Sun 23 Dec 22:22:56 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 2ii1-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ii1-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ii1-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ii1-3.6-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/2ii1-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ii1-3.6-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 22:23:04 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/2ii1-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ii1-3.6-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 757 and 0 Target number of residues in the AU: 757 Target solvent content: 0.6310 Checking the provided sequence file Detected sequence length: 301 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1204 Adjusted target solvent content: 0.41 Input MTZ file: 2ii1-3.6-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: 1 Cell parameters: 43.759 69.605 94.984 73.954 88.905 86.625 Input sequence file: 2ii1-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 9632 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: 91.283 3.600 Wilson plot Bfac: 66.82 11359 reflections ( 91.15 % complete ) and 0 restraints for refining 10638 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3206 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2894 (Rfree = 0.000) for 10638 atoms. Found 46 (68 requested) and removed 276 (34 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 3.76 Search for helices and strands: 0 residues in 0 chains, 10521 seeds are put forward NCS extension: 0 residues added, 10521 seeds are put forward Round 1: 352 peptides, 76 chains. Longest chain 9 peptides. Score 0.251 Round 2: 423 peptides, 84 chains. Longest chain 9 peptides. Score 0.312 Round 3: 469 peptides, 87 chains. Longest chain 13 peptides. Score 0.363 Round 4: 465 peptides, 84 chains. Longest chain 12 peptides. Score 0.376 Round 5: 461 peptides, 81 chains. Longest chain 13 peptides. Score 0.389 Taking the results from Round 5 Chains 83, Residues 380, Estimated correctness of the model 0.0 % 7 chains (38 residues) have been docked in sequence ------------------------------------------------------ 11359 reflections ( 91.15 % complete ) and 20624 restraints for refining 8731 atoms. 19098 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2096 (Rfree = 0.000) for 8731 atoms. Found 36 (56 requested) and removed 55 (28 requested) atoms. Cycle 2: After refmac, R = 0.2093 (Rfree = 0.000) for 8629 atoms. Found 41 (55 requested) and removed 43 (27 requested) atoms. Cycle 3: After refmac, R = 0.2053 (Rfree = 0.000) for 8597 atoms. Found 23 (55 requested) and removed 44 (27 requested) atoms. Cycle 4: After refmac, R = 0.1980 (Rfree = 0.000) for 8550 atoms. Found 28 (55 requested) and removed 46 (27 requested) atoms. Cycle 5: After refmac, R = 0.1908 (Rfree = 0.000) for 8513 atoms. Found 27 (54 requested) and removed 37 (27 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 3.80 Search for helices and strands: 0 residues in 0 chains, 8669 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 8681 seeds are put forward Round 1: 428 peptides, 90 chains. Longest chain 8 peptides. Score 0.280 Round 2: 484 peptides, 90 chains. Longest chain 11 peptides. Score 0.366 Round 3: 489 peptides, 87 chains. Longest chain 14 peptides. Score 0.392 Round 4: 525 peptides, 89 chains. Longest chain 15 peptides. Score 0.431 Round 5: 521 peptides, 90 chains. Longest chain 16 peptides. Score 0.419 Taking the results from Round 4 Chains 91, Residues 436, Estimated correctness of the model 0.0 % 9 chains (65 residues) have been docked in sequence ------------------------------------------------------ 11359 reflections ( 91.15 % complete ) and 20444 restraints for refining 8731 atoms. 18622 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1999 (Rfree = 0.000) for 8731 atoms. Found 45 (56 requested) and removed 49 (28 requested) atoms. Cycle 7: After refmac, R = 0.1892 (Rfree = 0.000) for 8669 atoms. Found 27 (55 requested) and removed 55 (27 requested) atoms. Cycle 8: After refmac, R = 0.1871 (Rfree = 0.000) for 8620 atoms. Found 35 (55 requested) and removed 53 (27 requested) atoms. Cycle 9: After refmac, R = 0.1777 (Rfree = 0.000) for 8582 atoms. Found 29 (55 requested) and removed 41 (27 requested) atoms. Cycle 10: After refmac, R = 0.1765 (Rfree = 0.000) for 8551 atoms. Found 31 (54 requested) and removed 39 (27 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.79 Search for helices and strands: 0 residues in 0 chains, 8773 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 8790 seeds are put forward Round 1: 386 peptides, 81 chains. Longest chain 8 peptides. Score 0.273 Round 2: 487 peptides, 84 chains. Longest chain 26 peptides. Score 0.408 Round 3: 490 peptides, 87 chains. Longest chain 17 peptides. Score 0.394 Round 4: 482 peptides, 83 chains. Longest chain 13 peptides. Score 0.407 Round 5: 487 peptides, 81 chains. Longest chain 22 peptides. Score 0.426 Taking the results from Round 5 Chains 83, Residues 406, Estimated correctness of the model 0.0 % 8 chains (53 residues) have been docked in sequence ------------------------------------------------------ 11359 reflections ( 91.15 % complete ) and 20575 restraints for refining 8731 atoms. 18878 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1876 (Rfree = 0.000) for 8731 atoms. Found 34 (56 requested) and removed 49 (28 requested) atoms. Cycle 12: After refmac, R = 0.1821 (Rfree = 0.000) for 8699 atoms. Found 37 (55 requested) and removed 37 (27 requested) atoms. Cycle 13: After refmac, R = 0.1767 (Rfree = 0.000) for 8687 atoms. Found 47 (55 requested) and removed 35 (27 requested) atoms. Cycle 14: After refmac, R = 0.1660 (Rfree = 0.000) for 8689 atoms. Found 29 (55 requested) and removed 38 (27 requested) atoms. Cycle 15: After refmac, R = 0.1839 (Rfree = 0.000) for 8678 atoms. Found 55 (55 requested) and removed 37 (27 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 3.78 Search for helices and strands: 0 residues in 0 chains, 8880 seeds are put forward NCS extension: 30 residues added (3 deleted due to clashes), 8910 seeds are put forward Round 1: 443 peptides, 96 chains. Longest chain 10 peptides. Score 0.265 Round 2: 465 peptides, 87 chains. Longest chain 12 peptides. Score 0.357 Round 3: 476 peptides, 85 chains. Longest chain 12 peptides. Score 0.386 Round 4: 466 peptides, 81 chains. Longest chain 13 peptides. Score 0.396 Round 5: 489 peptides, 86 chains. Longest chain 16 peptides. Score 0.399 Taking the results from Round 5 Chains 89, Residues 403, Estimated correctness of the model 0.0 % 9 chains (55 residues) have been docked in sequence ------------------------------------------------------ 11359 reflections ( 91.15 % complete ) and 20793 restraints for refining 8730 atoms. 19154 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1770 (Rfree = 0.000) for 8730 atoms. Found 34 (56 requested) and removed 42 (28 requested) atoms. Cycle 17: After refmac, R = 0.1789 (Rfree = 0.000) for 8700 atoms. Found 36 (55 requested) and removed 42 (27 requested) atoms. Cycle 18: After refmac, R = 0.1609 (Rfree = 0.000) for 8675 atoms. Found 28 (55 requested) and removed 36 (27 requested) atoms. Cycle 19: After refmac, R = 0.1386 (Rfree = 0.000) for 8659 atoms. Found 10 (55 requested) and removed 29 (27 requested) atoms. Cycle 20: After refmac, R = 0.1403 (Rfree = 0.000) for 8637 atoms. Found 7 (55 requested) and removed 36 (27 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.34 3.77 Search for helices and strands: 0 residues in 0 chains, 8799 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 8814 seeds are put forward Round 1: 473 peptides, 95 chains. Longest chain 10 peptides. Score 0.318 Round 2: 499 peptides, 86 chains. Longest chain 14 peptides. Score 0.413 Round 3: 518 peptides, 87 chains. Longest chain 16 peptides. Score 0.433 Round 4: 515 peptides, 85 chains. Longest chain 19 peptides. Score 0.441 Round 5: 522 peptides, 86 chains. Longest chain 18 peptides. Score 0.445 Taking the results from Round 5 Chains 86, Residues 436, Estimated correctness of the model 0.0 % 11 chains (49 residues) have been docked in sequence ------------------------------------------------------ 11359 reflections ( 91.15 % complete ) and 20630 restraints for refining 8730 atoms. 18873 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1705 (Rfree = 0.000) for 8730 atoms. Found 22 (56 requested) and removed 42 (28 requested) atoms. Cycle 22: After refmac, R = 0.1598 (Rfree = 0.000) for 8685 atoms. Found 23 (55 requested) and removed 39 (27 requested) atoms. Cycle 23: After refmac, R = 0.1478 (Rfree = 0.000) for 8651 atoms. Found 24 (55 requested) and removed 35 (27 requested) atoms. Cycle 24: After refmac, R = 0.1489 (Rfree = 0.000) for 8631 atoms. Found 28 (55 requested) and removed 35 (27 requested) atoms. Cycle 25: After refmac, R = 0.1370 (Rfree = 0.000) for 8615 atoms. Found 12 (55 requested) and removed 33 (27 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 3.75 Search for helices and strands: 0 residues in 0 chains, 8797 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 8819 seeds are put forward Round 1: 442 peptides, 90 chains. Longest chain 10 peptides. Score 0.303 Round 2: 442 peptides, 79 chains. Longest chain 16 peptides. Score 0.374 Round 3: 454 peptides, 71 chains. Longest chain 15 peptides. Score 0.441 Round 4: 436 peptides, 69 chains. Longest chain 17 peptides. Score 0.428 Round 5: 439 peptides, 72 chains. Longest chain 15 peptides. Score 0.414 Taking the results from Round 3 Chains 73, Residues 383, Estimated correctness of the model 0.0 % 8 chains (44 residues) have been docked in sequence ------------------------------------------------------ 11359 reflections ( 91.15 % complete ) and 20818 restraints for refining 8730 atoms. 19242 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1593 (Rfree = 0.000) for 8730 atoms. Found 34 (56 requested) and removed 44 (28 requested) atoms. Cycle 27: After refmac, R = 0.1537 (Rfree = 0.000) for 8698 atoms. Found 38 (55 requested) and removed 30 (27 requested) atoms. Cycle 28: After refmac, R = 0.1406 (Rfree = 0.000) for 8695 atoms. Found 40 (55 requested) and removed 34 (27 requested) atoms. Cycle 29: After refmac, R = 0.1416 (Rfree = 0.000) for 8691 atoms. Found 36 (55 requested) and removed 35 (27 requested) atoms. Cycle 30: After refmac, R = 0.1356 (Rfree = 0.000) for 8684 atoms. Found 31 (55 requested) and removed 33 (27 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.35 3.78 Search for helices and strands: 0 residues in 0 chains, 8840 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 8852 seeds are put forward Round 1: 384 peptides, 77 chains. Longest chain 10 peptides. Score 0.297 Round 2: 427 peptides, 71 chains. Longest chain 15 peptides. Score 0.402 Round 3: 428 peptides, 72 chains. Longest chain 12 peptides. Score 0.398 Round 4: 438 peptides, 73 chains. Longest chain 13 peptides. Score 0.406 Round 5: 446 peptides, 74 chains. Longest chain 13 peptides. Score 0.411 Taking the results from Round 5 Chains 74, Residues 372, Estimated correctness of the model 0.0 % 10 chains (56 residues) have been docked in sequence ------------------------------------------------------ 11359 reflections ( 91.15 % complete ) and 20719 restraints for refining 8730 atoms. 19179 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1610 (Rfree = 0.000) for 8730 atoms. Found 34 (56 requested) and removed 36 (28 requested) atoms. Cycle 32: After refmac, R = 0.1493 (Rfree = 0.000) for 8714 atoms. Found 22 (55 requested) and removed 31 (27 requested) atoms. Cycle 33: After refmac, R = 0.1471 (Rfree = 0.000) for 8690 atoms. Found 30 (55 requested) and removed 31 (27 requested) atoms. Cycle 34: After refmac, R = 0.1341 (Rfree = 0.000) for 8688 atoms. Found 17 (55 requested) and removed 29 (27 requested) atoms. Cycle 35: After refmac, R = 0.1422 (Rfree = 0.000) for 8671 atoms. Found 37 (55 requested) and removed 32 (27 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.34 3.77 Search for helices and strands: 0 residues in 0 chains, 8827 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 8845 seeds are put forward Round 1: 378 peptides, 79 chains. Longest chain 12 peptides. Score 0.274 Round 2: 397 peptides, 71 chains. Longest chain 13 peptides. Score 0.358 Round 3: 412 peptides, 71 chains. Longest chain 13 peptides. Score 0.380 Round 4: 429 peptides, 66 chains. Longest chain 14 peptides. Score 0.437 Round 5: 410 peptides, 64 chains. Longest chain 16 peptides. Score 0.422 Taking the results from Round 4 Chains 66, Residues 363, Estimated correctness of the model 0.0 % 7 chains (46 residues) have been docked in sequence ------------------------------------------------------ 11359 reflections ( 91.15 % complete ) and 20790 restraints for refining 8730 atoms. 19271 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1542 (Rfree = 0.000) for 8730 atoms. Found 48 (56 requested) and removed 35 (28 requested) atoms. Cycle 37: After refmac, R = 0.1461 (Rfree = 0.000) for 8720 atoms. Found 33 (56 requested) and removed 33 (28 requested) atoms. Cycle 38: After refmac, R = 0.1374 (Rfree = 0.000) for 8707 atoms. Found 29 (55 requested) and removed 27 (27 requested) atoms. Cycle 39: After refmac, R = 0.1388 (Rfree = 0.000) for 8698 atoms. Found 32 (55 requested) and removed 30 (27 requested) atoms. Cycle 40: After refmac, R = 0.1370 (Rfree = 0.000) for 8692 atoms. Found 35 (55 requested) and removed 32 (27 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 3.78 Search for helices and strands: 0 residues in 0 chains, 8859 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 8877 seeds are put forward Round 1: 353 peptides, 75 chains. Longest chain 10 peptides. Score 0.260 Round 2: 384 peptides, 75 chains. Longest chain 12 peptides. Score 0.311 Round 3: 396 peptides, 70 chains. Longest chain 13 peptides. Score 0.363 Round 4: 396 peptides, 72 chains. Longest chain 11 peptides. Score 0.350 Round 5: 403 peptides, 72 chains. Longest chain 14 peptides. Score 0.360 Taking the results from Round 3 Chains 70, Residues 326, Estimated correctness of the model 0.0 % 7 chains (42 residues) have been docked in sequence ------------------------------------------------------ 11359 reflections ( 91.15 % complete ) and 21168 restraints for refining 8729 atoms. 19831 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1525 (Rfree = 0.000) for 8729 atoms. Found 40 (56 requested) and removed 34 (28 requested) atoms. Cycle 42: After refmac, R = 0.1474 (Rfree = 0.000) for 8721 atoms. Found 40 (56 requested) and removed 33 (28 requested) atoms. Cycle 43: After refmac, R = 0.1500 (Rfree = 0.000) for 8717 atoms. Found 51 (55 requested) and removed 30 (27 requested) atoms. Cycle 44: After refmac, R = 0.1487 (Rfree = 0.000) for 8729 atoms. Found 49 (56 requested) and removed 39 (28 requested) atoms. Cycle 45: After refmac, R = 0.1200 (Rfree = 0.000) for 8728 atoms. Found 10 (56 requested) and removed 30 (28 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.35 3.78 Search for helices and strands: 0 residues in 0 chains, 8910 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 8928 seeds are put forward Round 1: 303 peptides, 66 chains. Longest chain 9 peptides. Score 0.238 Round 2: 323 peptides, 62 chains. Longest chain 10 peptides. Score 0.301 Round 3: 352 peptides, 65 chains. Longest chain 14 peptides. Score 0.328 Round 4: 349 peptides, 61 chains. Longest chain 12 peptides. Score 0.350 Round 5: 344 peptides, 64 chains. Longest chain 13 peptides. Score 0.322 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 61, Residues 288, Estimated correctness of the model 0.0 % 6 chains (31 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 2ii1-3_warpNtrace.pdb as input Building loops using Loopy2018 61 chains (288 residues) following loop building 6 chains (31 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11359 reflections ( 91.15 % complete ) and 21413 restraints for refining 8731 atoms. 20238 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1500 (Rfree = 0.000) for 8731 atoms. Found 0 (56 requested) and removed 28 (28 requested) atoms. Cycle 47: After refmac, R = 0.1566 (Rfree = 0.000) for 8687 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 48: After refmac, R = 0.1525 (Rfree = 0.000) for 8653 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.1442 (Rfree = 0.000) for 8622 atoms. TimeTaking 101.38