null Tue 25 Dec 19:27:57 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 2okc-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2okc-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2okc-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okc-3.2-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/2okc-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okc-3.2-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 ============================================================ Tue 25 Dec 19:28:13 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/2okc-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okc-3.2-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 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-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: 19 Cell parameters: 75.340 85.750 152.600 90.000 90.000 90.000 Input sequence file: 2okc-3.2-parrot-hancs.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 7891 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3190 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2735 (Rfree = 0.000) for 7891 atoms. Found 70 (70 requested) and removed 60 (35 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.24 3.20 Search for helices and strands: 0 residues in 0 chains, 8067 seeds are put forward NCS extension: 0 residues added, 8067 seeds are put forward Round 1: 369 peptides, 76 chains. Longest chain 12 peptides. Score 0.290 Round 2: 465 peptides, 78 chains. Longest chain 18 peptides. Score 0.436 Round 3: 484 peptides, 80 chains. Longest chain 17 peptides. Score 0.452 Round 4: 499 peptides, 76 chains. Longest chain 16 peptides. Score 0.499 Round 5: 520 peptides, 78 chains. Longest chain 17 peptides. Score 0.517 Taking the results from Round 5 Chains 79, Residues 442, Estimated correctness of the model 16.8 % 5 chains (39 residues) have been docked in sequence ------------------------------------------------------ 15216 reflections ( 89.87 % complete ) and 14314 restraints for refining 6499 atoms. 12509 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2577 (Rfree = 0.000) for 6499 atoms. Found 56 (58 requested) and removed 45 (29 requested) atoms. Cycle 2: After refmac, R = 0.2395 (Rfree = 0.000) for 6461 atoms. Found 21 (58 requested) and removed 43 (29 requested) atoms. Cycle 3: After refmac, R = 0.2402 (Rfree = 0.000) for 6418 atoms. Found 23 (57 requested) and removed 30 (28 requested) atoms. Cycle 4: After refmac, R = 0.2307 (Rfree = 0.000) for 6395 atoms. Found 24 (57 requested) and removed 32 (28 requested) atoms. Cycle 5: After refmac, R = 0.2266 (Rfree = 0.000) for 6374 atoms. Found 24 (57 requested) and removed 34 (28 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.20 3.16 Search for helices and strands: 0 residues in 0 chains, 6581 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 6595 seeds are put forward Round 1: 483 peptides, 83 chains. Longest chain 19 peptides. Score 0.431 Round 2: 528 peptides, 75 chains. Longest chain 21 peptides. Score 0.545 Round 3: 513 peptides, 69 chains. Longest chain 23 peptides. Score 0.561 Round 4: 535 peptides, 68 chains. Longest chain 22 peptides. Score 0.594 Round 5: 535 peptides, 69 chains. Longest chain 21 peptides. Score 0.588 Taking the results from Round 4 Chains 70, Residues 467, Estimated correctness of the model 39.4 % 8 chains (78 residues) have been docked in sequence ------------------------------------------------------ 15216 reflections ( 89.87 % complete ) and 14035 restraints for refining 6499 atoms. 11983 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2559 (Rfree = 0.000) for 6499 atoms. Found 42 (58 requested) and removed 50 (29 requested) atoms. Cycle 7: After refmac, R = 0.2373 (Rfree = 0.000) for 6470 atoms. Found 11 (58 requested) and removed 39 (29 requested) atoms. Cycle 8: After refmac, R = 0.2348 (Rfree = 0.000) for 6430 atoms. Found 17 (57 requested) and removed 33 (28 requested) atoms. Cycle 9: After refmac, R = 0.2278 (Rfree = 0.000) for 6407 atoms. Found 13 (57 requested) and removed 28 (28 requested) atoms. Cycle 10: After refmac, R = 0.2227 (Rfree = 0.000) for 6381 atoms. Found 13 (57 requested) and removed 28 (28 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.24 3.20 Search for helices and strands: 0 residues in 0 chains, 6578 seeds are put forward NCS extension: 17 residues added (4 deleted due to clashes), 6595 seeds are put forward Round 1: 469 peptides, 81 chains. Longest chain 13 peptides. Score 0.422 Round 2: 485 peptides, 69 chains. Longest chain 23 peptides. Score 0.523 Round 3: 496 peptides, 70 chains. Longest chain 18 peptides. Score 0.532 Round 4: 497 peptides, 64 chains. Longest chain 25 peptides. Score 0.569 Round 5: 513 peptides, 66 chains. Longest chain 20 peptides. Score 0.578 Taking the results from Round 5 Chains 66, Residues 447, Estimated correctness of the model 35.0 % 4 chains (22 residues) have been docked in sequence ------------------------------------------------------ 15216 reflections ( 89.87 % complete ) and 14656 restraints for refining 6499 atoms. 12868 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2572 (Rfree = 0.000) for 6499 atoms. Found 48 (58 requested) and removed 32 (29 requested) atoms. Cycle 12: After refmac, R = 0.2481 (Rfree = 0.000) for 6496 atoms. Found 19 (58 requested) and removed 35 (29 requested) atoms. Cycle 13: After refmac, R = 0.2524 (Rfree = 0.000) for 6473 atoms. Found 18 (58 requested) and removed 34 (29 requested) atoms. Cycle 14: After refmac, R = 0.2502 (Rfree = 0.000) for 6445 atoms. Found 13 (57 requested) and removed 29 (28 requested) atoms. Cycle 15: After refmac, R = 0.2462 (Rfree = 0.000) for 6415 atoms. Found 21 (57 requested) and removed 28 (28 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.22 3.18 Search for helices and strands: 0 residues in 0 chains, 6613 seeds are put forward NCS extension: 22 residues added (4 deleted due to clashes), 6635 seeds are put forward Round 1: 440 peptides, 74 chains. Longest chain 16 peptides. Score 0.424 Round 2: 486 peptides, 69 chains. Longest chain 16 peptides. Score 0.524 Round 3: 475 peptides, 69 chains. Longest chain 32 peptides. Score 0.509 Round 4: 496 peptides, 65 chains. Longest chain 38 peptides. Score 0.562 Round 5: 500 peptides, 63 chains. Longest chain 31 peptides. Score 0.578 Taking the results from Round 5 Chains 63, Residues 437, Estimated correctness of the model 35.0 % 4 chains (49 residues) have been docked in sequence ------------------------------------------------------ 15216 reflections ( 89.87 % complete ) and 14131 restraints for refining 6498 atoms. 12251 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2684 (Rfree = 0.000) for 6498 atoms. Found 44 (58 requested) and removed 42 (29 requested) atoms. Cycle 17: After refmac, R = 0.2611 (Rfree = 0.000) for 6480 atoms. Found 14 (58 requested) and removed 36 (29 requested) atoms. Cycle 18: After refmac, R = 0.2548 (Rfree = 0.000) for 6450 atoms. Found 13 (57 requested) and removed 37 (28 requested) atoms. Cycle 19: After refmac, R = 0.2523 (Rfree = 0.000) for 6424 atoms. Found 10 (57 requested) and removed 30 (28 requested) atoms. Cycle 20: After refmac, R = 0.2424 (Rfree = 0.000) for 6401 atoms. Found 12 (57 requested) and removed 28 (28 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.19 3.15 Search for helices and strands: 0 residues in 0 chains, 6584 seeds are put forward NCS extension: 39 residues added (2 deleted due to clashes), 6623 seeds are put forward Round 1: 448 peptides, 83 chains. Longest chain 26 peptides. Score 0.375 Round 2: 468 peptides, 70 chains. Longest chain 37 peptides. Score 0.493 Round 3: 489 peptides, 67 chains. Longest chain 38 peptides. Score 0.541 Round 4: 490 peptides, 71 chains. Longest chain 24 peptides. Score 0.518 Round 5: 477 peptides, 66 chains. Longest chain 36 peptides. Score 0.530 Taking the results from Round 3 Chains 68, Residues 422, Estimated correctness of the model 24.2 % 8 chains (79 residues) have been docked in sequence ------------------------------------------------------ 15216 reflections ( 89.87 % complete ) and 13783 restraints for refining 6499 atoms. 11846 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2539 (Rfree = 0.000) for 6499 atoms. Found 44 (58 requested) and removed 47 (29 requested) atoms. Cycle 22: After refmac, R = 0.2452 (Rfree = 0.000) for 6469 atoms. Found 29 (58 requested) and removed 38 (29 requested) atoms. Cycle 23: After refmac, R = 0.2382 (Rfree = 0.000) for 6440 atoms. Found 31 (57 requested) and removed 33 (28 requested) atoms. Cycle 24: After refmac, R = 0.2277 (Rfree = 0.000) for 6425 atoms. Found 15 (57 requested) and removed 33 (28 requested) atoms. Cycle 25: After refmac, R = 0.2216 (Rfree = 0.000) for 6397 atoms. Found 10 (57 requested) and removed 29 (28 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.21 3.17 Search for helices and strands: 0 residues in 0 chains, 6554 seeds are put forward NCS extension: 33 residues added (3 deleted due to clashes), 6587 seeds are put forward Round 1: 389 peptides, 70 chains. Longest chain 17 peptides. Score 0.369 Round 2: 421 peptides, 67 chains. Longest chain 21 peptides. Score 0.442 Round 3: 430 peptides, 69 chains. Longest chain 20 peptides. Score 0.442 Round 4: 438 peptides, 65 chains. Longest chain 19 peptides. Score 0.481 Round 5: 448 peptides, 66 chains. Longest chain 23 peptides. Score 0.489 Taking the results from Round 5 Chains 69, Residues 382, Estimated correctness of the model 7.7 % 8 chains (53 residues) have been docked in sequence ------------------------------------------------------ 15216 reflections ( 89.87 % complete ) and 14630 restraints for refining 6498 atoms. 13011 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2812 (Rfree = 0.000) for 6498 atoms. Found 43 (58 requested) and removed 51 (29 requested) atoms. Cycle 27: After refmac, R = 0.2607 (Rfree = 0.000) for 6459 atoms. Found 24 (58 requested) and removed 31 (29 requested) atoms. Cycle 28: After refmac, R = 0.2400 (Rfree = 0.000) for 6446 atoms. Found 13 (57 requested) and removed 30 (28 requested) atoms. Cycle 29: After refmac, R = 0.2384 (Rfree = 0.000) for 6422 atoms. Found 33 (57 requested) and removed 30 (28 requested) atoms. Cycle 30: After refmac, R = 0.2289 (Rfree = 0.000) for 6415 atoms. Found 18 (57 requested) and removed 36 (28 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.20 3.16 Search for helices and strands: 0 residues in 0 chains, 6579 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 6604 seeds are put forward Round 1: 355 peptides, 71 chains. Longest chain 12 peptides. Score 0.302 Round 2: 390 peptides, 67 chains. Longest chain 13 peptides. Score 0.392 Round 3: 402 peptides, 65 chains. Longest chain 14 peptides. Score 0.426 Round 4: 401 peptides, 64 chains. Longest chain 21 peptides. Score 0.431 Round 5: 385 peptides, 61 chains. Longest chain 14 peptides. Score 0.427 Taking the results from Round 4 Chains 64, Residues 337, Estimated correctness of the model 0.0 % 4 chains (22 residues) have been docked in sequence ------------------------------------------------------ 15216 reflections ( 89.87 % complete ) and 15020 restraints for refining 6500 atoms. 13680 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2335 (Rfree = 0.000) for 6500 atoms. Found 29 (58 requested) and removed 34 (29 requested) atoms. Cycle 32: After refmac, R = 0.2208 (Rfree = 0.000) for 6485 atoms. Found 9 (58 requested) and removed 32 (29 requested) atoms. Cycle 33: After refmac, R = 0.2203 (Rfree = 0.000) for 6451 atoms. Found 16 (57 requested) and removed 31 (28 requested) atoms. Cycle 34: After refmac, R = 0.2167 (Rfree = 0.000) for 6431 atoms. Found 28 (57 requested) and removed 29 (28 requested) atoms. Cycle 35: After refmac, R = 0.2132 (Rfree = 0.000) for 6417 atoms. Found 32 (57 requested) and removed 29 (28 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.18 3.14 Search for helices and strands: 0 residues in 0 chains, 6611 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 6645 seeds are put forward Round 1: 370 peptides, 72 chains. Longest chain 10 peptides. Score 0.322 Round 2: 409 peptides, 76 chains. Longest chain 11 peptides. Score 0.360 Round 3: 417 peptides, 72 chains. Longest chain 13 peptides. Score 0.401 Round 4: 441 peptides, 75 chains. Longest chain 13 peptides. Score 0.419 Round 5: 439 peptides, 73 chains. Longest chain 13 peptides. Score 0.429 Taking the results from Round 5 Chains 73, Residues 366, Estimated correctness of the model 0.0 % 9 chains (39 residues) have been docked in sequence ------------------------------------------------------ 15216 reflections ( 89.87 % complete ) and 14786 restraints for refining 6500 atoms. 13309 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2307 (Rfree = 0.000) for 6500 atoms. Found 25 (58 requested) and removed 52 (29 requested) atoms. Cycle 37: After refmac, R = 0.2172 (Rfree = 0.000) for 6467 atoms. Found 25 (58 requested) and removed 30 (29 requested) atoms. Cycle 38: After refmac, R = 0.2099 (Rfree = 0.000) for 6455 atoms. Found 25 (57 requested) and removed 28 (28 requested) atoms. Cycle 39: After refmac, R = 0.2017 (Rfree = 0.000) for 6444 atoms. Found 14 (57 requested) and removed 31 (28 requested) atoms. Cycle 40: After refmac, R = 0.1985 (Rfree = 0.000) for 6419 atoms. Found 5 (57 requested) and removed 28 (28 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.22 3.18 Search for helices and strands: 0 residues in 0 chains, 6555 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 6573 seeds are put forward Round 1: 376 peptides, 76 chains. Longest chain 9 peptides. Score 0.302 Round 2: 412 peptides, 71 chains. Longest chain 12 peptides. Score 0.400 Round 3: 414 peptides, 67 chains. Longest chain 15 peptides. Score 0.431 Round 4: 397 peptides, 67 chains. Longest chain 13 peptides. Score 0.404 Round 5: 400 peptides, 65 chains. Longest chain 15 peptides. Score 0.422 Taking the results from Round 3 Chains 68, Residues 347, Estimated correctness of the model 0.0 % 8 chains (40 residues) have been docked in sequence ------------------------------------------------------ 15216 reflections ( 89.87 % complete ) and 14810 restraints for refining 6500 atoms. 13398 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2161 (Rfree = 0.000) for 6500 atoms. Found 29 (58 requested) and removed 33 (29 requested) atoms. Cycle 42: After refmac, R = 0.2082 (Rfree = 0.000) for 6476 atoms. Found 25 (58 requested) and removed 32 (29 requested) atoms. Cycle 43: After refmac, R = 0.1986 (Rfree = 0.000) for 6455 atoms. Found 11 (58 requested) and removed 31 (29 requested) atoms. Cycle 44: After refmac, R = 0.1962 (Rfree = 0.000) for 6429 atoms. Found 11 (57 requested) and removed 30 (28 requested) atoms. Cycle 45: After refmac, R = 0.1940 (Rfree = 0.000) for 6404 atoms. Found 10 (57 requested) and removed 30 (28 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.21 3.17 Search for helices and strands: 0 residues in 0 chains, 6522 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 6543 seeds are put forward Round 1: 349 peptides, 69 chains. Longest chain 11 peptides. Score 0.307 Round 2: 391 peptides, 66 chains. Longest chain 15 peptides. Score 0.401 Round 3: 386 peptides, 64 chains. Longest chain 12 peptides. Score 0.407 Round 4: 380 peptides, 66 chains. Longest chain 13 peptides. Score 0.383 Round 5: 410 peptides, 69 chains. Longest chain 13 peptides. Score 0.411 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 69, Residues 341, Estimated correctness of the model 0.0 % 8 chains (35 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 2okc-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 303 A and 316 A 68 chains (348 residues) following loop building 7 chains (47 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 15216 reflections ( 89.87 % complete ) and 14778 restraints for refining 6500 atoms. 13380 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2455 (Rfree = 0.000) for 6500 atoms. Found 0 (58 requested) and removed 29 (29 requested) atoms. Cycle 47: After refmac, R = 0.2243 (Rfree = 0.000) for 6445 atoms. Found 0 (58 requested) and removed 29 (29 requested) atoms. Cycle 48: After refmac, R = 0.2089 (Rfree = 0.000) for 6399 atoms. Found 0 (57 requested) and removed 28 (28 requested) atoms. Cycle 49: After refmac, R = 0.2032 (Rfree = 0.000) for 6365 atoms. Found 0 (57 requested) and removed 28 (28 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:18:32 GMT 2018 Job finished. TimeTaking 110.58 Used memory is bytes: 22302264