null Sun 23 Dec 22:23:10 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 2hi0-1.5-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hi0-1.5-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hi0-1.5-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hi0-1.5-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/2hi0-1.5-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hi0-1.5-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 22:23:18 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/2hi0-1.5-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hi0-1.5-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 497 and 0 Target number of residues in the AU: 497 Target solvent content: 0.4220 Checking the provided sequence file Detected sequence length: 240 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 480 Adjusted target solvent content: 0.44 Input MTZ file: 2hi0-1.5-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: 4 Cell parameters: 58.636 38.695 103.583 90.000 98.094 90.000 Input sequence file: 2hi0-1.5-parrot-hancs.fasta_lf Building free atoms model in initial map for 3840 target number of atoms Had to go as low as 0.30 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 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: 102.551 1.510 Wilson plot Bfac: 10.68 72257 reflections ( 99.17 % complete ) and 0 restraints for refining 4251 atoms. Observations/parameters ratio is 4.25 ------------------------------------------------------ Starting model: R = 0.3335 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2909 (Rfree = 0.000) for 4251 atoms. Found 324 (324 requested) and removed 170 (162 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.51 1.64 NCS extension: 0 residues added, 4405 seeds are put forward Round 1: 439 peptides, 24 chains. Longest chain 49 peptides. Score 0.910 Round 2: 457 peptides, 10 chains. Longest chain 86 peptides. Score 0.958 Round 3: 462 peptides, 9 chains. Longest chain 108 peptides. Score 0.961 Round 4: 467 peptides, 8 chains. Longest chain 98 peptides. Score 0.965 Round 5: 467 peptides, 7 chains. Longest chain 148 peptides. Score 0.967 Taking the results from Round 5 Chains 7, Residues 460, Estimated correctness of the model 99.9 % 4 chains (378 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 66 B and 69 B 6 chains (462 residues) following loop building 3 chains (380 residues) in sequence following loop building ------------------------------------------------------ 72257 reflections ( 99.17 % complete ) and 4636 restraints for refining 4165 atoms. 1302 conditional restraints added. Observations/parameters ratio is 4.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2774 (Rfree = 0.000) for 4165 atoms. Found 226 (317 requested) and removed 57 (158 requested) atoms. Cycle 2: After refmac, R = 0.2557 (Rfree = 0.000) for 4333 atoms. Found 170 (330 requested) and removed 19 (165 requested) atoms. Cycle 3: After refmac, R = 0.2263 (Rfree = 0.000) for 4477 atoms. Found 164 (342 requested) and removed 34 (171 requested) atoms. Cycle 4: After refmac, R = 0.2119 (Rfree = 0.000) for 4599 atoms. Found 130 (351 requested) and removed 33 (175 requested) atoms. Cycle 5: After refmac, R = 0.2017 (Rfree = 0.000) for 4686 atoms. Found 132 (358 requested) and removed 23 (179 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.46 1.58 NCS extension: 14 residues added (3 deleted due to clashes), 4810 seeds are put forward Round 1: 470 peptides, 5 chains. Longest chain 163 peptides. Score 0.972 Round 2: 470 peptides, 5 chains. Longest chain 163 peptides. Score 0.972 Round 3: 469 peptides, 6 chains. Longest chain 163 peptides. Score 0.970 Round 4: 469 peptides, 6 chains. Longest chain 148 peptides. Score 0.970 Round 5: 470 peptides, 5 chains. Longest chain 163 peptides. Score 0.972 Taking the results from Round 5 Chains 6, Residues 465, Estimated correctness of the model 100.0 % 5 chains (462 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 162 A and 168 A Built loop between residues 148 B and 152 B Built loop between residues 164 B and 167 B 2 chains (472 residues) following loop building 2 chains (472 residues) in sequence following loop building ------------------------------------------------------ 72257 reflections ( 99.17 % complete ) and 4320 restraints for refining 4566 atoms. 595 conditional restraints added. Observations/parameters ratio is 3.96 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2330 (Rfree = 0.000) for 4566 atoms. Found 159 (348 requested) and removed 52 (174 requested) atoms. Cycle 7: After refmac, R = 0.2047 (Rfree = 0.000) for 4671 atoms. Found 149 (356 requested) and removed 23 (178 requested) atoms. Cycle 8: After refmac, R = 0.1937 (Rfree = 0.000) for 4786 atoms. Found 136 (366 requested) and removed 37 (183 requested) atoms. Cycle 9: After refmac, R = 0.1875 (Rfree = 0.000) for 4875 atoms. Found 135 (372 requested) and removed 29 (186 requested) atoms. Cycle 10: After refmac, R = 0.1832 (Rfree = 0.000) for 4970 atoms. Found 116 (380 requested) and removed 44 (190 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.47 1.59 NCS extension: 0 residues added, 5042 seeds are put forward Round 1: 471 peptides, 5 chains. Longest chain 165 peptides. Score 0.973 Round 2: 471 peptides, 5 chains. Longest chain 165 peptides. Score 0.973 Round 3: 472 peptides, 4 chains. Longest chain 165 peptides. Score 0.975 Round 4: 472 peptides, 4 chains. Longest chain 165 peptides. Score 0.975 Round 5: 472 peptides, 5 chains. Longest chain 165 peptides. Score 0.973 Taking the results from Round 4 Chains 5, Residues 468, Estimated correctness of the model 100.0 % 4 chains (465 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 162 B and 168 B 3 chains (470 residues) following loop building 3 chains (470 residues) in sequence following loop building ------------------------------------------------------ 72257 reflections ( 99.17 % complete ) and 4547 restraints for refining 4716 atoms. 836 conditional restraints added. Observations/parameters ratio is 3.83 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2198 (Rfree = 0.000) for 4716 atoms. Found 163 (359 requested) and removed 46 (179 requested) atoms. Cycle 12: After refmac, R = 0.1948 (Rfree = 0.000) for 4824 atoms. Found 138 (368 requested) and removed 23 (184 requested) atoms. Cycle 13: After refmac, R = 0.1861 (Rfree = 0.000) for 4928 atoms. Found 129 (376 requested) and removed 32 (188 requested) atoms. Cycle 14: After refmac, R = 0.1808 (Rfree = 0.000) for 5019 atoms. Found 108 (383 requested) and removed 34 (191 requested) atoms. Cycle 15: After refmac, R = 0.1785 (Rfree = 0.000) for 5077 atoms. Found 146 (388 requested) and removed 54 (194 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.46 1.58 NCS extension: 109 residues added (127 deleted due to clashes), 5278 seeds are put forward Round 1: 470 peptides, 4 chains. Longest chain 165 peptides. Score 0.975 Round 2: 470 peptides, 6 chains. Longest chain 165 peptides. Score 0.970 Round 3: 470 peptides, 4 chains. Longest chain 165 peptides. Score 0.975 Round 4: 471 peptides, 5 chains. Longest chain 165 peptides. Score 0.973 Round 5: 470 peptides, 4 chains. Longest chain 165 peptides. Score 0.975 Taking the results from Round 5 Chains 5, Residues 466, Estimated correctness of the model 100.0 % 4 chains (463 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 165 A and 168 A Built loop between residues 162 B and 168 B 2 chains (470 residues) following loop building 2 chains (470 residues) in sequence following loop building ------------------------------------------------------ 72257 reflections ( 99.17 % complete ) and 4605 restraints for refining 4785 atoms. 892 conditional restraints added. Observations/parameters ratio is 3.78 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2169 (Rfree = 0.000) for 4785 atoms. Found 191 (365 requested) and removed 54 (182 requested) atoms. Cycle 17: After refmac, R = 0.1916 (Rfree = 0.000) for 4914 atoms. Found 173 (375 requested) and removed 23 (187 requested) atoms. Cycle 18: After refmac, R = 0.1850 (Rfree = 0.000) for 5051 atoms. Found 141 (386 requested) and removed 35 (193 requested) atoms. Cycle 19: After refmac, R = 0.1796 (Rfree = 0.000) for 5141 atoms. Found 110 (393 requested) and removed 60 (196 requested) atoms. Cycle 20: After refmac, R = 0.1762 (Rfree = 0.000) for 5180 atoms. Found 152 (388 requested) and removed 48 (198 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.46 1.58 NCS extension: 0 residues added, 5284 seeds are put forward Round 1: 471 peptides, 4 chains. Longest chain 165 peptides. Score 0.975 Round 2: 470 peptides, 6 chains. Longest chain 165 peptides. Score 0.970 Round 3: 471 peptides, 4 chains. Longest chain 165 peptides. Score 0.975 Round 4: 470 peptides, 6 chains. Longest chain 165 peptides. Score 0.970 Round 5: 470 peptides, 5 chains. Longest chain 165 peptides. Score 0.972 Taking the results from Round 3 Chains 5, Residues 467, Estimated correctness of the model 100.0 % 4 chains (462 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 160 A and 168 A 4 chains (473 residues) following loop building 3 chains (469 residues) in sequence following loop building ------------------------------------------------------ 72257 reflections ( 99.17 % complete ) and 4828 restraints for refining 4877 atoms. 1105 conditional restraints added. Observations/parameters ratio is 3.70 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2137 (Rfree = 0.000) for 4877 atoms. Found 223 (365 requested) and removed 64 (186 requested) atoms. Cycle 22: After refmac, R = 0.1914 (Rfree = 0.000) for 5029 atoms. Found 153 (376 requested) and removed 38 (192 requested) atoms. Cycle 23: After refmac, R = 0.1841 (Rfree = 0.000) for 5126 atoms. Found 140 (384 requested) and removed 54 (196 requested) atoms. Cycle 24: After refmac, R = 0.1801 (Rfree = 0.000) for 5199 atoms. Found 137 (389 requested) and removed 58 (198 requested) atoms. Cycle 25: After refmac, R = 0.1771 (Rfree = 0.000) for 5266 atoms. Found 138 (394 requested) and removed 84 (201 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.46 1.58 NCS extension: 4 residues added (1 deleted due to clashes), 5327 seeds are put forward Round 1: 471 peptides, 4 chains. Longest chain 165 peptides. Score 0.975 Round 2: 470 peptides, 5 chains. Longest chain 165 peptides. Score 0.972 Round 3: 471 peptides, 4 chains. Longest chain 165 peptides. Score 0.975 Round 4: 469 peptides, 4 chains. Longest chain 164 peptides. Score 0.974 Round 5: 469 peptides, 8 chains. Longest chain 90 peptides. Score 0.966 Taking the results from Round 3 Chains 4, Residues 467, Estimated correctness of the model 100.0 % 4 chains (467 residues) have been docked in sequence Building loops using Loopy2018 4 chains (467 residues) following loop building 4 chains (467 residues) in sequence following loop building ------------------------------------------------------ 72257 reflections ( 99.17 % complete ) and 4827 restraints for refining 4868 atoms. 1133 conditional restraints added. Observations/parameters ratio is 3.71 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2143 (Rfree = 0.000) for 4868 atoms. Found 232 (356 requested) and removed 31 (185 requested) atoms. Cycle 27: After refmac, R = 0.1929 (Rfree = 0.000) for 5061 atoms. Found 152 (371 requested) and removed 33 (193 requested) atoms. Cycle 28: After refmac, R = 0.1845 (Rfree = 0.000) for 5168 atoms. Found 115 (379 requested) and removed 41 (197 requested) atoms. Cycle 29: After refmac, R = 0.1802 (Rfree = 0.000) for 5223 atoms. Found 130 (384 requested) and removed 45 (200 requested) atoms. Cycle 30: After refmac, R = 0.1778 (Rfree = 0.000) for 5298 atoms. Found 141 (389 requested) and removed 62 (202 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.46 1.58 NCS extension: 0 residues added, 5377 seeds are put forward Round 1: 469 peptides, 6 chains. Longest chain 116 peptides. Score 0.970 Round 2: 470 peptides, 5 chains. Longest chain 165 peptides. Score 0.972 Round 3: 471 peptides, 5 chains. Longest chain 165 peptides. Score 0.973 Round 4: 471 peptides, 4 chains. Longest chain 165 peptides. Score 0.975 Round 5: 471 peptides, 4 chains. Longest chain 165 peptides. Score 0.975 Taking the results from Round 5 Chains 4, Residues 467, Estimated correctness of the model 100.0 % 4 chains (467 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 165 A and 168 A Built loop between residues 165 B and 168 B 2 chains (471 residues) following loop building 2 chains (471 residues) in sequence following loop building ------------------------------------------------------ 72257 reflections ( 99.17 % complete ) and 4859 restraints for refining 4937 atoms. 1137 conditional restraints added. Observations/parameters ratio is 3.66 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2183 (Rfree = 0.000) for 4937 atoms. Found 228 (361 requested) and removed 46 (188 requested) atoms. Cycle 32: After refmac, R = 0.1943 (Rfree = 0.000) for 5114 atoms. Found 160 (374 requested) and removed 41 (195 requested) atoms. Cycle 33: After refmac, R = 0.1856 (Rfree = 0.000) for 5216 atoms. Found 131 (383 requested) and removed 43 (199 requested) atoms. Cycle 34: After refmac, R = 0.1807 (Rfree = 0.000) for 5288 atoms. Found 133 (388 requested) and removed 57 (202 requested) atoms. Cycle 35: After refmac, R = 0.1783 (Rfree = 0.000) for 5350 atoms. Found 128 (393 requested) and removed 64 (204 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.46 1.58 NCS extension: 0 residues added, 5414 seeds are put forward Round 1: 471 peptides, 4 chains. Longest chain 164 peptides. Score 0.975 Round 2: 470 peptides, 6 chains. Longest chain 165 peptides. Score 0.970 Round 3: 472 peptides, 4 chains. Longest chain 165 peptides. Score 0.975 Round 4: 471 peptides, 5 chains. Longest chain 165 peptides. Score 0.973 Round 5: 472 peptides, 5 chains. Longest chain 165 peptides. Score 0.973 Taking the results from Round 3 Chains 5, Residues 468, Estimated correctness of the model 100.0 % 4 chains (464 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 165 A and 168 A Built loop between residues 161 B and 168 B 2 chains (472 residues) following loop building 2 chains (472 residues) in sequence following loop building ------------------------------------------------------ 72257 reflections ( 99.17 % complete ) and 4928 restraints for refining 4970 atoms. 1198 conditional restraints added. Observations/parameters ratio is 3.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2183 (Rfree = 0.000) for 4970 atoms. Found 239 (364 requested) and removed 44 (189 requested) atoms. Cycle 37: After refmac, R = 0.1962 (Rfree = 0.000) for 5160 atoms. Found 131 (378 requested) and removed 37 (197 requested) atoms. Cycle 38: After refmac, R = 0.1868 (Rfree = 0.000) for 5236 atoms. Found 127 (384 requested) and removed 37 (200 requested) atoms. Cycle 39: After refmac, R = 0.1821 (Rfree = 0.000) for 5308 atoms. Found 139 (390 requested) and removed 36 (203 requested) atoms. Cycle 40: After refmac, R = 0.1799 (Rfree = 0.000) for 5393 atoms. Found 122 (396 requested) and removed 57 (206 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.46 1.58 NCS extension: 114 residues added (124 deleted due to clashes), 5573 seeds are put forward Round 1: 469 peptides, 6 chains. Longest chain 147 peptides. Score 0.970 Round 2: 469 peptides, 6 chains. Longest chain 147 peptides. Score 0.970 Round 3: 469 peptides, 6 chains. Longest chain 147 peptides. Score 0.970 Round 4: 470 peptides, 5 chains. Longest chain 164 peptides. Score 0.972 Round 5: 469 peptides, 6 chains. Longest chain 164 peptides. Score 0.970 Taking the results from Round 4 Chains 6, Residues 465, Estimated correctness of the model 100.0 % 5 chains (461 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 147 A and 151 A 5 chains (468 residues) following loop building 4 chains (464 residues) in sequence following loop building ------------------------------------------------------ 72257 reflections ( 99.17 % complete ) and 5133 restraints for refining 5000 atoms. 1459 conditional restraints added. Observations/parameters ratio is 3.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2182 (Rfree = 0.000) for 5000 atoms. Found 227 (366 requested) and removed 27 (190 requested) atoms. Cycle 42: After refmac, R = 0.1951 (Rfree = 0.000) for 5189 atoms. Found 148 (380 requested) and removed 24 (198 requested) atoms. Cycle 43: After refmac, R = 0.1882 (Rfree = 0.000) for 5295 atoms. Found 119 (389 requested) and removed 34 (202 requested) atoms. Cycle 44: After refmac, R = 0.1830 (Rfree = 0.000) for 5364 atoms. Found 121 (394 requested) and removed 32 (205 requested) atoms. Cycle 45: After refmac, R = 0.1791 (Rfree = 0.000) for 5440 atoms. Found 112 (399 requested) and removed 40 (208 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.46 1.58 NCS extension: 1 residues added (2 deleted due to clashes), 5513 seeds are put forward Round 1: 472 peptides, 4 chains. Longest chain 164 peptides. Score 0.975 Round 2: 472 peptides, 4 chains. Longest chain 165 peptides. Score 0.975 Round 3: 471 peptides, 5 chains. Longest chain 165 peptides. Score 0.973 Round 4: 472 peptides, 4 chains. Longest chain 165 peptides. Score 0.975 Round 5: 471 peptides, 5 chains. Longest chain 165 peptides. Score 0.973 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 468, Estimated correctness of the model 100.0 % 4 chains (463 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 160 A and 168 A 4 chains (475 residues) following loop building 3 chains (470 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 72257 reflections ( 99.17 % complete ) and 3735 restraints for refining 3670 atoms. Observations/parameters ratio is 4.92 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2806 (Rfree = 0.000) for 3670 atoms. Found 202 (269 requested) and removed 0 (269 requested) atoms. Cycle 47: After refmac, R = 0.2351 (Rfree = 0.000) for 3670 atoms. Found 101 (283 requested) and removed 0 (147 requested) atoms. Cycle 48: After refmac, R = 0.2160 (Rfree = 0.000) for 3670 atoms. Found 66 (291 requested) and removed 4 (151 requested) atoms. Cycle 49: After refmac, R = 0.2051 (Rfree = 0.000) for 3670 atoms. Found 42 (295 requested) and removed 5 (153 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:44:44 GMT 2018 Job finished. TimeTaking 81.57 Used memory is bytes: 4933288