Mon 24 Dec 00:59:28 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2p10-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2p10-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2p10-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p10-3.2-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2p10-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p10-3.2-parrot-mrncs ############### 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 00:59:33 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/mrncs/ArpWArp/wArpResults/WorkingDir/2p10-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p10-3.2-parrot-mrncs/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-mrncs.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-mrncs.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 15244 atoms. Observations/parameters ratio is 0.59 ------------------------------------------------------ Starting model: R = 0.2979 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2607 (Rfree = 0.000) for 15244 atoms. Found 136 (136 requested) and removed 111 (68 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.20 2.80 Search for helices and strands: 0 residues in 0 chains, 15626 seeds are put forward NCS extension: 0 residues added, 15626 seeds are put forward Round 1: 977 peptides, 149 chains. Longest chain 29 peptides. Score 0.458 Round 2: 1092 peptides, 135 chains. Longest chain 31 peptides. Score 0.565 Round 3: 1103 peptides, 130 chains. Longest chain 38 peptides. Score 0.584 Round 4: 1148 peptides, 118 chains. Longest chain 44 peptides. Score 0.635 Round 5: 1147 peptides, 115 chains. Longest chain 31 peptides. Score 0.642 Taking the results from Round 5 Chains 127, Residues 1032, Estimated correctness of the model 51.9 % 25 chains (329 residues) have been docked in sequence ------------------------------------------------------ 36121 reflections ( 97.38 % complete ) and 24438 restraints for refining 12526 atoms. 19334 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2397 (Rfree = 0.000) for 12526 atoms. Found 112 (112 requested) and removed 116 (56 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2196 (Rfree = 0.000) for 12366 atoms. Found 60 (112 requested) and removed 75 (56 requested) atoms. Cycle 3: After refmac, R = 0.2114 (Rfree = 0.000) for 12272 atoms. Found 41 (110 requested) and removed 63 (55 requested) atoms. Cycle 4: After refmac, R = 0.2048 (Rfree = 0.000) for 12213 atoms. Found 24 (109 requested) and removed 55 (54 requested) atoms. Cycle 5: After refmac, R = 0.2018 (Rfree = 0.000) for 12150 atoms. Found 35 (109 requested) and removed 55 (54 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.16 2.76 Search for helices and strands: 0 residues in 0 chains, 12617 seeds are put forward NCS extension: 14 residues added (8 deleted due to clashes), 12631 seeds are put forward Round 1: 1115 peptides, 134 chains. Longest chain 31 peptides. Score 0.580 Round 2: 1180 peptides, 122 chains. Longest chain 37 peptides. Score 0.642 Round 3: 1177 peptides, 110 chains. Longest chain 37 peptides. Score 0.667 Round 4: 1187 peptides, 110 chains. Longest chain 42 peptides. Score 0.671 Round 5: 1168 peptides, 113 chains. Longest chain 38 peptides. Score 0.656 Taking the results from Round 4 Chains 130, Residues 1077, Estimated correctness of the model 58.8 % 29 chains (420 residues) have been docked in sequence ------------------------------------------------------ 36121 reflections ( 97.38 % complete ) and 23493 restraints for refining 12533 atoms. 17909 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2347 (Rfree = 0.000) for 12533 atoms. Found 110 (112 requested) and removed 103 (56 requested) atoms. Cycle 7: After refmac, R = 0.2143 (Rfree = 0.000) for 12462 atoms. Found 36 (112 requested) and removed 69 (56 requested) atoms. Cycle 8: After refmac, R = 0.2057 (Rfree = 0.000) for 12371 atoms. Found 30 (111 requested) and removed 59 (55 requested) atoms. Cycle 9: After refmac, R = 0.2022 (Rfree = 0.000) for 12316 atoms. Found 21 (110 requested) and removed 55 (55 requested) atoms. Cycle 10: After refmac, R = 0.2025 (Rfree = 0.000) for 12261 atoms. Found 25 (110 requested) and removed 55 (55 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.18 2.78 Search for helices and strands: 0 residues in 0 chains, 12687 seeds are put forward NCS extension: 21 residues added (17 deleted due to clashes), 12708 seeds are put forward Round 1: 1131 peptides, 129 chains. Longest chain 31 peptides. Score 0.601 Round 2: 1191 peptides, 123 chains. Longest chain 40 peptides. Score 0.645 Round 3: 1198 peptides, 111 chains. Longest chain 47 peptides. Score 0.674 Round 4: 1185 peptides, 113 chains. Longest chain 48 peptides. Score 0.664 Round 5: 1184 peptides, 116 chains. Longest chain 40 peptides. Score 0.657 Taking the results from Round 3 Chains 132, Residues 1087, Estimated correctness of the model 59.5 % 32 chains (435 residues) have been docked in sequence ------------------------------------------------------ 36121 reflections ( 97.38 % complete ) and 23329 restraints for refining 12532 atoms. 17685 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2252 (Rfree = 0.000) for 12532 atoms. Found 73 (112 requested) and removed 99 (56 requested) atoms. Cycle 12: After refmac, R = 0.2091 (Rfree = 0.000) for 12435 atoms. Found 53 (112 requested) and removed 65 (56 requested) atoms. Cycle 13: After refmac, R = 0.2007 (Rfree = 0.000) for 12396 atoms. Found 20 (111 requested) and removed 59 (55 requested) atoms. Cycle 14: After refmac, R = 0.1982 (Rfree = 0.000) for 12336 atoms. Found 16 (110 requested) and removed 56 (55 requested) atoms. Cycle 15: After refmac, R = 0.1981 (Rfree = 0.000) for 12277 atoms. Found 19 (110 requested) and removed 55 (55 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.18 2.78 Search for helices and strands: 0 residues in 0 chains, 12687 seeds are put forward NCS extension: 14 residues added (8 deleted due to clashes), 12701 seeds are put forward Round 1: 1089 peptides, 130 chains. Longest chain 29 peptides. Score 0.576 Round 2: 1171 peptides, 122 chains. Longest chain 34 peptides. Score 0.637 Round 3: 1148 peptides, 111 chains. Longest chain 41 peptides. Score 0.651 Round 4: 1155 peptides, 118 chains. Longest chain 41 peptides. Score 0.639 Round 5: 1182 peptides, 112 chains. Longest chain 70 peptides. Score 0.665 Taking the results from Round 5 Chains 121, Residues 1070, Estimated correctness of the model 57.4 % 23 chains (382 residues) have been docked in sequence ------------------------------------------------------ 36121 reflections ( 97.38 % complete ) and 23908 restraints for refining 12532 atoms. 18422 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2277 (Rfree = 0.000) for 12532 atoms. Found 112 (112 requested) and removed 98 (56 requested) atoms. Cycle 17: After refmac, R = 0.2053 (Rfree = 0.000) for 12486 atoms. Found 31 (112 requested) and removed 61 (56 requested) atoms. Cycle 18: After refmac, R = 0.1961 (Rfree = 0.000) for 12421 atoms. Found 15 (111 requested) and removed 57 (55 requested) atoms. Cycle 19: After refmac, R = 0.1919 (Rfree = 0.000) for 12352 atoms. Found 23 (111 requested) and removed 56 (55 requested) atoms. Cycle 20: After refmac, R = 0.1845 (Rfree = 0.000) for 12291 atoms. Found 34 (110 requested) and removed 55 (55 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.17 2.77 Search for helices and strands: 0 residues in 0 chains, 12744 seeds are put forward NCS extension: 10 residues added (15 deleted due to clashes), 12754 seeds are put forward Round 1: 1111 peptides, 131 chains. Longest chain 39 peptides. Score 0.585 Round 2: 1200 peptides, 119 chains. Longest chain 40 peptides. Score 0.658 Round 3: 1187 peptides, 108 chains. Longest chain 61 peptides. Score 0.675 Round 4: 1175 peptides, 113 chains. Longest chain 65 peptides. Score 0.659 Round 5: 1171 peptides, 123 chains. Longest chain 38 peptides. Score 0.635 Taking the results from Round 3 Chains 131, Residues 1079, Estimated correctness of the model 59.7 % 27 chains (429 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 36121 reflections ( 97.38 % complete ) and 23769 restraints for refining 12532 atoms. 18100 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2250 (Rfree = 0.000) for 12532 atoms. Found 98 (112 requested) and removed 87 (56 requested) atoms. Cycle 22: After refmac, R = 0.2055 (Rfree = 0.000) for 12500 atoms. Found 42 (112 requested) and removed 65 (56 requested) atoms. Cycle 23: After refmac, R = 0.1960 (Rfree = 0.000) for 12455 atoms. Found 21 (111 requested) and removed 58 (55 requested) atoms. Cycle 24: After refmac, R = 0.1926 (Rfree = 0.000) for 12407 atoms. Found 19 (111 requested) and removed 58 (55 requested) atoms. Cycle 25: After refmac, R = 0.1905 (Rfree = 0.000) for 12359 atoms. Found 24 (110 requested) and removed 55 (55 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.16 2.76 Search for helices and strands: 0 residues in 0 chains, 12750 seeds are put forward NCS extension: 14 residues added (10 deleted due to clashes), 12764 seeds are put forward Round 1: 1108 peptides, 130 chains. Longest chain 41 peptides. Score 0.586 Round 2: 1161 peptides, 114 chains. Longest chain 64 peptides. Score 0.650 Round 3: 1164 peptides, 112 chains. Longest chain 41 peptides. Score 0.656 Round 4: 1164 peptides, 112 chains. Longest chain 53 peptides. Score 0.656 Round 5: 1154 peptides, 115 chains. Longest chain 42 peptides. Score 0.645 Taking the results from Round 4 Chains 128, Residues 1052, Estimated correctness of the model 55.3 % 27 chains (385 residues) have been docked in sequence ------------------------------------------------------ 36121 reflections ( 97.38 % complete ) and 24087 restraints for refining 12532 atoms. 18687 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2207 (Rfree = 0.000) for 12532 atoms. Found 82 (112 requested) and removed 91 (56 requested) atoms. Cycle 27: After refmac, R = 0.2045 (Rfree = 0.000) for 12480 atoms. Found 31 (112 requested) and removed 67 (56 requested) atoms. Cycle 28: After refmac, R = 0.1968 (Rfree = 0.000) for 12419 atoms. Found 19 (111 requested) and removed 55 (55 requested) atoms. Cycle 29: After refmac, R = 0.1973 (Rfree = 0.000) for 12370 atoms. Found 30 (111 requested) and removed 55 (55 requested) atoms. Cycle 30: After refmac, R = 0.1923 (Rfree = 0.000) for 12329 atoms. Found 33 (110 requested) and removed 55 (55 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 2.77 Search for helices and strands: 0 residues in 0 chains, 12744 seeds are put forward NCS extension: 23 residues added (51 deleted due to clashes), 12767 seeds are put forward Round 1: 1097 peptides, 122 chains. Longest chain 32 peptides. Score 0.600 Round 2: 1184 peptides, 109 chains. Longest chain 51 peptides. Score 0.672 Round 3: 1155 peptides, 116 chains. Longest chain 30 peptides. Score 0.643 Round 4: 1151 peptides, 105 chains. Longest chain 54 peptides. Score 0.666 Round 5: 1140 peptides, 106 chains. Longest chain 49 peptides. Score 0.658 Taking the results from Round 2 Chains 124, Residues 1075, Estimated correctness of the model 59.0 % 23 chains (415 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 36121 reflections ( 97.38 % complete ) and 23720 restraints for refining 12529 atoms. 18109 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2165 (Rfree = 0.000) for 12529 atoms. Found 96 (112 requested) and removed 105 (56 requested) atoms. Cycle 32: After refmac, R = 0.2008 (Rfree = 0.000) for 12486 atoms. Found 43 (112 requested) and removed 68 (56 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.1959 (Rfree = 0.000) for 12444 atoms. Found 28 (111 requested) and removed 58 (55 requested) atoms. Cycle 34: After refmac, R = 0.1933 (Rfree = 0.000) for 12403 atoms. Found 38 (111 requested) and removed 55 (55 requested) atoms. Cycle 35: After refmac, R = 0.1877 (Rfree = 0.000) for 12374 atoms. Found 18 (111 requested) and removed 55 (55 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.18 2.78 Search for helices and strands: 0 residues in 0 chains, 12758 seeds are put forward NCS extension: 16 residues added (25 deleted due to clashes), 12774 seeds are put forward Round 1: 1060 peptides, 126 chains. Longest chain 35 peptides. Score 0.570 Round 2: 1120 peptides, 122 chains. Longest chain 53 peptides. Score 0.612 Round 3: 1088 peptides, 112 chains. Longest chain 38 peptides. Score 0.620 Round 4: 1105 peptides, 111 chains. Longest chain 37 peptides. Score 0.630 Round 5: 1101 peptides, 117 chains. Longest chain 41 peptides. Score 0.614 Taking the results from Round 4 Chains 125, Residues 994, Estimated correctness of the model 48.9 % 22 chains (367 residues) have been docked in sequence ------------------------------------------------------ 36121 reflections ( 97.38 % complete ) and 24617 restraints for refining 12533 atoms. 19525 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2153 (Rfree = 0.000) for 12533 atoms. Found 83 (112 requested) and removed 90 (56 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2013 (Rfree = 0.000) for 12489 atoms. Found 48 (112 requested) and removed 70 (56 requested) atoms. Cycle 38: After refmac, R = 0.1971 (Rfree = 0.000) for 12449 atoms. Found 30 (111 requested) and removed 55 (55 requested) atoms. Cycle 39: After refmac, R = 0.1954 (Rfree = 0.000) for 12416 atoms. Found 21 (111 requested) and removed 55 (55 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1968 (Rfree = 0.000) for 12376 atoms. Found 24 (111 requested) and removed 57 (55 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.18 2.78 Search for helices and strands: 0 residues in 0 chains, 12766 seeds are put forward NCS extension: 19 residues added (11 deleted due to clashes), 12785 seeds are put forward Round 1: 1049 peptides, 136 chains. Longest chain 29 peptides. Score 0.538 Round 2: 1126 peptides, 124 chains. Longest chain 38 peptides. Score 0.610 Round 3: 1126 peptides, 125 chains. Longest chain 45 peptides. Score 0.608 Round 4: 1103 peptides, 116 chains. Longest chain 29 peptides. Score 0.618 Round 5: 1098 peptides, 127 chains. Longest chain 32 peptides. Score 0.588 Taking the results from Round 4 Chains 129, Residues 987, Estimated correctness of the model 45.8 % 23 chains (305 residues) have been docked in sequence ------------------------------------------------------ 36121 reflections ( 97.38 % complete ) and 25566 restraints for refining 12531 atoms. 20746 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2227 (Rfree = 0.000) for 12531 atoms. Found 112 (112 requested) and removed 93 (56 requested) atoms. Cycle 42: After refmac, R = 0.2076 (Rfree = 0.000) for 12508 atoms. Found 37 (112 requested) and removed 61 (56 requested) atoms. Cycle 43: After refmac, R = 0.2038 (Rfree = 0.000) for 12460 atoms. Found 26 (112 requested) and removed 57 (56 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.2043 (Rfree = 0.000) for 12418 atoms. Found 38 (111 requested) and removed 55 (55 requested) atoms. Cycle 45: After refmac, R = 0.2029 (Rfree = 0.000) for 12389 atoms. Found 30 (111 requested) and removed 56 (55 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 2.78 Search for helices and strands: 0 residues in 0 chains, 12788 seeds are put forward NCS extension: 11 residues added (7 deleted due to clashes), 12799 seeds are put forward Round 1: 969 peptides, 134 chains. Longest chain 21 peptides. Score 0.495 Round 2: 1062 peptides, 126 chains. Longest chain 39 peptides. Score 0.571 Round 3: 1083 peptides, 128 chains. Longest chain 41 peptides. Score 0.578 Round 4: 1058 peptides, 119 chains. Longest chain 30 peptides. Score 0.587 Round 5: 1079 peptides, 123 chains. Longest chain 29 peptides. Score 0.588 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 134, Residues 956, Estimated correctness of the model 37.8 % 17 chains (205 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 Built loop between residues 42 A and 48 A Built loop between residues 66 A and 70 A 131 chains (961 residues) following loop building 15 chains (213 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 36121 reflections ( 97.38 % complete ) and 26425 restraints for refining 12530 atoms. 22148 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2238 (Rfree = 0.000) for 12530 atoms. Found 0 (112 requested) and removed 24 (56 requested) atoms. Cycle 47: After refmac, R = 0.2168 (Rfree = 0.000) for 12476 atoms. Found 0 (112 requested) and removed 19 (56 requested) atoms. Cycle 48: After refmac, R = 0.2149 (Rfree = 0.000) for 12440 atoms. Found 0 (111 requested) and removed 9 (55 requested) atoms. Cycle 49: After refmac, R = 0.2108 (Rfree = 0.000) for 12421 atoms. TimeTaking 193.18