Sun 23 Dec 22:23:05 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vm8-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vm8-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vm8-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vm8-3.4-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/1vm8-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vm8-3.4-parrot-hancs ############### 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 22:23:15 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/hancs/ArpWArp/wArpResults/WorkingDir/1vm8-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vm8-3.4-parrot-hancs/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 846 and 0 Target number of residues in the AU: 846 Target solvent content: 0.6311 Checking the provided sequence file Detected sequence length: 534 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 1068 Adjusted target solvent content: 0.53 Input MTZ file: 1vm8-3.4-parrot-hancs.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: 80.094 73.402 107.132 90.000 99.827 90.000 Input sequence file: 1vm8-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 8544 target number of atoms Had to go as low as 0.60 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: 105.560 3.400 Wilson plot Bfac: 67.13 16970 reflections ( 99.23 % complete ) and 0 restraints for refining 9487 atoms. Observations/parameters ratio is 0.45 ------------------------------------------------------ Starting model: R = 0.3250 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2905 (Rfree = 0.000) for 9487 atoms. Found 71 (71 requested) and removed 162 (35 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.28 3.15 Search for helices and strands: 0 residues in 0 chains, 9594 seeds are put forward NCS extension: 0 residues added, 9594 seeds are put forward Round 1: 433 peptides, 81 chains. Longest chain 17 peptides. Score 0.333 Round 2: 512 peptides, 82 chains. Longest chain 20 peptides. Score 0.432 Round 3: 543 peptides, 86 chains. Longest chain 17 peptides. Score 0.449 Round 4: 530 peptides, 82 chains. Longest chain 17 peptides. Score 0.455 Round 5: 568 peptides, 78 chains. Longest chain 23 peptides. Score 0.520 Taking the results from Round 5 Chains 81, Residues 490, Estimated correctness of the model 0.4 % 5 chains (46 residues) have been docked in sequence ------------------------------------------------------ 16970 reflections ( 99.23 % complete ) and 17767 restraints for refining 7767 atoms. 15746 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2352 (Rfree = 0.000) for 7767 atoms. Found 51 (58 requested) and removed 79 (29 requested) atoms. Cycle 2: After refmac, R = 0.2155 (Rfree = 0.000) for 7661 atoms. Found 31 (58 requested) and removed 57 (29 requested) atoms. Cycle 3: After refmac, R = 0.2070 (Rfree = 0.000) for 7599 atoms. Found 21 (57 requested) and removed 34 (28 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2011 (Rfree = 0.000) for 7566 atoms. Found 18 (57 requested) and removed 39 (28 requested) atoms. Cycle 5: After refmac, R = 0.1937 (Rfree = 0.000) for 7532 atoms. Found 11 (56 requested) and removed 32 (28 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.28 3.15 Search for helices and strands: 0 residues in 0 chains, 7783 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 7808 seeds are put forward Round 1: 504 peptides, 89 chains. Longest chain 20 peptides. Score 0.383 Round 2: 551 peptides, 87 chains. Longest chain 16 peptides. Score 0.453 Round 3: 566 peptides, 84 chains. Longest chain 22 peptides. Score 0.487 Round 4: 565 peptides, 81 chains. Longest chain 20 peptides. Score 0.501 Round 5: 591 peptides, 83 chains. Longest chain 27 peptides. Score 0.520 Taking the results from Round 5 Chains 86, Residues 508, Estimated correctness of the model 0.4 % 4 chains (33 residues) have been docked in sequence ------------------------------------------------------ 16970 reflections ( 99.23 % complete ) and 17684 restraints for refining 7768 atoms. 15656 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2190 (Rfree = 0.000) for 7768 atoms. Found 42 (58 requested) and removed 51 (29 requested) atoms. Cycle 7: After refmac, R = 0.2074 (Rfree = 0.000) for 7722 atoms. Found 30 (58 requested) and removed 39 (29 requested) atoms. Cycle 8: After refmac, R = 0.2054 (Rfree = 0.000) for 7683 atoms. Found 21 (58 requested) and removed 38 (29 requested) atoms. Cycle 9: After refmac, R = 0.2035 (Rfree = 0.000) for 7644 atoms. Found 20 (57 requested) and removed 38 (28 requested) atoms. Cycle 10: After refmac, R = 0.1977 (Rfree = 0.000) for 7615 atoms. Found 27 (57 requested) and removed 37 (28 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.27 3.14 Search for helices and strands: 0 residues in 0 chains, 7928 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 7943 seeds are put forward Round 1: 491 peptides, 88 chains. Longest chain 19 peptides. Score 0.371 Round 2: 535 peptides, 81 chains. Longest chain 20 peptides. Score 0.466 Round 3: 544 peptides, 80 chains. Longest chain 20 peptides. Score 0.482 Round 4: 533 peptides, 76 chains. Longest chain 21 peptides. Score 0.490 Round 5: 535 peptides, 74 chains. Longest chain 20 peptides. Score 0.502 Taking the results from Round 5 Chains 75, Residues 461, Estimated correctness of the model 0.0 % 3 chains (25 residues) have been docked in sequence ------------------------------------------------------ 16970 reflections ( 99.23 % complete ) and 17665 restraints for refining 7768 atoms. 15810 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2176 (Rfree = 0.000) for 7768 atoms. Found 40 (58 requested) and removed 47 (29 requested) atoms. Cycle 12: After refmac, R = 0.2029 (Rfree = 0.000) for 7721 atoms. Found 24 (58 requested) and removed 36 (29 requested) atoms. Cycle 13: After refmac, R = 0.2011 (Rfree = 0.000) for 7688 atoms. Found 18 (58 requested) and removed 36 (29 requested) atoms. Cycle 14: After refmac, R = 0.1945 (Rfree = 0.000) for 7661 atoms. Found 13 (57 requested) and removed 33 (28 requested) atoms. Cycle 15: After refmac, R = 0.1927 (Rfree = 0.000) for 7623 atoms. Found 19 (57 requested) and removed 34 (28 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.28 3.15 Search for helices and strands: 0 residues in 0 chains, 7869 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 7883 seeds are put forward Round 1: 493 peptides, 86 chains. Longest chain 22 peptides. Score 0.385 Round 2: 536 peptides, 80 chains. Longest chain 25 peptides. Score 0.472 Round 3: 565 peptides, 83 chains. Longest chain 25 peptides. Score 0.491 Round 4: 559 peptides, 74 chains. Longest chain 25 peptides. Score 0.530 Round 5: 554 peptides, 72 chains. Longest chain 24 peptides. Score 0.534 Taking the results from Round 5 Chains 73, Residues 482, Estimated correctness of the model 5.7 % 6 chains (55 residues) have been docked in sequence ------------------------------------------------------ 16970 reflections ( 99.23 % complete ) and 17091 restraints for refining 7767 atoms. 15030 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2195 (Rfree = 0.000) for 7767 atoms. Found 52 (58 requested) and removed 42 (29 requested) atoms. Cycle 17: After refmac, R = 0.2076 (Rfree = 0.000) for 7750 atoms. Found 22 (58 requested) and removed 35 (29 requested) atoms. Cycle 18: After refmac, R = 0.2016 (Rfree = 0.000) for 7715 atoms. Found 33 (58 requested) and removed 30 (29 requested) atoms. Cycle 19: After refmac, R = 0.1988 (Rfree = 0.000) for 7695 atoms. Found 27 (58 requested) and removed 33 (29 requested) atoms. Cycle 20: After refmac, R = 0.1887 (Rfree = 0.000) for 7674 atoms. Found 11 (58 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.29 3.16 Search for helices and strands: 0 residues in 0 chains, 7884 seeds are put forward NCS extension: 23 residues added (4 deleted due to clashes), 7907 seeds are put forward Round 1: 482 peptides, 87 chains. Longest chain 15 peptides. Score 0.365 Round 2: 546 peptides, 80 chains. Longest chain 19 peptides. Score 0.484 Round 3: 562 peptides, 80 chains. Longest chain 22 peptides. Score 0.503 Round 4: 564 peptides, 81 chains. Longest chain 20 peptides. Score 0.500 Round 5: 573 peptides, 80 chains. Longest chain 21 peptides. Score 0.515 Taking the results from Round 5 Chains 83, Residues 493, Estimated correctness of the model 0.0 % 8 chains (54 residues) have been docked in sequence ------------------------------------------------------ 16970 reflections ( 99.23 % complete ) and 17240 restraints for refining 7767 atoms. 15183 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2167 (Rfree = 0.000) for 7767 atoms. Found 48 (58 requested) and removed 47 (29 requested) atoms. Cycle 22: After refmac, R = 0.2048 (Rfree = 0.000) for 7737 atoms. Found 18 (58 requested) and removed 33 (29 requested) atoms. Cycle 23: After refmac, R = 0.2010 (Rfree = 0.000) for 7705 atoms. Found 26 (58 requested) and removed 40 (29 requested) atoms. Cycle 24: After refmac, R = 0.1937 (Rfree = 0.000) for 7676 atoms. Found 23 (58 requested) and removed 33 (29 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1884 (Rfree = 0.000) for 7659 atoms. Found 17 (57 requested) and removed 30 (28 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.29 3.16 Search for helices and strands: 0 residues in 0 chains, 7882 seeds are put forward NCS extension: 21 residues added (4 deleted due to clashes), 7903 seeds are put forward Round 1: 480 peptides, 87 chains. Longest chain 17 peptides. Score 0.362 Round 2: 549 peptides, 84 chains. Longest chain 18 peptides. Score 0.467 Round 3: 562 peptides, 85 chains. Longest chain 19 peptides. Score 0.477 Round 4: 574 peptides, 87 chains. Longest chain 21 peptides. Score 0.481 Round 5: 567 peptides, 81 chains. Longest chain 32 peptides. Score 0.503 Taking the results from Round 5 Chains 83, Residues 486, Estimated correctness of the model 0.0 % 8 chains (65 residues) have been docked in sequence ------------------------------------------------------ 16970 reflections ( 99.23 % complete ) and 17034 restraints for refining 7766 atoms. 14974 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2137 (Rfree = 0.000) for 7766 atoms. Found 58 (58 requested) and removed 48 (29 requested) atoms. Cycle 27: After refmac, R = 0.1969 (Rfree = 0.000) for 7744 atoms. Found 22 (58 requested) and removed 34 (29 requested) atoms. Cycle 28: After refmac, R = 0.1961 (Rfree = 0.000) for 7726 atoms. Found 29 (58 requested) and removed 33 (29 requested) atoms. Cycle 29: After refmac, R = 0.1949 (Rfree = 0.000) for 7713 atoms. Found 25 (58 requested) and removed 31 (29 requested) atoms. Cycle 30: After refmac, R = 0.1872 (Rfree = 0.000) for 7695 atoms. Found 14 (58 requested) and removed 30 (29 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.28 3.15 Search for helices and strands: 0 residues in 0 chains, 7894 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 7910 seeds are put forward Round 1: 446 peptides, 82 chains. Longest chain 17 peptides. Score 0.345 Round 2: 480 peptides, 75 chains. Longest chain 17 peptides. Score 0.431 Round 3: 509 peptides, 76 chains. Longest chain 22 peptides. Score 0.461 Round 4: 515 peptides, 80 chains. Longest chain 23 peptides. Score 0.447 Round 5: 508 peptides, 77 chains. Longest chain 23 peptides. Score 0.455 Taking the results from Round 3 Chains 78, Residues 433, Estimated correctness of the model 0.0 % 5 chains (35 residues) have been docked in sequence ------------------------------------------------------ 16970 reflections ( 99.23 % complete ) and 17699 restraints for refining 7766 atoms. 15936 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2095 (Rfree = 0.000) for 7766 atoms. Found 41 (58 requested) and removed 34 (29 requested) atoms. Cycle 32: After refmac, R = 0.2010 (Rfree = 0.000) for 7753 atoms. Found 27 (58 requested) and removed 36 (29 requested) atoms. Cycle 33: After refmac, R = 0.1922 (Rfree = 0.000) for 7735 atoms. Found 21 (58 requested) and removed 30 (29 requested) atoms. Cycle 34: After refmac, R = 0.1874 (Rfree = 0.000) for 7711 atoms. Found 12 (58 requested) and removed 30 (29 requested) atoms. Cycle 35: After refmac, R = 0.1868 (Rfree = 0.000) for 7683 atoms. Found 26 (58 requested) and removed 30 (29 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.29 3.16 Search for helices and strands: 0 residues in 0 chains, 7892 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 7913 seeds are put forward Round 1: 410 peptides, 74 chains. Longest chain 15 peptides. Score 0.343 Round 2: 453 peptides, 70 chains. Longest chain 18 peptides. Score 0.424 Round 3: 457 peptides, 74 chains. Longest chain 18 peptides. Score 0.407 Round 4: 496 peptides, 80 chains. Longest chain 18 peptides. Score 0.423 Round 5: 505 peptides, 81 chains. Longest chain 16 peptides. Score 0.429 Taking the results from Round 5 Chains 81, Residues 424, Estimated correctness of the model 0.0 % 10 chains (75 residues) have been docked in sequence ------------------------------------------------------ 16970 reflections ( 99.23 % complete ) and 17454 restraints for refining 7768 atoms. 15582 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2080 (Rfree = 0.000) for 7768 atoms. Found 47 (58 requested) and removed 43 (29 requested) atoms. Cycle 37: After refmac, R = 0.1996 (Rfree = 0.000) for 7747 atoms. Found 28 (58 requested) and removed 40 (29 requested) atoms. Cycle 38: After refmac, R = 0.1990 (Rfree = 0.000) for 7719 atoms. Found 35 (58 requested) and removed 31 (29 requested) atoms. Cycle 39: After refmac, R = 0.1874 (Rfree = 0.000) for 7718 atoms. Found 30 (58 requested) and removed 30 (29 requested) atoms. Cycle 40: After refmac, R = 0.1839 (Rfree = 0.000) for 7712 atoms. Found 14 (58 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.29 3.16 Search for helices and strands: 0 residues in 0 chains, 7897 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 7913 seeds are put forward Round 1: 444 peptides, 90 chains. Longest chain 16 peptides. Score 0.295 Round 2: 507 peptides, 89 chains. Longest chain 15 peptides. Score 0.387 Round 3: 513 peptides, 79 chains. Longest chain 19 peptides. Score 0.450 Round 4: 511 peptides, 80 chains. Longest chain 16 peptides. Score 0.442 Round 5: 528 peptides, 78 chains. Longest chain 20 peptides. Score 0.473 Taking the results from Round 5 Chains 79, Residues 450, Estimated correctness of the model 0.0 % 5 chains (27 residues) have been docked in sequence ------------------------------------------------------ 16970 reflections ( 99.23 % complete ) and 17678 restraints for refining 7768 atoms. 15895 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2059 (Rfree = 0.000) for 7768 atoms. Found 50 (58 requested) and removed 41 (29 requested) atoms. Cycle 42: After refmac, R = 0.2014 (Rfree = 0.000) for 7757 atoms. Found 38 (58 requested) and removed 36 (29 requested) atoms. Cycle 43: After refmac, R = 0.1934 (Rfree = 0.000) for 7749 atoms. Found 40 (58 requested) and removed 32 (29 requested) atoms. Cycle 44: After refmac, R = 0.1906 (Rfree = 0.000) for 7746 atoms. Found 34 (58 requested) and removed 31 (29 requested) atoms. Cycle 45: After refmac, R = 0.1849 (Rfree = 0.000) for 7737 atoms. Found 19 (58 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.28 3.15 Search for helices and strands: 0 residues in 0 chains, 7912 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 7932 seeds are put forward Round 1: 399 peptides, 81 chains. Longest chain 11 peptides. Score 0.284 Round 2: 464 peptides, 77 chains. Longest chain 14 peptides. Score 0.399 Round 3: 449 peptides, 76 chains. Longest chain 14 peptides. Score 0.385 Round 4: 457 peptides, 71 chains. Longest chain 20 peptides. Score 0.424 Round 5: 455 peptides, 79 chains. Longest chain 12 peptides. Score 0.375 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 73, Residues 386, Estimated correctness of the model 0.0 % 5 chains (29 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 1vm8-3_warpNtrace.pdb as input Building loops using Loopy2018 73 chains (386 residues) following loop building 5 chains (29 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16970 reflections ( 99.23 % complete ) and 18054 restraints for refining 7768 atoms. 16487 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1948 (Rfree = 0.000) for 7768 atoms. Found 0 (58 requested) and removed 29 (29 requested) atoms. Cycle 47: After refmac, R = 0.1936 (Rfree = 0.000) for 7725 atoms. Found 0 (58 requested) and removed 22 (29 requested) atoms. Cycle 48: After refmac, R = 0.1905 (Rfree = 0.000) for 7693 atoms. Found 0 (58 requested) and removed 20 (29 requested) atoms. Cycle 49: After refmac, R = 0.1881 (Rfree = 0.000) for 7668 atoms. TimeTaking 93.53