Mon 24 Dec 07:39:26 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2go7-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2go7-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2go7-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2go7-3.6-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2go7-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2go7-3.6-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:39:30 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/noncs/ArpWArp/wArpResults/WorkingDir/2go7-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2go7-3.6-parrot-noncs/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 810 and 0 Target number of residues in the AU: 810 Target solvent content: 0.6427 Checking the provided sequence file Detected sequence length: 207 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 828 Adjusted target solvent content: 0.63 Input MTZ file: 2go7-3.6-parrot-noncs.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: 169 Cell parameters: 155.000 155.000 88.440 90.000 90.000 120.000 Input sequence file: 2go7-3.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 6624 target number of atoms Had to go as low as 1.10 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: 134.234 3.600 Wilson plot Bfac: 73.62 14169 reflections ( 99.78 % complete ) and 0 restraints for refining 7387 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3603 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3258 (Rfree = 0.000) for 7387 atoms. Found 47 (47 requested) and removed 40 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.43 2.87 Search for helices and strands: 0 residues in 0 chains, 7541 seeds are put forward NCS extension: 0 residues added, 7541 seeds are put forward Round 1: 359 peptides, 72 chains. Longest chain 11 peptides. Score 0.282 Round 2: 493 peptides, 80 chains. Longest chain 12 peptides. Score 0.421 Round 3: 513 peptides, 68 chains. Longest chain 21 peptides. Score 0.511 Round 4: 503 peptides, 65 chains. Longest chain 19 peptides. Score 0.515 Round 5: 517 peptides, 62 chains. Longest chain 23 peptides. Score 0.546 Taking the results from Round 5 Chains 64, Residues 455, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 14169 reflections ( 99.78 % complete ) and 13057 restraints for refining 6004 atoms. 11251 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2794 (Rfree = 0.000) for 6004 atoms. Found 37 (38 requested) and removed 41 (19 requested) atoms. Cycle 2: After refmac, R = 0.2662 (Rfree = 0.000) for 5893 atoms. Found 21 (38 requested) and removed 33 (19 requested) atoms. Cycle 3: After refmac, R = 0.2621 (Rfree = 0.000) for 5823 atoms. Found 24 (37 requested) and removed 26 (18 requested) atoms. Cycle 4: After refmac, R = 0.2506 (Rfree = 0.000) for 5772 atoms. Found 21 (37 requested) and removed 28 (18 requested) atoms. Cycle 5: After refmac, R = 0.2492 (Rfree = 0.000) for 5729 atoms. Found 20 (36 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.44 2.88 Search for helices and strands: 0 residues in 0 chains, 5980 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 5997 seeds are put forward Round 1: 461 peptides, 77 chains. Longest chain 13 peptides. Score 0.397 Round 2: 486 peptides, 63 chains. Longest chain 23 peptides. Score 0.506 Round 3: 513 peptides, 70 chains. Longest chain 20 peptides. Score 0.500 Round 4: 526 peptides, 63 chains. Longest chain 26 peptides. Score 0.551 Round 5: 506 peptides, 61 chains. Longest chain 20 peptides. Score 0.539 Taking the results from Round 4 Chains 66, Residues 463, Estimated correctness of the model 0.0 % 4 chains (52 residues) have been docked in sequence ------------------------------------------------------ 14169 reflections ( 99.78 % complete ) and 12467 restraints for refining 6001 atoms. 10476 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2820 (Rfree = 0.000) for 6001 atoms. Found 38 (38 requested) and removed 50 (19 requested) atoms. Cycle 7: After refmac, R = 0.2503 (Rfree = 0.000) for 5893 atoms. Found 38 (38 requested) and removed 40 (19 requested) atoms. Cycle 8: After refmac, R = 0.2395 (Rfree = 0.000) for 5832 atoms. Found 17 (37 requested) and removed 40 (18 requested) atoms. Cycle 9: After refmac, R = 0.2444 (Rfree = 0.000) for 5759 atoms. Found 36 (37 requested) and removed 62 (18 requested) atoms. Cycle 10: After refmac, R = 0.2304 (Rfree = 0.000) for 5698 atoms. Found 24 (36 requested) and removed 35 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 2.87 Search for helices and strands: 0 residues in 0 chains, 5906 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 5934 seeds are put forward Round 1: 469 peptides, 77 chains. Longest chain 15 peptides. Score 0.407 Round 2: 512 peptides, 75 chains. Longest chain 18 peptides. Score 0.473 Round 3: 522 peptides, 67 chains. Longest chain 22 peptides. Score 0.526 Round 4: 521 peptides, 64 chains. Longest chain 22 peptides. Score 0.541 Round 5: 527 peptides, 67 chains. Longest chain 28 peptides. Score 0.532 Taking the results from Round 4 Chains 68, Residues 457, Estimated correctness of the model 0.0 % 4 chains (42 residues) have been docked in sequence ------------------------------------------------------ 14169 reflections ( 99.78 % complete ) and 12462 restraints for refining 6003 atoms. 10560 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2556 (Rfree = 0.000) for 6003 atoms. Found 38 (38 requested) and removed 36 (19 requested) atoms. Cycle 12: After refmac, R = 0.2419 (Rfree = 0.000) for 5926 atoms. Found 28 (38 requested) and removed 30 (19 requested) atoms. Cycle 13: After refmac, R = 0.2304 (Rfree = 0.000) for 5871 atoms. Found 28 (38 requested) and removed 30 (19 requested) atoms. Cycle 14: After refmac, R = 0.2246 (Rfree = 0.000) for 5828 atoms. Found 10 (37 requested) and removed 22 (18 requested) atoms. Cycle 15: After refmac, R = 0.2229 (Rfree = 0.000) for 5788 atoms. Found 17 (37 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 2.87 Search for helices and strands: 0 residues in 0 chains, 6031 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 6058 seeds are put forward Round 1: 453 peptides, 76 chains. Longest chain 15 peptides. Score 0.392 Round 2: 496 peptides, 71 chains. Longest chain 18 peptides. Score 0.475 Round 3: 520 peptides, 70 chains. Longest chain 22 peptides. Score 0.509 Round 4: 518 peptides, 69 chains. Longest chain 24 peptides. Score 0.512 Round 5: 530 peptides, 71 chains. Longest chain 17 peptides. Score 0.515 Taking the results from Round 5 Chains 71, Residues 459, Estimated correctness of the model 0.0 % 3 chains (40 residues) have been docked in sequence ------------------------------------------------------ 14169 reflections ( 99.78 % complete ) and 12570 restraints for refining 6003 atoms. 10647 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2450 (Rfree = 0.000) for 6003 atoms. Found 38 (38 requested) and removed 35 (19 requested) atoms. Cycle 17: After refmac, R = 0.2230 (Rfree = 0.000) for 5957 atoms. Found 21 (38 requested) and removed 35 (19 requested) atoms. Cycle 18: After refmac, R = 0.2197 (Rfree = 0.000) for 5916 atoms. Found 17 (38 requested) and removed 26 (19 requested) atoms. Cycle 19: After refmac, R = 0.2010 (Rfree = 0.000) for 5891 atoms. Found 5 (37 requested) and removed 24 (18 requested) atoms. Cycle 20: After refmac, R = 0.1974 (Rfree = 0.000) for 5860 atoms. Found 12 (37 requested) and removed 32 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.40 2.85 Search for helices and strands: 0 residues in 0 chains, 6074 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 6092 seeds are put forward Round 1: 431 peptides, 69 chains. Longest chain 16 peptides. Score 0.403 Round 2: 481 peptides, 66 chains. Longest chain 24 peptides. Score 0.484 Round 3: 488 peptides, 63 chains. Longest chain 31 peptides. Score 0.508 Round 4: 490 peptides, 70 chains. Longest chain 22 peptides. Score 0.473 Round 5: 491 peptides, 69 chains. Longest chain 26 peptides. Score 0.480 Taking the results from Round 3 Chains 65, Residues 425, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 14169 reflections ( 99.78 % complete ) and 12997 restraints for refining 6004 atoms. 11296 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2683 (Rfree = 0.000) for 6004 atoms. Found 38 (38 requested) and removed 43 (19 requested) atoms. Cycle 22: After refmac, R = 0.2236 (Rfree = 0.000) for 5960 atoms. Found 28 (38 requested) and removed 52 (19 requested) atoms. Cycle 23: After refmac, R = 0.2185 (Rfree = 0.000) for 5910 atoms. Found 18 (38 requested) and removed 29 (19 requested) atoms. Cycle 24: After refmac, R = 0.2163 (Rfree = 0.000) for 5884 atoms. Found 25 (37 requested) and removed 26 (18 requested) atoms. Cycle 25: After refmac, R = 0.2146 (Rfree = 0.000) for 5871 atoms. Found 14 (37 requested) and removed 28 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.42 2.86 Search for helices and strands: 0 residues in 0 chains, 6082 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 6104 seeds are put forward Round 1: 454 peptides, 80 chains. Longest chain 16 peptides. Score 0.370 Round 2: 488 peptides, 71 chains. Longest chain 18 peptides. Score 0.465 Round 3: 488 peptides, 73 chains. Longest chain 20 peptides. Score 0.454 Round 4: 496 peptides, 66 chains. Longest chain 23 peptides. Score 0.502 Round 5: 489 peptides, 69 chains. Longest chain 20 peptides. Score 0.477 Taking the results from Round 4 Chains 68, Residues 430, Estimated correctness of the model 0.0 % 3 chains (52 residues) have been docked in sequence ------------------------------------------------------ 14169 reflections ( 99.78 % complete ) and 12591 restraints for refining 6004 atoms. 10734 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2504 (Rfree = 0.000) for 6004 atoms. Found 38 (38 requested) and removed 27 (19 requested) atoms. Cycle 27: After refmac, R = 0.2274 (Rfree = 0.000) for 5972 atoms. Found 30 (38 requested) and removed 33 (19 requested) atoms. Cycle 28: After refmac, R = 0.2137 (Rfree = 0.000) for 5926 atoms. Found 14 (38 requested) and removed 25 (19 requested) atoms. Cycle 29: After refmac, R = 0.2086 (Rfree = 0.000) for 5900 atoms. Found 20 (37 requested) and removed 35 (18 requested) atoms. Cycle 30: After refmac, R = 0.2029 (Rfree = 0.000) for 5874 atoms. Found 16 (37 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.39 2.84 Search for helices and strands: 0 residues in 0 chains, 6096 seeds are put forward NCS extension: 18 residues added (4 deleted due to clashes), 6114 seeds are put forward Round 1: 407 peptides, 76 chains. Longest chain 15 peptides. Score 0.328 Round 2: 440 peptides, 69 chains. Longest chain 25 peptides. Score 0.415 Round 3: 465 peptides, 69 chains. Longest chain 20 peptides. Score 0.448 Round 4: 449 peptides, 62 chains. Longest chain 22 peptides. Score 0.467 Round 5: 470 peptides, 65 chains. Longest chain 22 peptides. Score 0.476 Taking the results from Round 5 Chains 65, Residues 405, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14169 reflections ( 99.78 % complete ) and 13046 restraints for refining 6001 atoms. 11491 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2315 (Rfree = 0.000) for 6001 atoms. Found 38 (38 requested) and removed 33 (19 requested) atoms. Cycle 32: After refmac, R = 0.2158 (Rfree = 0.000) for 5983 atoms. Found 24 (38 requested) and removed 31 (19 requested) atoms. Cycle 33: After refmac, R = 0.2043 (Rfree = 0.000) for 5966 atoms. Found 19 (38 requested) and removed 25 (19 requested) atoms. Cycle 34: After refmac, R = 0.2022 (Rfree = 0.000) for 5950 atoms. Found 19 (38 requested) and removed 33 (19 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1968 (Rfree = 0.000) for 5930 atoms. Found 24 (38 requested) and removed 20 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.42 2.86 Search for helices and strands: 0 residues in 0 chains, 6207 seeds are put forward NCS extension: 38 residues added (1 deleted due to clashes), 6245 seeds are put forward Round 1: 405 peptides, 74 chains. Longest chain 12 peptides. Score 0.337 Round 2: 470 peptides, 70 chains. Longest chain 17 peptides. Score 0.448 Round 3: 472 peptides, 71 chains. Longest chain 18 peptides. Score 0.445 Round 4: 480 peptides, 68 chains. Longest chain 20 peptides. Score 0.472 Round 5: 468 peptides, 69 chains. Longest chain 18 peptides. Score 0.451 Taking the results from Round 4 Chains 69, Residues 412, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 14169 reflections ( 99.78 % complete ) and 13027 restraints for refining 6004 atoms. 11359 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2364 (Rfree = 0.000) for 6004 atoms. Found 36 (38 requested) and removed 26 (19 requested) atoms. Cycle 37: After refmac, R = 0.2122 (Rfree = 0.000) for 5977 atoms. Found 17 (38 requested) and removed 21 (19 requested) atoms. Cycle 38: After refmac, R = 0.2103 (Rfree = 0.000) for 5952 atoms. Found 10 (38 requested) and removed 21 (19 requested) atoms. Cycle 39: After refmac, R = 0.1987 (Rfree = 0.000) for 5921 atoms. Found 9 (38 requested) and removed 19 (19 requested) atoms. Cycle 40: After refmac, R = 0.1999 (Rfree = 0.000) for 5906 atoms. Found 8 (37 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.43 2.87 Search for helices and strands: 0 residues in 0 chains, 6115 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 6136 seeds are put forward Round 1: 405 peptides, 77 chains. Longest chain 11 peptides. Score 0.319 Round 2: 459 peptides, 72 chains. Longest chain 20 peptides. Score 0.423 Round 3: 462 peptides, 67 chains. Longest chain 18 peptides. Score 0.455 Round 4: 457 peptides, 71 chains. Longest chain 20 peptides. Score 0.426 Round 5: 476 peptides, 69 chains. Longest chain 21 peptides. Score 0.461 Taking the results from Round 5 Chains 69, Residues 407, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 14169 reflections ( 99.78 % complete ) and 13305 restraints for refining 6002 atoms. 11746 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2228 (Rfree = 0.000) for 6002 atoms. Found 29 (38 requested) and removed 33 (19 requested) atoms. Cycle 42: After refmac, R = 0.2011 (Rfree = 0.000) for 5973 atoms. Found 16 (38 requested) and removed 21 (19 requested) atoms. Cycle 43: After refmac, R = 0.1983 (Rfree = 0.000) for 5951 atoms. Found 11 (38 requested) and removed 21 (19 requested) atoms. Cycle 44: After refmac, R = 0.1931 (Rfree = 0.000) for 5932 atoms. Found 9 (38 requested) and removed 24 (19 requested) atoms. Cycle 45: After refmac, R = 0.1963 (Rfree = 0.000) for 5911 atoms. Found 20 (37 requested) and removed 20 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.41 2.86 Search for helices and strands: 0 residues in 0 chains, 6131 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 6159 seeds are put forward Round 1: 384 peptides, 71 chains. Longest chain 14 peptides. Score 0.326 Round 2: 421 peptides, 68 chains. Longest chain 14 peptides. Score 0.396 Round 3: 420 peptides, 65 chains. Longest chain 17 peptides. Score 0.412 Round 4: 429 peptides, 66 chains. Longest chain 14 peptides. Score 0.418 Round 5: 422 peptides, 62 chains. Longest chain 22 peptides. Score 0.433 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 62, Residues 360, 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 2go7-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14169 reflections ( 99.78 % complete ) and 13424 restraints for refining 6004 atoms. 12046 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2327 (Rfree = 0.000) for 6004 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.2305 (Rfree = 0.000) for 5963 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 48: After refmac, R = 0.2105 (Rfree = 0.000) for 5935 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 49: After refmac, R = 0.2201 (Rfree = 0.000) for 5906 atoms. TimeTaking 67.03