Sun 23 Dec 22:22:44 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 2gvh-2.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gvh-2.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gvh-2.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvh-2.6-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/2gvh-2.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvh-2.6-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 22:22:53 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/2gvh-2.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvh-2.6-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 856 and 0 Target number of residues in the AU: 856 Target solvent content: 0.6147 Checking the provided sequence file Detected sequence length: 288 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 864 Adjusted target solvent content: 0.61 Input MTZ file: 2gvh-2.6-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: 78 Cell parameters: 121.211 121.211 81.834 90.000 90.000 90.000 Input sequence file: 2gvh-2.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 6912 target number of atoms Had to go as low as 0.80 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 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: 121.211 2.600 Wilson plot Bfac: 58.86 32893 reflections ( 89.68 % complete ) and 0 restraints for refining 7665 atoms. Observations/parameters ratio is 1.07 ------------------------------------------------------ Starting model: R = 0.3560 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2714 (Rfree = 0.000) for 7665 atoms. Found 119 (124 requested) and removed 100 (62 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.85 2.46 NCS extension: 0 residues added, 7684 seeds are put forward Round 1: 473 peptides, 74 chains. Longest chain 22 peptides. Score 0.433 Round 2: 556 peptides, 69 chains. Longest chain 24 peptides. Score 0.559 Round 3: 561 peptides, 63 chains. Longest chain 26 peptides. Score 0.594 Round 4: 574 peptides, 63 chains. Longest chain 39 peptides. Score 0.607 Round 5: 587 peptides, 61 chains. Longest chain 31 peptides. Score 0.629 Taking the results from Round 5 Chains 70, Residues 526, Estimated correctness of the model 73.4 % 13 chains (177 residues) have been docked in sequence ------------------------------------------------------ 32893 reflections ( 89.68 % complete ) and 11903 restraints for refining 6442 atoms. 9206 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3096 (Rfree = 0.000) for 6442 atoms. Found 93 (104 requested) and removed 87 (52 requested) atoms. Cycle 2: After refmac, R = 0.2937 (Rfree = 0.000) for 6351 atoms. Found 90 (104 requested) and removed 72 (52 requested) atoms. Cycle 3: After refmac, R = 0.2850 (Rfree = 0.000) for 6326 atoms. Found 67 (103 requested) and removed 73 (51 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2785 (Rfree = 0.000) for 6285 atoms. Found 68 (102 requested) and removed 65 (51 requested) atoms. Cycle 5: After refmac, R = 0.2680 (Rfree = 0.000) for 6269 atoms. Found 41 (101 requested) and removed 58 (50 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.93 2.52 NCS extension: 127 residues added (38 deleted due to clashes), 6421 seeds are put forward Round 1: 559 peptides, 62 chains. Longest chain 42 peptides. Score 0.596 Round 2: 561 peptides, 57 chains. Longest chain 45 peptides. Score 0.622 Round 3: 581 peptides, 52 chains. Longest chain 42 peptides. Score 0.662 Round 4: 591 peptides, 53 chains. Longest chain 48 peptides. Score 0.667 Round 5: 592 peptides, 49 chains. Longest chain 51 peptides. Score 0.685 Taking the results from Round 5 Chains 54, Residues 543, Estimated correctness of the model 80.2 % 11 chains (189 residues) have been docked in sequence ------------------------------------------------------ 32893 reflections ( 89.68 % complete ) and 11676 restraints for refining 6444 atoms. 8830 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3020 (Rfree = 0.000) for 6444 atoms. Found 104 (104 requested) and removed 86 (52 requested) atoms. Cycle 7: After refmac, R = 0.2739 (Rfree = 0.000) for 6439 atoms. Found 70 (104 requested) and removed 70 (52 requested) atoms. Cycle 8: After refmac, R = 0.2676 (Rfree = 0.000) for 6411 atoms. Found 62 (104 requested) and removed 65 (52 requested) atoms. Cycle 9: After refmac, R = 0.2545 (Rfree = 0.000) for 6399 atoms. Found 53 (103 requested) and removed 53 (51 requested) atoms. Cycle 10: After refmac, R = 0.2543 (Rfree = 0.000) for 6390 atoms. Found 42 (103 requested) and removed 58 (51 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.93 2.52 NCS extension: 55 residues added (34 deleted due to clashes), 6449 seeds are put forward Round 1: 570 peptides, 59 chains. Longest chain 48 peptides. Score 0.621 Round 2: 591 peptides, 51 chains. Longest chain 62 peptides. Score 0.675 Round 3: 588 peptides, 49 chains. Longest chain 44 peptides. Score 0.681 Round 4: 602 peptides, 48 chains. Longest chain 60 peptides. Score 0.697 Round 5: 602 peptides, 49 chains. Longest chain 53 peptides. Score 0.693 Taking the results from Round 4 Chains 58, Residues 554, Estimated correctness of the model 81.6 % 12 chains (229 residues) have been docked in sequence ------------------------------------------------------ 32893 reflections ( 89.68 % complete ) and 11133 restraints for refining 6441 atoms. 8100 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2824 (Rfree = 0.000) for 6441 atoms. Found 74 (104 requested) and removed 82 (52 requested) atoms. Cycle 12: After refmac, R = 0.2624 (Rfree = 0.000) for 6409 atoms. Found 77 (104 requested) and removed 67 (52 requested) atoms. Cycle 13: After refmac, R = 0.2486 (Rfree = 0.000) for 6398 atoms. Found 54 (104 requested) and removed 60 (52 requested) atoms. Cycle 14: After refmac, R = 0.2495 (Rfree = 0.000) for 6379 atoms. Found 43 (103 requested) and removed 53 (51 requested) atoms. Cycle 15: After refmac, R = 0.2261 (Rfree = 0.000) for 6364 atoms. Found 27 (103 requested) and removed 53 (51 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.94 2.53 NCS extension: 162 residues added (109 deleted due to clashes), 6517 seeds are put forward Round 1: 571 peptides, 56 chains. Longest chain 46 peptides. Score 0.636 Round 2: 595 peptides, 42 chains. Longest chain 61 peptides. Score 0.715 Round 3: 585 peptides, 48 chains. Longest chain 40 peptides. Score 0.683 Round 4: 613 peptides, 46 chains. Longest chain 40 peptides. Score 0.714 Round 5: 604 peptides, 46 chains. Longest chain 49 peptides. Score 0.707 Taking the results from Round 2 Chains 53, Residues 553, Estimated correctness of the model 83.6 % 16 chains (324 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 245 A and 252 A Built loop between residues 193 C and 197 C 48 chains (555 residues) following loop building 14 chains (333 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 32893 reflections ( 89.68 % complete ) and 10118 restraints for refining 6444 atoms. 6642 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2628 (Rfree = 0.000) for 6444 atoms. Found 66 (104 requested) and removed 79 (52 requested) atoms. Cycle 17: After refmac, R = 0.2433 (Rfree = 0.000) for 6396 atoms. Found 52 (102 requested) and removed 64 (52 requested) atoms. Cycle 18: After refmac, R = 0.2336 (Rfree = 0.000) for 6355 atoms. Found 47 (99 requested) and removed 58 (51 requested) atoms. Cycle 19: After refmac, R = 0.2313 (Rfree = 0.000) for 6335 atoms. Found 45 (96 requested) and removed 54 (51 requested) atoms. Cycle 20: After refmac, R = 0.2266 (Rfree = 0.000) for 6314 atoms. Found 42 (94 requested) and removed 52 (51 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.95 2.54 NCS extension: 173 residues added (153 deleted due to clashes), 6497 seeds are put forward Round 1: 563 peptides, 49 chains. Longest chain 51 peptides. Score 0.659 Round 2: 610 peptides, 42 chains. Longest chain 48 peptides. Score 0.727 Round 3: 600 peptides, 38 chains. Longest chain 55 peptides. Score 0.734 Round 4: 598 peptides, 41 chains. Longest chain 61 peptides. Score 0.721 Round 5: 610 peptides, 40 chains. Longest chain 74 peptides. Score 0.734 Taking the results from Round 5 Chains 50, Residues 570, Estimated correctness of the model 85.5 % 10 chains (299 residues) have been docked in sequence Building loops using Loopy2018 50 chains (570 residues) following loop building 10 chains (299 residues) in sequence following loop building ------------------------------------------------------ 32893 reflections ( 89.68 % complete ) and 10404 restraints for refining 6442 atoms. 6995 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2654 (Rfree = 0.000) for 6442 atoms. Found 94 (94 requested) and removed 79 (52 requested) atoms. Cycle 22: After refmac, R = 0.2454 (Rfree = 0.000) for 6439 atoms. Found 53 (92 requested) and removed 58 (52 requested) atoms. Cycle 23: After refmac, R = 0.2372 (Rfree = 0.000) for 6416 atoms. Found 42 (89 requested) and removed 54 (52 requested) atoms. Cycle 24: After refmac, R = 0.2337 (Rfree = 0.000) for 6390 atoms. Found 29 (87 requested) and removed 56 (51 requested) atoms. Cycle 25: After refmac, R = 0.2277 (Rfree = 0.000) for 6352 atoms. Found 40 (84 requested) and removed 53 (51 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.95 2.54 NCS extension: 175 residues added (145 deleted due to clashes), 6519 seeds are put forward Round 1: 571 peptides, 46 chains. Longest chain 43 peptides. Score 0.679 Round 2: 595 peptides, 41 chains. Longest chain 48 peptides. Score 0.719 Round 3: 588 peptides, 41 chains. Longest chain 49 peptides. Score 0.714 Round 4: 586 peptides, 41 chains. Longest chain 51 peptides. Score 0.712 Round 5: 592 peptides, 36 chains. Longest chain 74 peptides. Score 0.736 Taking the results from Round 5 Chains 42, Residues 556, Estimated correctness of the model 85.7 % 13 chains (326 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 245 A and 249 A Built loop between residues 118 B and 122 B 40 chains (561 residues) following loop building 11 chains (332 residues) in sequence following loop building ------------------------------------------------------ 32893 reflections ( 89.68 % complete ) and 10170 restraints for refining 6444 atoms. 6705 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2740 (Rfree = 0.000) for 6444 atoms. Found 83 (83 requested) and removed 78 (52 requested) atoms. Cycle 27: After refmac, R = 0.2463 (Rfree = 0.000) for 6418 atoms. Found 79 (81 requested) and removed 71 (52 requested) atoms. Cycle 28: After refmac, R = 0.2357 (Rfree = 0.000) for 6410 atoms. Found 72 (79 requested) and removed 59 (52 requested) atoms. Cycle 29: After refmac, R = 0.2302 (Rfree = 0.000) for 6414 atoms. Found 58 (77 requested) and removed 56 (52 requested) atoms. Cycle 30: After refmac, R = 0.2103 (Rfree = 0.000) for 6402 atoms. Found 35 (75 requested) and removed 55 (52 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.97 2.56 NCS extension: 218 residues added (191 deleted due to clashes), 6630 seeds are put forward Round 1: 586 peptides, 41 chains. Longest chain 67 peptides. Score 0.712 Round 2: 600 peptides, 38 chains. Longest chain 68 peptides. Score 0.734 Round 3: 616 peptides, 37 chains. Longest chain 58 peptides. Score 0.749 Round 4: 627 peptides, 35 chains. Longest chain 68 peptides. Score 0.764 Round 5: 624 peptides, 36 chains. Longest chain 68 peptides. Score 0.759 Taking the results from Round 4 Chains 42, Residues 592, Estimated correctness of the model 88.4 % 12 chains (333 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 216 A and 219 A Built loop between residues 248 C and 252 C 40 chains (596 residues) following loop building 10 chains (338 residues) in sequence following loop building ------------------------------------------------------ 32893 reflections ( 89.68 % complete ) and 9875 restraints for refining 6442 atoms. 6273 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2535 (Rfree = 0.000) for 6442 atoms. Found 73 (73 requested) and removed 67 (52 requested) atoms. Cycle 32: After refmac, R = 0.2347 (Rfree = 0.000) for 6423 atoms. Found 57 (71 requested) and removed 57 (52 requested) atoms. Cycle 33: After refmac, R = 0.2285 (Rfree = 0.000) for 6409 atoms. Found 46 (69 requested) and removed 55 (52 requested) atoms. Cycle 34: After refmac, R = 0.2227 (Rfree = 0.000) for 6393 atoms. Found 42 (66 requested) and removed 52 (51 requested) atoms. Cycle 35: After refmac, R = 0.2211 (Rfree = 0.000) for 6371 atoms. Found 49 (64 requested) and removed 54 (51 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.99 2.58 NCS extension: 168 residues added (90 deleted due to clashes), 6557 seeds are put forward Round 1: 592 peptides, 45 chains. Longest chain 57 peptides. Score 0.701 Round 2: 597 peptides, 39 chains. Longest chain 62 peptides. Score 0.728 Round 3: 617 peptides, 35 chains. Longest chain 71 peptides. Score 0.757 Round 4: 614 peptides, 39 chains. Longest chain 59 peptides. Score 0.741 Round 5: 610 peptides, 42 chains. Longest chain 72 peptides. Score 0.727 Taking the results from Round 3 Chains 42, Residues 582, Estimated correctness of the model 87.7 % 13 chains (358 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 82 A and 89 A 40 chains (585 residues) following loop building 12 chains (364 residues) in sequence following loop building ------------------------------------------------------ 32893 reflections ( 89.68 % complete ) and 9877 restraints for refining 6443 atoms. 6156 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2477 (Rfree = 0.000) for 6443 atoms. Found 62 (62 requested) and removed 69 (52 requested) atoms. Cycle 37: After refmac, R = 0.2317 (Rfree = 0.000) for 6416 atoms. Found 57 (60 requested) and removed 61 (52 requested) atoms. Cycle 38: After refmac, R = 0.2207 (Rfree = 0.000) for 6408 atoms. Found 51 (58 requested) and removed 54 (51 requested) atoms. Cycle 39: After refmac, R = 0.2150 (Rfree = 0.000) for 6404 atoms. Found 44 (56 requested) and removed 55 (51 requested) atoms. Cycle 40: After refmac, R = 0.2129 (Rfree = 0.000) for 6390 atoms. Found 33 (54 requested) and removed 57 (51 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.97 2.56 NCS extension: 378 residues added (186 deleted due to clashes), 6753 seeds are put forward Round 1: 570 peptides, 43 chains. Longest chain 72 peptides. Score 0.691 Round 2: 591 peptides, 41 chains. Longest chain 54 peptides. Score 0.716 Round 3: 596 peptides, 39 chains. Longest chain 73 peptides. Score 0.728 Round 4: 594 peptides, 37 chains. Longest chain 54 peptides. Score 0.734 Round 5: 587 peptides, 40 chains. Longest chain 75 peptides. Score 0.717 Taking the results from Round 4 Chains 43, Residues 557, Estimated correctness of the model 85.5 % 12 chains (302 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 38 A and 48 A Built loop between residues 216 A and 220 A Built loop between residues 84 C and 89 C Built loop between residues 246 B and 251 B 37 chains (575 residues) following loop building 8 chains (322 residues) in sequence following loop building ------------------------------------------------------ 32893 reflections ( 89.68 % complete ) and 10428 restraints for refining 6444 atoms. 6911 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2476 (Rfree = 0.000) for 6444 atoms. Found 52 (52 requested) and removed 70 (52 requested) atoms. Cycle 42: After refmac, R = 0.2335 (Rfree = 0.000) for 6414 atoms. Found 52 (52 requested) and removed 59 (52 requested) atoms. Cycle 43: After refmac, R = 0.2225 (Rfree = 0.000) for 6396 atoms. Found 51 (51 requested) and removed 59 (51 requested) atoms. Cycle 44: After refmac, R = 0.2186 (Rfree = 0.000) for 6385 atoms. Found 51 (51 requested) and removed 51 (51 requested) atoms. Cycle 45: After refmac, R = 0.2110 (Rfree = 0.000) for 6379 atoms. Found 46 (51 requested) and removed 55 (51 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.97 2.56 NCS extension: 161 residues added (158 deleted due to clashes), 6548 seeds are put forward Round 1: 576 peptides, 46 chains. Longest chain 60 peptides. Score 0.684 Round 2: 599 peptides, 33 chains. Longest chain 67 peptides. Score 0.752 Round 3: 600 peptides, 39 chains. Longest chain 54 peptides. Score 0.731 Round 4: 616 peptides, 38 chains. Longest chain 63 peptides. Score 0.746 Round 5: 616 peptides, 36 chains. Longest chain 61 peptides. Score 0.753 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 42, Residues 580, Estimated correctness of the model 87.3 % 17 chains (383 residues) have been docked in sequence Sequence coverage is 65 % Consider running further cycles of model building using 2gvh-2_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 205 A and 208 A Built loop between residues 37 C and 49 C Built loop between residues 66 C and 73 C Built loop between residues 85 C and 90 C Built loop between residues 114 C and 119 C Built loop between residues 197 C and 200 C Built loop between residues 246 C and 249 C Built loop between residues 215 B and 220 B Built loop between residues 229 B and 234 B 27 chains (612 residues) following loop building 8 chains (422 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 32893 reflections ( 89.68 % complete ) and 9087 restraints for refining 6443 atoms. 5089 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2658 (Rfree = 0.000) for 6443 atoms. Found 0 (52 requested) and removed 52 (52 requested) atoms. Cycle 47: After refmac, R = 0.2422 (Rfree = 0.000) for 6373 atoms. Found 0 (51 requested) and removed 22 (51 requested) atoms. Cycle 48: After refmac, R = 0.2303 (Rfree = 0.000) for 6339 atoms. Found 0 (51 requested) and removed 11 (51 requested) atoms. Cycle 49: After refmac, R = 0.2262 (Rfree = 0.000) for 6320 atoms. TimeTaking 98.87