Mon 24 Dec 00:32:07 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 1vkn-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vkn-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vkn-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkn-4.0-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/1vkn-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkn-4.0-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 ============================================================ Mon 24 Dec 00:32:11 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/1vkn-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkn-4.0-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 918 and 0 Target number of residues in the AU: 918 Target solvent content: 0.6615 Checking the provided sequence file Detected sequence length: 351 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1404 Adjusted target solvent content: 0.48 Input MTZ file: 1vkn-4.0-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: 4 Cell parameters: 85.135 92.128 101.299 90.000 112.538 90.000 Input sequence file: 1vkn-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 11232 target number of atoms Had to go as low as 0.80 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: 93.562 4.000 Wilson plot Bfac: 85.81 12267 reflections ( 98.92 % complete ) and 0 restraints for refining 12445 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3212 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2915 (Rfree = 0.000) for 12445 atoms. Found 59 (59 requested) and removed 80 (29 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.75 3.85 Search for helices and strands: 0 residues in 0 chains, 12642 seeds are put forward NCS extension: 0 residues added, 12642 seeds are put forward Round 1: 476 peptides, 93 chains. Longest chain 14 peptides. Score 0.304 Round 2: 629 peptides, 107 chains. Longest chain 13 peptides. Score 0.411 Round 3: 651 peptides, 102 chains. Longest chain 21 peptides. Score 0.457 Round 4: 700 peptides, 98 chains. Longest chain 18 peptides. Score 0.522 Round 5: 691 peptides, 95 chains. Longest chain 24 peptides. Score 0.526 Taking the results from Round 5 Chains 96, Residues 596, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 12267 reflections ( 98.92 % complete ) and 23896 restraints for refining 10138 atoms. 21566 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2145 (Rfree = 0.000) for 10138 atoms. Found 42 (48 requested) and removed 53 (24 requested) atoms. Cycle 2: After refmac, R = 0.2071 (Rfree = 0.000) for 9961 atoms. Found 47 (48 requested) and removed 51 (24 requested) atoms. Cycle 3: After refmac, R = 0.2012 (Rfree = 0.000) for 9875 atoms. Found 47 (47 requested) and removed 55 (23 requested) atoms. Cycle 4: After refmac, R = 0.1908 (Rfree = 0.000) for 9811 atoms. Found 46 (46 requested) and removed 54 (23 requested) atoms. Cycle 5: After refmac, R = 0.1500 (Rfree = 0.000) for 9766 atoms. Found 16 (46 requested) and removed 28 (23 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.73 3.83 Search for helices and strands: 0 residues in 0 chains, 10079 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 10093 seeds are put forward Round 1: 603 peptides, 110 chains. Longest chain 14 peptides. Score 0.368 Round 2: 679 peptides, 102 chains. Longest chain 21 peptides. Score 0.485 Round 3: 727 peptides, 109 chains. Longest chain 22 peptides. Score 0.502 Round 4: 723 peptides, 104 chains. Longest chain 24 peptides. Score 0.519 Round 5: 736 peptides, 104 chains. Longest chain 23 peptides. Score 0.531 Taking the results from Round 5 Chains 106, Residues 632, Estimated correctness of the model 0.0 % 5 chains (32 residues) have been docked in sequence ------------------------------------------------------ 12267 reflections ( 98.92 % complete ) and 23669 restraints for refining 10141 atoms. 21168 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2006 (Rfree = 0.000) for 10141 atoms. Found 48 (48 requested) and removed 68 (24 requested) atoms. Cycle 7: After refmac, R = 0.1921 (Rfree = 0.000) for 10040 atoms. Found 48 (48 requested) and removed 59 (24 requested) atoms. Cycle 8: After refmac, R = 0.1888 (Rfree = 0.000) for 9986 atoms. Found 47 (47 requested) and removed 55 (23 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.1794 (Rfree = 0.000) for 9946 atoms. Found 47 (47 requested) and removed 52 (23 requested) atoms. Cycle 10: After refmac, R = 0.1797 (Rfree = 0.000) for 9890 atoms. Found 47 (47 requested) and removed 43 (23 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.78 3.88 Search for helices and strands: 0 residues in 0 chains, 10286 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 10302 seeds are put forward Round 1: 576 peptides, 115 chains. Longest chain 11 peptides. Score 0.312 Round 2: 679 peptides, 117 chains. Longest chain 16 peptides. Score 0.418 Round 3: 668 peptides, 104 chains. Longest chain 22 peptides. Score 0.465 Round 4: 681 peptides, 106 chains. Longest chain 16 peptides. Score 0.469 Round 5: 696 peptides, 100 chains. Longest chain 22 peptides. Score 0.510 Taking the results from Round 5 Chains 102, Residues 596, Estimated correctness of the model 0.0 % 4 chains (39 residues) have been docked in sequence ------------------------------------------------------ 12267 reflections ( 98.92 % complete ) and 23665 restraints for refining 10141 atoms. 21259 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1994 (Rfree = 0.000) for 10141 atoms. Found 48 (48 requested) and removed 58 (24 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.1831 (Rfree = 0.000) for 10049 atoms. Found 48 (48 requested) and removed 51 (24 requested) atoms. Cycle 13: After refmac, R = 0.1417 (Rfree = 0.000) for 10019 atoms. Found 16 (47 requested) and removed 37 (23 requested) atoms. Cycle 14: After refmac, R = 0.1321 (Rfree = 0.000) for 9979 atoms. Found 7 (47 requested) and removed 28 (23 requested) atoms. Cycle 15: After refmac, R = 0.1288 (Rfree = 0.000) for 9944 atoms. Found 10 (47 requested) and removed 27 (23 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.77 3.87 Search for helices and strands: 0 residues in 0 chains, 10234 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 10260 seeds are put forward Round 1: 601 peptides, 112 chains. Longest chain 16 peptides. Score 0.356 Round 2: 643 peptides, 104 chains. Longest chain 17 peptides. Score 0.439 Round 3: 668 peptides, 110 chains. Longest chain 18 peptides. Score 0.438 Round 4: 647 peptides, 104 chains. Longest chain 15 peptides. Score 0.444 Round 5: 653 peptides, 102 chains. Longest chain 17 peptides. Score 0.459 Taking the results from Round 5 Chains 102, Residues 551, Estimated correctness of the model 0.0 % 4 chains (22 residues) have been docked in sequence ------------------------------------------------------ 12267 reflections ( 98.92 % complete ) and 24095 restraints for refining 10142 atoms. 21939 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1886 (Rfree = 0.000) for 10142 atoms. Found 48 (48 requested) and removed 107 (24 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.1787 (Rfree = 0.000) for 10012 atoms. Found 47 (47 requested) and removed 40 (23 requested) atoms. Cycle 18: After refmac, R = 0.1752 (Rfree = 0.000) for 9980 atoms. Found 47 (47 requested) and removed 39 (23 requested) atoms. Cycle 19: After refmac, R = 0.1667 (Rfree = 0.000) for 9948 atoms. Found 47 (47 requested) and removed 44 (23 requested) atoms. Cycle 20: After refmac, R = 0.1217 (Rfree = 0.000) for 9921 atoms. Found 16 (47 requested) and removed 28 (23 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.77 3.87 Search for helices and strands: 0 residues in 0 chains, 10216 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 10233 seeds are put forward Round 1: 539 peptides, 110 chains. Longest chain 12 peptides. Score 0.293 Round 2: 623 peptides, 106 chains. Longest chain 22 peptides. Score 0.409 Round 3: 605 peptides, 102 chains. Longest chain 16 peptides. Score 0.408 Round 4: 625 peptides, 109 chains. Longest chain 14 peptides. Score 0.397 Round 5: 638 peptides, 99 chains. Longest chain 20 peptides. Score 0.457 Taking the results from Round 5 Chains 102, Residues 539, Estimated correctness of the model 0.0 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 12267 reflections ( 98.92 % complete ) and 23984 restraints for refining 10139 atoms. 21847 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1789 (Rfree = 0.000) for 10139 atoms. Found 48 (48 requested) and removed 46 (24 requested) atoms. Cycle 22: After refmac, R = 0.1837 (Rfree = 0.000) for 10048 atoms. Found 48 (48 requested) and removed 42 (24 requested) atoms. Cycle 23: After refmac, R = 0.1816 (Rfree = 0.000) for 10007 atoms. Found 47 (47 requested) and removed 46 (23 requested) atoms. Cycle 24: After refmac, R = 0.1739 (Rfree = 0.000) for 9975 atoms. Found 47 (47 requested) and removed 50 (23 requested) atoms. Cycle 25: After refmac, R = 0.1790 (Rfree = 0.000) for 9947 atoms. Found 47 (47 requested) and removed 32 (23 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.77 3.87 Search for helices and strands: 0 residues in 0 chains, 10330 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 10354 seeds are put forward Round 1: 479 peptides, 100 chains. Longest chain 10 peptides. Score 0.271 Round 2: 567 peptides, 98 chains. Longest chain 16 peptides. Score 0.385 Round 3: 575 peptides, 91 chains. Longest chain 18 peptides. Score 0.428 Round 4: 580 peptides, 96 chains. Longest chain 19 peptides. Score 0.409 Round 5: 568 peptides, 91 chains. Longest chain 18 peptides. Score 0.420 Taking the results from Round 3 Chains 92, Residues 484, Estimated correctness of the model 0.0 % 4 chains (26 residues) have been docked in sequence ------------------------------------------------------ 12267 reflections ( 98.92 % complete ) and 24048 restraints for refining 10143 atoms. 22119 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1699 (Rfree = 0.000) for 10143 atoms. Found 48 (48 requested) and removed 43 (24 requested) atoms. Cycle 27: After refmac, R = 0.1734 (Rfree = 0.000) for 10093 atoms. Found 48 (48 requested) and removed 42 (24 requested) atoms. Cycle 28: After refmac, R = 0.1705 (Rfree = 0.000) for 10070 atoms. Found 47 (47 requested) and removed 40 (23 requested) atoms. Cycle 29: After refmac, R = 0.1660 (Rfree = 0.000) for 10038 atoms. Found 47 (47 requested) and removed 38 (23 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1220 (Rfree = 0.000) for 10011 atoms. Found 14 (47 requested) and removed 31 (23 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.76 3.86 Search for helices and strands: 0 residues in 0 chains, 10302 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 10316 seeds are put forward Round 1: 452 peptides, 96 chains. Longest chain 8 peptides. Score 0.258 Round 2: 523 peptides, 96 chains. Longest chain 11 peptides. Score 0.345 Round 3: 543 peptides, 97 chains. Longest chain 13 peptides. Score 0.363 Round 4: 565 peptides, 98 chains. Longest chain 14 peptides. Score 0.383 Round 5: 563 peptides, 92 chains. Longest chain 14 peptides. Score 0.410 Taking the results from Round 5 Chains 93, Residues 471, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 12267 reflections ( 98.92 % complete ) and 24305 restraints for refining 10140 atoms. 22477 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1756 (Rfree = 0.000) for 10140 atoms. Found 48 (48 requested) and removed 50 (24 requested) atoms. Cycle 32: After refmac, R = 0.1735 (Rfree = 0.000) for 10085 atoms. Found 48 (48 requested) and removed 42 (24 requested) atoms. Cycle 33: After refmac, R = 0.1654 (Rfree = 0.000) for 10059 atoms. Found 47 (47 requested) and removed 43 (23 requested) atoms. Cycle 34: After refmac, R = 0.1197 (Rfree = 0.000) for 10034 atoms. Found 14 (47 requested) and removed 28 (23 requested) atoms. Cycle 35: After refmac, R = 0.1091 (Rfree = 0.000) for 10008 atoms. Found 13 (47 requested) and removed 29 (23 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.78 3.88 Search for helices and strands: 0 residues in 0 chains, 10250 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 10263 seeds are put forward Round 1: 442 peptides, 94 chains. Longest chain 10 peptides. Score 0.256 Round 2: 511 peptides, 92 chains. Longest chain 15 peptides. Score 0.351 Round 3: 528 peptides, 96 chains. Longest chain 12 peptides. Score 0.351 Round 4: 530 peptides, 92 chains. Longest chain 14 peptides. Score 0.373 Round 5: 538 peptides, 98 chains. Longest chain 15 peptides. Score 0.352 Taking the results from Round 4 Chains 92, Residues 438, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 12267 reflections ( 98.92 % complete ) and 24432 restraints for refining 10139 atoms. 22751 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1736 (Rfree = 0.000) for 10139 atoms. Found 48 (48 requested) and removed 47 (24 requested) atoms. Cycle 37: After refmac, R = 0.1645 (Rfree = 0.000) for 10084 atoms. Found 48 (48 requested) and removed 45 (24 requested) atoms. Cycle 38: After refmac, R = 0.1152 (Rfree = 0.000) for 10063 atoms. Found 21 (47 requested) and removed 28 (23 requested) atoms. Cycle 39: After refmac, R = 0.1049 (Rfree = 0.000) for 10034 atoms. Found 8 (47 requested) and removed 30 (23 requested) atoms. Cycle 40: After refmac, R = 0.1004 (Rfree = 0.000) for 10000 atoms. Found 6 (47 requested) and removed 27 (23 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.76 3.86 Search for helices and strands: 0 residues in 0 chains, 10255 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 10268 seeds are put forward Round 1: 362 peptides, 78 chains. Longest chain 9 peptides. Score 0.238 Round 2: 395 peptides, 77 chains. Longest chain 10 peptides. Score 0.288 Round 3: 405 peptides, 75 chains. Longest chain 9 peptides. Score 0.312 Round 4: 437 peptides, 82 chains. Longest chain 11 peptides. Score 0.314 Round 5: 449 peptides, 83 chains. Longest chain 15 peptides. Score 0.323 Taking the results from Round 5 Chains 83, Residues 366, Estimated correctness of the model 0.0 % 4 chains (16 residues) have been docked in sequence ------------------------------------------------------ 12267 reflections ( 98.92 % complete ) and 24973 restraints for refining 10143 atoms. 23560 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1757 (Rfree = 0.000) for 10143 atoms. Found 48 (48 requested) and removed 60 (24 requested) atoms. Cycle 42: After refmac, R = 0.1797 (Rfree = 0.000) for 10069 atoms. Found 48 (48 requested) and removed 46 (24 requested) atoms. Cycle 43: After refmac, R = 0.1703 (Rfree = 0.000) for 10027 atoms. Found 47 (47 requested) and removed 50 (23 requested) atoms. Cycle 44: After refmac, R = 0.1759 (Rfree = 0.000) for 10004 atoms. Found 47 (47 requested) and removed 44 (23 requested) atoms. Cycle 45: After refmac, R = 0.1178 (Rfree = 0.000) for 9984 atoms. Found 17 (47 requested) and removed 25 (23 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.77 3.87 Search for helices and strands: 0 residues in 0 chains, 10278 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 10297 seeds are put forward Round 1: 375 peptides, 84 chains. Longest chain 9 peptides. Score 0.222 Round 2: 424 peptides, 84 chains. Longest chain 11 peptides. Score 0.287 Round 3: 434 peptides, 82 chains. Longest chain 12 peptides. Score 0.310 Round 4: 429 peptides, 80 chains. Longest chain 19 peptides. Score 0.315 Round 5: 428 peptides, 81 chains. Longest chain 16 peptides. Score 0.308 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 80, Residues 349, 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 1vkn-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12267 reflections ( 98.92 % complete ) and 24413 restraints for refining 9961 atoms. 23097 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1695 (Rfree = 0.000) for 9961 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 47: After refmac, R = 0.2013 (Rfree = 0.000) for 9898 atoms. Found 0 (47 requested) and removed 23 (23 requested) atoms. Cycle 48: After refmac, R = 0.1870 (Rfree = 0.000) for 9837 atoms. Found 0 (46 requested) and removed 23 (23 requested) atoms. Cycle 49: After refmac, R = 0.1920 (Rfree = 0.000) for 9787 atoms. TimeTaking 90.3