Sun 23 Dec 23:58:43 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vr0-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vr0-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vr0-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr0-3.4-parrot-mrncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr0-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr0-3.4-parrot-mrncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 23:58:47 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr0-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr0-3.4-parrot-mrncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 510 and 0 Target number of residues in the AU: 510 Target solvent content: 0.6232 Checking the provided sequence file Detected sequence length: 247 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 741 Adjusted target solvent content: 0.45 Input MTZ file: 1vr0-3.4-parrot-mrncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 20 Cell parameters: 46.686 69.193 453.518 90.000 90.000 90.000 Input sequence file: 1vr0-3.4-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5928 target number of atoms Had to go as low as 0.65 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 226.759 3.400 Wilson plot Bfac: 62.77 10631 reflections ( 99.67 % complete ) and 0 restraints for refining 6535 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3134 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2909 (Rfree = 0.000) for 6535 atoms. Found 49 (49 requested) and removed 151 (24 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.24 3.46 Search for helices and strands: 0 residues in 0 chains, 6584 seeds are put forward NCS extension: 0 residues added, 6584 seeds are put forward Round 1: 328 peptides, 63 chains. Longest chain 13 peptides. Score 0.352 Round 2: 392 peptides, 62 chains. Longest chain 21 peptides. Score 0.494 Round 3: 397 peptides, 55 chains. Longest chain 18 peptides. Score 0.559 Round 4: 417 peptides, 55 chains. Longest chain 38 peptides. Score 0.593 Round 5: 409 peptides, 53 chains. Longest chain 25 peptides. Score 0.595 Taking the results from Round 5 Chains 53, Residues 356, Estimated correctness of the model 27.0 % 3 chains (34 residues) have been docked in sequence ------------------------------------------------------ 10631 reflections ( 99.67 % complete ) and 11686 restraints for refining 5387 atoms. 10215 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2769 (Rfree = 0.000) for 5387 atoms. Found 22 (40 requested) and removed 48 (20 requested) atoms. Cycle 2: After refmac, R = 0.2479 (Rfree = 0.000) for 5279 atoms. Found 17 (40 requested) and removed 37 (20 requested) atoms. Cycle 3: After refmac, R = 0.2246 (Rfree = 0.000) for 5223 atoms. Found 14 (39 requested) and removed 31 (19 requested) atoms. Cycle 4: After refmac, R = 0.2096 (Rfree = 0.000) for 5190 atoms. Found 7 (39 requested) and removed 27 (19 requested) atoms. Cycle 5: After refmac, R = 0.2073 (Rfree = 0.000) for 5159 atoms. Found 9 (39 requested) and removed 26 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.22 3.44 Search for helices and strands: 0 residues in 0 chains, 5335 seeds are put forward NCS extension: 12 residues added (7 deleted due to clashes), 5347 seeds are put forward Round 1: 363 peptides, 58 chains. Longest chain 18 peptides. Score 0.471 Round 2: 394 peptides, 56 chains. Longest chain 22 peptides. Score 0.546 Round 3: 386 peptides, 50 chains. Longest chain 38 peptides. Score 0.579 Round 4: 407 peptides, 49 chains. Longest chain 30 peptides. Score 0.620 Round 5: 405 peptides, 48 chains. Longest chain 43 peptides. Score 0.624 Taking the results from Round 5 Chains 48, Residues 357, Estimated correctness of the model 36.3 % 1 chains (42 residues) have been docked in sequence ------------------------------------------------------ 10631 reflections ( 99.67 % complete ) and 12014 restraints for refining 5390 atoms. 10495 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2295 (Rfree = 0.000) for 5390 atoms. Found 36 (40 requested) and removed 50 (20 requested) atoms. Cycle 7: After refmac, R = 0.2045 (Rfree = 0.000) for 5350 atoms. Found 16 (40 requested) and removed 32 (20 requested) atoms. Cycle 8: After refmac, R = 0.2080 (Rfree = 0.000) for 5327 atoms. Found 13 (40 requested) and removed 27 (20 requested) atoms. Cycle 9: After refmac, R = 0.1882 (Rfree = 0.000) for 5304 atoms. Found 7 (40 requested) and removed 25 (20 requested) atoms. Cycle 10: After refmac, R = 0.1893 (Rfree = 0.000) for 5280 atoms. Found 6 (39 requested) and removed 25 (19 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.24 3.46 Search for helices and strands: 0 residues in 0 chains, 5447 seeds are put forward NCS extension: 41 residues added (2 deleted due to clashes), 5488 seeds are put forward Round 1: 351 peptides, 61 chains. Longest chain 17 peptides. Score 0.420 Round 2: 402 peptides, 59 chains. Longest chain 50 peptides. Score 0.537 Round 3: 399 peptides, 59 chains. Longest chain 29 peptides. Score 0.532 Round 4: 421 peptides, 61 chains. Longest chain 36 peptides. Score 0.555 Round 5: 410 peptides, 60 chains. Longest chain 25 peptides. Score 0.543 Taking the results from Round 4 Chains 63, Residues 360, Estimated correctness of the model 13.3 % 3 chains (47 residues) have been docked in sequence ------------------------------------------------------ 10631 reflections ( 99.67 % complete ) and 11972 restraints for refining 5389 atoms. 10439 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2291 (Rfree = 0.000) for 5389 atoms. Found 35 (40 requested) and removed 51 (20 requested) atoms. Cycle 12: After refmac, R = 0.2153 (Rfree = 0.000) for 5364 atoms. Found 10 (40 requested) and removed 34 (20 requested) atoms. Cycle 13: After refmac, R = 0.2178 (Rfree = 0.000) for 5335 atoms. Found 8 (40 requested) and removed 27 (20 requested) atoms. Cycle 14: After refmac, R = 0.1992 (Rfree = 0.000) for 5310 atoms. Found 4 (40 requested) and removed 23 (20 requested) atoms. Cycle 15: After refmac, R = 0.1942 (Rfree = 0.000) for 5288 atoms. Found 7 (39 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.23 3.45 Search for helices and strands: 0 residues in 0 chains, 5469 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 5482 seeds are put forward Round 1: 346 peptides, 58 chains. Longest chain 21 peptides. Score 0.437 Round 2: 386 peptides, 55 chains. Longest chain 31 peptides. Score 0.540 Round 3: 389 peptides, 54 chains. Longest chain 19 peptides. Score 0.553 Round 4: 411 peptides, 55 chains. Longest chain 19 peptides. Score 0.583 Round 5: 413 peptides, 56 chains. Longest chain 24 peptides. Score 0.579 Taking the results from Round 4 Chains 55, Residues 356, Estimated correctness of the model 23.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 10631 reflections ( 99.67 % complete ) and 12233 restraints for refining 5390 atoms. 10811 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2229 (Rfree = 0.000) for 5390 atoms. Found 40 (40 requested) and removed 29 (20 requested) atoms. Cycle 17: After refmac, R = 0.2013 (Rfree = 0.000) for 5385 atoms. Found 16 (40 requested) and removed 24 (20 requested) atoms. Cycle 18: After refmac, R = 0.1958 (Rfree = 0.000) for 5368 atoms. Found 8 (40 requested) and removed 24 (20 requested) atoms. Cycle 19: After refmac, R = 0.1922 (Rfree = 0.000) for 5351 atoms. Found 10 (40 requested) and removed 20 (20 requested) atoms. Cycle 20: After refmac, R = 0.1919 (Rfree = 0.000) for 5337 atoms. Found 8 (40 requested) and removed 21 (20 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.24 3.46 Search for helices and strands: 0 residues in 0 chains, 5520 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 5543 seeds are put forward Round 1: 373 peptides, 55 chains. Longest chain 19 peptides. Score 0.516 Round 2: 371 peptides, 51 chains. Longest chain 23 peptides. Score 0.545 Round 3: 405 peptides, 53 chains. Longest chain 20 peptides. Score 0.588 Round 4: 388 peptides, 52 chains. Longest chain 18 peptides. Score 0.567 Round 5: 389 peptides, 53 chains. Longest chain 20 peptides. Score 0.561 Taking the results from Round 3 Chains 53, Residues 352, Estimated correctness of the model 24.7 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 10631 reflections ( 99.67 % complete ) and 12144 restraints for refining 5389 atoms. 10725 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2098 (Rfree = 0.000) for 5389 atoms. Found 30 (40 requested) and removed 29 (20 requested) atoms. Cycle 22: After refmac, R = 0.1868 (Rfree = 0.000) for 5380 atoms. Found 11 (40 requested) and removed 23 (20 requested) atoms. Cycle 23: After refmac, R = 0.1802 (Rfree = 0.000) for 5366 atoms. Found 10 (40 requested) and removed 20 (20 requested) atoms. Cycle 24: After refmac, R = 0.1781 (Rfree = 0.000) for 5353 atoms. Found 5 (40 requested) and removed 22 (20 requested) atoms. Cycle 25: After refmac, R = 0.1778 (Rfree = 0.000) for 5334 atoms. Found 8 (40 requested) and removed 20 (20 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.24 3.46 Search for helices and strands: 0 residues in 0 chains, 5500 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 5517 seeds are put forward Round 1: 317 peptides, 52 chains. Longest chain 15 peptides. Score 0.430 Round 2: 372 peptides, 51 chains. Longest chain 24 peptides. Score 0.547 Round 3: 367 peptides, 54 chains. Longest chain 17 peptides. Score 0.513 Round 4: 382 peptides, 48 chains. Longest chain 18 peptides. Score 0.587 Round 5: 375 peptides, 52 chains. Longest chain 21 peptides. Score 0.544 Taking the results from Round 4 Chains 48, Residues 334, Estimated correctness of the model 24.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10631 reflections ( 99.67 % complete ) and 12388 restraints for refining 5390 atoms. 11100 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2008 (Rfree = 0.000) for 5390 atoms. Found 26 (40 requested) and removed 26 (20 requested) atoms. Cycle 27: After refmac, R = 0.1819 (Rfree = 0.000) for 5379 atoms. Found 12 (40 requested) and removed 22 (20 requested) atoms. Cycle 28: After refmac, R = 0.1739 (Rfree = 0.000) for 5364 atoms. Found 12 (40 requested) and removed 22 (20 requested) atoms. Cycle 29: After refmac, R = 0.1672 (Rfree = 0.000) for 5350 atoms. Found 6 (40 requested) and removed 20 (20 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1630 (Rfree = 0.000) for 5334 atoms. Found 8 (40 requested) and removed 21 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.23 3.45 Search for helices and strands: 0 residues in 0 chains, 5523 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 5542 seeds are put forward Round 1: 302 peptides, 51 chains. Longest chain 12 peptides. Score 0.408 Round 2: 350 peptides, 47 chains. Longest chain 26 peptides. Score 0.539 Round 3: 342 peptides, 49 chains. Longest chain 24 peptides. Score 0.507 Round 4: 365 peptides, 54 chains. Longest chain 27 peptides. Score 0.509 Round 5: 370 peptides, 49 chains. Longest chain 26 peptides. Score 0.559 Taking the results from Round 5 Chains 50, Residues 321, Estimated correctness of the model 14.7 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 10631 reflections ( 99.67 % complete ) and 12301 restraints for refining 5389 atoms. 11032 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2106 (Rfree = 0.000) for 5389 atoms. Found 38 (40 requested) and removed 25 (20 requested) atoms. Cycle 32: After refmac, R = 0.1899 (Rfree = 0.000) for 5387 atoms. Found 14 (40 requested) and removed 25 (20 requested) atoms. Cycle 33: After refmac, R = 0.1831 (Rfree = 0.000) for 5372 atoms. Found 12 (40 requested) and removed 22 (20 requested) atoms. Cycle 34: After refmac, R = 0.1807 (Rfree = 0.000) for 5361 atoms. Found 9 (40 requested) and removed 21 (20 requested) atoms. Cycle 35: After refmac, R = 0.1795 (Rfree = 0.000) for 5345 atoms. Found 9 (40 requested) and removed 22 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.23 3.45 Search for helices and strands: 0 residues in 0 chains, 5494 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 5512 seeds are put forward Round 1: 315 peptides, 58 chains. Longest chain 14 peptides. Score 0.370 Round 2: 348 peptides, 50 chains. Longest chain 16 peptides. Score 0.510 Round 3: 348 peptides, 54 chains. Longest chain 16 peptides. Score 0.476 Round 4: 332 peptides, 54 chains. Longest chain 19 peptides. Score 0.444 Round 5: 355 peptides, 55 chains. Longest chain 19 peptides. Score 0.481 Taking the results from Round 2 Chains 50, Residues 298, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10631 reflections ( 99.67 % complete ) and 12479 restraints for refining 5390 atoms. 11337 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1917 (Rfree = 0.000) for 5390 atoms. Found 20 (40 requested) and removed 22 (20 requested) atoms. Cycle 37: After refmac, R = 0.1784 (Rfree = 0.000) for 5384 atoms. Found 9 (40 requested) and removed 20 (20 requested) atoms. Cycle 38: After refmac, R = 0.1733 (Rfree = 0.000) for 5371 atoms. Found 6 (40 requested) and removed 21 (20 requested) atoms. Cycle 39: After refmac, R = 0.1710 (Rfree = 0.000) for 5354 atoms. Found 7 (40 requested) and removed 20 (20 requested) atoms. Cycle 40: After refmac, R = 0.1733 (Rfree = 0.000) for 5341 atoms. Found 8 (40 requested) and removed 20 (20 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.24 3.46 Search for helices and strands: 0 residues in 0 chains, 5474 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 5489 seeds are put forward Round 1: 287 peptides, 55 chains. Longest chain 11 peptides. Score 0.335 Round 2: 328 peptides, 53 chains. Longest chain 16 peptides. Score 0.444 Round 3: 335 peptides, 52 chains. Longest chain 12 peptides. Score 0.468 Round 4: 320 peptides, 49 chains. Longest chain 15 peptides. Score 0.464 Round 5: 323 peptides, 49 chains. Longest chain 18 peptides. Score 0.470 Taking the results from Round 5 Chains 49, Residues 274, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10631 reflections ( 99.67 % complete ) and 12579 restraints for refining 5390 atoms. 11532 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2020 (Rfree = 0.000) for 5390 atoms. Found 15 (40 requested) and removed 27 (20 requested) atoms. Cycle 42: After refmac, R = 0.1860 (Rfree = 0.000) for 5373 atoms. Found 12 (40 requested) and removed 23 (20 requested) atoms. Cycle 43: After refmac, R = 0.1767 (Rfree = 0.000) for 5358 atoms. Found 9 (40 requested) and removed 23 (20 requested) atoms. Cycle 44: After refmac, R = 0.1745 (Rfree = 0.000) for 5343 atoms. Found 6 (40 requested) and removed 21 (20 requested) atoms. Cycle 45: After refmac, R = 0.1781 (Rfree = 0.000) for 5325 atoms. Found 12 (40 requested) and removed 20 (20 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.24 3.46 Search for helices and strands: 0 residues in 0 chains, 5457 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 5476 seeds are put forward Round 1: 286 peptides, 52 chains. Longest chain 11 peptides. Score 0.362 Round 2: 308 peptides, 48 chains. Longest chain 18 peptides. Score 0.448 Round 3: 294 peptides, 48 chains. Longest chain 11 peptides. Score 0.418 Round 4: 286 peptides, 49 chains. Longest chain 14 peptides. Score 0.391 Round 5: 285 peptides, 46 chains. Longest chain 11 peptides. Score 0.418 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 48, Residues 260, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vr0-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10631 reflections ( 99.67 % complete ) and 12689 restraints for refining 5389 atoms. 11697 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1873 (Rfree = 0.000) for 5389 atoms. Found 0 (40 requested) and removed 13 (20 requested) atoms. Cycle 47: After refmac, R = 0.1844 (Rfree = 0.000) for 5374 atoms. Found 0 (40 requested) and removed 2 (20 requested) atoms. Cycle 48: After refmac, R = 0.1809 (Rfree = 0.000) for 5371 atoms. Found 0 (40 requested) and removed 10 (20 requested) atoms. Cycle 49: After refmac, R = 0.1856 (Rfree = 0.000) for 5360 atoms. TimeTaking 59.2