Sun 23 Dec 22:23:05 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 2hhz-2.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hhz-2.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hhz-2.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hhz-2.0-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/2hhz-2.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hhz-2.0-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 22:23:13 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/2hhz-2.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hhz-2.0-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 126 and 0 Target number of residues in the AU: 126 Target solvent content: 0.5372 Checking the provided sequence file Detected sequence length: 150 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 150 Adjusted target solvent content: 0.45 Input MTZ file: 2hhz-2.0-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: 71.030 71.030 58.410 90.000 90.000 90.000 Input sequence file: 2hhz-2.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1200 target number of atoms Had to go as low as 0.50 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: 50.226 1.999 Wilson plot Bfac: 32.02 10546 reflections ( 99.73 % complete ) and 0 restraints for refining 1331 atoms. Observations/parameters ratio is 1.98 ------------------------------------------------------ Starting model: R = 0.3303 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3066 (Rfree = 0.000) for 1331 atoms. Found 25 (45 requested) and removed 39 (22 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.31 2.47 Round 1: 93 peptides, 9 chains. Longest chain 44 peptides. Score 0.723 Round 2: 99 peptides, 8 chains. Longest chain 26 peptides. Score 0.781 Round 3: 103 peptides, 7 chains. Longest chain 46 peptides. Score 0.821 Round 4: 111 peptides, 8 chains. Longest chain 34 peptides. Score 0.831 Round 5: 117 peptides, 5 chains. Longest chain 41 peptides. Score 0.897 Taking the results from Round 5 Chains 5, Residues 112, Estimated correctness of the model 98.9 % 3 chains (104 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 46 A and 49 A 4 chains (114 residues) following loop building 2 chains (106 residues) in sequence following loop building ------------------------------------------------------ 10546 reflections ( 99.73 % complete ) and 1346 restraints for refining 1162 atoms. 446 conditional restraints added. Observations/parameters ratio is 2.27 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2959 (Rfree = 0.000) for 1162 atoms. Found 34 (39 requested) and removed 22 (19 requested) atoms. Cycle 2: After refmac, R = 0.2621 (Rfree = 0.000) for 1165 atoms. Found 19 (39 requested) and removed 20 (20 requested) atoms. Cycle 3: After refmac, R = 0.2501 (Rfree = 0.000) for 1157 atoms. Found 23 (37 requested) and removed 11 (19 requested) atoms. Cycle 4: After refmac, R = 0.2367 (Rfree = 0.000) for 1161 atoms. Found 21 (38 requested) and removed 8 (20 requested) atoms. Cycle 5: After refmac, R = 0.2296 (Rfree = 0.000) for 1171 atoms. Found 19 (38 requested) and removed 17 (20 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.25 2.41 Round 1: 117 peptides, 5 chains. Longest chain 49 peptides. Score 0.897 Round 2: 120 peptides, 5 chains. Longest chain 51 peptides. Score 0.904 Round 3: 125 peptides, 3 chains. Longest chain 94 peptides. Score 0.937 Round 4: 123 peptides, 6 chains. Longest chain 51 peptides. Score 0.897 Round 5: 125 peptides, 5 chains. Longest chain 61 peptides. Score 0.914 Taking the results from Round 3 Chains 3, Residues 122, Estimated correctness of the model 99.6 % 2 chains (118 residues) have been docked in sequence Building loops using Loopy2018 3 chains (122 residues) following loop building 2 chains (118 residues) in sequence following loop building ------------------------------------------------------ 10546 reflections ( 99.73 % complete ) and 1255 restraints for refining 1164 atoms. 264 conditional restraints added. Observations/parameters ratio is 2.27 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2440 (Rfree = 0.000) for 1164 atoms. Found 30 (37 requested) and removed 19 (19 requested) atoms. Cycle 7: After refmac, R = 0.2243 (Rfree = 0.000) for 1174 atoms. Found 27 (37 requested) and removed 16 (20 requested) atoms. Cycle 8: After refmac, R = 0.2159 (Rfree = 0.000) for 1184 atoms. Found 26 (36 requested) and removed 16 (20 requested) atoms. Cycle 9: After refmac, R = 0.2108 (Rfree = 0.000) for 1194 atoms. Found 22 (35 requested) and removed 19 (20 requested) atoms. Cycle 10: After refmac, R = 0.2081 (Rfree = 0.000) for 1197 atoms. Found 27 (35 requested) and removed 17 (20 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.25 2.41 Round 1: 118 peptides, 5 chains. Longest chain 51 peptides. Score 0.900 Round 2: 125 peptides, 3 chains. Longest chain 94 peptides. Score 0.937 Round 3: 122 peptides, 6 chains. Longest chain 44 peptides. Score 0.895 Round 4: 125 peptides, 3 chains. Longest chain 94 peptides. Score 0.937 Round 5: 119 peptides, 7 chains. Longest chain 44 peptides. Score 0.873 Taking the results from Round 4 Chains 3, Residues 122, Estimated correctness of the model 99.6 % 2 chains (118 residues) have been docked in sequence Building loops using Loopy2018 3 chains (122 residues) following loop building 2 chains (118 residues) in sequence following loop building ------------------------------------------------------ 10546 reflections ( 99.73 % complete ) and 1258 restraints for refining 1164 atoms. 267 conditional restraints added. Observations/parameters ratio is 2.27 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2266 (Rfree = 0.000) for 1164 atoms. Found 31 (33 requested) and removed 20 (19 requested) atoms. Cycle 12: After refmac, R = 0.2119 (Rfree = 0.000) for 1175 atoms. Found 23 (33 requested) and removed 12 (20 requested) atoms. Cycle 13: After refmac, R = 0.2053 (Rfree = 0.000) for 1186 atoms. Found 28 (32 requested) and removed 17 (20 requested) atoms. Cycle 14: After refmac, R = 0.2019 (Rfree = 0.000) for 1197 atoms. Found 28 (32 requested) and removed 20 (20 requested) atoms. Cycle 15: After refmac, R = 0.1995 (Rfree = 0.000) for 1205 atoms. Found 26 (31 requested) and removed 22 (20 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.23 2.38 Round 1: 121 peptides, 6 chains. Longest chain 43 peptides. Score 0.893 Round 2: 125 peptides, 4 chains. Longest chain 79 peptides. Score 0.926 Round 3: 125 peptides, 4 chains. Longest chain 82 peptides. Score 0.926 Round 4: 121 peptides, 7 chains. Longest chain 69 peptides. Score 0.879 Round 5: 123 peptides, 6 chains. Longest chain 39 peptides. Score 0.897 Taking the results from Round 3 Chains 4, Residues 121, Estimated correctness of the model 99.4 % 2 chains (106 residues) have been docked in sequence Building loops using Loopy2018 4 chains (121 residues) following loop building 2 chains (106 residues) in sequence following loop building ------------------------------------------------------ 10546 reflections ( 99.73 % complete ) and 1368 restraints for refining 1164 atoms. 438 conditional restraints added. Observations/parameters ratio is 2.27 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2269 (Rfree = 0.000) for 1164 atoms. Found 29 (29 requested) and removed 19 (19 requested) atoms. Cycle 17: After refmac, R = 0.2142 (Rfree = 0.000) for 1170 atoms. Found 22 (29 requested) and removed 14 (20 requested) atoms. Cycle 18: After refmac, R = 0.2070 (Rfree = 0.000) for 1177 atoms. Found 25 (28 requested) and removed 9 (20 requested) atoms. Cycle 19: After refmac, R = 0.2038 (Rfree = 0.000) for 1193 atoms. Found 20 (28 requested) and removed 17 (20 requested) atoms. Cycle 20: After refmac, R = 0.2023 (Rfree = 0.000) for 1195 atoms. Found 26 (27 requested) and removed 18 (20 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.25 2.41 Round 1: 123 peptides, 5 chains. Longest chain 51 peptides. Score 0.910 Round 2: 116 peptides, 4 chains. Longest chain 63 peptides. Score 0.909 Round 3: 122 peptides, 6 chains. Longest chain 51 peptides. Score 0.895 Round 4: 125 peptides, 3 chains. Longest chain 95 peptides. Score 0.937 Round 5: 122 peptides, 5 chains. Longest chain 79 peptides. Score 0.908 Taking the results from Round 4 Chains 3, Residues 122, Estimated correctness of the model 99.6 % 2 chains (119 residues) have been docked in sequence Building loops using Loopy2018 3 chains (122 residues) following loop building 2 chains (119 residues) in sequence following loop building ------------------------------------------------------ 10546 reflections ( 99.73 % complete ) and 1219 restraints for refining 1164 atoms. 227 conditional restraints added. Observations/parameters ratio is 2.27 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2252 (Rfree = 0.000) for 1164 atoms. Found 26 (26 requested) and removed 19 (19 requested) atoms. Cycle 22: After refmac, R = 0.2084 (Rfree = 0.000) for 1170 atoms. Found 19 (26 requested) and removed 10 (20 requested) atoms. Cycle 23: After refmac, R = 0.2009 (Rfree = 0.000) for 1179 atoms. Found 12 (25 requested) and removed 11 (20 requested) atoms. Cycle 24: After refmac, R = 0.1961 (Rfree = 0.000) for 1179 atoms. Found 18 (24 requested) and removed 10 (20 requested) atoms. Cycle 25: After refmac, R = 0.1957 (Rfree = 0.000) for 1186 atoms. Found 15 (23 requested) and removed 15 (20 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.24 2.39 Round 1: 123 peptides, 7 chains. Longest chain 51 peptides. Score 0.884 Round 2: 123 peptides, 3 chains. Longest chain 92 peptides. Score 0.934 Round 3: 126 peptides, 6 chains. Longest chain 51 peptides. Score 0.904 Round 4: 119 peptides, 7 chains. Longest chain 45 peptides. Score 0.873 Round 5: 127 peptides, 4 chains. Longest chain 79 peptides. Score 0.929 Taking the results from Round 2 Chains 3, Residues 120, Estimated correctness of the model 99.5 % 2 chains (116 residues) have been docked in sequence Building loops using Loopy2018 3 chains (120 residues) following loop building 2 chains (116 residues) in sequence following loop building ------------------------------------------------------ 10546 reflections ( 99.73 % complete ) and 1274 restraints for refining 1164 atoms. 303 conditional restraints added. Observations/parameters ratio is 2.27 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2229 (Rfree = 0.000) for 1164 atoms. Found 22 (22 requested) and removed 20 (19 requested) atoms. Cycle 27: After refmac, R = 0.2088 (Rfree = 0.000) for 1166 atoms. Found 22 (22 requested) and removed 8 (20 requested) atoms. Cycle 28: After refmac, R = 0.1994 (Rfree = 0.000) for 1180 atoms. Found 11 (22 requested) and removed 6 (20 requested) atoms. Cycle 29: After refmac, R = 0.1960 (Rfree = 0.000) for 1183 atoms. Found 13 (21 requested) and removed 9 (20 requested) atoms. Cycle 30: After refmac, R = 0.1935 (Rfree = 0.000) for 1187 atoms. Found 16 (20 requested) and removed 10 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.24 2.39 Round 1: 119 peptides, 5 chains. Longest chain 48 peptides. Score 0.902 Round 2: 122 peptides, 4 chains. Longest chain 81 peptides. Score 0.920 Round 3: 117 peptides, 6 chains. Longest chain 57 peptides. Score 0.883 Round 4: 123 peptides, 4 chains. Longest chain 85 peptides. Score 0.922 Round 5: 117 peptides, 6 chains. Longest chain 48 peptides. Score 0.883 Taking the results from Round 4 Chains 4, Residues 119, Estimated correctness of the model 99.3 % 2 chains (109 residues) have been docked in sequence Building loops using Loopy2018 4 chains (119 residues) following loop building 2 chains (109 residues) in sequence following loop building ------------------------------------------------------ 10546 reflections ( 99.73 % complete ) and 1355 restraints for refining 1164 atoms. 421 conditional restraints added. Observations/parameters ratio is 2.27 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2253 (Rfree = 0.000) for 1164 atoms. Found 19 (19 requested) and removed 21 (19 requested) atoms. Cycle 32: After refmac, R = 0.2142 (Rfree = 0.000) for 1161 atoms. Found 13 (19 requested) and removed 7 (19 requested) atoms. Cycle 33: After refmac, R = 0.2075 (Rfree = 0.000) for 1166 atoms. Found 16 (20 requested) and removed 5 (20 requested) atoms. Cycle 34: After refmac, R = 0.2030 (Rfree = 0.000) for 1177 atoms. Found 10 (20 requested) and removed 9 (20 requested) atoms. Cycle 35: After refmac, R = 0.1999 (Rfree = 0.000) for 1177 atoms. Found 17 (20 requested) and removed 6 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.24 2.39 Round 1: 122 peptides, 5 chains. Longest chain 50 peptides. Score 0.908 Round 2: 120 peptides, 4 chains. Longest chain 75 peptides. Score 0.917 Round 3: 121 peptides, 5 chains. Longest chain 48 peptides. Score 0.906 Round 4: 122 peptides, 6 chains. Longest chain 66 peptides. Score 0.895 Round 5: 121 peptides, 6 chains. Longest chain 44 peptides. Score 0.893 Taking the results from Round 2 Chains 4, Residues 116, Estimated correctness of the model 99.3 % 3 chains (113 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 81 A and 84 A 3 chains (118 residues) following loop building 2 chains (115 residues) in sequence following loop building ------------------------------------------------------ 10546 reflections ( 99.73 % complete ) and 1306 restraints for refining 1164 atoms. 347 conditional restraints added. Observations/parameters ratio is 2.27 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2174 (Rfree = 0.000) for 1164 atoms. Found 19 (19 requested) and removed 20 (19 requested) atoms. Cycle 37: After refmac, R = 0.2074 (Rfree = 0.000) for 1162 atoms. Found 19 (19 requested) and removed 5 (19 requested) atoms. Cycle 38: After refmac, R = 0.2018 (Rfree = 0.000) for 1176 atoms. Found 17 (20 requested) and removed 9 (20 requested) atoms. Cycle 39: After refmac, R = 0.1991 (Rfree = 0.000) for 1182 atoms. Found 18 (20 requested) and removed 9 (20 requested) atoms. Cycle 40: After refmac, R = 0.1965 (Rfree = 0.000) for 1190 atoms. Found 13 (20 requested) and removed 8 (20 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.23 2.38 Round 1: 118 peptides, 6 chains. Longest chain 48 peptides. Score 0.886 Round 2: 122 peptides, 5 chains. Longest chain 66 peptides. Score 0.908 Round 3: 124 peptides, 5 chains. Longest chain 51 peptides. Score 0.912 Round 4: 119 peptides, 5 chains. Longest chain 65 peptides. Score 0.902 Round 5: 123 peptides, 6 chains. Longest chain 39 peptides. Score 0.897 Taking the results from Round 3 Chains 5, Residues 119, Estimated correctness of the model 99.2 % 3 chains (108 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 53 A and 56 A 4 chains (121 residues) following loop building 2 chains (110 residues) in sequence following loop building ------------------------------------------------------ 10546 reflections ( 99.73 % complete ) and 1356 restraints for refining 1164 atoms. 410 conditional restraints added. Observations/parameters ratio is 2.27 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2274 (Rfree = 0.000) for 1164 atoms. Found 19 (19 requested) and removed 20 (19 requested) atoms. Cycle 42: After refmac, R = 0.2135 (Rfree = 0.000) for 1163 atoms. Found 13 (19 requested) and removed 3 (19 requested) atoms. Cycle 43: After refmac, R = 0.2073 (Rfree = 0.000) for 1172 atoms. Found 11 (20 requested) and removed 4 (20 requested) atoms. Cycle 44: After refmac, R = 0.2021 (Rfree = 0.000) for 1179 atoms. Found 13 (20 requested) and removed 4 (20 requested) atoms. Cycle 45: After refmac, R = 0.1998 (Rfree = 0.000) for 1187 atoms. Found 9 (20 requested) and removed 3 (20 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.23 2.38 Round 1: 122 peptides, 6 chains. Longest chain 51 peptides. Score 0.895 Round 2: 125 peptides, 5 chains. Longest chain 66 peptides. Score 0.914 Round 3: 120 peptides, 6 chains. Longest chain 47 peptides. Score 0.890 Round 4: 125 peptides, 5 chains. Longest chain 66 peptides. Score 0.914 Round 5: 126 peptides, 4 chains. Longest chain 49 peptides. Score 0.927 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 122, Estimated correctness of the model 99.4 % 3 chains (118 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 50 A 3 chains (124 residues) following loop building 2 chains (120 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 10546 reflections ( 99.73 % complete ) and 1004 restraints for refining 981 atoms. Observations/parameters ratio is 2.69 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2894 (Rfree = 0.000) for 981 atoms. Found 5 (16 requested) and removed 0 (16 requested) atoms. Cycle 47: After refmac, R = 0.2715 (Rfree = 0.000) for 981 atoms. Found 2 (16 requested) and removed 0 (16 requested) atoms. Cycle 48: After refmac, R = 0.2639 (Rfree = 0.000) for 981 atoms. Found 2 (16 requested) and removed 0 (16 requested) atoms. Cycle 49: After refmac, R = 0.2575 (Rfree = 0.000) for 981 atoms. Found 4 (16 requested) and removed 0 (16 requested) atoms. Writing output files ... TimeTaking 28.32