Sun 23 Dec 22:22:52 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 2prv-1.3-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2prv-1.3-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2prv-1.3-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prv-1.3-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/2prv-1.3-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prv-1.3-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 22:23:02 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/2prv-1.3-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prv-1.3-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 321 and 0 Target number of residues in the AU: 321 Target solvent content: 0.4359 Checking the provided sequence file Detected sequence length: 153 Maximum limit of NCS related copies: 16 Number of NCS-related molecules: 2 Adjusted target number of residues: 306 Adjusted target solvent content: 0.46 Input MTZ file: 2prv-1.3-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: 1 Cell parameters: 40.107 45.170 48.067 84.512 67.558 73.075 Input sequence file: 2prv-1.3-parrot-hancs.fasta_lf Building free atoms model in initial map for 2448 target number of atoms Had to go as low as 0.60 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: 44.420 1.300 Wilson plot Bfac: 12.49 69437 reflections ( 94.64 % complete ) and 0 restraints for refining 2714 atoms. Observations/parameters ratio is 6.40 ------------------------------------------------------ Starting model: R = 0.4225 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3854 (Rfree = 0.000) for 2714 atoms. Found 156 (317 requested) and removed 169 (158 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.56 1.65 Round 1: 109 peptides, 23 chains. Longest chain 8 peptides. Score 0.272 Round 2: 104 peptides, 23 chains. Longest chain 7 peptides. Score 0.242 Round 3: 121 peptides, 23 chains. Longest chain 10 peptides. Score 0.340 Round 4: 114 peptides, 21 chains. Longest chain 11 peptides. Score 0.348 Round 5: 113 peptides, 20 chains. Longest chain 9 peptides. Score 0.367 Taking the results from Round 5 Chains 20, Residues 93, Estimated correctness of the model 92.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 69437 reflections ( 94.64 % complete ) and 5010 restraints for refining 2554 atoms. 4658 conditional restraints added. Observations/parameters ratio is 6.80 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3874 (Rfree = 0.000) for 2554 atoms. Found 149 (298 requested) and removed 42 (149 requested) atoms. Cycle 2: After refmac, R = 0.3615 (Rfree = 0.000) for 2661 atoms. Found 125 (311 requested) and removed 22 (155 requested) atoms. Cycle 3: After refmac, R = 0.3444 (Rfree = 0.000) for 2760 atoms. Found 124 (323 requested) and removed 7 (161 requested) atoms. Cycle 4: After refmac, R = 0.3314 (Rfree = 0.000) for 2874 atoms. Found 110 (336 requested) and removed 8 (168 requested) atoms. Cycle 5: After refmac, R = 0.3236 (Rfree = 0.000) for 2972 atoms. Found 91 (348 requested) and removed 8 (174 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.46 1.54 Round 1: 108 peptides, 20 chains. Longest chain 10 peptides. Score 0.339 Round 2: 132 peptides, 20 chains. Longest chain 10 peptides. Score 0.465 Round 3: 139 peptides, 20 chains. Longest chain 12 peptides. Score 0.498 Round 4: 149 peptides, 20 chains. Longest chain 18 peptides. Score 0.543 Round 5: 140 peptides, 19 chains. Longest chain 18 peptides. Score 0.523 Taking the results from Round 4 Chains 20, Residues 129, Estimated correctness of the model 95.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 69437 reflections ( 94.64 % complete ) and 5799 restraints for refining 2996 atoms. 5303 conditional restraints added. Observations/parameters ratio is 5.79 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3406 (Rfree = 0.000) for 2996 atoms. Found 155 (350 requested) and removed 16 (175 requested) atoms. Cycle 7: After refmac, R = 0.3241 (Rfree = 0.000) for 3135 atoms. Found 105 (366 requested) and removed 10 (183 requested) atoms. Cycle 8: After refmac, R = 0.3135 (Rfree = 0.000) for 3230 atoms. Found 95 (377 requested) and removed 3 (188 requested) atoms. Cycle 9: After refmac, R = 0.3051 (Rfree = 0.000) for 3317 atoms. Found 104 (388 requested) and removed 3 (194 requested) atoms. Cycle 10: After refmac, R = 0.2999 (Rfree = 0.000) for 3415 atoms. Found 98 (399 requested) and removed 1 (199 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.44 1.52 Round 1: 125 peptides, 16 chains. Longest chain 17 peptides. Score 0.516 Round 2: 134 peptides, 17 chains. Longest chain 17 peptides. Score 0.536 Round 3: 144 peptides, 17 chains. Longest chain 17 peptides. Score 0.579 Round 4: 148 peptides, 17 chains. Longest chain 17 peptides. Score 0.595 Round 5: 139 peptides, 17 chains. Longest chain 14 peptides. Score 0.558 Taking the results from Round 4 Chains 17, Residues 131, Estimated correctness of the model 96.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 69437 reflections ( 94.64 % complete ) and 7089 restraints for refining 3393 atoms. 6582 conditional restraints added. Observations/parameters ratio is 5.12 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3118 (Rfree = 0.000) for 3393 atoms. Found 161 (396 requested) and removed 12 (198 requested) atoms. Cycle 12: After refmac, R = 0.2985 (Rfree = 0.000) for 3541 atoms. Found 112 (414 requested) and removed 3 (207 requested) atoms. Cycle 13: After refmac, R = 0.2908 (Rfree = 0.000) for 3648 atoms. Found 105 (426 requested) and removed 2 (213 requested) atoms. Cycle 14: After refmac, R = 0.2848 (Rfree = 0.000) for 3747 atoms. Found 105 (438 requested) and removed 3 (219 requested) atoms. Cycle 15: After refmac, R = 0.2813 (Rfree = 0.000) for 3844 atoms. Found 90 (450 requested) and removed 7 (225 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.43 1.51 Round 1: 145 peptides, 19 chains. Longest chain 17 peptides. Score 0.545 Round 2: 135 peptides, 15 chains. Longest chain 19 peptides. Score 0.580 Round 3: 149 peptides, 17 chains. Longest chain 17 peptides. Score 0.599 Round 4: 138 peptides, 15 chains. Longest chain 17 peptides. Score 0.592 Round 5: 153 peptides, 15 chains. Longest chain 27 peptides. Score 0.649 Taking the results from Round 5 Chains 15, Residues 138, Estimated correctness of the model 97.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 69437 reflections ( 94.64 % complete ) and 8131 restraints for refining 3769 atoms. 7594 conditional restraints added. Observations/parameters ratio is 4.61 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2965 (Rfree = 0.000) for 3769 atoms. Found 159 (440 requested) and removed 14 (220 requested) atoms. Cycle 17: After refmac, R = 0.2843 (Rfree = 0.000) for 3913 atoms. Found 112 (457 requested) and removed 4 (228 requested) atoms. Cycle 18: After refmac, R = 0.2774 (Rfree = 0.000) for 4019 atoms. Found 97 (470 requested) and removed 5 (235 requested) atoms. Cycle 19: After refmac, R = 0.2716 (Rfree = 0.000) for 4109 atoms. Found 91 (480 requested) and removed 2 (240 requested) atoms. Cycle 20: After refmac, R = 0.2663 (Rfree = 0.000) for 4197 atoms. Found 99 (490 requested) and removed 0 (245 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.42 1.50 Round 1: 131 peptides, 16 chains. Longest chain 15 peptides. Score 0.543 Round 2: 136 peptides, 14 chains. Longest chain 18 peptides. Score 0.603 Round 3: 143 peptides, 14 chains. Longest chain 19 peptides. Score 0.630 Round 4: 142 peptides, 14 chains. Longest chain 19 peptides. Score 0.626 Round 5: 144 peptides, 16 chains. Longest chain 19 peptides. Score 0.598 Taking the results from Round 3 Chains 14, Residues 129, Estimated correctness of the model 97.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 69437 reflections ( 94.64 % complete ) and 9631 restraints for refining 4112 atoms. 9129 conditional restraints added. Observations/parameters ratio is 4.22 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2786 (Rfree = 0.000) for 4112 atoms. Found 151 (480 requested) and removed 13 (240 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2697 (Rfree = 0.000) for 4250 atoms. Found 105 (496 requested) and removed 5 (248 requested) atoms. Cycle 23: After refmac, R = 0.2640 (Rfree = 0.000) for 4349 atoms. Found 81 (508 requested) and removed 7 (254 requested) atoms. Cycle 24: After refmac, R = 0.2599 (Rfree = 0.000) for 4419 atoms. Found 86 (517 requested) and removed 5 (258 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.2570 (Rfree = 0.000) for 4498 atoms. Found 85 (526 requested) and removed 4 (263 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.41 1.49 Round 1: 147 peptides, 16 chains. Longest chain 26 peptides. Score 0.609 Round 2: 139 peptides, 13 chains. Longest chain 26 peptides. Score 0.633 Round 3: 134 peptides, 13 chains. Longest chain 26 peptides. Score 0.614 Round 4: 142 peptides, 14 chains. Longest chain 26 peptides. Score 0.626 Round 5: 139 peptides, 14 chains. Longest chain 26 peptides. Score 0.615 Taking the results from Round 2 Chains 13, Residues 126, Estimated correctness of the model 97.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 69437 reflections ( 94.64 % complete ) and 10775 restraints for refining 4402 atoms. 10284 conditional restraints added. Observations/parameters ratio is 3.94 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2668 (Rfree = 0.000) for 4402 atoms. Found 157 (514 requested) and removed 7 (257 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2587 (Rfree = 0.000) for 4552 atoms. Found 111 (532 requested) and removed 5 (266 requested) atoms. Cycle 28: After refmac, R = 0.2531 (Rfree = 0.000) for 4657 atoms. Found 85 (544 requested) and removed 3 (272 requested) atoms. Cycle 29: After refmac, R = 0.2496 (Rfree = 0.000) for 4732 atoms. Found 93 (554 requested) and removed 4 (277 requested) atoms. Cycle 30: After refmac, R = 0.2466 (Rfree = 0.000) for 4820 atoms. Found 70 (563 requested) and removed 7 (281 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.41 1.49 Round 1: 134 peptides, 15 chains. Longest chain 26 peptides. Score 0.576 Round 2: 137 peptides, 15 chains. Longest chain 26 peptides. Score 0.588 Round 3: 131 peptides, 13 chains. Longest chain 26 peptides. Score 0.602 Round 4: 139 peptides, 14 chains. Longest chain 27 peptides. Score 0.615 Round 5: 141 peptides, 15 chains. Longest chain 27 peptides. Score 0.604 Taking the results from Round 4 Chains 14, Residues 125, Estimated correctness of the model 97.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 69437 reflections ( 94.64 % complete ) and 11921 restraints for refining 4673 atoms. 11435 conditional restraints added. Observations/parameters ratio is 3.71 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2605 (Rfree = 0.000) for 4673 atoms. Found 204 (546 requested) and removed 9 (273 requested) atoms. Cycle 32: After refmac, R = 0.2525 (Rfree = 0.000) for 4868 atoms. Found 112 (569 requested) and removed 3 (284 requested) atoms. Cycle 33: After refmac, R = 0.2456 (Rfree = 0.000) for 4975 atoms. Found 87 (582 requested) and removed 5 (291 requested) atoms. Cycle 34: After refmac, R = 0.2414 (Rfree = 0.000) for 5052 atoms. Found 88 (591 requested) and removed 3 (295 requested) atoms. Cycle 35: After refmac, R = 0.2393 (Rfree = 0.000) for 5132 atoms. Found 83 (600 requested) and removed 7 (300 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.41 1.49 Round 1: 130 peptides, 17 chains. Longest chain 14 peptides. Score 0.518 Round 2: 141 peptides, 14 chains. Longest chain 27 peptides. Score 0.623 Round 3: 141 peptides, 15 chains. Longest chain 27 peptides. Score 0.604 Round 4: 144 peptides, 16 chains. Longest chain 17 peptides. Score 0.598 Round 5: 142 peptides, 19 chains. Longest chain 14 peptides. Score 0.532 Taking the results from Round 2 Chains 14, Residues 127, Estimated correctness of the model 97.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 69437 reflections ( 94.64 % complete ) and 13050 restraints for refining 4945 atoms. 12556 conditional restraints added. Observations/parameters ratio is 3.51 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2499 (Rfree = 0.000) for 4945 atoms. Found 192 (578 requested) and removed 7 (289 requested) atoms. Cycle 37: After refmac, R = 0.2448 (Rfree = 0.000) for 5130 atoms. Found 118 (599 requested) and removed 5 (299 requested) atoms. Cycle 38: After refmac, R = 0.2390 (Rfree = 0.000) for 5242 atoms. Found 89 (613 requested) and removed 4 (306 requested) atoms. Cycle 39: After refmac, R = 0.2356 (Rfree = 0.000) for 5320 atoms. Found 91 (622 requested) and removed 5 (311 requested) atoms. Cycle 40: After refmac, R = 0.2323 (Rfree = 0.000) for 5403 atoms. Found 90 (632 requested) and removed 11 (316 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.40 1.48 Round 1: 112 peptides, 13 chains. Longest chain 16 peptides. Score 0.520 Round 2: 126 peptides, 15 chains. Longest chain 16 peptides. Score 0.541 Round 3: 122 peptides, 14 chains. Longest chain 17 peptides. Score 0.544 Round 4: 130 peptides, 14 chains. Longest chain 26 peptides. Score 0.579 Round 5: 131 peptides, 17 chains. Longest chain 26 peptides. Score 0.523 Taking the results from Round 4 Chains 14, Residues 116, Estimated correctness of the model 96.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 69437 reflections ( 94.64 % complete ) and 13919 restraints for refining 5129 atoms. 13469 conditional restraints added. Observations/parameters ratio is 3.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2506 (Rfree = 0.000) for 5129 atoms. Found 228 (599 requested) and removed 12 (299 requested) atoms. Cycle 42: After refmac, R = 0.2424 (Rfree = 0.000) for 5345 atoms. Found 137 (625 requested) and removed 10 (312 requested) atoms. Cycle 43: After refmac, R = 0.2358 (Rfree = 0.000) for 5472 atoms. Found 96 (639 requested) and removed 16 (319 requested) atoms. Cycle 44: After refmac, R = 0.2304 (Rfree = 0.000) for 5545 atoms. Found 104 (649 requested) and removed 11 (324 requested) atoms. Cycle 45: After refmac, R = 0.2281 (Rfree = 0.000) for 5635 atoms. Found 101 (659 requested) and removed 22 (329 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.40 1.48 Round 1: 119 peptides, 16 chains. Longest chain 14 peptides. Score 0.488 Round 2: 119 peptides, 13 chains. Longest chain 26 peptides. Score 0.552 Round 3: 121 peptides, 13 chains. Longest chain 26 peptides. Score 0.561 Round 4: 115 peptides, 14 chains. Longest chain 26 peptides. Score 0.513 Round 5: 124 peptides, 14 chains. Longest chain 22 peptides. Score 0.553 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 0, Residues 0, Estimated correctness of the model 96.1 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2prv-1_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 69437 reflections ( 94.64 % complete ) and 14856 restraints for refining 5361 atoms. 14437 conditional restraints added. Observations/parameters ratio is 3.24 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2425 (Rfree = 0.000) for 5361 atoms. Found 0 (626 requested) and removed 1 (313 requested) atoms. Cycle 47: After refmac, R = 0.2376 (Rfree = 0.000) for 5360 atoms. Found 0 (626 requested) and removed 2 (313 requested) atoms. Cycle 48: After refmac, R = 0.2353 (Rfree = 0.000) for 5358 atoms. Found 0 (626 requested) and removed 0 (313 requested) atoms. Cycle 49: After refmac, R = 0.2341 (Rfree = 0.000) for 5357 atoms. Found 0 (626 requested) and removed 0 (313 requested) atoms. Writing output files ... TimeTaking 68.15