Sun 23 Dec 22:22:59 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 1vm8-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vm8-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vm8-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vm8-3.6-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/1vm8-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vm8-3.6-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 22:23:09 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/1vm8-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vm8-3.6-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 818 and 0 Target number of residues in the AU: 818 Target solvent content: 0.6433 Checking the provided sequence file Detected sequence length: 534 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 1068 Adjusted target solvent content: 0.53 Input MTZ file: 1vm8-3.6-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: 4 Cell parameters: 80.094 73.402 107.132 90.000 99.827 90.000 Input sequence file: 1vm8-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 8544 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: 105.560 3.600 Wilson plot Bfac: 73.86 14307 reflections ( 99.11 % complete ) and 0 restraints for refining 9509 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3256 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2893 (Rfree = 0.000) for 9509 atoms. Found 61 (61 requested) and removed 92 (30 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.49 3.35 Search for helices and strands: 0 residues in 0 chains, 9652 seeds are put forward NCS extension: 0 residues added, 9652 seeds are put forward Round 1: 401 peptides, 85 chains. Longest chain 13 peptides. Score 0.262 Round 2: 517 peptides, 85 chains. Longest chain 15 peptides. Score 0.422 Round 3: 540 peptides, 79 chains. Longest chain 17 peptides. Score 0.482 Round 4: 540 peptides, 80 chains. Longest chain 18 peptides. Score 0.477 Round 5: 550 peptides, 80 chains. Longest chain 18 peptides. Score 0.489 Taking the results from Round 5 Chains 84, Residues 470, Estimated correctness of the model 0.0 % 7 chains (74 residues) have been docked in sequence ------------------------------------------------------ 14307 reflections ( 99.11 % complete ) and 17682 restraints for refining 7744 atoms. 15638 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2310 (Rfree = 0.000) for 7744 atoms. Found 34 (49 requested) and removed 59 (24 requested) atoms. Cycle 2: After refmac, R = 0.2208 (Rfree = 0.000) for 7635 atoms. Found 20 (49 requested) and removed 61 (24 requested) atoms. Cycle 3: After refmac, R = 0.2111 (Rfree = 0.000) for 7557 atoms. Found 16 (48 requested) and removed 48 (24 requested) atoms. Cycle 4: After refmac, R = 0.2027 (Rfree = 0.000) for 7501 atoms. Found 25 (48 requested) and removed 35 (24 requested) atoms. Cycle 5: After refmac, R = 0.1960 (Rfree = 0.000) for 7472 atoms. Found 18 (48 requested) and removed 42 (24 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 3.32 Search for helices and strands: 0 residues in 0 chains, 7693 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 7707 seeds are put forward Round 1: 483 peptides, 88 chains. Longest chain 14 peptides. Score 0.361 Round 2: 524 peptides, 78 chains. Longest chain 16 peptides. Score 0.469 Round 3: 553 peptides, 77 chains. Longest chain 20 peptides. Score 0.508 Round 4: 557 peptides, 73 chains. Longest chain 26 peptides. Score 0.532 Round 5: 545 peptides, 74 chains. Longest chain 24 peptides. Score 0.514 Taking the results from Round 4 Chains 76, Residues 484, Estimated correctness of the model 0.0 % 5 chains (37 residues) have been docked in sequence ------------------------------------------------------ 14307 reflections ( 99.11 % complete ) and 17756 restraints for refining 7745 atoms. 15792 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2101 (Rfree = 0.000) for 7745 atoms. Found 44 (49 requested) and removed 75 (24 requested) atoms. Cycle 7: After refmac, R = 0.1955 (Rfree = 0.000) for 7659 atoms. Found 22 (49 requested) and removed 55 (24 requested) atoms. Cycle 8: After refmac, R = 0.1918 (Rfree = 0.000) for 7600 atoms. Found 13 (48 requested) and removed 40 (24 requested) atoms. Cycle 9: After refmac, R = 0.1885 (Rfree = 0.000) for 7562 atoms. Found 9 (48 requested) and removed 38 (24 requested) atoms. Cycle 10: After refmac, R = 0.1869 (Rfree = 0.000) for 7525 atoms. Found 12 (48 requested) and removed 37 (24 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.45 3.31 Search for helices and strands: 0 residues in 0 chains, 7732 seeds are put forward NCS extension: 46 residues added (0 deleted due to clashes), 7778 seeds are put forward Round 1: 511 peptides, 94 chains. Longest chain 16 peptides. Score 0.364 Round 2: 545 peptides, 82 chains. Longest chain 17 peptides. Score 0.473 Round 3: 540 peptides, 81 chains. Longest chain 14 peptides. Score 0.472 Round 4: 548 peptides, 83 chains. Longest chain 17 peptides. Score 0.471 Round 5: 526 peptides, 77 chains. Longest chain 17 peptides. Score 0.476 Taking the results from Round 5 Chains 80, Residues 449, Estimated correctness of the model 0.0 % 5 chains (30 residues) have been docked in sequence ------------------------------------------------------ 14307 reflections ( 99.11 % complete ) and 18040 restraints for refining 7744 atoms. 16248 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2126 (Rfree = 0.000) for 7744 atoms. Found 39 (49 requested) and removed 50 (24 requested) atoms. Cycle 12: After refmac, R = 0.1978 (Rfree = 0.000) for 7673 atoms. Found 33 (49 requested) and removed 46 (24 requested) atoms. Cycle 13: After refmac, R = 0.1910 (Rfree = 0.000) for 7638 atoms. Found 23 (49 requested) and removed 34 (24 requested) atoms. Cycle 14: After refmac, R = 0.1845 (Rfree = 0.000) for 7611 atoms. Found 8 (48 requested) and removed 34 (24 requested) atoms. Cycle 15: After refmac, R = 0.1789 (Rfree = 0.000) for 7569 atoms. Found 13 (48 requested) and removed 28 (24 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.46 3.32 Search for helices and strands: 0 residues in 0 chains, 7797 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 7815 seeds are put forward Round 1: 486 peptides, 90 chains. Longest chain 12 peptides. Score 0.353 Round 2: 520 peptides, 85 chains. Longest chain 14 peptides. Score 0.426 Round 3: 526 peptides, 81 chains. Longest chain 20 peptides. Score 0.455 Round 4: 530 peptides, 75 chains. Longest chain 23 peptides. Score 0.492 Round 5: 530 peptides, 79 chains. Longest chain 20 peptides. Score 0.470 Taking the results from Round 4 Chains 78, Residues 455, Estimated correctness of the model 0.0 % 4 chains (32 residues) have been docked in sequence ------------------------------------------------------ 14307 reflections ( 99.11 % complete ) and 17861 restraints for refining 7745 atoms. 16028 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2045 (Rfree = 0.000) for 7745 atoms. Found 34 (49 requested) and removed 59 (24 requested) atoms. Cycle 17: After refmac, R = 0.1915 (Rfree = 0.000) for 7678 atoms. Found 19 (49 requested) and removed 35 (24 requested) atoms. Cycle 18: After refmac, R = 0.1931 (Rfree = 0.000) for 7647 atoms. Found 21 (49 requested) and removed 41 (24 requested) atoms. Cycle 19: After refmac, R = 0.1807 (Rfree = 0.000) for 7611 atoms. Found 15 (48 requested) and removed 36 (24 requested) atoms. Cycle 20: After refmac, R = 0.1856 (Rfree = 0.000) for 7574 atoms. Found 19 (48 requested) and removed 34 (24 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.44 3.31 Search for helices and strands: 0 residues in 0 chains, 7765 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 7792 seeds are put forward Round 1: 451 peptides, 86 chains. Longest chain 10 peptides. Score 0.328 Round 2: 502 peptides, 80 chains. Longest chain 15 peptides. Score 0.431 Round 3: 475 peptides, 73 chains. Longest chain 18 peptides. Score 0.435 Round 4: 519 peptides, 79 chains. Longest chain 18 peptides. Score 0.457 Round 5: 503 peptides, 72 chains. Longest chain 21 peptides. Score 0.475 Taking the results from Round 5 Chains 73, Residues 431, Estimated correctness of the model 0.0 % 4 chains (37 residues) have been docked in sequence ------------------------------------------------------ 14307 reflections ( 99.11 % complete ) and 17730 restraints for refining 7743 atoms. 15949 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2074 (Rfree = 0.000) for 7743 atoms. Found 40 (49 requested) and removed 49 (24 requested) atoms. Cycle 22: After refmac, R = 0.1903 (Rfree = 0.000) for 7693 atoms. Found 25 (49 requested) and removed 44 (24 requested) atoms. Cycle 23: After refmac, R = 0.1874 (Rfree = 0.000) for 7654 atoms. Found 21 (49 requested) and removed 38 (24 requested) atoms. Cycle 24: After refmac, R = 0.1809 (Rfree = 0.000) for 7623 atoms. Found 15 (48 requested) and removed 36 (24 requested) atoms. Cycle 25: After refmac, R = 0.1764 (Rfree = 0.000) for 7593 atoms. Found 8 (48 requested) and removed 34 (24 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.46 3.32 Search for helices and strands: 0 residues in 0 chains, 7786 seeds are put forward NCS extension: 36 residues added (0 deleted due to clashes), 7822 seeds are put forward Round 1: 438 peptides, 80 chains. Longest chain 14 peptides. Score 0.346 Round 2: 486 peptides, 76 chains. Longest chain 15 peptides. Score 0.433 Round 3: 484 peptides, 72 chains. Longest chain 16 peptides. Score 0.452 Round 4: 492 peptides, 72 chains. Longest chain 16 peptides. Score 0.462 Round 5: 484 peptides, 73 chains. Longest chain 18 peptides. Score 0.447 Taking the results from Round 4 Chains 73, Residues 420, Estimated correctness of the model 0.0 % 6 chains (41 residues) have been docked in sequence ------------------------------------------------------ 14307 reflections ( 99.11 % complete ) and 17964 restraints for refining 7745 atoms. 16253 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2074 (Rfree = 0.000) for 7745 atoms. Found 36 (49 requested) and removed 42 (24 requested) atoms. Cycle 27: After refmac, R = 0.1906 (Rfree = 0.000) for 7703 atoms. Found 16 (49 requested) and removed 30 (24 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1873 (Rfree = 0.000) for 7666 atoms. Found 19 (49 requested) and removed 26 (24 requested) atoms. Cycle 29: After refmac, R = 0.1909 (Rfree = 0.000) for 7644 atoms. Found 29 (49 requested) and removed 36 (24 requested) atoms. Cycle 30: After refmac, R = 0.1894 (Rfree = 0.000) for 7620 atoms. Found 23 (48 requested) and removed 32 (24 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.46 3.32 Search for helices and strands: 0 residues in 0 chains, 7821 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 7839 seeds are put forward Round 1: 414 peptides, 82 chains. Longest chain 10 peptides. Score 0.300 Round 2: 464 peptides, 78 chains. Longest chain 14 peptides. Score 0.393 Round 3: 485 peptides, 75 chains. Longest chain 15 peptides. Score 0.437 Round 4: 468 peptides, 72 chains. Longest chain 17 peptides. Score 0.432 Round 5: 492 peptides, 77 chains. Longest chain 16 peptides. Score 0.435 Taking the results from Round 3 Chains 76, Residues 410, Estimated correctness of the model 0.0 % 5 chains (32 residues) have been docked in sequence ------------------------------------------------------ 14307 reflections ( 99.11 % complete ) and 18028 restraints for refining 7744 atoms. 16400 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2066 (Rfree = 0.000) for 7744 atoms. Found 36 (49 requested) and removed 43 (24 requested) atoms. Cycle 32: After refmac, R = 0.1967 (Rfree = 0.000) for 7697 atoms. Found 45 (49 requested) and removed 45 (24 requested) atoms. Cycle 33: After refmac, R = 0.1846 (Rfree = 0.000) for 7679 atoms. Found 34 (49 requested) and removed 34 (24 requested) atoms. Cycle 34: After refmac, R = 0.1819 (Rfree = 0.000) for 7667 atoms. Found 30 (49 requested) and removed 34 (24 requested) atoms. Cycle 35: After refmac, R = 0.1825 (Rfree = 0.000) for 7654 atoms. Found 37 (49 requested) and removed 31 (24 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.42 3.29 Search for helices and strands: 0 residues in 0 chains, 7878 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 7899 seeds are put forward Round 1: 422 peptides, 87 chains. Longest chain 13 peptides. Score 0.281 Round 2: 481 peptides, 81 chains. Longest chain 14 peptides. Score 0.398 Round 3: 464 peptides, 77 chains. Longest chain 14 peptides. Score 0.399 Round 4: 475 peptides, 80 chains. Longest chain 14 peptides. Score 0.396 Round 5: 495 peptides, 79 chains. Longest chain 15 peptides. Score 0.427 Taking the results from Round 5 Chains 80, Residues 416, Estimated correctness of the model 0.0 % 3 chains (15 residues) have been docked in sequence ------------------------------------------------------ 14307 reflections ( 99.11 % complete ) and 18040 restraints for refining 7745 atoms. 16424 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1986 (Rfree = 0.000) for 7745 atoms. Found 40 (49 requested) and removed 39 (24 requested) atoms. Cycle 37: After refmac, R = 0.1950 (Rfree = 0.000) for 7714 atoms. Found 47 (49 requested) and removed 37 (24 requested) atoms. Cycle 38: After refmac, R = 0.1854 (Rfree = 0.000) for 7707 atoms. Found 30 (49 requested) and removed 33 (24 requested) atoms. Cycle 39: After refmac, R = 0.1817 (Rfree = 0.000) for 7688 atoms. Found 33 (49 requested) and removed 30 (24 requested) atoms. Cycle 40: After refmac, R = 0.1586 (Rfree = 0.000) for 7684 atoms. Found 10 (49 requested) and removed 28 (24 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.45 3.31 Search for helices and strands: 0 residues in 0 chains, 7843 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 7856 seeds are put forward Round 1: 425 peptides, 85 chains. Longest chain 14 peptides. Score 0.298 Round 2: 461 peptides, 78 chains. Longest chain 15 peptides. Score 0.389 Round 3: 441 peptides, 71 chains. Longest chain 17 peptides. Score 0.403 Round 4: 438 peptides, 66 chains. Longest chain 21 peptides. Score 0.428 Round 5: 445 peptides, 68 chains. Longest chain 15 peptides. Score 0.426 Taking the results from Round 4 Chains 67, Residues 372, Estimated correctness of the model 0.0 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 14307 reflections ( 99.11 % complete ) and 18097 restraints for refining 7744 atoms. 16580 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1973 (Rfree = 0.000) for 7744 atoms. Found 49 (49 requested) and removed 38 (24 requested) atoms. Cycle 42: After refmac, R = 0.1849 (Rfree = 0.000) for 7722 atoms. Found 41 (49 requested) and removed 33 (24 requested) atoms. Cycle 43: After refmac, R = 0.1806 (Rfree = 0.000) for 7699 atoms. Found 40 (49 requested) and removed 29 (24 requested) atoms. Cycle 44: After refmac, R = 0.1724 (Rfree = 0.000) for 7694 atoms. Found 33 (49 requested) and removed 33 (24 requested) atoms. Cycle 45: After refmac, R = 0.1696 (Rfree = 0.000) for 7683 atoms. Found 28 (49 requested) and removed 29 (24 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.45 3.31 Search for helices and strands: 0 residues in 0 chains, 7865 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 7882 seeds are put forward Round 1: 382 peptides, 74 chains. Longest chain 13 peptides. Score 0.303 Round 2: 402 peptides, 72 chains. Longest chain 13 peptides. Score 0.344 Round 3: 412 peptides, 67 chains. Longest chain 26 peptides. Score 0.388 Round 4: 413 peptides, 70 chains. Longest chain 13 peptides. Score 0.371 Round 5: 424 peptides, 65 chains. Longest chain 28 peptides. Score 0.416 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 66, Residues 359, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1vm8-3_warpNtrace.pdb as input Building loops using Loopy2018 66 chains (359 residues) following loop building 2 chains (21 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14307 reflections ( 99.11 % complete ) and 18194 restraints for refining 7744 atoms. 16754 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1838 (Rfree = 0.000) for 7744 atoms. Found 0 (49 requested) and removed 24 (24 requested) atoms. Cycle 47: After refmac, R = 0.1840 (Rfree = 0.000) for 7696 atoms. Found 0 (49 requested) and removed 24 (24 requested) atoms. Cycle 48: After refmac, R = 0.1816 (Rfree = 0.000) for 7657 atoms. Found 0 (49 requested) and removed 24 (24 requested) atoms. Cycle 49: After refmac, R = 0.1743 (Rfree = 0.000) for 7626 atoms. TimeTaking 91.92