null Mon 24 Dec 07:30:54 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2f4l-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2f4l-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2f4l-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4l-4.0-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2f4l-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4l-4.0-parrot-noncs ############### 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 07:30:59 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/noncs/ArpWArp/wArpResults/WorkingDir/2f4l-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2f4l-4.0-parrot-noncs/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-noncs.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-noncs.fasta_lf Building free atoms model in initial map for 9504 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: 86.372 4.000 Wilson plot Bfac: 80.01 11382 reflections ( 99.54 % complete ) and 0 restraints for refining 10518 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3369 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3398 (Rfree = 0.000) for 10518 atoms. Found 49 (49 requested) and removed 164 (24 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.71 3.71 Search for helices and strands: 0 residues in 0 chains, 10501 seeds are put forward NCS extension: 0 residues added, 10501 seeds are put forward Round 1: 380 peptides, 81 chains. Longest chain 8 peptides. Score 0.253 Round 2: 488 peptides, 89 chains. Longest chain 14 peptides. Score 0.356 Round 3: 526 peptides, 90 chains. Longest chain 15 peptides. Score 0.399 Round 4: 537 peptides, 89 chains. Longest chain 13 peptides. Score 0.418 Round 5: 537 peptides, 83 chains. Longest chain 20 peptides. Score 0.449 Taking the results from Round 5 Chains 87, Residues 454, Estimated correctness of the model 0.0 % 6 chains (52 residues) have been docked in sequence ------------------------------------------------------ 11382 reflections ( 99.54 % complete ) and 20318 restraints for refining 8579 atoms. 18431 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2648 (Rfree = 0.000) for 8579 atoms. Found 40 (40 requested) and removed 73 (20 requested) atoms. Cycle 2: After refmac, R = 0.2681 (Rfree = 0.000) for 8393 atoms. Found 38 (40 requested) and removed 56 (20 requested) atoms. Cycle 3: After refmac, R = 0.2604 (Rfree = 0.000) for 8306 atoms. Found 36 (39 requested) and removed 55 (19 requested) atoms. Cycle 4: After refmac, R = 0.2233 (Rfree = 0.000) for 8235 atoms. Found 14 (39 requested) and removed 36 (19 requested) atoms. Cycle 5: After refmac, R = 0.2145 (Rfree = 0.000) for 8179 atoms. Found 11 (39 requested) and removed 30 (19 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.68 3.68 Search for helices and strands: 0 residues in 0 chains, 8352 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 8368 seeds are put forward Round 1: 470 peptides, 99 chains. Longest chain 11 peptides. Score 0.275 Round 2: 545 peptides, 91 chains. Longest chain 14 peptides. Score 0.417 Round 3: 578 peptides, 96 chains. Longest chain 15 peptides. Score 0.431 Round 4: 562 peptides, 81 chains. Longest chain 18 peptides. Score 0.488 Round 5: 588 peptides, 84 chains. Longest chain 21 peptides. Score 0.503 Taking the results from Round 5 Chains 85, Residues 504, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 11382 reflections ( 99.54 % complete ) and 19766 restraints for refining 8404 atoms. 17796 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2203 (Rfree = 0.000) for 8404 atoms. Found 33 (39 requested) and removed 69 (19 requested) atoms. Cycle 7: After refmac, R = 0.2253 (Rfree = 0.000) for 8295 atoms. Found 35 (39 requested) and removed 52 (19 requested) atoms. Cycle 8: After refmac, R = 0.2006 (Rfree = 0.000) for 8249 atoms. Found 23 (39 requested) and removed 41 (19 requested) atoms. Cycle 9: After refmac, R = 0.1816 (Rfree = 0.000) for 8205 atoms. Found 11 (39 requested) and removed 25 (19 requested) atoms. Cycle 10: After refmac, R = 0.1837 (Rfree = 0.000) for 8180 atoms. Found 7 (38 requested) and removed 25 (19 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.67 3.67 Search for helices and strands: 0 residues in 0 chains, 8408 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 8422 seeds are put forward Round 1: 496 peptides, 100 chains. Longest chain 12 peptides. Score 0.305 Round 2: 555 peptides, 93 chains. Longest chain 13 peptides. Score 0.419 Round 3: 543 peptides, 91 chains. Longest chain 14 peptides. Score 0.415 Round 4: 572 peptides, 92 chains. Longest chain 16 peptides. Score 0.444 Round 5: 586 peptides, 97 chains. Longest chain 13 peptides. Score 0.435 Taking the results from Round 4 Chains 92, Residues 480, Estimated correctness of the model 0.0 % 5 chains (36 residues) have been docked in sequence ------------------------------------------------------ 11382 reflections ( 99.54 % complete ) and 19983 restraints for refining 8578 atoms. 18037 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2395 (Rfree = 0.000) for 8578 atoms. Found 37 (40 requested) and removed 64 (20 requested) atoms. Cycle 12: After refmac, R = 0.2211 (Rfree = 0.000) for 8492 atoms. Found 30 (40 requested) and removed 37 (20 requested) atoms. Cycle 13: After refmac, R = 0.1997 (Rfree = 0.000) for 8439 atoms. Found 7 (40 requested) and removed 35 (20 requested) atoms. Cycle 14: After refmac, R = 0.2076 (Rfree = 0.000) for 8378 atoms. Found 21 (39 requested) and removed 30 (19 requested) atoms. Cycle 15: After refmac, R = 0.2155 (Rfree = 0.000) for 8352 atoms. Found 30 (39 requested) and removed 30 (19 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.59 3.59 Search for helices and strands: 0 residues in 0 chains, 8520 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 8537 seeds are put forward Round 1: 460 peptides, 95 chains. Longest chain 11 peptides. Score 0.284 Round 2: 518 peptides, 92 chains. Longest chain 18 peptides. Score 0.378 Round 3: 570 peptides, 91 chains. Longest chain 16 peptides. Score 0.447 Round 4: 570 peptides, 86 chains. Longest chain 17 peptides. Score 0.472 Round 5: 572 peptides, 86 chains. Longest chain 18 peptides. Score 0.475 Taking the results from Round 5 Chains 86, Residues 486, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 11382 reflections ( 99.54 % complete ) and 20284 restraints for refining 8583 atoms. 18385 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2278 (Rfree = 0.000) for 8583 atoms. Found 40 (40 requested) and removed 48 (20 requested) atoms. Cycle 17: After refmac, R = 0.2138 (Rfree = 0.000) for 8511 atoms. Found 40 (40 requested) and removed 76 (20 requested) atoms. Cycle 18: After refmac, R = 0.1920 (Rfree = 0.000) for 8445 atoms. Found 16 (40 requested) and removed 33 (20 requested) atoms. Cycle 19: After refmac, R = 0.1730 (Rfree = 0.000) for 8406 atoms. Found 9 (40 requested) and removed 26 (20 requested) atoms. Cycle 20: After refmac, R = 0.1691 (Rfree = 0.000) for 8381 atoms. Found 9 (39 requested) and removed 23 (19 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.65 3.65 Search for helices and strands: 0 residues in 0 chains, 8532 seeds are put forward NCS extension: 10 residues added (4 deleted due to clashes), 8542 seeds are put forward Round 1: 419 peptides, 81 chains. Longest chain 12 peptides. Score 0.309 Round 2: 501 peptides, 85 chains. Longest chain 14 peptides. Score 0.395 Round 3: 480 peptides, 72 chains. Longest chain 19 peptides. Score 0.440 Round 4: 508 peptides, 80 chains. Longest chain 13 peptides. Score 0.430 Round 5: 515 peptides, 81 chains. Longest chain 14 peptides. Score 0.434 Taking the results from Round 3 Chains 74, Residues 408, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 11382 reflections ( 99.54 % complete ) and 20648 restraints for refining 8582 atoms. 19041 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1925 (Rfree = 0.000) for 8582 atoms. Found 31 (40 requested) and removed 38 (20 requested) atoms. Cycle 22: After refmac, R = 0.1928 (Rfree = 0.000) for 8505 atoms. Found 40 (40 requested) and removed 32 (20 requested) atoms. Cycle 23: After refmac, R = 0.1937 (Rfree = 0.000) for 8481 atoms. Found 39 (40 requested) and removed 29 (20 requested) atoms. Cycle 24: After refmac, R = 0.1598 (Rfree = 0.000) for 8458 atoms. Found 12 (40 requested) and removed 26 (20 requested) atoms. Cycle 25: After refmac, R = 0.1610 (Rfree = 0.000) for 8419 atoms. Found 22 (40 requested) and removed 24 (20 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.70 3.70 Search for helices and strands: 0 residues in 0 chains, 8566 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 8586 seeds are put forward Round 1: 415 peptides, 88 chains. Longest chain 11 peptides. Score 0.262 Round 2: 489 peptides, 92 chains. Longest chain 12 peptides. Score 0.340 Round 3: 481 peptides, 87 chains. Longest chain 14 peptides. Score 0.358 Round 4: 508 peptides, 84 chains. Longest chain 15 peptides. Score 0.409 Round 5: 509 peptides, 83 chains. Longest chain 17 peptides. Score 0.416 Taking the results from Round 5 Chains 83, Residues 426, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 11382 reflections ( 99.54 % complete ) and 20820 restraints for refining 8580 atoms. 19183 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2045 (Rfree = 0.000) for 8580 atoms. Found 36 (40 requested) and removed 38 (20 requested) atoms. Cycle 27: After refmac, R = 0.2009 (Rfree = 0.000) for 8515 atoms. Found 40 (40 requested) and removed 30 (20 requested) atoms. Cycle 28: After refmac, R = 0.1991 (Rfree = 0.000) for 8478 atoms. Found 40 (40 requested) and removed 31 (20 requested) atoms. Cycle 29: After refmac, R = 0.1579 (Rfree = 0.000) for 8455 atoms. Found 14 (40 requested) and removed 24 (20 requested) atoms. Cycle 30: After refmac, R = 0.1479 (Rfree = 0.000) for 8417 atoms. Found 13 (40 requested) and removed 23 (20 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.70 3.70 Search for helices and strands: 0 residues in 0 chains, 8584 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 8601 seeds are put forward Round 1: 366 peptides, 77 chains. Longest chain 11 peptides. Score 0.257 Round 2: 456 peptides, 78 chains. Longest chain 16 peptides. Score 0.376 Round 3: 467 peptides, 76 chains. Longest chain 19 peptides. Score 0.401 Round 4: 483 peptides, 78 chains. Longest chain 19 peptides. Score 0.411 Round 5: 482 peptides, 82 chains. Longest chain 13 peptides. Score 0.387 Taking the results from Round 4 Chains 80, Residues 405, Estimated correctness of the model 0.0 % 3 chains (33 residues) have been docked in sequence ------------------------------------------------------ 11382 reflections ( 99.54 % complete ) and 20444 restraints for refining 8582 atoms. 18779 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2070 (Rfree = 0.000) for 8582 atoms. Found 40 (40 requested) and removed 50 (20 requested) atoms. Cycle 32: After refmac, R = 0.2113 (Rfree = 0.000) for 8504 atoms. Found 40 (40 requested) and removed 33 (20 requested) atoms. Cycle 33: After refmac, R = 0.2039 (Rfree = 0.000) for 8438 atoms. Found 40 (40 requested) and removed 30 (20 requested) atoms. Cycle 34: After refmac, R = 0.2039 (Rfree = 0.000) for 8396 atoms. Found 40 (40 requested) and removed 31 (20 requested) atoms. Cycle 35: After refmac, R = 0.2023 (Rfree = 0.000) for 8372 atoms. Found 39 (39 requested) and removed 30 (19 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.66 3.66 Search for helices and strands: 0 residues in 0 chains, 8549 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 8568 seeds are put forward Round 1: 336 peptides, 75 chains. Longest chain 8 peptides. Score 0.224 Round 2: 403 peptides, 79 chains. Longest chain 13 peptides. Score 0.299 Round 3: 402 peptides, 72 chains. Longest chain 13 peptides. Score 0.339 Round 4: 406 peptides, 71 chains. Longest chain 13 peptides. Score 0.350 Round 5: 413 peptides, 68 chains. Longest chain 15 peptides. Score 0.377 Taking the results from Round 5 Chains 68, Residues 345, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 11382 reflections ( 99.54 % complete ) and 19773 restraints for refining 8249 atoms. 18449 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1963 (Rfree = 0.000) for 8249 atoms. Found 39 (39 requested) and removed 53 (19 requested) atoms. Cycle 37: After refmac, R = 0.2104 (Rfree = 0.000) for 8174 atoms. Found 39 (39 requested) and removed 36 (19 requested) atoms. Cycle 38: After refmac, R = 0.1875 (Rfree = 0.000) for 8134 atoms. Found 38 (38 requested) and removed 32 (19 requested) atoms. Cycle 39: After refmac, R = 0.1979 (Rfree = 0.000) for 8106 atoms. Found 38 (38 requested) and removed 28 (19 requested) atoms. Cycle 40: After refmac, R = 0.1499 (Rfree = 0.000) for 8097 atoms. Found 15 (38 requested) and removed 30 (19 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.64 3.64 Search for helices and strands: 0 residues in 0 chains, 8234 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 8249 seeds are put forward Round 1: 365 peptides, 81 chains. Longest chain 9 peptides. Score 0.231 Round 2: 444 peptides, 84 chains. Longest chain 17 peptides. Score 0.326 Round 3: 426 peptides, 77 chains. Longest chain 15 peptides. Score 0.342 Round 4: 423 peptides, 68 chains. Longest chain 18 peptides. Score 0.390 Round 5: 442 peptides, 77 chains. Longest chain 14 peptides. Score 0.364 Taking the results from Round 4 Chains 70, Residues 355, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 11382 reflections ( 99.54 % complete ) and 19299 restraints for refining 8260 atoms. 17890 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2011 (Rfree = 0.000) for 8260 atoms. Found 39 (39 requested) and removed 79 (19 requested) atoms. Cycle 42: After refmac, R = 0.1955 (Rfree = 0.000) for 8188 atoms. Found 39 (39 requested) and removed 39 (19 requested) atoms. Cycle 43: After refmac, R = 0.1987 (Rfree = 0.000) for 8162 atoms. Found 38 (38 requested) and removed 35 (19 requested) atoms. Cycle 44: After refmac, R = 0.1748 (Rfree = 0.000) for 8145 atoms. Found 26 (38 requested) and removed 27 (19 requested) atoms. Cycle 45: After refmac, R = 0.1752 (Rfree = 0.000) for 8125 atoms. Found 32 (38 requested) and removed 31 (19 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.67 3.67 Search for helices and strands: 0 residues in 0 chains, 8277 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 8300 seeds are put forward Round 1: 327 peptides, 70 chains. Longest chain 12 peptides. Score 0.243 Round 2: 349 peptides, 64 chains. Longest chain 14 peptides. Score 0.313 Round 3: 370 peptides, 66 chains. Longest chain 13 peptides. Score 0.331 Round 4: 379 peptides, 67 chains. Longest chain 13 peptides. Score 0.337 Round 5: 389 peptides, 65 chains. Longest chain 14 peptides. Score 0.363 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 65, Residues 324, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 2f4l-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11382 reflections ( 99.54 % complete ) and 19477 restraints for refining 8222 atoms. 18207 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1807 (Rfree = 0.000) for 8222 atoms. Found 0 (39 requested) and removed 19 (19 requested) atoms. Cycle 47: After refmac, R = 0.1685 (Rfree = 0.000) for 8164 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 48: After refmac, R = 0.1669 (Rfree = 0.000) for 8137 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Cycle 49: After refmac, R = 0.1715 (Rfree = 0.000) for 8115 atoms. Found 0 (38 requested) and removed 19 (19 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:54:35 GMT 2018 Job finished. TimeTaking 83.69 Used memory is bytes: 17884376