null Sun 23 Dec 22:22:55 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 2hsb-1.9-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hsb-1.9-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hsb-1.9-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hsb-1.9-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/2hsb-1.9-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hsb-1.9-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 22:23:04 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/2hsb-1.9-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hsb-1.9-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 127 and 0 Target number of residues in the AU: 127 Target solvent content: 0.5351 Checking the provided sequence file Detected sequence length: 126 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 126 Adjusted target solvent content: 0.54 Input MTZ file: 2hsb-1.9-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: 96 Cell parameters: 60.666 60.666 80.341 90.000 90.000 90.000 Input sequence file: 2hsb-1.9-parrot-hancs.fasta_lf Building free atoms model in initial map for 1008 target number of atoms Had to go as low as 0.55 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 1 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: 48.414 1.950 Wilson plot Bfac: 30.72 11459 reflections ( 99.96 % complete ) and 0 restraints for refining 1129 atoms. Observations/parameters ratio is 2.54 ------------------------------------------------------ Starting model: R = 0.3344 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2829 (Rfree = 0.000) for 1129 atoms. Found 39 (41 requested) and removed 20 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.25 2.13 Round 1: 98 peptides, 11 chains. Longest chain 31 peptides. Score 0.695 Round 2: 105 peptides, 7 chains. Longest chain 54 peptides. Score 0.826 Round 3: 110 peptides, 5 chains. Longest chain 61 peptides. Score 0.878 Round 4: 115 peptides, 5 chains. Longest chain 65 peptides. Score 0.891 Round 5: 117 peptides, 5 chains. Longest chain 48 peptides. Score 0.896 Taking the results from Round 5 Chains 5, Residues 112, Estimated correctness of the model 99.0 % 3 chains (102 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 A and 54 A Built loop between residues 69 A and 80 A 2 chains (121 residues) following loop building 1 chains (117 residues) in sequence following loop building ------------------------------------------------------ 11459 reflections ( 99.96 % complete ) and 1169 restraints for refining 1103 atoms. 188 conditional restraints added. Observations/parameters ratio is 2.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2781 (Rfree = 0.000) for 1103 atoms. Found 39 (40 requested) and removed 23 (20 requested) atoms. Cycle 2: After refmac, R = 0.2532 (Rfree = 0.000) for 1111 atoms. Found 29 (40 requested) and removed 20 (20 requested) atoms. Cycle 3: After refmac, R = 0.2359 (Rfree = 0.000) for 1116 atoms. Found 23 (39 requested) and removed 19 (20 requested) atoms. Cycle 4: After refmac, R = 0.2261 (Rfree = 0.000) for 1118 atoms. Found 29 (39 requested) and removed 14 (20 requested) atoms. Cycle 5: After refmac, R = 0.2221 (Rfree = 0.000) for 1131 atoms. Found 21 (39 requested) and removed 17 (20 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.17 2.06 Round 1: 117 peptides, 4 chains. Longest chain 49 peptides. Score 0.909 Round 2: 119 peptides, 3 chains. Longest chain 56 peptides. Score 0.926 Round 3: 115 peptides, 3 chains. Longest chain 51 peptides. Score 0.918 Round 4: 119 peptides, 3 chains. Longest chain 65 peptides. Score 0.926 Round 5: 116 peptides, 5 chains. Longest chain 49 peptides. Score 0.894 Taking the results from Round 4 Chains 3, Residues 116, Estimated correctness of the model 99.4 % 2 chains (111 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 A and 55 A 2 chains (122 residues) following loop building 1 chains (117 residues) in sequence following loop building ------------------------------------------------------ 11459 reflections ( 99.96 % complete ) and 1184 restraints for refining 1133 atoms. 199 conditional restraints added. Observations/parameters ratio is 2.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2459 (Rfree = 0.000) for 1133 atoms. Found 28 (38 requested) and removed 22 (20 requested) atoms. Cycle 7: After refmac, R = 0.2244 (Rfree = 0.000) for 1139 atoms. Found 17 (37 requested) and removed 20 (20 requested) atoms. Cycle 8: After refmac, R = 0.2149 (Rfree = 0.000) for 1134 atoms. Found 21 (36 requested) and removed 13 (20 requested) atoms. Cycle 9: After refmac, R = 0.2085 (Rfree = 0.000) for 1140 atoms. Found 26 (36 requested) and removed 21 (21 requested) atoms. Cycle 10: After refmac, R = 0.2051 (Rfree = 0.000) for 1142 atoms. Found 22 (35 requested) and removed 19 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.16 2.05 Round 1: 123 peptides, 2 chains. Longest chain 74 peptides. Score 0.943 Round 2: 119 peptides, 2 chains. Longest chain 69 peptides. Score 0.937 Round 3: 121 peptides, 4 chains. Longest chain 51 peptides. Score 0.917 Round 4: 119 peptides, 3 chains. Longest chain 49 peptides. Score 0.926 Round 5: 122 peptides, 3 chains. Longest chain 57 peptides. Score 0.931 Taking the results from Round 1 Chains 2, Residues 121, Estimated correctness of the model 99.7 % 2 chains (121 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 49 A and 53 A 1 chains (124 residues) following loop building 1 chains (124 residues) in sequence following loop building ------------------------------------------------------ 11459 reflections ( 99.96 % complete ) and 1122 restraints for refining 1136 atoms. 102 conditional restraints added. Observations/parameters ratio is 2.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2327 (Rfree = 0.000) for 1136 atoms. Found 34 (34 requested) and removed 21 (20 requested) atoms. Cycle 12: After refmac, R = 0.2159 (Rfree = 0.000) for 1146 atoms. Found 23 (34 requested) and removed 21 (21 requested) atoms. Cycle 13: After refmac, R = 0.2065 (Rfree = 0.000) for 1146 atoms. Found 24 (33 requested) and removed 21 (21 requested) atoms. Cycle 14: After refmac, R = 0.2038 (Rfree = 0.000) for 1146 atoms. Found 27 (32 requested) and removed 22 (21 requested) atoms. Cycle 15: After refmac, R = 0.2007 (Rfree = 0.000) for 1150 atoms. Found 26 (31 requested) and removed 14 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.17 2.06 Round 1: 124 peptides, 2 chains. Longest chain 75 peptides. Score 0.945 Round 2: 122 peptides, 3 chains. Longest chain 51 peptides. Score 0.931 Round 3: 124 peptides, 2 chains. Longest chain 76 peptides. Score 0.945 Round 4: 121 peptides, 4 chains. Longest chain 51 peptides. Score 0.917 Round 5: 123 peptides, 2 chains. Longest chain 75 peptides. Score 0.943 Taking the results from Round 3 Chains 2, Residues 122, Estimated correctness of the model 99.7 % 2 chains (122 residues) have been docked in sequence Building loops using Loopy2018 2 chains (122 residues) following loop building 2 chains (122 residues) in sequence following loop building ------------------------------------------------------ 11459 reflections ( 99.96 % complete ) and 1135 restraints for refining 1147 atoms. 133 conditional restraints added. Observations/parameters ratio is 2.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2239 (Rfree = 0.000) for 1147 atoms. Found 23 (30 requested) and removed 22 (21 requested) atoms. Cycle 17: After refmac, R = 0.2124 (Rfree = 0.000) for 1145 atoms. Found 17 (29 requested) and removed 19 (21 requested) atoms. Cycle 18: After refmac, R = 0.2017 (Rfree = 0.000) for 1143 atoms. Found 26 (29 requested) and removed 12 (21 requested) atoms. Cycle 19: After refmac, R = 0.1976 (Rfree = 0.000) for 1157 atoms. Found 16 (29 requested) and removed 16 (21 requested) atoms. Cycle 20: After refmac, R = 0.1971 (Rfree = 0.000) for 1155 atoms. Found 17 (28 requested) and removed 10 (21 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.16 2.05 Round 1: 125 peptides, 1 chains. Longest chain 125 peptides. Score 0.956 Round 2: 124 peptides, 2 chains. Longest chain 74 peptides. Score 0.945 Round 3: 119 peptides, 4 chains. Longest chain 48 peptides. Score 0.913 Round 4: 122 peptides, 2 chains. Longest chain 74 peptides. Score 0.942 Round 5: 119 peptides, 2 chains. Longest chain 69 peptides. Score 0.937 Taking the results from Round 1 Chains 1, Residues 124, Estimated correctness of the model 99.8 % 1 chains (124 residues) have been docked in sequence ------------------------------------------------------ 11459 reflections ( 99.96 % complete ) and 1118 restraints for refining 1156 atoms. 98 conditional restraints added. Observations/parameters ratio is 2.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2246 (Rfree = 0.000) for 1156 atoms. Found 27 (27 requested) and removed 23 (21 requested) atoms. Cycle 22: After refmac, R = 0.2126 (Rfree = 0.000) for 1160 atoms. Found 16 (26 requested) and removed 21 (21 requested) atoms. Cycle 23: After refmac, R = 0.2094 (Rfree = 0.000) for 1153 atoms. Found 25 (25 requested) and removed 17 (21 requested) atoms. Cycle 24: After refmac, R = 0.2049 (Rfree = 0.000) for 1160 atoms. Found 11 (24 requested) and removed 21 (21 requested) atoms. Cycle 25: After refmac, R = 0.2021 (Rfree = 0.000) for 1148 atoms. Found 24 (24 requested) and removed 7 (21 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.17 2.06 Round 1: 121 peptides, 2 chains. Longest chain 73 peptides. Score 0.940 Round 2: 125 peptides, 1 chains. Longest chain 125 peptides. Score 0.956 Round 3: 125 peptides, 1 chains. Longest chain 125 peptides. Score 0.956 Round 4: 120 peptides, 3 chains. Longest chain 66 peptides. Score 0.928 Round 5: 123 peptides, 2 chains. Longest chain 75 peptides. Score 0.943 Taking the results from Round 3 Chains 1, Residues 124, Estimated correctness of the model 99.8 % 1 chains (124 residues) have been docked in sequence ------------------------------------------------------ 11459 reflections ( 99.96 % complete ) and 1121 restraints for refining 1149 atoms. 101 conditional restraints added. Observations/parameters ratio is 2.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2271 (Rfree = 0.000) for 1149 atoms. Found 24 (24 requested) and removed 24 (21 requested) atoms. Cycle 27: After refmac, R = 0.2124 (Rfree = 0.000) for 1147 atoms. Found 22 (23 requested) and removed 21 (21 requested) atoms. Cycle 28: After refmac, R = 0.2051 (Rfree = 0.000) for 1148 atoms. Found 22 (22 requested) and removed 15 (21 requested) atoms. Cycle 29: After refmac, R = 0.2000 (Rfree = 0.000) for 1154 atoms. Found 19 (21 requested) and removed 20 (21 requested) atoms. Cycle 30: After refmac, R = 0.1994 (Rfree = 0.000) for 1151 atoms. Found 21 (21 requested) and removed 12 (21 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.16 2.05 Round 1: 121 peptides, 2 chains. Longest chain 73 peptides. Score 0.940 Round 2: 121 peptides, 2 chains. Longest chain 73 peptides. Score 0.940 Round 3: 119 peptides, 4 chains. Longest chain 48 peptides. Score 0.913 Round 4: 121 peptides, 2 chains. Longest chain 73 peptides. Score 0.940 Round 5: 120 peptides, 3 chains. Longest chain 51 peptides. Score 0.928 Taking the results from Round 4 Chains 2, Residues 119, Estimated correctness of the model 99.6 % 2 chains (119 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 A and 54 A 1 chains (124 residues) following loop building 1 chains (124 residues) in sequence following loop building ------------------------------------------------------ 11459 reflections ( 99.96 % complete ) and 1118 restraints for refining 1149 atoms. 98 conditional restraints added. Observations/parameters ratio is 2.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2302 (Rfree = 0.000) for 1149 atoms. Found 21 (21 requested) and removed 25 (21 requested) atoms. Cycle 32: After refmac, R = 0.2106 (Rfree = 0.000) for 1145 atoms. Found 21 (21 requested) and removed 21 (21 requested) atoms. Cycle 33: After refmac, R = 0.2043 (Rfree = 0.000) for 1142 atoms. Found 21 (21 requested) and removed 13 (21 requested) atoms. Cycle 34: After refmac, R = 0.2005 (Rfree = 0.000) for 1148 atoms. Found 13 (21 requested) and removed 17 (21 requested) atoms. Cycle 35: After refmac, R = 0.1994 (Rfree = 0.000) for 1141 atoms. Found 21 (21 requested) and removed 12 (21 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.17 2.06 Round 1: 120 peptides, 2 chains. Longest chain 72 peptides. Score 0.939 Round 2: 121 peptides, 2 chains. Longest chain 73 peptides. Score 0.940 Round 3: 119 peptides, 4 chains. Longest chain 48 peptides. Score 0.913 Round 4: 120 peptides, 2 chains. Longest chain 72 peptides. Score 0.939 Round 5: 120 peptides, 3 chains. Longest chain 51 peptides. Score 0.928 Taking the results from Round 2 Chains 2, Residues 119, Estimated correctness of the model 99.6 % 2 chains (119 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 A and 54 A 1 chains (124 residues) following loop building 1 chains (124 residues) in sequence following loop building ------------------------------------------------------ 11459 reflections ( 99.96 % complete ) and 1127 restraints for refining 1149 atoms. 107 conditional restraints added. Observations/parameters ratio is 2.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2365 (Rfree = 0.000) for 1149 atoms. Found 21 (21 requested) and removed 24 (21 requested) atoms. Cycle 37: After refmac, R = 0.2188 (Rfree = 0.000) for 1145 atoms. Found 21 (21 requested) and removed 21 (21 requested) atoms. Cycle 38: After refmac, R = 0.2124 (Rfree = 0.000) for 1145 atoms. Found 21 (21 requested) and removed 16 (21 requested) atoms. Cycle 39: After refmac, R = 0.2093 (Rfree = 0.000) for 1149 atoms. Found 21 (21 requested) and removed 15 (21 requested) atoms. Cycle 40: After refmac, R = 0.2084 (Rfree = 0.000) for 1154 atoms. Found 19 (21 requested) and removed 15 (21 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.17 2.06 Round 1: 121 peptides, 2 chains. Longest chain 73 peptides. Score 0.940 Round 2: 121 peptides, 2 chains. Longest chain 73 peptides. Score 0.940 Round 3: 119 peptides, 3 chains. Longest chain 50 peptides. Score 0.926 Round 4: 119 peptides, 4 chains. Longest chain 56 peptides. Score 0.913 Round 5: 119 peptides, 3 chains. Longest chain 50 peptides. Score 0.926 Taking the results from Round 2 Chains 2, Residues 119, Estimated correctness of the model 99.6 % 2 chains (119 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 A and 54 A 1 chains (124 residues) following loop building 1 chains (124 residues) in sequence following loop building ------------------------------------------------------ 11459 reflections ( 99.96 % complete ) and 1122 restraints for refining 1152 atoms. 102 conditional restraints added. Observations/parameters ratio is 2.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2349 (Rfree = 0.000) for 1152 atoms. Found 21 (21 requested) and removed 25 (21 requested) atoms. Cycle 42: After refmac, R = 0.2181 (Rfree = 0.000) for 1147 atoms. Found 21 (21 requested) and removed 21 (21 requested) atoms. Cycle 43: After refmac, R = 0.2118 (Rfree = 0.000) for 1147 atoms. Found 19 (21 requested) and removed 13 (21 requested) atoms. Cycle 44: After refmac, R = 0.2093 (Rfree = 0.000) for 1151 atoms. Found 21 (21 requested) and removed 6 (21 requested) atoms. Cycle 45: After refmac, R = 0.2084 (Rfree = 0.000) for 1165 atoms. Found 19 (21 requested) and removed 14 (21 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.17 2.06 Round 1: 121 peptides, 2 chains. Longest chain 73 peptides. Score 0.940 Round 2: 121 peptides, 2 chains. Longest chain 73 peptides. Score 0.940 Round 3: 120 peptides, 3 chains. Longest chain 51 peptides. Score 0.928 Round 4: 120 peptides, 3 chains. Longest chain 66 peptides. Score 0.928 Round 5: 119 peptides, 4 chains. Longest chain 51 peptides. Score 0.913 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 2, Residues 119, Estimated correctness of the model 99.6 % 2 chains (119 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 48 A and 54 A 1 chains (124 residues) following loop building 1 chains (124 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 11459 reflections ( 99.96 % complete ) and 1020 restraints for refining 1006 atoms. Observations/parameters ratio is 2.85 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2735 (Rfree = 0.000) for 1006 atoms. Found 9 (18 requested) and removed 0 (18 requested) atoms. Cycle 47: After refmac, R = 0.2568 (Rfree = 0.000) for 1006 atoms. Found 3 (18 requested) and removed 0 (18 requested) atoms. Cycle 48: After refmac, R = 0.2472 (Rfree = 0.000) for 1006 atoms. Found 2 (18 requested) and removed 0 (18 requested) atoms. Cycle 49: After refmac, R = 0.2402 (Rfree = 0.000) for 1006 atoms. Found 6 (18 requested) and removed 1 (18 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:51:36 GMT 2018 Job finished. TimeTaking 28.67 Used memory is bytes: 1555416