null Sun 23 Dec 22:22:41 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 2f4l-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2f4l-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2f4l-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4l-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/2f4l-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4l-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 22:22:50 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/2f4l-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4l-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 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-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: 19 Cell parameters: 80.030 103.980 155.130 90.000 90.000 90.000 Input sequence file: 2f4l-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 9504 target number of atoms Had to go as low as 0.65 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 10555 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.2942 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2793 (Rfree = 0.000) for 10555 atoms. Found 79 (79 requested) and removed 66 (39 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 3.33 Search for helices and strands: 0 residues in 0 chains, 10716 seeds are put forward NCS extension: 0 residues added, 10716 seeds are put forward Round 1: 642 peptides, 103 chains. Longest chain 22 peptides. Score 0.470 Round 2: 819 peptides, 95 chains. Longest chain 30 peptides. Score 0.672 Round 3: 841 peptides, 82 chains. Longest chain 36 peptides. Score 0.731 Round 4: 851 peptides, 81 chains. Longest chain 40 peptides. Score 0.740 Round 5: 863 peptides, 79 chains. Longest chain 34 peptides. Score 0.753 Taking the results from Round 5 Chains 88, Residues 784, Estimated correctness of the model 70.5 % 13 chains (207 residues) have been docked in sequence Building loops using Loopy2018 88 chains (784 residues) following loop building 13 chains (207 residues) in sequence following loop building ------------------------------------------------------ 18383 reflections ( 99.71 % complete ) and 16395 restraints for refining 8638 atoms. 12562 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2407 (Rfree = 0.000) for 8638 atoms. Found 57 (65 requested) and removed 69 (32 requested) atoms. Cycle 2: After refmac, R = 0.2244 (Rfree = 0.000) for 8445 atoms. Found 23 (64 requested) and removed 44 (32 requested) atoms. Cycle 3: After refmac, R = 0.2202 (Rfree = 0.000) for 8360 atoms. Found 18 (60 requested) and removed 44 (31 requested) atoms. Cycle 4: After refmac, R = 0.2130 (Rfree = 0.000) for 8292 atoms. Found 18 (58 requested) and removed 37 (31 requested) atoms. Cycle 5: After refmac, R = 0.2124 (Rfree = 0.000) for 8246 atoms. Found 19 (57 requested) and removed 40 (31 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.33 3.33 Search for helices and strands: 0 residues in 0 chains, 8401 seeds are put forward NCS extension: 12 residues added (15 deleted due to clashes), 8413 seeds are put forward Round 1: 807 peptides, 94 chains. Longest chain 36 peptides. Score 0.666 Round 2: 852 peptides, 73 chains. Longest chain 35 peptides. Score 0.764 Round 3: 859 peptides, 76 chains. Longest chain 43 peptides. Score 0.760 Round 4: 882 peptides, 72 chains. Longest chain 40 peptides. Score 0.784 Round 5: 866 peptides, 71 chains. Longest chain 38 peptides. Score 0.778 Taking the results from Round 4 Chains 82, Residues 810, Estimated correctness of the model 76.9 % 17 chains (344 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 29 A and 33 A Built loop between residues 276 B and 279 B Built loop between residues 266 D and 277 D 78 chains (815 residues) following loop building 14 chains (359 residues) in sequence following loop building ------------------------------------------------------ 18383 reflections ( 99.71 % complete ) and 15025 restraints for refining 8641 atoms. 10629 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2595 (Rfree = 0.000) for 8641 atoms. Found 58 (58 requested) and removed 186 (32 requested) atoms. Cycle 7: After refmac, R = 0.2370 (Rfree = 0.000) for 8448 atoms. Found 42 (56 requested) and removed 43 (32 requested) atoms. Cycle 8: After refmac, R = 0.2337 (Rfree = 0.000) for 8406 atoms. Found 34 (54 requested) and removed 40 (31 requested) atoms. Cycle 9: After refmac, R = 0.2243 (Rfree = 0.000) for 8377 atoms. Found 22 (53 requested) and removed 41 (31 requested) atoms. Cycle 10: After refmac, R = 0.2251 (Rfree = 0.000) for 8326 atoms. Found 24 (52 requested) and removed 38 (31 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.31 3.31 Search for helices and strands: 0 residues in 0 chains, 8487 seeds are put forward NCS extension: 11 residues added (18 deleted due to clashes), 8498 seeds are put forward Round 1: 775 peptides, 89 chains. Longest chain 31 peptides. Score 0.659 Round 2: 834 peptides, 78 chains. Longest chain 39 peptides. Score 0.738 Round 3: 829 peptides, 75 chains. Longest chain 36 peptides. Score 0.744 Round 4: 811 peptides, 72 chains. Longest chain 36 peptides. Score 0.742 Round 5: 813 peptides, 73 chains. Longest chain 51 peptides. Score 0.740 Taking the results from Round 3 Chains 89, Residues 754, Estimated correctness of the model 68.5 % 12 chains (229 residues) have been docked in sequence Building loops using Loopy2018 89 chains (754 residues) following loop building 12 chains (229 residues) in sequence following loop building ------------------------------------------------------ 18383 reflections ( 99.71 % complete ) and 16764 restraints for refining 8639 atoms. 12968 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2463 (Rfree = 0.000) for 8639 atoms. Found 49 (52 requested) and removed 81 (32 requested) atoms. Cycle 12: After refmac, R = 0.2324 (Rfree = 0.000) for 8565 atoms. Found 27 (50 requested) and removed 55 (32 requested) atoms. Cycle 13: After refmac, R = 0.2212 (Rfree = 0.000) for 8516 atoms. Found 22 (49 requested) and removed 40 (32 requested) atoms. Cycle 14: After refmac, R = 0.2194 (Rfree = 0.000) for 8463 atoms. Found 32 (47 requested) and removed 39 (32 requested) atoms. Cycle 15: After refmac, R = 0.2110 (Rfree = 0.000) for 8431 atoms. Found 23 (45 requested) and removed 39 (31 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 3.35 Search for helices and strands: 0 residues in 0 chains, 8555 seeds are put forward NCS extension: 48 residues added (7 deleted due to clashes), 8603 seeds are put forward Round 1: 738 peptides, 85 chains. Longest chain 35 peptides. Score 0.643 Round 2: 819 peptides, 78 chains. Longest chain 35 peptides. Score 0.729 Round 3: 833 peptides, 79 chains. Longest chain 38 peptides. Score 0.735 Round 4: 827 peptides, 80 chains. Longest chain 31 peptides. Score 0.728 Round 5: 798 peptides, 83 chains. Longest chain 41 peptides. Score 0.698 Taking the results from Round 3 Chains 85, Residues 754, Estimated correctness of the model 66.4 % 13 chains (259 residues) have been docked in sequence Building loops using Loopy2018 85 chains (754 residues) following loop building 13 chains (259 residues) in sequence following loop building ------------------------------------------------------ 18383 reflections ( 99.71 % complete ) and 16150 restraints for refining 8640 atoms. 12206 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2545 (Rfree = 0.000) for 8640 atoms. Found 45 (45 requested) and removed 71 (32 requested) atoms. Cycle 17: After refmac, R = 0.2344 (Rfree = 0.000) for 8552 atoms. Found 33 (44 requested) and removed 51 (32 requested) atoms. Cycle 18: After refmac, R = 0.2347 (Rfree = 0.000) for 8500 atoms. Found 37 (42 requested) and removed 42 (32 requested) atoms. Cycle 19: After refmac, R = 0.2274 (Rfree = 0.000) for 8469 atoms. Found 24 (41 requested) and removed 39 (32 requested) atoms. Cycle 20: After refmac, R = 0.2271 (Rfree = 0.000) for 8421 atoms. Found 32 (39 requested) and removed 38 (31 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.29 3.29 Search for helices and strands: 0 residues in 0 chains, 8544 seeds are put forward NCS extension: 22 residues added (19 deleted due to clashes), 8566 seeds are put forward Round 1: 687 peptides, 95 chains. Longest chain 29 peptides. Score 0.555 Round 2: 749 peptides, 79 chains. Longest chain 58 peptides. Score 0.675 Round 3: 743 peptides, 81 chains. Longest chain 32 peptides. Score 0.663 Round 4: 738 peptides, 74 chains. Longest chain 37 peptides. Score 0.684 Round 5: 788 peptides, 84 chains. Longest chain 31 peptides. Score 0.687 Taking the results from Round 5 Chains 86, Residues 704, Estimated correctness of the model 54.5 % 5 chains (98 residues) have been docked in sequence ------------------------------------------------------ 18383 reflections ( 99.71 % complete ) and 18200 restraints for refining 8641 atoms. 15072 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2619 (Rfree = 0.000) for 8641 atoms. Found 39 (39 requested) and removed 71 (32 requested) atoms. Cycle 22: After refmac, R = 0.2464 (Rfree = 0.000) for 8558 atoms. Found 39 (39 requested) and removed 43 (32 requested) atoms. Cycle 23: After refmac, R = 0.2329 (Rfree = 0.000) for 8527 atoms. Found 38 (38 requested) and removed 42 (32 requested) atoms. Cycle 24: After refmac, R = 0.2302 (Rfree = 0.000) for 8512 atoms. Found 36 (38 requested) and removed 45 (32 requested) atoms. Cycle 25: After refmac, R = 0.2264 (Rfree = 0.000) for 8492 atoms. Found 22 (38 requested) and removed 42 (32 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.34 3.34 Search for helices and strands: 0 residues in 0 chains, 8627 seeds are put forward NCS extension: 9 residues added (7 deleted due to clashes), 8636 seeds are put forward Round 1: 646 peptides, 90 chains. Longest chain 26 peptides. Score 0.536 Round 2: 715 peptides, 86 chains. Longest chain 24 peptides. Score 0.620 Round 3: 719 peptides, 80 chains. Longest chain 39 peptides. Score 0.647 Round 4: 730 peptides, 78 chains. Longest chain 25 peptides. Score 0.663 Round 5: 728 peptides, 84 chains. Longest chain 32 peptides. Score 0.639 Taking the results from Round 4 Chains 85, Residues 652, Estimated correctness of the model 47.9 % 8 chains (124 residues) have been docked in sequence ------------------------------------------------------ 18383 reflections ( 99.71 % complete ) and 18126 restraints for refining 8640 atoms. 15145 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2513 (Rfree = 0.000) for 8640 atoms. Found 39 (39 requested) and removed 59 (32 requested) atoms. Cycle 27: After refmac, R = 0.2387 (Rfree = 0.000) for 8565 atoms. Found 39 (39 requested) and removed 44 (32 requested) atoms. Cycle 28: After refmac, R = 0.2272 (Rfree = 0.000) for 8539 atoms. Found 38 (38 requested) and removed 41 (32 requested) atoms. Cycle 29: After refmac, R = 0.2239 (Rfree = 0.000) for 8513 atoms. Found 38 (38 requested) and removed 40 (32 requested) atoms. Cycle 30: After refmac, R = 0.2205 (Rfree = 0.000) for 8498 atoms. Found 36 (38 requested) and removed 42 (32 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.35 3.35 Search for helices and strands: 0 residues in 0 chains, 8638 seeds are put forward NCS extension: 26 residues added (10 deleted due to clashes), 8664 seeds are put forward Round 1: 646 peptides, 98 chains. Longest chain 23 peptides. Score 0.498 Round 2: 723 peptides, 97 chains. Longest chain 27 peptides. Score 0.582 Round 3: 725 peptides, 87 chains. Longest chain 26 peptides. Score 0.624 Round 4: 713 peptides, 94 chains. Longest chain 24 peptides. Score 0.585 Round 5: 707 peptides, 87 chains. Longest chain 25 peptides. Score 0.608 Taking the results from Round 3 Chains 91, Residues 638, Estimated correctness of the model 36.3 % 7 chains (101 residues) have been docked in sequence ------------------------------------------------------ 18383 reflections ( 99.71 % complete ) and 18265 restraints for refining 8641 atoms. 15368 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2895 (Rfree = 0.000) for 8641 atoms. Found 39 (39 requested) and removed 76 (32 requested) atoms. Cycle 32: After refmac, R = 0.2487 (Rfree = 0.000) for 8537 atoms. Found 38 (38 requested) and removed 44 (32 requested) atoms. Cycle 33: After refmac, R = 0.2417 (Rfree = 0.000) for 8494 atoms. Found 38 (38 requested) and removed 40 (32 requested) atoms. Cycle 34: After refmac, R = 0.2172 (Rfree = 0.000) for 8475 atoms. Found 26 (38 requested) and removed 33 (32 requested) atoms. Cycle 35: After refmac, R = 0.2130 (Rfree = 0.000) for 8455 atoms. Found 21 (38 requested) and removed 36 (31 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.35 3.35 Search for helices and strands: 0 residues in 0 chains, 8550 seeds are put forward NCS extension: 23 residues added (5 deleted due to clashes), 8573 seeds are put forward Round 1: 620 peptides, 91 chains. Longest chain 26 peptides. Score 0.504 Round 2: 678 peptides, 87 chains. Longest chain 28 peptides. Score 0.581 Round 3: 661 peptides, 83 chains. Longest chain 25 peptides. Score 0.582 Round 4: 660 peptides, 75 chains. Longest chain 26 peptides. Score 0.615 Round 5: 661 peptides, 80 chains. Longest chain 29 peptides. Score 0.595 Taking the results from Round 4 Chains 78, Residues 585, Estimated correctness of the model 33.5 % 8 chains (118 residues) have been docked in sequence ------------------------------------------------------ 18383 reflections ( 99.71 % complete ) and 18619 restraints for refining 8641 atoms. 15888 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2852 (Rfree = 0.000) for 8641 atoms. Found 39 (39 requested) and removed 66 (32 requested) atoms. Cycle 37: After refmac, R = 0.2496 (Rfree = 0.000) for 8543 atoms. Found 39 (39 requested) and removed 48 (32 requested) atoms. Cycle 38: After refmac, R = 0.2361 (Rfree = 0.000) for 8493 atoms. Found 38 (38 requested) and removed 36 (32 requested) atoms. Cycle 39: After refmac, R = 0.2333 (Rfree = 0.000) for 8474 atoms. Found 38 (38 requested) and removed 38 (32 requested) atoms. Cycle 40: After refmac, R = 0.2217 (Rfree = 0.000) for 8467 atoms. Found 33 (38 requested) and removed 35 (31 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 3.33 Search for helices and strands: 0 residues in 0 chains, 8598 seeds are put forward NCS extension: 12 residues added (9 deleted due to clashes), 8610 seeds are put forward Round 1: 574 peptides, 91 chains. Longest chain 22 peptides. Score 0.452 Round 2: 635 peptides, 88 chains. Longest chain 26 peptides. Score 0.534 Round 3: 623 peptides, 80 chains. Longest chain 27 peptides. Score 0.558 Round 4: 660 peptides, 81 chains. Longest chain 27 peptides. Score 0.590 Round 5: 660 peptides, 80 chains. Longest chain 30 peptides. Score 0.594 Taking the results from Round 5 Chains 85, Residues 580, Estimated correctness of the model 26.7 % 6 chains (76 residues) have been docked in sequence ------------------------------------------------------ 18383 reflections ( 99.71 % complete ) and 18795 restraints for refining 8640 atoms. 16248 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2458 (Rfree = 0.000) for 8640 atoms. Found 39 (39 requested) and removed 52 (32 requested) atoms. Cycle 42: After refmac, R = 0.2270 (Rfree = 0.000) for 8595 atoms. Found 39 (39 requested) and removed 38 (32 requested) atoms. Cycle 43: After refmac, R = 0.2258 (Rfree = 0.000) for 8583 atoms. Found 38 (38 requested) and removed 41 (32 requested) atoms. Cycle 44: After refmac, R = 0.2199 (Rfree = 0.000) for 8561 atoms. Found 38 (38 requested) and removed 37 (32 requested) atoms. Cycle 45: After refmac, R = 0.2174 (Rfree = 0.000) for 8551 atoms. Found 38 (38 requested) and removed 33 (32 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.32 3.32 Search for helices and strands: 0 residues in 0 chains, 8685 seeds are put forward NCS extension: 8 residues added (7 deleted due to clashes), 8693 seeds are put forward Round 1: 543 peptides, 87 chains. Longest chain 17 peptides. Score 0.436 Round 2: 598 peptides, 80 chains. Longest chain 22 peptides. Score 0.532 Round 3: 598 peptides, 75 chains. Longest chain 24 peptides. Score 0.556 Round 4: 606 peptides, 79 chains. Longest chain 26 peptides. Score 0.545 Round 5: 632 peptides, 78 chains. Longest chain 22 peptides. Score 0.576 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 82, Residues 554, Estimated correctness of the model 20.7 % 5 chains (58 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 2f4l-3_warpNtrace.pdb as input Building loops using Loopy2018 82 chains (554 residues) following loop building 5 chains (58 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 18383 reflections ( 99.71 % complete ) and 18957 restraints for refining 8641 atoms. 16594 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2458 (Rfree = 0.000) for 8641 atoms. Found 0 (39 requested) and removed 32 (32 requested) atoms. Cycle 47: After refmac, R = 0.2265 (Rfree = 0.000) for 8571 atoms. Found 0 (39 requested) and removed 32 (32 requested) atoms. Cycle 48: After refmac, R = 0.2194 (Rfree = 0.000) for 8517 atoms. Found 0 (38 requested) and removed 32 (32 requested) atoms. Cycle 49: After refmac, R = 0.2190 (Rfree = 0.000) for 8472 atoms. Found 0 (38 requested) and removed 32 (32 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:16:01 GMT 2018 Job finished. TimeTaking 113.34 Used memory is bytes: 22101848