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 2hti-2.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hti-2.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hti-2.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hti-2.4-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/2hti-2.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hti-2.4-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 22:22:58 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/2hti-2.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hti-2.4-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 140 and 0 Target number of residues in the AU: 140 Target solvent content: 0.6100 Checking the provided sequence file Detected sequence length: 185 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 185 Adjusted target solvent content: 0.48 Input MTZ file: 2hti-2.4-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: 178 Cell parameters: 72.007 72.007 129.790 90.000 90.000 120.000 Input sequence file: 2hti-2.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1480 target number of atoms Had to go as low as 0.35 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: 28.784 2.410 Wilson plot Bfac: 55.76 8159 reflections ( 99.39 % complete ) and 0 restraints for refining 1645 atoms. Observations/parameters ratio is 1.24 ------------------------------------------------------ Starting model: R = 0.3621 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3282 (Rfree = 0.000) for 1645 atoms. Found 30 (33 requested) and removed 31 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.92 3.00 Round 1: 81 peptides, 10 chains. Longest chain 15 peptides. Score 0.534 Round 2: 93 peptides, 8 chains. Longest chain 21 peptides. Score 0.668 Round 3: 111 peptides, 9 chains. Longest chain 29 peptides. Score 0.732 Round 4: 116 peptides, 8 chains. Longest chain 31 peptides. Score 0.774 Round 5: 112 peptides, 7 chains. Longest chain 31 peptides. Score 0.778 Taking the results from Round 5 Chains 7, Residues 105, Estimated correctness of the model 91.8 % 3 chains (74 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 47 A and 50 A 6 chains (107 residues) following loop building 2 chains (76 residues) in sequence following loop building ------------------------------------------------------ 8159 reflections ( 99.39 % complete ) and 1869 restraints for refining 1255 atoms. 1128 conditional restraints added. Observations/parameters ratio is 1.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3093 (Rfree = 0.000) for 1255 atoms. Found 25 (25 requested) and removed 21 (12 requested) atoms. Cycle 2: After refmac, R = 0.2756 (Rfree = 0.000) for 1233 atoms. Found 12 (24 requested) and removed 15 (12 requested) atoms. Cycle 3: After refmac, R = 0.2707 (Rfree = 0.000) for 1204 atoms. Found 13 (23 requested) and removed 15 (12 requested) atoms. Cycle 4: After refmac, R = 0.2578 (Rfree = 0.000) for 1192 atoms. Found 14 (23 requested) and removed 13 (12 requested) atoms. Cycle 5: After refmac, R = 0.2428 (Rfree = 0.000) for 1182 atoms. Found 5 (22 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.79 2.87 Round 1: 107 peptides, 9 chains. Longest chain 43 peptides. Score 0.714 Round 2: 114 peptides, 6 chains. Longest chain 34 peptides. Score 0.804 Round 3: 118 peptides, 7 chains. Longest chain 44 peptides. Score 0.800 Round 4: 118 peptides, 7 chains. Longest chain 33 peptides. Score 0.800 Round 5: 117 peptides, 8 chains. Longest chain 46 peptides. Score 0.778 Taking the results from Round 2 Chains 6, Residues 108, Estimated correctness of the model 93.5 % 4 chains (97 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 50 A and 54 A 5 chains (111 residues) following loop building 3 chains (100 residues) in sequence following loop building ------------------------------------------------------ 8159 reflections ( 99.39 % complete ) and 1430 restraints for refining 1206 atoms. 578 conditional restraints added. Observations/parameters ratio is 1.69 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2674 (Rfree = 0.000) for 1206 atoms. Found 22 (22 requested) and removed 15 (12 requested) atoms. Cycle 7: After refmac, R = 0.2423 (Rfree = 0.000) for 1200 atoms. Found 15 (21 requested) and removed 14 (12 requested) atoms. Cycle 8: After refmac, R = 0.2350 (Rfree = 0.000) for 1189 atoms. Found 11 (21 requested) and removed 12 (12 requested) atoms. Cycle 9: After refmac, R = 0.2295 (Rfree = 0.000) for 1179 atoms. Found 8 (19 requested) and removed 11 (11 requested) atoms. Cycle 10: After refmac, R = 0.2283 (Rfree = 0.000) for 1170 atoms. Found 8 (19 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.81 2.89 Round 1: 116 peptides, 7 chains. Longest chain 36 peptides. Score 0.793 Round 2: 120 peptides, 5 chains. Longest chain 64 peptides. Score 0.840 Round 3: 114 peptides, 8 chains. Longest chain 27 peptides. Score 0.766 Round 4: 108 peptides, 5 chains. Longest chain 48 peptides. Score 0.802 Round 5: 109 peptides, 6 chains. Longest chain 40 peptides. Score 0.787 Taking the results from Round 2 Chains 6, Residues 115, Estimated correctness of the model 95.5 % 4 chains (105 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 34 A and 36 A 5 chains (116 residues) following loop building 3 chains (106 residues) in sequence following loop building ------------------------------------------------------ 8159 reflections ( 99.39 % complete ) and 1369 restraints for refining 1181 atoms. 476 conditional restraints added. Observations/parameters ratio is 1.73 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2649 (Rfree = 0.000) for 1181 atoms. Found 18 (18 requested) and removed 17 (11 requested) atoms. Cycle 12: After refmac, R = 0.2331 (Rfree = 0.000) for 1174 atoms. Found 18 (18 requested) and removed 13 (11 requested) atoms. Cycle 13: After refmac, R = 0.2297 (Rfree = 0.000) for 1172 atoms. Found 17 (17 requested) and removed 12 (11 requested) atoms. Cycle 14: After refmac, R = 0.2220 (Rfree = 0.000) for 1172 atoms. Found 13 (17 requested) and removed 11 (11 requested) atoms. Cycle 15: After refmac, R = 0.2151 (Rfree = 0.000) for 1171 atoms. Found 13 (17 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.80 2.88 Round 1: 115 peptides, 5 chains. Longest chain 43 peptides. Score 0.825 Round 2: 118 peptides, 5 chains. Longest chain 68 peptides. Score 0.835 Round 3: 119 peptides, 6 chains. Longest chain 37 peptides. Score 0.821 Round 4: 116 peptides, 6 chains. Longest chain 32 peptides. Score 0.811 Round 5: 110 peptides, 5 chains. Longest chain 41 peptides. Score 0.809 Taking the results from Round 2 Chains 5, Residues 113, Estimated correctness of the model 95.2 % 3 chains (101 residues) have been docked in sequence Building loops using Loopy2018 5 chains (113 residues) following loop building 3 chains (101 residues) in sequence following loop building ------------------------------------------------------ 8159 reflections ( 99.39 % complete ) and 1416 restraints for refining 1178 atoms. 547 conditional restraints added. Observations/parameters ratio is 1.73 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2419 (Rfree = 0.000) for 1178 atoms. Found 16 (16 requested) and removed 18 (11 requested) atoms. Cycle 17: After refmac, R = 0.2194 (Rfree = 0.000) for 1168 atoms. Found 15 (16 requested) and removed 12 (11 requested) atoms. Cycle 18: After refmac, R = 0.2098 (Rfree = 0.000) for 1167 atoms. Found 12 (15 requested) and removed 11 (11 requested) atoms. Cycle 19: After refmac, R = 0.2039 (Rfree = 0.000) for 1166 atoms. Found 9 (15 requested) and removed 11 (11 requested) atoms. Cycle 20: After refmac, R = 0.2012 (Rfree = 0.000) for 1160 atoms. Found 10 (14 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.80 2.88 Round 1: 120 peptides, 4 chains. Longest chain 36 peptides. Score 0.856 Round 2: 119 peptides, 5 chains. Longest chain 37 peptides. Score 0.838 Round 3: 121 peptides, 4 chains. Longest chain 38 peptides. Score 0.859 Round 4: 114 peptides, 6 chains. Longest chain 35 peptides. Score 0.804 Round 5: 117 peptides, 6 chains. Longest chain 32 peptides. Score 0.814 Taking the results from Round 3 Chains 7, Residues 117, Estimated correctness of the model 96.4 % 4 chains (113 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 A and 52 A 5 chains (119 residues) following loop building 3 chains (116 residues) in sequence following loop building ------------------------------------------------------ 8159 reflections ( 99.39 % complete ) and 1318 restraints for refining 1197 atoms. 368 conditional restraints added. Observations/parameters ratio is 1.70 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2385 (Rfree = 0.000) for 1197 atoms. Found 14 (14 requested) and removed 19 (12 requested) atoms. Cycle 22: After refmac, R = 0.2127 (Rfree = 0.000) for 1186 atoms. Found 14 (14 requested) and removed 12 (12 requested) atoms. Cycle 23: After refmac, R = 0.2003 (Rfree = 0.000) for 1186 atoms. Found 4 (13 requested) and removed 12 (11 requested) atoms. Cycle 24: After refmac, R = 0.1977 (Rfree = 0.000) for 1175 atoms. Found 6 (12 requested) and removed 12 (11 requested) atoms. Cycle 25: After refmac, R = 0.1999 (Rfree = 0.000) for 1168 atoms. Found 5 (12 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.78 2.86 Round 1: 121 peptides, 4 chains. Longest chain 39 peptides. Score 0.859 Round 2: 119 peptides, 5 chains. Longest chain 37 peptides. Score 0.838 Round 3: 115 peptides, 7 chains. Longest chain 35 peptides. Score 0.789 Round 4: 119 peptides, 6 chains. Longest chain 38 peptides. Score 0.821 Round 5: 117 peptides, 7 chains. Longest chain 30 peptides. Score 0.796 Taking the results from Round 1 Chains 7, Residues 117, Estimated correctness of the model 96.4 % 4 chains (112 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 A and 52 A 5 chains (118 residues) following loop building 3 chains (115 residues) in sequence following loop building ------------------------------------------------------ 8159 reflections ( 99.39 % complete ) and 1312 restraints for refining 1184 atoms. 371 conditional restraints added. Observations/parameters ratio is 1.72 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2321 (Rfree = 0.000) for 1184 atoms. Found 11 (11 requested) and removed 16 (11 requested) atoms. Cycle 27: After refmac, R = 0.2066 (Rfree = 0.000) for 1174 atoms. Found 7 (11 requested) and removed 13 (11 requested) atoms. Cycle 28: After refmac, R = 0.1960 (Rfree = 0.000) for 1165 atoms. Found 9 (11 requested) and removed 11 (11 requested) atoms. Cycle 29: After refmac, R = 0.1921 (Rfree = 0.000) for 1157 atoms. Found 7 (11 requested) and removed 12 (11 requested) atoms. Cycle 30: After refmac, R = 0.1912 (Rfree = 0.000) for 1151 atoms. Found 6 (11 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.78 2.86 Round 1: 115 peptides, 5 chains. Longest chain 35 peptides. Score 0.825 Round 2: 117 peptides, 5 chains. Longest chain 49 peptides. Score 0.832 Round 3: 117 peptides, 3 chains. Longest chain 63 peptides. Score 0.864 Round 4: 115 peptides, 6 chains. Longest chain 47 peptides. Score 0.808 Round 5: 120 peptides, 3 chains. Longest chain 66 peptides. Score 0.871 Taking the results from Round 5 Chains 4, Residues 117, Estimated correctness of the model 97.0 % 3 chains (116 residues) have been docked in sequence Building loops using Loopy2018 4 chains (117 residues) following loop building 4 chains (117 residues) in sequence following loop building ------------------------------------------------------ 8159 reflections ( 99.39 % complete ) and 1295 restraints for refining 1180 atoms. 350 conditional restraints added. Observations/parameters ratio is 1.73 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2233 (Rfree = 0.000) for 1180 atoms. Found 11 (11 requested) and removed 19 (11 requested) atoms. Cycle 32: After refmac, R = 0.1955 (Rfree = 0.000) for 1167 atoms. Found 11 (11 requested) and removed 12 (11 requested) atoms. Cycle 33: After refmac, R = 0.1887 (Rfree = 0.000) for 1163 atoms. Found 11 (11 requested) and removed 11 (11 requested) atoms. Cycle 34: After refmac, R = 0.1842 (Rfree = 0.000) for 1163 atoms. Found 8 (11 requested) and removed 12 (11 requested) atoms. Cycle 35: After refmac, R = 0.1827 (Rfree = 0.000) for 1158 atoms. Found 11 (11 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.78 2.86 Round 1: 116 peptides, 6 chains. Longest chain 37 peptides. Score 0.811 Round 2: 115 peptides, 6 chains. Longest chain 38 peptides. Score 0.808 Round 3: 119 peptides, 7 chains. Longest chain 38 peptides. Score 0.803 Round 4: 120 peptides, 5 chains. Longest chain 38 peptides. Score 0.840 Round 5: 115 peptides, 6 chains. Longest chain 34 peptides. Score 0.808 Taking the results from Round 4 Chains 8, Residues 115, Estimated correctness of the model 95.5 % 4 chains (100 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 A and 52 A 6 chains (117 residues) following loop building 3 chains (103 residues) in sequence following loop building ------------------------------------------------------ 8159 reflections ( 99.39 % complete ) and 1415 restraints for refining 1183 atoms. 530 conditional restraints added. Observations/parameters ratio is 1.72 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2265 (Rfree = 0.000) for 1183 atoms. Found 11 (11 requested) and removed 18 (11 requested) atoms. Cycle 37: After refmac, R = 0.2049 (Rfree = 0.000) for 1174 atoms. Found 10 (11 requested) and removed 12 (11 requested) atoms. Cycle 38: After refmac, R = 0.2028 (Rfree = 0.000) for 1170 atoms. Found 9 (11 requested) and removed 11 (11 requested) atoms. Cycle 39: After refmac, R = 0.1969 (Rfree = 0.000) for 1168 atoms. Found 8 (11 requested) and removed 13 (11 requested) atoms. Cycle 40: After refmac, R = 0.1939 (Rfree = 0.000) for 1162 atoms. Found 8 (11 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.78 2.86 Round 1: 111 peptides, 6 chains. Longest chain 37 peptides. Score 0.794 Round 2: 117 peptides, 6 chains. Longest chain 38 peptides. Score 0.814 Round 3: 114 peptides, 6 chains. Longest chain 34 peptides. Score 0.804 Round 4: 118 peptides, 5 chains. Longest chain 35 peptides. Score 0.835 Round 5: 114 peptides, 7 chains. Longest chain 31 peptides. Score 0.786 Taking the results from Round 4 Chains 9, Residues 113, Estimated correctness of the model 95.2 % 5 chains (105 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 A and 52 A 7 chains (115 residues) following loop building 4 chains (108 residues) in sequence following loop building ------------------------------------------------------ 8159 reflections ( 99.39 % complete ) and 1409 restraints for refining 1205 atoms. 502 conditional restraints added. Observations/parameters ratio is 1.69 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2387 (Rfree = 0.000) for 1205 atoms. Found 12 (12 requested) and removed 17 (12 requested) atoms. Cycle 42: After refmac, R = 0.2059 (Rfree = 0.000) for 1197 atoms. Found 11 (12 requested) and removed 13 (12 requested) atoms. Cycle 43: After refmac, R = 0.1935 (Rfree = 0.000) for 1193 atoms. Found 7 (12 requested) and removed 12 (12 requested) atoms. Cycle 44: After refmac, R = 0.1910 (Rfree = 0.000) for 1187 atoms. Found 11 (11 requested) and removed 11 (11 requested) atoms. Cycle 45: After refmac, R = 0.1912 (Rfree = 0.000) for 1185 atoms. Found 5 (11 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.78 2.86 Round 1: 113 peptides, 5 chains. Longest chain 31 peptides. Score 0.819 Round 2: 118 peptides, 4 chains. Longest chain 65 peptides. Score 0.851 Round 3: 115 peptides, 8 chains. Longest chain 21 peptides. Score 0.770 Round 4: 122 peptides, 4 chains. Longest chain 35 peptides. Score 0.861 Round 5: 120 peptides, 5 chains. Longest chain 37 peptides. Score 0.840 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 118, Estimated correctness of the model 96.5 % 4 chains (114 residues) have been docked in sequence Sequence coverage is 95 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 47 A and 51 A 4 chains (119 residues) following loop building 3 chains (117 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 8159 reflections ( 99.39 % complete ) and 953 restraints for refining 937 atoms. Observations/parameters ratio is 2.18 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3169 (Rfree = 0.000) for 937 atoms. Found 9 (9 requested) and removed 0 (9 requested) atoms. Cycle 47: After refmac, R = 0.2839 (Rfree = 0.000) for 937 atoms. Found 8 (9 requested) and removed 0 (9 requested) atoms. Cycle 48: After refmac, R = 0.2641 (Rfree = 0.000) for 937 atoms. Found 4 (9 requested) and removed 4 (9 requested) atoms. Cycle 49: After refmac, R = 0.2611 (Rfree = 0.000) for 937 atoms. TimeTaking 31.17