Mon 24 Dec 07:54:52 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 2p10-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2p10-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2p10-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p10-3.4-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/2p10-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p10-3.4-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 07:54:57 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/2p10-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p10-3.4-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 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-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: 2p10-3.4-parrot-noncs.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 3.400 Wilson plot Bfac: 69.77 30063 reflections ( 97.25 % complete ) and 0 restraints for refining 15118 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.3012 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2527 (Rfree = 0.000) for 15118 atoms. Found 114 (114 requested) and removed 77 (57 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 2.91 Search for helices and strands: 0 residues in 0 chains, 15529 seeds are put forward NCS extension: 0 residues added, 15529 seeds are put forward Round 1: 906 peptides, 147 chains. Longest chain 25 peptides. Score 0.416 Round 2: 1057 peptides, 142 chains. Longest chain 24 peptides. Score 0.527 Round 3: 1078 peptides, 129 chains. Longest chain 33 peptides. Score 0.573 Round 4: 1103 peptides, 126 chains. Longest chain 34 peptides. Score 0.593 Round 5: 1126 peptides, 131 chains. Longest chain 28 peptides. Score 0.593 Taking the results from Round 5 Chains 146, Residues 995, Estimated correctness of the model 26.4 % 27 chains (247 residues) have been docked in sequence ------------------------------------------------------ 30063 reflections ( 97.25 % complete ) and 25609 restraints for refining 12480 atoms. 21016 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2279 (Rfree = 0.000) for 12480 atoms. Found 94 (94 requested) and removed 109 (47 requested) atoms. Cycle 2: After refmac, R = 0.2032 (Rfree = 0.000) for 12311 atoms. Found 56 (94 requested) and removed 60 (47 requested) atoms. Cycle 3: After refmac, R = 0.1911 (Rfree = 0.000) for 12234 atoms. Found 36 (92 requested) and removed 60 (46 requested) atoms. Cycle 4: After refmac, R = 0.1856 (Rfree = 0.000) for 12172 atoms. Found 36 (92 requested) and removed 54 (46 requested) atoms. Cycle 5: After refmac, R = 0.1816 (Rfree = 0.000) for 12127 atoms. Found 27 (91 requested) and removed 48 (45 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.32 2.90 Search for helices and strands: 0 residues in 0 chains, 12643 seeds are put forward NCS extension: 11 residues added (8 deleted due to clashes), 12654 seeds are put forward Round 1: 1026 peptides, 135 chains. Longest chain 27 peptides. Score 0.527 Round 2: 1106 peptides, 125 chains. Longest chain 33 peptides. Score 0.597 Round 3: 1133 peptides, 130 chains. Longest chain 31 peptides. Score 0.600 Round 4: 1136 peptides, 120 chains. Longest chain 39 peptides. Score 0.625 Round 5: 1108 peptides, 117 chains. Longest chain 43 peptides. Score 0.618 Taking the results from Round 4 Chains 143, Residues 1016, Estimated correctness of the model 36.6 % 26 chains (253 residues) have been docked in sequence ------------------------------------------------------ 30063 reflections ( 97.25 % complete ) and 25357 restraints for refining 12481 atoms. 20628 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2215 (Rfree = 0.000) for 12481 atoms. Found 94 (94 requested) and removed 112 (47 requested) atoms. Cycle 7: After refmac, R = 0.1991 (Rfree = 0.000) for 12366 atoms. Found 59 (94 requested) and removed 67 (47 requested) atoms. Cycle 8: After refmac, R = 0.1894 (Rfree = 0.000) for 12298 atoms. Found 45 (93 requested) and removed 69 (46 requested) atoms. Cycle 9: After refmac, R = 0.1859 (Rfree = 0.000) for 12253 atoms. Found 34 (92 requested) and removed 53 (46 requested) atoms. Cycle 10: After refmac, R = 0.1797 (Rfree = 0.000) for 12203 atoms. Found 37 (92 requested) and removed 52 (46 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.32 2.90 Search for helices and strands: 0 residues in 0 chains, 12624 seeds are put forward NCS extension: 20 residues added (4 deleted due to clashes), 12644 seeds are put forward Round 1: 1031 peptides, 142 chains. Longest chain 28 peptides. Score 0.511 Round 2: 1097 peptides, 126 chains. Longest chain 35 peptides. Score 0.590 Round 3: 1126 peptides, 128 chains. Longest chain 37 peptides. Score 0.601 Round 4: 1119 peptides, 129 chains. Longest chain 35 peptides. Score 0.595 Round 5: 1129 peptides, 122 chains. Longest chain 38 peptides. Score 0.617 Taking the results from Round 5 Chains 140, Residues 1007, Estimated correctness of the model 34.1 % 24 chains (238 residues) have been docked in sequence ------------------------------------------------------ 30063 reflections ( 97.25 % complete ) and 25698 restraints for refining 12482 atoms. 21079 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2199 (Rfree = 0.000) for 12482 atoms. Found 94 (94 requested) and removed 105 (47 requested) atoms. Cycle 12: After refmac, R = 0.1974 (Rfree = 0.000) for 12398 atoms. Found 45 (94 requested) and removed 77 (47 requested) atoms. Cycle 13: After refmac, R = 0.1921 (Rfree = 0.000) for 12322 atoms. Found 32 (93 requested) and removed 66 (46 requested) atoms. Cycle 14: After refmac, R = 0.1855 (Rfree = 0.000) for 12266 atoms. Found 31 (92 requested) and removed 49 (46 requested) atoms. Cycle 15: After refmac, R = 0.1812 (Rfree = 0.000) for 12227 atoms. Found 30 (92 requested) and removed 47 (46 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.31 2.89 Search for helices and strands: 0 residues in 0 chains, 12678 seeds are put forward NCS extension: 17 residues added (7 deleted due to clashes), 12695 seeds are put forward Round 1: 1031 peptides, 145 chains. Longest chain 29 peptides. Score 0.503 Round 2: 1090 peptides, 124 chains. Longest chain 31 peptides. Score 0.591 Round 3: 1092 peptides, 128 chains. Longest chain 28 peptides. Score 0.583 Round 4: 1109 peptides, 119 chains. Longest chain 43 peptides. Score 0.613 Round 5: 1120 peptides, 127 chains. Longest chain 38 peptides. Score 0.600 Taking the results from Round 4 Chains 132, Residues 990, Estimated correctness of the model 32.9 % 20 chains (232 residues) have been docked in sequence ------------------------------------------------------ 30063 reflections ( 97.25 % complete ) and 25688 restraints for refining 12480 atoms. 21130 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2135 (Rfree = 0.000) for 12480 atoms. Found 79 (94 requested) and removed 101 (47 requested) atoms. Cycle 17: After refmac, R = 0.1967 (Rfree = 0.000) for 12414 atoms. Found 43 (94 requested) and removed 63 (47 requested) atoms. Cycle 18: After refmac, R = 0.1924 (Rfree = 0.000) for 12371 atoms. Found 33 (93 requested) and removed 54 (46 requested) atoms. Cycle 19: After refmac, R = 0.1871 (Rfree = 0.000) for 12328 atoms. Found 28 (93 requested) and removed 49 (46 requested) atoms. Cycle 20: After refmac, R = 0.1834 (Rfree = 0.000) for 12292 atoms. Found 26 (92 requested) and removed 48 (46 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.31 2.89 Search for helices and strands: 0 residues in 0 chains, 12746 seeds are put forward NCS extension: 27 residues added (16 deleted due to clashes), 12773 seeds are put forward Round 1: 988 peptides, 142 chains. Longest chain 29 peptides. Score 0.485 Round 2: 1038 peptides, 126 chains. Longest chain 33 peptides. Score 0.558 Round 3: 1044 peptides, 131 chains. Longest chain 36 peptides. Score 0.548 Round 4: 1094 peptides, 131 chains. Longest chain 27 peptides. Score 0.576 Round 5: 1070 peptides, 125 chains. Longest chain 32 peptides. Score 0.578 Taking the results from Round 5 Chains 134, Residues 945, Estimated correctness of the model 21.3 % 16 chains (175 residues) have been docked in sequence ------------------------------------------------------ 30063 reflections ( 97.25 % complete ) and 26257 restraints for refining 12482 atoms. 22035 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2104 (Rfree = 0.000) for 12482 atoms. Found 81 (94 requested) and removed 88 (47 requested) atoms. Cycle 22: After refmac, R = 0.1913 (Rfree = 0.000) for 12430 atoms. Found 38 (94 requested) and removed 58 (47 requested) atoms. Cycle 23: After refmac, R = 0.1841 (Rfree = 0.000) for 12385 atoms. Found 24 (93 requested) and removed 47 (46 requested) atoms. Cycle 24: After refmac, R = 0.1807 (Rfree = 0.000) for 12352 atoms. Found 19 (93 requested) and removed 48 (46 requested) atoms. Cycle 25: After refmac, R = 0.1795 (Rfree = 0.000) for 12306 atoms. Found 23 (93 requested) and removed 46 (46 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.31 2.89 Search for helices and strands: 0 residues in 0 chains, 12710 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 12728 seeds are put forward Round 1: 950 peptides, 142 chains. Longest chain 22 peptides. Score 0.460 Round 2: 1007 peptides, 124 chains. Longest chain 27 peptides. Score 0.545 Round 3: 1030 peptides, 123 chains. Longest chain 32 peptides. Score 0.561 Round 4: 1032 peptides, 116 chains. Longest chain 31 peptides. Score 0.580 Round 5: 1044 peptides, 123 chains. Longest chain 33 peptides. Score 0.569 Taking the results from Round 4 Chains 130, Residues 916, Estimated correctness of the model 22.0 % 19 chains (234 residues) have been docked in sequence ------------------------------------------------------ 30063 reflections ( 97.25 % complete ) and 25763 restraints for refining 12481 atoms. 21392 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2114 (Rfree = 0.000) for 12481 atoms. Found 78 (94 requested) and removed 86 (47 requested) atoms. Cycle 27: After refmac, R = 0.1907 (Rfree = 0.000) for 12409 atoms. Found 40 (94 requested) and removed 57 (47 requested) atoms. Cycle 28: After refmac, R = 0.1833 (Rfree = 0.000) for 12368 atoms. Found 22 (93 requested) and removed 50 (46 requested) atoms. Cycle 29: After refmac, R = 0.1785 (Rfree = 0.000) for 12330 atoms. Found 11 (93 requested) and removed 47 (46 requested) atoms. Cycle 30: After refmac, R = 0.1784 (Rfree = 0.000) for 12282 atoms. Found 12 (92 requested) and removed 46 (46 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.32 2.90 Search for helices and strands: 0 residues in 0 chains, 12644 seeds are put forward NCS extension: 8 residues added (10 deleted due to clashes), 12652 seeds are put forward Round 1: 934 peptides, 136 chains. Longest chain 27 peptides. Score 0.467 Round 2: 1003 peptides, 131 chains. Longest chain 31 peptides. Score 0.524 Round 3: 1025 peptides, 126 chains. Longest chain 27 peptides. Score 0.550 Round 4: 1016 peptides, 129 chains. Longest chain 24 peptides. Score 0.537 Round 5: 1023 peptides, 132 chains. Longest chain 27 peptides. Score 0.533 Taking the results from Round 3 Chains 133, Residues 899, Estimated correctness of the model 11.5 % 20 chains (167 residues) have been docked in sequence ------------------------------------------------------ 30063 reflections ( 97.25 % complete ) and 26516 restraints for refining 12482 atoms. 22526 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2060 (Rfree = 0.000) for 12482 atoms. Found 76 (94 requested) and removed 69 (47 requested) atoms. Cycle 32: After refmac, R = 0.1915 (Rfree = 0.000) for 12449 atoms. Found 29 (94 requested) and removed 54 (47 requested) atoms. Cycle 33: After refmac, R = 0.1850 (Rfree = 0.000) for 12396 atoms. Found 25 (93 requested) and removed 46 (46 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1791 (Rfree = 0.000) for 12358 atoms. Found 22 (93 requested) and removed 48 (46 requested) atoms. Cycle 35: After refmac, R = 0.1761 (Rfree = 0.000) for 12321 atoms. Found 10 (93 requested) and removed 46 (46 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 2.89 Search for helices and strands: 0 residues in 0 chains, 12737 seeds are put forward NCS extension: 15 residues added (15 deleted due to clashes), 12752 seeds are put forward Round 1: 895 peptides, 144 chains. Longest chain 26 peptides. Score 0.418 Round 2: 956 peptides, 129 chains. Longest chain 27 peptides. Score 0.501 Round 3: 959 peptides, 125 chains. Longest chain 30 peptides. Score 0.514 Round 4: 954 peptides, 125 chains. Longest chain 32 peptides. Score 0.511 Round 5: 976 peptides, 129 chains. Longest chain 26 peptides. Score 0.513 Taking the results from Round 3 Chains 128, Residues 834, Estimated correctness of the model 0.0 % 10 chains (104 residues) have been docked in sequence ------------------------------------------------------ 30063 reflections ( 97.25 % complete ) and 27792 restraints for refining 12482 atoms. 24215 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1969 (Rfree = 0.000) for 12482 atoms. Found 71 (94 requested) and removed 62 (47 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.1807 (Rfree = 0.000) for 12466 atoms. Found 30 (94 requested) and removed 51 (47 requested) atoms. Cycle 38: After refmac, R = 0.1748 (Rfree = 0.000) for 12426 atoms. Found 25 (93 requested) and removed 47 (46 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1713 (Rfree = 0.000) for 12394 atoms. Found 13 (93 requested) and removed 46 (46 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1707 (Rfree = 0.000) for 12354 atoms. Found 13 (93 requested) and removed 47 (46 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 2.89 Search for helices and strands: 0 residues in 0 chains, 12793 seeds are put forward NCS extension: 15 residues added (23 deleted due to clashes), 12808 seeds are put forward Round 1: 893 peptides, 142 chains. Longest chain 19 peptides. Score 0.422 Round 2: 972 peptides, 131 chains. Longest chain 28 peptides. Score 0.505 Round 3: 981 peptides, 126 chains. Longest chain 28 peptides. Score 0.525 Round 4: 963 peptides, 123 chains. Longest chain 32 peptides. Score 0.522 Round 5: 992 peptides, 131 chains. Longest chain 28 peptides. Score 0.518 Taking the results from Round 3 Chains 132, Residues 855, Estimated correctness of the model 2.3 % 13 chains (136 residues) have been docked in sequence ------------------------------------------------------ 30063 reflections ( 97.25 % complete ) and 27322 restraints for refining 12483 atoms. 23568 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1955 (Rfree = 0.000) for 12483 atoms. Found 75 (94 requested) and removed 65 (47 requested) atoms. Cycle 42: After refmac, R = 0.1785 (Rfree = 0.000) for 12460 atoms. Found 23 (94 requested) and removed 50 (47 requested) atoms. Cycle 43: After refmac, R = 0.1734 (Rfree = 0.000) for 12415 atoms. Found 20 (93 requested) and removed 46 (46 requested) atoms. Cycle 44: After refmac, R = 0.1721 (Rfree = 0.000) for 12378 atoms. Found 18 (93 requested) and removed 46 (46 requested) atoms. Cycle 45: After refmac, R = 0.1722 (Rfree = 0.000) for 12342 atoms. Found 19 (93 requested) and removed 46 (46 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 2.91 Search for helices and strands: 0 residues in 0 chains, 12733 seeds are put forward NCS extension: 26 residues added (4 deleted due to clashes), 12759 seeds are put forward Round 1: 857 peptides, 140 chains. Longest chain 24 peptides. Score 0.403 Round 2: 932 peptides, 130 chains. Longest chain 29 peptides. Score 0.483 Round 3: 931 peptides, 130 chains. Longest chain 29 peptides. Score 0.483 Round 4: 955 peptides, 127 chains. Longest chain 29 peptides. Score 0.506 Round 5: 947 peptides, 123 chains. Longest chain 29 peptides. Score 0.512 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 132, Residues 824, Estimated correctness of the model 0.0 % 19 chains (173 residues) have been docked in sequence Sequence coverage is 20 % Consider running further cycles of model building using 2p10-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 164 A and 178 A 130 chains (828 residues) following loop building 18 chains (186 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 30063 reflections ( 97.25 % complete ) and 26911 restraints for refining 12481 atoms. 23198 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2086 (Rfree = 0.000) for 12481 atoms. Found 0 (94 requested) and removed 47 (47 requested) atoms. Cycle 47: After refmac, R = 0.1969 (Rfree = 0.000) for 12402 atoms. Found 0 (93 requested) and removed 46 (46 requested) atoms. Cycle 48: After refmac, R = 0.1947 (Rfree = 0.000) for 12340 atoms. Found 0 (93 requested) and removed 26 (46 requested) atoms. Cycle 49: After refmac, R = 0.1888 (Rfree = 0.000) for 12303 atoms. Found 0 (92 requested) and removed 13 (46 requested) atoms. Writing output files ... TimeTaking 155.68