null 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 2p10-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p10-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p10-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p10-3.4-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/2p10-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p10-3.4-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 22:23:17 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/2p10-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p10-3.4-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 1560 and 0 Target number of residues in the AU: 1560 Target solvent content: 0.6362 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: 2p10-3.4-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: 146 Cell parameters: 180.269 180.269 185.514 90.000 90.000 120.000 Input sequence file: 2p10-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 13728 target number of atoms Had to go as low as 0.85 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 3.400 Wilson plot Bfac: 69.77 30063 reflections ( 97.25 % complete ) and 0 restraints for refining 15108 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.3012 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2519 (Rfree = 0.000) for 15108 atoms. Found 114 (114 requested) and removed 83 (57 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 2.91 Search for helices and strands: 0 residues in 0 chains, 15452 seeds are put forward NCS extension: 0 residues added, 15452 seeds are put forward Round 1: 896 peptides, 151 chains. Longest chain 19 peptides. Score 0.397 Round 2: 1048 peptides, 137 chains. Longest chain 29 peptides. Score 0.535 Round 3: 1059 peptides, 125 chains. Longest chain 42 peptides. Score 0.572 Round 4: 1115 peptides, 127 chains. Longest chain 35 peptides. Score 0.597 Round 5: 1106 peptides, 115 chains. Longest chain 38 peptides. Score 0.621 Taking the results from Round 5 Chains 133, Residues 991, Estimated correctness of the model 35.4 % 30 chains (340 residues) have been docked in sequence ------------------------------------------------------ 30063 reflections ( 97.25 % complete ) and 25149 restraints for refining 12477 atoms. 20315 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2260 (Rfree = 0.000) for 12477 atoms. Found 94 (94 requested) and removed 130 (47 requested) atoms. Cycle 2: After refmac, R = 0.2035 (Rfree = 0.000) for 12272 atoms. Found 61 (93 requested) and removed 71 (46 requested) atoms. Cycle 3: After refmac, R = 0.1927 (Rfree = 0.000) for 12181 atoms. Found 40 (92 requested) and removed 54 (46 requested) atoms. Cycle 4: After refmac, R = 0.1847 (Rfree = 0.000) for 12114 atoms. Found 33 (91 requested) and removed 63 (45 requested) atoms. Cycle 5: After refmac, R = 0.1808 (Rfree = 0.000) for 12055 atoms. Found 28 (91 requested) and removed 53 (45 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.30 2.88 Search for helices and strands: 0 residues in 0 chains, 12514 seeds are put forward NCS extension: 18 residues added (21 deleted due to clashes), 12532 seeds are put forward Round 1: 996 peptides, 135 chains. Longest chain 29 peptides. Score 0.509 Round 2: 1104 peptides, 123 chains. Longest chain 45 peptides. Score 0.601 Round 3: 1145 peptides, 122 chains. Longest chain 47 peptides. Score 0.625 Round 4: 1126 peptides, 122 chains. Longest chain 41 peptides. Score 0.615 Round 5: 1133 peptides, 119 chains. Longest chain 43 peptides. Score 0.626 Taking the results from Round 5 Chains 135, Residues 1014, Estimated correctness of the model 36.9 % 27 chains (339 residues) have been docked in sequence ------------------------------------------------------ 30063 reflections ( 97.25 % complete ) and 24440 restraints for refining 12482 atoms. 19405 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2225 (Rfree = 0.000) for 12482 atoms. Found 89 (94 requested) and removed 108 (47 requested) atoms. Cycle 7: After refmac, R = 0.2015 (Rfree = 0.000) for 12369 atoms. Found 32 (94 requested) and removed 64 (47 requested) atoms. Cycle 8: After refmac, R = 0.1944 (Rfree = 0.000) for 12289 atoms. Found 30 (93 requested) and removed 65 (46 requested) atoms. Cycle 9: After refmac, R = 0.1927 (Rfree = 0.000) for 12229 atoms. Found 24 (92 requested) and removed 55 (46 requested) atoms. Cycle 10: After refmac, R = 0.1881 (Rfree = 0.000) for 12172 atoms. Found 27 (92 requested) and removed 50 (46 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.30 2.88 Search for helices and strands: 0 residues in 0 chains, 12614 seeds are put forward NCS extension: 8 residues added (15 deleted due to clashes), 12622 seeds are put forward Round 1: 1056 peptides, 143 chains. Longest chain 28 peptides. Score 0.524 Round 2: 1096 peptides, 122 chains. Longest chain 45 peptides. Score 0.600 Round 3: 1099 peptides, 114 chains. Longest chain 50 peptides. Score 0.620 Round 4: 1078 peptides, 123 chains. Longest chain 42 peptides. Score 0.587 Round 5: 1093 peptides, 118 chains. Longest chain 34 peptides. Score 0.608 Taking the results from Round 3 Chains 133, Residues 985, Estimated correctness of the model 35.1 % 23 chains (238 residues) have been docked in sequence ------------------------------------------------------ 30063 reflections ( 97.25 % complete ) and 25597 restraints for refining 12482 atoms. 20954 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2134 (Rfree = 0.000) for 12482 atoms. Found 94 (94 requested) and removed 96 (47 requested) atoms. Cycle 12: After refmac, R = 0.1955 (Rfree = 0.000) for 12425 atoms. Found 29 (94 requested) and removed 67 (47 requested) atoms. Cycle 13: After refmac, R = 0.1908 (Rfree = 0.000) for 12354 atoms. Found 35 (93 requested) and removed 53 (46 requested) atoms. Cycle 14: After refmac, R = 0.1889 (Rfree = 0.000) for 12320 atoms. Found 21 (93 requested) and removed 49 (46 requested) atoms. Cycle 15: After refmac, R = 0.1866 (Rfree = 0.000) for 12273 atoms. Found 27 (92 requested) and removed 47 (46 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.30 2.88 Search for helices and strands: 0 residues in 0 chains, 12676 seeds are put forward NCS extension: 21 residues added (18 deleted due to clashes), 12697 seeds are put forward Round 1: 1026 peptides, 137 chains. Longest chain 30 peptides. Score 0.522 Round 2: 1056 peptides, 127 chains. Longest chain 41 peptides. Score 0.565 Round 3: 1088 peptides, 118 chains. Longest chain 40 peptides. Score 0.605 Round 4: 1114 peptides, 121 chains. Longest chain 47 peptides. Score 0.611 Round 5: 1073 peptides, 117 chains. Longest chain 45 peptides. Score 0.600 Taking the results from Round 4 Chains 133, Residues 993, Estimated correctness of the model 32.2 % 20 chains (251 residues) have been docked in sequence ------------------------------------------------------ 30063 reflections ( 97.25 % complete ) and 25655 restraints for refining 12483 atoms. 20956 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2182 (Rfree = 0.000) for 12483 atoms. Found 89 (94 requested) and removed 93 (47 requested) atoms. Cycle 17: After refmac, R = 0.1988 (Rfree = 0.000) for 12409 atoms. Found 32 (94 requested) and removed 70 (47 requested) atoms. Cycle 18: After refmac, R = 0.1932 (Rfree = 0.000) for 12346 atoms. Found 22 (93 requested) and removed 56 (46 requested) atoms. Cycle 19: After refmac, R = 0.1876 (Rfree = 0.000) for 12281 atoms. Found 26 (92 requested) and removed 48 (46 requested) atoms. Cycle 20: After refmac, R = 0.1841 (Rfree = 0.000) for 12243 atoms. Found 26 (92 requested) and removed 50 (46 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.31 2.89 Search for helices and strands: 0 residues in 0 chains, 12630 seeds are put forward NCS extension: 16 residues added (23 deleted due to clashes), 12646 seeds are put forward Round 1: 1000 peptides, 142 chains. Longest chain 27 peptides. Score 0.492 Round 2: 1052 peptides, 115 chains. Longest chain 36 peptides. Score 0.593 Round 3: 1075 peptides, 129 chains. Longest chain 45 peptides. Score 0.571 Round 4: 1059 peptides, 121 chains. Longest chain 42 peptides. Score 0.582 Round 5: 1063 peptides, 123 chains. Longest chain 47 peptides. Score 0.579 Taking the results from Round 2 Chains 124, Residues 937, Estimated correctness of the model 26.4 % 20 chains (234 residues) have been docked in sequence ------------------------------------------------------ 30063 reflections ( 97.25 % complete ) and 25974 restraints for refining 12483 atoms. 21580 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2099 (Rfree = 0.000) for 12483 atoms. Found 79 (94 requested) and removed 81 (47 requested) atoms. Cycle 22: After refmac, R = 0.1949 (Rfree = 0.000) for 12432 atoms. Found 35 (94 requested) and removed 57 (47 requested) atoms. Cycle 23: After refmac, R = 0.1922 (Rfree = 0.000) for 12386 atoms. Found 21 (93 requested) and removed 50 (46 requested) atoms. Cycle 24: After refmac, R = 0.1882 (Rfree = 0.000) for 12340 atoms. Found 28 (93 requested) and removed 48 (46 requested) atoms. Cycle 25: After refmac, R = 0.1877 (Rfree = 0.000) for 12305 atoms. Found 28 (93 requested) and removed 46 (46 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.33 2.91 Search for helices and strands: 0 residues in 0 chains, 12697 seeds are put forward NCS extension: 20 residues added (9 deleted due to clashes), 12717 seeds are put forward Round 1: 950 peptides, 132 chains. Longest chain 28 peptides. Score 0.489 Round 2: 1053 peptides, 120 chains. Longest chain 40 peptides. Score 0.582 Round 3: 1029 peptides, 107 chains. Longest chain 35 peptides. Score 0.601 Round 4: 1026 peptides, 124 chains. Longest chain 41 peptides. Score 0.556 Round 5: 1023 peptides, 117 chains. Longest chain 33 peptides. Score 0.573 Taking the results from Round 3 Chains 116, Residues 922, Estimated correctness of the model 29.0 % 17 chains (207 residues) have been docked in sequence ------------------------------------------------------ 30063 reflections ( 97.25 % complete ) and 26133 restraints for refining 12483 atoms. 21880 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2065 (Rfree = 0.000) for 12483 atoms. Found 80 (94 requested) and removed 88 (47 requested) atoms. Cycle 27: After refmac, R = 0.1901 (Rfree = 0.000) for 12420 atoms. Found 39 (94 requested) and removed 53 (47 requested) atoms. Cycle 28: After refmac, R = 0.1859 (Rfree = 0.000) for 12374 atoms. Found 29 (93 requested) and removed 53 (46 requested) atoms. Cycle 29: After refmac, R = 0.1817 (Rfree = 0.000) for 12335 atoms. Found 25 (93 requested) and removed 48 (46 requested) atoms. Cycle 30: After refmac, R = 0.1775 (Rfree = 0.000) for 12298 atoms. Found 17 (92 requested) and removed 47 (46 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.32 2.90 Search for helices and strands: 0 residues in 0 chains, 12724 seeds are put forward NCS extension: 15 residues added (19 deleted due to clashes), 12739 seeds are put forward Round 1: 907 peptides, 133 chains. Longest chain 22 peptides. Score 0.458 Round 2: 1003 peptides, 114 chains. Longest chain 31 peptides. Score 0.569 Round 3: 1007 peptides, 117 chains. Longest chain 29 peptides. Score 0.564 Round 4: 1038 peptides, 113 chains. Longest chain 42 peptides. Score 0.591 Round 5: 1022 peptides, 115 chains. Longest chain 37 peptides. Score 0.577 Taking the results from Round 4 Chains 131, Residues 925, Estimated correctness of the model 25.7 % 24 chains (252 residues) have been docked in sequence ------------------------------------------------------ 30063 reflections ( 97.25 % complete ) and 25517 restraints for refining 12483 atoms. 21096 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2132 (Rfree = 0.000) for 12483 atoms. Found 94 (94 requested) and removed 96 (47 requested) atoms. Cycle 32: After refmac, R = 0.1936 (Rfree = 0.000) for 12419 atoms. Found 35 (94 requested) and removed 69 (47 requested) atoms. Cycle 33: After refmac, R = 0.1886 (Rfree = 0.000) for 12363 atoms. Found 35 (93 requested) and removed 47 (46 requested) atoms. Cycle 34: After refmac, R = 0.1821 (Rfree = 0.000) for 12337 atoms. Found 21 (93 requested) and removed 47 (46 requested) atoms. Cycle 35: After refmac, R = 0.1788 (Rfree = 0.000) for 12291 atoms. Found 21 (92 requested) and removed 47 (46 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.33 2.91 Search for helices and strands: 0 residues in 0 chains, 12712 seeds are put forward NCS extension: 11 residues added (6 deleted due to clashes), 12723 seeds are put forward Round 1: 855 peptides, 126 chains. Longest chain 20 peptides. Score 0.445 Round 2: 937 peptides, 122 chains. Longest chain 27 peptides. Score 0.509 Round 3: 972 peptides, 122 chains. Longest chain 26 peptides. Score 0.530 Round 4: 937 peptides, 116 chains. Longest chain 32 peptides. Score 0.526 Round 5: 954 peptides, 113 chains. Longest chain 33 peptides. Score 0.544 Taking the results from Round 5 Chains 122, Residues 841, Estimated correctness of the model 9.3 % 18 chains (179 residues) have been docked in sequence ------------------------------------------------------ 30063 reflections ( 97.25 % complete ) and 27056 restraints for refining 12482 atoms. 23256 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2137 (Rfree = 0.000) for 12482 atoms. Found 92 (94 requested) and removed 74 (47 requested) atoms. Cycle 37: After refmac, R = 0.1965 (Rfree = 0.000) for 12454 atoms. Found 37 (94 requested) and removed 61 (47 requested) atoms. Cycle 38: After refmac, R = 0.1877 (Rfree = 0.000) for 12404 atoms. Found 29 (93 requested) and removed 51 (46 requested) atoms. Cycle 39: After refmac, R = 0.1817 (Rfree = 0.000) for 12363 atoms. Found 23 (93 requested) and removed 47 (46 requested) atoms. Cycle 40: After refmac, R = 0.1776 (Rfree = 0.000) for 12329 atoms. Found 12 (93 requested) and removed 48 (46 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.32 2.90 Search for helices and strands: 0 residues in 0 chains, 12763 seeds are put forward NCS extension: 13 residues added (10 deleted due to clashes), 12776 seeds are put forward Round 1: 830 peptides, 129 chains. Longest chain 18 peptides. Score 0.418 Round 2: 954 peptides, 122 chains. Longest chain 29 peptides. Score 0.519 Round 3: 943 peptides, 119 chains. Longest chain 23 peptides. Score 0.521 Round 4: 947 peptides, 111 chains. Longest chain 31 peptides. Score 0.545 Round 5: 982 peptides, 121 chains. Longest chain 27 peptides. Score 0.539 Taking the results from Round 4 Chains 120, Residues 836, Estimated correctness of the model 9.7 % 19 chains (180 residues) have been docked in sequence ------------------------------------------------------ 30063 reflections ( 97.25 % complete ) and 26917 restraints for refining 12482 atoms. 23116 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2111 (Rfree = 0.000) for 12482 atoms. Found 94 (94 requested) and removed 76 (47 requested) atoms. Cycle 42: After refmac, R = 0.1930 (Rfree = 0.000) for 12479 atoms. Found 41 (94 requested) and removed 54 (47 requested) atoms. Cycle 43: After refmac, R = 0.1887 (Rfree = 0.000) for 12450 atoms. Found 35 (94 requested) and removed 49 (47 requested) atoms. Cycle 44: After refmac, R = 0.1824 (Rfree = 0.000) for 12415 atoms. Found 18 (93 requested) and removed 48 (46 requested) atoms. Cycle 45: After refmac, R = 0.1801 (Rfree = 0.000) for 12379 atoms. Found 25 (93 requested) and removed 49 (46 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 2.91 Search for helices and strands: 0 residues in 0 chains, 12811 seeds are put forward NCS extension: 11 residues added (5 deleted due to clashes), 12822 seeds are put forward Round 1: 848 peptides, 135 chains. Longest chain 17 peptides. Score 0.412 Round 2: 909 peptides, 122 chains. Longest chain 24 peptides. Score 0.492 Round 3: 908 peptides, 123 chains. Longest chain 21 peptides. Score 0.488 Round 4: 917 peptides, 117 chains. Longest chain 33 peptides. Score 0.511 Round 5: 877 peptides, 117 chains. Longest chain 21 peptides. Score 0.486 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 126, Residues 800, Estimated correctness of the model 0.0 % 18 chains (148 residues) have been docked in sequence Sequence coverage is 18 % Consider running further cycles of model building using 2p10-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 70 B and 83 B 125 chains (811 residues) following loop building 17 chains (160 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 30063 reflections ( 97.25 % complete ) and 27243 restraints for refining 12483 atoms. 23669 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2087 (Rfree = 0.000) for 12483 atoms. Found 0 (94 requested) and removed 47 (47 requested) atoms. Cycle 47: After refmac, R = 0.2015 (Rfree = 0.000) for 12398 atoms. Found 0 (93 requested) and removed 23 (46 requested) atoms. Cycle 48: After refmac, R = 0.1977 (Rfree = 0.000) for 12360 atoms. Found 0 (93 requested) and removed 13 (46 requested) atoms. Cycle 49: After refmac, R = 0.1950 (Rfree = 0.000) for 12336 atoms. Found 0 (93 requested) and removed 8 (46 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:11:18 GMT 2018 Job finished. TimeTaking 168.18 Used memory is bytes: 25835520