Mon 24 Dec 00:19:50 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 2g0t-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2g0t-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2g0t-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2g0t-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/2g0t-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2g0t-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 00:19:54 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/2g0t-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2g0t-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 897 and 0 Target number of residues in the AU: 897 Target solvent content: 0.5857 Checking the provided sequence file Detected sequence length: 350 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 700 Adjusted target solvent content: 0.68 Input MTZ file: 2g0t-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: 213 Cell parameters: 191.568 191.568 191.568 90.000 90.000 90.000 Input sequence file: 2g0t-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5600 target number of atoms Had to go as low as 0.95 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: 29.560 3.601 Wilson plot Bfac: 47.03 14436 reflections ( 99.70 % complete ) and 0 restraints for refining 6205 atoms. Observations/parameters ratio is 0.58 ------------------------------------------------------ Starting model: R = 0.3208 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3137 (Rfree = 0.000) for 6205 atoms. Found 39 (39 requested) and removed 60 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.07 2.39 Search for helices and strands: 0 residues in 0 chains, 6356 seeds are put forward NCS extension: 0 residues added, 6356 seeds are put forward Round 1: 438 peptides, 69 chains. Longest chain 19 peptides. Score 0.421 Round 2: 470 peptides, 61 chains. Longest chain 30 peptides. Score 0.508 Round 3: 510 peptides, 53 chains. Longest chain 36 peptides. Score 0.596 Round 4: 493 peptides, 52 chains. Longest chain 33 peptides. Score 0.583 Round 5: 502 peptides, 56 chains. Longest chain 34 peptides. Score 0.572 Taking the results from Round 3 Chains 62, Residues 457, Estimated correctness of the model 13.0 % 9 chains (131 residues) have been docked in sequence ------------------------------------------------------ 14436 reflections ( 99.70 % complete ) and 9389 restraints for refining 5119 atoms. 7125 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2732 (Rfree = 0.000) for 5119 atoms. Found 32 (32 requested) and removed 39 (16 requested) atoms. Cycle 2: After refmac, R = 0.2635 (Rfree = 0.000) for 5044 atoms. Found 32 (32 requested) and removed 32 (16 requested) atoms. Cycle 3: After refmac, R = 0.2561 (Rfree = 0.000) for 4996 atoms. Found 32 (32 requested) and removed 35 (16 requested) atoms. Cycle 4: After refmac, R = 0.2478 (Rfree = 0.000) for 4961 atoms. Found 24 (32 requested) and removed 26 (16 requested) atoms. Cycle 5: After refmac, R = 0.2464 (Rfree = 0.000) for 4942 atoms. Found 28 (31 requested) and removed 31 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.06 2.38 Search for helices and strands: 0 residues in 0 chains, 5129 seeds are put forward NCS extension: 48 residues added (3 deleted due to clashes), 5177 seeds are put forward Round 1: 475 peptides, 66 chains. Longest chain 22 peptides. Score 0.487 Round 2: 503 peptides, 55 chains. Longest chain 25 peptides. Score 0.579 Round 3: 469 peptides, 56 chains. Longest chain 25 peptides. Score 0.535 Round 4: 484 peptides, 55 chains. Longest chain 23 peptides. Score 0.557 Round 5: 476 peptides, 58 chains. Longest chain 19 peptides. Score 0.532 Taking the results from Round 2 Chains 57, Residues 448, Estimated correctness of the model 6.2 % 8 chains (94 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 14436 reflections ( 99.70 % complete ) and 9742 restraints for refining 5076 atoms. 7674 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2698 (Rfree = 0.000) for 5076 atoms. Found 32 (32 requested) and removed 31 (16 requested) atoms. Cycle 7: After refmac, R = 0.2455 (Rfree = 0.000) for 5046 atoms. Found 30 (32 requested) and removed 27 (16 requested) atoms. Cycle 8: After refmac, R = 0.2367 (Rfree = 0.000) for 5026 atoms. Found 26 (32 requested) and removed 26 (16 requested) atoms. Cycle 9: After refmac, R = 0.2390 (Rfree = 0.000) for 5007 atoms. Found 26 (32 requested) and removed 32 (16 requested) atoms. Cycle 10: After refmac, R = 0.2336 (Rfree = 0.000) for 4991 atoms. Found 20 (32 requested) and removed 33 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.06 2.38 Search for helices and strands: 0 residues in 0 chains, 5172 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 5195 seeds are put forward Round 1: 469 peptides, 63 chains. Longest chain 19 peptides. Score 0.496 Round 2: 483 peptides, 54 chains. Longest chain 28 peptides. Score 0.562 Round 3: 479 peptides, 54 chains. Longest chain 26 peptides. Score 0.557 Round 4: 491 peptides, 56 chains. Longest chain 24 peptides. Score 0.560 Round 5: 483 peptides, 51 chains. Longest chain 23 peptides. Score 0.577 Taking the results from Round 5 Chains 55, Residues 432, Estimated correctness of the model 5.4 % 5 chains (58 residues) have been docked in sequence ------------------------------------------------------ 14436 reflections ( 99.70 % complete ) and 10113 restraints for refining 5075 atoms. 8213 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2800 (Rfree = 0.000) for 5075 atoms. Found 32 (32 requested) and removed 29 (16 requested) atoms. Cycle 12: After refmac, R = 0.2600 (Rfree = 0.000) for 5046 atoms. Found 31 (32 requested) and removed 33 (16 requested) atoms. Cycle 13: After refmac, R = 0.2486 (Rfree = 0.000) for 5028 atoms. Found 23 (32 requested) and removed 30 (16 requested) atoms. Cycle 14: After refmac, R = 0.2491 (Rfree = 0.000) for 5004 atoms. Found 24 (32 requested) and removed 29 (16 requested) atoms. Cycle 15: After refmac, R = 0.2419 (Rfree = 0.000) for 4986 atoms. Found 25 (32 requested) and removed 36 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.06 2.38 Search for helices and strands: 0 residues in 0 chains, 5170 seeds are put forward NCS extension: 30 residues added (5 deleted due to clashes), 5200 seeds are put forward Round 1: 446 peptides, 56 chains. Longest chain 26 peptides. Score 0.507 Round 2: 487 peptides, 53 chains. Longest chain 28 peptides. Score 0.571 Round 3: 483 peptides, 49 chains. Longest chain 39 peptides. Score 0.588 Round 4: 480 peptides, 43 chains. Longest chain 30 peptides. Score 0.615 Round 5: 494 peptides, 51 chains. Longest chain 31 peptides. Score 0.589 Taking the results from Round 4 Chains 50, Residues 437, Estimated correctness of the model 20.4 % 6 chains (80 residues) have been docked in sequence ------------------------------------------------------ 14436 reflections ( 99.70 % complete ) and 9958 restraints for refining 5076 atoms. 7962 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2731 (Rfree = 0.000) for 5076 atoms. Found 32 (32 requested) and removed 33 (16 requested) atoms. Cycle 17: After refmac, R = 0.2516 (Rfree = 0.000) for 5037 atoms. Found 32 (32 requested) and removed 33 (16 requested) atoms. Cycle 18: After refmac, R = 0.2400 (Rfree = 0.000) for 5021 atoms. Found 24 (32 requested) and removed 24 (16 requested) atoms. Cycle 19: After refmac, R = 0.2330 (Rfree = 0.000) for 5015 atoms. Found 18 (32 requested) and removed 25 (16 requested) atoms. Cycle 20: After refmac, R = 0.2284 (Rfree = 0.000) for 5001 atoms. Found 15 (32 requested) and removed 27 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.08 2.40 Search for helices and strands: 0 residues in 0 chains, 5170 seeds are put forward NCS extension: 27 residues added (10 deleted due to clashes), 5197 seeds are put forward Round 1: 466 peptides, 55 chains. Longest chain 26 peptides. Score 0.537 Round 2: 490 peptides, 52 chains. Longest chain 33 peptides. Score 0.580 Round 3: 482 peptides, 45 chains. Longest chain 32 peptides. Score 0.607 Round 4: 500 peptides, 54 chains. Longest chain 35 peptides. Score 0.580 Round 5: 497 peptides, 51 chains. Longest chain 28 peptides. Score 0.592 Taking the results from Round 3 Chains 49, Residues 437, Estimated correctness of the model 17.3 % 6 chains (101 residues) have been docked in sequence ------------------------------------------------------ 14436 reflections ( 99.70 % complete ) and 9726 restraints for refining 5075 atoms. 7660 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2598 (Rfree = 0.000) for 5075 atoms. Found 32 (32 requested) and removed 35 (16 requested) atoms. Cycle 22: After refmac, R = 0.2394 (Rfree = 0.000) for 5041 atoms. Found 30 (32 requested) and removed 27 (16 requested) atoms. Cycle 23: After refmac, R = 0.2271 (Rfree = 0.000) for 5037 atoms. Found 16 (32 requested) and removed 31 (16 requested) atoms. Cycle 24: After refmac, R = 0.2226 (Rfree = 0.000) for 5012 atoms. Found 16 (32 requested) and removed 30 (16 requested) atoms. Cycle 25: After refmac, R = 0.2180 (Rfree = 0.000) for 4989 atoms. Found 17 (32 requested) and removed 21 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.08 2.40 Search for helices and strands: 0 residues in 0 chains, 5198 seeds are put forward NCS extension: 24 residues added (6 deleted due to clashes), 5222 seeds are put forward Round 1: 456 peptides, 59 chains. Longest chain 26 peptides. Score 0.502 Round 2: 495 peptides, 55 chains. Longest chain 27 peptides. Score 0.570 Round 3: 488 peptides, 52 chains. Longest chain 30 peptides. Score 0.578 Round 4: 502 peptides, 48 chains. Longest chain 40 peptides. Score 0.613 Round 5: 490 peptides, 49 chains. Longest chain 29 peptides. Score 0.595 Taking the results from Round 4 Chains 54, Residues 454, Estimated correctness of the model 19.6 % 6 chains (100 residues) have been docked in sequence ------------------------------------------------------ 14436 reflections ( 99.70 % complete ) and 9615 restraints for refining 5076 atoms. 7470 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2668 (Rfree = 0.000) for 5076 atoms. Found 32 (32 requested) and removed 41 (16 requested) atoms. Cycle 27: After refmac, R = 0.2492 (Rfree = 0.000) for 5038 atoms. Found 28 (32 requested) and removed 32 (16 requested) atoms. Cycle 28: After refmac, R = 0.2392 (Rfree = 0.000) for 5012 atoms. Found 14 (32 requested) and removed 28 (16 requested) atoms. Cycle 29: After refmac, R = 0.2325 (Rfree = 0.000) for 4991 atoms. Found 19 (32 requested) and removed 28 (16 requested) atoms. Cycle 30: After refmac, R = 0.2291 (Rfree = 0.000) for 4970 atoms. Found 13 (31 requested) and removed 31 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.06 2.38 Search for helices and strands: 0 residues in 0 chains, 5141 seeds are put forward NCS extension: 34 residues added (11 deleted due to clashes), 5175 seeds are put forward Round 1: 451 peptides, 60 chains. Longest chain 19 peptides. Score 0.491 Round 2: 488 peptides, 49 chains. Longest chain 32 peptides. Score 0.593 Round 3: 485 peptides, 53 chains. Longest chain 21 peptides. Score 0.569 Round 4: 489 peptides, 47 chains. Longest chain 29 peptides. Score 0.604 Round 5: 489 peptides, 50 chains. Longest chain 31 peptides. Score 0.589 Taking the results from Round 4 Chains 49, Residues 442, Estimated correctness of the model 16.1 % 5 chains (67 residues) have been docked in sequence ------------------------------------------------------ 14436 reflections ( 99.70 % complete ) and 9974 restraints for refining 5075 atoms. 8002 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2711 (Rfree = 0.000) for 5075 atoms. Found 32 (32 requested) and removed 36 (16 requested) atoms. Cycle 32: After refmac, R = 0.2546 (Rfree = 0.000) for 5046 atoms. Found 29 (32 requested) and removed 26 (16 requested) atoms. Cycle 33: After refmac, R = 0.2418 (Rfree = 0.000) for 5033 atoms. Found 32 (32 requested) and removed 29 (16 requested) atoms. Cycle 34: After refmac, R = 0.2288 (Rfree = 0.000) for 5023 atoms. Found 13 (32 requested) and removed 26 (16 requested) atoms. Cycle 35: After refmac, R = 0.2221 (Rfree = 0.000) for 5002 atoms. Found 8 (32 requested) and removed 23 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.06 2.38 Search for helices and strands: 0 residues in 0 chains, 5155 seeds are put forward NCS extension: 25 residues added (8 deleted due to clashes), 5180 seeds are put forward Round 1: 448 peptides, 61 chains. Longest chain 20 peptides. Score 0.481 Round 2: 486 peptides, 57 chains. Longest chain 21 peptides. Score 0.549 Round 3: 488 peptides, 57 chains. Longest chain 26 peptides. Score 0.551 Round 4: 498 peptides, 55 chains. Longest chain 34 peptides. Score 0.573 Round 5: 522 peptides, 59 chains. Longest chain 31 peptides. Score 0.579 Taking the results from Round 5 Chains 66, Residues 463, Estimated correctness of the model 6.2 % 6 chains (68 residues) have been docked in sequence ------------------------------------------------------ 14436 reflections ( 99.70 % complete ) and 10142 restraints for refining 5075 atoms. 8125 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2724 (Rfree = 0.000) for 5075 atoms. Found 32 (32 requested) and removed 36 (16 requested) atoms. Cycle 37: After refmac, R = 0.2489 (Rfree = 0.000) for 5052 atoms. Found 19 (32 requested) and removed 34 (16 requested) atoms. Cycle 38: After refmac, R = 0.2376 (Rfree = 0.000) for 5023 atoms. Found 18 (32 requested) and removed 27 (16 requested) atoms. Cycle 39: After refmac, R = 0.2324 (Rfree = 0.000) for 5007 atoms. Found 7 (32 requested) and removed 27 (16 requested) atoms. Cycle 40: After refmac, R = 0.2298 (Rfree = 0.000) for 4982 atoms. Found 13 (31 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.09 2.40 Search for helices and strands: 0 residues in 0 chains, 5165 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 5177 seeds are put forward Round 1: 444 peptides, 64 chains. Longest chain 26 peptides. Score 0.458 Round 2: 486 peptides, 52 chains. Longest chain 27 peptides. Score 0.575 Round 3: 499 peptides, 53 chains. Longest chain 20 peptides. Score 0.584 Round 4: 510 peptides, 54 chains. Longest chain 22 peptides. Score 0.591 Round 5: 532 peptides, 54 chains. Longest chain 30 peptides. Score 0.614 Taking the results from Round 5 Chains 58, Residues 478, Estimated correctness of the model 20.0 % 6 chains (58 residues) have been docked in sequence ------------------------------------------------------ 14436 reflections ( 99.70 % complete ) and 10068 restraints for refining 5075 atoms. 8009 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2765 (Rfree = 0.000) for 5075 atoms. Found 32 (32 requested) and removed 23 (16 requested) atoms. Cycle 42: After refmac, R = 0.2551 (Rfree = 0.000) for 5052 atoms. Found 29 (32 requested) and removed 32 (16 requested) atoms. Cycle 43: After refmac, R = 0.2442 (Rfree = 0.000) for 5031 atoms. Found 16 (32 requested) and removed 24 (16 requested) atoms. Cycle 44: After refmac, R = 0.2371 (Rfree = 0.000) for 5011 atoms. Found 22 (32 requested) and removed 28 (16 requested) atoms. Cycle 45: After refmac, R = 0.2315 (Rfree = 0.000) for 4995 atoms. Found 14 (32 requested) and removed 27 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.06 2.38 Search for helices and strands: 0 residues in 0 chains, 5135 seeds are put forward NCS extension: 19 residues added (7 deleted due to clashes), 5154 seeds are put forward Round 1: 462 peptides, 63 chains. Longest chain 19 peptides. Score 0.487 Round 2: 484 peptides, 58 chains. Longest chain 31 peptides. Score 0.541 Round 3: 478 peptides, 53 chains. Longest chain 29 peptides. Score 0.561 Round 4: 477 peptides, 52 chains. Longest chain 23 peptides. Score 0.565 Round 5: 505 peptides, 54 chains. Longest chain 31 peptides. Score 0.586 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 60, Residues 451, Estimated correctness of the model 9.0 % 6 chains (56 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 2g0t-3_warpNtrace.pdb as input Building loops using Loopy2018 60 chains (451 residues) following loop building 6 chains (56 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. Failed to save intermediate PDB 14436 reflections ( 99.70 % complete ) and 10227 restraints for refining 5075 atoms. 8299 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2712 (Rfree = 0.000) for 5075 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2522 (Rfree = 0.000) for 5038 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2450 (Rfree = 0.000) for 5008 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.2406 (Rfree = 0.000) for 4987 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Writing output files ... TimeTaking 158.73