Sun 23 Dec 22:22:46 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 1vm8-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vm8-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vm8-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vm8-3.2-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/1vm8-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vm8-3.2-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 22:22:54 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/1vm8-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vm8-3.2-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 870 and 0 Target number of residues in the AU: 870 Target solvent content: 0.6207 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: 1vm8-3.2-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: 1vm8-3.2-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 3.200 Wilson plot Bfac: 61.74 Failed to save intermediate PDB 20337 reflections ( 99.36 % complete ) and 0 restraints for refining 9513 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3264 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2755 (Rfree = 0.000) for 9513 atoms. Found 68 (85 requested) and removed 263 (42 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.15 3.03 Search for helices and strands: 0 residues in 0 chains, 9447 seeds are put forward NCS extension: 0 residues added, 9447 seeds are put forward Round 1: 402 peptides, 80 chains. Longest chain 12 peptides. Score 0.295 Round 2: 497 peptides, 85 chains. Longest chain 18 peptides. Score 0.396 Round 3: 528 peptides, 82 chains. Longest chain 34 peptides. Score 0.452 Round 4: 552 peptides, 82 chains. Longest chain 17 peptides. Score 0.481 Round 5: 565 peptides, 84 chains. Longest chain 20 peptides. Score 0.486 Taking the results from Round 5 Chains 89, Residues 481, Estimated correctness of the model 6.7 % 9 chains (66 residues) have been docked in sequence ------------------------------------------------------ 20337 reflections ( 99.36 % complete ) and 17646 restraints for refining 7799 atoms. 15619 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2558 (Rfree = 0.000) for 7799 atoms. Found 70 (70 requested) and removed 92 (35 requested) atoms. Cycle 2: After refmac, R = 0.2340 (Rfree = 0.000) for 7719 atoms. Found 29 (69 requested) and removed 48 (34 requested) atoms. Cycle 3: After refmac, R = 0.2224 (Rfree = 0.000) for 7668 atoms. Found 22 (69 requested) and removed 42 (34 requested) atoms. Cycle 4: After refmac, R = 0.2212 (Rfree = 0.000) for 7613 atoms. Found 19 (68 requested) and removed 43 (34 requested) atoms. Cycle 5: After refmac, R = 0.2198 (Rfree = 0.000) for 7577 atoms. Found 18 (68 requested) and removed 39 (34 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.13 3.01 Search for helices and strands: 0 residues in 0 chains, 7786 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 7809 seeds are put forward Round 1: 515 peptides, 92 chains. Longest chain 16 peptides. Score 0.381 Round 2: 594 peptides, 86 chains. Longest chain 22 peptides. Score 0.509 Round 3: 586 peptides, 89 chains. Longest chain 21 peptides. Score 0.485 Round 4: 616 peptides, 92 chains. Longest chain 25 peptides. Score 0.504 Round 5: 584 peptides, 81 chains. Longest chain 21 peptides. Score 0.522 Taking the results from Round 5 Chains 81, Residues 503, Estimated correctness of the model 18.3 % 4 chains (43 residues) have been docked in sequence ------------------------------------------------------ 20337 reflections ( 99.36 % complete ) and 17341 restraints for refining 7797 atoms. 15264 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2434 (Rfree = 0.000) for 7797 atoms. Found 56 (70 requested) and removed 53 (35 requested) atoms. Cycle 7: After refmac, R = 0.2250 (Rfree = 0.000) for 7758 atoms. Found 24 (70 requested) and removed 43 (35 requested) atoms. Cycle 8: After refmac, R = 0.2180 (Rfree = 0.000) for 7712 atoms. Found 20 (69 requested) and removed 40 (34 requested) atoms. Cycle 9: After refmac, R = 0.2194 (Rfree = 0.000) for 7676 atoms. Found 26 (69 requested) and removed 39 (34 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2140 (Rfree = 0.000) for 7659 atoms. Found 31 (68 requested) and removed 35 (34 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.16 3.04 Search for helices and strands: 0 residues in 0 chains, 7912 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 7929 seeds are put forward Round 1: 545 peptides, 97 chains. Longest chain 22 peptides. Score 0.392 Round 2: 572 peptides, 85 chains. Longest chain 19 peptides. Score 0.489 Round 3: 580 peptides, 92 chains. Longest chain 18 peptides. Score 0.462 Round 4: 593 peptides, 83 chains. Longest chain 34 peptides. Score 0.523 Round 5: 602 peptides, 78 chains. Longest chain 24 peptides. Score 0.556 Taking the results from Round 5 Chains 78, Residues 524, Estimated correctness of the model 28.7 % 5 chains (36 residues) have been docked in sequence ------------------------------------------------------ 20337 reflections ( 99.36 % complete ) and 17153 restraints for refining 7799 atoms. 15035 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2302 (Rfree = 0.000) for 7799 atoms. Found 56 (70 requested) and removed 40 (35 requested) atoms. Cycle 12: After refmac, R = 0.2073 (Rfree = 0.000) for 7786 atoms. Found 17 (70 requested) and removed 38 (35 requested) atoms. Cycle 13: After refmac, R = 0.2003 (Rfree = 0.000) for 7739 atoms. Found 11 (69 requested) and removed 40 (34 requested) atoms. Cycle 14: After refmac, R = 0.1975 (Rfree = 0.000) for 7697 atoms. Found 12 (69 requested) and removed 36 (34 requested) atoms. Cycle 15: After refmac, R = 0.1968 (Rfree = 0.000) for 7663 atoms. Found 8 (68 requested) and removed 34 (34 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.14 3.02 Search for helices and strands: 0 residues in 0 chains, 7901 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 7923 seeds are put forward Round 1: 546 peptides, 87 chains. Longest chain 19 peptides. Score 0.447 Round 2: 563 peptides, 82 chains. Longest chain 24 peptides. Score 0.494 Round 3: 595 peptides, 82 chains. Longest chain 28 peptides. Score 0.530 Round 4: 609 peptides, 88 chains. Longest chain 23 peptides. Score 0.516 Round 5: 587 peptides, 71 chains. Longest chain 27 peptides. Score 0.574 Taking the results from Round 5 Chains 77, Residues 516, Estimated correctness of the model 33.9 % 8 chains (102 residues) have been docked in sequence ------------------------------------------------------ 20337 reflections ( 99.36 % complete ) and 16377 restraints for refining 7799 atoms. 14016 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2356 (Rfree = 0.000) for 7799 atoms. Found 64 (70 requested) and removed 63 (35 requested) atoms. Cycle 17: After refmac, R = 0.2142 (Rfree = 0.000) for 7770 atoms. Found 25 (70 requested) and removed 40 (35 requested) atoms. Cycle 18: After refmac, R = 0.2070 (Rfree = 0.000) for 7733 atoms. Found 18 (69 requested) and removed 37 (34 requested) atoms. Cycle 19: After refmac, R = 0.2037 (Rfree = 0.000) for 7703 atoms. Found 20 (69 requested) and removed 35 (34 requested) atoms. Cycle 20: After refmac, R = 0.1977 (Rfree = 0.000) for 7680 atoms. Found 17 (68 requested) and removed 35 (34 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.12 3.00 Search for helices and strands: 0 residues in 0 chains, 7897 seeds are put forward NCS extension: 26 residues added (4 deleted due to clashes), 7923 seeds are put forward Round 1: 495 peptides, 81 chains. Longest chain 22 peptides. Score 0.416 Round 2: 551 peptides, 82 chains. Longest chain 22 peptides. Score 0.480 Round 3: 551 peptides, 79 chains. Longest chain 24 peptides. Score 0.495 Round 4: 555 peptides, 72 chains. Longest chain 24 peptides. Score 0.535 Round 5: 583 peptides, 84 chains. Longest chain 26 peptides. Score 0.506 Taking the results from Round 4 Chains 74, Residues 483, Estimated correctness of the model 22.4 % 7 chains (66 residues) have been docked in sequence ------------------------------------------------------ 20337 reflections ( 99.36 % complete ) and 17262 restraints for refining 7800 atoms. 15177 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2293 (Rfree = 0.000) for 7800 atoms. Found 47 (70 requested) and removed 46 (35 requested) atoms. Cycle 22: After refmac, R = 0.2126 (Rfree = 0.000) for 7780 atoms. Found 13 (70 requested) and removed 37 (35 requested) atoms. Cycle 23: After refmac, R = 0.2064 (Rfree = 0.000) for 7745 atoms. Found 14 (69 requested) and removed 34 (34 requested) atoms. Cycle 24: After refmac, R = 0.2048 (Rfree = 0.000) for 7716 atoms. Found 9 (69 requested) and removed 34 (34 requested) atoms. Cycle 25: After refmac, R = 0.2025 (Rfree = 0.000) for 7687 atoms. Found 10 (69 requested) and removed 34 (34 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.15 3.03 Search for helices and strands: 0 residues in 0 chains, 7863 seeds are put forward NCS extension: 34 residues added (2 deleted due to clashes), 7897 seeds are put forward Round 1: 508 peptides, 86 chains. Longest chain 23 peptides. Score 0.405 Round 2: 546 peptides, 81 chains. Longest chain 25 peptides. Score 0.479 Round 3: 556 peptides, 82 chains. Longest chain 18 peptides. Score 0.486 Round 4: 572 peptides, 81 chains. Longest chain 25 peptides. Score 0.509 Round 5: 570 peptides, 82 chains. Longest chain 21 peptides. Score 0.502 Taking the results from Round 4 Chains 88, Residues 491, Estimated correctness of the model 14.2 % 8 chains (60 residues) have been docked in sequence ------------------------------------------------------ 20337 reflections ( 99.36 % complete ) and 17202 restraints for refining 7799 atoms. 15132 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2278 (Rfree = 0.000) for 7799 atoms. Found 50 (70 requested) and removed 40 (35 requested) atoms. Cycle 27: After refmac, R = 0.2122 (Rfree = 0.000) for 7786 atoms. Found 27 (70 requested) and removed 39 (35 requested) atoms. Cycle 28: After refmac, R = 0.2091 (Rfree = 0.000) for 7758 atoms. Found 25 (69 requested) and removed 34 (34 requested) atoms. Cycle 29: After refmac, R = 0.2086 (Rfree = 0.000) for 7739 atoms. Found 21 (69 requested) and removed 34 (34 requested) atoms. Cycle 30: After refmac, R = 0.2064 (Rfree = 0.000) for 7722 atoms. Found 16 (69 requested) and removed 34 (34 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.13 3.01 Search for helices and strands: 0 residues in 0 chains, 7911 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 7927 seeds are put forward Round 1: 503 peptides, 87 chains. Longest chain 14 peptides. Score 0.393 Round 2: 551 peptides, 82 chains. Longest chain 22 peptides. Score 0.480 Round 3: 541 peptides, 79 chains. Longest chain 20 peptides. Score 0.483 Round 4: 529 peptides, 75 chains. Longest chain 14 peptides. Score 0.490 Round 5: 525 peptides, 78 chains. Longest chain 22 peptides. Score 0.470 Taking the results from Round 4 Chains 76, Residues 454, Estimated correctness of the model 8.1 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 20337 reflections ( 99.36 % complete ) and 17810 restraints for refining 7800 atoms. 16029 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2159 (Rfree = 0.000) for 7800 atoms. Found 49 (70 requested) and removed 38 (35 requested) atoms. Cycle 32: After refmac, R = 0.2019 (Rfree = 0.000) for 7801 atoms. Found 14 (70 requested) and removed 35 (35 requested) atoms. Cycle 33: After refmac, R = 0.1967 (Rfree = 0.000) for 7776 atoms. Found 17 (69 requested) and removed 34 (34 requested) atoms. Cycle 34: After refmac, R = 0.1940 (Rfree = 0.000) for 7754 atoms. Found 11 (69 requested) and removed 34 (34 requested) atoms. Cycle 35: After refmac, R = 0.1936 (Rfree = 0.000) for 7725 atoms. Found 16 (69 requested) and removed 35 (34 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.14 3.02 Search for helices and strands: 0 residues in 0 chains, 7892 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 7911 seeds are put forward Round 1: 480 peptides, 89 chains. Longest chain 16 peptides. Score 0.351 Round 2: 514 peptides, 85 chains. Longest chain 20 peptides. Score 0.418 Round 3: 541 peptides, 82 chains. Longest chain 24 peptides. Score 0.468 Round 4: 528 peptides, 85 chains. Longest chain 15 peptides. Score 0.436 Round 5: 535 peptides, 82 chains. Longest chain 15 peptides. Score 0.461 Taking the results from Round 3 Chains 84, Residues 459, Estimated correctness of the model 0.7 % 8 chains (80 residues) have been docked in sequence ------------------------------------------------------ 20337 reflections ( 99.36 % complete ) and 16955 restraints for refining 7800 atoms. 14917 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2153 (Rfree = 0.000) for 7800 atoms. Found 54 (70 requested) and removed 42 (35 requested) atoms. Cycle 37: After refmac, R = 0.1988 (Rfree = 0.000) for 7793 atoms. Found 30 (70 requested) and removed 36 (35 requested) atoms. Cycle 38: After refmac, R = 0.1947 (Rfree = 0.000) for 7777 atoms. Found 16 (69 requested) and removed 34 (34 requested) atoms. Cycle 39: After refmac, R = 0.1932 (Rfree = 0.000) for 7748 atoms. Found 14 (69 requested) and removed 34 (34 requested) atoms. Cycle 40: After refmac, R = 0.2097 (Rfree = 0.000) for 7716 atoms. Found 44 (69 requested) and removed 35 (34 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.12 3.00 Search for helices and strands: 0 residues in 0 chains, 7906 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 7930 seeds are put forward Round 1: 445 peptides, 87 chains. Longest chain 25 peptides. Score 0.314 Round 2: 497 peptides, 87 chains. Longest chain 18 peptides. Score 0.385 Round 3: 497 peptides, 86 chains. Longest chain 23 peptides. Score 0.391 Round 4: 515 peptides, 76 chains. Longest chain 41 peptides. Score 0.468 Round 5: 504 peptides, 83 chains. Longest chain 20 peptides. Score 0.417 Taking the results from Round 4 Chains 78, Residues 439, Estimated correctness of the model 0.7 % 3 chains (35 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 20337 reflections ( 99.36 % complete ) and 17569 restraints for refining 7798 atoms. 15756 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2167 (Rfree = 0.000) for 7798 atoms. Found 51 (70 requested) and removed 35 (35 requested) atoms. Cycle 42: After refmac, R = 0.2048 (Rfree = 0.000) for 7797 atoms. Found 20 (70 requested) and removed 35 (35 requested) atoms. Cycle 43: After refmac, R = 0.2025 (Rfree = 0.000) for 7771 atoms. Found 18 (69 requested) and removed 34 (34 requested) atoms. Cycle 44: After refmac, R = 0.2000 (Rfree = 0.000) for 7751 atoms. Found 10 (69 requested) and removed 34 (34 requested) atoms. Cycle 45: After refmac, R = 0.1986 (Rfree = 0.000) for 7724 atoms. Found 8 (69 requested) and removed 35 (34 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.14 3.02 Search for helices and strands: 0 residues in 0 chains, 7875 seeds are put forward NCS extension: 50 residues added (3 deleted due to clashes), 7925 seeds are put forward Round 1: 400 peptides, 77 chains. Longest chain 20 peptides. Score 0.310 Round 2: 464 peptides, 79 chains. Longest chain 13 peptides. Score 0.387 Round 3: 480 peptides, 78 chains. Longest chain 20 peptides. Score 0.414 Round 4: 465 peptides, 71 chains. Longest chain 14 peptides. Score 0.434 Round 5: 474 peptides, 77 chains. Longest chain 24 peptides. Score 0.412 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 71, Residues 394, Estimated correctness of the model 0.0 % 6 chains (41 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 1vm8-3_warpNtrace.pdb as input Building loops using Loopy2018 71 chains (394 residues) following loop building 6 chains (41 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 20337 reflections ( 99.36 % complete ) and 17800 restraints for refining 7798 atoms. 16178 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2052 (Rfree = 0.000) for 7798 atoms. Found 0 (70 requested) and removed 19 (35 requested) atoms. Cycle 47: After refmac, R = 0.2025 (Rfree = 0.000) for 7769 atoms. Found 0 (69 requested) and removed 10 (34 requested) atoms. Cycle 48: After refmac, R = 0.1981 (Rfree = 0.000) for 7755 atoms. Found 0 (69 requested) and removed 20 (34 requested) atoms. Cycle 49: After refmac, R = 0.1955 (Rfree = 0.000) for 7729 atoms. TimeTaking 99.1