Report on BUSTER refinement run in directory 1pmq_01_MapOnly

N.B. initial structure has some really bad geometry restraint violations 
     logs/screen_initial.txt
     WARNING: Have |delta/sigma| deviations > 5.0 sigma. Number of outliers for each term: 
     WARNING:        49 bond lengths. Worst is    15.5 sigs     0.86 Angs A|501:N19=H19 (880)
     WARNING:        13 bond angles.  Worst is    12.1 sigs   108.55 degs A|502:C8=N7=C5 (ANP)
     WARNING:         1 planes.       Worst is    11.9 sigs     0.24 Angs A|501:N49=C50=N54=C55 (880)
     WARNING:         1 idealD contacts. Worst     5.1 sigs     2.67 Angs A|283:SG(CYS)=A|346:NZ(LYS)
N.B. final structure has some really bad geometry restraint violations
This is serious - check the final map with visualise_geometry_coot 
     logs/screen_final.txt
     WARNING: Have |delta/sigma| deviations > 5.0 sigma. Number of outliers for each term: 
     WARNING:        49 bond lengths. Worst is    15.5 sigs     0.86 Angs A|501:N19=H19 (880)
     WARNING:        13 bond angles.  Worst is    12.1 sigs   108.55 degs A|502:C8=N7=C5 (ANP)
     WARNING:         1 planes.       Worst is    11.9 sigs     0.24 Angs A|501:N49=C50=N54=C55 (880)
     WARNING:         1 idealD contacts. Worst     5.1 sigs     2.67 Angs A|283:SG(CYS)=A|346:NZ(LYS)

Refinement vital statistics
initial final
Ncycles big 0 2
Ncycles small 0 0
X-ray weight n/a n/a
Rwork 0.2253 0.2231
Rfree 0.2636 0.2619
100*(Rfree-Rwork) 3.8% 3.9%
LLGwork
(cumulative Log-Likelihood Gain, working set)		 0 0.0000
LLGfree
(cumulative Log-Likelihood Gain, free set)		 0 0.0000
High resolution limit in Å n/a n/a
Low resolution limit in Å n/a n/a
Number of waters 54 54
help? see BUSTER wiki Refinement vital statistics

Graph of R/Rfree against cycle of refinement

svg

reciprocal space correlation coefficient plots
start
svg
mtv svg agr png pdf 		final
svg
mtv svg agr png pdf
help? see BUSTER wiki interpreting reciprocal-space CC plots

Run conditions
refine command /mnt/scratch_fs1/osmart/autobuster/Server/autoBUSTER/bin/linux64/refine -p 1pmq_hydrogenate_880.pdb -m 1pmq/1pmq.mtz -d 1pmq_01_MapOnly -l 880.grade_PDB_ligand.cif -M MapOnly -report
BUSTER version, run at, by user ?, Mon Jun 16 15:21:43 BST 2014, osmart
in directory /home/osmart/2014/06/erice_workshop/1pmq_tutorial
nthreads, hostname, OS 6, hypatia, Ubuntu precise (12.04.4 LTS)
buster-report command /home/osmart/autobuster/Server/scripts/buster-report -d 1pmq_01_MapOnly -dr 1pmq_01_MapOnly.report -f
buster-report version, run at, by user 1.1.4 <July 25 2015>, Sat Jul 25 18:42:14 2015, osmart
buster-report run on refine directory /home/osmart/2014/06/erice_workshop/1pmq_tutorial/1pmq_01_MapOnly
buster-report output directory /home/osmart/2014/06/erice_workshop/1pmq_tutorial/1pmq_01_MapOnly.report
final pdb coordinates 1pmq_01_MapOnly.report.pdb
final mtzfile 1pmq_01_MapOnly.report.mtz
this report pdf version report.pdf
this report tsv version report.tsv
this report xml version report.xml
help? see BUSTER wiki Run conditions table
Main X-ray Ligand analysis Geometry details Refinement progress Real-space correlation coefficients MolProbity analysis