Mon 24 Dec 00:06:12 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2g0t-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2g0t-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2g0t-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2g0t-3.4-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2g0t-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2g0t-3.4-parrot-mrncs ############### 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 00:06:17 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/mrncs/ArpWArp/wArpResults/WorkingDir/2g0t-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2g0t-3.4-parrot-mrncs/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-mrncs.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-mrncs.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 6264 atoms. Observations/parameters ratio is 0.68 ------------------------------------------------------ Starting model: R = 0.3195 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2537 (Rfree = 0.000) for 6264 atoms. Found 47 (47 requested) and removed 53 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.90 2.26 Search for helices and strands: 0 residues in 0 chains, 6381 seeds are put forward NCS extension: 0 residues added, 6381 seeds are put forward Round 1: 440 peptides, 66 chains. Longest chain 17 peptides. Score 0.441 Round 2: 495 peptides, 66 chains. Longest chain 21 peptides. Score 0.511 Round 3: 517 peptides, 62 chains. Longest chain 21 peptides. Score 0.558 Round 4: 528 peptides, 53 chains. Longest chain 26 peptides. Score 0.615 Round 5: 531 peptides, 54 chains. Longest chain 36 peptides. Score 0.613 Taking the results from Round 4 Chains 59, Residues 475, Estimated correctness of the model 33.5 % 6 chains (68 residues) have been docked in sequence ------------------------------------------------------ 17072 reflections ( 99.75 % complete ) and 10067 restraints for refining 5194 atoms. 7946 conditional restraints added. Observations/parameters ratio is 0.82 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2654 (Rfree = 0.000) for 5194 atoms. Found 39 (39 requested) and removed 34 (19 requested) atoms. Cycle 2: After refmac, R = 0.2478 (Rfree = 0.000) for 5139 atoms. Found 39 (39 requested) and removed 35 (19 requested) atoms. Cycle 3: After refmac, R = 0.2392 (Rfree = 0.000) for 5097 atoms. Found 27 (38 requested) and removed 28 (19 requested) atoms. Cycle 4: After refmac, R = 0.2308 (Rfree = 0.000) for 5071 atoms. Found 21 (38 requested) and removed 28 (19 requested) atoms. Cycle 5: After refmac, R = 0.2268 (Rfree = 0.000) for 5044 atoms. Found 21 (38 requested) and removed 26 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.89 2.25 Search for helices and strands: 0 residues in 0 chains, 5223 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 5246 seeds are put forward Round 1: 491 peptides, 57 chains. Longest chain 26 peptides. Score 0.555 Round 2: 537 peptides, 53 chains. Longest chain 26 peptides. Score 0.624 Round 3: 528 peptides, 54 chains. Longest chain 25 peptides. Score 0.610 Round 4: 552 peptides, 53 chains. Longest chain 28 peptides. Score 0.639 Round 5: 557 peptides, 49 chains. Longest chain 39 peptides. Score 0.661 Taking the results from Round 5 Chains 55, Residues 508, Estimated correctness of the model 47.3 % 11 chains (180 residues) have been docked in sequence ------------------------------------------------------ 17072 reflections ( 99.75 % complete ) and 8638 restraints for refining 5092 atoms. 5936 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2742 (Rfree = 0.000) for 5092 atoms. Found 38 (38 requested) and removed 39 (19 requested) atoms. Cycle 7: After refmac, R = 0.2583 (Rfree = 0.000) for 5057 atoms. Found 38 (38 requested) and removed 27 (19 requested) atoms. Cycle 8: After refmac, R = 0.2504 (Rfree = 0.000) for 5036 atoms. Found 25 (38 requested) and removed 35 (19 requested) atoms. Cycle 9: After refmac, R = 0.2425 (Rfree = 0.000) for 5014 atoms. Found 19 (37 requested) and removed 27 (18 requested) atoms. Cycle 10: After refmac, R = 0.2407 (Rfree = 0.000) for 4995 atoms. Found 17 (37 requested) and removed 30 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.95 2.30 Search for helices and strands: 0 residues in 0 chains, 5146 seeds are put forward NCS extension: 18 residues added (14 deleted due to clashes), 5164 seeds are put forward Round 1: 538 peptides, 54 chains. Longest chain 47 peptides. Score 0.620 Round 2: 559 peptides, 46 chains. Longest chain 49 peptides. Score 0.676 Round 3: 553 peptides, 51 chains. Longest chain 32 peptides. Score 0.649 Round 4: 547 peptides, 46 chains. Longest chain 38 peptides. Score 0.666 Round 5: 563 peptides, 50 chains. Longest chain 36 peptides. Score 0.662 Taking the results from Round 2 Chains 51, Residues 513, Estimated correctness of the model 51.5 % 9 chains (197 residues) have been docked in sequence ------------------------------------------------------ 17072 reflections ( 99.75 % complete ) and 8455 restraints for refining 5091 atoms. 5679 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2712 (Rfree = 0.000) for 5091 atoms. Found 38 (38 requested) and removed 57 (19 requested) atoms. Cycle 12: After refmac, R = 0.2592 (Rfree = 0.000) for 5042 atoms. Found 38 (38 requested) and removed 31 (19 requested) atoms. Cycle 13: After refmac, R = 0.2493 (Rfree = 0.000) for 5031 atoms. Found 23 (38 requested) and removed 31 (19 requested) atoms. Cycle 14: After refmac, R = 0.2449 (Rfree = 0.000) for 5003 atoms. Found 24 (37 requested) and removed 30 (18 requested) atoms. Cycle 15: After refmac, R = 0.2456 (Rfree = 0.000) for 4988 atoms. Found 22 (37 requested) and removed 25 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.95 2.30 Search for helices and strands: 0 residues in 0 chains, 5162 seeds are put forward NCS extension: 28 residues added (21 deleted due to clashes), 5190 seeds are put forward Round 1: 524 peptides, 44 chains. Longest chain 45 peptides. Score 0.653 Round 2: 541 peptides, 43 chains. Longest chain 40 peptides. Score 0.673 Round 3: 538 peptides, 50 chains. Longest chain 47 peptides. Score 0.639 Round 4: 545 peptides, 44 chains. Longest chain 51 peptides. Score 0.673 Round 5: 536 peptides, 49 chains. Longest chain 38 peptides. Score 0.642 Taking the results from Round 4 Chains 50, Residues 501, Estimated correctness of the model 50.7 % 8 chains (189 residues) have been docked in sequence ------------------------------------------------------ 17072 reflections ( 99.75 % complete ) and 8780 restraints for refining 5091 atoms. 6068 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2754 (Rfree = 0.000) for 5091 atoms. Found 38 (38 requested) and removed 53 (19 requested) atoms. Cycle 17: After refmac, R = 0.2580 (Rfree = 0.000) for 5050 atoms. Found 33 (38 requested) and removed 27 (19 requested) atoms. Cycle 18: After refmac, R = 0.2458 (Rfree = 0.000) for 5036 atoms. Found 17 (38 requested) and removed 29 (19 requested) atoms. Cycle 19: After refmac, R = 0.2400 (Rfree = 0.000) for 5013 atoms. Found 11 (37 requested) and removed 24 (18 requested) atoms. Cycle 20: After refmac, R = 0.2353 (Rfree = 0.000) for 4999 atoms. Found 21 (37 requested) and removed 21 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.90 2.26 Search for helices and strands: 0 residues in 0 chains, 5171 seeds are put forward NCS extension: 32 residues added (13 deleted due to clashes), 5203 seeds are put forward Round 1: 515 peptides, 58 chains. Longest chain 31 peptides. Score 0.576 Round 2: 526 peptides, 47 chains. Longest chain 45 peptides. Score 0.641 Round 3: 521 peptides, 48 chains. Longest chain 32 peptides. Score 0.632 Round 4: 543 peptides, 48 chains. Longest chain 30 peptides. Score 0.653 Round 5: 556 peptides, 46 chains. Longest chain 45 peptides. Score 0.674 Taking the results from Round 5 Chains 50, Residues 510, Estimated correctness of the model 50.9 % 8 chains (155 residues) have been docked in sequence ------------------------------------------------------ 17072 reflections ( 99.75 % complete ) and 9095 restraints for refining 5090 atoms. 6502 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2667 (Rfree = 0.000) for 5090 atoms. Found 38 (38 requested) and removed 35 (19 requested) atoms. Cycle 22: After refmac, R = 0.2482 (Rfree = 0.000) for 5069 atoms. Found 38 (38 requested) and removed 33 (19 requested) atoms. Cycle 23: After refmac, R = 0.2360 (Rfree = 0.000) for 5063 atoms. Found 25 (38 requested) and removed 25 (19 requested) atoms. Cycle 24: After refmac, R = 0.2266 (Rfree = 0.000) for 5058 atoms. Found 17 (38 requested) and removed 26 (19 requested) atoms. Cycle 25: After refmac, R = 0.2227 (Rfree = 0.000) for 5045 atoms. Found 14 (38 requested) and removed 21 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.93 2.28 Search for helices and strands: 0 residues in 0 chains, 5191 seeds are put forward NCS extension: 37 residues added (16 deleted due to clashes), 5228 seeds are put forward Round 1: 518 peptides, 60 chains. Longest chain 30 peptides. Score 0.569 Round 2: 543 peptides, 44 chains. Longest chain 32 peptides. Score 0.671 Round 3: 555 peptides, 51 chains. Longest chain 36 peptides. Score 0.650 Round 4: 558 peptides, 45 chains. Longest chain 31 peptides. Score 0.680 Round 5: 552 peptides, 47 chains. Longest chain 33 peptides. Score 0.666 Taking the results from Round 4 Chains 49, Residues 513, Estimated correctness of the model 52.6 % 11 chains (193 residues) have been docked in sequence ------------------------------------------------------ 17072 reflections ( 99.75 % complete ) and 8651 restraints for refining 5091 atoms. 5929 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2675 (Rfree = 0.000) for 5091 atoms. Found 38 (38 requested) and removed 41 (19 requested) atoms. Cycle 27: After refmac, R = 0.2520 (Rfree = 0.000) for 5064 atoms. Found 35 (38 requested) and removed 27 (19 requested) atoms. Cycle 28: After refmac, R = 0.2418 (Rfree = 0.000) for 5058 atoms. Found 25 (38 requested) and removed 27 (19 requested) atoms. Cycle 29: After refmac, R = 0.2366 (Rfree = 0.000) for 5044 atoms. Found 19 (38 requested) and removed 22 (19 requested) atoms. Cycle 30: After refmac, R = 0.2323 (Rfree = 0.000) for 5030 atoms. Found 23 (38 requested) and removed 23 (19 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.94 2.29 Search for helices and strands: 0 residues in 0 chains, 5183 seeds are put forward NCS extension: 25 residues added (11 deleted due to clashes), 5208 seeds are put forward Round 1: 510 peptides, 51 chains. Longest chain 29 peptides. Score 0.606 Round 2: 530 peptides, 49 chains. Longest chain 42 peptides. Score 0.636 Round 3: 547 peptides, 46 chains. Longest chain 34 peptides. Score 0.666 Round 4: 529 peptides, 47 chains. Longest chain 54 peptides. Score 0.644 Round 5: 535 peptides, 45 chains. Longest chain 37 peptides. Score 0.659 Taking the results from Round 3 Chains 50, Residues 501, Estimated correctness of the model 48.7 % 11 chains (211 residues) have been docked in sequence ------------------------------------------------------ 17072 reflections ( 99.75 % complete ) and 8628 restraints for refining 5091 atoms. 5834 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2651 (Rfree = 0.000) for 5091 atoms. Found 38 (38 requested) and removed 33 (19 requested) atoms. Cycle 32: After refmac, R = 0.2490 (Rfree = 0.000) for 5072 atoms. Found 38 (38 requested) and removed 27 (19 requested) atoms. Cycle 33: After refmac, R = 0.2381 (Rfree = 0.000) for 5070 atoms. Found 38 (38 requested) and removed 24 (19 requested) atoms. Cycle 34: After refmac, R = 0.2295 (Rfree = 0.000) for 5073 atoms. Found 22 (38 requested) and removed 23 (19 requested) atoms. Cycle 35: After refmac, R = 0.2250 (Rfree = 0.000) for 5060 atoms. Found 23 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.91 2.26 Search for helices and strands: 0 residues in 0 chains, 5208 seeds are put forward NCS extension: 16 residues added (18 deleted due to clashes), 5224 seeds are put forward Round 1: 511 peptides, 54 chains. Longest chain 30 peptides. Score 0.592 Round 2: 538 peptides, 49 chains. Longest chain 32 peptides. Score 0.643 Round 3: 545 peptides, 49 chains. Longest chain 33 peptides. Score 0.650 Round 4: 547 peptides, 52 chains. Longest chain 33 peptides. Score 0.638 Round 5: 552 peptides, 50 chains. Longest chain 38 peptides. Score 0.652 Taking the results from Round 5 Chains 57, Residues 502, Estimated correctness of the model 44.7 % 12 chains (200 residues) have been docked in sequence ------------------------------------------------------ 17072 reflections ( 99.75 % complete ) and 8578 restraints for refining 5091 atoms. 5853 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2666 (Rfree = 0.000) for 5091 atoms. Found 38 (38 requested) and removed 36 (19 requested) atoms. Cycle 37: After refmac, R = 0.2489 (Rfree = 0.000) for 5066 atoms. Found 38 (38 requested) and removed 27 (19 requested) atoms. Cycle 38: After refmac, R = 0.2396 (Rfree = 0.000) for 5068 atoms. Found 20 (38 requested) and removed 21 (19 requested) atoms. Cycle 39: After refmac, R = 0.2344 (Rfree = 0.000) for 5052 atoms. Found 17 (38 requested) and removed 19 (19 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.2301 (Rfree = 0.000) for 5042 atoms. Found 13 (38 requested) and removed 20 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.97 2.31 Search for helices and strands: 0 residues in 0 chains, 5194 seeds are put forward NCS extension: 37 residues added (16 deleted due to clashes), 5231 seeds are put forward Round 1: 506 peptides, 53 chains. Longest chain 27 peptides. Score 0.592 Round 2: 533 peptides, 44 chains. Longest chain 42 peptides. Score 0.662 Round 3: 518 peptides, 48 chains. Longest chain 38 peptides. Score 0.629 Round 4: 520 peptides, 47 chains. Longest chain 33 peptides. Score 0.635 Round 5: 519 peptides, 43 chains. Longest chain 39 peptides. Score 0.653 Taking the results from Round 2 Chains 47, Residues 489, Estimated correctness of the model 47.6 % 11 chains (179 residues) have been docked in sequence ------------------------------------------------------ 17072 reflections ( 99.75 % complete ) and 8870 restraints for refining 5092 atoms. 6229 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2587 (Rfree = 0.000) for 5092 atoms. Found 38 (38 requested) and removed 38 (19 requested) atoms. Cycle 42: After refmac, R = 0.2431 (Rfree = 0.000) for 5075 atoms. Found 27 (38 requested) and removed 24 (19 requested) atoms. Cycle 43: After refmac, R = 0.2333 (Rfree = 0.000) for 5064 atoms. Found 19 (38 requested) and removed 27 (19 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.2256 (Rfree = 0.000) for 5052 atoms. Found 15 (38 requested) and removed 24 (19 requested) atoms. Cycle 45: After refmac, R = 0.2229 (Rfree = 0.000) for 5039 atoms. Found 13 (38 requested) and removed 19 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.90 2.26 Search for helices and strands: 0 residues in 0 chains, 5150 seeds are put forward NCS extension: 20 residues added (6 deleted due to clashes), 5170 seeds are put forward Round 1: 490 peptides, 55 chains. Longest chain 23 peptides. Score 0.564 Round 2: 522 peptides, 47 chains. Longest chain 30 peptides. Score 0.637 Round 3: 525 peptides, 51 chains. Longest chain 27 peptides. Score 0.621 Round 4: 524 peptides, 46 chains. Longest chain 34 peptides. Score 0.644 Round 5: 542 peptides, 53 chains. Longest chain 32 peptides. Score 0.629 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 53, Residues 478, Estimated correctness of the model 42.4 % 9 chains (190 residues) have been docked in sequence Sequence coverage is 39 % Consider running further cycles of model building using 2g0t-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 213 A and 218 A 51 chains (481 residues) following loop building 8 chains (194 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17072 reflections ( 99.75 % complete ) and 8840 restraints for refining 5092 atoms. 6249 conditional restraints added. Observations/parameters ratio is 0.84 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2529 (Rfree = 0.000) for 5092 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.2413 (Rfree = 0.000) for 5046 atoms. Found 0 (38 requested) and removed 12 (19 requested) atoms. Cycle 48: After refmac, R = 0.2341 (Rfree = 0.000) for 5027 atoms. Found 0 (38 requested) and removed 4 (19 requested) atoms. Cycle 49: After refmac, R = 0.2294 (Rfree = 0.000) for 5022 atoms. Found 0 (37 requested) and removed 2 (18 requested) atoms. Writing output files ... TimeTaking 173.38