Mon 24 Dec 01:04:17 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-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2f4l-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2f4l-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4l-4.0-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-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4l-4.0-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 01:04:22 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-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4l-4.0-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 828 and 0 Target number of residues in the AU: 828 Target solvent content: 0.6529 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-4.0-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-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 9504 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: 86.372 4.000 Wilson plot Bfac: 80.01 11382 reflections ( 99.54 % complete ) and 0 restraints for refining 10541 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3101 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3259 (Rfree = 0.000) for 10541 atoms. Found 50 (50 requested) and removed 108 (25 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.71 3.71 Search for helices and strands: 0 residues in 0 chains, 10610 seeds are put forward NCS extension: 0 residues added, 10610 seeds are put forward Round 1: 442 peptides, 86 chains. Longest chain 11 peptides. Score 0.311 Round 2: 597 peptides, 100 chains. Longest chain 13 peptides. Score 0.433 Round 3: 642 peptides, 97 chains. Longest chain 17 peptides. Score 0.499 Round 4: 696 peptides, 97 chains. Longest chain 22 peptides. Score 0.555 Round 5: 711 peptides, 91 chains. Longest chain 29 peptides. Score 0.595 Taking the results from Round 5 Chains 96, Residues 620, Estimated correctness of the model 0.0 % 9 chains (76 residues) have been docked in sequence ------------------------------------------------------ 11382 reflections ( 99.54 % complete ) and 18882 restraints for refining 8580 atoms. 16241 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2402 (Rfree = 0.000) for 8580 atoms. Found 32 (40 requested) and removed 70 (20 requested) atoms. Cycle 2: After refmac, R = 0.2223 (Rfree = 0.000) for 8356 atoms. Found 14 (40 requested) and removed 41 (20 requested) atoms. Cycle 3: After refmac, R = 0.2167 (Rfree = 0.000) for 8268 atoms. Found 15 (39 requested) and removed 26 (19 requested) atoms. Cycle 4: After refmac, R = 0.2114 (Rfree = 0.000) for 8238 atoms. Found 5 (39 requested) and removed 25 (19 requested) atoms. Cycle 5: After refmac, R = 0.2088 (Rfree = 0.000) for 8206 atoms. Found 5 (39 requested) and removed 21 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.67 3.67 Search for helices and strands: 0 residues in 0 chains, 8360 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 8374 seeds are put forward Round 1: 587 peptides, 97 chains. Longest chain 16 peptides. Score 0.436 Round 2: 667 peptides, 92 chains. Longest chain 27 peptides. Score 0.548 Round 3: 677 peptides, 95 chains. Longest chain 20 peptides. Score 0.545 Round 4: 710 peptides, 86 chains. Longest chain 35 peptides. Score 0.615 Round 5: 706 peptides, 80 chains. Longest chain 25 peptides. Score 0.636 Taking the results from Round 5 Chains 89, Residues 626, Estimated correctness of the model 0.1 % 9 chains (98 residues) have been docked in sequence ------------------------------------------------------ 11382 reflections ( 99.54 % complete ) and 18739 restraints for refining 8582 atoms. 15952 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2278 (Rfree = 0.000) for 8582 atoms. Found 39 (40 requested) and removed 64 (20 requested) atoms. Cycle 7: After refmac, R = 0.2151 (Rfree = 0.000) for 8434 atoms. Found 17 (40 requested) and removed 38 (20 requested) atoms. Cycle 8: After refmac, R = 0.2144 (Rfree = 0.000) for 8376 atoms. Found 14 (39 requested) and removed 25 (19 requested) atoms. Cycle 9: After refmac, R = 0.2119 (Rfree = 0.000) for 8354 atoms. Found 6 (39 requested) and removed 23 (19 requested) atoms. Cycle 10: After refmac, R = 0.2106 (Rfree = 0.000) for 8328 atoms. Found 8 (39 requested) and removed 23 (19 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.70 3.70 Search for helices and strands: 0 residues in 0 chains, 8474 seeds are put forward NCS extension: 34 residues added (2 deleted due to clashes), 8508 seeds are put forward Round 1: 544 peptides, 96 chains. Longest chain 15 peptides. Score 0.389 Round 2: 610 peptides, 87 chains. Longest chain 16 peptides. Score 0.512 Round 3: 643 peptides, 88 chains. Longest chain 20 peptides. Score 0.542 Round 4: 650 peptides, 86 chains. Longest chain 19 peptides. Score 0.558 Round 5: 657 peptides, 83 chains. Longest chain 21 peptides. Score 0.578 Taking the results from Round 5 Chains 85, Residues 574, Estimated correctness of the model 0.0 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 11382 reflections ( 99.54 % complete ) and 19871 restraints for refining 8581 atoms. 17559 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2326 (Rfree = 0.000) for 8581 atoms. Found 23 (40 requested) and removed 47 (20 requested) atoms. Cycle 12: After refmac, R = 0.2423 (Rfree = 0.000) for 8476 atoms. Found 37 (40 requested) and removed 48 (20 requested) atoms. Cycle 13: After refmac, R = 0.1951 (Rfree = 0.000) for 8406 atoms. Found 15 (40 requested) and removed 31 (20 requested) atoms. Cycle 14: After refmac, R = 0.1868 (Rfree = 0.000) for 8355 atoms. Found 17 (39 requested) and removed 30 (19 requested) atoms. Cycle 15: After refmac, R = 0.1813 (Rfree = 0.000) for 8324 atoms. Found 3 (39 requested) and removed 27 (19 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.74 3.74 Search for helices and strands: 0 residues in 0 chains, 8429 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 8445 seeds are put forward Round 1: 512 peptides, 95 chains. Longest chain 15 peptides. Score 0.354 Round 2: 613 peptides, 95 chains. Longest chain 21 peptides. Score 0.476 Round 3: 608 peptides, 91 chains. Longest chain 15 peptides. Score 0.490 Round 4: 585 peptides, 81 chains. Longest chain 19 peptides. Score 0.514 Round 5: 599 peptides, 81 chains. Longest chain 23 peptides. Score 0.529 Taking the results from Round 5 Chains 83, Residues 518, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 11382 reflections ( 99.54 % complete ) and 20360 restraints for refining 8579 atoms. 18285 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2198 (Rfree = 0.000) for 8579 atoms. Found 18 (40 requested) and removed 39 (20 requested) atoms. Cycle 17: After refmac, R = 0.2167 (Rfree = 0.000) for 8487 atoms. Found 36 (40 requested) and removed 48 (20 requested) atoms. Cycle 18: After refmac, R = 0.2251 (Rfree = 0.000) for 8447 atoms. Found 32 (40 requested) and removed 31 (20 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2011 (Rfree = 0.000) for 8406 atoms. Found 26 (40 requested) and removed 32 (20 requested) atoms. Cycle 20: After refmac, R = 0.1930 (Rfree = 0.000) for 8374 atoms. Found 17 (39 requested) and removed 28 (19 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.65 3.65 Search for helices and strands: 0 residues in 0 chains, 8527 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 8547 seeds are put forward Round 1: 478 peptides, 93 chains. Longest chain 15 peptides. Score 0.320 Round 2: 544 peptides, 86 chains. Longest chain 17 peptides. Score 0.442 Round 3: 575 peptides, 90 chains. Longest chain 15 peptides. Score 0.458 Round 4: 558 peptides, 88 chains. Longest chain 17 peptides. Score 0.448 Round 5: 592 peptides, 87 chains. Longest chain 21 peptides. Score 0.492 Taking the results from Round 5 Chains 87, Residues 505, Estimated correctness of the model 0.0 % 3 chains (11 residues) have been docked in sequence ------------------------------------------------------ 11382 reflections ( 99.54 % complete ) and 20356 restraints for refining 8582 atoms. 18397 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2159 (Rfree = 0.000) for 8582 atoms. Found 40 (40 requested) and removed 57 (20 requested) atoms. Cycle 22: After refmac, R = 0.2100 (Rfree = 0.000) for 8508 atoms. Found 40 (40 requested) and removed 49 (20 requested) atoms. Cycle 23: After refmac, R = 0.1895 (Rfree = 0.000) for 8458 atoms. Found 34 (40 requested) and removed 25 (20 requested) atoms. Cycle 24: After refmac, R = 0.1717 (Rfree = 0.000) for 8422 atoms. Found 20 (40 requested) and removed 29 (20 requested) atoms. Cycle 25: After refmac, R = 0.1768 (Rfree = 0.000) for 8393 atoms. Found 25 (39 requested) and removed 37 (19 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.66 3.66 Search for helices and strands: 0 residues in 0 chains, 8622 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 8644 seeds are put forward Round 1: 408 peptides, 84 chains. Longest chain 9 peptides. Score 0.276 Round 2: 493 peptides, 86 chains. Longest chain 20 peptides. Score 0.379 Round 3: 508 peptides, 84 chains. Longest chain 15 peptides. Score 0.409 Round 4: 532 peptides, 91 chains. Longest chain 13 peptides. Score 0.401 Round 5: 523 peptides, 78 chains. Longest chain 17 peptides. Score 0.459 Taking the results from Round 5 Chains 79, Residues 445, Estimated correctness of the model 0.0 % 3 chains (27 residues) have been docked in sequence ------------------------------------------------------ 11382 reflections ( 99.54 % complete ) and 20467 restraints for refining 8582 atoms. 18686 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1949 (Rfree = 0.000) for 8582 atoms. Found 40 (40 requested) and removed 42 (20 requested) atoms. Cycle 27: After refmac, R = 0.1767 (Rfree = 0.000) for 8547 atoms. Found 13 (40 requested) and removed 26 (20 requested) atoms. Cycle 28: After refmac, R = 0.1751 (Rfree = 0.000) for 8526 atoms. Found 12 (40 requested) and removed 23 (20 requested) atoms. Cycle 29: After refmac, R = 0.1605 (Rfree = 0.000) for 8509 atoms. Found 10 (40 requested) and removed 27 (20 requested) atoms. Cycle 30: After refmac, R = 0.1530 (Rfree = 0.000) for 8481 atoms. Found 15 (40 requested) and removed 27 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.71 3.71 Search for helices and strands: 0 residues in 0 chains, 8637 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 8662 seeds are put forward Round 1: 462 peptides, 92 chains. Longest chain 10 peptides. Score 0.304 Round 2: 531 peptides, 86 chains. Longest chain 15 peptides. Score 0.427 Round 3: 525 peptides, 82 chains. Longest chain 16 peptides. Score 0.440 Round 4: 532 peptides, 85 chains. Longest chain 15 peptides. Score 0.433 Round 5: 551 peptides, 84 chains. Longest chain 24 peptides. Score 0.461 Taking the results from Round 5 Chains 85, Residues 467, Estimated correctness of the model 0.0 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 11382 reflections ( 99.54 % complete ) and 20412 restraints for refining 8583 atoms. 18571 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1925 (Rfree = 0.000) for 8583 atoms. Found 30 (40 requested) and removed 29 (20 requested) atoms. Cycle 32: After refmac, R = 0.1825 (Rfree = 0.000) for 8544 atoms. Found 30 (40 requested) and removed 31 (20 requested) atoms. Cycle 33: After refmac, R = 0.1932 (Rfree = 0.000) for 8524 atoms. Found 40 (40 requested) and removed 33 (20 requested) atoms. Cycle 34: After refmac, R = 0.1918 (Rfree = 0.000) for 8508 atoms. Found 40 (40 requested) and removed 35 (20 requested) atoms. Cycle 35: After refmac, R = 0.1498 (Rfree = 0.000) for 8482 atoms. Found 17 (40 requested) and removed 25 (20 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.70 3.70 Search for helices and strands: 0 residues in 0 chains, 8652 seeds are put forward NCS extension: 9 residues added (3 deleted due to clashes), 8661 seeds are put forward Round 1: 430 peptides, 86 chains. Longest chain 12 peptides. Score 0.295 Round 2: 479 peptides, 79 chains. Longest chain 15 peptides. Score 0.400 Round 3: 497 peptides, 82 chains. Longest chain 15 peptides. Score 0.406 Round 4: 500 peptides, 76 chains. Longest chain 17 peptides. Score 0.442 Round 5: 496 peptides, 80 chains. Longest chain 15 peptides. Score 0.416 Taking the results from Round 4 Chains 76, Residues 424, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 11382 reflections ( 99.54 % complete ) and 20891 restraints for refining 8582 atoms. 19257 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1915 (Rfree = 0.000) for 8582 atoms. Found 34 (40 requested) and removed 43 (20 requested) atoms. Cycle 37: After refmac, R = 0.1856 (Rfree = 0.000) for 8542 atoms. Found 40 (40 requested) and removed 28 (20 requested) atoms. Cycle 38: After refmac, R = 0.1773 (Rfree = 0.000) for 8535 atoms. Found 35 (40 requested) and removed 21 (20 requested) atoms. Cycle 39: After refmac, R = 0.1705 (Rfree = 0.000) for 8527 atoms. Found 36 (40 requested) and removed 20 (20 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1709 (Rfree = 0.000) for 8530 atoms. Found 40 (40 requested) and removed 23 (20 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.71 3.71 Search for helices and strands: 0 residues in 0 chains, 8718 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 8738 seeds are put forward Round 1: 409 peptides, 83 chains. Longest chain 11 peptides. Score 0.283 Round 2: 461 peptides, 80 chains. Longest chain 17 peptides. Score 0.371 Round 3: 471 peptides, 80 chains. Longest chain 19 peptides. Score 0.384 Round 4: 491 peptides, 82 chains. Longest chain 17 peptides. Score 0.399 Round 5: 497 peptides, 83 chains. Longest chain 18 peptides. Score 0.401 Taking the results from Round 5 Chains 85, Residues 414, Estimated correctness of the model 0.0 % 5 chains (41 residues) have been docked in sequence ------------------------------------------------------ 11382 reflections ( 99.54 % complete ) and 20668 restraints for refining 8582 atoms. 18953 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2000 (Rfree = 0.000) for 8582 atoms. Found 40 (40 requested) and removed 32 (20 requested) atoms. Cycle 42: After refmac, R = 0.1981 (Rfree = 0.000) for 8527 atoms. Found 40 (40 requested) and removed 38 (20 requested) atoms. Cycle 43: After refmac, R = 0.1994 (Rfree = 0.000) for 8500 atoms. Found 40 (40 requested) and removed 28 (20 requested) atoms. Cycle 44: After refmac, R = 0.1499 (Rfree = 0.000) for 8482 atoms. Found 15 (40 requested) and removed 27 (20 requested) atoms. Cycle 45: After refmac, R = 0.1421 (Rfree = 0.000) for 8445 atoms. Found 22 (40 requested) and removed 25 (20 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.71 3.71 Search for helices and strands: 0 residues in 0 chains, 8634 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 8650 seeds are put forward Round 1: 357 peptides, 76 chains. Longest chain 10 peptides. Score 0.250 Round 2: 433 peptides, 82 chains. Longest chain 12 peptides. Score 0.322 Round 3: 455 peptides, 82 chains. Longest chain 13 peptides. Score 0.352 Round 4: 453 peptides, 78 chains. Longest chain 16 peptides. Score 0.372 Round 5: 447 peptides, 74 chains. Longest chain 21 peptides. Score 0.387 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 76, Residues 373, Estimated correctness of the model 0.0 % 3 chains (24 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2f4l-4_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 36 A and 46 A 74 chains (377 residues) following loop building 2 chains (33 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11382 reflections ( 99.54 % complete ) and 20642 restraints for refining 8572 atoms. 19103 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1851 (Rfree = 0.000) for 8572 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 47: After refmac, R = 0.1778 (Rfree = 0.000) for 8516 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 48: After refmac, R = 0.1600 (Rfree = 0.000) for 8486 atoms. Found 0 (40 requested) and removed 20 (20 requested) atoms. Cycle 49: After refmac, R = 0.1720 (Rfree = 0.000) for 8453 atoms. TimeTaking 82.38