null Sun 23 Dec 22:22:49 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 1vr8-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vr8-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vr8-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr8-3.2-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/1vr8-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr8-3.2-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 22:22:59 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/1vr8-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr8-3.2-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 124 and 0 Target number of residues in the AU: 124 Target solvent content: 0.6040 Checking the provided sequence file Detected sequence length: 142 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 142 Adjusted target solvent content: 0.55 Input MTZ file: 1vr8-3.2-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: 154 Cell parameters: 57.762 57.762 87.976 90.000 90.000 120.000 Input sequence file: 1vr8-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1136 target number of atoms Had to go as low as 0.75 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 Loops will be built when appropriate and at the last cycle Resolution range: 50.023 3.200 Wilson plot Bfac: 53.05 3034 reflections ( 99.80 % complete ) and 0 restraints for refining 1270 atoms. Observations/parameters ratio is 0.60 ------------------------------------------------------ Starting model: R = 0.3244 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2260 (Rfree = 0.000) for 1270 atoms. Found 11 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.05 2.85 Search for helices and strands: 0 residues in 0 chains, 1290 seeds are put forward Round 1: 87 peptides, 12 chains. Longest chain 15 peptides. Score 0.546 Round 2: 93 peptides, 10 chains. Longest chain 18 peptides. Score 0.652 Round 3: 115 peptides, 10 chains. Longest chain 35 peptides. Score 0.768 Round 4: 112 peptides, 8 chains. Longest chain 23 peptides. Score 0.797 Round 5: 111 peptides, 8 chains. Longest chain 28 peptides. Score 0.793 Taking the results from Round 4 Chains 9, Residues 104, Estimated correctness of the model 83.0 % 4 chains (69 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 102 A and 107 A 8 chains (108 residues) following loop building 3 chains (73 residues) in sequence following loop building ------------------------------------------------------ 3034 reflections ( 99.80 % complete ) and 1732 restraints for refining 1178 atoms. 987 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2692 (Rfree = 0.000) for 1178 atoms. Found 10 (10 requested) and removed 20 (5 requested) atoms. Cycle 2: After refmac, R = 0.2402 (Rfree = 0.000) for 1144 atoms. Found 9 (10 requested) and removed 7 (5 requested) atoms. Cycle 3: After refmac, R = 0.2259 (Rfree = 0.000) for 1136 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. Cycle 4: After refmac, R = 0.2158 (Rfree = 0.000) for 1130 atoms. Found 4 (9 requested) and removed 5 (5 requested) atoms. Cycle 5: After refmac, R = 0.2139 (Rfree = 0.000) for 1126 atoms. Found 2 (9 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.03 2.83 Search for helices and strands: 0 residues in 0 chains, 1142 seeds are put forward Round 1: 109 peptides, 11 chains. Longest chain 20 peptides. Score 0.717 Round 2: 113 peptides, 7 chains. Longest chain 39 peptides. Score 0.820 Round 3: 116 peptides, 8 chains. Longest chain 37 peptides. Score 0.812 Round 4: 112 peptides, 7 chains. Longest chain 37 peptides. Score 0.816 Round 5: 111 peptides, 8 chains. Longest chain 43 peptides. Score 0.793 Taking the results from Round 2 Chains 8, Residues 106, Estimated correctness of the model 86.3 % 3 chains (79 residues) have been docked in sequence Building loops using Loopy2018 8 chains (106 residues) following loop building 3 chains (79 residues) in sequence following loop building ------------------------------------------------------ 3034 reflections ( 99.80 % complete ) and 1531 restraints for refining 1079 atoms. 774 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2437 (Rfree = 0.000) for 1079 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 7: After refmac, R = 0.2195 (Rfree = 0.000) for 1070 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. Cycle 8: After refmac, R = 0.2125 (Rfree = 0.000) for 1066 atoms. Found 5 (8 requested) and removed 4 (4 requested) atoms. Cycle 9: After refmac, R = 0.2094 (Rfree = 0.000) for 1066 atoms. Found 4 (8 requested) and removed 4 (4 requested) atoms. Cycle 10: After refmac, R = 0.2068 (Rfree = 0.000) for 1064 atoms. Found 2 (7 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.01 2.82 Search for helices and strands: 0 residues in 0 chains, 1084 seeds are put forward Round 1: 112 peptides, 9 chains. Longest chain 39 peptides. Score 0.777 Round 2: 120 peptides, 6 chains. Longest chain 39 peptides. Score 0.859 Round 3: 123 peptides, 8 chains. Longest chain 39 peptides. Score 0.836 Round 4: 120 peptides, 8 chains. Longest chain 39 peptides. Score 0.826 Round 5: 112 peptides, 9 chains. Longest chain 29 peptides. Score 0.777 Taking the results from Round 2 Chains 7, Residues 114, Estimated correctness of the model 91.3 % 3 chains (98 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 39 A and 44 A 6 chains (118 residues) following loop building 2 chains (102 residues) in sequence following loop building ------------------------------------------------------ 3034 reflections ( 99.80 % complete ) and 1304 restraints for refining 1094 atoms. 378 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2291 (Rfree = 0.000) for 1094 atoms. Found 7 (7 requested) and removed 8 (4 requested) atoms. Cycle 12: After refmac, R = 0.2096 (Rfree = 0.000) for 1091 atoms. Found 7 (7 requested) and removed 6 (4 requested) atoms. Cycle 13: After refmac, R = 0.2035 (Rfree = 0.000) for 1090 atoms. Found 7 (7 requested) and removed 5 (4 requested) atoms. Cycle 14: After refmac, R = 0.1974 (Rfree = 0.000) for 1092 atoms. Found 3 (7 requested) and removed 5 (4 requested) atoms. Cycle 15: After refmac, R = 0.1929 (Rfree = 0.000) for 1089 atoms. Found 4 (6 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.98 2.79 Search for helices and strands: 0 residues in 0 chains, 1113 seeds are put forward Round 1: 113 peptides, 6 chains. Longest chain 35 peptides. Score 0.838 Round 2: 124 peptides, 6 chains. Longest chain 40 peptides. Score 0.870 Round 3: 121 peptides, 6 chains. Longest chain 35 peptides. Score 0.862 Round 4: 123 peptides, 6 chains. Longest chain 38 peptides. Score 0.867 Round 5: 118 peptides, 11 chains. Longest chain 19 peptides. Score 0.760 Taking the results from Round 2 Chains 7, Residues 118, Estimated correctness of the model 92.5 % 3 chains (97 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 34 A and 41 A 5 chains (121 residues) following loop building 2 chains (103 residues) in sequence following loop building ------------------------------------------------------ 3034 reflections ( 99.80 % complete ) and 1252 restraints for refining 1080 atoms. 307 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2309 (Rfree = 0.000) for 1080 atoms. Found 6 (6 requested) and removed 12 (4 requested) atoms. Cycle 17: After refmac, R = 0.2086 (Rfree = 0.000) for 1074 atoms. Found 6 (6 requested) and removed 5 (4 requested) atoms. Cycle 18: After refmac, R = 0.1956 (Rfree = 0.000) for 1071 atoms. Found 6 (6 requested) and removed 4 (4 requested) atoms. Cycle 19: After refmac, R = 0.1906 (Rfree = 0.000) for 1072 atoms. Found 6 (6 requested) and removed 4 (4 requested) atoms. Cycle 20: After refmac, R = 0.1858 (Rfree = 0.000) for 1073 atoms. Found 6 (6 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.00 2.81 Search for helices and strands: 0 residues in 0 chains, 1100 seeds are put forward Round 1: 109 peptides, 9 chains. Longest chain 19 peptides. Score 0.763 Round 2: 111 peptides, 7 chains. Longest chain 37 peptides. Score 0.813 Round 3: 114 peptides, 9 chains. Longest chain 27 peptides. Score 0.785 Round 4: 115 peptides, 8 chains. Longest chain 25 peptides. Score 0.808 Round 5: 106 peptides, 8 chains. Longest chain 31 peptides. Score 0.772 Taking the results from Round 2 Chains 8, Residues 104, Estimated correctness of the model 85.3 % 3 chains (78 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 41 A and 44 A 7 chains (106 residues) following loop building 2 chains (80 residues) in sequence following loop building ------------------------------------------------------ 3034 reflections ( 99.80 % complete ) and 1481 restraints for refining 1041 atoms. 701 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2154 (Rfree = 0.000) for 1041 atoms. Found 5 (5 requested) and removed 9 (4 requested) atoms. Cycle 22: After refmac, R = 0.1885 (Rfree = 0.000) for 1035 atoms. Found 5 (5 requested) and removed 4 (4 requested) atoms. Cycle 23: After refmac, R = 0.1784 (Rfree = 0.000) for 1036 atoms. Found 5 (5 requested) and removed 4 (4 requested) atoms. Cycle 24: After refmac, R = 0.1742 (Rfree = 0.000) for 1036 atoms. Found 5 (5 requested) and removed 4 (4 requested) atoms. Cycle 25: After refmac, R = 0.1721 (Rfree = 0.000) for 1036 atoms. Found 3 (5 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.01 2.82 Search for helices and strands: 0 residues in 0 chains, 1059 seeds are put forward Round 1: 109 peptides, 11 chains. Longest chain 19 peptides. Score 0.717 Round 2: 117 peptides, 7 chains. Longest chain 36 peptides. Score 0.833 Round 3: 111 peptides, 8 chains. Longest chain 42 peptides. Score 0.793 Round 4: 120 peptides, 7 chains. Longest chain 24 peptides. Score 0.843 Round 5: 116 peptides, 5 chains. Longest chain 42 peptides. Score 0.863 Taking the results from Round 5 Chains 5, Residues 111, Estimated correctness of the model 91.7 % 4 chains (101 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 14 A and 21 A Built loop between residues 48 A and 51 A 3 chains (119 residues) following loop building 2 chains (109 residues) in sequence following loop building ------------------------------------------------------ 3034 reflections ( 99.80 % complete ) and 1269 restraints for refining 1101 atoms. 313 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2175 (Rfree = 0.000) for 1101 atoms. Found 4 (4 requested) and removed 10 (4 requested) atoms. Cycle 27: After refmac, R = 0.1918 (Rfree = 0.000) for 1090 atoms. Found 4 (4 requested) and removed 4 (4 requested) atoms. Cycle 28: After refmac, R = 0.1800 (Rfree = 0.000) for 1087 atoms. Found 4 (4 requested) and removed 4 (4 requested) atoms. Cycle 29: After refmac, R = 0.1817 (Rfree = 0.000) for 1087 atoms. Found 4 (4 requested) and removed 4 (4 requested) atoms. Cycle 30: After refmac, R = 0.1791 (Rfree = 0.000) for 1087 atoms. Found 4 (4 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.00 2.81 Search for helices and strands: 0 residues in 0 chains, 1110 seeds are put forward Round 1: 99 peptides, 8 chains. Longest chain 42 peptides. Score 0.740 Round 2: 113 peptides, 7 chains. Longest chain 26 peptides. Score 0.820 Round 3: 116 peptides, 5 chains. Longest chain 42 peptides. Score 0.863 Round 4: 114 peptides, 5 chains. Longest chain 51 peptides. Score 0.858 Round 5: 107 peptides, 7 chains. Longest chain 45 peptides. Score 0.797 Taking the results from Round 3 Chains 8, Residues 111, Estimated correctness of the model 91.7 % 3 chains (85 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 A and 51 A 6 chains (112 residues) following loop building 2 chains (87 residues) in sequence following loop building ------------------------------------------------------ 3034 reflections ( 99.80 % complete ) and 1362 restraints for refining 1052 atoms. 542 conditional restraints added. Observations/parameters ratio is 0.72 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2048 (Rfree = 0.000) for 1052 atoms. Found 4 (4 requested) and removed 8 (4 requested) atoms. Cycle 32: After refmac, R = 0.2026 (Rfree = 0.000) for 1046 atoms. Found 4 (4 requested) and removed 5 (4 requested) atoms. Cycle 33: After refmac, R = 0.1879 (Rfree = 0.000) for 1043 atoms. Found 4 (4 requested) and removed 4 (4 requested) atoms. Cycle 34: After refmac, R = 0.1866 (Rfree = 0.000) for 1043 atoms. Found 4 (4 requested) and removed 4 (4 requested) atoms. Cycle 35: After refmac, R = 0.1852 (Rfree = 0.000) for 1041 atoms. Found 4 (4 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.00 2.81 Search for helices and strands: 0 residues in 0 chains, 1069 seeds are put forward Round 1: 111 peptides, 9 chains. Longest chain 24 peptides. Score 0.772 Round 2: 118 peptides, 8 chains. Longest chain 29 peptides. Score 0.819 Round 3: 119 peptides, 6 chains. Longest chain 29 peptides. Score 0.856 Round 4: 112 peptides, 8 chains. Longest chain 29 peptides. Score 0.797 Round 5: 110 peptides, 8 chains. Longest chain 29 peptides. Score 0.789 Taking the results from Round 3 Chains 8, Residues 113, Estimated correctness of the model 90.9 % 4 chains (80 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 113 A and 116 A 7 chains (115 residues) following loop building 3 chains (82 residues) in sequence following loop building ------------------------------------------------------ 3034 reflections ( 99.80 % complete ) and 1374 restraints for refining 1037 atoms. 555 conditional restraints added. Observations/parameters ratio is 0.73 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2370 (Rfree = 0.000) for 1037 atoms. Found 4 (4 requested) and removed 6 (4 requested) atoms. Cycle 37: After refmac, R = 0.2092 (Rfree = 0.000) for 1034 atoms. Found 4 (4 requested) and removed 4 (4 requested) atoms. Cycle 38: After refmac, R = 0.1930 (Rfree = 0.000) for 1033 atoms. Found 3 (4 requested) and removed 4 (4 requested) atoms. Cycle 39: After refmac, R = 0.1901 (Rfree = 0.000) for 1032 atoms. Found 1 (4 requested) and removed 4 (4 requested) atoms. Cycle 40: After refmac, R = 0.1897 (Rfree = 0.000) for 1029 atoms. Found 2 (4 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.05 2.85 Search for helices and strands: 0 residues in 0 chains, 1055 seeds are put forward Round 1: 110 peptides, 9 chains. Longest chain 36 peptides. Score 0.768 Round 2: 119 peptides, 5 chains. Longest chain 45 peptides. Score 0.871 Round 3: 116 peptides, 6 chains. Longest chain 45 peptides. Score 0.847 Round 4: 114 peptides, 7 chains. Longest chain 30 peptides. Score 0.823 Round 5: 113 peptides, 7 chains. Longest chain 46 peptides. Score 0.820 Taking the results from Round 2 Chains 7, Residues 114, Estimated correctness of the model 92.6 % 3 chains (94 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 36 A and 42 A 5 chains (118 residues) following loop building 2 chains (99 residues) in sequence following loop building ------------------------------------------------------ 3034 reflections ( 99.80 % complete ) and 1346 restraints for refining 1082 atoms. 448 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2212 (Rfree = 0.000) for 1082 atoms. Found 4 (4 requested) and removed 12 (4 requested) atoms. Cycle 42: After refmac, R = 0.1933 (Rfree = 0.000) for 1073 atoms. Found 4 (4 requested) and removed 5 (4 requested) atoms. Cycle 43: After refmac, R = 0.1816 (Rfree = 0.000) for 1070 atoms. Found 4 (4 requested) and removed 4 (4 requested) atoms. Cycle 44: After refmac, R = 0.1721 (Rfree = 0.000) for 1070 atoms. Found 3 (4 requested) and removed 4 (4 requested) atoms. Cycle 45: After refmac, R = 0.1647 (Rfree = 0.000) for 1069 atoms. Found 1 (4 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.99 2.80 Search for helices and strands: 0 residues in 0 chains, 1088 seeds are put forward Round 1: 119 peptides, 9 chains. Longest chain 38 peptides. Score 0.804 Round 2: 118 peptides, 6 chains. Longest chain 38 peptides. Score 0.853 Round 3: 110 peptides, 9 chains. Longest chain 29 peptides. Score 0.768 Round 4: 118 peptides, 6 chains. Longest chain 38 peptides. Score 0.853 Round 5: 116 peptides, 7 chains. Longest chain 32 peptides. Score 0.830 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 112, Estimated correctness of the model 90.6 % 3 chains (94 residues) have been docked in sequence Sequence coverage is 83 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 40 A and 50 A 4 chains (115 residues) following loop building 2 chains (103 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 3034 reflections ( 99.80 % complete ) and 917 restraints for refining 894 atoms. Observations/parameters ratio is 0.85 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3344 (Rfree = 0.000) for 894 atoms. Found 4 (4 requested) and removed 0 (4 requested) atoms. Cycle 47: After refmac, R = 0.3161 (Rfree = 0.000) for 894 atoms. Found 4 (4 requested) and removed 1 (4 requested) atoms. Cycle 48: After refmac, R = 0.3031 (Rfree = 0.000) for 894 atoms. Found 4 (4 requested) and removed 1 (4 requested) atoms. Cycle 49: After refmac, R = 0.2995 (Rfree = 0.000) for 894 atoms. Found 4 (4 requested) and removed 0 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:50:27 GMT 2018 Job finished. TimeTaking 27.62 Used memory is bytes: 194432