null Mon 24 Dec 07:56:14 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 2hx1-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2hx1-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2hx1-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hx1-3.2-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/2hx1-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hx1-3.2-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 07:56:18 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/noncs/ArpWArp/wArpResults/WorkingDir/2hx1-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hx1-3.2-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 896 and 0 Target number of residues in the AU: 896 Target solvent content: 0.5911 Checking the provided sequence file Detected sequence length: 284 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1136 Adjusted target solvent content: 0.48 Input MTZ file: 2hx1-3.2-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: 19 Cell parameters: 65.624 119.462 151.274 90.000 90.000 90.000 Input sequence file: 2hx1-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 9088 target number of atoms Had to go as low as 0.70 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: 93.753 3.200 Wilson plot Bfac: 48.97 20273 reflections ( 99.79 % complete ) and 0 restraints for refining 10151 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.3286 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3049 (Rfree = 0.000) for 10151 atoms. Found 91 (91 requested) and removed 75 (45 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.97 3.05 Search for helices and strands: 0 residues in 0 chains, 10352 seeds are put forward NCS extension: 0 residues added, 10352 seeds are put forward Round 1: 582 peptides, 109 chains. Longest chain 18 peptides. Score 0.381 Round 2: 722 peptides, 112 chains. Longest chain 36 peptides. Score 0.536 Round 3: 775 peptides, 99 chains. Longest chain 32 peptides. Score 0.646 Round 4: 748 peptides, 89 chains. Longest chain 22 peptides. Score 0.661 Round 5: 809 peptides, 99 chains. Longest chain 34 peptides. Score 0.675 Taking the results from Round 5 Chains 100, Residues 710, Estimated correctness of the model 59.7 % 4 chains (59 residues) have been docked in sequence ------------------------------------------------------ 20273 reflections ( 99.79 % complete ) and 17082 restraints for refining 8293 atoms. 14139 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2911 (Rfree = 0.000) for 8293 atoms. Found 74 (74 requested) and removed 68 (37 requested) atoms. Cycle 2: After refmac, R = 0.2714 (Rfree = 0.000) for 8193 atoms. Found 62 (74 requested) and removed 53 (37 requested) atoms. Cycle 3: After refmac, R = 0.2805 (Rfree = 0.000) for 8165 atoms. Found 59 (73 requested) and removed 64 (36 requested) atoms. Cycle 4: After refmac, R = 0.2590 (Rfree = 0.000) for 8136 atoms. Found 43 (73 requested) and removed 46 (36 requested) atoms. Cycle 5: After refmac, R = 0.2560 (Rfree = 0.000) for 8112 atoms. Found 39 (72 requested) and removed 43 (36 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.00 3.08 Search for helices and strands: 0 residues in 0 chains, 8373 seeds are put forward NCS extension: 20 residues added (18 deleted due to clashes), 8393 seeds are put forward Round 1: 724 peptides, 103 chains. Longest chain 25 peptides. Score 0.580 Round 2: 789 peptides, 85 chains. Longest chain 34 peptides. Score 0.709 Round 3: 808 peptides, 87 chains. Longest chain 47 peptides. Score 0.717 Round 4: 791 peptides, 84 chains. Longest chain 25 peptides. Score 0.714 Round 5: 782 peptides, 74 chains. Longest chain 37 peptides. Score 0.742 Taking the results from Round 5 Chains 78, Residues 708, Estimated correctness of the model 73.6 % 5 chains (81 residues) have been docked in sequence Building loops using Loopy2018 78 chains (708 residues) following loop building 5 chains (81 residues) in sequence following loop building ------------------------------------------------------ 20273 reflections ( 99.79 % complete ) and 17142 restraints for refining 8297 atoms. 14082 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2775 (Rfree = 0.000) for 8297 atoms. Found 73 (74 requested) and removed 70 (37 requested) atoms. Cycle 7: After refmac, R = 0.2707 (Rfree = 0.000) for 8249 atoms. Found 46 (73 requested) and removed 98 (37 requested) atoms. Cycle 8: After refmac, R = 0.2560 (Rfree = 0.000) for 8175 atoms. Found 36 (70 requested) and removed 48 (36 requested) atoms. Cycle 9: After refmac, R = 0.2558 (Rfree = 0.000) for 8144 atoms. Found 40 (69 requested) and removed 40 (36 requested) atoms. Cycle 10: After refmac, R = 0.2563 (Rfree = 0.000) for 8133 atoms. Found 41 (67 requested) and removed 43 (36 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.00 3.08 Search for helices and strands: 0 residues in 0 chains, 8353 seeds are put forward NCS extension: 24 residues added (11 deleted due to clashes), 8377 seeds are put forward Round 1: 740 peptides, 95 chains. Longest chain 27 peptides. Score 0.630 Round 2: 808 peptides, 85 chains. Longest chain 33 peptides. Score 0.723 Round 3: 822 peptides, 88 chains. Longest chain 29 peptides. Score 0.723 Round 4: 806 peptides, 79 chains. Longest chain 30 peptides. Score 0.742 Round 5: 780 peptides, 89 chains. Longest chain 21 peptides. Score 0.688 Taking the results from Round 4 Chains 83, Residues 727, Estimated correctness of the model 73.6 % 5 chains (95 residues) have been docked in sequence Building loops using Loopy2018 83 chains (727 residues) following loop building 5 chains (95 residues) in sequence following loop building ------------------------------------------------------ 20273 reflections ( 99.79 % complete ) and 16722 restraints for refining 8297 atoms. 13481 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2971 (Rfree = 0.000) for 8297 atoms. Found 67 (67 requested) and removed 69 (37 requested) atoms. Cycle 12: After refmac, R = 0.2865 (Rfree = 0.000) for 8237 atoms. Found 65 (65 requested) and removed 49 (37 requested) atoms. Cycle 13: After refmac, R = 0.2669 (Rfree = 0.000) for 8222 atoms. Found 61 (64 requested) and removed 48 (37 requested) atoms. Cycle 14: After refmac, R = 0.2582 (Rfree = 0.000) for 8210 atoms. Found 38 (61 requested) and removed 44 (36 requested) atoms. Cycle 15: After refmac, R = 0.2497 (Rfree = 0.000) for 8182 atoms. Found 33 (60 requested) and removed 40 (36 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.00 3.08 Search for helices and strands: 0 residues in 0 chains, 8399 seeds are put forward NCS extension: 16 residues added (12 deleted due to clashes), 8415 seeds are put forward Round 1: 716 peptides, 93 chains. Longest chain 23 peptides. Score 0.616 Round 2: 772 peptides, 82 chains. Longest chain 32 peptides. Score 0.707 Round 3: 777 peptides, 82 chains. Longest chain 26 peptides. Score 0.711 Round 4: 785 peptides, 81 chains. Longest chain 25 peptides. Score 0.720 Round 5: 755 peptides, 85 chains. Longest chain 31 peptides. Score 0.683 Taking the results from Round 4 Chains 88, Residues 704, Estimated correctness of the model 69.3 % 5 chains (72 residues) have been docked in sequence Building loops using Loopy2018 88 chains (704 residues) following loop building 5 chains (72 residues) in sequence following loop building ------------------------------------------------------ 20273 reflections ( 99.79 % complete ) and 17144 restraints for refining 8296 atoms. 14117 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2830 (Rfree = 0.000) for 8296 atoms. Found 59 (59 requested) and removed 61 (37 requested) atoms. Cycle 17: After refmac, R = 0.2553 (Rfree = 0.000) for 8247 atoms. Found 51 (58 requested) and removed 57 (37 requested) atoms. Cycle 18: After refmac, R = 0.2457 (Rfree = 0.000) for 8218 atoms. Found 37 (55 requested) and removed 48 (36 requested) atoms. Cycle 19: After refmac, R = 0.2444 (Rfree = 0.000) for 8186 atoms. Found 53 (54 requested) and removed 38 (36 requested) atoms. Cycle 20: After refmac, R = 0.2382 (Rfree = 0.000) for 8187 atoms. Found 52 (53 requested) and removed 43 (36 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.01 3.09 Search for helices and strands: 0 residues in 0 chains, 8400 seeds are put forward NCS extension: 13 residues added (10 deleted due to clashes), 8413 seeds are put forward Round 1: 691 peptides, 95 chains. Longest chain 20 peptides. Score 0.582 Round 2: 741 peptides, 76 chains. Longest chain 40 peptides. Score 0.705 Round 3: 743 peptides, 80 chains. Longest chain 34 peptides. Score 0.692 Round 4: 740 peptides, 81 chains. Longest chain 22 peptides. Score 0.686 Round 5: 766 peptides, 87 chains. Longest chain 30 peptides. Score 0.684 Taking the results from Round 2 Chains 78, Residues 665, Estimated correctness of the model 66.2 % 4 chains (88 residues) have been docked in sequence Building loops using Loopy2018 78 chains (665 residues) following loop building 4 chains (88 residues) in sequence following loop building ------------------------------------------------------ 20273 reflections ( 99.79 % complete ) and 17263 restraints for refining 8296 atoms. 14349 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2815 (Rfree = 0.000) for 8296 atoms. Found 52 (52 requested) and removed 56 (37 requested) atoms. Cycle 22: After refmac, R = 0.2567 (Rfree = 0.000) for 8261 atoms. Found 50 (50 requested) and removed 46 (37 requested) atoms. Cycle 23: After refmac, R = 0.2484 (Rfree = 0.000) for 8249 atoms. Found 49 (49 requested) and removed 41 (37 requested) atoms. Cycle 24: After refmac, R = 0.2412 (Rfree = 0.000) for 8246 atoms. Found 44 (47 requested) and removed 43 (37 requested) atoms. Cycle 25: After refmac, R = 0.2402 (Rfree = 0.000) for 8234 atoms. Found 46 (46 requested) and removed 44 (37 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.01 3.09 Search for helices and strands: 0 residues in 0 chains, 8445 seeds are put forward NCS extension: 29 residues added (6 deleted due to clashes), 8474 seeds are put forward Round 1: 661 peptides, 94 chains. Longest chain 21 peptides. Score 0.555 Round 2: 737 peptides, 80 chains. Longest chain 25 peptides. Score 0.687 Round 3: 737 peptides, 85 chains. Longest chain 33 peptides. Score 0.668 Round 4: 729 peptides, 83 chains. Longest chain 39 peptides. Score 0.669 Round 5: 735 peptides, 88 chains. Longest chain 25 peptides. Score 0.654 Taking the results from Round 2 Chains 84, Residues 657, Estimated correctness of the model 62.4 % 4 chains (61 residues) have been docked in sequence ------------------------------------------------------ 20273 reflections ( 99.79 % complete ) and 17324 restraints for refining 8294 atoms. 14544 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2519 (Rfree = 0.000) for 8294 atoms. Found 44 (44 requested) and removed 50 (37 requested) atoms. Cycle 27: After refmac, R = 0.2446 (Rfree = 0.000) for 8270 atoms. Found 44 (44 requested) and removed 41 (37 requested) atoms. Cycle 28: After refmac, R = 0.2261 (Rfree = 0.000) for 8256 atoms. Found 39 (44 requested) and removed 40 (37 requested) atoms. Cycle 29: After refmac, R = 0.2179 (Rfree = 0.000) for 8243 atoms. Found 17 (44 requested) and removed 40 (37 requested) atoms. Cycle 30: After refmac, R = 0.2157 (Rfree = 0.000) for 8208 atoms. Found 24 (44 requested) and removed 37 (36 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.03 3.11 Search for helices and strands: 0 residues in 0 chains, 8392 seeds are put forward NCS extension: 12 residues added (10 deleted due to clashes), 8404 seeds are put forward Round 1: 681 peptides, 88 chains. Longest chain 21 peptides. Score 0.604 Round 2: 749 peptides, 81 chains. Longest chain 27 peptides. Score 0.693 Round 3: 761 peptides, 85 chains. Longest chain 33 peptides. Score 0.688 Round 4: 753 peptides, 83 chains. Longest chain 29 peptides. Score 0.689 Round 5: 742 peptides, 86 chains. Longest chain 35 peptides. Score 0.668 Taking the results from Round 2 Chains 88, Residues 668, Estimated correctness of the model 63.7 % 7 chains (90 residues) have been docked in sequence ------------------------------------------------------ 20273 reflections ( 99.79 % complete ) and 16979 restraints for refining 8296 atoms. 14040 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2569 (Rfree = 0.000) for 8296 atoms. Found 44 (44 requested) and removed 52 (37 requested) atoms. Cycle 32: After refmac, R = 0.2515 (Rfree = 0.000) for 8270 atoms. Found 44 (44 requested) and removed 42 (37 requested) atoms. Cycle 33: After refmac, R = 0.2385 (Rfree = 0.000) for 8249 atoms. Found 40 (44 requested) and removed 39 (37 requested) atoms. Cycle 34: After refmac, R = 0.2485 (Rfree = 0.000) for 8240 atoms. Found 44 (44 requested) and removed 41 (37 requested) atoms. Cycle 35: After refmac, R = 0.2233 (Rfree = 0.000) for 8227 atoms. Found 37 (44 requested) and removed 37 (36 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.04 3.12 Search for helices and strands: 0 residues in 0 chains, 8419 seeds are put forward NCS extension: 13 residues added (6 deleted due to clashes), 8432 seeds are put forward Round 1: 645 peptides, 83 chains. Longest chain 23 peptides. Score 0.590 Round 2: 713 peptides, 86 chains. Longest chain 24 peptides. Score 0.643 Round 3: 706 peptides, 85 chains. Longest chain 37 peptides. Score 0.640 Round 4: 712 peptides, 84 chains. Longest chain 45 peptides. Score 0.650 Round 5: 715 peptides, 90 chains. Longest chain 35 peptides. Score 0.628 Taking the results from Round 4 Chains 87, Residues 628, Estimated correctness of the model 53.8 % 4 chains (71 residues) have been docked in sequence ------------------------------------------------------ 20273 reflections ( 99.79 % complete ) and 17382 restraints for refining 8297 atoms. 14649 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2653 (Rfree = 0.000) for 8297 atoms. Found 44 (44 requested) and removed 47 (37 requested) atoms. Cycle 37: After refmac, R = 0.2393 (Rfree = 0.000) for 8265 atoms. Found 44 (44 requested) and removed 38 (37 requested) atoms. Cycle 38: After refmac, R = 0.2419 (Rfree = 0.000) for 8253 atoms. Found 40 (44 requested) and removed 39 (37 requested) atoms. Cycle 39: After refmac, R = 0.2447 (Rfree = 0.000) for 8247 atoms. Found 44 (44 requested) and removed 39 (37 requested) atoms. Cycle 40: After refmac, R = 0.2375 (Rfree = 0.000) for 8235 atoms. Found 44 (44 requested) and removed 40 (37 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.99 3.07 Search for helices and strands: 0 residues in 0 chains, 8453 seeds are put forward NCS extension: 23 residues added (13 deleted due to clashes), 8476 seeds are put forward Round 1: 615 peptides, 94 chains. Longest chain 14 peptides. Score 0.503 Round 2: 675 peptides, 89 chains. Longest chain 32 peptides. Score 0.593 Round 3: 655 peptides, 85 chains. Longest chain 31 peptides. Score 0.591 Round 4: 671 peptides, 79 chains. Longest chain 28 peptides. Score 0.633 Round 5: 657 peptides, 81 chains. Longest chain 31 peptides. Score 0.611 Taking the results from Round 4 Chains 83, Residues 592, Estimated correctness of the model 49.7 % 3 chains (59 residues) have been docked in sequence ------------------------------------------------------ 20273 reflections ( 99.79 % complete ) and 17611 restraints for refining 8297 atoms. 15104 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2552 (Rfree = 0.000) for 8297 atoms. Found 44 (44 requested) and removed 52 (37 requested) atoms. Cycle 42: After refmac, R = 0.2419 (Rfree = 0.000) for 8259 atoms. Found 44 (44 requested) and removed 41 (37 requested) atoms. Cycle 43: After refmac, R = 0.2350 (Rfree = 0.000) for 8247 atoms. Found 44 (44 requested) and removed 39 (37 requested) atoms. Cycle 44: After refmac, R = 0.2349 (Rfree = 0.000) for 8242 atoms. Found 43 (44 requested) and removed 42 (37 requested) atoms. Cycle 45: After refmac, R = 0.2329 (Rfree = 0.000) for 8235 atoms. Found 39 (44 requested) and removed 39 (36 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.96 3.04 Search for helices and strands: 0 residues in 0 chains, 8425 seeds are put forward NCS extension: 16 residues added (9 deleted due to clashes), 8441 seeds are put forward Round 1: 614 peptides, 98 chains. Longest chain 22 peptides. Score 0.482 Round 2: 667 peptides, 90 chains. Longest chain 34 peptides. Score 0.580 Round 3: 651 peptides, 86 chains. Longest chain 35 peptides. Score 0.582 Round 4: 648 peptides, 82 chains. Longest chain 37 peptides. Score 0.598 Round 5: 637 peptides, 83 chains. Longest chain 28 peptides. Score 0.582 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 84, Residues 566, Estimated correctness of the model 40.5 % 3 chains (56 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 2hx1-3_warpNtrace.pdb as input Building loops using Loopy2018 84 chains (566 residues) following loop building 3 chains (56 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 20273 reflections ( 99.79 % complete ) and 17747 restraints for refining 8296 atoms. 15353 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2595 (Rfree = 0.000) for 8296 atoms. Found 0 (44 requested) and removed 37 (37 requested) atoms. Cycle 47: After refmac, R = 0.2441 (Rfree = 0.000) for 8244 atoms. Found 0 (44 requested) and removed 34 (37 requested) atoms. Cycle 48: After refmac, R = 0.2482 (Rfree = 0.000) for 8202 atoms. Found 0 (44 requested) and removed 36 (36 requested) atoms. Cycle 49: After refmac, R = 0.2425 (Rfree = 0.000) for 8157 atoms. Found 0 (44 requested) and removed 36 (36 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:21:07 GMT 2018 Job finished. TimeTaking 84.89 Used memory is bytes: 13925696