null Sun 23 Dec 22:22:46 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 2etj-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2etj-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2etj-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etj-3.4-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/2etj-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etj-3.4-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 22:22:56 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/2etj-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2etj-3.4-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 159 and 0 Target number of residues in the AU: 159 Target solvent content: 0.6363 Checking the provided sequence file Detected sequence length: 250 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 250 Adjusted target solvent content: 0.43 Input MTZ file: 2etj-3.4-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: 144 Cell parameters: 51.821 51.821 76.293 90.000 90.000 120.000 Input sequence file: 2etj-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2000 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 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 Loops will be built when appropriate and at the last cycle Resolution range: 24.534 3.401 Wilson plot Bfac: 69.61 3136 reflections ( 99.71 % complete ) and 0 restraints for refining 2219 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3377 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3447 (Rfree = 0.000) for 2219 atoms. Found 16 (16 requested) and removed 30 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.52 3.87 Search for helices and strands: 0 residues in 0 chains, 2234 seeds are put forward Round 1: 63 peptides, 11 chains. Longest chain 10 peptides. Score 0.331 Round 2: 91 peptides, 15 chains. Longest chain 16 peptides. Score 0.407 Round 3: 88 peptides, 15 chains. Longest chain 11 peptides. Score 0.386 Round 4: 100 peptides, 17 chains. Longest chain 12 peptides. Score 0.409 Round 5: 88 peptides, 13 chains. Longest chain 15 peptides. Score 0.446 Taking the results from Round 5 Chains 14, Residues 75, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 3136 reflections ( 99.71 % complete ) and 4428 restraints for refining 1818 atoms. 4105 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3049 (Rfree = 0.000) for 1818 atoms. Found 5 (13 requested) and removed 41 (6 requested) atoms. Cycle 2: After refmac, R = 0.2811 (Rfree = 0.000) for 1756 atoms. Found 12 (13 requested) and removed 24 (6 requested) atoms. Cycle 3: After refmac, R = 0.2896 (Rfree = 0.000) for 1719 atoms. Found 9 (13 requested) and removed 22 (6 requested) atoms. Cycle 4: After refmac, R = 0.2473 (Rfree = 0.000) for 1695 atoms. Found 5 (12 requested) and removed 13 (6 requested) atoms. Cycle 5: After refmac, R = 0.2792 (Rfree = 0.000) for 1681 atoms. Found 9 (12 requested) and removed 21 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 3.79 Search for helices and strands: 0 residues in 0 chains, 1745 seeds are put forward Round 1: 69 peptides, 15 chains. Longest chain 7 peptides. Score 0.243 Round 2: 98 peptides, 19 chains. Longest chain 8 peptides. Score 0.336 Round 3: 102 peptides, 18 chains. Longest chain 13 peptides. Score 0.393 Round 4: 111 peptides, 20 chains. Longest chain 10 peptides. Score 0.396 Round 5: 121 peptides, 22 chains. Longest chain 15 peptides. Score 0.406 Taking the results from Round 5 Chains 22, Residues 99, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3136 reflections ( 99.71 % complete ) and 3612 restraints for refining 1611 atoms. 3222 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2904 (Rfree = 0.000) for 1611 atoms. Found 9 (12 requested) and removed 32 (6 requested) atoms. Cycle 7: After refmac, R = 0.2640 (Rfree = 0.000) for 1570 atoms. Found 9 (11 requested) and removed 13 (5 requested) atoms. Cycle 8: After refmac, R = 0.2679 (Rfree = 0.000) for 1546 atoms. Found 6 (11 requested) and removed 12 (5 requested) atoms. Cycle 9: After refmac, R = 0.2641 (Rfree = 0.000) for 1528 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 10: After refmac, R = 0.2667 (Rfree = 0.000) for 1518 atoms. Found 9 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.41 3.75 Search for helices and strands: 0 residues in 0 chains, 1604 seeds are put forward Round 1: 92 peptides, 18 chains. Longest chain 9 peptides. Score 0.323 Round 2: 113 peptides, 19 chains. Longest chain 12 peptides. Score 0.437 Round 3: 113 peptides, 20 chains. Longest chain 13 peptides. Score 0.410 Round 4: 115 peptides, 19 chains. Longest chain 14 peptides. Score 0.450 Round 5: 113 peptides, 19 chains. Longest chain 14 peptides. Score 0.437 Taking the results from Round 4 Chains 20, Residues 96, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 3136 reflections ( 99.71 % complete ) and 3417 restraints for refining 1611 atoms. 3021 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2899 (Rfree = 0.000) for 1611 atoms. Found 9 (12 requested) and removed 25 (6 requested) atoms. Cycle 12: After refmac, R = 0.3171 (Rfree = 0.000) for 1579 atoms. Found 12 (12 requested) and removed 28 (6 requested) atoms. Cycle 13: After refmac, R = 0.2666 (Rfree = 0.000) for 1546 atoms. Found 8 (11 requested) and removed 16 (5 requested) atoms. Cycle 14: After refmac, R = 0.2858 (Rfree = 0.000) for 1532 atoms. Found 10 (11 requested) and removed 13 (5 requested) atoms. Cycle 15: After refmac, R = 0.2548 (Rfree = 0.000) for 1523 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.41 3.75 Search for helices and strands: 0 residues in 0 chains, 1625 seeds are put forward Round 1: 88 peptides, 17 chains. Longest chain 9 peptides. Score 0.324 Round 2: 107 peptides, 20 chains. Longest chain 10 peptides. Score 0.369 Round 3: 99 peptides, 18 chains. Longest chain 10 peptides. Score 0.373 Round 4: 104 peptides, 17 chains. Longest chain 10 peptides. Score 0.435 Round 5: 99 peptides, 16 chains. Longest chain 12 peptides. Score 0.431 Taking the results from Round 4 Chains 17, Residues 87, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3136 reflections ( 99.71 % complete ) and 3440 restraints for refining 1563 atoms. 3093 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2844 (Rfree = 0.000) for 1563 atoms. Found 11 (11 requested) and removed 22 (5 requested) atoms. Cycle 17: After refmac, R = 0.2377 (Rfree = 0.000) for 1548 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 18: After refmac, R = 0.2537 (Rfree = 0.000) for 1539 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 19: After refmac, R = 0.2580 (Rfree = 0.000) for 1533 atoms. Found 11 (11 requested) and removed 14 (5 requested) atoms. Cycle 20: After refmac, R = 0.2654 (Rfree = 0.000) for 1522 atoms. Found 11 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.41 3.75 Search for helices and strands: 0 residues in 0 chains, 1611 seeds are put forward Round 1: 84 peptides, 15 chains. Longest chain 10 peptides. Score 0.357 Round 2: 109 peptides, 17 chains. Longest chain 17 peptides. Score 0.467 Round 3: 108 peptides, 18 chains. Longest chain 8 peptides. Score 0.433 Round 4: 110 peptides, 16 chains. Longest chain 17 peptides. Score 0.500 Round 5: 110 peptides, 16 chains. Longest chain 15 peptides. Score 0.500 Taking the results from Round 5 Chains 16, Residues 94, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3136 reflections ( 99.71 % complete ) and 3471 restraints for refining 1601 atoms. 3097 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2584 (Rfree = 0.000) for 1601 atoms. Found 10 (12 requested) and removed 33 (6 requested) atoms. Cycle 22: After refmac, R = 0.2440 (Rfree = 0.000) for 1567 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 23: After refmac, R = 0.2283 (Rfree = 0.000) for 1558 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 24: After refmac, R = 0.2292 (Rfree = 0.000) for 1554 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 25: After refmac, R = 0.2595 (Rfree = 0.000) for 1545 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.48 3.82 Search for helices and strands: 0 residues in 0 chains, 1616 seeds are put forward Round 1: 76 peptides, 17 chains. Longest chain 7 peptides. Score 0.233 Round 2: 100 peptides, 17 chains. Longest chain 10 peptides. Score 0.409 Round 3: 101 peptides, 16 chains. Longest chain 10 peptides. Score 0.444 Round 4: 103 peptides, 16 chains. Longest chain 10 peptides. Score 0.457 Round 5: 99 peptides, 13 chains. Longest chain 17 peptides. Score 0.514 Taking the results from Round 5 Chains 13, Residues 86, Estimated correctness of the model 0.0 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 3136 reflections ( 99.71 % complete ) and 3458 restraints for refining 1638 atoms. 3092 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2516 (Rfree = 0.000) for 1638 atoms. Found 12 (12 requested) and removed 26 (6 requested) atoms. Cycle 27: After refmac, R = 0.2930 (Rfree = 0.000) for 1616 atoms. Found 12 (12 requested) and removed 23 (6 requested) atoms. Cycle 28: After refmac, R = 0.2706 (Rfree = 0.000) for 1597 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 29: After refmac, R = 0.2610 (Rfree = 0.000) for 1583 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 30: After refmac, R = 0.2285 (Rfree = 0.000) for 1576 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.52 3.87 Search for helices and strands: 0 residues in 0 chains, 1634 seeds are put forward Round 1: 80 peptides, 16 chains. Longest chain 10 peptides. Score 0.296 Round 2: 89 peptides, 14 chains. Longest chain 17 peptides. Score 0.423 Round 3: 90 peptides, 16 chains. Longest chain 10 peptides. Score 0.370 Round 4: 81 peptides, 12 chains. Longest chain 16 peptides. Score 0.429 Round 5: 93 peptides, 15 chains. Longest chain 14 peptides. Score 0.420 Taking the results from Round 4 Chains 12, Residues 69, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3136 reflections ( 99.71 % complete ) and 3521 restraints for refining 1609 atoms. 3236 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2692 (Rfree = 0.000) for 1609 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 32: After refmac, R = 0.2411 (Rfree = 0.000) for 1591 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 33: After refmac, R = 0.2668 (Rfree = 0.000) for 1585 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 34: After refmac, R = 0.2690 (Rfree = 0.000) for 1574 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 35: After refmac, R = 0.2696 (Rfree = 0.000) for 1569 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.68 4.04 Search for helices and strands: 0 residues in 0 chains, 1622 seeds are put forward Round 1: 65 peptides, 14 chains. Longest chain 8 peptides. Score 0.244 Round 2: 78 peptides, 15 chains. Longest chain 10 peptides. Score 0.313 Round 3: 82 peptides, 16 chains. Longest chain 9 peptides. Score 0.311 Round 4: 75 peptides, 12 chains. Longest chain 12 peptides. Score 0.387 Round 5: 84 peptides, 14 chains. Longest chain 13 peptides. Score 0.388 Taking the results from Round 5 Chains 14, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3136 reflections ( 99.71 % complete ) and 3415 restraints for refining 1559 atoms. 3149 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2878 (Rfree = 0.000) for 1559 atoms. Found 11 (11 requested) and removed 16 (5 requested) atoms. Cycle 37: After refmac, R = 0.2874 (Rfree = 0.000) for 1545 atoms. Found 11 (11 requested) and removed 15 (5 requested) atoms. Cycle 38: After refmac, R = 0.2456 (Rfree = 0.000) for 1532 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 39: After refmac, R = 0.2343 (Rfree = 0.000) for 1526 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 40: After refmac, R = 0.2351 (Rfree = 0.000) for 1525 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 3.87 Search for helices and strands: 0 residues in 0 chains, 1608 seeds are put forward Round 1: 65 peptides, 13 chains. Longest chain 12 peptides. Score 0.278 Round 2: 70 peptides, 13 chains. Longest chain 11 peptides. Score 0.318 Round 3: 68 peptides, 13 chains. Longest chain 12 peptides. Score 0.302 Round 4: 73 peptides, 13 chains. Longest chain 10 peptides. Score 0.340 Round 5: 67 peptides, 10 chains. Longest chain 14 peptides. Score 0.394 Taking the results from Round 5 Chains 10, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3136 reflections ( 99.71 % complete ) and 3675 restraints for refining 1573 atoms. 3457 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2570 (Rfree = 0.000) for 1573 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 42: After refmac, R = 0.2519 (Rfree = 0.000) for 1560 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 43: After refmac, R = 0.2731 (Rfree = 0.000) for 1556 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. Cycle 44: After refmac, R = 0.2576 (Rfree = 0.000) for 1551 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. Cycle 45: After refmac, R = 0.2649 (Rfree = 0.000) for 1542 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.47 3.81 Search for helices and strands: 0 residues in 0 chains, 1602 seeds are put forward Round 1: 49 peptides, 11 chains. Longest chain 7 peptides. Score 0.214 Round 2: 49 peptides, 9 chains. Longest chain 9 peptides. Score 0.289 Round 3: 62 peptides, 10 chains. Longest chain 12 peptides. Score 0.357 Round 4: 63 peptides, 11 chains. Longest chain 9 peptides. Score 0.331 Round 5: 66 peptides, 11 chains. Longest chain 13 peptides. Score 0.354 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 52, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2etj-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3136 reflections ( 99.71 % complete ) and 3332 restraints for refining 1493 atoms. 3134 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2582 (Rfree = 0.000) for 1493 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2527 (Rfree = 0.000) for 1478 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2817 (Rfree = 0.000) for 1470 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2856 (Rfree = 0.000) for 1462 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:53:24 GMT 2018 Job finished. TimeTaking 30.63 Used memory is bytes: 7878376