Mon 24 Dec 07:55:10 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 2okc-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2okc-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2okc-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2okc-3.2-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/2okc-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2okc-3.2-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 07:55:15 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/2okc-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2okc-3.2-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 662 and 0 Target number of residues in the AU: 662 Target solvent content: 0.6366 Checking the provided sequence file Detected sequence length: 445 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 890 Adjusted target solvent content: 0.51 Input MTZ file: 2okc-3.2-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: 75.340 85.750 152.600 90.000 90.000 90.000 Input sequence file: 2okc-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 7120 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: 28.546 3.200 Wilson plot Bfac: 69.89 15216 reflections ( 89.87 % complete ) and 0 restraints for refining 7954 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3217 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2566 (Rfree = 0.000) for 7954 atoms. Found 70 (71 requested) and removed 76 (35 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.24 3.20 Search for helices and strands: 0 residues in 0 chains, 8138 seeds are put forward NCS extension: 0 residues added, 8138 seeds are put forward Round 1: 352 peptides, 69 chains. Longest chain 14 peptides. Score 0.312 Round 2: 456 peptides, 77 chains. Longest chain 16 peptides. Score 0.429 Round 3: 494 peptides, 75 chains. Longest chain 18 peptides. Score 0.499 Round 4: 500 peptides, 69 chains. Longest chain 18 peptides. Score 0.543 Round 5: 511 peptides, 68 chains. Longest chain 27 peptides. Score 0.564 Taking the results from Round 5 Chains 69, Residues 443, Estimated correctness of the model 31.0 % 6 chains (40 residues) have been docked in sequence ------------------------------------------------------ 15216 reflections ( 89.87 % complete ) and 14469 restraints for refining 6499 atoms. 12650 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2584 (Rfree = 0.000) for 6499 atoms. Found 40 (58 requested) and removed 54 (29 requested) atoms. Cycle 2: After refmac, R = 0.2464 (Rfree = 0.000) for 6418 atoms. Found 20 (58 requested) and removed 48 (29 requested) atoms. Cycle 3: After refmac, R = 0.2467 (Rfree = 0.000) for 6368 atoms. Found 17 (57 requested) and removed 36 (28 requested) atoms. Cycle 4: After refmac, R = 0.2480 (Rfree = 0.000) for 6334 atoms. Found 19 (56 requested) and removed 48 (28 requested) atoms. Cycle 5: After refmac, R = 0.2452 (Rfree = 0.000) for 6296 atoms. Found 14 (56 requested) and removed 36 (28 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.22 3.18 Search for helices and strands: 0 residues in 0 chains, 6498 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 6515 seeds are put forward Round 1: 452 peptides, 77 chains. Longest chain 21 peptides. Score 0.423 Round 2: 497 peptides, 66 chains. Longest chain 20 peptides. Score 0.557 Round 3: 520 peptides, 69 chains. Longest chain 20 peptides. Score 0.570 Round 4: 506 peptides, 68 chains. Longest chain 20 peptides. Score 0.557 Round 5: 513 peptides, 70 chains. Longest chain 23 peptides. Score 0.555 Taking the results from Round 3 Chains 70, Residues 451, Estimated correctness of the model 32.7 % 5 chains (29 residues) have been docked in sequence ------------------------------------------------------ 15216 reflections ( 89.87 % complete ) and 14600 restraints for refining 6500 atoms. 12795 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2482 (Rfree = 0.000) for 6500 atoms. Found 43 (58 requested) and removed 62 (29 requested) atoms. Cycle 7: After refmac, R = 0.2408 (Rfree = 0.000) for 6458 atoms. Found 43 (58 requested) and removed 49 (29 requested) atoms. Cycle 8: After refmac, R = 0.2263 (Rfree = 0.000) for 6433 atoms. Found 29 (57 requested) and removed 37 (28 requested) atoms. Cycle 9: After refmac, R = 0.2307 (Rfree = 0.000) for 6404 atoms. Found 30 (57 requested) and removed 39 (28 requested) atoms. Cycle 10: After refmac, R = 0.2146 (Rfree = 0.000) for 6377 atoms. Found 21 (57 requested) and removed 30 (28 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.22 3.18 Search for helices and strands: 0 residues in 0 chains, 6576 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 6593 seeds are put forward Round 1: 442 peptides, 80 chains. Longest chain 14 peptides. Score 0.386 Round 2: 483 peptides, 75 chains. Longest chain 14 peptides. Score 0.483 Round 3: 495 peptides, 79 chains. Longest chain 14 peptides. Score 0.475 Round 4: 515 peptides, 80 chains. Longest chain 20 peptides. Score 0.497 Round 5: 496 peptides, 72 chains. Longest chain 20 peptides. Score 0.520 Taking the results from Round 5 Chains 73, Residues 424, Estimated correctness of the model 17.7 % 6 chains (31 residues) have been docked in sequence ------------------------------------------------------ 15216 reflections ( 89.87 % complete ) and 14597 restraints for refining 6500 atoms. 12908 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2516 (Rfree = 0.000) for 6500 atoms. Found 41 (58 requested) and removed 49 (29 requested) atoms. Cycle 12: After refmac, R = 0.2396 (Rfree = 0.000) for 6481 atoms. Found 17 (58 requested) and removed 37 (29 requested) atoms. Cycle 13: After refmac, R = 0.2455 (Rfree = 0.000) for 6448 atoms. Found 25 (57 requested) and removed 40 (28 requested) atoms. Cycle 14: After refmac, R = 0.2392 (Rfree = 0.000) for 6420 atoms. Found 28 (57 requested) and removed 31 (28 requested) atoms. Cycle 15: After refmac, R = 0.2221 (Rfree = 0.000) for 6409 atoms. Found 9 (57 requested) and removed 32 (28 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.23 3.19 Search for helices and strands: 0 residues in 0 chains, 6585 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 6604 seeds are put forward Round 1: 436 peptides, 76 chains. Longest chain 14 peptides. Score 0.404 Round 2: 471 peptides, 71 chains. Longest chain 21 peptides. Score 0.491 Round 3: 485 peptides, 69 chains. Longest chain 18 peptides. Score 0.523 Round 4: 490 peptides, 67 chains. Longest chain 24 peptides. Score 0.542 Round 5: 488 peptides, 66 chains. Longest chain 23 peptides. Score 0.545 Taking the results from Round 5 Chains 68, Residues 422, Estimated correctness of the model 25.4 % 5 chains (34 residues) have been docked in sequence ------------------------------------------------------ 15216 reflections ( 89.87 % complete ) and 14589 restraints for refining 6498 atoms. 12877 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2463 (Rfree = 0.000) for 6498 atoms. Found 40 (58 requested) and removed 43 (29 requested) atoms. Cycle 17: After refmac, R = 0.2408 (Rfree = 0.000) for 6482 atoms. Found 37 (58 requested) and removed 36 (29 requested) atoms. Cycle 18: After refmac, R = 0.2184 (Rfree = 0.000) for 6470 atoms. Found 15 (58 requested) and removed 37 (29 requested) atoms. Cycle 19: After refmac, R = 0.2194 (Rfree = 0.000) for 6423 atoms. Found 17 (57 requested) and removed 31 (28 requested) atoms. Cycle 20: After refmac, R = 0.2136 (Rfree = 0.000) for 6391 atoms. Found 15 (57 requested) and removed 29 (28 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.25 3.21 Search for helices and strands: 0 residues in 0 chains, 6565 seeds are put forward NCS extension: 28 residues added (2 deleted due to clashes), 6593 seeds are put forward Round 1: 417 peptides, 76 chains. Longest chain 18 peptides. Score 0.373 Round 2: 456 peptides, 75 chains. Longest chain 23 peptides. Score 0.442 Round 3: 469 peptides, 71 chains. Longest chain 28 peptides. Score 0.488 Round 4: 466 peptides, 67 chains. Longest chain 25 peptides. Score 0.509 Round 5: 478 peptides, 72 chains. Longest chain 16 peptides. Score 0.494 Taking the results from Round 4 Chains 69, Residues 399, Estimated correctness of the model 14.2 % 5 chains (50 residues) have been docked in sequence ------------------------------------------------------ 15216 reflections ( 89.87 % complete ) and 14422 restraints for refining 6500 atoms. 12730 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2840 (Rfree = 0.000) for 6500 atoms. Found 58 (58 requested) and removed 58 (29 requested) atoms. Cycle 22: After refmac, R = 0.2509 (Rfree = 0.000) for 6457 atoms. Found 30 (58 requested) and removed 34 (29 requested) atoms. Cycle 23: After refmac, R = 0.2235 (Rfree = 0.000) for 6446 atoms. Found 17 (57 requested) and removed 34 (28 requested) atoms. Cycle 24: After refmac, R = 0.2363 (Rfree = 0.000) for 6413 atoms. Found 57 (57 requested) and removed 30 (28 requested) atoms. Cycle 25: After refmac, R = 0.2358 (Rfree = 0.000) for 6426 atoms. Found 57 (57 requested) and removed 37 (28 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.28 3.24 Search for helices and strands: 0 residues in 0 chains, 6645 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 6656 seeds are put forward Round 1: 354 peptides, 68 chains. Longest chain 11 peptides. Score 0.323 Round 2: 395 peptides, 66 chains. Longest chain 12 peptides. Score 0.407 Round 3: 413 peptides, 62 chains. Longest chain 18 peptides. Score 0.463 Round 4: 422 peptides, 61 chains. Longest chain 16 peptides. Score 0.483 Round 5: 433 peptides, 68 chains. Longest chain 21 peptides. Score 0.454 Taking the results from Round 4 Chains 61, Residues 361, Estimated correctness of the model 5.7 % 6 chains (43 residues) have been docked in sequence ------------------------------------------------------ 15216 reflections ( 89.87 % complete ) and 14562 restraints for refining 6499 atoms. 13047 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2563 (Rfree = 0.000) for 6499 atoms. Found 44 (58 requested) and removed 66 (29 requested) atoms. Cycle 27: After refmac, R = 0.2533 (Rfree = 0.000) for 6451 atoms. Found 55 (58 requested) and removed 38 (29 requested) atoms. Cycle 28: After refmac, R = 0.2514 (Rfree = 0.000) for 6451 atoms. Found 58 (58 requested) and removed 38 (29 requested) atoms. Cycle 29: After refmac, R = 0.2188 (Rfree = 0.000) for 6460 atoms. Found 12 (58 requested) and removed 34 (29 requested) atoms. Cycle 30: After refmac, R = 0.2377 (Rfree = 0.000) for 6427 atoms. Found 53 (57 requested) and removed 34 (28 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.24 3.20 Search for helices and strands: 0 residues in 0 chains, 6582 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 6601 seeds are put forward Round 1: 370 peptides, 72 chains. Longest chain 13 peptides. Score 0.322 Round 2: 411 peptides, 69 chains. Longest chain 15 peptides. Score 0.412 Round 3: 422 peptides, 68 chains. Longest chain 15 peptides. Score 0.437 Round 4: 428 peptides, 62 chains. Longest chain 17 peptides. Score 0.486 Round 5: 425 peptides, 66 chains. Longest chain 16 peptides. Score 0.455 Taking the results from Round 4 Chains 64, Residues 366, Estimated correctness of the model 6.7 % 6 chains (42 residues) have been docked in sequence ------------------------------------------------------ 15216 reflections ( 89.87 % complete ) and 14587 restraints for refining 6500 atoms. 13072 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2499 (Rfree = 0.000) for 6500 atoms. Found 49 (58 requested) and removed 41 (29 requested) atoms. Cycle 32: After refmac, R = 0.2347 (Rfree = 0.000) for 6484 atoms. Found 28 (58 requested) and removed 34 (29 requested) atoms. Cycle 33: After refmac, R = 0.2395 (Rfree = 0.000) for 6465 atoms. Found 37 (58 requested) and removed 34 (29 requested) atoms. Cycle 34: After refmac, R = 0.2408 (Rfree = 0.000) for 6449 atoms. Found 52 (58 requested) and removed 36 (29 requested) atoms. Cycle 35: After refmac, R = 0.2512 (Rfree = 0.000) for 6450 atoms. Found 58 (58 requested) and removed 38 (29 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.20 3.16 Search for helices and strands: 0 residues in 0 chains, 6629 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 6648 seeds are put forward Round 1: 351 peptides, 66 chains. Longest chain 12 peptides. Score 0.333 Round 2: 390 peptides, 65 chains. Longest chain 13 peptides. Score 0.406 Round 3: 389 peptides, 57 chains. Longest chain 22 peptides. Score 0.461 Round 4: 379 peptides, 58 chains. Longest chain 17 peptides. Score 0.438 Round 5: 386 peptides, 59 chains. Longest chain 15 peptides. Score 0.442 Taking the results from Round 3 Chains 58, Residues 332, Estimated correctness of the model 0.0 % 3 chains (33 residues) have been docked in sequence ------------------------------------------------------ 15216 reflections ( 89.87 % complete ) and 14739 restraints for refining 6500 atoms. 13351 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2470 (Rfree = 0.000) for 6500 atoms. Found 58 (58 requested) and removed 39 (29 requested) atoms. Cycle 37: After refmac, R = 0.2555 (Rfree = 0.000) for 6494 atoms. Found 58 (58 requested) and removed 40 (29 requested) atoms. Cycle 38: After refmac, R = 0.2193 (Rfree = 0.000) for 6497 atoms. Found 21 (58 requested) and removed 35 (29 requested) atoms. Cycle 39: After refmac, R = 0.2169 (Rfree = 0.000) for 6473 atoms. Found 18 (58 requested) and removed 34 (29 requested) atoms. Cycle 40: After refmac, R = 0.2152 (Rfree = 0.000) for 6454 atoms. Found 18 (57 requested) and removed 35 (28 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.23 3.19 Search for helices and strands: 0 residues in 0 chains, 6577 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 6593 seeds are put forward Round 1: 315 peptides, 64 chains. Longest chain 10 peptides. Score 0.283 Round 2: 361 peptides, 58 chains. Longest chain 14 peptides. Score 0.409 Round 3: 360 peptides, 58 chains. Longest chain 14 peptides. Score 0.407 Round 4: 403 peptides, 65 chains. Longest chain 13 peptides. Score 0.427 Round 5: 380 peptides, 59 chains. Longest chain 15 peptides. Score 0.433 Taking the results from Round 5 Chains 61, Residues 321, Estimated correctness of the model 0.0 % 6 chains (47 residues) have been docked in sequence ------------------------------------------------------ 15216 reflections ( 89.87 % complete ) and 14609 restraints for refining 6500 atoms. 13252 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2343 (Rfree = 0.000) for 6500 atoms. Found 36 (58 requested) and removed 37 (29 requested) atoms. Cycle 42: After refmac, R = 0.2398 (Rfree = 0.000) for 6480 atoms. Found 58 (58 requested) and removed 39 (29 requested) atoms. Cycle 43: After refmac, R = 0.2355 (Rfree = 0.000) for 6491 atoms. Found 58 (58 requested) and removed 36 (29 requested) atoms. Cycle 44: After refmac, R = 0.2180 (Rfree = 0.000) for 6505 atoms. Found 52 (58 requested) and removed 35 (29 requested) atoms. Cycle 45: After refmac, R = 0.2121 (Rfree = 0.000) for 6512 atoms. Found 35 (58 requested) and removed 36 (29 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.21 3.17 Search for helices and strands: 0 residues in 0 chains, 6664 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 6683 seeds are put forward Round 1: 318 peptides, 61 chains. Longest chain 11 peptides. Score 0.312 Round 2: 351 peptides, 59 chains. Longest chain 12 peptides. Score 0.385 Round 3: 380 peptides, 63 chains. Longest chain 12 peptides. Score 0.404 Round 4: 370 peptides, 63 chains. Longest chain 12 peptides. Score 0.388 Round 5: 360 peptides, 58 chains. Longest chain 14 peptides. Score 0.407 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 58, Residues 302, Estimated correctness of the model 0.0 % 6 chains (35 residues) have been docked in sequence Sequence coverage is 11 % Consider running further cycles of model building using 2okc-3_warpNtrace.pdb as input Building loops using Loopy2018 58 chains (302 residues) following loop building 6 chains (35 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 15216 reflections ( 89.87 % complete ) and 15050 restraints for refining 6499 atoms. 13812 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2317 (Rfree = 0.000) for 6499 atoms. Found 0 (58 requested) and removed 29 (29 requested) atoms. Cycle 47: After refmac, R = 0.2431 (Rfree = 0.000) for 6440 atoms. Found 0 (58 requested) and removed 29 (29 requested) atoms. Cycle 48: After refmac, R = 0.2241 (Rfree = 0.000) for 6399 atoms. Found 0 (57 requested) and removed 28 (28 requested) atoms. Cycle 49: After refmac, R = 0.2194 (Rfree = 0.000) for 6368 atoms. TimeTaking 69.53