Mon 24 Dec 00:10:39 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-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2f4l-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2f4l-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4l-3.6-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-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4l-3.6-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 ============================================================ Mon 24 Dec 00:10:44 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-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4l-3.6-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 850 and 0 Target number of residues in the AU: 850 Target solvent content: 0.6436 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-3.6-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-3.6-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 3.600 Wilson plot Bfac: 74.06 15528 reflections ( 99.66 % complete ) and 0 restraints for refining 10581 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.2985 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3008 (Rfree = 0.000) for 10581 atoms. Found 67 (67 requested) and removed 139 (33 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.42 3.42 Search for helices and strands: 0 residues in 0 chains, 10642 seeds are put forward NCS extension: 0 residues added, 10642 seeds are put forward Round 1: 621 peptides, 101 chains. Longest chain 16 peptides. Score 0.456 Round 2: 765 peptides, 91 chains. Longest chain 27 peptides. Score 0.643 Round 3: 816 peptides, 81 chains. Longest chain 41 peptides. Score 0.717 Round 4: 808 peptides, 76 chains. Longest chain 49 peptides. Score 0.728 Round 5: 836 peptides, 75 chains. Longest chain 50 peptides. Score 0.749 Taking the results from Round 5 Chains 93, Residues 761, Estimated correctness of the model 63.6 % 19 chains (188 residues) have been docked in sequence Building loops using Loopy2018 93 chains (761 residues) following loop building 19 chains (188 residues) in sequence following loop building ------------------------------------------------------ 15528 reflections ( 99.66 % complete ) and 16690 restraints for refining 8609 atoms. 13113 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2490 (Rfree = 0.000) for 8609 atoms. Found 41 (55 requested) and removed 89 (27 requested) atoms. Cycle 2: After refmac, R = 0.2411 (Rfree = 0.000) for 8383 atoms. Found 49 (53 requested) and removed 65 (27 requested) atoms. Cycle 3: After refmac, R = 0.2312 (Rfree = 0.000) for 8297 atoms. Found 38 (51 requested) and removed 44 (26 requested) atoms. Cycle 4: After refmac, R = 0.2111 (Rfree = 0.000) for 8226 atoms. Found 16 (50 requested) and removed 45 (26 requested) atoms. Cycle 5: After refmac, R = 0.2204 (Rfree = 0.000) for 8161 atoms. Found 32 (48 requested) and removed 39 (26 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.44 3.44 Search for helices and strands: 0 residues in 0 chains, 8354 seeds are put forward NCS extension: 14 residues added (25 deleted due to clashes), 8368 seeds are put forward Round 1: 746 peptides, 103 chains. Longest chain 25 peptides. Score 0.578 Round 2: 787 peptides, 90 chains. Longest chain 32 peptides. Score 0.665 Round 3: 799 peptides, 86 chains. Longest chain 40 peptides. Score 0.688 Round 4: 838 peptides, 85 chains. Longest chain 46 peptides. Score 0.719 Round 5: 843 peptides, 86 chains. Longest chain 31 peptides. Score 0.719 Taking the results from Round 5 Chains 99, Residues 757, Estimated correctness of the model 55.3 % 10 chains (105 residues) have been docked in sequence Building loops using Loopy2018 99 chains (757 residues) following loop building 9 chains (105 residues) in sequence following loop building ------------------------------------------------------ 15528 reflections ( 99.66 % complete ) and 17847 restraints for refining 8612 atoms. 14543 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2570 (Rfree = 0.000) for 8612 atoms. Found 49 (49 requested) and removed 96 (27 requested) atoms. Cycle 7: After refmac, R = 0.2393 (Rfree = 0.000) for 8439 atoms. Found 37 (48 requested) and removed 52 (27 requested) atoms. Cycle 8: After refmac, R = 0.2253 (Rfree = 0.000) for 8369 atoms. Found 39 (46 requested) and removed 42 (27 requested) atoms. Cycle 9: After refmac, R = 0.2168 (Rfree = 0.000) for 8332 atoms. Found 27 (45 requested) and removed 36 (26 requested) atoms. Cycle 10: After refmac, R = 0.2125 (Rfree = 0.000) for 8297 atoms. Found 30 (43 requested) and removed 32 (26 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.46 3.46 Search for helices and strands: 0 residues in 0 chains, 8449 seeds are put forward NCS extension: 26 residues added (6 deleted due to clashes), 8475 seeds are put forward Round 1: 740 peptides, 101 chains. Longest chain 26 peptides. Score 0.581 Round 2: 778 peptides, 85 chains. Longest chain 51 peptides. Score 0.676 Round 3: 828 peptides, 89 chains. Longest chain 51 peptides. Score 0.699 Round 4: 804 peptides, 90 chains. Longest chain 31 peptides. Score 0.678 Round 5: 822 peptides, 92 chains. Longest chain 32 peptides. Score 0.685 Taking the results from Round 3 Chains 99, Residues 739, Estimated correctness of the model 49.3 % 9 chains (136 residues) have been docked in sequence ------------------------------------------------------ 15528 reflections ( 99.66 % complete ) and 17609 restraints for refining 8614 atoms. 14231 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2530 (Rfree = 0.000) for 8614 atoms. Found 44 (44 requested) and removed 78 (27 requested) atoms. Cycle 12: After refmac, R = 0.2520 (Rfree = 0.000) for 8476 atoms. Found 44 (44 requested) and removed 60 (27 requested) atoms. Cycle 13: After refmac, R = 0.2429 (Rfree = 0.000) for 8405 atoms. Found 43 (43 requested) and removed 35 (27 requested) atoms. Cycle 14: After refmac, R = 0.2377 (Rfree = 0.000) for 8372 atoms. Found 41 (42 requested) and removed 38 (26 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2340 (Rfree = 0.000) for 8344 atoms. Found 42 (42 requested) and removed 34 (26 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.43 3.43 Search for helices and strands: 0 residues in 0 chains, 8524 seeds are put forward NCS extension: 22 residues added (19 deleted due to clashes), 8546 seeds are put forward Round 1: 664 peptides, 100 chains. Longest chain 23 peptides. Score 0.508 Round 2: 747 peptides, 89 chains. Longest chain 39 peptides. Score 0.636 Round 3: 745 peptides, 93 chains. Longest chain 22 peptides. Score 0.618 Round 4: 731 peptides, 89 chains. Longest chain 25 peptides. Score 0.622 Round 5: 762 peptides, 93 chains. Longest chain 29 peptides. Score 0.633 Taking the results from Round 2 Chains 94, Residues 658, Estimated correctness of the model 28.2 % 6 chains (66 residues) have been docked in sequence ------------------------------------------------------ 15528 reflections ( 99.66 % complete ) and 18861 restraints for refining 8604 atoms. 16062 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2630 (Rfree = 0.000) for 8604 atoms. Found 44 (44 requested) and removed 66 (27 requested) atoms. Cycle 17: After refmac, R = 0.2537 (Rfree = 0.000) for 8505 atoms. Found 44 (44 requested) and removed 50 (27 requested) atoms. Cycle 18: After refmac, R = 0.2126 (Rfree = 0.000) for 8456 atoms. Found 22 (43 requested) and removed 35 (27 requested) atoms. Cycle 19: After refmac, R = 0.2068 (Rfree = 0.000) for 8417 atoms. Found 14 (43 requested) and removed 37 (27 requested) atoms. Cycle 20: After refmac, R = 0.2330 (Rfree = 0.000) for 8380 atoms. Found 42 (42 requested) and removed 33 (26 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.46 3.46 Search for helices and strands: 0 residues in 0 chains, 8548 seeds are put forward NCS extension: 18 residues added (4 deleted due to clashes), 8566 seeds are put forward Round 1: 627 peptides, 98 chains. Longest chain 18 peptides. Score 0.477 Round 2: 728 peptides, 86 chains. Longest chain 33 peptides. Score 0.631 Round 3: 698 peptides, 88 chains. Longest chain 25 peptides. Score 0.596 Round 4: 731 peptides, 87 chains. Longest chain 32 peptides. Score 0.630 Round 5: 736 peptides, 88 chains. Longest chain 20 peptides. Score 0.630 Taking the results from Round 2 Chains 90, Residues 642, Estimated correctness of the model 26.4 % 7 chains (130 residues) have been docked in sequence ------------------------------------------------------ 15528 reflections ( 99.66 % complete ) and 18134 restraints for refining 8614 atoms. 15124 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2417 (Rfree = 0.000) for 8614 atoms. Found 41 (44 requested) and removed 52 (27 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2416 (Rfree = 0.000) for 8543 atoms. Found 44 (44 requested) and removed 40 (27 requested) atoms. Cycle 23: After refmac, R = 0.2435 (Rfree = 0.000) for 8511 atoms. Found 43 (43 requested) and removed 43 (27 requested) atoms. Cycle 24: After refmac, R = 0.2494 (Rfree = 0.000) for 8485 atoms. Found 43 (43 requested) and removed 48 (27 requested) atoms. Cycle 25: After refmac, R = 0.2430 (Rfree = 0.000) for 8461 atoms. Found 43 (43 requested) and removed 38 (27 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.44 3.44 Search for helices and strands: 0 residues in 0 chains, 8597 seeds are put forward NCS extension: 19 residues added (6 deleted due to clashes), 8616 seeds are put forward Round 1: 585 peptides, 95 chains. Longest chain 21 peptides. Score 0.444 Round 2: 654 peptides, 84 chains. Longest chain 23 peptides. Score 0.571 Round 3: 687 peptides, 87 chains. Longest chain 22 peptides. Score 0.590 Round 4: 694 peptides, 84 chains. Longest chain 27 peptides. Score 0.609 Round 5: 675 peptides, 88 chains. Longest chain 21 peptides. Score 0.574 Taking the results from Round 4 Chains 87, Residues 610, Estimated correctness of the model 18.1 % 6 chains (69 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 15528 reflections ( 99.66 % complete ) and 18797 restraints for refining 8614 atoms. 16179 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2528 (Rfree = 0.000) for 8614 atoms. Found 44 (44 requested) and removed 44 (27 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2457 (Rfree = 0.000) for 8542 atoms. Found 44 (44 requested) and removed 43 (27 requested) atoms. Cycle 28: After refmac, R = 0.2140 (Rfree = 0.000) for 8489 atoms. Found 26 (43 requested) and removed 32 (27 requested) atoms. Cycle 29: After refmac, R = 0.2062 (Rfree = 0.000) for 8457 atoms. Found 15 (43 requested) and removed 31 (27 requested) atoms. Cycle 30: After refmac, R = 0.2266 (Rfree = 0.000) for 8425 atoms. Found 43 (43 requested) and removed 38 (27 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.43 3.43 Search for helices and strands: 0 residues in 0 chains, 8566 seeds are put forward NCS extension: 21 residues added (8 deleted due to clashes), 8587 seeds are put forward Round 1: 539 peptides, 95 chains. Longest chain 13 peptides. Score 0.388 Round 2: 623 peptides, 101 chains. Longest chain 15 peptides. Score 0.458 Round 3: 635 peptides, 90 chains. Longest chain 20 peptides. Score 0.524 Round 4: 649 peptides, 91 chains. Longest chain 20 peptides. Score 0.534 Round 5: 647 peptides, 89 chains. Longest chain 22 peptides. Score 0.542 Taking the results from Round 5 Chains 90, Residues 558, Estimated correctness of the model 0.0 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 15528 reflections ( 99.66 % complete ) and 19777 restraints for refining 8615 atoms. 17500 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2329 (Rfree = 0.000) for 8615 atoms. Found 44 (44 requested) and removed 48 (27 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2303 (Rfree = 0.000) for 8568 atoms. Found 44 (44 requested) and removed 44 (27 requested) atoms. Cycle 33: After refmac, R = 0.2336 (Rfree = 0.000) for 8533 atoms. Found 43 (43 requested) and removed 57 (27 requested) atoms. Cycle 34: After refmac, R = 0.2287 (Rfree = 0.000) for 8480 atoms. Found 43 (43 requested) and removed 44 (27 requested) atoms. Cycle 35: After refmac, R = 0.2311 (Rfree = 0.000) for 8443 atoms. Found 43 (43 requested) and removed 34 (27 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.40 3.40 Search for helices and strands: 0 residues in 0 chains, 8607 seeds are put forward NCS extension: 13 residues added (5 deleted due to clashes), 8620 seeds are put forward Round 1: 513 peptides, 88 chains. Longest chain 16 peptides. Score 0.394 Round 2: 625 peptides, 98 chains. Longest chain 16 peptides. Score 0.475 Round 3: 603 peptides, 85 chains. Longest chain 22 peptides. Score 0.514 Round 4: 592 peptides, 87 chains. Longest chain 19 peptides. Score 0.492 Round 5: 585 peptides, 86 chains. Longest chain 19 peptides. Score 0.489 Taking the results from Round 3 Chains 88, Residues 518, Estimated correctness of the model 0.0 % 4 chains (42 residues) have been docked in sequence ------------------------------------------------------ 15528 reflections ( 99.66 % complete ) and 19203 restraints for refining 8472 atoms. 17055 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2430 (Rfree = 0.000) for 8472 atoms. Found 43 (43 requested) and removed 54 (27 requested) atoms. Cycle 37: After refmac, R = 0.2212 (Rfree = 0.000) for 8410 atoms. Found 43 (43 requested) and removed 43 (27 requested) atoms. Cycle 38: After refmac, R = 0.2171 (Rfree = 0.000) for 8374 atoms. Found 42 (42 requested) and removed 37 (26 requested) atoms. Cycle 39: After refmac, R = 0.2072 (Rfree = 0.000) for 8366 atoms. Found 42 (42 requested) and removed 29 (26 requested) atoms. Cycle 40: After refmac, R = 0.1992 (Rfree = 0.000) for 8366 atoms. Found 37 (42 requested) and removed 28 (26 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 3.39 Search for helices and strands: 0 residues in 0 chains, 8504 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 8523 seeds are put forward Round 1: 479 peptides, 87 chains. Longest chain 15 peptides. Score 0.355 Round 2: 565 peptides, 86 chains. Longest chain 21 peptides. Score 0.467 Round 3: 548 peptides, 82 chains. Longest chain 19 peptides. Score 0.467 Round 4: 567 peptides, 82 chains. Longest chain 22 peptides. Score 0.489 Round 5: 578 peptides, 80 chains. Longest chain 30 peptides. Score 0.511 Taking the results from Round 5 Chains 80, Residues 498, Estimated correctness of the model 0.0 % 3 chains (37 residues) have been docked in sequence ------------------------------------------------------ 15528 reflections ( 99.66 % complete ) and 19588 restraints for refining 8615 atoms. 17519 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2415 (Rfree = 0.000) for 8615 atoms. Found 44 (44 requested) and removed 49 (27 requested) atoms. Cycle 42: After refmac, R = 0.2336 (Rfree = 0.000) for 8557 atoms. Found 44 (44 requested) and removed 37 (27 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2024 (Rfree = 0.000) for 8536 atoms. Found 19 (43 requested) and removed 33 (27 requested) atoms. Cycle 44: After refmac, R = 0.1910 (Rfree = 0.000) for 8509 atoms. Found 7 (43 requested) and removed 32 (27 requested) atoms. Cycle 45: After refmac, R = 0.1905 (Rfree = 0.000) for 8479 atoms. Found 13 (43 requested) and removed 30 (27 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.39 3.39 Search for helices and strands: 0 residues in 0 chains, 8589 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 8608 seeds are put forward Round 1: 452 peptides, 86 chains. Longest chain 13 peptides. Score 0.325 Round 2: 520 peptides, 90 chains. Longest chain 21 peptides. Score 0.391 Round 3: 499 peptides, 79 chains. Longest chain 12 peptides. Score 0.425 Round 4: 509 peptides, 81 chains. Longest chain 17 peptides. Score 0.426 Round 5: 503 peptides, 80 chains. Longest chain 18 peptides. Score 0.424 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 81, Residues 428, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence Sequence coverage is 1 % Consider running further cycles of model building using 2f4l-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 15528 reflections ( 99.66 % complete ) and 20307 restraints for refining 8613 atoms. 18661 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2376 (Rfree = 0.000) for 8613 atoms. Found 0 (44 requested) and removed 27 (27 requested) atoms. Cycle 47: After refmac, R = 0.2417 (Rfree = 0.000) for 8543 atoms. Found 0 (44 requested) and removed 27 (27 requested) atoms. Cycle 48: After refmac, R = 0.2282 (Rfree = 0.000) for 8495 atoms. Found 0 (43 requested) and removed 27 (27 requested) atoms. Cycle 49: After refmac, R = 0.2241 (Rfree = 0.000) for 8446 atoms. TimeTaking 103.45