Sun 23 Dec 23:46:12 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 2p10-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2p10-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2p10-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p10-3.4-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/2p10-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p10-3.4-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 ============================================================ Sun 23 Dec 23:46:16 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/2p10-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p10-3.4-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 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-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: 2p10-3.4-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 3.400 Wilson plot Bfac: 69.77 30063 reflections ( 97.25 % complete ) and 0 restraints for refining 15262 atoms. Observations/parameters ratio is 0.49 ------------------------------------------------------ Starting model: R = 0.2991 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2626 (Rfree = 0.000) for 15262 atoms. Found 115 (115 requested) and removed 79 (57 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.35 2.93 Search for helices and strands: 0 residues in 0 chains, 15650 seeds are put forward NCS extension: 0 residues added, 15650 seeds are put forward Round 1: 863 peptides, 141 chains. Longest chain 19 peptides. Score 0.405 Round 2: 1042 peptides, 129 chains. Longest chain 30 peptides. Score 0.552 Round 3: 1054 peptides, 132 chains. Longest chain 35 peptides. Score 0.551 Round 4: 1090 peptides, 118 chains. Longest chain 38 peptides. Score 0.606 Round 5: 1098 peptides, 112 chains. Longest chain 35 peptides. Score 0.625 Taking the results from Round 5 Chains 125, Residues 986, Estimated correctness of the model 36.6 % 23 chains (285 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 30063 reflections ( 97.25 % complete ) and 25146 restraints for refining 12481 atoms. 20358 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2277 (Rfree = 0.000) for 12481 atoms. Found 94 (94 requested) and removed 121 (47 requested) atoms. Cycle 2: After refmac, R = 0.2077 (Rfree = 0.000) for 12253 atoms. Found 45 (94 requested) and removed 67 (47 requested) atoms. Cycle 3: After refmac, R = 0.1988 (Rfree = 0.000) for 12147 atoms. Found 43 (92 requested) and removed 56 (46 requested) atoms. Cycle 4: After refmac, R = 0.1940 (Rfree = 0.000) for 12076 atoms. Found 26 (91 requested) and removed 57 (45 requested) atoms. Cycle 5: After refmac, R = 0.1960 (Rfree = 0.000) for 12012 atoms. Found 42 (90 requested) and removed 53 (45 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.31 2.89 Search for helices and strands: 0 residues in 0 chains, 12465 seeds are put forward NCS extension: 27 residues added (4 deleted due to clashes), 12492 seeds are put forward Round 1: 1016 peptides, 134 chains. Longest chain 37 peptides. Score 0.524 Round 2: 1102 peptides, 125 chains. Longest chain 34 peptides. Score 0.595 Round 3: 1128 peptides, 121 chains. Longest chain 34 peptides. Score 0.618 Round 4: 1106 peptides, 120 chains. Longest chain 30 peptides. Score 0.610 Round 5: 1109 peptides, 122 chains. Longest chain 33 peptides. Score 0.606 Taking the results from Round 3 Chains 135, Residues 1007, Estimated correctness of the model 34.4 % 26 chains (308 residues) have been docked in sequence ------------------------------------------------------ 30063 reflections ( 97.25 % complete ) and 25030 restraints for refining 12480 atoms. 20099 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2205 (Rfree = 0.000) for 12480 atoms. Found 94 (94 requested) and removed 102 (47 requested) atoms. Cycle 7: After refmac, R = 0.1975 (Rfree = 0.000) for 12382 atoms. Found 46 (94 requested) and removed 70 (47 requested) atoms. Cycle 8: After refmac, R = 0.1952 (Rfree = 0.000) for 12297 atoms. Found 48 (93 requested) and removed 56 (46 requested) atoms. Cycle 9: After refmac, R = 0.1905 (Rfree = 0.000) for 12243 atoms. Found 47 (92 requested) and removed 58 (46 requested) atoms. Cycle 10: After refmac, R = 0.1852 (Rfree = 0.000) for 12195 atoms. Found 30 (92 requested) and removed 51 (46 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.31 2.89 Search for helices and strands: 0 residues in 0 chains, 12637 seeds are put forward NCS extension: 14 residues added (9 deleted due to clashes), 12651 seeds are put forward Round 1: 1016 peptides, 136 chains. Longest chain 28 peptides. Score 0.518 Round 2: 1126 peptides, 118 chains. Longest chain 34 peptides. Score 0.624 Round 3: 1118 peptides, 126 chains. Longest chain 35 peptides. Score 0.601 Round 4: 1134 peptides, 124 chains. Longest chain 54 peptides. Score 0.614 Round 5: 1094 peptides, 118 chains. Longest chain 34 peptides. Score 0.608 Taking the results from Round 2 Chains 130, Residues 1008, Estimated correctness of the model 36.3 % 22 chains (246 residues) have been docked in sequence ------------------------------------------------------ 30063 reflections ( 97.25 % complete ) and 25403 restraints for refining 12480 atoms. 20713 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2055 (Rfree = 0.000) for 12480 atoms. Found 78 (94 requested) and removed 111 (47 requested) atoms. Cycle 12: After refmac, R = 0.1883 (Rfree = 0.000) for 12385 atoms. Found 42 (93 requested) and removed 79 (46 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1836 (Rfree = 0.000) for 12312 atoms. Found 31 (93 requested) and removed 57 (46 requested) atoms. Cycle 14: After refmac, R = 0.1801 (Rfree = 0.000) for 12266 atoms. Found 25 (92 requested) and removed 51 (46 requested) atoms. Cycle 15: After refmac, R = 0.1765 (Rfree = 0.000) for 12224 atoms. Found 29 (92 requested) and removed 47 (46 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.32 2.90 Search for helices and strands: 0 residues in 0 chains, 12605 seeds are put forward NCS extension: 12 residues added (17 deleted due to clashes), 12617 seeds are put forward Round 1: 997 peptides, 145 chains. Longest chain 25 peptides. Score 0.482 Round 2: 1070 peptides, 124 chains. Longest chain 37 peptides. Score 0.581 Round 3: 1085 peptides, 116 chains. Longest chain 36 peptides. Score 0.608 Round 4: 1080 peptides, 117 chains. Longest chain 34 peptides. Score 0.603 Round 5: 1107 peptides, 120 chains. Longest chain 45 peptides. Score 0.610 Taking the results from Round 5 Chains 136, Residues 987, Estimated correctness of the model 31.9 % 27 chains (333 residues) have been docked in sequence ------------------------------------------------------ 30063 reflections ( 97.25 % complete ) and 24587 restraints for refining 12482 atoms. 19666 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2195 (Rfree = 0.000) for 12482 atoms. Found 94 (94 requested) and removed 103 (47 requested) atoms. Cycle 17: After refmac, R = 0.1981 (Rfree = 0.000) for 12397 atoms. Found 33 (94 requested) and removed 73 (47 requested) atoms. Cycle 18: After refmac, R = 0.1919 (Rfree = 0.000) for 12326 atoms. Found 28 (93 requested) and removed 50 (46 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1856 (Rfree = 0.000) for 12283 atoms. Found 26 (92 requested) and removed 49 (46 requested) atoms. Cycle 20: After refmac, R = 0.1808 (Rfree = 0.000) for 12240 atoms. Found 22 (92 requested) and removed 47 (46 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.32 2.90 Search for helices and strands: 0 residues in 0 chains, 12613 seeds are put forward NCS extension: 29 residues added (18 deleted due to clashes), 12642 seeds are put forward Round 1: 981 peptides, 141 chains. Longest chain 25 peptides. Score 0.483 Round 2: 1076 peptides, 121 chains. Longest chain 50 peptides. Score 0.591 Round 3: 1054 peptides, 114 chains. Longest chain 30 peptides. Score 0.597 Round 4: 1097 peptides, 117 chains. Longest chain 30 peptides. Score 0.612 Round 5: 1068 peptides, 116 chains. Longest chain 28 peptides. Score 0.599 Taking the results from Round 4 Chains 134, Residues 980, Estimated correctness of the model 32.5 % 24 chains (260 residues) have been docked in sequence ------------------------------------------------------ 30063 reflections ( 97.25 % complete ) and 25413 restraints for refining 12482 atoms. 20737 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2158 (Rfree = 0.000) for 12482 atoms. Found 82 (94 requested) and removed 79 (47 requested) atoms. Cycle 22: After refmac, R = 0.1959 (Rfree = 0.000) for 12406 atoms. Found 28 (94 requested) and removed 61 (47 requested) atoms. Cycle 23: After refmac, R = 0.1909 (Rfree = 0.000) for 12333 atoms. Found 33 (93 requested) and removed 48 (46 requested) atoms. Cycle 24: After refmac, R = 0.1845 (Rfree = 0.000) for 12279 atoms. Found 25 (93 requested) and removed 49 (46 requested) atoms. Cycle 25: After refmac, R = 0.1827 (Rfree = 0.000) for 12237 atoms. Found 25 (92 requested) and removed 50 (46 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.30 2.88 Search for helices and strands: 0 residues in 0 chains, 12695 seeds are put forward NCS extension: 11 residues added (8 deleted due to clashes), 12706 seeds are put forward Round 1: 946 peptides, 138 chains. Longest chain 20 peptides. Score 0.469 Round 2: 1041 peptides, 126 chains. Longest chain 23 peptides. Score 0.559 Round 3: 1035 peptides, 118 chains. Longest chain 37 peptides. Score 0.577 Round 4: 1067 peptides, 121 chains. Longest chain 32 peptides. Score 0.587 Round 5: 1052 peptides, 125 chains. Longest chain 23 peptides. Score 0.568 Taking the results from Round 4 Chains 130, Residues 946, Estimated correctness of the model 24.4 % 17 chains (188 residues) have been docked in sequence ------------------------------------------------------ 30063 reflections ( 97.25 % complete ) and 26528 restraints for refining 12483 atoms. 22249 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2092 (Rfree = 0.000) for 12483 atoms. Found 76 (94 requested) and removed 68 (47 requested) atoms. Cycle 27: After refmac, R = 0.1948 (Rfree = 0.000) for 12438 atoms. Found 32 (94 requested) and removed 55 (47 requested) atoms. Cycle 28: After refmac, R = 0.1908 (Rfree = 0.000) for 12382 atoms. Found 43 (93 requested) and removed 57 (46 requested) atoms. Cycle 29: After refmac, R = 0.1850 (Rfree = 0.000) for 12343 atoms. Found 23 (93 requested) and removed 57 (46 requested) atoms. Cycle 30: After refmac, R = 0.1798 (Rfree = 0.000) for 12289 atoms. Found 25 (92 requested) and removed 48 (46 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.28 2.87 Search for helices and strands: 0 residues in 0 chains, 12727 seeds are put forward NCS extension: 16 residues added (8 deleted due to clashes), 12743 seeds are put forward Round 1: 921 peptides, 136 chains. Longest chain 26 peptides. Score 0.459 Round 2: 987 peptides, 133 chains. Longest chain 28 peptides. Score 0.509 Round 3: 1023 peptides, 133 chains. Longest chain 31 peptides. Score 0.531 Round 4: 1013 peptides, 121 chains. Longest chain 26 peptides. Score 0.557 Round 5: 1013 peptides, 119 chains. Longest chain 31 peptides. Score 0.562 Taking the results from Round 5 Chains 126, Residues 894, Estimated correctness of the model 15.8 % 14 chains (163 residues) have been docked in sequence ------------------------------------------------------ 30063 reflections ( 97.25 % complete ) and 26798 restraints for refining 12481 atoms. 22816 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2094 (Rfree = 0.000) for 12481 atoms. Found 94 (94 requested) and removed 74 (47 requested) atoms. Cycle 32: After refmac, R = 0.1906 (Rfree = 0.000) for 12460 atoms. Found 30 (94 requested) and removed 63 (47 requested) atoms. Cycle 33: After refmac, R = 0.1886 (Rfree = 0.000) for 12384 atoms. Found 37 (93 requested) and removed 54 (46 requested) atoms. Cycle 34: After refmac, R = 0.1820 (Rfree = 0.000) for 12349 atoms. Found 21 (93 requested) and removed 49 (46 requested) atoms. Cycle 35: After refmac, R = 0.1785 (Rfree = 0.000) for 12313 atoms. Found 19 (93 requested) and removed 48 (46 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.31 2.89 Search for helices and strands: 0 residues in 0 chains, 12707 seeds are put forward NCS extension: 8 residues added (17 deleted due to clashes), 12715 seeds are put forward Round 1: 853 peptides, 128 chains. Longest chain 31 peptides. Score 0.437 Round 2: 963 peptides, 123 chains. Longest chain 37 peptides. Score 0.522 Round 3: 986 peptides, 123 chains. Longest chain 37 peptides. Score 0.536 Round 4: 968 peptides, 115 chains. Longest chain 37 peptides. Score 0.547 Round 5: 971 peptides, 126 chains. Longest chain 26 peptides. Score 0.519 Taking the results from Round 4 Chains 124, Residues 853, Estimated correctness of the model 10.4 % 20 chains (203 residues) have been docked in sequence ------------------------------------------------------ 30063 reflections ( 97.25 % complete ) and 26433 restraints for refining 12483 atoms. 22466 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2063 (Rfree = 0.000) for 12483 atoms. Found 72 (94 requested) and removed 70 (47 requested) atoms. Cycle 37: After refmac, R = 0.1874 (Rfree = 0.000) for 12434 atoms. Found 30 (94 requested) and removed 59 (47 requested) atoms. Cycle 38: After refmac, R = 0.1807 (Rfree = 0.000) for 12378 atoms. Found 31 (93 requested) and removed 49 (46 requested) atoms. Cycle 39: After refmac, R = 0.1765 (Rfree = 0.000) for 12344 atoms. Found 25 (93 requested) and removed 49 (46 requested) atoms. Cycle 40: After refmac, R = 0.1731 (Rfree = 0.000) for 12309 atoms. Found 21 (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, 12735 seeds are put forward NCS extension: 20 residues added (15 deleted due to clashes), 12755 seeds are put forward Round 1: 852 peptides, 136 chains. Longest chain 25 peptides. Score 0.412 Round 2: 934 peptides, 127 chains. Longest chain 25 peptides. Score 0.493 Round 3: 948 peptides, 129 chains. Longest chain 24 peptides. Score 0.496 Round 4: 908 peptides, 120 chains. Longest chain 20 peptides. Score 0.497 Round 5: 927 peptides, 127 chains. Longest chain 19 peptides. Score 0.489 Taking the results from Round 4 Chains 127, Residues 788, Estimated correctness of the model 0.0 % 17 chains (114 residues) have been docked in sequence ------------------------------------------------------ 30063 reflections ( 97.25 % complete ) and 28129 restraints for refining 12481 atoms. 24738 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1954 (Rfree = 0.000) for 12481 atoms. Found 74 (94 requested) and removed 62 (47 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.1837 (Rfree = 0.000) for 12459 atoms. Found 32 (94 requested) and removed 52 (47 requested) atoms. Cycle 43: After refmac, R = 0.1784 (Rfree = 0.000) for 12418 atoms. Found 30 (93 requested) and removed 53 (46 requested) atoms. Cycle 44: After refmac, R = 0.1738 (Rfree = 0.000) for 12372 atoms. Found 32 (93 requested) and removed 51 (46 requested) atoms. Cycle 45: After refmac, R = 0.1676 (Rfree = 0.000) for 12341 atoms. Found 26 (93 requested) and removed 46 (46 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.32 2.90 Search for helices and strands: 0 residues in 0 chains, 12741 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 12757 seeds are put forward Round 1: 827 peptides, 141 chains. Longest chain 18 peptides. Score 0.379 Round 2: 883 peptides, 132 chains. Longest chain 19 peptides. Score 0.445 Round 3: 906 peptides, 122 chains. Longest chain 29 peptides. Score 0.490 Round 4: 897 peptides, 120 chains. Longest chain 22 peptides. Score 0.490 Round 5: 907 peptides, 119 chains. Longest chain 30 peptides. Score 0.499 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 127, Residues 788, Estimated correctness of the model 0.0 % 17 chains (126 residues) have been docked in sequence Sequence coverage is 15 % Consider running further cycles of model building using 2p10-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 244 A and 253 A Built loop between residues 184 C and 196 C Built loop between residues 63 B and 69 B 122 chains (801 residues) following loop building 14 chains (150 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 30063 reflections ( 97.25 % complete ) and 27129 restraints for refining 12483 atoms. 23625 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2037 (Rfree = 0.000) for 12483 atoms. Found 0 (94 requested) and removed 40 (47 requested) atoms. Cycle 47: After refmac, R = 0.1944 (Rfree = 0.000) for 12392 atoms. Found 0 (93 requested) and removed 28 (46 requested) atoms. Cycle 48: After refmac, R = 0.1886 (Rfree = 0.000) for 12345 atoms. Found 0 (93 requested) and removed 18 (46 requested) atoms. Cycle 49: After refmac, R = 0.1848 (Rfree = 0.000) for 12316 atoms. Found 0 (93 requested) and removed 9 (46 requested) atoms. Writing output files ... TimeTaking 149.97