null Mon 24 Dec 07:34:55 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2p10-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2p10-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2p10-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p10-3.2-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2p10-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p10-3.2-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:35:00 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/noncs/ArpWArp/wArpResults/WorkingDir/2p10-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p10-3.2-parrot-noncs/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-noncs.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-noncs.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 15106 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Starting model: R = 0.3018 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2574 (Rfree = 0.000) for 15106 atoms. Found 135 (135 requested) and removed 107 (67 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.19 2.79 Search for helices and strands: 0 residues in 0 chains, 15492 seeds are put forward NCS extension: 0 residues added, 15492 seeds are put forward Round 1: 941 peptides, 157 chains. Longest chain 18 peptides. Score 0.410 Round 2: 1127 peptides, 147 chains. Longest chain 22 peptides. Score 0.554 Round 3: 1170 peptides, 133 chains. Longest chain 37 peptides. Score 0.611 Round 4: 1192 peptides, 125 chains. Longest chain 36 peptides. Score 0.641 Round 5: 1211 peptides, 121 chains. Longest chain 35 peptides. Score 0.658 Taking the results from Round 5 Chains 140, Residues 1090, Estimated correctness of the model 55.7 % 35 chains (445 residues) have been docked in sequence ------------------------------------------------------ 36121 reflections ( 97.38 % complete ) and 23221 restraints for refining 12529 atoms. 17624 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2476 (Rfree = 0.000) for 12529 atoms. Found 112 (112 requested) and removed 126 (56 requested) atoms. Cycle 2: After refmac, R = 0.2284 (Rfree = 0.000) for 12342 atoms. Found 76 (112 requested) and removed 86 (56 requested) atoms. Cycle 3: After refmac, R = 0.2156 (Rfree = 0.000) for 12263 atoms. Found 45 (110 requested) and removed 63 (55 requested) atoms. Cycle 4: After refmac, R = 0.2072 (Rfree = 0.000) for 12208 atoms. Found 34 (109 requested) and removed 55 (54 requested) atoms. Cycle 5: After refmac, R = 0.2021 (Rfree = 0.000) for 12158 atoms. Found 24 (109 requested) and removed 56 (54 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.17 2.77 Search for helices and strands: 0 residues in 0 chains, 12582 seeds are put forward NCS extension: 29 residues added (20 deleted due to clashes), 12611 seeds are put forward Round 1: 1116 peptides, 132 chains. Longest chain 38 peptides. Score 0.586 Round 2: 1163 peptides, 122 chains. Longest chain 39 peptides. Score 0.633 Round 3: 1173 peptides, 123 chains. Longest chain 40 peptides. Score 0.636 Round 4: 1178 peptides, 123 chains. Longest chain 36 peptides. Score 0.638 Round 5: 1167 peptides, 122 chains. Longest chain 38 peptides. Score 0.635 Taking the results from Round 4 Chains 127, Residues 1055, Estimated correctness of the model 50.9 % 30 chains (434 residues) have been docked in sequence ------------------------------------------------------ 36121 reflections ( 97.38 % complete ) and 23723 restraints for refining 12530 atoms. 18253 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2365 (Rfree = 0.000) for 12530 atoms. Found 99 (112 requested) and removed 97 (56 requested) atoms. Cycle 7: After refmac, R = 0.2182 (Rfree = 0.000) for 12452 atoms. Found 48 (112 requested) and removed 70 (56 requested) atoms. Cycle 8: After refmac, R = 0.2094 (Rfree = 0.000) for 12372 atoms. Found 33 (111 requested) and removed 58 (55 requested) atoms. Cycle 9: After refmac, R = 0.2042 (Rfree = 0.000) for 12319 atoms. Found 27 (110 requested) and removed 56 (55 requested) atoms. Cycle 10: After refmac, R = 0.2000 (Rfree = 0.000) for 12275 atoms. Found 23 (110 requested) and removed 56 (55 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.19 2.79 Search for helices and strands: 0 residues in 0 chains, 12712 seeds are put forward NCS extension: 18 residues added (20 deleted due to clashes), 12730 seeds are put forward Round 1: 1106 peptides, 137 chains. Longest chain 39 peptides. Score 0.568 Round 2: 1148 peptides, 123 chains. Longest chain 51 peptides. Score 0.624 Round 3: 1149 peptides, 116 chains. Longest chain 57 peptides. Score 0.640 Round 4: 1163 peptides, 125 chains. Longest chain 54 peptides. Score 0.627 Round 5: 1169 peptides, 128 chains. Longest chain 51 peptides. Score 0.623 Taking the results from Round 3 Chains 127, Residues 1033, Estimated correctness of the model 51.4 % 25 chains (369 residues) have been docked in sequence ------------------------------------------------------ 36121 reflections ( 97.38 % complete ) and 24381 restraints for refining 12531 atoms. 19059 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2303 (Rfree = 0.000) for 12531 atoms. Found 104 (112 requested) and removed 108 (56 requested) atoms. Cycle 12: After refmac, R = 0.2130 (Rfree = 0.000) for 12475 atoms. Found 47 (112 requested) and removed 63 (56 requested) atoms. Cycle 13: After refmac, R = 0.2057 (Rfree = 0.000) for 12432 atoms. Found 29 (111 requested) and removed 56 (55 requested) atoms. Cycle 14: After refmac, R = 0.2033 (Rfree = 0.000) for 12389 atoms. Found 23 (111 requested) and removed 55 (55 requested) atoms. Cycle 15: After refmac, R = 0.2013 (Rfree = 0.000) for 12342 atoms. Found 26 (110 requested) and removed 58 (55 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.19 2.79 Search for helices and strands: 0 residues in 0 chains, 12764 seeds are put forward NCS extension: 16 residues added (23 deleted due to clashes), 12780 seeds are put forward Round 1: 1073 peptides, 127 chains. Longest chain 55 peptides. Score 0.575 Round 2: 1164 peptides, 119 chains. Longest chain 40 peptides. Score 0.641 Round 3: 1166 peptides, 123 chains. Longest chain 47 peptides. Score 0.633 Round 4: 1182 peptides, 120 chains. Longest chain 47 peptides. Score 0.647 Round 5: 1192 peptides, 123 chains. Longest chain 57 peptides. Score 0.645 Taking the results from Round 4 Chains 131, Residues 1062, Estimated correctness of the model 53.1 % 25 chains (384 residues) have been docked in sequence ------------------------------------------------------ 36121 reflections ( 97.38 % complete ) and 23996 restraints for refining 12532 atoms. 18559 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2338 (Rfree = 0.000) for 12532 atoms. Found 95 (112 requested) and removed 102 (56 requested) atoms. Cycle 17: After refmac, R = 0.2152 (Rfree = 0.000) for 12457 atoms. Found 36 (112 requested) and removed 69 (56 requested) atoms. Cycle 18: After refmac, R = 0.2086 (Rfree = 0.000) for 12393 atoms. Found 30 (111 requested) and removed 58 (55 requested) atoms. Cycle 19: After refmac, R = 0.2051 (Rfree = 0.000) for 12355 atoms. Found 23 (110 requested) and removed 59 (55 requested) atoms. Cycle 20: After refmac, R = 0.2028 (Rfree = 0.000) for 12297 atoms. Found 32 (110 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, 12734 seeds are put forward NCS extension: 32 residues added (9 deleted due to clashes), 12766 seeds are put forward Round 1: 1095 peptides, 136 chains. Longest chain 48 peptides. Score 0.564 Round 2: 1164 peptides, 127 chains. Longest chain 38 peptides. Score 0.622 Round 3: 1178 peptides, 122 chains. Longest chain 30 peptides. Score 0.641 Round 4: 1183 peptides, 123 chains. Longest chain 34 peptides. Score 0.641 Round 5: 1184 peptides, 124 chains. Longest chain 42 peptides. Score 0.639 Taking the results from Round 4 Chains 141, Residues 1060, Estimated correctness of the model 51.6 % 24 chains (285 residues) have been docked in sequence ------------------------------------------------------ 36121 reflections ( 97.38 % complete ) and 25368 restraints for refining 12533 atoms. 20370 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2233 (Rfree = 0.000) for 12533 atoms. Found 82 (112 requested) and removed 96 (56 requested) atoms. Cycle 22: After refmac, R = 0.2054 (Rfree = 0.000) for 12476 atoms. Found 25 (112 requested) and removed 69 (56 requested) atoms. Cycle 23: After refmac, R = 0.2011 (Rfree = 0.000) for 12400 atoms. Found 43 (111 requested) and removed 65 (55 requested) atoms. Cycle 24: After refmac, R = 0.1979 (Rfree = 0.000) for 12345 atoms. Found 41 (111 requested) and removed 60 (55 requested) atoms. Cycle 25: After refmac, R = 0.2087 (Rfree = 0.000) for 12310 atoms. Found 89 (110 requested) and removed 56 (55 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.16 2.76 Search for helices and strands: 0 residues in 0 chains, 12780 seeds are put forward NCS extension: 7 residues added (16 deleted due to clashes), 12787 seeds are put forward Round 1: 1080 peptides, 130 chains. Longest chain 32 peptides. Score 0.571 Round 2: 1167 peptides, 123 chains. Longest chain 39 peptides. Score 0.633 Round 3: 1173 peptides, 124 chains. Longest chain 40 peptides. Score 0.634 Round 4: 1174 peptides, 125 chains. Longest chain 36 peptides. Score 0.632 Round 5: 1200 peptides, 118 chains. Longest chain 41 peptides. Score 0.660 Taking the results from Round 5 Chains 136, Residues 1082, Estimated correctness of the model 56.2 % 22 chains (347 residues) have been docked in sequence ------------------------------------------------------ 36121 reflections ( 97.38 % complete ) and 24244 restraints for refining 12532 atoms. 18813 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2268 (Rfree = 0.000) for 12532 atoms. Found 112 (112 requested) and removed 96 (56 requested) atoms. Cycle 27: After refmac, R = 0.2084 (Rfree = 0.000) for 12501 atoms. Found 38 (112 requested) and removed 68 (56 requested) atoms. Cycle 28: After refmac, R = 0.2060 (Rfree = 0.000) for 12435 atoms. Found 26 (111 requested) and removed 57 (55 requested) atoms. Cycle 29: After refmac, R = 0.1947 (Rfree = 0.000) for 12384 atoms. Found 20 (111 requested) and removed 57 (55 requested) atoms. Cycle 30: After refmac, R = 0.1924 (Rfree = 0.000) for 12338 atoms. Found 17 (110 requested) and removed 55 (55 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.16 2.76 Search for helices and strands: 0 residues in 0 chains, 12730 seeds are put forward NCS extension: 7 residues added (13 deleted due to clashes), 12737 seeds are put forward Round 1: 1030 peptides, 133 chains. Longest chain 32 peptides. Score 0.535 Round 2: 1102 peptides, 118 chains. Longest chain 37 peptides. Score 0.612 Round 3: 1078 peptides, 119 chains. Longest chain 31 peptides. Score 0.597 Round 4: 1103 peptides, 110 chains. Longest chain 42 peptides. Score 0.632 Round 5: 1115 peptides, 110 chains. Longest chain 44 peptides. Score 0.638 Taking the results from Round 5 Chains 121, Residues 1005, Estimated correctness of the model 50.9 % 26 chains (349 residues) have been docked in sequence ------------------------------------------------------ 36121 reflections ( 97.38 % complete ) and 24630 restraints for refining 12532 atoms. 19542 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2201 (Rfree = 0.000) for 12532 atoms. Found 112 (112 requested) and removed 87 (56 requested) atoms. Cycle 32: After refmac, R = 0.1993 (Rfree = 0.000) for 12513 atoms. Found 37 (112 requested) and removed 66 (56 requested) atoms. Cycle 33: After refmac, R = 0.2235 (Rfree = 0.000) for 12461 atoms. Found 105 (112 requested) and removed 60 (56 requested) atoms. Cycle 34: After refmac, R = 0.1871 (Rfree = 0.000) for 12480 atoms. Found 42 (112 requested) and removed 60 (56 requested) atoms. Cycle 35: After refmac, R = 0.1845 (Rfree = 0.000) for 12437 atoms. Found 35 (111 requested) and removed 56 (55 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.16 2.76 Search for helices and strands: 0 residues in 0 chains, 12909 seeds are put forward NCS extension: 13 residues added (22 deleted due to clashes), 12922 seeds are put forward Round 1: 1050 peptides, 131 chains. Longest chain 27 peptides. Score 0.552 Round 2: 1109 peptides, 115 chains. Longest chain 40 peptides. Score 0.623 Round 3: 1113 peptides, 108 chains. Longest chain 50 peptides. Score 0.641 Round 4: 1093 peptides, 113 chains. Longest chain 37 peptides. Score 0.620 Round 5: 1101 peptides, 110 chains. Longest chain 34 peptides. Score 0.631 Taking the results from Round 3 Chains 120, Residues 1005, Estimated correctness of the model 51.6 % 24 chains (308 residues) have been docked in sequence ------------------------------------------------------ 36121 reflections ( 97.38 % complete ) and 24988 restraints for refining 12528 atoms. 20028 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2070 (Rfree = 0.000) for 12528 atoms. Found 80 (112 requested) and removed 87 (56 requested) atoms. Cycle 37: After refmac, R = 0.1994 (Rfree = 0.000) for 12487 atoms. Found 48 (112 requested) and removed 63 (56 requested) atoms. Cycle 38: After refmac, R = 0.1879 (Rfree = 0.000) for 12457 atoms. Found 26 (111 requested) and removed 57 (55 requested) atoms. Cycle 39: After refmac, R = 0.1929 (Rfree = 0.000) for 12416 atoms. Found 27 (111 requested) and removed 57 (55 requested) atoms. Cycle 40: After refmac, R = 0.1861 (Rfree = 0.000) for 12374 atoms. Found 34 (111 requested) and removed 55 (55 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.17 2.77 Search for helices and strands: 0 residues in 0 chains, 12772 seeds are put forward NCS extension: 28 residues added (20 deleted due to clashes), 12800 seeds are put forward Round 1: 988 peptides, 139 chains. Longest chain 25 peptides. Score 0.493 Round 2: 1064 peptides, 119 chains. Longest chain 33 peptides. Score 0.590 Round 3: 1107 peptides, 122 chains. Longest chain 40 peptides. Score 0.605 Round 4: 1064 peptides, 115 chains. Longest chain 43 peptides. Score 0.600 Round 5: 1068 peptides, 131 chains. Longest chain 34 peptides. Score 0.562 Taking the results from Round 3 Chains 131, Residues 985, Estimated correctness of the model 42.4 % 17 chains (193 residues) have been docked in sequence ------------------------------------------------------ 36121 reflections ( 97.38 % complete ) and 26295 restraints for refining 12531 atoms. 21814 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2053 (Rfree = 0.000) for 12531 atoms. Found 78 (112 requested) and removed 82 (56 requested) atoms. Cycle 42: After refmac, R = 0.1892 (Rfree = 0.000) for 12498 atoms. Found 31 (112 requested) and removed 58 (56 requested) atoms. Cycle 43: After refmac, R = 0.1960 (Rfree = 0.000) for 12455 atoms. Found 65 (111 requested) and removed 56 (55 requested) atoms. Cycle 44: After refmac, R = 0.1809 (Rfree = 0.000) for 12446 atoms. Found 27 (111 requested) and removed 56 (55 requested) atoms. Cycle 45: After refmac, R = 0.2070 (Rfree = 0.000) for 12411 atoms. Found 111 (111 requested) and removed 57 (55 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.15 2.75 Search for helices and strands: 0 residues in 0 chains, 12922 seeds are put forward NCS extension: 24 residues added (23 deleted due to clashes), 12946 seeds are put forward Round 1: 1014 peptides, 137 chains. Longest chain 23 peptides. Score 0.515 Round 2: 1049 peptides, 123 chains. Longest chain 40 peptides. Score 0.572 Round 3: 1051 peptides, 124 chains. Longest chain 34 peptides. Score 0.570 Round 4: 1097 peptides, 117 chains. Longest chain 54 peptides. Score 0.612 Round 5: 1060 peptides, 114 chains. Longest chain 32 peptides. Score 0.600 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 125, Residues 980, Estimated correctness of the model 44.3 % 15 chains (215 residues) have been docked in sequence Sequence coverage is 21 % Consider running further cycles of model building using 2p10-3_warpNtrace.pdb as input Building loops using Loopy2018 125 chains (980 residues) following loop building 15 chains (215 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 36121 reflections ( 97.38 % complete ) and 26002 restraints for refining 12530 atoms. 21480 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2123 (Rfree = 0.000) for 12530 atoms. Found 0 (112 requested) and removed 49 (56 requested) atoms. Cycle 47: After refmac, R = 0.2012 (Rfree = 0.000) for 12443 atoms. Found 0 (112 requested) and removed 12 (56 requested) atoms. Cycle 48: After refmac, R = 0.1999 (Rfree = 0.000) for 12417 atoms. Found 0 (111 requested) and removed 1 (55 requested) atoms. Cycle 49: After refmac, R = 0.2014 (Rfree = 0.000) for 12408 atoms. Found 0 (111 requested) and removed 6 (55 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 10:18:33 GMT 2018 Job finished. TimeTaking 163.64 Used memory is bytes: 8409304