null Sun 23 Dec 22:22:49 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 1vkz-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkz-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkz-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkz-4.0-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/1vkz-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkz-4.0-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 22:22:58 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/1vkz-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkz-4.0-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 603 and 0 Target number of residues in the AU: 603 Target solvent content: 0.6147 Checking the provided sequence file Detected sequence length: 412 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 824 Adjusted target solvent content: 0.47 Input MTZ file: 1vkz-4.0-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: 63.745 78.443 85.018 90.000 95.062 90.000 Input sequence file: 1vkz-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 6592 target number of atoms Had to go as low as 0.60 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: 19.959 4.001 Wilson plot Bfac: 58.96 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 6916 reflections ( 96.32 % complete ) and 0 restraints for refining 7267 atoms. Observations/parameters ratio is 0.24 ------------------------------------------------------ Starting model: R = 0.2990 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2905 (Rfree = 0.000) for 7267 atoms. Found 26 (34 requested) and removed 340 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.35 3.49 Search for helices and strands: 0 residues in 0 chains, 6990 seeds are put forward NCS extension: 0 residues added, 6990 seeds are put forward Round 1: 224 peptides, 49 chains. Longest chain 12 peptides. Score 0.235 Round 2: 290 peptides, 55 chains. Longest chain 14 peptides. Score 0.324 Round 3: 331 peptides, 59 chains. Longest chain 12 peptides. Score 0.372 Round 4: 346 peptides, 63 chains. Longest chain 14 peptides. Score 0.368 Round 5: 349 peptides, 61 chains. Longest chain 12 peptides. Score 0.390 Taking the results from Round 5 Chains 63, Residues 288, Estimated correctness of the model 0.0 % 13 chains (64 residues) have been docked in sequence ------------------------------------------------------ 6916 reflections ( 96.32 % complete ) and 13819 restraints for refining 5953 atoms. 12577 conditional restraints added. Observations/parameters ratio is 0.29 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2734 (Rfree = 0.000) for 5953 atoms. Found 23 (28 requested) and removed 87 (14 requested) atoms. Cycle 2: After refmac, R = 0.2594 (Rfree = 0.000) for 5765 atoms. Found 27 (27 requested) and removed 61 (13 requested) atoms. Cycle 3: After refmac, R = 0.2120 (Rfree = 0.000) for 5646 atoms. Found 23 (27 requested) and removed 58 (13 requested) atoms. Cycle 4: After refmac, R = 0.2327 (Rfree = 0.000) for 5564 atoms. Found 25 (26 requested) and removed 43 (13 requested) atoms. Cycle 5: After refmac, R = 0.2366 (Rfree = 0.000) for 5519 atoms. Found 26 (26 requested) and removed 43 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.35 3.49 Search for helices and strands: 0 residues in 0 chains, 5667 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 5680 seeds are put forward Round 1: 333 peptides, 67 chains. Longest chain 11 peptides. Score 0.308 Round 2: 380 peptides, 63 chains. Longest chain 12 peptides. Score 0.432 Round 3: 382 peptides, 59 chains. Longest chain 13 peptides. Score 0.467 Round 4: 396 peptides, 65 chains. Longest chain 12 peptides. Score 0.445 Round 5: 422 peptides, 64 chains. Longest chain 18 peptides. Score 0.498 Taking the results from Round 5 Chains 67, Residues 358, Estimated correctness of the model 0.0 % 5 chains (46 residues) have been docked in sequence ------------------------------------------------------ 6916 reflections ( 96.32 % complete ) and 12612 restraints for refining 5666 atoms. 11088 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2216 (Rfree = 0.000) for 5666 atoms. Found 26 (26 requested) and removed 109 (13 requested) atoms. Cycle 7: After refmac, R = 0.1974 (Rfree = 0.000) for 5525 atoms. Found 26 (26 requested) and removed 72 (13 requested) atoms. Cycle 8: After refmac, R = 0.1812 (Rfree = 0.000) for 5453 atoms. Found 19 (26 requested) and removed 26 (13 requested) atoms. Cycle 9: After refmac, R = 0.1533 (Rfree = 0.000) for 5425 atoms. Found 10 (25 requested) and removed 25 (12 requested) atoms. Cycle 10: After refmac, R = 0.1712 (Rfree = 0.000) for 5388 atoms. Found 18 (25 requested) and removed 22 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.33 3.47 Search for helices and strands: 0 residues in 0 chains, 5540 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 5552 seeds are put forward Round 1: 376 peptides, 73 chains. Longest chain 11 peptides. Score 0.344 Round 2: 404 peptides, 61 chains. Longest chain 18 peptides. Score 0.489 Round 3: 420 peptides, 58 chains. Longest chain 17 peptides. Score 0.537 Round 4: 423 peptides, 62 chains. Longest chain 20 peptides. Score 0.514 Round 5: 413 peptides, 62 chains. Longest chain 15 peptides. Score 0.497 Taking the results from Round 3 Chains 61, Residues 362, Estimated correctness of the model 0.0 % 8 chains (60 residues) have been docked in sequence ------------------------------------------------------ 6916 reflections ( 96.32 % complete ) and 12186 restraints for refining 5687 atoms. 10624 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2233 (Rfree = 0.000) for 5687 atoms. Found 27 (27 requested) and removed 66 (13 requested) atoms. Cycle 12: After refmac, R = 0.2246 (Rfree = 0.000) for 5560 atoms. Found 26 (26 requested) and removed 38 (13 requested) atoms. Cycle 13: After refmac, R = 0.1800 (Rfree = 0.000) for 5484 atoms. Found 15 (26 requested) and removed 25 (13 requested) atoms. Cycle 14: After refmac, R = 0.1609 (Rfree = 0.000) for 5441 atoms. Found 11 (25 requested) and removed 29 (12 requested) atoms. Cycle 15: After refmac, R = 0.1590 (Rfree = 0.000) for 5404 atoms. Found 11 (25 requested) and removed 21 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.42 3.56 Search for helices and strands: 0 residues in 0 chains, 5540 seeds are put forward NCS extension: 30 residues added (1 deleted due to clashes), 5570 seeds are put forward Round 1: 314 peptides, 61 chains. Longest chain 11 peptides. Score 0.321 Round 2: 370 peptides, 60 chains. Longest chain 15 peptides. Score 0.438 Round 3: 410 peptides, 65 chains. Longest chain 17 peptides. Score 0.470 Round 4: 391 peptides, 60 chains. Longest chain 14 peptides. Score 0.475 Round 5: 395 peptides, 55 chains. Longest chain 16 peptides. Score 0.519 Taking the results from Round 5 Chains 56, Residues 340, Estimated correctness of the model 0.0 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 6916 reflections ( 96.32 % complete ) and 13024 restraints for refining 5744 atoms. 11646 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2618 (Rfree = 0.000) for 5744 atoms. Found 27 (27 requested) and removed 70 (13 requested) atoms. Cycle 17: After refmac, R = 0.2336 (Rfree = 0.000) for 5625 atoms. Found 27 (27 requested) and removed 49 (13 requested) atoms. Cycle 18: After refmac, R = 0.1923 (Rfree = 0.000) for 5561 atoms. Found 21 (26 requested) and removed 28 (13 requested) atoms. Cycle 19: After refmac, R = 0.1678 (Rfree = 0.000) for 5515 atoms. Found 22 (26 requested) and removed 21 (13 requested) atoms. Cycle 20: After refmac, R = 0.1579 (Rfree = 0.000) for 5498 atoms. Found 9 (26 requested) and removed 26 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.45 3.59 Search for helices and strands: 0 residues in 0 chains, 5634 seeds are put forward NCS extension: 17 residues added (4 deleted due to clashes), 5651 seeds are put forward Round 1: 309 peptides, 63 chains. Longest chain 11 peptides. Score 0.293 Round 2: 349 peptides, 56 chains. Longest chain 14 peptides. Score 0.431 Round 3: 367 peptides, 53 chains. Longest chain 16 peptides. Score 0.487 Round 4: 378 peptides, 56 chains. Longest chain 15 peptides. Score 0.483 Round 5: 374 peptides, 59 chains. Longest chain 21 peptides. Score 0.453 Taking the results from Round 3 Chains 53, Residues 314, Estimated correctness of the model 0.0 % 4 chains (34 residues) have been docked in sequence ------------------------------------------------------ 6916 reflections ( 96.32 % complete ) and 12501 restraints for refining 5632 atoms. 11153 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2523 (Rfree = 0.000) for 5632 atoms. Found 26 (26 requested) and removed 75 (13 requested) atoms. Cycle 22: After refmac, R = 0.2487 (Rfree = 0.000) for 5517 atoms. Found 26 (26 requested) and removed 48 (13 requested) atoms. Cycle 23: After refmac, R = 0.1959 (Rfree = 0.000) for 5440 atoms. Found 24 (26 requested) and removed 31 (13 requested) atoms. Cycle 24: After refmac, R = 0.1754 (Rfree = 0.000) for 5406 atoms. Found 19 (25 requested) and removed 23 (12 requested) atoms. Cycle 25: After refmac, R = 0.1779 (Rfree = 0.000) for 5385 atoms. Found 22 (25 requested) and removed 20 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.43 3.57 Search for helices and strands: 0 residues in 0 chains, 5511 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 5531 seeds are put forward Round 1: 305 peptides, 59 chains. Longest chain 13 peptides. Score 0.320 Round 2: 359 peptides, 60 chains. Longest chain 12 peptides. Score 0.417 Round 3: 384 peptides, 66 chains. Longest chain 13 peptides. Score 0.416 Round 4: 390 peptides, 66 chains. Longest chain 13 peptides. Score 0.427 Round 5: 379 peptides, 59 chains. Longest chain 15 peptides. Score 0.461 Taking the results from Round 5 Chains 59, Residues 320, Estimated correctness of the model 0.0 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 6916 reflections ( 96.32 % complete ) and 12703 restraints for refining 5640 atoms. 11391 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2594 (Rfree = 0.000) for 5640 atoms. Found 26 (26 requested) and removed 80 (13 requested) atoms. Cycle 27: After refmac, R = 0.2583 (Rfree = 0.000) for 5516 atoms. Found 26 (26 requested) and removed 63 (13 requested) atoms. Cycle 28: After refmac, R = 0.1909 (Rfree = 0.000) for 5417 atoms. Found 25 (26 requested) and removed 24 (13 requested) atoms. Cycle 29: After refmac, R = 0.1710 (Rfree = 0.000) for 5385 atoms. Found 18 (25 requested) and removed 19 (12 requested) atoms. Cycle 30: After refmac, R = 0.1707 (Rfree = 0.000) for 5371 atoms. Found 20 (25 requested) and removed 19 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.42 3.56 Search for helices and strands: 0 residues in 0 chains, 5510 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 5525 seeds are put forward Round 1: 281 peptides, 57 chains. Longest chain 10 peptides. Score 0.287 Round 2: 348 peptides, 56 chains. Longest chain 16 peptides. Score 0.429 Round 3: 361 peptides, 63 chains. Longest chain 12 peptides. Score 0.397 Round 4: 368 peptides, 60 chains. Longest chain 17 peptides. Score 0.434 Round 5: 368 peptides, 58 chains. Longest chain 14 peptides. Score 0.450 Taking the results from Round 5 Chains 59, Residues 310, Estimated correctness of the model 0.0 % 7 chains (48 residues) have been docked in sequence ------------------------------------------------------ 6916 reflections ( 96.32 % complete ) and 12416 restraints for refining 5668 atoms. 11062 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2631 (Rfree = 0.000) for 5668 atoms. Found 26 (26 requested) and removed 86 (13 requested) atoms. Cycle 32: After refmac, R = 0.2372 (Rfree = 0.000) for 5513 atoms. Found 26 (26 requested) and removed 49 (13 requested) atoms. Cycle 33: After refmac, R = 0.2279 (Rfree = 0.000) for 5451 atoms. Found 26 (26 requested) and removed 34 (13 requested) atoms. Cycle 34: After refmac, R = 0.2260 (Rfree = 0.000) for 5409 atoms. Found 25 (25 requested) and removed 28 (12 requested) atoms. Cycle 35: After refmac, R = 0.1828 (Rfree = 0.000) for 5382 atoms. Found 25 (25 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.39 3.53 Search for helices and strands: 0 residues in 0 chains, 5489 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 5505 seeds are put forward Round 1: 263 peptides, 55 chains. Longest chain 10 peptides. Score 0.266 Round 2: 286 peptides, 51 chains. Longest chain 11 peptides. Score 0.351 Round 3: 311 peptides, 51 chains. Longest chain 16 peptides. Score 0.401 Round 4: 293 peptides, 50 chains. Longest chain 12 peptides. Score 0.374 Round 5: 287 peptides, 48 chains. Longest chain 15 peptides. Score 0.380 Taking the results from Round 3 Chains 51, Residues 260, Estimated correctness of the model 0.0 % 6 chains (34 residues) have been docked in sequence ------------------------------------------------------ 6916 reflections ( 96.32 % complete ) and 12036 restraints for refining 5359 atoms. 10952 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2449 (Rfree = 0.000) for 5359 atoms. Found 25 (25 requested) and removed 40 (12 requested) atoms. Cycle 37: After refmac, R = 0.2472 (Rfree = 0.000) for 5311 atoms. Found 25 (25 requested) and removed 36 (12 requested) atoms. Cycle 38: After refmac, R = 0.2276 (Rfree = 0.000) for 5252 atoms. Found 25 (25 requested) and removed 31 (12 requested) atoms. Cycle 39: After refmac, R = 0.2270 (Rfree = 0.000) for 5212 atoms. Found 24 (24 requested) and removed 28 (12 requested) atoms. Cycle 40: After refmac, R = 0.2270 (Rfree = 0.000) for 5191 atoms. Found 24 (24 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 3.62 Search for helices and strands: 0 residues in 0 chains, 5300 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 5315 seeds are put forward Round 1: 263 peptides, 55 chains. Longest chain 10 peptides. Score 0.266 Round 2: 284 peptides, 48 chains. Longest chain 13 peptides. Score 0.374 Round 3: 304 peptides, 51 chains. Longest chain 17 peptides. Score 0.387 Round 4: 319 peptides, 54 chains. Longest chain 15 peptides. Score 0.391 Round 5: 317 peptides, 54 chains. Longest chain 14 peptides. Score 0.387 Taking the results from Round 4 Chains 54, Residues 265, Estimated correctness of the model 0.0 % 6 chains (32 residues) have been docked in sequence ------------------------------------------------------ 6916 reflections ( 96.32 % complete ) and 10890 restraints for refining 5047 atoms. 9804 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2720 (Rfree = 0.000) for 5047 atoms. Found 23 (23 requested) and removed 44 (11 requested) atoms. Cycle 42: After refmac, R = 0.2563 (Rfree = 0.000) for 4962 atoms. Found 23 (23 requested) and removed 31 (11 requested) atoms. Cycle 43: After refmac, R = 0.2513 (Rfree = 0.000) for 4926 atoms. Found 23 (23 requested) and removed 26 (11 requested) atoms. Cycle 44: After refmac, R = 0.2390 (Rfree = 0.000) for 4887 atoms. Found 23 (23 requested) and removed 26 (11 requested) atoms. Cycle 45: After refmac, R = 0.2012 (Rfree = 0.000) for 4859 atoms. Found 22 (23 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.48 3.62 Search for helices and strands: 0 residues in 0 chains, 4977 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 4990 seeds are put forward Round 1: 208 peptides, 45 chains. Longest chain 12 peptides. Score 0.236 Round 2: 284 peptides, 54 chains. Longest chain 12 peptides. Score 0.321 Round 3: 307 peptides, 55 chains. Longest chain 12 peptides. Score 0.359 Round 4: 319 peptides, 52 chains. Longest chain 12 peptides. Score 0.408 Round 5: 299 peptides, 46 chains. Longest chain 16 peptides. Score 0.420 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 46, Residues 253, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1vkz-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6916 reflections ( 96.32 % complete ) and 10442 restraints for refining 4804 atoms. 9476 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2693 (Rfree = 0.000) for 4804 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2680 (Rfree = 0.000) for 4753 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2677 (Rfree = 0.000) for 4708 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.2605 (Rfree = 0.000) for 4673 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:34:33 GMT 2018 Job finished. TimeTaking 71.74 Used memory is bytes: 3044392