Report on BUSTER refinement run in directory 1pmq_02

Report on BUSTER refinement run in directory 1pmq_02_refine

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:        47 bond lengths. Worst is    15.5 sigs     0.86 Angs A|501:N19=H19 (880)
     WARNING:        12 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:         1 bond angles.  Worst is     5.7 sigs   140.85 degs A|501:C50=N54=C55 (880)

Refinement vital statistics
	initial	final
N_cycles big	`0`	`5`
N_cycles small	`0`	`285`
X-ray weight	`4.00`	`4.49`
R_work	`0.2253`	`0.2062`
R_free	`0.2636`	`0.2362`
*100(R_free-R_work)**	`3.8%`	`3.0%`
LLG_work (cumulative Log-Likelihood Gain, working set)	`0`	`0.1125`
LLG_free (cumulative Log-Likelihood Gain, free set)	`0`	`0.0802`
RMS bond in Å	`0.0166`	`0.0090`
RMS angle in degrees	`1.46`	`0.99`
High resolution limit in Å	`2.10`	`2.10`
Low resolution limit in Å	`16.94`	`16.94`
Number of waters	`54`	`54`
help? see BUSTER wiki Refinement vital statistics

Graph of R/Rfree against cycle of refinement

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

Run conditions
refine command	`/software/GPhL/BUSTER_stable_production_20140512/autoBUSTER/bin/linux64/refine -p 1pmq_hydrogenate_880.pdb -m 1pmq/1pmq.mtz -d 1pmq_02_refine -l 880.grade_PDB_ligand.cif -M TLSbasic`
BUSTER version, run at, by user	`2.10.1, Thu May 29 07:26:35 BST 2014, osmart`
in directory	`/home/osmart/erice_workshop/1pmq_tutorial`
nthreads, hostname, OS	`2, fuji01vm, Ubuntu precise (12.04.4 LTS)`
buster-report command	`/home/software/GPhL/BUSTER_stable_production_20140512/scripts/buster-report -d 1pmq_02_refine`
buster-report version, run at, by user	`1.1.2 <May 05 2014>, Thu May 29 08:37:45 2014, osmart`
buster-report run on refine directory	`/home/osmart/erice_workshop/1pmq_tutorial/1pmq_02_refine`
buster-report output directory	`/home/osmart/erice_workshop/1pmq_tutorial/1pmq_02_refine-report`
final pdb coordinates	`1pmq_02_refine.pdb`
final mtzfile	`1pmq_02_refine.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