Sun 23 Dec 23:41:46 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 2ii1-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ii1-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ii1-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ii1-3.4-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/2ii1-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ii1-3.4-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 ============================================================ Sun 23 Dec 23:41:51 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/2ii1-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ii1-3.4-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 774 and 0 Target number of residues in the AU: 774 Target solvent content: 0.6227 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: 2ii1-3.4-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: 1 Cell parameters: 43.759 69.605 94.984 73.954 88.905 86.625 Input sequence file: 2ii1-3.4-parrot-mrncs.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 3.400 Wilson plot Bfac: 62.70 13485 reflections ( 91.19 % complete ) and 0 restraints for refining 10733 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3119 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2848 (Rfree = 0.000) for 10733 atoms. Found 71 (81 requested) and removed 145 (40 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.21 3.62 Search for helices and strands: 0 residues in 0 chains, 10756 seeds are put forward NCS extension: 0 residues added, 10756 seeds are put forward Round 1: 330 peptides, 74 chains. Longest chain 8 peptides. Score 0.228 Round 2: 409 peptides, 82 chains. Longest chain 13 peptides. Score 0.303 Round 3: 442 peptides, 85 chains. Longest chain 12 peptides. Score 0.335 Round 4: 488 peptides, 90 chains. Longest chain 13 peptides. Score 0.372 Round 5: 507 peptides, 82 chains. Longest chain 20 peptides. Score 0.448 Taking the results from Round 5 Chains 84, Residues 425, Estimated correctness of the model 0.0 % 12 chains (64 residues) have been docked in sequence ------------------------------------------------------ 13485 reflections ( 91.19 % complete ) and 20152 restraints for refining 8757 atoms. 18372 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2336 (Rfree = 0.000) for 8757 atoms. Found 31 (66 requested) and removed 66 (33 requested) atoms. Cycle 2: After refmac, R = 0.2274 (Rfree = 0.000) for 8647 atoms. Found 42 (65 requested) and removed 44 (32 requested) atoms. Cycle 3: After refmac, R = 0.1920 (Rfree = 0.000) for 8609 atoms. Found 17 (65 requested) and removed 40 (32 requested) atoms. Cycle 4: After refmac, R = 0.1883 (Rfree = 0.000) for 8550 atoms. Found 8 (64 requested) and removed 34 (32 requested) atoms. Cycle 5: After refmac, R = 0.1875 (Rfree = 0.000) for 8502 atoms. Found 5 (64 requested) and removed 34 (32 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.18 3.59 Search for helices and strands: 0 residues in 0 chains, 8637 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 8653 seeds are put forward Round 1: 406 peptides, 87 chains. Longest chain 12 peptides. Score 0.265 Round 2: 494 peptides, 89 chains. Longest chain 15 peptides. Score 0.387 Round 3: 506 peptides, 90 chains. Longest chain 22 peptides. Score 0.398 Round 4: 503 peptides, 85 chains. Longest chain 15 peptides. Score 0.424 Round 5: 504 peptides, 85 chains. Longest chain 19 peptides. Score 0.426 Taking the results from Round 5 Chains 86, Residues 419, Estimated correctness of the model 0.0 % 17 chains (82 residues) have been docked in sequence ------------------------------------------------------ 13485 reflections ( 91.19 % complete ) and 19994 restraints for refining 8604 atoms. 18193 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2062 (Rfree = 0.000) for 8604 atoms. Found 39 (64 requested) and removed 59 (32 requested) atoms. Cycle 7: After refmac, R = 0.2010 (Rfree = 0.000) for 8542 atoms. Found 31 (64 requested) and removed 46 (32 requested) atoms. Cycle 8: After refmac, R = 0.1929 (Rfree = 0.000) for 8489 atoms. Found 21 (64 requested) and removed 38 (32 requested) atoms. Cycle 9: After refmac, R = 0.1960 (Rfree = 0.000) for 8446 atoms. Found 34 (63 requested) and removed 37 (31 requested) atoms. Cycle 10: After refmac, R = 0.1640 (Rfree = 0.000) for 8418 atoms. Found 13 (63 requested) and removed 33 (31 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.18 3.59 Search for helices and strands: 0 residues in 0 chains, 8563 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 8581 seeds are put forward Round 1: 454 peptides, 94 chains. Longest chain 9 peptides. Score 0.295 Round 2: 515 peptides, 92 chains. Longest chain 16 peptides. Score 0.399 Round 3: 502 peptides, 91 chains. Longest chain 14 peptides. Score 0.387 Round 4: 523 peptides, 90 chains. Longest chain 14 peptides. Score 0.422 Round 5: 533 peptides, 94 chains. Longest chain 14 peptides. Score 0.412 Taking the results from Round 4 Chains 91, Residues 433, Estimated correctness of the model 0.0 % 8 chains (42 residues) have been docked in sequence ------------------------------------------------------ 13485 reflections ( 91.19 % complete ) and 19562 restraints for refining 8482 atoms. 17826 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2058 (Rfree = 0.000) for 8482 atoms. Found 34 (64 requested) and removed 57 (32 requested) atoms. Cycle 12: After refmac, R = 0.2037 (Rfree = 0.000) for 8426 atoms. Found 46 (63 requested) and removed 45 (31 requested) atoms. Cycle 13: After refmac, R = 0.2016 (Rfree = 0.000) for 8400 atoms. Found 42 (63 requested) and removed 45 (31 requested) atoms. Cycle 14: After refmac, R = 0.1900 (Rfree = 0.000) for 8380 atoms. Found 36 (63 requested) and removed 31 (31 requested) atoms. Cycle 15: After refmac, R = 0.1642 (Rfree = 0.000) for 8375 atoms. Found 17 (63 requested) and removed 31 (31 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.17 3.58 Search for helices and strands: 0 residues in 0 chains, 8524 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 8540 seeds are put forward Round 1: 454 peptides, 95 chains. Longest chain 10 peptides. Score 0.289 Round 2: 514 peptides, 96 chains. Longest chain 11 peptides. Score 0.373 Round 3: 518 peptides, 95 chains. Longest chain 11 peptides. Score 0.385 Round 4: 511 peptides, 92 chains. Longest chain 15 peptides. Score 0.393 Round 5: 500 peptides, 91 chains. Longest chain 12 peptides. Score 0.384 Taking the results from Round 4 Chains 92, Residues 419, Estimated correctness of the model 0.0 % 7 chains (42 residues) have been docked in sequence ------------------------------------------------------ 13485 reflections ( 91.19 % complete ) and 20017 restraints for refining 8565 atoms. 18326 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1941 (Rfree = 0.000) for 8565 atoms. Found 35 (64 requested) and removed 65 (32 requested) atoms. Cycle 17: After refmac, R = 0.1883 (Rfree = 0.000) for 8516 atoms. Found 37 (64 requested) and removed 44 (32 requested) atoms. Cycle 18: After refmac, R = 0.1829 (Rfree = 0.000) for 8495 atoms. Found 43 (64 requested) and removed 42 (32 requested) atoms. Cycle 19: After refmac, R = 0.1564 (Rfree = 0.000) for 8485 atoms. Found 14 (64 requested) and removed 33 (32 requested) atoms. Cycle 20: After refmac, R = 0.1535 (Rfree = 0.000) for 8454 atoms. Found 11 (63 requested) and removed 34 (31 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.20 3.61 Search for helices and strands: 0 residues in 0 chains, 8566 seeds are put forward NCS extension: 29 residues added (0 deleted due to clashes), 8595 seeds are put forward Round 1: 427 peptides, 92 chains. Longest chain 9 peptides. Score 0.266 Round 2: 478 peptides, 86 chains. Longest chain 14 peptides. Score 0.383 Round 3: 492 peptides, 91 chains. Longest chain 12 peptides. Score 0.372 Round 4: 499 peptides, 92 chains. Longest chain 10 peptides. Score 0.376 Round 5: 504 peptides, 88 chains. Longest chain 16 peptides. Score 0.408 Taking the results from Round 5 Chains 88, Residues 416, Estimated correctness of the model 0.0 % 10 chains (47 residues) have been docked in sequence ------------------------------------------------------ 13485 reflections ( 91.19 % complete ) and 20180 restraints for refining 8714 atoms. 18503 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1964 (Rfree = 0.000) for 8714 atoms. Found 47 (65 requested) and removed 49 (32 requested) atoms. Cycle 22: After refmac, R = 0.1913 (Rfree = 0.000) for 8683 atoms. Found 45 (65 requested) and removed 47 (32 requested) atoms. Cycle 23: After refmac, R = 0.1577 (Rfree = 0.000) for 8665 atoms. Found 13 (65 requested) and removed 39 (32 requested) atoms. Cycle 24: After refmac, R = 0.1532 (Rfree = 0.000) for 8626 atoms. Found 7 (65 requested) and removed 35 (32 requested) atoms. Cycle 25: After refmac, R = 0.1614 (Rfree = 0.000) for 8590 atoms. Found 11 (64 requested) and removed 36 (32 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.20 3.61 Search for helices and strands: 0 residues in 0 chains, 8706 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 8723 seeds are put forward Round 1: 433 peptides, 92 chains. Longest chain 10 peptides. Score 0.275 Round 2: 485 peptides, 92 chains. Longest chain 12 peptides. Score 0.355 Round 3: 475 peptides, 80 chains. Longest chain 16 peptides. Score 0.415 Round 4: 513 peptides, 90 chains. Longest chain 15 peptides. Score 0.408 Round 5: 488 peptides, 87 chains. Longest chain 14 peptides. Score 0.391 Taking the results from Round 3 Chains 84, Residues 395, Estimated correctness of the model 0.0 % 13 chains (72 residues) have been docked in sequence ------------------------------------------------------ 13485 reflections ( 91.19 % complete ) and 20421 restraints for refining 8758 atoms. 18742 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1921 (Rfree = 0.000) for 8758 atoms. Found 49 (66 requested) and removed 48 (33 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.1795 (Rfree = 0.000) for 8748 atoms. Found 50 (66 requested) and removed 36 (33 requested) atoms. Cycle 28: After refmac, R = 0.1738 (Rfree = 0.000) for 8746 atoms. Found 59 (66 requested) and removed 43 (33 requested) atoms. Cycle 29: After refmac, R = 0.1682 (Rfree = 0.000) for 8752 atoms. Found 50 (66 requested) and removed 39 (33 requested) atoms. Cycle 30: After refmac, R = 0.1403 (Rfree = 0.000) for 8749 atoms. Found 15 (66 requested) and removed 37 (33 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.18 3.59 Search for helices and strands: 0 residues in 0 chains, 8886 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 8914 seeds are put forward Round 1: 405 peptides, 85 chains. Longest chain 11 peptides. Score 0.277 Round 2: 462 peptides, 89 chains. Longest chain 12 peptides. Score 0.340 Round 3: 489 peptides, 91 chains. Longest chain 13 peptides. Score 0.368 Round 4: 467 peptides, 82 chains. Longest chain 15 peptides. Score 0.391 Round 5: 467 peptides, 80 chains. Longest chain 17 peptides. Score 0.404 Taking the results from Round 5 Chains 82, Residues 387, Estimated correctness of the model 0.0 % 9 chains (39 residues) have been docked in sequence ------------------------------------------------------ 13485 reflections ( 91.19 % complete ) and 20558 restraints for refining 8758 atoms. 19003 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1783 (Rfree = 0.000) for 8758 atoms. Found 45 (66 requested) and removed 48 (33 requested) atoms. Cycle 32: After refmac, R = 0.1709 (Rfree = 0.000) for 8732 atoms. Found 66 (66 requested) and removed 41 (33 requested) atoms. Cycle 33: After refmac, R = 0.1717 (Rfree = 0.000) for 8736 atoms. Found 48 (66 requested) and removed 43 (33 requested) atoms. Cycle 34: After refmac, R = 0.1640 (Rfree = 0.000) for 8726 atoms. Found 51 (65 requested) and removed 36 (32 requested) atoms. Cycle 35: After refmac, R = 0.1338 (Rfree = 0.000) for 8729 atoms. Found 11 (65 requested) and removed 33 (32 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.16 3.57 Search for helices and strands: 0 residues in 0 chains, 8822 seeds are put forward NCS extension: 34 residues added (2 deleted due to clashes), 8856 seeds are put forward Round 1: 388 peptides, 81 chains. Longest chain 12 peptides. Score 0.276 Round 2: 414 peptides, 70 chains. Longest chain 15 peptides. Score 0.390 Round 3: 432 peptides, 78 chains. Longest chain 17 peptides. Score 0.365 Round 4: 423 peptides, 74 chains. Longest chain 15 peptides. Score 0.377 Round 5: 405 peptides, 73 chains. Longest chain 13 peptides. Score 0.357 Taking the results from Round 2 Chains 72, Residues 344, Estimated correctness of the model 0.0 % 10 chains (46 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 13485 reflections ( 91.19 % complete ) and 20328 restraints for refining 8695 atoms. 18905 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1683 (Rfree = 0.000) for 8695 atoms. Found 52 (65 requested) and removed 51 (32 requested) atoms. Cycle 37: After refmac, R = 0.1659 (Rfree = 0.000) for 8680 atoms. Found 54 (65 requested) and removed 42 (32 requested) atoms. Cycle 38: After refmac, R = 0.1627 (Rfree = 0.000) for 8679 atoms. Found 38 (65 requested) and removed 41 (32 requested) atoms. Cycle 39: After refmac, R = 0.1595 (Rfree = 0.000) for 8675 atoms. Found 36 (65 requested) and removed 38 (32 requested) atoms. Cycle 40: After refmac, R = 0.1587 (Rfree = 0.000) for 8666 atoms. Found 35 (65 requested) and removed 35 (32 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.18 3.59 Search for helices and strands: 0 residues in 0 chains, 8842 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 8868 seeds are put forward Round 1: 357 peptides, 74 chains. Longest chain 11 peptides. Score 0.274 Round 2: 386 peptides, 73 chains. Longest chain 11 peptides. Score 0.327 Round 3: 391 peptides, 73 chains. Longest chain 12 peptides. Score 0.335 Round 4: 395 peptides, 74 chains. Longest chain 11 peptides. Score 0.335 Round 5: 394 peptides, 69 chains. Longest chain 11 peptides. Score 0.366 Taking the results from Round 5 Chains 69, Residues 325, Estimated correctness of the model 0.0 % 4 chains (22 residues) have been docked in sequence ------------------------------------------------------ 13485 reflections ( 91.19 % complete ) and 21010 restraints for refining 8757 atoms. 19721 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1697 (Rfree = 0.000) for 8757 atoms. Found 40 (66 requested) and removed 43 (33 requested) atoms. Cycle 42: After refmac, R = 0.1636 (Rfree = 0.000) for 8741 atoms. Found 47 (66 requested) and removed 34 (33 requested) atoms. Cycle 43: After refmac, R = 0.1589 (Rfree = 0.000) for 8742 atoms. Found 45 (66 requested) and removed 36 (33 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1559 (Rfree = 0.000) for 8744 atoms. Found 41 (66 requested) and removed 39 (33 requested) atoms. Cycle 45: After refmac, R = 0.1494 (Rfree = 0.000) for 8740 atoms. Found 37 (66 requested) and removed 39 (33 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.15 3.56 Search for helices and strands: 0 residues in 0 chains, 8876 seeds are put forward NCS extension: 12 residues added (0 deleted due to clashes), 8888 seeds are put forward Round 1: 328 peptides, 69 chains. Longest chain 9 peptides. Score 0.260 Round 2: 385 peptides, 71 chains. Longest chain 12 peptides. Score 0.339 Round 3: 361 peptides, 61 chains. Longest chain 16 peptides. Score 0.369 Round 4: 344 peptides, 60 chains. Longest chain 14 peptides. Score 0.350 Round 5: 341 peptides, 60 chains. Longest chain 17 peptides. Score 0.345 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 61, Residues 300, Estimated correctness of the model 0.0 % 11 chains (64 residues) have been docked in sequence Sequence coverage is 21 % Consider running further cycles of model building using 2ii1-3_warpNtrace.pdb as input Building loops using Loopy2018 61 chains (300 residues) following loop building 11 chains (64 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13485 reflections ( 91.19 % complete ) and 20684 restraints for refining 8757 atoms. 19377 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1606 (Rfree = 0.000) for 8757 atoms. Found 0 (66 requested) and removed 33 (33 requested) atoms. Cycle 47: After refmac, R = 0.1577 (Rfree = 0.000) for 8715 atoms. Found 0 (65 requested) and removed 32 (32 requested) atoms. Cycle 48: After refmac, R = 0.1488 (Rfree = 0.000) for 8676 atoms. Found 0 (65 requested) and removed 32 (32 requested) atoms. Cycle 49: After refmac, R = 0.1427 (Rfree = 0.000) for 8638 atoms. TimeTaking 96.77