Mon 24 Dec 07:42:18 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 2f4l-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2f4l-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2f4l-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4l-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/2f4l-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4l-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 07:42:22 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/2f4l-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4l-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 864 and 0 Target number of residues in the AU: 864 Target solvent content: 0.6378 Checking the provided sequence file Detected sequence length: 297 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1188 Adjusted target solvent content: 0.50 Input MTZ file: 2f4l-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: 19 Cell parameters: 80.030 103.980 155.130 90.000 90.000 90.000 Input sequence file: 2f4l-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 9504 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: 86.372 3.400 Wilson plot Bfac: 70.63 18383 reflections ( 99.71 % complete ) and 0 restraints for refining 10521 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3329 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3027 (Rfree = 0.000) for 10521 atoms. Found 79 (79 requested) and removed 116 (39 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.30 3.30 Search for helices and strands: 0 residues in 0 chains, 10585 seeds are put forward NCS extension: 0 residues added, 10585 seeds are put forward Round 1: 516 peptides, 103 chains. Longest chain 15 peptides. Score 0.315 Round 2: 622 peptides, 103 chains. Longest chain 14 peptides. Score 0.447 Round 3: 661 peptides, 97 chains. Longest chain 19 peptides. Score 0.519 Round 4: 711 peptides, 93 chains. Longest chain 20 peptides. Score 0.587 Round 5: 708 peptides, 91 chains. Longest chain 23 peptides. Score 0.593 Taking the results from Round 5 Chains 95, Residues 617, Estimated correctness of the model 26.4 % 9 chains (64 residues) have been docked in sequence ------------------------------------------------------ 18383 reflections ( 99.71 % complete ) and 19016 restraints for refining 8639 atoms. 16456 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2666 (Rfree = 0.000) for 8639 atoms. Found 56 (65 requested) and removed 76 (32 requested) atoms. Cycle 2: After refmac, R = 0.2469 (Rfree = 0.000) for 8489 atoms. Found 40 (65 requested) and removed 53 (32 requested) atoms. Cycle 3: After refmac, R = 0.2350 (Rfree = 0.000) for 8423 atoms. Found 28 (63 requested) and removed 45 (31 requested) atoms. Cycle 4: After refmac, R = 0.2297 (Rfree = 0.000) for 8377 atoms. Found 21 (63 requested) and removed 45 (31 requested) atoms. Cycle 5: After refmac, R = 0.2312 (Rfree = 0.000) for 8333 atoms. Found 25 (63 requested) and removed 38 (31 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.31 3.31 Search for helices and strands: 0 residues in 0 chains, 8463 seeds are put forward NCS extension: 16 residues added (3 deleted due to clashes), 8479 seeds are put forward Round 1: 617 peptides, 101 chains. Longest chain 17 peptides. Score 0.451 Round 2: 702 peptides, 94 chains. Longest chain 30 peptides. Score 0.574 Round 3: 698 peptides, 88 chains. Longest chain 36 peptides. Score 0.596 Round 4: 702 peptides, 93 chains. Longest chain 24 peptides. Score 0.578 Round 5: 695 peptides, 90 chains. Longest chain 22 peptides. Score 0.585 Taking the results from Round 3 Chains 89, Residues 610, Estimated correctness of the model 27.4 % 5 chains (63 residues) have been docked in sequence ------------------------------------------------------ 18383 reflections ( 99.71 % complete ) and 18964 restraints for refining 8640 atoms. 16391 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2518 (Rfree = 0.000) for 8640 atoms. Found 59 (65 requested) and removed 70 (32 requested) atoms. Cycle 7: After refmac, R = 0.2357 (Rfree = 0.000) for 8543 atoms. Found 37 (65 requested) and removed 44 (32 requested) atoms. Cycle 8: After refmac, R = 0.2318 (Rfree = 0.000) for 8483 atoms. Found 39 (64 requested) and removed 44 (32 requested) atoms. Cycle 9: After refmac, R = 0.2239 (Rfree = 0.000) for 8437 atoms. Found 31 (64 requested) and removed 46 (32 requested) atoms. Cycle 10: After refmac, R = 0.2264 (Rfree = 0.000) for 8382 atoms. Found 44 (63 requested) and removed 41 (31 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.34 3.34 Search for helices and strands: 0 residues in 0 chains, 8575 seeds are put forward NCS extension: 63 residues added (15 deleted due to clashes), 8638 seeds are put forward Round 1: 625 peptides, 104 chains. Longest chain 18 peptides. Score 0.445 Round 2: 692 peptides, 94 chains. Longest chain 26 peptides. Score 0.564 Round 3: 693 peptides, 91 chains. Longest chain 24 peptides. Score 0.578 Round 4: 701 peptides, 90 chains. Longest chain 25 peptides. Score 0.590 Round 5: 706 peptides, 87 chains. Longest chain 31 peptides. Score 0.607 Taking the results from Round 5 Chains 88, Residues 619, Estimated correctness of the model 30.9 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 18383 reflections ( 99.71 % complete ) and 19211 restraints for refining 8640 atoms. 16753 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2821 (Rfree = 0.000) for 8640 atoms. Found 65 (65 requested) and removed 70 (32 requested) atoms. Cycle 12: After refmac, R = 0.2496 (Rfree = 0.000) for 8539 atoms. Found 61 (65 requested) and removed 56 (32 requested) atoms. Cycle 13: After refmac, R = 0.2374 (Rfree = 0.000) for 8508 atoms. Found 47 (64 requested) and removed 40 (32 requested) atoms. Cycle 14: After refmac, R = 0.2313 (Rfree = 0.000) for 8479 atoms. Found 41 (64 requested) and removed 34 (32 requested) atoms. Cycle 15: After refmac, R = 0.2281 (Rfree = 0.000) for 8457 atoms. Found 33 (64 requested) and removed 41 (32 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.30 3.30 Search for helices and strands: 0 residues in 0 chains, 8588 seeds are put forward NCS extension: 16 residues added (6 deleted due to clashes), 8604 seeds are put forward Round 1: 583 peptides, 98 chains. Longest chain 19 peptides. Score 0.426 Round 2: 666 peptides, 96 chains. Longest chain 20 peptides. Score 0.529 Round 3: 682 peptides, 92 chains. Longest chain 25 peptides. Score 0.563 Round 4: 705 peptides, 99 chains. Longest chain 28 peptides. Score 0.555 Round 5: 702 peptides, 91 chains. Longest chain 23 peptides. Score 0.587 Taking the results from Round 5 Chains 94, Residues 611, Estimated correctness of the model 24.4 % 9 chains (63 residues) have been docked in sequence ------------------------------------------------------ 18383 reflections ( 99.71 % complete ) and 18843 restraints for refining 8636 atoms. 16292 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2705 (Rfree = 0.000) for 8636 atoms. Found 65 (65 requested) and removed 68 (32 requested) atoms. Cycle 17: After refmac, R = 0.2291 (Rfree = 0.000) for 8569 atoms. Found 43 (65 requested) and removed 44 (32 requested) atoms. Cycle 18: After refmac, R = 0.2224 (Rfree = 0.000) for 8516 atoms. Found 40 (64 requested) and removed 38 (32 requested) atoms. Cycle 19: After refmac, R = 0.2190 (Rfree = 0.000) for 8486 atoms. Found 36 (64 requested) and removed 35 (32 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2311 (Rfree = 0.000) for 8464 atoms. Found 46 (64 requested) and removed 40 (32 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.28 3.28 Search for helices and strands: 0 residues in 0 chains, 8664 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 8681 seeds are put forward Round 1: 583 peptides, 104 chains. Longest chain 11 peptides. Score 0.395 Round 2: 668 peptides, 98 chains. Longest chain 19 peptides. Score 0.522 Round 3: 673 peptides, 94 chains. Longest chain 23 peptides. Score 0.545 Round 4: 652 peptides, 91 chains. Longest chain 29 peptides. Score 0.538 Round 5: 661 peptides, 88 chains. Longest chain 24 peptides. Score 0.560 Taking the results from Round 5 Chains 89, Residues 573, Estimated correctness of the model 15.1 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 18383 reflections ( 99.71 % complete ) and 19327 restraints for refining 8639 atoms. 17042 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2502 (Rfree = 0.000) for 8639 atoms. Found 65 (65 requested) and removed 39 (32 requested) atoms. Cycle 22: After refmac, R = 0.2327 (Rfree = 0.000) for 8589 atoms. Found 51 (65 requested) and removed 39 (32 requested) atoms. Cycle 23: After refmac, R = 0.2173 (Rfree = 0.000) for 8567 atoms. Found 22 (64 requested) and removed 35 (32 requested) atoms. Cycle 24: After refmac, R = 0.2256 (Rfree = 0.000) for 8531 atoms. Found 47 (64 requested) and removed 34 (32 requested) atoms. Cycle 25: After refmac, R = 0.2243 (Rfree = 0.000) for 8525 atoms. Found 43 (64 requested) and removed 41 (32 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.28 3.28 Search for helices and strands: 0 residues in 0 chains, 8644 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 8669 seeds are put forward Round 1: 595 peptides, 104 chains. Longest chain 20 peptides. Score 0.410 Round 2: 597 peptides, 91 chains. Longest chain 20 peptides. Score 0.478 Round 3: 630 peptides, 92 chains. Longest chain 21 peptides. Score 0.510 Round 4: 605 peptides, 89 chains. Longest chain 20 peptides. Score 0.497 Round 5: 655 peptides, 94 chains. Longest chain 17 peptides. Score 0.527 Taking the results from Round 5 Chains 95, Residues 561, Estimated correctness of the model 3.1 % 5 chains (45 residues) have been docked in sequence ------------------------------------------------------ 18383 reflections ( 99.71 % complete ) and 19186 restraints for refining 8638 atoms. 16887 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2573 (Rfree = 0.000) for 8638 atoms. Found 65 (65 requested) and removed 50 (32 requested) atoms. Cycle 27: After refmac, R = 0.2292 (Rfree = 0.000) for 8584 atoms. Found 41 (65 requested) and removed 44 (32 requested) atoms. Cycle 28: After refmac, R = 0.2208 (Rfree = 0.000) for 8545 atoms. Found 21 (64 requested) and removed 37 (32 requested) atoms. Cycle 29: After refmac, R = 0.2232 (Rfree = 0.000) for 8509 atoms. Found 35 (64 requested) and removed 40 (32 requested) atoms. Cycle 30: After refmac, R = 0.2179 (Rfree = 0.000) for 8486 atoms. Found 32 (64 requested) and removed 33 (32 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.27 3.27 Search for helices and strands: 0 residues in 0 chains, 8612 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 8627 seeds are put forward Round 1: 476 peptides, 91 chains. Longest chain 13 peptides. Score 0.329 Round 2: 562 peptides, 90 chains. Longest chain 20 peptides. Score 0.443 Round 3: 588 peptides, 90 chains. Longest chain 19 peptides. Score 0.473 Round 4: 584 peptides, 88 chains. Longest chain 20 peptides. Score 0.478 Round 5: 573 peptides, 87 chains. Longest chain 25 peptides. Score 0.471 Taking the results from Round 4 Chains 90, Residues 496, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 18383 reflections ( 99.71 % complete ) and 19462 restraints for refining 8640 atoms. 17485 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2830 (Rfree = 0.000) for 8640 atoms. Found 65 (65 requested) and removed 68 (32 requested) atoms. Cycle 32: After refmac, R = 0.2651 (Rfree = 0.000) for 8556 atoms. Found 65 (65 requested) and removed 53 (32 requested) atoms. Cycle 33: After refmac, R = 0.2328 (Rfree = 0.000) for 8512 atoms. Found 48 (64 requested) and removed 43 (32 requested) atoms. Cycle 34: After refmac, R = 0.2494 (Rfree = 0.000) for 8473 atoms. Found 64 (64 requested) and removed 41 (32 requested) atoms. Cycle 35: After refmac, R = 0.2705 (Rfree = 0.000) for 8463 atoms. Found 64 (64 requested) and removed 46 (32 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.33 3.33 Search for helices and strands: 0 residues in 0 chains, 8613 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 8635 seeds are put forward Round 1: 421 peptides, 83 chains. Longest chain 10 peptides. Score 0.300 Round 2: 535 peptides, 92 chains. Longest chain 15 peptides. Score 0.399 Round 3: 550 peptides, 81 chains. Longest chain 19 peptides. Score 0.475 Round 4: 550 peptides, 84 chains. Longest chain 22 peptides. Score 0.460 Round 5: 546 peptides, 79 chains. Longest chain 22 peptides. Score 0.480 Taking the results from Round 5 Chains 81, Residues 467, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 18383 reflections ( 99.71 % complete ) and 18847 restraints for refining 8401 atoms. 17003 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2709 (Rfree = 0.000) for 8401 atoms. Found 63 (63 requested) and removed 65 (31 requested) atoms. Cycle 37: After refmac, R = 0.2611 (Rfree = 0.000) for 8336 atoms. Found 63 (63 requested) and removed 62 (31 requested) atoms. Cycle 38: After refmac, R = 0.2820 (Rfree = 0.000) for 8276 atoms. Found 62 (62 requested) and removed 56 (31 requested) atoms. Cycle 39: After refmac, R = 0.2554 (Rfree = 0.000) for 8237 atoms. Found 62 (62 requested) and removed 39 (31 requested) atoms. Cycle 40: After refmac, R = 0.2505 (Rfree = 0.000) for 8223 atoms. Found 62 (62 requested) and removed 43 (31 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 3.35 Search for helices and strands: 0 residues in 0 chains, 8450 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 8471 seeds are put forward Round 1: 403 peptides, 81 chains. Longest chain 13 peptides. Score 0.287 Round 2: 478 peptides, 80 chains. Longest chain 14 peptides. Score 0.393 Round 3: 505 peptides, 77 chains. Longest chain 20 peptides. Score 0.443 Round 4: 536 peptides, 84 chains. Longest chain 17 peptides. Score 0.443 Round 5: 525 peptides, 79 chains. Longest chain 17 peptides. Score 0.456 Taking the results from Round 5 Chains 79, Residues 446, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 18383 reflections ( 99.71 % complete ) and 18728 restraints for refining 8244 atoms. 17023 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2777 (Rfree = 0.000) for 8244 atoms. Found 62 (62 requested) and removed 55 (31 requested) atoms. Cycle 42: After refmac, R = 0.2628 (Rfree = 0.000) for 8187 atoms. Found 62 (62 requested) and removed 49 (31 requested) atoms. Cycle 43: After refmac, R = 0.2548 (Rfree = 0.000) for 8162 atoms. Found 61 (61 requested) and removed 41 (30 requested) atoms. Cycle 44: After refmac, R = 0.2440 (Rfree = 0.000) for 8156 atoms. Found 61 (61 requested) and removed 44 (30 requested) atoms. Cycle 45: After refmac, R = 0.2369 (Rfree = 0.000) for 8153 atoms. Found 61 (61 requested) and removed 30 (30 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.31 3.31 Search for helices and strands: 0 residues in 0 chains, 8367 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 8392 seeds are put forward Round 1: 400 peptides, 85 chains. Longest chain 11 peptides. Score 0.258 Round 2: 480 peptides, 85 chains. Longest chain 24 peptides. Score 0.368 Round 3: 517 peptides, 87 chains. Longest chain 16 peptides. Score 0.404 Round 4: 532 peptides, 77 chains. Longest chain 22 peptides. Score 0.475 Round 5: 488 peptides, 77 chains. Longest chain 16 peptides. Score 0.422 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 78, Residues 455, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence Sequence coverage is 4 % Consider running further cycles of model building using 2f4l-3_warpNtrace.pdb as input Building loops using Loopy2018 78 chains (455 residues) following loop building 3 chains (22 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 18383 reflections ( 99.71 % complete ) and 18291 restraints for refining 8232 atoms. 16475 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2566 (Rfree = 0.000) for 8232 atoms. Found 0 (62 requested) and removed 31 (31 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2437 (Rfree = 0.000) for 8154 atoms. Found 0 (61 requested) and removed 30 (30 requested) atoms. Cycle 48: After refmac, R = 0.2676 (Rfree = 0.000) for 8079 atoms. Found 0 (61 requested) and removed 30 (30 requested) atoms. Cycle 49: After refmac, R = 0.2399 (Rfree = 0.000) for 8019 atoms. TimeTaking 84.23