Mon 24 Dec 07:33:25 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2g0t-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2g0t-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2g0t-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2g0t-3.4-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2g0t-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2g0t-3.4-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:33:29 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/noncs/ArpWArp/wArpResults/WorkingDir/2g0t-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2g0t-3.4-parrot-noncs/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 924 and 0 Target number of residues in the AU: 924 Target solvent content: 0.5732 Checking the provided sequence file Detected sequence length: 350 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 700 Adjusted target solvent content: 0.68 Input MTZ file: 2g0t-3.4-parrot-noncs.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: 213 Cell parameters: 191.568 191.568 191.568 90.000 90.000 90.000 Input sequence file: 2g0t-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 5600 target number of atoms Had to go as low as 0.95 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: 29.560 3.400 Wilson plot Bfac: 42.73 17072 reflections ( 99.75 % complete ) and 0 restraints for refining 6259 atoms. Observations/parameters ratio is 0.68 ------------------------------------------------------ Starting model: R = 0.3271 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2777 (Rfree = 0.000) for 6259 atoms. Found 47 (47 requested) and removed 63 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.96 2.30 Search for helices and strands: 0 residues in 0 chains, 6386 seeds are put forward NCS extension: 0 residues added, 6386 seeds are put forward Round 1: 440 peptides, 71 chains. Longest chain 16 peptides. Score 0.412 Round 2: 490 peptides, 60 chains. Longest chain 27 peptides. Score 0.538 Round 3: 505 peptides, 56 chains. Longest chain 26 peptides. Score 0.576 Round 4: 521 peptides, 58 chains. Longest chain 32 peptides. Score 0.583 Round 5: 517 peptides, 49 chains. Longest chain 48 peptides. Score 0.623 Taking the results from Round 5 Chains 56, Residues 468, Estimated correctness of the model 36.0 % 11 chains (151 residues) have been docked in sequence ------------------------------------------------------ 17072 reflections ( 99.75 % complete ) and 9354 restraints for refining 5252 atoms. 6944 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2810 (Rfree = 0.000) for 5252 atoms. Found 39 (39 requested) and removed 45 (19 requested) atoms. Cycle 2: After refmac, R = 0.2666 (Rfree = 0.000) for 5177 atoms. Found 39 (39 requested) and removed 32 (19 requested) atoms. Cycle 3: After refmac, R = 0.2563 (Rfree = 0.000) for 5161 atoms. Found 33 (39 requested) and removed 40 (19 requested) atoms. Cycle 4: After refmac, R = 0.2526 (Rfree = 0.000) for 5135 atoms. Found 32 (38 requested) and removed 35 (19 requested) atoms. Cycle 5: After refmac, R = 0.2484 (Rfree = 0.000) for 5112 atoms. Found 29 (38 requested) and removed 33 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.91 2.26 Search for helices and strands: 0 residues in 0 chains, 5292 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 5316 seeds are put forward Round 1: 486 peptides, 61 chains. Longest chain 20 peptides. Score 0.528 Round 2: 523 peptides, 59 chains. Longest chain 28 peptides. Score 0.580 Round 3: 528 peptides, 51 chains. Longest chain 32 peptides. Score 0.624 Round 4: 531 peptides, 55 chains. Longest chain 40 peptides. Score 0.608 Round 5: 530 peptides, 50 chains. Longest chain 47 peptides. Score 0.631 Taking the results from Round 5 Chains 59, Residues 480, Estimated correctness of the model 38.5 % 7 chains (95 residues) have been docked in sequence ------------------------------------------------------ 17072 reflections ( 99.75 % complete ) and 9589 restraints for refining 5091 atoms. 7413 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2775 (Rfree = 0.000) for 5091 atoms. Found 38 (38 requested) and removed 46 (19 requested) atoms. Cycle 7: After refmac, R = 0.2585 (Rfree = 0.000) for 5041 atoms. Found 29 (38 requested) and removed 32 (19 requested) atoms. Cycle 8: After refmac, R = 0.2498 (Rfree = 0.000) for 5014 atoms. Found 23 (38 requested) and removed 32 (19 requested) atoms. Cycle 9: After refmac, R = 0.2430 (Rfree = 0.000) for 4994 atoms. Found 22 (37 requested) and removed 27 (18 requested) atoms. Cycle 10: After refmac, R = 0.2433 (Rfree = 0.000) for 4973 atoms. Found 27 (37 requested) and removed 25 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.90 2.26 Search for helices and strands: 0 residues in 0 chains, 5174 seeds are put forward NCS extension: 21 residues added (3 deleted due to clashes), 5195 seeds are put forward Round 1: 512 peptides, 59 chains. Longest chain 29 peptides. Score 0.568 Round 2: 552 peptides, 46 chains. Longest chain 38 peptides. Score 0.670 Round 3: 533 peptides, 50 chains. Longest chain 40 peptides. Score 0.634 Round 4: 552 peptides, 46 chains. Longest chain 39 peptides. Score 0.670 Round 5: 528 peptides, 44 chains. Longest chain 37 peptides. Score 0.657 Taking the results from Round 4 Chains 56, Residues 506, Estimated correctness of the model 49.8 % 11 chains (200 residues) have been docked in sequence ------------------------------------------------------ 17072 reflections ( 99.75 % complete ) and 8513 restraints for refining 5091 atoms. 5774 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2889 (Rfree = 0.000) for 5091 atoms. Found 38 (38 requested) and removed 50 (19 requested) atoms. Cycle 12: After refmac, R = 0.2701 (Rfree = 0.000) for 5045 atoms. Found 38 (38 requested) and removed 31 (19 requested) atoms. Cycle 13: After refmac, R = 0.2600 (Rfree = 0.000) for 5031 atoms. Found 38 (38 requested) and removed 26 (19 requested) atoms. Cycle 14: After refmac, R = 0.2530 (Rfree = 0.000) for 5032 atoms. Found 26 (38 requested) and removed 26 (19 requested) atoms. Cycle 15: After refmac, R = 0.2459 (Rfree = 0.000) for 5022 atoms. Found 23 (37 requested) and removed 22 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.91 2.26 Search for helices and strands: 0 residues in 0 chains, 5192 seeds are put forward NCS extension: 17 residues added (11 deleted due to clashes), 5209 seeds are put forward Round 1: 515 peptides, 57 chains. Longest chain 24 peptides. Score 0.581 Round 2: 532 peptides, 55 chains. Longest chain 30 peptides. Score 0.609 Round 3: 526 peptides, 52 chains. Longest chain 31 peptides. Score 0.618 Round 4: 549 peptides, 52 chains. Longest chain 29 peptides. Score 0.640 Round 5: 551 peptides, 50 chains. Longest chain 34 peptides. Score 0.651 Taking the results from Round 5 Chains 62, Residues 501, Estimated correctness of the model 44.4 % 11 chains (143 residues) have been docked in sequence ------------------------------------------------------ 17072 reflections ( 99.75 % complete ) and 8927 restraints for refining 5092 atoms. 6479 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2736 (Rfree = 0.000) for 5092 atoms. Found 38 (38 requested) and removed 40 (19 requested) atoms. Cycle 17: After refmac, R = 0.2580 (Rfree = 0.000) for 5065 atoms. Found 27 (38 requested) and removed 33 (19 requested) atoms. Cycle 18: After refmac, R = 0.2497 (Rfree = 0.000) for 5046 atoms. Found 25 (38 requested) and removed 29 (19 requested) atoms. Cycle 19: After refmac, R = 0.2450 (Rfree = 0.000) for 5034 atoms. Found 21 (38 requested) and removed 28 (19 requested) atoms. Cycle 20: After refmac, R = 0.2394 (Rfree = 0.000) for 5021 atoms. Found 24 (37 requested) and removed 26 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.91 2.26 Search for helices and strands: 0 residues in 0 chains, 5187 seeds are put forward NCS extension: 13 residues added (5 deleted due to clashes), 5200 seeds are put forward Round 1: 506 peptides, 59 chains. Longest chain 19 peptides. Score 0.561 Round 2: 538 peptides, 52 chains. Longest chain 31 peptides. Score 0.630 Round 3: 543 peptides, 51 chains. Longest chain 51 peptides. Score 0.639 Round 4: 533 peptides, 54 chains. Longest chain 37 peptides. Score 0.615 Round 5: 522 peptides, 54 chains. Longest chain 38 peptides. Score 0.604 Taking the results from Round 3 Chains 60, Residues 492, Estimated correctness of the model 40.9 % 7 chains (114 residues) have been docked in sequence ------------------------------------------------------ 17072 reflections ( 99.75 % complete ) and 9193 restraints for refining 5092 atoms. 6810 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2725 (Rfree = 0.000) for 5092 atoms. Found 38 (38 requested) and removed 47 (19 requested) atoms. Cycle 22: After refmac, R = 0.2540 (Rfree = 0.000) for 5058 atoms. Found 30 (38 requested) and removed 26 (19 requested) atoms. Cycle 23: After refmac, R = 0.2441 (Rfree = 0.000) for 5050 atoms. Found 18 (38 requested) and removed 25 (19 requested) atoms. Cycle 24: After refmac, R = 0.2382 (Rfree = 0.000) for 5033 atoms. Found 11 (38 requested) and removed 22 (19 requested) atoms. Cycle 25: After refmac, R = 0.2349 (Rfree = 0.000) for 5013 atoms. Found 11 (37 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.93 2.28 Search for helices and strands: 0 residues in 0 chains, 5166 seeds are put forward NCS extension: 39 residues added (13 deleted due to clashes), 5205 seeds are put forward Round 1: 493 peptides, 57 chains. Longest chain 26 peptides. Score 0.557 Round 2: 506 peptides, 48 chains. Longest chain 33 peptides. Score 0.617 Round 3: 524 peptides, 48 chains. Longest chain 27 peptides. Score 0.635 Round 4: 535 peptides, 56 chains. Longest chain 24 peptides. Score 0.607 Round 5: 528 peptides, 53 chains. Longest chain 39 peptides. Score 0.615 Taking the results from Round 3 Chains 55, Residues 476, Estimated correctness of the model 39.7 % 8 chains (135 residues) have been docked in sequence ------------------------------------------------------ 17072 reflections ( 99.75 % complete ) and 9206 restraints for refining 5092 atoms. 6847 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2645 (Rfree = 0.000) for 5092 atoms. Found 38 (38 requested) and removed 32 (19 requested) atoms. Cycle 27: After refmac, R = 0.2496 (Rfree = 0.000) for 5072 atoms. Found 26 (38 requested) and removed 28 (19 requested) atoms. Cycle 28: After refmac, R = 0.2414 (Rfree = 0.000) for 5058 atoms. Found 13 (38 requested) and removed 27 (19 requested) atoms. Cycle 29: After refmac, R = 0.2392 (Rfree = 0.000) for 5032 atoms. Found 10 (38 requested) and removed 30 (19 requested) atoms. Cycle 30: After refmac, R = 0.2402 (Rfree = 0.000) for 5010 atoms. Found 19 (37 requested) and removed 32 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.90 2.26 Search for helices and strands: 0 residues in 0 chains, 5164 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 5184 seeds are put forward Round 1: 491 peptides, 61 chains. Longest chain 26 peptides. Score 0.533 Round 2: 526 peptides, 51 chains. Longest chain 37 peptides. Score 0.622 Round 3: 536 peptides, 51 chains. Longest chain 37 peptides. Score 0.632 Round 4: 530 peptides, 48 chains. Longest chain 51 peptides. Score 0.640 Round 5: 506 peptides, 51 chains. Longest chain 26 peptides. Score 0.602 Taking the results from Round 4 Chains 50, Residues 482, Estimated correctness of the model 41.2 % 6 chains (131 residues) have been docked in sequence ------------------------------------------------------ 17072 reflections ( 99.75 % complete ) and 9279 restraints for refining 5090 atoms. 6911 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2694 (Rfree = 0.000) for 5090 atoms. Found 38 (38 requested) and removed 36 (19 requested) atoms. Cycle 32: After refmac, R = 0.2532 (Rfree = 0.000) for 5058 atoms. Found 38 (38 requested) and removed 26 (19 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2436 (Rfree = 0.000) for 5054 atoms. Found 21 (38 requested) and removed 27 (19 requested) atoms. Cycle 34: After refmac, R = 0.2374 (Rfree = 0.000) for 5037 atoms. Found 25 (38 requested) and removed 30 (19 requested) atoms. Cycle 35: After refmac, R = 0.2325 (Rfree = 0.000) for 5020 atoms. Found 22 (37 requested) and removed 23 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.90 2.26 Search for helices and strands: 0 residues in 0 chains, 5151 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 5179 seeds are put forward Round 1: 517 peptides, 61 chains. Longest chain 37 peptides. Score 0.563 Round 2: 539 peptides, 52 chains. Longest chain 35 peptides. Score 0.631 Round 3: 528 peptides, 45 chains. Longest chain 43 peptides. Score 0.652 Round 4: 528 peptides, 54 chains. Longest chain 37 peptides. Score 0.610 Round 5: 522 peptides, 52 chains. Longest chain 30 peptides. Score 0.614 Taking the results from Round 3 Chains 55, Residues 483, Estimated correctness of the model 44.7 % 8 chains (155 residues) have been docked in sequence ------------------------------------------------------ 17072 reflections ( 99.75 % complete ) and 8851 restraints for refining 5091 atoms. 6350 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2691 (Rfree = 0.000) for 5091 atoms. Found 38 (38 requested) and removed 44 (19 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2516 (Rfree = 0.000) for 5063 atoms. Found 32 (38 requested) and removed 30 (19 requested) atoms. Cycle 38: After refmac, R = 0.2498 (Rfree = 0.000) for 5049 atoms. Found 28 (38 requested) and removed 27 (19 requested) atoms. Cycle 39: After refmac, R = 0.2440 (Rfree = 0.000) for 5045 atoms. Found 21 (38 requested) and removed 25 (19 requested) atoms. Cycle 40: After refmac, R = 0.2415 (Rfree = 0.000) for 5033 atoms. Found 16 (38 requested) and removed 22 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.91 2.26 Search for helices and strands: 0 residues in 0 chains, 5212 seeds are put forward NCS extension: 27 residues added (13 deleted due to clashes), 5239 seeds are put forward Round 1: 472 peptides, 58 chains. Longest chain 22 peptides. Score 0.527 Round 2: 509 peptides, 48 chains. Longest chain 34 peptides. Score 0.620 Round 3: 525 peptides, 49 chains. Longest chain 37 peptides. Score 0.631 Round 4: 519 peptides, 57 chains. Longest chain 23 peptides. Score 0.586 Round 5: 504 peptides, 43 chains. Longest chain 41 peptides. Score 0.639 Taking the results from Round 5 Chains 48, Residues 461, Estimated correctness of the model 40.9 % 8 chains (168 residues) have been docked in sequence ------------------------------------------------------ 17072 reflections ( 99.75 % complete ) and 8924 restraints for refining 5092 atoms. 6473 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2648 (Rfree = 0.000) for 5092 atoms. Found 38 (38 requested) and removed 43 (19 requested) atoms. Cycle 42: After refmac, R = 0.2476 (Rfree = 0.000) for 5070 atoms. Found 34 (38 requested) and removed 26 (19 requested) atoms. Cycle 43: After refmac, R = 0.2372 (Rfree = 0.000) for 5069 atoms. Found 21 (38 requested) and removed 27 (19 requested) atoms. Cycle 44: After refmac, R = 0.2320 (Rfree = 0.000) for 5054 atoms. Found 14 (38 requested) and removed 28 (19 requested) atoms. Cycle 45: After refmac, R = 0.2291 (Rfree = 0.000) for 5035 atoms. Found 16 (38 requested) and removed 22 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.90 2.26 Search for helices and strands: 0 residues in 0 chains, 5176 seeds are put forward NCS extension: 26 residues added (21 deleted due to clashes), 5202 seeds are put forward Round 1: 466 peptides, 53 chains. Longest chain 27 peptides. Score 0.547 Round 2: 508 peptides, 51 chains. Longest chain 29 peptides. Score 0.604 Round 3: 505 peptides, 52 chains. Longest chain 31 peptides. Score 0.596 Round 4: 516 peptides, 48 chains. Longest chain 33 peptides. Score 0.627 Round 5: 514 peptides, 50 chains. Longest chain 30 peptides. Score 0.615 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 49, Residues 468, Estimated correctness of the model 37.2 % 7 chains (140 residues) have been docked in sequence Sequence coverage is 29 % Consider running further cycles of model building using 2g0t-3_warpNtrace.pdb as input Building loops using Loopy2018 49 chains (468 residues) following loop building 7 chains (140 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17072 reflections ( 99.75 % complete ) and 9121 restraints for refining 5092 atoms. 6726 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2545 (Rfree = 0.000) for 5092 atoms. Found 0 (38 requested) and removed 17 (19 requested) atoms. Cycle 47: After refmac, R = 0.2458 (Rfree = 0.000) for 5050 atoms. Found 0 (38 requested) and removed 13 (19 requested) atoms. Cycle 48: After refmac, R = 0.2426 (Rfree = 0.000) for 5030 atoms. Found 0 (38 requested) and removed 10 (19 requested) atoms. Cycle 49: After refmac, R = 0.2379 (Rfree = 0.000) for 5017 atoms. TimeTaking 170.87