null 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 2p10-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p10-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p10-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p10-4.0-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/2p10-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p10-4.0-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 22:23:15 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/2p10-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p10-4.0-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 1409 and 0 Target number of residues in the AU: 1409 Target solvent content: 0.6714 Checking the provided sequence file Detected sequence length: 286 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1716 Adjusted target solvent content: 0.60 Input MTZ file: 2p10-4.0-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: 146 Cell parameters: 180.269 180.269 185.514 90.000 90.000 120.000 Input sequence file: 2p10-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 13728 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: 119.449 4.001 Wilson plot Bfac: 93.52 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 18377 reflections ( 96.69 % complete ) and 0 restraints for refining 15107 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3179 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3136 (Rfree = 0.000) for 15107 atoms. Found 71 (71 requested) and removed 341 (35 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.84 3.36 Search for helices and strands: 0 residues in 0 chains, 15120 seeds are put forward NCS extension: 0 residues added, 15120 seeds are put forward Round 1: 641 peptides, 116 chains. Longest chain 12 peptides. Score 0.321 Round 2: 800 peptides, 116 chains. Longest chain 21 peptides. Score 0.438 Round 3: 824 peptides, 107 chains. Longest chain 27 peptides. Score 0.481 Round 4: 880 peptides, 111 chains. Longest chain 26 peptides. Score 0.505 Round 5: 883 peptides, 113 chains. Longest chain 28 peptides. Score 0.501 Taking the results from Round 4 Chains 120, Residues 769, Estimated correctness of the model 0.0 % 19 chains (136 residues) have been docked in sequence ------------------------------------------------------ 18377 reflections ( 96.69 % complete ) and 27778 restraints for refining 12324 atoms. 24414 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2462 (Rfree = 0.000) for 12324 atoms. Found 58 (58 requested) and removed 111 (29 requested) atoms. Cycle 2: After refmac, R = 0.2297 (Rfree = 0.000) for 11957 atoms. Found 58 (58 requested) and removed 118 (29 requested) atoms. Cycle 3: After refmac, R = 0.2207 (Rfree = 0.000) for 11748 atoms. Found 56 (56 requested) and removed 100 (28 requested) atoms. Cycle 4: After refmac, R = 0.2150 (Rfree = 0.000) for 11616 atoms. Found 55 (55 requested) and removed 86 (27 requested) atoms. Cycle 5: After refmac, R = 0.2019 (Rfree = 0.000) for 11537 atoms. Found 55 (55 requested) and removed 73 (27 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.82 3.34 Search for helices and strands: 0 residues in 0 chains, 11999 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 12022 seeds are put forward Round 1: 806 peptides, 132 chains. Longest chain 16 peptides. Score 0.392 Round 2: 901 peptides, 114 chains. Longest chain 24 peptides. Score 0.509 Round 3: 884 peptides, 97 chains. Longest chain 22 peptides. Score 0.547 Round 4: 888 peptides, 103 chains. Longest chain 24 peptides. Score 0.532 Round 5: 885 peptides, 97 chains. Longest chain 24 peptides. Score 0.547 Taking the results from Round 5 Chains 106, Residues 788, Estimated correctness of the model 0.0 % 15 chains (149 residues) have been docked in sequence ------------------------------------------------------ 18377 reflections ( 96.69 % complete ) and 26674 restraints for refining 12084 atoms. 23226 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2160 (Rfree = 0.000) for 12084 atoms. Found 57 (57 requested) and removed 228 (28 requested) atoms. Cycle 7: After refmac, R = 0.1988 (Rfree = 0.000) for 11765 atoms. Found 51 (56 requested) and removed 86 (28 requested) atoms. Cycle 8: After refmac, R = 0.1898 (Rfree = 0.000) for 11654 atoms. Found 55 (55 requested) and removed 190 (27 requested) atoms. Cycle 9: After refmac, R = 0.1924 (Rfree = 0.000) for 11486 atoms. Found 54 (54 requested) and removed 130 (27 requested) atoms. Cycle 10: After refmac, R = 0.1646 (Rfree = 0.000) for 11366 atoms. Found 26 (54 requested) and removed 82 (27 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.84 3.36 Search for helices and strands: 0 residues in 0 chains, 11764 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 11791 seeds are put forward Round 1: 810 peptides, 133 chains. Longest chain 20 peptides. Score 0.392 Round 2: 848 peptides, 113 chains. Longest chain 19 peptides. Score 0.479 Round 3: 873 peptides, 106 chains. Longest chain 25 peptides. Score 0.515 Round 4: 880 peptides, 112 chains. Longest chain 27 peptides. Score 0.502 Round 5: 879 peptides, 113 chains. Longest chain 22 peptides. Score 0.498 Taking the results from Round 3 Chains 117, Residues 767, Estimated correctness of the model 0.0 % 19 chains (144 residues) have been docked in sequence ------------------------------------------------------ 18377 reflections ( 96.69 % complete ) and 26165 restraints for refining 11995 atoms. 22832 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2182 (Rfree = 0.000) for 11995 atoms. Found 56 (56 requested) and removed 173 (28 requested) atoms. Cycle 12: After refmac, R = 0.2010 (Rfree = 0.000) for 11782 atoms. Found 56 (56 requested) and removed 99 (28 requested) atoms. Cycle 13: After refmac, R = 0.1979 (Rfree = 0.000) for 11683 atoms. Found 55 (55 requested) and removed 88 (27 requested) atoms. Cycle 14: After refmac, R = 0.1904 (Rfree = 0.000) for 11602 atoms. Found 55 (55 requested) and removed 71 (27 requested) atoms. Cycle 15: After refmac, R = 0.1839 (Rfree = 0.000) for 11562 atoms. Found 45 (55 requested) and removed 78 (27 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.79 3.31 Search for helices and strands: 0 residues in 0 chains, 12000 seeds are put forward NCS extension: 13 residues added (7 deleted due to clashes), 12013 seeds are put forward Round 1: 769 peptides, 129 chains. Longest chain 18 peptides. Score 0.375 Round 2: 830 peptides, 107 chains. Longest chain 26 peptides. Score 0.485 Round 3: 849 peptides, 115 chains. Longest chain 23 peptides. Score 0.474 Round 4: 830 peptides, 114 chains. Longest chain 24 peptides. Score 0.464 Round 5: 843 peptides, 108 chains. Longest chain 23 peptides. Score 0.490 Taking the results from Round 5 Chains 113, Residues 735, Estimated correctness of the model 0.0 % 9 chains (73 residues) have been docked in sequence ------------------------------------------------------ 18377 reflections ( 96.69 % complete ) and 28661 restraints for refining 12394 atoms. 25630 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2093 (Rfree = 0.000) for 12394 atoms. Found 57 (58 requested) and removed 101 (29 requested) atoms. Cycle 17: After refmac, R = 0.2009 (Rfree = 0.000) for 12244 atoms. Found 58 (58 requested) and removed 74 (29 requested) atoms. Cycle 18: After refmac, R = 0.1936 (Rfree = 0.000) for 12167 atoms. Found 58 (58 requested) and removed 71 (29 requested) atoms. Cycle 19: After refmac, R = 0.1596 (Rfree = 0.000) for 12103 atoms. Found 15 (57 requested) and removed 49 (28 requested) atoms. Cycle 20: After refmac, R = 0.1548 (Rfree = 0.000) for 12037 atoms. Found 5 (57 requested) and removed 65 (28 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.81 3.33 Search for helices and strands: 0 residues in 0 chains, 12422 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 12443 seeds are put forward Round 1: 724 peptides, 121 chains. Longest chain 17 peptides. Score 0.368 Round 2: 798 peptides, 111 chains. Longest chain 17 peptides. Score 0.452 Round 3: 842 peptides, 117 chains. Longest chain 21 peptides. Score 0.463 Round 4: 818 peptides, 109 chains. Longest chain 19 peptides. Score 0.471 Round 5: 816 peptides, 105 chains. Longest chain 21 peptides. Score 0.482 Taking the results from Round 5 Chains 113, Residues 711, Estimated correctness of the model 0.0 % 18 chains (134 residues) have been docked in sequence ------------------------------------------------------ 18377 reflections ( 96.69 % complete ) and 28022 restraints for refining 12393 atoms. 24906 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2073 (Rfree = 0.000) for 12393 atoms. Found 47 (58 requested) and removed 80 (29 requested) atoms. Cycle 22: After refmac, R = 0.2043 (Rfree = 0.000) for 12248 atoms. Found 54 (58 requested) and removed 72 (29 requested) atoms. Cycle 23: After refmac, R = 0.1981 (Rfree = 0.000) for 12165 atoms. Found 55 (58 requested) and removed 70 (29 requested) atoms. Cycle 24: After refmac, R = 0.1927 (Rfree = 0.000) for 12117 atoms. Found 45 (57 requested) and removed 57 (28 requested) atoms. Cycle 25: After refmac, R = 0.1917 (Rfree = 0.000) for 12081 atoms. Found 57 (57 requested) and removed 54 (28 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.84 3.36 Search for helices and strands: 0 residues in 0 chains, 12507 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 12529 seeds are put forward Round 1: 743 peptides, 130 chains. Longest chain 16 peptides. Score 0.353 Round 2: 795 peptides, 118 chains. Longest chain 17 peptides. Score 0.428 Round 3: 808 peptides, 119 chains. Longest chain 18 peptides. Score 0.434 Round 4: 838 peptides, 114 chains. Longest chain 17 peptides. Score 0.469 Round 5: 828 peptides, 113 chains. Longest chain 18 peptides. Score 0.466 Taking the results from Round 4 Chains 114, Residues 724, Estimated correctness of the model 0.0 % 8 chains (37 residues) have been docked in sequence ------------------------------------------------------ 18377 reflections ( 96.69 % complete ) and 28969 restraints for refining 12396 atoms. 26101 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2052 (Rfree = 0.000) for 12396 atoms. Found 49 (58 requested) and removed 87 (29 requested) atoms. Cycle 27: After refmac, R = 0.2005 (Rfree = 0.000) for 12249 atoms. Found 58 (58 requested) and removed 61 (29 requested) atoms. Cycle 28: After refmac, R = 0.1921 (Rfree = 0.000) for 12186 atoms. Found 44 (58 requested) and removed 61 (29 requested) atoms. Cycle 29: After refmac, R = 0.1599 (Rfree = 0.000) for 12107 atoms. Found 13 (57 requested) and removed 45 (28 requested) atoms. Cycle 30: After refmac, R = 0.1823 (Rfree = 0.000) for 12043 atoms. Found 57 (57 requested) and removed 53 (28 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.81 3.33 Search for helices and strands: 0 residues in 0 chains, 12449 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 12467 seeds are put forward Round 1: 672 peptides, 121 chains. Longest chain 17 peptides. Score 0.328 Round 2: 753 peptides, 117 chains. Longest chain 17 peptides. Score 0.402 Round 3: 793 peptides, 117 chains. Longest chain 19 peptides. Score 0.430 Round 4: 789 peptides, 108 chains. Longest chain 25 peptides. Score 0.455 Round 5: 760 peptides, 109 chains. Longest chain 19 peptides. Score 0.432 Taking the results from Round 4 Chains 112, Residues 681, Estimated correctness of the model 0.0 % 9 chains (70 residues) have been docked in sequence ------------------------------------------------------ 18377 reflections ( 96.69 % complete ) and 28695 restraints for refining 12395 atoms. 25898 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1916 (Rfree = 0.000) for 12395 atoms. Found 53 (58 requested) and removed 78 (29 requested) atoms. Cycle 32: After refmac, R = 0.1995 (Rfree = 0.000) for 12278 atoms. Found 58 (58 requested) and removed 64 (29 requested) atoms. Cycle 33: After refmac, R = 0.1954 (Rfree = 0.000) for 12193 atoms. Found 58 (58 requested) and removed 91 (29 requested) atoms. Cycle 34: After refmac, R = 0.1915 (Rfree = 0.000) for 12110 atoms. Found 57 (57 requested) and removed 44 (28 requested) atoms. Cycle 35: After refmac, R = 0.1905 (Rfree = 0.000) for 12042 atoms. Found 57 (57 requested) and removed 58 (28 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.80 3.32 Search for helices and strands: 0 residues in 0 chains, 12517 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 12536 seeds are put forward Round 1: 637 peptides, 122 chains. Longest chain 15 peptides. Score 0.297 Round 2: 744 peptides, 118 chains. Longest chain 14 peptides. Score 0.392 Round 3: 785 peptides, 116 chains. Longest chain 20 peptides. Score 0.427 Round 4: 767 peptides, 116 chains. Longest chain 19 peptides. Score 0.415 Round 5: 782 peptides, 114 chains. Longest chain 20 peptides. Score 0.432 Taking the results from Round 5 Chains 115, Residues 668, Estimated correctness of the model 0.0 % 9 chains (68 residues) have been docked in sequence ------------------------------------------------------ 18377 reflections ( 96.69 % complete ) and 28698 restraints for refining 12394 atoms. 25948 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1961 (Rfree = 0.000) for 12394 atoms. Found 48 (58 requested) and removed 76 (29 requested) atoms. Cycle 37: After refmac, R = 0.1902 (Rfree = 0.000) for 12257 atoms. Found 58 (58 requested) and removed 55 (29 requested) atoms. Cycle 38: After refmac, R = 0.1879 (Rfree = 0.000) for 12198 atoms. Found 58 (58 requested) and removed 61 (29 requested) atoms. Cycle 39: After refmac, R = 0.1829 (Rfree = 0.000) for 12141 atoms. Found 57 (57 requested) and removed 53 (28 requested) atoms. Cycle 40: After refmac, R = 0.1763 (Rfree = 0.000) for 12122 atoms. Found 57 (57 requested) and removed 54 (28 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.79 3.31 Search for helices and strands: 0 residues in 0 chains, 12532 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 12552 seeds are put forward Round 1: 595 peptides, 116 chains. Longest chain 12 peptides. Score 0.284 Round 2: 670 peptides, 110 chains. Longest chain 23 peptides. Score 0.364 Round 3: 715 peptides, 118 chains. Longest chain 15 peptides. Score 0.371 Round 4: 744 peptides, 102 chains. Longest chain 26 peptides. Score 0.443 Round 5: 731 peptides, 113 chains. Longest chain 26 peptides. Score 0.399 Taking the results from Round 4 Chains 103, Residues 642, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 18377 reflections ( 96.69 % complete ) and 29048 restraints for refining 12397 atoms. 26528 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1929 (Rfree = 0.000) for 12397 atoms. Found 58 (58 requested) and removed 90 (29 requested) atoms. Cycle 42: After refmac, R = 0.1859 (Rfree = 0.000) for 12301 atoms. Found 58 (58 requested) and removed 83 (29 requested) atoms. Cycle 43: After refmac, R = 0.1832 (Rfree = 0.000) for 12236 atoms. Found 58 (58 requested) and removed 68 (29 requested) atoms. Cycle 44: After refmac, R = 0.1820 (Rfree = 0.000) for 12177 atoms. Found 55 (58 requested) and removed 65 (29 requested) atoms. Cycle 45: After refmac, R = 0.1796 (Rfree = 0.000) for 12126 atoms. Found 57 (57 requested) and removed 56 (28 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.85 3.36 Search for helices and strands: 0 residues in 0 chains, 12489 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 12501 seeds are put forward Round 1: 615 peptides, 121 chains. Longest chain 12 peptides. Score 0.283 Round 2: 702 peptides, 118 chains. Longest chain 17 peptides. Score 0.361 Round 3: 698 peptides, 116 chains. Longest chain 15 peptides. Score 0.365 Round 4: 713 peptides, 117 chains. Longest chain 15 peptides. Score 0.373 Round 5: 758 peptides, 119 chains. Longest chain 14 peptides. Score 0.399 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 119, Residues 639, Estimated correctness of the model 0.0 % 6 chains (35 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2p10-4_warpNtrace.pdb as input Building loops using Loopy2018 119 chains (639 residues) following loop building 6 chains (35 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 18377 reflections ( 96.69 % complete ) and 29082 restraints for refining 12395 atoms. 26560 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1832 (Rfree = 0.000) for 12395 atoms. Found 0 (58 requested) and removed 29 (29 requested) atoms. Cycle 47: After refmac, R = 0.1821 (Rfree = 0.000) for 12295 atoms. Found 0 (58 requested) and removed 29 (29 requested) atoms. Cycle 48: After refmac, R = 0.1764 (Rfree = 0.000) for 12215 atoms. Found 0 (58 requested) and removed 29 (29 requested) atoms. Cycle 49: After refmac, R = 0.1399 (Rfree = 0.000) for 12153 atoms. Found 0 (57 requested) and removed 28 (28 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:01:07 GMT 2018 Job finished. TimeTaking 158.04 Used memory is bytes: 14878656