Sun 23 Dec 22:22:59 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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pbl-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pbl-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pbl-3.8-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-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pbl-3.8-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 22:23:09 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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pbl-3.8-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 656 and 0 Target number of residues in the AU: 656 Target solvent content: 0.6484 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-3.8-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-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 8384 target number of atoms Had to go as low as 0.75 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 3.800 Wilson plot Bfac: 77.07 9891 reflections ( 98.93 % complete ) and 0 restraints for refining 9269 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3600 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4088 (Rfree = 0.000) for 9269 atoms. Found 50 (50 requested) and removed 71 (25 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.43 3.72 Search for helices and strands: 0 residues in 0 chains, 9475 seeds are put forward NCS extension: 0 residues added, 9475 seeds are put forward Round 1: 285 peptides, 66 chains. Longest chain 8 peptides. Score 0.209 Round 2: 402 peptides, 82 chains. Longest chain 10 peptides. Score 0.302 Round 3: 443 peptides, 80 chains. Longest chain 17 peptides. Score 0.384 Round 4: 474 peptides, 80 chains. Longest chain 13 peptides. Score 0.432 Round 5: 476 peptides, 75 chains. Longest chain 17 peptides. Score 0.467 Taking the results from Round 5 Chains 77, Residues 401, Estimated correctness of the model 0.0 % 13 chains (87 residues) have been docked in sequence ------------------------------------------------------ 9891 reflections ( 98.93 % complete ) and 17109 restraints for refining 7582 atoms. 15331 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3509 (Rfree = 0.000) for 7582 atoms. Found 41 (41 requested) and removed 104 (20 requested) atoms. Cycle 2: After refmac, R = 0.3364 (Rfree = 0.000) for 7334 atoms. Found 41 (41 requested) and removed 53 (20 requested) atoms. Cycle 3: After refmac, R = 0.2598 (Rfree = 0.000) for 7219 atoms. Found 40 (40 requested) and removed 44 (20 requested) atoms. Cycle 4: After refmac, R = 0.2923 (Rfree = 0.000) for 7168 atoms. Found 39 (39 requested) and removed 47 (19 requested) atoms. Cycle 5: After refmac, R = 0.3025 (Rfree = 0.000) for 7126 atoms. Found 39 (39 requested) and removed 53 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.49 3.78 Search for helices and strands: 0 residues in 0 chains, 7429 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 7448 seeds are put forward Round 1: 439 peptides, 82 chains. Longest chain 18 peptides. Score 0.364 Round 2: 508 peptides, 82 chains. Longest chain 18 peptides. Score 0.469 Round 3: 536 peptides, 77 chains. Longest chain 19 peptides. Score 0.538 Round 4: 532 peptides, 76 chains. Longest chain 18 peptides. Score 0.539 Round 5: 538 peptides, 71 chains. Longest chain 22 peptides. Score 0.575 Taking the results from Round 5 Chains 74, Residues 467, Estimated correctness of the model 0.0 % 6 chains (60 residues) have been docked in sequence ------------------------------------------------------ 9891 reflections ( 98.93 % complete ) and 16630 restraints for refining 7457 atoms. 14627 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3123 (Rfree = 0.000) for 7457 atoms. Found 41 (41 requested) and removed 120 (20 requested) atoms. Cycle 7: After refmac, R = 0.2957 (Rfree = 0.000) for 7249 atoms. Found 40 (40 requested) and removed 60 (20 requested) atoms. Cycle 8: After refmac, R = 0.2814 (Rfree = 0.000) for 7153 atoms. Found 39 (39 requested) and removed 44 (19 requested) atoms. Cycle 9: After refmac, R = 0.2812 (Rfree = 0.000) for 7100 atoms. Found 39 (39 requested) and removed 44 (19 requested) atoms. Cycle 10: After refmac, R = 0.2652 (Rfree = 0.000) for 7056 atoms. Found 39 (39 requested) and removed 37 (19 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.46 3.75 Search for helices and strands: 0 residues in 0 chains, 7344 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 7357 seeds are put forward Round 1: 451 peptides, 86 chains. Longest chain 16 peptides. Score 0.356 Round 2: 491 peptides, 77 chains. Longest chain 14 peptides. Score 0.476 Round 3: 487 peptides, 74 chains. Longest chain 20 peptides. Score 0.489 Round 4: 517 peptides, 74 chains. Longest chain 19 peptides. Score 0.530 Round 5: 525 peptides, 75 chains. Longest chain 20 peptides. Score 0.535 Taking the results from Round 5 Chains 79, Residues 450, Estimated correctness of the model 0.0 % 6 chains (50 residues) have been docked in sequence ------------------------------------------------------ 9891 reflections ( 98.93 % complete ) and 16923 restraints for refining 7496 atoms. 15050 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3082 (Rfree = 0.000) for 7496 atoms. Found 41 (41 requested) and removed 78 (20 requested) atoms. Cycle 12: After refmac, R = 0.2982 (Rfree = 0.000) for 7348 atoms. Found 41 (41 requested) and removed 55 (20 requested) atoms. Cycle 13: After refmac, R = 0.2799 (Rfree = 0.000) for 7274 atoms. Found 40 (40 requested) and removed 38 (20 requested) atoms. Cycle 14: After refmac, R = 0.2703 (Rfree = 0.000) for 7241 atoms. Found 40 (40 requested) and removed 41 (20 requested) atoms. Cycle 15: After refmac, R = 0.2651 (Rfree = 0.000) for 7206 atoms. Found 39 (39 requested) and removed 28 (19 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.46 3.75 Search for helices and strands: 0 residues in 0 chains, 7547 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 7566 seeds are put forward Round 1: 431 peptides, 82 chains. Longest chain 11 peptides. Score 0.350 Round 2: 504 peptides, 85 chains. Longest chain 15 peptides. Score 0.445 Round 3: 523 peptides, 84 chains. Longest chain 13 peptides. Score 0.479 Round 4: 535 peptides, 83 chains. Longest chain 15 peptides. Score 0.501 Round 5: 533 peptides, 87 chains. Longest chain 13 peptides. Score 0.474 Taking the results from Round 4 Chains 86, Residues 452, Estimated correctness of the model 0.0 % 10 chains (81 residues) have been docked in sequence ------------------------------------------------------ 9891 reflections ( 98.93 % complete ) and 16589 restraints for refining 7582 atoms. 14602 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2842 (Rfree = 0.000) for 7582 atoms. Found 41 (41 requested) and removed 101 (20 requested) atoms. Cycle 17: After refmac, R = 0.2699 (Rfree = 0.000) for 7418 atoms. Found 41 (41 requested) and removed 48 (20 requested) atoms. Cycle 18: After refmac, R = 0.2643 (Rfree = 0.000) for 7342 atoms. Found 40 (40 requested) and removed 35 (20 requested) atoms. Cycle 19: After refmac, R = 0.2561 (Rfree = 0.000) for 7309 atoms. Found 40 (40 requested) and removed 33 (20 requested) atoms. Cycle 20: After refmac, R = 0.2531 (Rfree = 0.000) for 7287 atoms. Found 40 (40 requested) and removed 35 (20 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.51 3.80 Search for helices and strands: 0 residues in 0 chains, 7577 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 7592 seeds are put forward Round 1: 413 peptides, 81 chains. Longest chain 11 peptides. Score 0.327 Round 2: 470 peptides, 79 chains. Longest chain 17 peptides. Score 0.432 Round 3: 488 peptides, 78 chains. Longest chain 16 peptides. Score 0.466 Round 4: 491 peptides, 77 chains. Longest chain 14 peptides. Score 0.476 Round 5: 493 peptides, 75 chains. Longest chain 17 peptides. Score 0.491 Taking the results from Round 5 Chains 77, Residues 418, Estimated correctness of the model 0.0 % 6 chains (40 residues) have been docked in sequence ------------------------------------------------------ 9891 reflections ( 98.93 % complete ) and 16941 restraints for refining 7549 atoms. 15186 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2827 (Rfree = 0.000) for 7549 atoms. Found 41 (41 requested) and removed 93 (20 requested) atoms. Cycle 22: After refmac, R = 0.2763 (Rfree = 0.000) for 7420 atoms. Found 41 (41 requested) and removed 59 (20 requested) atoms. Cycle 23: After refmac, R = 0.2694 (Rfree = 0.000) for 7333 atoms. Found 40 (40 requested) and removed 40 (20 requested) atoms. Cycle 24: After refmac, R = 0.2622 (Rfree = 0.000) for 7298 atoms. Found 40 (40 requested) and removed 39 (20 requested) atoms. Cycle 25: After refmac, R = 0.2620 (Rfree = 0.000) for 7259 atoms. Found 40 (40 requested) and removed 37 (20 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.49 3.78 Search for helices and strands: 0 residues in 0 chains, 7476 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 7491 seeds are put forward Round 1: 398 peptides, 81 chains. Longest chain 10 peptides. Score 0.302 Round 2: 471 peptides, 75 chains. Longest chain 25 peptides. Score 0.460 Round 3: 439 peptides, 69 chains. Longest chain 13 peptides. Score 0.451 Round 4: 432 peptides, 70 chains. Longest chain 15 peptides. Score 0.434 Round 5: 429 peptides, 65 chains. Longest chain 18 peptides. Score 0.462 Taking the results from Round 5 Chains 65, Residues 364, Estimated correctness of the model 0.0 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 9891 reflections ( 98.93 % complete ) and 17716 restraints for refining 7583 atoms. 16218 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2988 (Rfree = 0.000) for 7583 atoms. Found 41 (41 requested) and removed 85 (20 requested) atoms. Cycle 27: After refmac, R = 0.2949 (Rfree = 0.000) for 7462 atoms. Found 41 (41 requested) and removed 43 (20 requested) atoms. Cycle 28: After refmac, R = 0.2916 (Rfree = 0.000) for 7400 atoms. Found 41 (41 requested) and removed 45 (20 requested) atoms. Cycle 29: After refmac, R = 0.2822 (Rfree = 0.000) for 7347 atoms. Found 40 (40 requested) and removed 32 (20 requested) atoms. Cycle 30: After refmac, R = 0.2835 (Rfree = 0.000) for 7326 atoms. Found 40 (40 requested) and removed 35 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.48 3.77 Search for helices and strands: 0 residues in 0 chains, 7546 seeds are put forward NCS extension: 23 residues added (4 deleted due to clashes), 7569 seeds are put forward Round 1: 327 peptides, 71 chains. Longest chain 10 peptides. Score 0.249 Round 2: 388 peptides, 72 chains. Longest chain 11 peptides. Score 0.349 Round 3: 412 peptides, 70 chains. Longest chain 17 peptides. Score 0.403 Round 4: 409 peptides, 70 chains. Longest chain 13 peptides. Score 0.398 Round 5: 422 peptides, 69 chains. Longest chain 12 peptides. Score 0.425 Taking the results from Round 5 Chains 69, Residues 353, Estimated correctness of the model 0.0 % 4 chains (16 residues) have been docked in sequence ------------------------------------------------------ 9891 reflections ( 98.93 % complete ) and 17030 restraints for refining 7344 atoms. 15639 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2996 (Rfree = 0.000) for 7344 atoms. Found 40 (40 requested) and removed 75 (20 requested) atoms. Cycle 32: After refmac, R = 0.2955 (Rfree = 0.000) for 7224 atoms. Found 40 (40 requested) and removed 48 (20 requested) atoms. Cycle 33: After refmac, R = 0.2908 (Rfree = 0.000) for 7175 atoms. Found 39 (39 requested) and removed 31 (19 requested) atoms. Cycle 34: After refmac, R = 0.2012 (Rfree = 0.000) for 7136 atoms. Found 39 (39 requested) and removed 24 (19 requested) atoms. Cycle 35: After refmac, R = 0.2380 (Rfree = 0.000) for 7136 atoms. Found 39 (39 requested) and removed 33 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.51 3.80 Search for helices and strands: 0 residues in 0 chains, 7347 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 7360 seeds are put forward Round 1: 334 peptides, 71 chains. Longest chain 9 peptides. Score 0.262 Round 2: 406 peptides, 73 chains. Longest chain 15 peptides. Score 0.372 Round 3: 441 peptides, 77 chains. Longest chain 11 peptides. Score 0.401 Round 4: 424 peptides, 73 chains. Longest chain 16 peptides. Score 0.401 Round 5: 415 peptides, 72 chains. Longest chain 15 peptides. Score 0.394 Taking the results from Round 4 Chains 74, Residues 351, Estimated correctness of the model 0.0 % 6 chains (32 residues) have been docked in sequence ------------------------------------------------------ 9891 reflections ( 98.93 % complete ) and 16106 restraints for refining 7134 atoms. 14670 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3015 (Rfree = 0.000) for 7134 atoms. Found 39 (39 requested) and removed 93 (19 requested) atoms. Cycle 37: After refmac, R = 0.2751 (Rfree = 0.000) for 7018 atoms. Found 38 (38 requested) and removed 40 (19 requested) atoms. Cycle 38: After refmac, R = 0.2619 (Rfree = 0.000) for 6979 atoms. Found 38 (38 requested) and removed 38 (19 requested) atoms. Cycle 39: After refmac, R = 0.1859 (Rfree = 0.000) for 6954 atoms. Found 38 (38 requested) and removed 23 (19 requested) atoms. Cycle 40: After refmac, R = 0.1667 (Rfree = 0.000) for 6953 atoms. Found 38 (38 requested) and removed 21 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.49 3.78 Search for helices and strands: 0 residues in 0 chains, 7222 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 7240 seeds are put forward Round 1: 289 peptides, 63 chains. Longest chain 8 peptides. Score 0.240 Round 2: 381 peptides, 68 chains. Longest chain 17 peptides. Score 0.366 Round 3: 383 peptides, 68 chains. Longest chain 13 peptides. Score 0.370 Round 4: 365 peptides, 65 chains. Longest chain 12 peptides. Score 0.361 Round 5: 363 peptides, 62 chains. Longest chain 13 peptides. Score 0.380 Taking the results from Round 5 Chains 62, Residues 301, Estimated correctness of the model 0.0 % 4 chains (13 residues) have been docked in sequence ------------------------------------------------------ 9891 reflections ( 98.93 % complete ) and 16578 restraints for refining 7104 atoms. 15406 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2816 (Rfree = 0.000) for 7104 atoms. Found 39 (39 requested) and removed 56 (19 requested) atoms. Cycle 42: After refmac, R = 0.2727 (Rfree = 0.000) for 7037 atoms. Found 38 (38 requested) and removed 44 (19 requested) atoms. Cycle 43: After refmac, R = 0.2700 (Rfree = 0.000) for 6993 atoms. Found 38 (38 requested) and removed 37 (19 requested) atoms. Cycle 44: After refmac, R = 0.1958 (Rfree = 0.000) for 6967 atoms. Found 38 (38 requested) and removed 24 (19 requested) atoms. Cycle 45: After refmac, R = 0.1685 (Rfree = 0.000) for 6966 atoms. Found 34 (38 requested) and removed 22 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.51 3.80 Search for helices and strands: 0 residues in 0 chains, 7177 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 7189 seeds are put forward Round 1: 261 peptides, 56 chains. Longest chain 11 peptides. Score 0.243 Round 2: 308 peptides, 61 chains. Longest chain 12 peptides. Score 0.292 Round 3: 317 peptides, 57 chains. Longest chain 13 peptides. Score 0.338 Round 4: 322 peptides, 59 chains. Longest chain 15 peptides. Score 0.332 Round 5: 305 peptides, 55 chains. Longest chain 17 peptides. Score 0.333 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 57, Residues 260, Estimated correctness of the model 0.0 % 6 chains (23 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2pbl-3_warpNtrace.pdb as input Building loops using Loopy2018 57 chains (260 residues) following loop building 6 chains (23 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 9891 reflections ( 98.93 % complete ) and 15799 restraints for refining 6906 atoms. 14756 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2712 (Rfree = 0.000) for 6906 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2848 (Rfree = 0.000) for 6844 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.2757 (Rfree = 0.000) for 6798 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.1975 (Rfree = 0.000) for 6752 atoms. TimeTaking 87.67