Mon 24 Dec 00:13:26 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 2okc-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2okc-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2okc-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2okc-3.2-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/2okc-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2okc-3.2-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 00:13:31 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/2okc-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2okc-3.2-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 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-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: 75.340 85.750 152.600 90.000 90.000 90.000 Input sequence file: 2okc-3.2-parrot-mrncs.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 7925 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3170 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2535 (Rfree = 0.000) for 7925 atoms. Found 51 (71 requested) and removed 57 (35 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.24 3.20 Search for helices and strands: 0 residues in 0 chains, 8103 seeds are put forward NCS extension: 0 residues added, 8103 seeds are put forward Round 1: 396 peptides, 74 chains. Longest chain 13 peptides. Score 0.352 Round 2: 475 peptides, 76 chains. Longest chain 20 peptides. Score 0.464 Round 3: 518 peptides, 74 chains. Longest chain 21 peptides. Score 0.538 Round 4: 513 peptides, 73 chains. Longest chain 22 peptides. Score 0.537 Round 5: 522 peptides, 72 chains. Longest chain 22 peptides. Score 0.555 Taking the results from Round 5 Chains 74, Residues 450, Estimated correctness of the model 28.4 % 7 chains (63 residues) have been docked in sequence ------------------------------------------------------ 15216 reflections ( 89.87 % complete ) and 14116 restraints for refining 6499 atoms. 12182 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2553 (Rfree = 0.000) for 6499 atoms. Found 47 (58 requested) and removed 50 (29 requested) atoms. Cycle 2: After refmac, R = 0.2475 (Rfree = 0.000) for 6425 atoms. Found 41 (58 requested) and removed 46 (29 requested) atoms. Cycle 3: After refmac, R = 0.2400 (Rfree = 0.000) for 6391 atoms. Found 29 (57 requested) and removed 38 (28 requested) atoms. Cycle 4: After refmac, R = 0.2290 (Rfree = 0.000) for 6357 atoms. Found 12 (57 requested) and removed 36 (28 requested) atoms. Cycle 5: After refmac, R = 0.2304 (Rfree = 0.000) for 6321 atoms. Found 19 (56 requested) and removed 38 (28 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.24 3.20 Search for helices and strands: 0 residues in 0 chains, 6539 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 6557 seeds are put forward Round 1: 438 peptides, 73 chains. Longest chain 19 peptides. Score 0.428 Round 2: 504 peptides, 72 chains. Longest chain 27 peptides. Score 0.531 Round 3: 509 peptides, 72 chains. Longest chain 27 peptides. Score 0.538 Round 4: 520 peptides, 70 chains. Longest chain 25 peptides. Score 0.564 Round 5: 504 peptides, 68 chains. Longest chain 27 peptides. Score 0.555 Taking the results from Round 4 Chains 70, Residues 450, Estimated correctness of the model 31.0 % 8 chains (50 residues) have been docked in sequence ------------------------------------------------------ 15216 reflections ( 89.87 % complete ) and 14373 restraints for refining 6500 atoms. 12505 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2403 (Rfree = 0.000) for 6500 atoms. Found 57 (58 requested) and removed 44 (29 requested) atoms. Cycle 7: After refmac, R = 0.2265 (Rfree = 0.000) for 6478 atoms. Found 29 (58 requested) and removed 31 (29 requested) atoms. Cycle 8: After refmac, R = 0.2242 (Rfree = 0.000) for 6457 atoms. Found 34 (58 requested) and removed 35 (29 requested) atoms. Cycle 9: After refmac, R = 0.2182 (Rfree = 0.000) for 6443 atoms. Found 24 (57 requested) and removed 30 (28 requested) atoms. Cycle 10: After refmac, R = 0.2151 (Rfree = 0.000) for 6423 atoms. Found 21 (57 requested) and removed 31 (28 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.22 3.18 Search for helices and strands: 0 residues in 0 chains, 6611 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 6629 seeds are put forward Round 1: 424 peptides, 69 chains. Longest chain 16 peptides. Score 0.433 Round 2: 472 peptides, 69 chains. Longest chain 19 peptides. Score 0.505 Round 3: 500 peptides, 69 chains. Longest chain 24 peptides. Score 0.543 Round 4: 517 peptides, 67 chains. Longest chain 22 peptides. Score 0.577 Round 5: 525 peptides, 76 chains. Longest chain 19 peptides. Score 0.535 Taking the results from Round 4 Chains 70, Residues 450, Estimated correctness of the model 34.7 % 10 chains (77 residues) have been docked in sequence ------------------------------------------------------ 15216 reflections ( 89.87 % complete ) and 13884 restraints for refining 6500 atoms. 11887 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2317 (Rfree = 0.000) for 6500 atoms. Found 33 (58 requested) and removed 48 (29 requested) atoms. Cycle 12: After refmac, R = 0.2261 (Rfree = 0.000) for 6456 atoms. Found 39 (58 requested) and removed 41 (29 requested) atoms. Cycle 13: After refmac, R = 0.2042 (Rfree = 0.000) for 6429 atoms. Found 18 (57 requested) and removed 35 (28 requested) atoms. Cycle 14: After refmac, R = 0.1943 (Rfree = 0.000) for 6400 atoms. Found 17 (57 requested) and removed 32 (28 requested) atoms. Cycle 15: After refmac, R = 0.1925 (Rfree = 0.000) for 6373 atoms. Found 12 (57 requested) and removed 30 (28 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.23 3.19 Search for helices and strands: 0 residues in 0 chains, 6561 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 6587 seeds are put forward Round 1: 421 peptides, 71 chains. Longest chain 17 peptides. Score 0.414 Round 2: 476 peptides, 71 chains. Longest chain 17 peptides. Score 0.498 Round 3: 499 peptides, 66 chains. Longest chain 22 peptides. Score 0.560 Round 4: 482 peptides, 64 chains. Longest chain 23 peptides. Score 0.549 Round 5: 490 peptides, 63 chains. Longest chain 27 peptides. Score 0.566 Taking the results from Round 5 Chains 67, Residues 427, Estimated correctness of the model 31.6 % 9 chains (76 residues) have been docked in sequence ------------------------------------------------------ 15216 reflections ( 89.87 % complete ) and 13852 restraints for refining 6500 atoms. 11922 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2380 (Rfree = 0.000) for 6500 atoms. Found 48 (58 requested) and removed 55 (29 requested) atoms. Cycle 17: After refmac, R = 0.2333 (Rfree = 0.000) for 6471 atoms. Found 12 (58 requested) and removed 41 (29 requested) atoms. Cycle 18: After refmac, R = 0.2246 (Rfree = 0.000) for 6432 atoms. Found 20 (57 requested) and removed 34 (28 requested) atoms. Cycle 19: After refmac, R = 0.2258 (Rfree = 0.000) for 6411 atoms. Found 25 (57 requested) and removed 36 (28 requested) atoms. Cycle 20: After refmac, R = 0.2220 (Rfree = 0.000) for 6389 atoms. Found 20 (57 requested) and removed 33 (28 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.21 3.17 Search for helices and strands: 0 residues in 0 chains, 6588 seeds are put forward NCS extension: 27 residues added (3 deleted due to clashes), 6615 seeds are put forward Round 1: 439 peptides, 78 chains. Longest chain 14 peptides. Score 0.395 Round 2: 479 peptides, 72 chains. Longest chain 23 peptides. Score 0.496 Round 3: 478 peptides, 71 chains. Longest chain 21 peptides. Score 0.501 Round 4: 480 peptides, 68 chains. Longest chain 25 peptides. Score 0.522 Round 5: 499 peptides, 73 chains. Longest chain 21 peptides. Score 0.518 Taking the results from Round 4 Chains 72, Residues 412, Estimated correctness of the model 18.3 % 5 chains (42 residues) have been docked in sequence ------------------------------------------------------ 15216 reflections ( 89.87 % complete ) and 14379 restraints for refining 6499 atoms. 12671 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2391 (Rfree = 0.000) for 6499 atoms. Found 40 (58 requested) and removed 54 (29 requested) atoms. Cycle 22: After refmac, R = 0.2288 (Rfree = 0.000) for 6464 atoms. Found 33 (58 requested) and removed 35 (29 requested) atoms. Cycle 23: After refmac, R = 0.2290 (Rfree = 0.000) for 6450 atoms. Found 24 (57 requested) and removed 37 (28 requested) atoms. Cycle 24: After refmac, R = 0.2301 (Rfree = 0.000) for 6435 atoms. Found 36 (57 requested) and removed 43 (28 requested) atoms. Cycle 25: After refmac, R = 0.2123 (Rfree = 0.000) for 6417 atoms. Found 12 (57 requested) and removed 31 (28 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.19 3.15 Search for helices and strands: 0 residues in 0 chains, 6607 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 6622 seeds are put forward Round 1: 414 peptides, 79 chains. Longest chain 17 peptides. Score 0.346 Round 2: 448 peptides, 67 chains. Longest chain 18 peptides. Score 0.483 Round 3: 448 peptides, 64 chains. Longest chain 21 peptides. Score 0.502 Round 4: 455 peptides, 66 chains. Longest chain 25 peptides. Score 0.499 Round 5: 442 peptides, 65 chains. Longest chain 20 peptides. Score 0.487 Taking the results from Round 3 Chains 66, Residues 384, Estimated correctness of the model 12.0 % 7 chains (52 residues) have been docked in sequence ------------------------------------------------------ 15216 reflections ( 89.87 % complete ) and 14301 restraints for refining 6499 atoms. 12686 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2270 (Rfree = 0.000) for 6499 atoms. Found 38 (58 requested) and removed 38 (29 requested) atoms. Cycle 27: After refmac, R = 0.2183 (Rfree = 0.000) for 6488 atoms. Found 31 (58 requested) and removed 35 (29 requested) atoms. Cycle 28: After refmac, R = 0.2418 (Rfree = 0.000) for 6472 atoms. Found 58 (58 requested) and removed 36 (29 requested) atoms. Cycle 29: After refmac, R = 0.2081 (Rfree = 0.000) for 6487 atoms. Found 25 (58 requested) and removed 33 (29 requested) atoms. Cycle 30: After refmac, R = 0.2005 (Rfree = 0.000) for 6469 atoms. Found 15 (58 requested) and removed 32 (29 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.20 3.16 Search for helices and strands: 0 residues in 0 chains, 6640 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 6654 seeds are put forward Round 1: 403 peptides, 75 chains. Longest chain 13 peptides. Score 0.357 Round 2: 447 peptides, 73 chains. Longest chain 15 peptides. Score 0.442 Round 3: 444 peptides, 71 chains. Longest chain 14 peptides. Score 0.450 Round 4: 458 peptides, 70 chains. Longest chain 16 peptides. Score 0.478 Round 5: 455 peptides, 70 chains. Longest chain 20 peptides. Score 0.474 Taking the results from Round 4 Chains 71, Residues 388, Estimated correctness of the model 4.1 % 6 chains (51 residues) have been docked in sequence ------------------------------------------------------ 15216 reflections ( 89.87 % complete ) and 14280 restraints for refining 6500 atoms. 12628 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2222 (Rfree = 0.000) for 6500 atoms. Found 35 (58 requested) and removed 37 (29 requested) atoms. Cycle 32: After refmac, R = 0.2110 (Rfree = 0.000) for 6470 atoms. Found 17 (58 requested) and removed 34 (29 requested) atoms. Cycle 33: After refmac, R = 0.2041 (Rfree = 0.000) for 6439 atoms. Found 14 (57 requested) and removed 33 (28 requested) atoms. Cycle 34: After refmac, R = 0.2033 (Rfree = 0.000) for 6405 atoms. Found 21 (57 requested) and removed 32 (28 requested) atoms. Cycle 35: After refmac, R = 0.2005 (Rfree = 0.000) for 6387 atoms. Found 17 (57 requested) and removed 30 (28 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.22 3.18 Search for helices and strands: 0 residues in 0 chains, 6537 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 6555 seeds are put forward Round 1: 361 peptides, 68 chains. Longest chain 14 peptides. Score 0.336 Round 2: 393 peptides, 62 chains. Longest chain 17 peptides. Score 0.432 Round 3: 409 peptides, 70 chains. Longest chain 16 peptides. Score 0.402 Round 4: 409 peptides, 67 chains. Longest chain 15 peptides. Score 0.423 Round 5: 408 peptides, 67 chains. Longest chain 13 peptides. Score 0.421 Taking the results from Round 2 Chains 66, Residues 331, Estimated correctness of the model 0.0 % 8 chains (57 residues) have been docked in sequence ------------------------------------------------------ 15216 reflections ( 89.87 % complete ) and 14474 restraints for refining 6500 atoms. 13040 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2228 (Rfree = 0.000) for 6500 atoms. Found 39 (58 requested) and removed 66 (29 requested) atoms. Cycle 37: After refmac, R = 0.2139 (Rfree = 0.000) for 6463 atoms. Found 35 (58 requested) and removed 32 (29 requested) atoms. Cycle 38: After refmac, R = 0.2329 (Rfree = 0.000) for 6460 atoms. Found 58 (58 requested) and removed 37 (29 requested) atoms. Cycle 39: After refmac, R = 0.2081 (Rfree = 0.000) for 6465 atoms. Found 27 (58 requested) and removed 36 (29 requested) atoms. Cycle 40: After refmac, R = 0.2077 (Rfree = 0.000) for 6450 atoms. Found 24 (57 requested) and removed 35 (28 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.19 3.15 Search for helices and strands: 0 residues in 0 chains, 6611 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 6623 seeds are put forward Round 1: 294 peptides, 61 chains. Longest chain 11 peptides. Score 0.267 Round 2: 339 peptides, 54 chains. Longest chain 13 peptides. Score 0.402 Round 3: 361 peptides, 63 chains. Longest chain 12 peptides. Score 0.373 Round 4: 362 peptides, 59 chains. Longest chain 15 peptides. Score 0.403 Round 5: 374 peptides, 62 chains. Longest chain 15 peptides. Score 0.402 Taking the results from Round 4 Chains 60, Residues 303, Estimated correctness of the model 0.0 % 7 chains (51 residues) have been docked in sequence ------------------------------------------------------ 15216 reflections ( 89.87 % complete ) and 14700 restraints for refining 6500 atoms. 13407 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2225 (Rfree = 0.000) for 6500 atoms. Found 42 (58 requested) and removed 43 (29 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2063 (Rfree = 0.000) for 6484 atoms. Found 23 (58 requested) and removed 36 (29 requested) atoms. Cycle 43: After refmac, R = 0.2046 (Rfree = 0.000) for 6458 atoms. Found 29 (58 requested) and removed 33 (29 requested) atoms. Cycle 44: After refmac, R = 0.2022 (Rfree = 0.000) for 6447 atoms. Found 34 (57 requested) and removed 30 (28 requested) atoms. Cycle 45: After refmac, R = 0.1868 (Rfree = 0.000) for 6443 atoms. Found 13 (57 requested) and removed 30 (28 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 3.14 Search for helices and strands: 0 residues in 0 chains, 6599 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 6624 seeds are put forward Round 1: 302 peptides, 62 chains. Longest chain 10 peptides. Score 0.275 Round 2: 326 peptides, 61 chains. Longest chain 15 peptides. Score 0.327 Round 3: 350 peptides, 62 chains. Longest chain 14 peptides. Score 0.361 Round 4: 377 peptides, 63 chains. Longest chain 14 peptides. Score 0.399 Round 5: 354 peptides, 62 chains. Longest chain 14 peptides. Score 0.368 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 64, Residues 314, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 2okc-3_warpNtrace.pdb as input Building loops using Loopy2018 64 chains (314 residues) following loop building 3 chains (16 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 15216 reflections ( 89.87 % complete ) and 14859 restraints for refining 6500 atoms. 13627 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2183 (Rfree = 0.000) for 6500 atoms. Found 0 (58 requested) and removed 29 (29 requested) atoms. Cycle 47: After refmac, R = 0.2072 (Rfree = 0.000) for 6454 atoms. Found 0 (58 requested) and removed 29 (29 requested) atoms. Cycle 48: After refmac, R = 0.2013 (Rfree = 0.000) for 6410 atoms. Found 0 (57 requested) and removed 28 (28 requested) atoms. Cycle 49: After refmac, R = 0.2089 (Rfree = 0.000) for 6377 atoms. TimeTaking 78.73