Sun 23 Dec 22:23:08 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 1vl6-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vl6-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vl6-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl6-4.0-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/1vl6-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl6-4.0-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 22:23:18 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/1vl6-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl6-4.0-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 1174 and 0 Target number of residues in the AU: 1174 Target solvent content: 0.6750 Checking the provided sequence file Detected sequence length: 388 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1552 Adjusted target solvent content: 0.57 Input MTZ file: 1vl6-4.0-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: 170 Cell parameters: 144.124 144.124 163.018 90.000 90.000 120.000 Input sequence file: 1vl6-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 12416 target number of atoms Had to go as low as 0.90 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: 124.815 4.000 Wilson plot Bfac: 96.72 16252 reflections ( 99.83 % complete ) and 0 restraints for refining 13784 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3464 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3319 (Rfree = 0.000) for 13784 atoms. Found 65 (65 requested) and removed 76 (32 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.90 3.55 Search for helices and strands: 0 residues in 0 chains, 14003 seeds are put forward NCS extension: 0 residues added, 14003 seeds are put forward Round 1: 496 peptides, 92 chains. Longest chain 11 peptides. Score 0.303 Round 2: 671 peptides, 101 chains. Longest chain 19 peptides. Score 0.423 Round 3: 736 peptides, 102 chains. Longest chain 21 peptides. Score 0.472 Round 4: 780 peptides, 100 chains. Longest chain 21 peptides. Score 0.511 Round 5: 766 peptides, 86 chains. Longest chain 36 peptides. Score 0.547 Taking the results from Round 5 Chains 92, Residues 680, Estimated correctness of the model 0.0 % 13 chains (134 residues) have been docked in sequence ------------------------------------------------------ 16252 reflections ( 99.83 % complete ) and 25370 restraints for refining 11204 atoms. 22293 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2608 (Rfree = 0.000) for 11204 atoms. Found 53 (53 requested) and removed 73 (26 requested) atoms. Cycle 2: After refmac, R = 0.2548 (Rfree = 0.000) for 10995 atoms. Found 23 (53 requested) and removed 39 (26 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2498 (Rfree = 0.000) for 10952 atoms. Found 14 (52 requested) and removed 35 (26 requested) atoms. Cycle 4: After refmac, R = 0.2450 (Rfree = 0.000) for 10913 atoms. Found 8 (51 requested) and removed 30 (25 requested) atoms. Cycle 5: After refmac, R = 0.2412 (Rfree = 0.000) for 10872 atoms. Found 6 (51 requested) and removed 28 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.87 3.52 Search for helices and strands: 0 residues in 0 chains, 11204 seeds are put forward NCS extension: 42 residues added (1 deleted due to clashes), 11246 seeds are put forward Round 1: 730 peptides, 116 chains. Longest chain 15 peptides. Score 0.417 Round 2: 815 peptides, 97 chains. Longest chain 43 peptides. Score 0.546 Round 3: 784 peptides, 96 chains. Longest chain 22 peptides. Score 0.527 Round 4: 797 peptides, 94 chains. Longest chain 21 peptides. Score 0.543 Round 5: 793 peptides, 89 chains. Longest chain 26 peptides. Score 0.556 Taking the results from Round 5 Chains 95, Residues 704, Estimated correctness of the model 0.0 % 6 chains (63 residues) have been docked in sequence ------------------------------------------------------ 16252 reflections ( 99.83 % complete ) and 25873 restraints for refining 11210 atoms. 22942 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2433 (Rfree = 0.000) for 11210 atoms. Found 36 (53 requested) and removed 67 (26 requested) atoms. Cycle 7: After refmac, R = 0.2278 (Rfree = 0.000) for 11046 atoms. Found 20 (53 requested) and removed 42 (26 requested) atoms. Cycle 8: After refmac, R = 0.2210 (Rfree = 0.000) for 10966 atoms. Found 11 (52 requested) and removed 41 (26 requested) atoms. Cycle 9: After refmac, R = 0.2218 (Rfree = 0.000) for 10909 atoms. Found 14 (51 requested) and removed 32 (25 requested) atoms. Cycle 10: After refmac, R = 0.2186 (Rfree = 0.000) for 10867 atoms. Found 5 (51 requested) and removed 26 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.87 3.52 Search for helices and strands: 0 residues in 0 chains, 11228 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 11250 seeds are put forward Round 1: 719 peptides, 118 chains. Longest chain 14 peptides. Score 0.401 Round 2: 790 peptides, 107 chains. Longest chain 21 peptides. Score 0.495 Failed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDB Round 3: 800 peptides, 105 chains. Longest chain 24 peptides. Score 0.509 Round 4: 801 peptides, 91 chains. Longest chain 23 peptides. Score 0.555 Round 5: 817 peptides, 104 chains. Longest chain 23 peptides. Score 0.525 Taking the results from Round 4 Chains 95, Residues 710, Estimated correctness of the model 0.0 % 5 chains (54 residues) have been docked in sequence ------------------------------------------------------ 16252 reflections ( 99.83 % complete ) and 25594 restraints for refining 11208 atoms. 22650 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2459 (Rfree = 0.000) for 11208 atoms. Found 45 (53 requested) and removed 48 (26 requested) atoms. Cycle 12: After refmac, R = 0.2406 (Rfree = 0.000) for 11126 atoms. Found 23 (53 requested) and removed 35 (26 requested) atoms. Cycle 13: After refmac, R = 0.2375 (Rfree = 0.000) for 11097 atoms. Found 6 (52 requested) and removed 29 (26 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2366 (Rfree = 0.000) for 11066 atoms. Found 5 (52 requested) and removed 30 (26 requested) atoms. Cycle 15: After refmac, R = 0.2357 (Rfree = 0.000) for 11038 atoms. Found 1 (52 requested) and removed 28 (26 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.86 3.51 Search for helices and strands: 0 residues in 0 chains, 11379 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 11408 seeds are put forward Round 1: 687 peptides, 117 chains. Longest chain 14 peptides. Score 0.377 Round 2: 756 peptides, 107 chains. Longest chain 18 peptides. Score 0.470 Round 3: 781 peptides, 104 chains. Longest chain 22 peptides. Score 0.499 Round 4: 775 peptides, 102 chains. Longest chain 24 peptides. Score 0.501 Round 5: 764 peptides, 98 chains. Longest chain 23 peptides. Score 0.506 Taking the results from Round 5 Chains 105, Residues 666, Estimated correctness of the model 0.0 % 9 chains (76 residues) have been docked in sequence ------------------------------------------------------ 16252 reflections ( 99.83 % complete ) and 25513 restraints for refining 11212 atoms. 22719 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2525 (Rfree = 0.000) for 11212 atoms. Found 43 (53 requested) and removed 61 (26 requested) atoms. Cycle 17: After refmac, R = 0.2178 (Rfree = 0.000) for 11082 atoms. Found 28 (53 requested) and removed 53 (26 requested) atoms. Cycle 18: After refmac, R = 0.2150 (Rfree = 0.000) for 10990 atoms. Found 27 (52 requested) and removed 56 (26 requested) atoms. Cycle 19: After refmac, R = 0.2002 (Rfree = 0.000) for 10917 atoms. Found 23 (52 requested) and removed 42 (26 requested) atoms. Cycle 20: After refmac, R = 0.1832 (Rfree = 0.000) for 10864 atoms. Found 9 (51 requested) and removed 41 (25 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.84 3.50 Search for helices and strands: 0 residues in 0 chains, 11204 seeds are put forward NCS extension: 22 residues added (5 deleted due to clashes), 11226 seeds are put forward Round 1: 647 peptides, 117 chains. Longest chain 15 peptides. Score 0.342 Round 2: 719 peptides, 108 chains. Longest chain 15 peptides. Score 0.437 Round 3: 736 peptides, 110 chains. Longest chain 23 peptides. Score 0.443 Round 4: 736 peptides, 108 chains. Longest chain 23 peptides. Score 0.451 Round 5: 760 peptides, 110 chains. Longest chain 20 peptides. Score 0.462 Taking the results from Round 5 Chains 114, Residues 650, Estimated correctness of the model 0.0 % 10 chains (67 residues) have been docked in sequence ------------------------------------------------------ 16252 reflections ( 99.83 % complete ) and 26147 restraints for refining 11210 atoms. 23477 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2123 (Rfree = 0.000) for 11210 atoms. Found 37 (53 requested) and removed 56 (26 requested) atoms. Cycle 22: After refmac, R = 0.1904 (Rfree = 0.000) for 11124 atoms. Found 14 (53 requested) and removed 36 (26 requested) atoms. Cycle 23: After refmac, R = 0.1749 (Rfree = 0.000) for 11071 atoms. Found 5 (52 requested) and removed 38 (26 requested) atoms. Cycle 24: After refmac, R = 0.1733 (Rfree = 0.000) for 11020 atoms. Found 6 (52 requested) and removed 31 (26 requested) atoms. Cycle 25: After refmac, R = 0.1741 (Rfree = 0.000) for 10989 atoms. Found 2 (52 requested) and removed 28 (26 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.85 3.51 Search for helices and strands: 0 residues in 0 chains, 11296 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 11317 seeds are put forward Round 1: 666 peptides, 119 chains. Longest chain 15 peptides. Score 0.352 Round 2: 724 peptides, 109 chains. Longest chain 17 peptides. Score 0.437 Round 3: 720 peptides, 107 chains. Longest chain 22 peptides. Score 0.441 Round 4: 747 peptides, 109 chains. Longest chain 19 peptides. Score 0.456 Round 5: 739 peptides, 115 chains. Longest chain 20 peptides. Score 0.428 Taking the results from Round 4 Chains 109, Residues 638, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 16252 reflections ( 99.83 % complete ) and 26874 restraints for refining 11211 atoms. 24431 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2098 (Rfree = 0.000) for 11211 atoms. Found 42 (53 requested) and removed 44 (26 requested) atoms. Cycle 27: After refmac, R = 0.2079 (Rfree = 0.000) for 11127 atoms. Found 53 (53 requested) and removed 42 (26 requested) atoms. Cycle 28: After refmac, R = 0.2050 (Rfree = 0.000) for 11063 atoms. Found 52 (52 requested) and removed 44 (26 requested) atoms. Cycle 29: After refmac, R = 0.1941 (Rfree = 0.000) for 11010 atoms. Found 50 (52 requested) and removed 43 (26 requested) atoms. Cycle 30: After refmac, R = 0.1881 (Rfree = 0.000) for 10980 atoms. Found 46 (52 requested) and removed 45 (26 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.88 3.53 Search for helices and strands: 0 residues in 0 chains, 11371 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 11395 seeds are put forward Round 1: 555 peptides, 113 chains. Longest chain 13 peptides. Score 0.273 Round 2: 638 peptides, 106 chains. Longest chain 14 peptides. Score 0.377 Round 3: 686 peptides, 109 chains. Longest chain 25 peptides. Score 0.406 Round 4: 695 peptides, 108 chains. Longest chain 17 peptides. Score 0.417 Round 5: 714 peptides, 107 chains. Longest chain 18 peptides. Score 0.436 Taking the results from Round 5 Chains 107, Residues 607, Estimated correctness of the model 0.0 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 16252 reflections ( 99.83 % complete ) and 26388 restraints for refining 11211 atoms. 24009 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2116 (Rfree = 0.000) for 11211 atoms. Found 53 (53 requested) and removed 62 (26 requested) atoms. Cycle 32: After refmac, R = 0.1987 (Rfree = 0.000) for 11139 atoms. Found 53 (53 requested) and removed 51 (26 requested) atoms. Cycle 33: After refmac, R = 0.1895 (Rfree = 0.000) for 11091 atoms. Found 52 (52 requested) and removed 56 (26 requested) atoms. Cycle 34: After refmac, R = 0.1515 (Rfree = 0.000) for 11051 atoms. Found 6 (52 requested) and removed 39 (26 requested) atoms. Cycle 35: After refmac, R = 0.1433 (Rfree = 0.000) for 10997 atoms. Found 11 (52 requested) and removed 46 (26 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.85 3.51 Search for helices and strands: 0 residues in 0 chains, 11273 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 11298 seeds are put forward Round 1: 530 peptides, 108 chains. Longest chain 13 peptides. Score 0.269 Round 2: 667 peptides, 117 chains. Longest chain 16 peptides. Score 0.360 Round 3: 672 peptides, 110 chains. Longest chain 19 peptides. Score 0.391 Round 4: 683 peptides, 110 chains. Longest chain 17 peptides. Score 0.400 Round 5: 693 peptides, 104 chains. Longest chain 19 peptides. Score 0.430 Taking the results from Round 5 Chains 105, Residues 589, Estimated correctness of the model 0.0 % 5 chains (40 residues) have been docked in sequence ------------------------------------------------------ 16252 reflections ( 99.83 % complete ) and 26402 restraints for refining 11212 atoms. 24017 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2043 (Rfree = 0.000) for 11212 atoms. Found 42 (53 requested) and removed 57 (26 requested) atoms. Cycle 37: After refmac, R = 0.2041 (Rfree = 0.000) for 11128 atoms. Found 53 (53 requested) and removed 56 (26 requested) atoms. Cycle 38: After refmac, R = 0.1937 (Rfree = 0.000) for 11087 atoms. Found 52 (52 requested) and removed 49 (26 requested) atoms. Cycle 39: After refmac, R = 0.1840 (Rfree = 0.000) for 11050 atoms. Found 52 (52 requested) and removed 46 (26 requested) atoms. Cycle 40: After refmac, R = 0.1542 (Rfree = 0.000) for 11022 atoms. Found 6 (52 requested) and removed 29 (26 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.87 3.52 Search for helices and strands: 0 residues in 0 chains, 11345 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 11365 seeds are put forward Round 1: 514 peptides, 105 chains. Longest chain 10 peptides. Score 0.266 Round 2: 626 peptides, 112 chains. Longest chain 13 peptides. Score 0.343 Round 3: 623 peptides, 101 chains. Longest chain 16 peptides. Score 0.383 Round 4: 637 peptides, 100 chains. Longest chain 14 peptides. Score 0.399 Round 5: 625 peptides, 99 chains. Longest chain 14 peptides. Score 0.392 Taking the results from Round 4 Chains 100, Residues 537, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 16252 reflections ( 99.83 % complete ) and 26946 restraints for refining 11213 atoms. 24866 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1991 (Rfree = 0.000) for 11213 atoms. Found 37 (53 requested) and removed 50 (26 requested) atoms. Cycle 42: After refmac, R = 0.1962 (Rfree = 0.000) for 11115 atoms. Found 53 (53 requested) and removed 45 (26 requested) atoms. Cycle 43: After refmac, R = 0.1854 (Rfree = 0.000) for 11078 atoms. Found 52 (52 requested) and removed 51 (26 requested) atoms. Cycle 44: After refmac, R = 0.1881 (Rfree = 0.000) for 11047 atoms. Found 52 (52 requested) and removed 53 (26 requested) atoms. Cycle 45: After refmac, R = 0.1836 (Rfree = 0.000) for 11029 atoms. Found 52 (52 requested) and removed 36 (26 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.86 3.51 Search for helices and strands: 0 residues in 0 chains, 11405 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 11421 seeds are put forward Round 1: 516 peptides, 104 chains. Longest chain 12 peptides. Score 0.272 Round 2: 609 peptides, 103 chains. Longest chain 16 peptides. Score 0.363 Round 3: 612 peptides, 101 chains. Longest chain 12 peptides. Score 0.373 Round 4: 617 peptides, 105 chains. Longest chain 14 peptides. Score 0.362 Round 5: 595 peptides, 101 chains. Longest chain 12 peptides. Score 0.358 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 102, Residues 511, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence Sequence coverage is 1 % Consider running further cycles of model building using 1vl6-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. Failed to save intermediate PDB 16252 reflections ( 99.83 % complete ) and 26858 restraints for refining 11213 atoms. 24881 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2022 (Rfree = 0.000) for 11213 atoms. Found 0 (53 requested) and removed 26 (26 requested) atoms. Cycle 47: After refmac, R = 0.1952 (Rfree = 0.000) for 11138 atoms. Found 0 (53 requested) and removed 26 (26 requested) atoms. Cycle 48: After refmac, R = 0.1900 (Rfree = 0.000) for 11068 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Cycle 49: After refmac, R = 0.1927 (Rfree = 0.000) for 11008 atoms. TimeTaking 133.8