Sun 23 Dec 23:42:12 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 2f4l-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2f4l-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2f4l-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4l-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/2f4l-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4l-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 ============================================================ Sun 23 Dec 23:42:17 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/2f4l-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4l-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 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-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: 19 Cell parameters: 80.030 103.980 155.130 90.000 90.000 90.000 Input sequence file: 2f4l-3.4-parrot-mrncs.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 10602 atoms. Observations/parameters ratio is 0.43 ------------------------------------------------------ Starting model: R = 0.2950 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2671 (Rfree = 0.000) for 10602 atoms. Found 80 (80 requested) and removed 88 (40 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.31 3.31 Search for helices and strands: 0 residues in 0 chains, 10698 seeds are put forward NCS extension: 0 residues added, 10698 seeds are put forward Round 1: 669 peptides, 102 chains. Longest chain 25 peptides. Score 0.505 Round 2: 814 peptides, 88 chains. Longest chain 26 peptides. Score 0.692 Round 3: 848 peptides, 83 chains. Longest chain 60 peptides. Score 0.732 Round 4: 861 peptides, 74 chains. Longest chain 48 peptides. Score 0.766 Round 5: 841 peptides, 69 chains. Longest chain 46 peptides. Score 0.769 Taking the results from Round 5 Chains 82, Residues 772, Estimated correctness of the model 73.9 % 13 chains (284 residues) have been docked in sequence Building loops using Loopy2018 82 chains (772 residues) following loop building 13 chains (284 residues) in sequence following loop building ------------------------------------------------------ 18383 reflections ( 99.71 % complete ) and 15741 restraints for refining 8639 atoms. 11657 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2528 (Rfree = 0.000) for 8639 atoms. Found 51 (65 requested) and removed 84 (32 requested) atoms. Cycle 2: After refmac, R = 0.2354 (Rfree = 0.000) for 8449 atoms. Found 26 (63 requested) and removed 54 (32 requested) atoms. Cycle 3: After refmac, R = 0.2303 (Rfree = 0.000) for 8347 atoms. Found 18 (60 requested) and removed 47 (31 requested) atoms. Cycle 4: After refmac, R = 0.2145 (Rfree = 0.000) for 8283 atoms. Found 13 (58 requested) and removed 40 (31 requested) atoms. Cycle 5: After refmac, R = 0.2234 (Rfree = 0.000) for 8240 atoms. Found 20 (57 requested) and removed 49 (31 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.33 3.33 Search for helices and strands: 0 residues in 0 chains, 8360 seeds are put forward NCS extension: 11 residues added (19 deleted due to clashes), 8371 seeds are put forward Round 1: 783 peptides, 89 chains. Longest chain 33 peptides. Score 0.665 Round 2: 822 peptides, 74 chains. Longest chain 39 peptides. Score 0.743 Round 3: 816 peptides, 69 chains. Longest chain 42 peptides. Score 0.754 Round 4: 858 peptides, 73 chains. Longest chain 37 peptides. Score 0.768 Round 5: 863 peptides, 82 chains. Longest chain 40 peptides. Score 0.745 Taking the results from Round 4 Chains 81, Residues 785, Estimated correctness of the model 73.7 % 9 chains (163 residues) have been docked in sequence Building loops using Loopy2018 81 chains (785 residues) following loop building 9 chains (163 residues) in sequence following loop building ------------------------------------------------------ 18383 reflections ( 99.71 % complete ) and 17193 restraints for refining 8641 atoms. 13529 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2562 (Rfree = 0.000) for 8641 atoms. Found 54 (58 requested) and removed 104 (32 requested) atoms. Cycle 7: After refmac, R = 0.2334 (Rfree = 0.000) for 8526 atoms. Found 39 (56 requested) and removed 56 (32 requested) atoms. Cycle 8: After refmac, R = 0.2257 (Rfree = 0.000) for 8480 atoms. Found 34 (55 requested) and removed 47 (32 requested) atoms. Cycle 9: After refmac, R = 0.2277 (Rfree = 0.000) for 8447 atoms. Found 36 (53 requested) and removed 44 (31 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2122 (Rfree = 0.000) for 8425 atoms. Found 21 (52 requested) and removed 41 (31 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.33 3.33 Search for helices and strands: 0 residues in 0 chains, 8562 seeds are put forward NCS extension: 31 residues added (4 deleted due to clashes), 8593 seeds are put forward Round 1: 798 peptides, 92 chains. Longest chain 32 peptides. Score 0.666 Round 2: 851 peptides, 81 chains. Longest chain 35 peptides. Score 0.740 Round 3: 840 peptides, 83 chains. Longest chain 37 peptides. Score 0.727 Round 4: 829 peptides, 85 chains. Longest chain 31 peptides. Score 0.713 Round 5: 808 peptides, 78 chains. Longest chain 35 peptides. Score 0.721 Taking the results from Round 2 Chains 85, Residues 770, Estimated correctness of the model 67.6 % 12 chains (200 residues) have been docked in sequence Building loops using Loopy2018 85 chains (770 residues) following loop building 12 chains (200 residues) in sequence following loop building ------------------------------------------------------ 18383 reflections ( 99.71 % complete ) and 17067 restraints for refining 8641 atoms. 13326 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2410 (Rfree = 0.000) for 8641 atoms. Found 38 (52 requested) and removed 64 (32 requested) atoms. Cycle 12: After refmac, R = 0.2249 (Rfree = 0.000) for 8566 atoms. Found 30 (51 requested) and removed 49 (32 requested) atoms. Cycle 13: After refmac, R = 0.2214 (Rfree = 0.000) for 8528 atoms. Found 14 (49 requested) and removed 44 (32 requested) atoms. Cycle 14: After refmac, R = 0.2187 (Rfree = 0.000) for 8478 atoms. Found 24 (47 requested) and removed 40 (32 requested) atoms. Cycle 15: After refmac, R = 0.2217 (Rfree = 0.000) for 8444 atoms. Found 27 (45 requested) and removed 37 (31 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.33 3.33 Search for helices and strands: 0 residues in 0 chains, 8580 seeds are put forward NCS extension: 8 residues added (18 deleted due to clashes), 8588 seeds are put forward Round 1: 741 peptides, 86 chains. Longest chain 30 peptides. Score 0.642 Round 2: 802 peptides, 81 chains. Longest chain 30 peptides. Score 0.707 Round 3: 803 peptides, 82 chains. Longest chain 32 peptides. Score 0.705 Round 4: 804 peptides, 72 chains. Longest chain 40 peptides. Score 0.738 Round 5: 797 peptides, 78 chains. Longest chain 29 peptides. Score 0.714 Taking the results from Round 4 Chains 80, Residues 732, Estimated correctness of the model 67.1 % 12 chains (220 residues) have been docked in sequence Building loops using Loopy2018 80 chains (732 residues) following loop building 11 chains (220 residues) in sequence following loop building ------------------------------------------------------ 18383 reflections ( 99.71 % complete ) and 17044 restraints for refining 8637 atoms. 13332 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2536 (Rfree = 0.000) for 8637 atoms. Found 45 (45 requested) and removed 82 (32 requested) atoms. Cycle 17: After refmac, R = 0.2505 (Rfree = 0.000) for 8530 atoms. Found 44 (44 requested) and removed 52 (32 requested) atoms. Cycle 18: After refmac, R = 0.2359 (Rfree = 0.000) for 8486 atoms. Found 24 (42 requested) and removed 40 (32 requested) atoms. Cycle 19: After refmac, R = 0.2287 (Rfree = 0.000) for 8449 atoms. Found 20 (40 requested) and removed 42 (31 requested) atoms. Cycle 20: After refmac, R = 0.2241 (Rfree = 0.000) for 8417 atoms. Found 17 (39 requested) and removed 41 (31 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.31 3.31 Search for helices and strands: 0 residues in 0 chains, 8565 seeds are put forward NCS extension: 15 residues added (6 deleted due to clashes), 8580 seeds are put forward Round 1: 691 peptides, 93 chains. Longest chain 21 peptides. Score 0.568 Round 2: 769 peptides, 78 chains. Longest chain 31 peptides. Score 0.694 Round 3: 759 peptides, 83 chains. Longest chain 43 peptides. Score 0.668 Round 4: 749 peptides, 72 chains. Longest chain 43 peptides. Score 0.700 Round 5: 759 peptides, 86 chains. Longest chain 32 peptides. Score 0.657 Taking the results from Round 4 Chains 81, Residues 677, Estimated correctness of the model 57.9 % 13 chains (205 residues) have been docked in sequence ------------------------------------------------------ 18383 reflections ( 99.71 % complete ) and 17468 restraints for refining 8641 atoms. 14091 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2493 (Rfree = 0.000) for 8641 atoms. Found 39 (39 requested) and removed 73 (32 requested) atoms. Cycle 22: After refmac, R = 0.2447 (Rfree = 0.000) for 8549 atoms. Found 31 (38 requested) and removed 43 (32 requested) atoms. Cycle 23: After refmac, R = 0.2404 (Rfree = 0.000) for 8501 atoms. Found 37 (38 requested) and removed 41 (32 requested) atoms. Cycle 24: After refmac, R = 0.2384 (Rfree = 0.000) for 8475 atoms. Found 38 (38 requested) and removed 48 (32 requested) atoms. Cycle 25: After refmac, R = 0.2347 (Rfree = 0.000) for 8436 atoms. Found 31 (38 requested) and removed 39 (31 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.31 3.31 Search for helices and strands: 0 residues in 0 chains, 8563 seeds are put forward NCS extension: 30 residues added (8 deleted due to clashes), 8593 seeds are put forward Round 1: 712 peptides, 92 chains. Longest chain 24 peptides. Score 0.592 Round 2: 780 peptides, 86 chains. Longest chain 27 peptides. Score 0.674 Round 3: 754 peptides, 86 chains. Longest chain 32 peptides. Score 0.653 Round 4: 763 peptides, 90 chains. Longest chain 34 peptides. Score 0.645 Round 5: 757 peptides, 83 chains. Longest chain 44 peptides. Score 0.666 Taking the results from Round 2 Chains 91, Residues 694, Estimated correctness of the model 50.9 % 7 chains (123 residues) have been docked in sequence ------------------------------------------------------ 18383 reflections ( 99.71 % complete ) and 17931 restraints for refining 8604 atoms. 14795 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2340 (Rfree = 0.000) for 8604 atoms. Found 38 (38 requested) and removed 82 (32 requested) atoms. Cycle 27: After refmac, R = 0.2250 (Rfree = 0.000) for 8510 atoms. Found 33 (38 requested) and removed 42 (32 requested) atoms. Cycle 28: After refmac, R = 0.2185 (Rfree = 0.000) for 8481 atoms. Found 22 (38 requested) and removed 34 (32 requested) atoms. Cycle 29: After refmac, R = 0.2175 (Rfree = 0.000) for 8455 atoms. Found 29 (38 requested) and removed 58 (31 requested) atoms. Cycle 30: After refmac, R = 0.2180 (Rfree = 0.000) for 8408 atoms. Found 24 (38 requested) and removed 34 (31 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.32 3.32 Search for helices and strands: 0 residues in 0 chains, 8542 seeds are put forward NCS extension: 13 residues added (6 deleted due to clashes), 8555 seeds are put forward Round 1: 667 peptides, 95 chains. Longest chain 25 peptides. Score 0.535 Round 2: 737 peptides, 81 chains. Longest chain 39 peptides. Score 0.658 Round 3: 769 peptides, 86 chains. Longest chain 29 peptides. Score 0.665 Round 4: 746 peptides, 85 chains. Longest chain 24 peptides. Score 0.650 Round 5: 752 peptides, 83 chains. Longest chain 35 peptides. Score 0.662 Taking the results from Round 3 Chains 93, Residues 683, Estimated correctness of the model 48.4 % 9 chains (132 residues) have been docked in sequence ------------------------------------------------------ 18383 reflections ( 99.71 % complete ) and 17769 restraints for refining 8640 atoms. 14619 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2341 (Rfree = 0.000) for 8640 atoms. Found 39 (39 requested) and removed 48 (32 requested) atoms. Cycle 32: After refmac, R = 0.2201 (Rfree = 0.000) for 8595 atoms. Found 32 (39 requested) and removed 41 (32 requested) atoms. Cycle 33: After refmac, R = 0.2126 (Rfree = 0.000) for 8566 atoms. Found 38 (38 requested) and removed 36 (32 requested) atoms. Cycle 34: After refmac, R = 0.2061 (Rfree = 0.000) for 8555 atoms. Found 27 (38 requested) and removed 40 (32 requested) atoms. Cycle 35: After refmac, R = 0.2045 (Rfree = 0.000) for 8530 atoms. Found 33 (38 requested) and removed 35 (32 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.35 3.35 Search for helices and strands: 0 residues in 0 chains, 8682 seeds are put forward NCS extension: 9 residues added (10 deleted due to clashes), 8691 seeds are put forward Round 1: 640 peptides, 88 chains. Longest chain 24 peptides. Score 0.539 Round 2: 707 peptides, 83 chains. Longest chain 25 peptides. Score 0.625 Round 3: 737 peptides, 83 chains. Longest chain 30 peptides. Score 0.650 Round 4: 729 peptides, 82 chains. Longest chain 34 peptides. Score 0.647 Round 5: 744 peptides, 86 chains. Longest chain 24 peptides. Score 0.645 Taking the results from Round 3 Chains 89, Residues 654, Estimated correctness of the model 44.1 % 9 chains (118 residues) have been docked in sequence ------------------------------------------------------ 18383 reflections ( 99.71 % complete ) and 18044 restraints for refining 8641 atoms. 15099 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2435 (Rfree = 0.000) for 8641 atoms. Found 39 (39 requested) and removed 77 (32 requested) atoms. Cycle 37: After refmac, R = 0.2249 (Rfree = 0.000) for 8576 atoms. Found 38 (38 requested) and removed 36 (32 requested) atoms. Cycle 38: After refmac, R = 0.2214 (Rfree = 0.000) for 8551 atoms. Found 36 (38 requested) and removed 33 (32 requested) atoms. Cycle 39: After refmac, R = 0.2023 (Rfree = 0.000) for 8537 atoms. Found 19 (38 requested) and removed 33 (32 requested) atoms. Cycle 40: After refmac, R = 0.1958 (Rfree = 0.000) for 8511 atoms. Found 18 (38 requested) and removed 38 (32 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 3.33 Search for helices and strands: 0 residues in 0 chains, 8626 seeds are put forward NCS extension: 20 residues added (7 deleted due to clashes), 8646 seeds are put forward Round 1: 594 peptides, 97 chains. Longest chain 18 peptides. Score 0.445 Round 2: 645 peptides, 83 chains. Longest chain 22 peptides. Score 0.567 Round 3: 684 peptides, 81 chains. Longest chain 26 peptides. Score 0.612 Round 4: 664 peptides, 82 chains. Longest chain 23 peptides. Score 0.589 Round 5: 659 peptides, 79 chains. Longest chain 21 peptides. Score 0.598 Taking the results from Round 3 Chains 89, Residues 603, Estimated correctness of the model 32.5 % 6 chains (96 residues) have been docked in sequence ------------------------------------------------------ 18383 reflections ( 99.71 % complete ) and 18363 restraints for refining 8640 atoms. 15666 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2367 (Rfree = 0.000) for 8640 atoms. Found 39 (39 requested) and removed 48 (32 requested) atoms. Cycle 42: After refmac, R = 0.2424 (Rfree = 0.000) for 8598 atoms. Found 39 (39 requested) and removed 39 (32 requested) atoms. Cycle 43: After refmac, R = 0.2257 (Rfree = 0.000) for 8573 atoms. Found 38 (38 requested) and removed 40 (32 requested) atoms. Cycle 44: After refmac, R = 0.2096 (Rfree = 0.000) for 8542 atoms. Found 24 (38 requested) and removed 35 (32 requested) atoms. Cycle 45: After refmac, R = 0.2032 (Rfree = 0.000) for 8515 atoms. Found 23 (38 requested) and removed 36 (32 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.32 3.32 Search for helices and strands: 0 residues in 0 chains, 8601 seeds are put forward NCS extension: 10 residues added (5 deleted due to clashes), 8611 seeds are put forward Round 1: 569 peptides, 91 chains. Longest chain 20 peptides. Score 0.446 Round 2: 627 peptides, 82 chains. Longest chain 26 peptides. Score 0.553 Round 3: 629 peptides, 78 chains. Longest chain 30 peptides. Score 0.573 Round 4: 610 peptides, 80 chains. Longest chain 26 peptides. Score 0.545 Round 5: 606 peptides, 79 chains. Longest chain 26 peptides. Score 0.545 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 80, Residues 551, Estimated correctness of the model 19.6 % 4 chains (77 residues) have been docked in sequence Sequence coverage is 13 % Consider running further cycles of model building using 2f4l-3_warpNtrace.pdb as input Building loops using Loopy2018 80 chains (551 residues) following loop building 4 chains (77 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 18383 reflections ( 99.71 % complete ) and 19004 restraints for refining 8641 atoms. 16594 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2502 (Rfree = 0.000) for 8641 atoms. Found 0 (39 requested) and removed 32 (32 requested) atoms. Cycle 47: After refmac, R = 0.2441 (Rfree = 0.000) for 8582 atoms. Found 0 (39 requested) and removed 32 (32 requested) atoms. Cycle 48: After refmac, R = 0.2420 (Rfree = 0.000) for 8535 atoms. Found 0 (38 requested) and removed 32 (32 requested) atoms. Cycle 49: After refmac, R = 0.2157 (Rfree = 0.000) for 8476 atoms. TimeTaking 110.22