null Sun 23 Dec 22:22:59 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 2p10-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p10-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p10-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p10-3.2-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/2p10-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p10-3.2-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 22:23:08 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/2p10-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p10-3.2-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 1597 and 0 Target number of residues in the AU: 1597 Target solvent content: 0.6275 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: 2p10-3.2-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: 2p10-3.2-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 3.200 Wilson plot Bfac: 65.16 36121 reflections ( 97.38 % complete ) and 0 restraints for refining 15115 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Starting model: R = 0.2983 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2446 (Rfree = 0.000) for 15115 atoms. Found 135 (135 requested) and removed 91 (67 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.18 2.78 Search for helices and strands: 0 residues in 0 chains, 15490 seeds are put forward NCS extension: 0 residues added, 15490 seeds are put forward Round 1: 978 peptides, 150 chains. Longest chain 25 peptides. Score 0.456 Round 2: 1133 peptides, 131 chains. Longest chain 28 peptides. Score 0.597 Round 3: 1184 peptides, 127 chains. Longest chain 36 peptides. Score 0.632 Round 4: 1202 peptides, 117 chains. Longest chain 36 peptides. Score 0.663 Round 5: 1237 peptides, 114 chains. Longest chain 47 peptides. Score 0.685 Taking the results from Round 5 Chains 129, Residues 1123, Estimated correctness of the model 61.9 % 29 chains (446 residues) have been docked in sequence ------------------------------------------------------ 36121 reflections ( 97.38 % complete ) and 22920 restraints for refining 12531 atoms. 17046 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2435 (Rfree = 0.000) for 12531 atoms. Found 112 (112 requested) and removed 123 (56 requested) atoms. Cycle 2: After refmac, R = 0.2221 (Rfree = 0.000) for 12335 atoms. Found 77 (112 requested) and removed 76 (56 requested) atoms. Cycle 3: After refmac, R = 0.2113 (Rfree = 0.000) for 12242 atoms. Found 54 (110 requested) and removed 65 (55 requested) atoms. Cycle 4: After refmac, R = 0.2049 (Rfree = 0.000) for 12162 atoms. Found 42 (109 requested) and removed 55 (54 requested) atoms. Cycle 5: After refmac, R = 0.1986 (Rfree = 0.000) for 12111 atoms. Found 39 (109 requested) and removed 55 (54 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.17 2.77 Search for helices and strands: 0 residues in 0 chains, 12526 seeds are put forward NCS extension: 23 residues added (20 deleted due to clashes), 12549 seeds are put forward Round 1: 1186 peptides, 126 chains. Longest chain 45 peptides. Score 0.635 Round 2: 1245 peptides, 111 chains. Longest chain 47 peptides. Score 0.694 Round 3: 1239 peptides, 111 chains. Longest chain 47 peptides. Score 0.692 Round 4: 1249 peptides, 106 chains. Longest chain 51 peptides. Score 0.706 Round 5: 1229 peptides, 117 chains. Longest chain 51 peptides. Score 0.675 Taking the results from Round 4 Chains 126, Residues 1143, Estimated correctness of the model 66.4 % 25 chains (486 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 65 A and 69 A Built loop between residues 245 A and 255 A Built loop between residues 240 B and 245 B Built loop between residues 263 B and 267 B 120 chains (1150 residues) following loop building 21 chains (505 residues) in sequence following loop building ------------------------------------------------------ 36121 reflections ( 97.38 % complete ) and 22175 restraints for refining 12506 atoms. 16126 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2428 (Rfree = 0.000) for 12506 atoms. Found 112 (112 requested) and removed 124 (56 requested) atoms. Cycle 7: After refmac, R = 0.2194 (Rfree = 0.000) for 12401 atoms. Found 71 (110 requested) and removed 81 (56 requested) atoms. Cycle 8: After refmac, R = 0.2078 (Rfree = 0.000) for 12344 atoms. Found 42 (107 requested) and removed 62 (55 requested) atoms. Cycle 9: After refmac, R = 0.2000 (Rfree = 0.000) for 12298 atoms. Found 24 (103 requested) and removed 58 (55 requested) atoms. Cycle 10: After refmac, R = 0.1959 (Rfree = 0.000) for 12245 atoms. Found 25 (101 requested) and removed 55 (55 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.17 2.77 Search for helices and strands: 0 residues in 0 chains, 12647 seeds are put forward NCS extension: 25 residues added (54 deleted due to clashes), 12672 seeds are put forward Round 1: 1168 peptides, 128 chains. Longest chain 50 peptides. Score 0.622 Round 2: 1206 peptides, 120 chains. Longest chain 41 peptides. Score 0.658 Round 3: 1197 peptides, 116 chains. Longest chain 51 peptides. Score 0.663 Round 4: 1219 peptides, 120 chains. Longest chain 46 peptides. Score 0.664 Round 5: 1209 peptides, 117 chains. Longest chain 43 peptides. Score 0.666 Taking the results from Round 5 Chains 136, Residues 1092, Estimated correctness of the model 57.6 % 29 chains (417 residues) have been docked in sequence ------------------------------------------------------ 36121 reflections ( 97.38 % complete ) and 23699 restraints for refining 12530 atoms. 18046 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2275 (Rfree = 0.000) for 12530 atoms. Found 98 (101 requested) and removed 96 (56 requested) atoms. Cycle 12: After refmac, R = 0.2070 (Rfree = 0.000) for 12486 atoms. Found 47 (101 requested) and removed 66 (56 requested) atoms. Cycle 13: After refmac, R = 0.1982 (Rfree = 0.000) for 12442 atoms. Found 39 (100 requested) and removed 55 (55 requested) atoms. Cycle 14: After refmac, R = 0.1996 (Rfree = 0.000) for 12402 atoms. Found 41 (100 requested) and removed 57 (55 requested) atoms. Cycle 15: After refmac, R = 0.1924 (Rfree = 0.000) for 12367 atoms. Found 38 (100 requested) and removed 57 (55 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.17 2.77 Search for helices and strands: 0 residues in 0 chains, 12779 seeds are put forward NCS extension: 13 residues added (9 deleted due to clashes), 12792 seeds are put forward Round 1: 1125 peptides, 132 chains. Longest chain 36 peptides. Score 0.590 Round 2: 1189 peptides, 121 chains. Longest chain 88 peptides. Score 0.648 Round 3: 1221 peptides, 116 chains. Longest chain 65 peptides. Score 0.674 Round 4: 1238 peptides, 119 chains. Longest chain 51 peptides. Score 0.675 Round 5: 1218 peptides, 107 chains. Longest chain 45 peptides. Score 0.691 Taking the results from Round 5 Chains 123, Residues 1111, Estimated correctness of the model 63.2 % 32 chains (518 residues) have been docked in sequence ------------------------------------------------------ 36121 reflections ( 97.38 % complete ) and 22538 restraints for refining 12528 atoms. 16441 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2320 (Rfree = 0.000) for 12528 atoms. Found 101 (101 requested) and removed 101 (56 requested) atoms. Cycle 17: After refmac, R = 0.2110 (Rfree = 0.000) for 12463 atoms. Found 45 (101 requested) and removed 72 (56 requested) atoms. Cycle 18: After refmac, R = 0.1948 (Rfree = 0.000) for 12406 atoms. Found 28 (100 requested) and removed 64 (55 requested) atoms. Cycle 19: After refmac, R = 0.2027 (Rfree = 0.000) for 12333 atoms. Found 57 (100 requested) and removed 62 (55 requested) atoms. Cycle 20: After refmac, R = 0.1854 (Rfree = 0.000) for 12301 atoms. Found 29 (99 requested) and removed 58 (55 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.17 2.77 Search for helices and strands: 0 residues in 0 chains, 12722 seeds are put forward NCS extension: 12 residues added (17 deleted due to clashes), 12734 seeds are put forward Round 1: 1099 peptides, 126 chains. Longest chain 43 peptides. Score 0.591 Round 2: 1161 peptides, 114 chains. Longest chain 45 peptides. Score 0.650 Round 3: 1162 peptides, 121 chains. Longest chain 47 peptides. Score 0.635 Round 4: 1166 peptides, 112 chains. Longest chain 41 peptides. Score 0.657 Round 5: 1164 peptides, 115 chains. Longest chain 34 peptides. Score 0.650 Taking the results from Round 4 Chains 137, Residues 1054, Estimated correctness of the model 55.5 % 29 chains (409 residues) have been docked in sequence ------------------------------------------------------ 36121 reflections ( 97.38 % complete ) and 23903 restraints for refining 12531 atoms. 18419 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2246 (Rfree = 0.000) for 12531 atoms. Found 101 (101 requested) and removed 94 (56 requested) atoms. Cycle 22: After refmac, R = 0.2030 (Rfree = 0.000) for 12498 atoms. Found 51 (101 requested) and removed 59 (56 requested) atoms. Cycle 23: After refmac, R = 0.1935 (Rfree = 0.000) for 12454 atoms. Found 30 (101 requested) and removed 57 (56 requested) atoms. Cycle 24: After refmac, R = 0.2097 (Rfree = 0.000) for 12411 atoms. Found 74 (100 requested) and removed 59 (55 requested) atoms. Cycle 25: After refmac, R = 0.1913 (Rfree = 0.000) for 12405 atoms. Found 43 (100 requested) and removed 57 (55 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.16 2.76 Search for helices and strands: 0 residues in 0 chains, 12843 seeds are put forward NCS extension: 10 residues added (8 deleted due to clashes), 12853 seeds are put forward Round 1: 1076 peptides, 141 chains. Longest chain 37 peptides. Score 0.541 Round 2: 1190 peptides, 109 chains. Longest chain 51 peptides. Score 0.675 Round 3: 1192 peptides, 120 chains. Longest chain 41 peptides. Score 0.652 Round 4: 1160 peptides, 119 chains. Longest chain 41 peptides. Score 0.639 Round 5: 1147 peptides, 109 chains. Longest chain 45 peptides. Score 0.655 Taking the results from Round 2 Chains 118, Residues 1081, Estimated correctness of the model 59.7 % 31 chains (463 residues) have been docked in sequence ------------------------------------------------------ 36121 reflections ( 97.38 % complete ) and 22881 restraints for refining 12532 atoms. 17073 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2155 (Rfree = 0.000) for 12532 atoms. Found 82 (101 requested) and removed 85 (56 requested) atoms. Cycle 27: After refmac, R = 0.2015 (Rfree = 0.000) for 12483 atoms. Found 29 (101 requested) and removed 66 (56 requested) atoms. Cycle 28: After refmac, R = 0.1954 (Rfree = 0.000) for 12417 atoms. Found 29 (100 requested) and removed 55 (55 requested) atoms. Cycle 29: After refmac, R = 0.1917 (Rfree = 0.000) for 12380 atoms. Found 15 (100 requested) and removed 55 (55 requested) atoms. Cycle 30: After refmac, R = 0.1902 (Rfree = 0.000) for 12331 atoms. Found 6 (99 requested) and removed 55 (55 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.19 2.79 Search for helices and strands: 0 residues in 0 chains, 12700 seeds are put forward NCS extension: 16 residues added (30 deleted due to clashes), 12716 seeds are put forward Round 1: 1078 peptides, 128 chains. Longest chain 35 peptides. Score 0.575 Round 2: 1157 peptides, 117 chains. Longest chain 43 peptides. Score 0.642 Round 3: 1135 peptides, 122 chains. Longest chain 35 peptides. Score 0.620 Round 4: 1128 peptides, 114 chains. Longest chain 35 peptides. Score 0.635 Round 5: 1135 peptides, 108 chains. Longest chain 37 peptides. Score 0.652 Taking the results from Round 5 Chains 118, Residues 1027, Estimated correctness of the model 54.3 % 23 chains (353 residues) have been docked in sequence ------------------------------------------------------ 36121 reflections ( 97.38 % complete ) and 24206 restraints for refining 12533 atoms. 18896 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2243 (Rfree = 0.000) for 12533 atoms. Found 101 (101 requested) and removed 95 (56 requested) atoms. Cycle 32: After refmac, R = 0.2030 (Rfree = 0.000) for 12497 atoms. Found 47 (101 requested) and removed 61 (56 requested) atoms. Cycle 33: After refmac, R = 0.1938 (Rfree = 0.000) for 12449 atoms. Found 21 (101 requested) and removed 58 (56 requested) atoms. Cycle 34: After refmac, R = 0.1976 (Rfree = 0.000) for 12390 atoms. Found 24 (100 requested) and removed 55 (55 requested) atoms. Cycle 35: After refmac, R = 0.1885 (Rfree = 0.000) for 12350 atoms. Found 18 (99 requested) and removed 56 (55 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.19 2.79 Search for helices and strands: 0 residues in 0 chains, 12719 seeds are put forward NCS extension: 12 residues added (17 deleted due to clashes), 12731 seeds are put forward Round 1: 1022 peptides, 129 chains. Longest chain 29 peptides. Score 0.541 Round 2: 1110 peptides, 120 chains. Longest chain 43 peptides. Score 0.612 Round 3: 1122 peptides, 112 chains. Longest chain 39 peptides. Score 0.636 Round 4: 1069 peptides, 116 chains. Longest chain 37 peptides. Score 0.600 Round 5: 1091 peptides, 112 chains. Longest chain 46 peptides. Score 0.621 Taking the results from Round 3 Chains 119, Residues 1010, Estimated correctness of the model 50.4 % 19 chains (327 residues) have been docked in sequence ------------------------------------------------------ 36121 reflections ( 97.38 % complete ) and 24809 restraints for refining 12532 atoms. 19760 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2155 (Rfree = 0.000) for 12532 atoms. Found 101 (101 requested) and removed 92 (56 requested) atoms. Cycle 37: After refmac, R = 0.1997 (Rfree = 0.000) for 12520 atoms. Found 47 (101 requested) and removed 60 (56 requested) atoms. Cycle 38: After refmac, R = 0.1982 (Rfree = 0.000) for 12482 atoms. Found 38 (101 requested) and removed 58 (56 requested) atoms. Cycle 39: After refmac, R = 0.1899 (Rfree = 0.000) for 12450 atoms. Found 22 (100 requested) and removed 58 (55 requested) atoms. Cycle 40: After refmac, R = 0.1911 (Rfree = 0.000) for 12402 atoms. Found 25 (100 requested) and removed 58 (55 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.20 2.80 Search for helices and strands: 0 residues in 0 chains, 12820 seeds are put forward NCS extension: 20 residues added (25 deleted due to clashes), 12840 seeds are put forward Round 1: 990 peptides, 126 chains. Longest chain 30 peptides. Score 0.530 Round 2: 1084 peptides, 116 chains. Longest chain 50 peptides. Score 0.608 Round 3: 1085 peptides, 113 chains. Longest chain 34 peptides. Score 0.616 Round 4: 1078 peptides, 115 chains. Longest chain 32 peptides. Score 0.607 Round 5: 1085 peptides, 114 chains. Longest chain 44 peptides. Score 0.613 Taking the results from Round 3 Chains 124, Residues 972, Estimated correctness of the model 45.3 % 28 chains (293 residues) have been docked in sequence ------------------------------------------------------ 36121 reflections ( 97.38 % complete ) and 25556 restraints for refining 12532 atoms. 20877 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2090 (Rfree = 0.000) for 12532 atoms. Found 94 (101 requested) and removed 78 (56 requested) atoms. Cycle 42: After refmac, R = 0.1962 (Rfree = 0.000) for 12504 atoms. Found 43 (101 requested) and removed 57 (56 requested) atoms. Cycle 43: After refmac, R = 0.1913 (Rfree = 0.000) for 12470 atoms. Found 27 (101 requested) and removed 56 (56 requested) atoms. Cycle 44: After refmac, R = 0.1894 (Rfree = 0.000) for 12424 atoms. Found 23 (100 requested) and removed 57 (55 requested) atoms. Cycle 45: After refmac, R = 0.1830 (Rfree = 0.000) for 12376 atoms. Found 21 (100 requested) and removed 56 (55 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.19 2.79 Search for helices and strands: 0 residues in 0 chains, 12767 seeds are put forward NCS extension: 10 residues added (23 deleted due to clashes), 12777 seeds are put forward Round 1: 1015 peptides, 129 chains. Longest chain 29 peptides. Score 0.537 Round 2: 1072 peptides, 116 chains. Longest chain 50 peptides. Score 0.602 Round 3: 1083 peptides, 113 chains. Longest chain 38 peptides. Score 0.615 Round 4: 1069 peptides, 111 chains. Longest chain 29 peptides. Score 0.612 Round 5: 1058 peptides, 114 chains. Longest chain 46 peptides. Score 0.599 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 124, Residues 970, Estimated correctness of the model 45.0 % 24 chains (318 residues) have been docked in sequence Sequence coverage is 32 % Consider running further cycles of model building using 2p10-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 182 A and 191 A Built loop between residues 106 B and 119 B 120 chains (987 residues) following loop building 22 chains (338 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 36121 reflections ( 97.38 % complete ) and 24900 restraints for refining 12532 atoms. 19907 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2194 (Rfree = 0.000) for 12532 atoms. Found 0 (101 requested) and removed 28 (56 requested) atoms. Cycle 47: After refmac, R = 0.2100 (Rfree = 0.000) for 12474 atoms. Found 0 (101 requested) and removed 7 (56 requested) atoms. Cycle 48: After refmac, R = 0.2093 (Rfree = 0.000) for 12453 atoms. Found 0 (100 requested) and removed 5 (55 requested) atoms. Cycle 49: After refmac, R = 0.2087 (Rfree = 0.000) for 12439 atoms. Found 0 (100 requested) and removed 11 (55 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 01:20:26 GMT 2018 Job finished. TimeTaking 177.46 Used memory is bytes: 17943776