Mon 24 Dec 00:48:44 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 2ii1-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ii1-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ii1-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ii1-3.6-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/2ii1-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ii1-3.6-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 00:48:49 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/2ii1-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ii1-3.6-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 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-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: 2ii1-3.6-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 3.600 Wilson plot Bfac: 66.82 11359 reflections ( 91.15 % complete ) and 0 restraints for refining 10610 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3209 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2815 (Rfree = 0.000) for 10610 atoms. Found 30 (68 requested) and removed 218 (34 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.32 3.75 Search for helices and strands: 0 residues in 0 chains, 10513 seeds are put forward NCS extension: 0 residues added, 10513 seeds are put forward Round 1: 308 peptides, 65 chains. Longest chain 10 peptides. Score 0.254 Round 2: 372 peptides, 67 chains. Longest chain 16 peptides. Score 0.346 Round 3: 422 peptides, 77 chains. Longest chain 11 peptides. Score 0.357 Round 4: 432 peptides, 77 chains. Longest chain 11 peptides. Score 0.372 Round 5: 459 peptides, 78 chains. Longest chain 13 peptides. Score 0.405 Taking the results from Round 5 Chains 78, Residues 381, Estimated correctness of the model 0.0 % 9 chains (51 residues) have been docked in sequence ------------------------------------------------------ 11359 reflections ( 91.15 % complete ) and 20571 restraints for refining 8729 atoms. 18999 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2159 (Rfree = 0.000) for 8729 atoms. Found 32 (56 requested) and removed 56 (28 requested) atoms. Cycle 2: After refmac, R = 0.2146 (Rfree = 0.000) for 8611 atoms. Found 29 (55 requested) and removed 45 (27 requested) atoms. Cycle 3: After refmac, R = 0.2056 (Rfree = 0.000) for 8557 atoms. Found 34 (55 requested) and removed 44 (27 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.1662 (Rfree = 0.000) for 8521 atoms. Found 7 (54 requested) and removed 34 (27 requested) atoms. Cycle 5: After refmac, R = 0.1651 (Rfree = 0.000) for 8482 atoms. Found 10 (54 requested) and removed 32 (27 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.36 3.79 Search for helices and strands: 0 residues in 0 chains, 8625 seeds are put forward NCS extension: 11 residues added (4 deleted due to clashes), 8636 seeds are put forward Round 1: 400 peptides, 82 chains. Longest chain 10 peptides. Score 0.289 Round 2: 471 peptides, 86 chains. Longest chain 16 peptides. Score 0.372 Round 3: 476 peptides, 84 chains. Longest chain 13 peptides. Score 0.392 Round 4: 457 peptides, 80 chains. Longest chain 14 peptides. Score 0.389 Round 5: 501 peptides, 83 chains. Longest chain 15 peptides. Score 0.434 Taking the results from Round 5 Chains 84, Residues 418, Estimated correctness of the model 0.0 % 11 chains (69 residues) have been docked in sequence ------------------------------------------------------ 11359 reflections ( 91.15 % complete ) and 20542 restraints for refining 8696 atoms. 18778 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2063 (Rfree = 0.000) for 8696 atoms. Found 25 (55 requested) and removed 52 (27 requested) atoms. Cycle 7: After refmac, R = 0.2017 (Rfree = 0.000) for 8642 atoms. Found 21 (55 requested) and removed 51 (27 requested) atoms. Cycle 8: After refmac, R = 0.1964 (Rfree = 0.000) for 8595 atoms. Found 14 (55 requested) and removed 41 (27 requested) atoms. Cycle 9: After refmac, R = 0.1881 (Rfree = 0.000) for 8558 atoms. Found 17 (54 requested) and removed 37 (27 requested) atoms. Cycle 10: After refmac, R = 0.1868 (Rfree = 0.000) for 8536 atoms. Found 19 (54 requested) and removed 37 (27 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.32 3.75 Search for helices and strands: 0 residues in 0 chains, 8696 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 8716 seeds are put forward Round 1: 410 peptides, 82 chains. Longest chain 10 peptides. Score 0.305 Round 2: 448 peptides, 81 chains. Longest chain 13 peptides. Score 0.370 Round 3: 462 peptides, 82 chains. Longest chain 13 peptides. Score 0.384 Round 4: 466 peptides, 82 chains. Longest chain 13 peptides. Score 0.390 Round 5: 481 peptides, 77 chains. Longest chain 14 peptides. Score 0.442 Taking the results from Round 5 Chains 78, Residues 404, Estimated correctness of the model 0.0 % 10 chains (58 residues) have been docked in sequence ------------------------------------------------------ 11359 reflections ( 91.15 % complete ) and 20726 restraints for refining 8730 atoms. 19051 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1975 (Rfree = 0.000) for 8730 atoms. Found 19 (56 requested) and removed 46 (28 requested) atoms. Cycle 12: After refmac, R = 0.1872 (Rfree = 0.000) for 8669 atoms. Found 21 (55 requested) and removed 36 (27 requested) atoms. Cycle 13: After refmac, R = 0.1923 (Rfree = 0.000) for 8643 atoms. Found 25 (55 requested) and removed 39 (27 requested) atoms. Cycle 14: After refmac, R = 0.1837 (Rfree = 0.000) for 8620 atoms. Found 15 (55 requested) and removed 31 (27 requested) atoms. Cycle 15: After refmac, R = 0.2025 (Rfree = 0.000) for 8596 atoms. Found 34 (55 requested) and removed 37 (27 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.32 3.75 Search for helices and strands: 0 residues in 0 chains, 8793 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 8809 seeds are put forward Round 1: 448 peptides, 90 chains. Longest chain 11 peptides. Score 0.312 Round 2: 504 peptides, 86 chains. Longest chain 15 peptides. Score 0.420 Round 3: 506 peptides, 85 chains. Longest chain 19 peptides. Score 0.429 Round 4: 515 peptides, 82 chains. Longest chain 19 peptides. Score 0.459 Round 5: 505 peptides, 82 chains. Longest chain 14 peptides. Score 0.445 Taking the results from Round 4 Chains 83, Residues 433, Estimated correctness of the model 0.0 % 6 chains (38 residues) have been docked in sequence ------------------------------------------------------ 11359 reflections ( 91.15 % complete ) and 20669 restraints for refining 8731 atoms. 18940 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1889 (Rfree = 0.000) for 8731 atoms. Found 24 (56 requested) and removed 44 (28 requested) atoms. Cycle 17: After refmac, R = 0.1957 (Rfree = 0.000) for 8686 atoms. Found 34 (55 requested) and removed 33 (27 requested) atoms. Cycle 18: After refmac, R = 0.1948 (Rfree = 0.000) for 8678 atoms. Found 47 (55 requested) and removed 32 (27 requested) atoms. Cycle 19: After refmac, R = 0.1872 (Rfree = 0.000) for 8681 atoms. Found 29 (55 requested) and removed 34 (27 requested) atoms. Cycle 20: After refmac, R = 0.1604 (Rfree = 0.000) for 8668 atoms. Found 9 (55 requested) and removed 28 (27 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.31 3.74 Search for helices and strands: 0 residues in 0 chains, 8823 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 8843 seeds are put forward Round 1: 438 peptides, 90 chains. Longest chain 9 peptides. Score 0.296 Round 2: 460 peptides, 78 chains. Longest chain 17 peptides. Score 0.406 Round 3: 481 peptides, 80 chains. Longest chain 15 peptides. Score 0.424 Round 4: 472 peptides, 78 chains. Longest chain 16 peptides. Score 0.423 Round 5: 470 peptides, 77 chains. Longest chain 17 peptides. Score 0.427 Taking the results from Round 5 Chains 77, Residues 393, Estimated correctness of the model 0.0 % 6 chains (31 residues) have been docked in sequence ------------------------------------------------------ 11359 reflections ( 91.15 % complete ) and 20870 restraints for refining 8729 atoms. 19300 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1831 (Rfree = 0.000) for 8729 atoms. Found 42 (56 requested) and removed 34 (28 requested) atoms. Cycle 22: After refmac, R = 0.1806 (Rfree = 0.000) for 8709 atoms. Found 33 (56 requested) and removed 31 (28 requested) atoms. Cycle 23: After refmac, R = 0.1730 (Rfree = 0.000) for 8696 atoms. Found 35 (55 requested) and removed 35 (27 requested) atoms. Cycle 24: After refmac, R = 0.1659 (Rfree = 0.000) for 8680 atoms. Found 35 (55 requested) and removed 31 (27 requested) atoms. Cycle 25: After refmac, R = 0.1383 (Rfree = 0.000) for 8674 atoms. Found 9 (55 requested) and removed 28 (27 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 3.75 Search for helices and strands: 0 residues in 0 chains, 8836 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 8862 seeds are put forward Round 1: 400 peptides, 82 chains. Longest chain 12 peptides. Score 0.289 Round 2: 452 peptides, 84 chains. Longest chain 14 peptides. Score 0.357 Round 3: 476 peptides, 82 chains. Longest chain 11 peptides. Score 0.405 Round 4: 473 peptides, 82 chains. Longest chain 17 peptides. Score 0.400 Round 5: 500 peptides, 86 chains. Longest chain 17 peptides. Score 0.414 Taking the results from Round 5 Chains 86, Residues 414, Estimated correctness of the model 0.0 % 9 chains (54 residues) have been docked in sequence ------------------------------------------------------ 11359 reflections ( 91.15 % complete ) and 20766 restraints for refining 8731 atoms. 19058 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1817 (Rfree = 0.000) for 8731 atoms. Found 40 (56 requested) and removed 37 (28 requested) atoms. Cycle 27: After refmac, R = 0.1822 (Rfree = 0.000) for 8707 atoms. Found 51 (56 requested) and removed 34 (28 requested) atoms. Cycle 28: After refmac, R = 0.1706 (Rfree = 0.000) for 8710 atoms. Found 38 (55 requested) and removed 30 (27 requested) atoms. Cycle 29: After refmac, R = 0.1445 (Rfree = 0.000) for 8708 atoms. Found 10 (55 requested) and removed 29 (27 requested) atoms. Cycle 30: After refmac, R = 0.1397 (Rfree = 0.000) for 8679 atoms. Found 8 (55 requested) and removed 29 (27 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 3.74 Search for helices and strands: 0 residues in 0 chains, 8843 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 8857 seeds are put forward Round 1: 388 peptides, 79 chains. Longest chain 10 peptides. Score 0.290 Round 2: 425 peptides, 78 chains. Longest chain 11 peptides. Score 0.355 Round 3: 457 peptides, 80 chains. Longest chain 12 peptides. Score 0.389 Round 4: 451 peptides, 77 chains. Longest chain 16 peptides. Score 0.400 Round 5: 449 peptides, 77 chains. Longest chain 13 peptides. Score 0.397 Taking the results from Round 4 Chains 78, Residues 374, Estimated correctness of the model 0.0 % 9 chains (45 residues) have been docked in sequence ------------------------------------------------------ 11359 reflections ( 91.15 % complete ) and 20988 restraints for refining 8730 atoms. 19463 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1793 (Rfree = 0.000) for 8730 atoms. Found 30 (56 requested) and removed 39 (28 requested) atoms. Cycle 32: After refmac, R = 0.1780 (Rfree = 0.000) for 8701 atoms. Found 47 (55 requested) and removed 32 (27 requested) atoms. Cycle 33: After refmac, R = 0.1690 (Rfree = 0.000) for 8705 atoms. Found 30 (55 requested) and removed 31 (27 requested) atoms. Cycle 34: After refmac, R = 0.1445 (Rfree = 0.000) for 8692 atoms. Found 8 (55 requested) and removed 28 (27 requested) atoms. Cycle 35: After refmac, R = 0.1407 (Rfree = 0.000) for 8667 atoms. Found 8 (55 requested) and removed 27 (27 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.30 3.73 Search for helices and strands: 0 residues in 0 chains, 8817 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 8832 seeds are put forward Round 1: 338 peptides, 69 chains. Longest chain 9 peptides. Score 0.277 Round 2: 403 peptides, 73 chains. Longest chain 13 peptides. Score 0.354 Round 3: 419 peptides, 70 chains. Longest chain 15 peptides. Score 0.397 Round 4: 416 peptides, 71 chains. Longest chain 11 peptides. Score 0.386 Round 5: 400 peptides, 67 chains. Longest chain 16 peptides. Score 0.388 Taking the results from Round 3 Chains 71, Residues 349, Estimated correctness of the model 0.0 % 8 chains (40 residues) have been docked in sequence ------------------------------------------------------ 11359 reflections ( 91.15 % complete ) and 21002 restraints for refining 8731 atoms. 19570 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1739 (Rfree = 0.000) for 8731 atoms. Found 29 (56 requested) and removed 34 (28 requested) atoms. Cycle 37: After refmac, R = 0.1757 (Rfree = 0.000) for 8706 atoms. Found 55 (55 requested) and removed 32 (27 requested) atoms. Cycle 38: After refmac, R = 0.1732 (Rfree = 0.000) for 8724 atoms. Found 56 (56 requested) and removed 32 (28 requested) atoms. Cycle 39: After refmac, R = 0.1699 (Rfree = 0.000) for 8746 atoms. Found 56 (56 requested) and removed 36 (28 requested) atoms. Cycle 40: After refmac, R = 0.1605 (Rfree = 0.000) for 8763 atoms. Found 43 (56 requested) and removed 31 (28 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.30 3.73 Search for helices and strands: 0 residues in 0 chains, 8956 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 8974 seeds are put forward Round 1: 338 peptides, 75 chains. Longest chain 9 peptides. Score 0.234 Round 2: 412 peptides, 78 chains. Longest chain 12 peptides. Score 0.335 Round 3: 401 peptides, 76 chains. Longest chain 11 peptides. Score 0.331 Round 4: 394 peptides, 72 chains. Longest chain 11 peptides. Score 0.346 Round 5: 410 peptides, 72 chains. Longest chain 11 peptides. Score 0.371 Taking the results from Round 5 Chains 73, Residues 338, Estimated correctness of the model 0.0 % 5 chains (28 residues) have been docked in sequence ------------------------------------------------------ 11359 reflections ( 91.15 % complete ) and 21510 restraints for refining 8731 atoms. 20157 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1716 (Rfree = 0.000) for 8731 atoms. Found 46 (56 requested) and removed 34 (28 requested) atoms. Cycle 42: After refmac, R = 0.1584 (Rfree = 0.000) for 8726 atoms. Found 46 (56 requested) and removed 31 (28 requested) atoms. Cycle 43: After refmac, R = 0.1530 (Rfree = 0.000) for 8735 atoms. Found 36 (56 requested) and removed 30 (28 requested) atoms. Cycle 44: After refmac, R = 0.1454 (Rfree = 0.000) for 8734 atoms. Found 26 (56 requested) and removed 30 (28 requested) atoms. Cycle 45: After refmac, R = 0.1418 (Rfree = 0.000) for 8723 atoms. Found 45 (56 requested) and removed 30 (28 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.29 3.71 Search for helices and strands: 0 residues in 0 chains, 8920 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 8933 seeds are put forward Round 1: 287 peptides, 63 chains. Longest chain 7 peptides. Score 0.232 Round 2: 332 peptides, 63 chains. Longest chain 10 peptides. Score 0.309 Round 3: 335 peptides, 62 chains. Longest chain 11 peptides. Score 0.321 Round 4: 330 peptides, 60 chains. Longest chain 15 peptides. Score 0.327 Round 5: 319 peptides, 57 chains. Longest chain 13 peptides. Score 0.330 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 58, Residues 262, Estimated correctness of the model 0.0 % 6 chains (28 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 58 chains (262 residues) following loop building 6 chains (28 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 11359 reflections ( 91.15 % complete ) and 21947 restraints for refining 8730 atoms. 20885 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1486 (Rfree = 0.000) for 8730 atoms. Found 0 (56 requested) and removed 28 (28 requested) atoms. Cycle 47: After refmac, R = 0.1513 (Rfree = 0.000) for 8686 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 48: After refmac, R = 0.1517 (Rfree = 0.000) for 8656 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Cycle 49: After refmac, R = 0.1385 (Rfree = 0.000) for 8624 atoms. Found 0 (55 requested) and removed 27 (27 requested) atoms. Writing output files ... TimeTaking 82.98