Sun 23 Dec 22:22:43 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 2pbl-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pbl-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pbl-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pbl-3.2-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/2pbl-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pbl-3.2-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 22:22:52 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/2pbl-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pbl-3.2-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 750 and 0 Target number of residues in the AU: 750 Target solvent content: 0.5980 Checking the provided sequence file Detected sequence length: 262 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1048 Adjusted target solvent content: 0.44 Input MTZ file: 2pbl-3.2-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: 4 Cell parameters: 77.197 74.438 95.727 90.000 113.394 90.000 Input sequence file: 2pbl-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 8384 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: 87.858 3.200 Wilson plot Bfac: 51.72 16523 reflections ( 99.29 % complete ) and 0 restraints for refining 9303 atoms. Observations/parameters ratio is 0.44 ------------------------------------------------------ Starting model: R = 0.3409 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4140 (Rfree = 0.000) for 9303 atoms. Found 83 (83 requested) and removed 235 (41 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.92 3.16 Search for helices and strands: 0 residues in 0 chains, 9387 seeds are put forward NCS extension: 0 residues added, 9387 seeds are put forward Round 1: 397 peptides, 79 chains. Longest chain 10 peptides. Score 0.315 Round 2: 488 peptides, 82 chains. Longest chain 15 peptides. Score 0.440 Round 3: 518 peptides, 84 chains. Longest chain 21 peptides. Score 0.471 Round 4: 525 peptides, 78 chains. Longest chain 21 peptides. Score 0.518 Round 5: 547 peptides, 76 chains. Longest chain 21 peptides. Score 0.558 Taking the results from Round 5 Chains 81, Residues 471, Estimated correctness of the model 29.2 % 20 chains (123 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 99.29 % complete ) and 15883 restraints for refining 7653 atoms. 13693 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3429 (Rfree = 0.000) for 7653 atoms. Found 68 (68 requested) and removed 163 (34 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.3252 (Rfree = 0.000) for 7456 atoms. Found 67 (67 requested) and removed 57 (33 requested) atoms. Cycle 3: After refmac, R = 0.3037 (Rfree = 0.000) for 7422 atoms. Found 67 (67 requested) and removed 53 (33 requested) atoms. Cycle 4: After refmac, R = 0.2798 (Rfree = 0.000) for 7413 atoms. Found 66 (66 requested) and removed 44 (33 requested) atoms. Cycle 5: After refmac, R = 0.2711 (Rfree = 0.000) for 7421 atoms. Found 66 (66 requested) and removed 44 (33 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.96 3.21 Search for helices and strands: 0 residues in 0 chains, 7797 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 7818 seeds are put forward Round 1: 561 peptides, 95 chains. Longest chain 22 peptides. Score 0.465 Round 2: 627 peptides, 93 chains. Longest chain 19 peptides. Score 0.565 Round 3: 654 peptides, 82 chains. Longest chain 30 peptides. Score 0.650 Round 4: 672 peptides, 84 chains. Longest chain 28 peptides. Score 0.659 Round 5: 701 peptides, 79 chains. Longest chain 22 peptides. Score 0.708 Taking the results from Round 5 Chains 84, Residues 622, Estimated correctness of the model 66.9 % 19 chains (184 residues) have been docked in sequence Building loops using Loopy2018 84 chains (622 residues) following loop building 19 chains (184 residues) in sequence following loop building ------------------------------------------------------ 16523 reflections ( 99.29 % complete ) and 14963 restraints for refining 7652 atoms. 11942 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3037 (Rfree = 0.000) for 7652 atoms. Found 68 (68 requested) and removed 116 (34 requested) atoms. Cycle 7: After refmac, R = 0.2720 (Rfree = 0.000) for 7536 atoms. Found 67 (67 requested) and removed 53 (34 requested) atoms. Cycle 8: After refmac, R = 0.2566 (Rfree = 0.000) for 7521 atoms. Found 64 (64 requested) and removed 51 (33 requested) atoms. Cycle 9: After refmac, R = 0.2440 (Rfree = 0.000) for 7511 atoms. Found 63 (63 requested) and removed 43 (33 requested) atoms. Cycle 10: After refmac, R = 0.2377 (Rfree = 0.000) for 7515 atoms. Found 62 (62 requested) and removed 36 (33 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.98 3.23 Search for helices and strands: 0 residues in 0 chains, 7851 seeds are put forward NCS extension: 22 residues added (8 deleted due to clashes), 7873 seeds are put forward Round 1: 607 peptides, 86 chains. Longest chain 21 peptides. Score 0.578 Round 2: 677 peptides, 85 chains. Longest chain 27 peptides. Score 0.660 Round 3: 688 peptides, 74 chains. Longest chain 33 peptides. Score 0.717 Round 4: 685 peptides, 80 chains. Longest chain 34 peptides. Score 0.690 Round 5: 656 peptides, 77 chains. Longest chain 26 peptides. Score 0.675 Taking the results from Round 3 Chains 79, Residues 614, Estimated correctness of the model 68.7 % 12 chains (176 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 213 B and 221 B 77 chains (619 residues) following loop building 11 chains (183 residues) in sequence following loop building ------------------------------------------------------ 16523 reflections ( 99.29 % complete ) and 14844 restraints for refining 7654 atoms. 11740 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2722 (Rfree = 0.000) for 7654 atoms. Found 61 (61 requested) and removed 75 (34 requested) atoms. Cycle 12: After refmac, R = 0.2536 (Rfree = 0.000) for 7585 atoms. Found 60 (60 requested) and removed 52 (34 requested) atoms. Cycle 13: After refmac, R = 0.2450 (Rfree = 0.000) for 7570 atoms. Found 58 (58 requested) and removed 40 (34 requested) atoms. Cycle 14: After refmac, R = 0.2386 (Rfree = 0.000) for 7572 atoms. Found 57 (57 requested) and removed 45 (34 requested) atoms. Cycle 15: After refmac, R = 0.2299 (Rfree = 0.000) for 7573 atoms. Found 56 (56 requested) and removed 41 (34 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.00 3.25 Search for helices and strands: 0 residues in 0 chains, 7893 seeds are put forward NCS extension: 21 residues added (64 deleted due to clashes), 7914 seeds are put forward Round 1: 652 peptides, 86 chains. Longest chain 28 peptides. Score 0.629 Round 2: 697 peptides, 80 chains. Longest chain 37 peptides. Score 0.701 Round 3: 712 peptides, 84 chains. Longest chain 29 peptides. Score 0.698 Round 4: 704 peptides, 82 chains. Longest chain 30 peptides. Score 0.699 Round 5: 723 peptides, 80 chains. Longest chain 31 peptides. Score 0.723 Taking the results from Round 5 Chains 84, Residues 643, Estimated correctness of the model 69.9 % 14 chains (183 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 212 B and 221 B 84 chains (650 residues) following loop building 13 chains (191 residues) in sequence following loop building ------------------------------------------------------ 16523 reflections ( 99.29 % complete ) and 14678 restraints for refining 7653 atoms. 11416 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2916 (Rfree = 0.000) for 7653 atoms. Found 54 (54 requested) and removed 87 (34 requested) atoms. Cycle 17: After refmac, R = 0.2698 (Rfree = 0.000) for 7574 atoms. Found 53 (53 requested) and removed 49 (34 requested) atoms. Cycle 18: After refmac, R = 0.2507 (Rfree = 0.000) for 7558 atoms. Found 52 (52 requested) and removed 43 (34 requested) atoms. Cycle 19: After refmac, R = 0.2451 (Rfree = 0.000) for 7560 atoms. Found 50 (50 requested) and removed 39 (33 requested) atoms. Cycle 20: After refmac, R = 0.2378 (Rfree = 0.000) for 7564 atoms. Found 48 (48 requested) and removed 36 (33 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.01 3.26 Search for helices and strands: 0 residues in 0 chains, 7922 seeds are put forward NCS extension: 27 residues added (32 deleted due to clashes), 7949 seeds are put forward Round 1: 584 peptides, 82 chains. Longest chain 26 peptides. Score 0.571 Round 2: 655 peptides, 78 chains. Longest chain 35 peptides. Score 0.670 Round 3: 682 peptides, 85 chains. Longest chain 33 peptides. Score 0.665 Round 4: 672 peptides, 84 chains. Longest chain 28 peptides. Score 0.659 Round 5: 670 peptides, 81 chains. Longest chain 35 peptides. Score 0.671 Taking the results from Round 5 Chains 81, Residues 589, Estimated correctness of the model 58.8 % 13 chains (138 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 99.29 % complete ) and 15613 restraints for refining 7654 atoms. 12839 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2797 (Rfree = 0.000) for 7654 atoms. Found 48 (48 requested) and removed 85 (34 requested) atoms. Cycle 22: After refmac, R = 0.2597 (Rfree = 0.000) for 7580 atoms. Found 48 (48 requested) and removed 41 (34 requested) atoms. Cycle 23: After refmac, R = 0.2571 (Rfree = 0.000) for 7574 atoms. Found 48 (48 requested) and removed 43 (34 requested) atoms. Cycle 24: After refmac, R = 0.2562 (Rfree = 0.000) for 7566 atoms. Found 48 (48 requested) and removed 41 (34 requested) atoms. Cycle 25: After refmac, R = 0.2483 (Rfree = 0.000) for 7565 atoms. Found 47 (47 requested) and removed 41 (33 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.01 3.26 Search for helices and strands: 0 residues in 0 chains, 7862 seeds are put forward NCS extension: 9 residues added (22 deleted due to clashes), 7871 seeds are put forward Round 1: 576 peptides, 81 chains. Longest chain 37 peptides. Score 0.567 Round 2: 621 peptides, 73 chains. Longest chain 38 peptides. Score 0.658 Round 3: 635 peptides, 80 chains. Longest chain 40 peptides. Score 0.640 Round 4: 642 peptides, 80 chains. Longest chain 31 peptides. Score 0.647 Round 5: 642 peptides, 74 chains. Longest chain 34 peptides. Score 0.675 Taking the results from Round 5 Chains 77, Residues 568, Estimated correctness of the model 59.7 % 11 chains (155 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 16523 reflections ( 99.29 % complete ) and 15499 restraints for refining 7654 atoms. 12689 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2791 (Rfree = 0.000) for 7654 atoms. Found 48 (48 requested) and removed 67 (34 requested) atoms. Cycle 27: After refmac, R = 0.2595 (Rfree = 0.000) for 7601 atoms. Found 48 (48 requested) and removed 43 (34 requested) atoms. Cycle 28: After refmac, R = 0.2502 (Rfree = 0.000) for 7596 atoms. Found 48 (48 requested) and removed 38 (34 requested) atoms. Cycle 29: After refmac, R = 0.2429 (Rfree = 0.000) for 7595 atoms. Found 48 (48 requested) and removed 36 (34 requested) atoms. Cycle 30: After refmac, R = 0.2333 (Rfree = 0.000) for 7592 atoms. Found 48 (48 requested) and removed 39 (34 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.98 3.23 Search for helices and strands: 0 residues in 0 chains, 7890 seeds are put forward NCS extension: 8 residues added (18 deleted due to clashes), 7898 seeds are put forward Round 1: 560 peptides, 82 chains. Longest chain 23 peptides. Score 0.541 Round 2: 603 peptides, 71 chains. Longest chain 24 peptides. Score 0.649 Round 3: 604 peptides, 71 chains. Longest chain 42 peptides. Score 0.650 Round 4: 606 peptides, 75 chains. Longest chain 25 peptides. Score 0.633 Round 5: 627 peptides, 74 chains. Longest chain 26 peptides. Score 0.660 Taking the results from Round 5 Chains 77, Residues 553, Estimated correctness of the model 56.2 % 13 chains (145 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 99.29 % complete ) and 15710 restraints for refining 7654 atoms. 13015 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2652 (Rfree = 0.000) for 7654 atoms. Found 48 (48 requested) and removed 62 (34 requested) atoms. Cycle 32: After refmac, R = 0.2519 (Rfree = 0.000) for 7606 atoms. Found 48 (48 requested) and removed 39 (34 requested) atoms. Cycle 33: After refmac, R = 0.2460 (Rfree = 0.000) for 7598 atoms. Found 48 (48 requested) and removed 36 (34 requested) atoms. Cycle 34: After refmac, R = 0.2382 (Rfree = 0.000) for 7598 atoms. Found 48 (48 requested) and removed 37 (34 requested) atoms. Cycle 35: After refmac, R = 0.2341 (Rfree = 0.000) for 7601 atoms. Found 48 (48 requested) and removed 38 (34 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.95 3.20 Search for helices and strands: 0 residues in 0 chains, 7891 seeds are put forward NCS extension: 17 residues added (18 deleted due to clashes), 7908 seeds are put forward Round 1: 586 peptides, 88 chains. Longest chain 21 peptides. Score 0.540 Round 2: 637 peptides, 78 chains. Longest chain 22 peptides. Score 0.651 Round 3: 636 peptides, 80 chains. Longest chain 21 peptides. Score 0.641 Round 4: 632 peptides, 80 chains. Longest chain 26 peptides. Score 0.637 Round 5: 641 peptides, 75 chains. Longest chain 33 peptides. Score 0.669 Taking the results from Round 5 Chains 79, Residues 566, Estimated correctness of the model 58.3 % 15 chains (161 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 99.29 % complete ) and 15471 restraints for refining 7654 atoms. 12714 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2662 (Rfree = 0.000) for 7654 atoms. Found 48 (48 requested) and removed 91 (34 requested) atoms. Cycle 37: After refmac, R = 0.2536 (Rfree = 0.000) for 7581 atoms. Found 48 (48 requested) and removed 42 (34 requested) atoms. Cycle 38: After refmac, R = 0.2360 (Rfree = 0.000) for 7567 atoms. Found 48 (48 requested) and removed 36 (34 requested) atoms. Cycle 39: After refmac, R = 0.2270 (Rfree = 0.000) for 7565 atoms. Found 48 (48 requested) and removed 37 (34 requested) atoms. Cycle 40: After refmac, R = 0.2271 (Rfree = 0.000) for 7564 atoms. Found 47 (47 requested) and removed 35 (33 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.96 3.21 Search for helices and strands: 0 residues in 0 chains, 7868 seeds are put forward NCS extension: 3 residues added (14 deleted due to clashes), 7871 seeds are put forward Round 1: 566 peptides, 85 chains. Longest chain 18 peptides. Score 0.531 Round 2: 595 peptides, 70 chains. Longest chain 26 peptides. Score 0.645 Round 3: 612 peptides, 74 chains. Longest chain 28 peptides. Score 0.644 Round 4: 597 peptides, 78 chains. Longest chain 18 peptides. Score 0.608 Round 5: 628 peptides, 78 chains. Longest chain 28 peptides. Score 0.642 Taking the results from Round 2 Chains 72, Residues 525, Estimated correctness of the model 52.6 % 8 chains (101 residues) have been docked in sequence ------------------------------------------------------ 16523 reflections ( 99.29 % complete ) and 16391 restraints for refining 7654 atoms. 13961 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2497 (Rfree = 0.000) for 7654 atoms. Found 48 (48 requested) and removed 59 (34 requested) atoms. Cycle 42: After refmac, R = 0.2361 (Rfree = 0.000) for 7620 atoms. Found 48 (48 requested) and removed 40 (34 requested) atoms. Cycle 43: After refmac, R = 0.2305 (Rfree = 0.000) for 7618 atoms. Found 48 (48 requested) and removed 41 (34 requested) atoms. Cycle 44: After refmac, R = 0.2242 (Rfree = 0.000) for 7615 atoms. Found 48 (48 requested) and removed 38 (34 requested) atoms. Cycle 45: After refmac, R = 0.2158 (Rfree = 0.000) for 7621 atoms. Found 48 (48 requested) and removed 37 (34 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.98 3.23 Search for helices and strands: 0 residues in 0 chains, 7913 seeds are put forward NCS extension: 15 residues added (5 deleted due to clashes), 7928 seeds are put forward Round 1: 526 peptides, 75 chains. Longest chain 21 peptides. Score 0.536 Round 2: 558 peptides, 74 chains. Longest chain 23 peptides. Score 0.583 Round 3: 576 peptides, 78 chains. Longest chain 25 peptides. Score 0.583 Round 4: 559 peptides, 69 chains. Longest chain 26 peptides. Score 0.610 Round 5: 564 peptides, 77 chains. Longest chain 26 peptides. Score 0.574 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 69, Residues 490, Estimated correctness of the model 43.7 % 8 chains (68 residues) have been docked in sequence Sequence coverage is 13 % Consider running further cycles of model building using 2pbl-3_warpNtrace.pdb as input Building loops using Loopy2018 69 chains (490 residues) following loop building 8 chains (68 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16523 reflections ( 99.29 % complete ) and 17123 restraints for refining 7654 atoms. 15012 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2401 (Rfree = 0.000) for 7654 atoms. Found 0 (48 requested) and removed 34 (34 requested) atoms. Cycle 47: After refmac, R = 0.2359 (Rfree = 0.000) for 7607 atoms. Found 0 (48 requested) and removed 34 (34 requested) atoms. Cycle 48: After refmac, R = 0.2239 (Rfree = 0.000) for 7566 atoms. Found 0 (47 requested) and removed 33 (33 requested) atoms. Cycle 49: After refmac, R = 0.2122 (Rfree = 0.000) for 7529 atoms. TimeTaking 98.82