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 1vm8-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vm8-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vm8-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vm8-4.0-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/1vm8-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vm8-4.0-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 22:23:05 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/1vm8-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vm8-4.0-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 762 and 0 Target number of residues in the AU: 762 Target solvent content: 0.6677 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: 1vm8-4.0-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: 1vm8-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 8544 target number of atoms Had to go as low as 0.65 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 4.000 Wilson plot Bfac: 90.76 10439 reflections ( 98.84 % complete ) and 0 restraints for refining 9436 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3301 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3330 (Rfree = 0.000) for 9436 atoms. Found 44 (44 requested) and removed 78 (22 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.80 3.65 Search for helices and strands: 0 residues in 0 chains, 9541 seeds are put forward NCS extension: 0 residues added, 9541 seeds are put forward Round 1: 292 peptides, 59 chains. Longest chain 14 peptides. Score 0.263 Round 2: 407 peptides, 75 chains. Longest chain 10 peptides. Score 0.333 Round 3: 460 peptides, 75 chains. Longest chain 16 peptides. Score 0.405 Round 4: 489 peptides, 79 chains. Longest chain 24 peptides. Score 0.420 Round 5: 492 peptides, 75 chains. Longest chain 23 peptides. Score 0.446 Taking the results from Round 5 Chains 78, Residues 417, Estimated correctness of the model 0.0 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 10439 reflections ( 98.84 % complete ) and 18728 restraints for refining 7713 atoms. 17070 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2306 (Rfree = 0.000) for 7713 atoms. Found 24 (36 requested) and removed 111 (18 requested) atoms. Cycle 2: After refmac, R = 0.2233 (Rfree = 0.000) for 7489 atoms. Found 32 (36 requested) and removed 104 (18 requested) atoms. Cycle 3: After refmac, R = 0.2094 (Rfree = 0.000) for 7357 atoms. Found 34 (35 requested) and removed 55 (17 requested) atoms. Cycle 4: After refmac, R = 0.1704 (Rfree = 0.000) for 7273 atoms. Found 10 (34 requested) and removed 38 (17 requested) atoms. Cycle 5: After refmac, R = 0.1603 (Rfree = 0.000) for 7219 atoms. Found 11 (34 requested) and removed 40 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.83 3.68 Search for helices and strands: 0 residues in 0 chains, 7438 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 7449 seeds are put forward Round 1: 436 peptides, 76 chains. Longest chain 18 peptides. Score 0.367 Round 2: 500 peptides, 77 chains. Longest chain 20 peptides. Score 0.445 Round 3: 508 peptides, 73 chains. Longest chain 19 peptides. Score 0.476 Round 4: 510 peptides, 78 chains. Longest chain 13 peptides. Score 0.452 Round 5: 504 peptides, 69 chains. Longest chain 20 peptides. Score 0.493 Taking the results from Round 5 Chains 73, Residues 435, Estimated correctness of the model 0.0 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 10439 reflections ( 98.84 % complete ) and 17663 restraints for refining 7555 atoms. 15899 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2161 (Rfree = 0.000) for 7555 atoms. Found 35 (35 requested) and removed 106 (17 requested) atoms. Cycle 7: After refmac, R = 0.2103 (Rfree = 0.000) for 7411 atoms. Found 35 (35 requested) and removed 61 (17 requested) atoms. Cycle 8: After refmac, R = 0.1927 (Rfree = 0.000) for 7331 atoms. Found 35 (35 requested) and removed 61 (17 requested) atoms. Cycle 9: After refmac, R = 0.1927 (Rfree = 0.000) for 7280 atoms. Found 33 (34 requested) and removed 64 (17 requested) atoms. Cycle 10: After refmac, R = 0.1868 (Rfree = 0.000) for 7235 atoms. Found 34 (34 requested) and removed 31 (17 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.78 3.63 Search for helices and strands: 0 residues in 0 chains, 7513 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 7527 seeds are put forward Round 1: 440 peptides, 82 chains. Longest chain 10 peptides. Score 0.337 Round 2: 497 peptides, 77 chains. Longest chain 16 peptides. Score 0.441 Round 3: 492 peptides, 70 chains. Longest chain 19 peptides. Score 0.473 Round 4: 519 peptides, 73 chains. Longest chain 18 peptides. Score 0.489 Round 5: 498 peptides, 70 chains. Longest chain 16 peptides. Score 0.480 Taking the results from Round 4 Chains 77, Residues 446, Estimated correctness of the model 0.0 % 7 chains (64 residues) have been docked in sequence ------------------------------------------------------ 10439 reflections ( 98.84 % complete ) and 17370 restraints for refining 7714 atoms. 15449 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2014 (Rfree = 0.000) for 7714 atoms. Found 36 (36 requested) and removed 75 (18 requested) atoms. Cycle 12: After refmac, R = 0.2022 (Rfree = 0.000) for 7596 atoms. Found 36 (36 requested) and removed 55 (18 requested) atoms. Cycle 13: After refmac, R = 0.1887 (Rfree = 0.000) for 7522 atoms. Found 36 (36 requested) and removed 56 (18 requested) atoms. Cycle 14: After refmac, R = 0.1992 (Rfree = 0.000) for 7466 atoms. Found 35 (35 requested) and removed 48 (17 requested) atoms. Cycle 15: After refmac, R = 0.1765 (Rfree = 0.000) for 7424 atoms. Found 35 (35 requested) and removed 40 (17 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.81 3.66 Search for helices and strands: 0 residues in 0 chains, 7689 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 7708 seeds are put forward Round 1: 425 peptides, 84 chains. Longest chain 11 peptides. Score 0.304 Round 2: 469 peptides, 74 chains. Longest chain 14 peptides. Score 0.422 Round 3: 490 peptides, 79 chains. Longest chain 17 peptides. Score 0.421 Round 4: 464 peptides, 66 chains. Longest chain 18 peptides. Score 0.461 Round 5: 469 peptides, 66 chains. Longest chain 16 peptides. Score 0.467 Taking the results from Round 5 Failed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDBFailed to save intermediate PDB Chains 67, Residues 403, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 10439 reflections ( 98.84 % complete ) and 18070 restraints for refining 7716 atoms. 16464 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1947 (Rfree = 0.000) for 7716 atoms. Found 34 (36 requested) and removed 69 (18 requested) atoms. Cycle 17: After refmac, R = 0.1891 (Rfree = 0.000) for 7637 atoms. Found 36 (36 requested) and removed 61 (18 requested) atoms. Cycle 18: After refmac, R = 0.1855 (Rfree = 0.000) for 7580 atoms. Found 35 (36 requested) and removed 46 (18 requested) atoms. Cycle 19: After refmac, R = 0.1795 (Rfree = 0.000) for 7547 atoms. Found 35 (35 requested) and removed 47 (17 requested) atoms. Cycle 20: After refmac, R = 0.1394 (Rfree = 0.000) for 7525 atoms. Found 9 (35 requested) and removed 27 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.80 3.65 Search for helices and strands: 0 residues in 0 chains, 7762 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 7773 seeds are put forward Round 1: 419 peptides, 83 chains. Longest chain 9 peptides. Score 0.301 Round 2: 461 peptides, 75 chains. Longest chain 14 peptides. Score 0.406 Round 3: 447 peptides, 73 chains. Longest chain 14 peptides. Score 0.399 Round 4: 461 peptides, 70 chains. Longest chain 17 peptides. Score 0.435 Round 5: 469 peptides, 72 chains. Longest chain 18 peptides. Score 0.434 Taking the results from Round 4 Chains 70, Residues 391, Estimated correctness of the model 0.0 % 2 chains (14 residues) have been docked in sequence ------------------------------------------------------ 10439 reflections ( 98.84 % complete ) and 18025 restraints for refining 7716 atoms. 16491 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2067 (Rfree = 0.000) for 7716 atoms. Found 36 (36 requested) and removed 75 (18 requested) atoms. Cycle 22: After refmac, R = 0.1876 (Rfree = 0.000) for 7629 atoms. Found 36 (36 requested) and removed 41 (18 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.1787 (Rfree = 0.000) for 7579 atoms. Found 36 (36 requested) and removed 43 (18 requested) atoms. Cycle 24: After refmac, R = 0.1801 (Rfree = 0.000) for 7543 atoms. Found 35 (35 requested) and removed 39 (17 requested) atoms. Cycle 25: After refmac, R = 0.1753 (Rfree = 0.000) for 7516 atoms. Found 35 (35 requested) and removed 30 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.84 3.69 Search for helices and strands: 0 residues in 0 chains, 7816 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 7834 seeds are put forward Round 1: 399 peptides, 81 chains. Longest chain 9 peptides. Score 0.284 Round 2: 444 peptides, 72 chains. Longest chain 13 peptides. Score 0.401 Round 3: 438 peptides, 75 chains. Longest chain 10 peptides. Score 0.376 Round 4: 463 peptides, 71 chains. Longest chain 16 peptides. Score 0.431 Round 5: 445 peptides, 70 chains. Longest chain 14 peptides. Score 0.414 Taking the results from Round 4 Chains 73, Residues 392, Estimated correctness of the model 0.0 % 3 chains (21 residues) have been docked in sequence ------------------------------------------------------ 10439 reflections ( 98.84 % complete ) and 17885 restraints for refining 7713 atoms. 16324 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1895 (Rfree = 0.000) for 7713 atoms. Found 36 (36 requested) and removed 56 (18 requested) atoms. Cycle 27: After refmac, R = 0.1859 (Rfree = 0.000) for 7640 atoms. Found 36 (36 requested) and removed 66 (18 requested) atoms. Cycle 28: After refmac, R = 0.1421 (Rfree = 0.000) for 7588 atoms. Found 13 (36 requested) and removed 40 (18 requested) atoms. Cycle 29: After refmac, R = 0.1335 (Rfree = 0.000) for 7537 atoms. Found 6 (35 requested) and removed 25 (17 requested) atoms. Cycle 30: After refmac, R = 0.1290 (Rfree = 0.000) for 7507 atoms. Found 5 (35 requested) and removed 28 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.81 3.66 Search for helices and strands: 0 residues in 0 chains, 7710 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 7723 seeds are put forward Round 1: 368 peptides, 78 chains. Longest chain 9 peptides. Score 0.257 Round 2: 421 peptides, 77 chains. Longest chain 12 peptides. Score 0.340 Round 3: 427 peptides, 75 chains. Longest chain 11 peptides. Score 0.361 Round 4: 449 peptides, 78 chains. Longest chain 16 peptides. Score 0.373 Round 5: 430 peptides, 72 chains. Longest chain 12 peptides. Score 0.383 Taking the results from Round 5 Chains 72, Residues 358, Estimated correctness of the model 0.0 % 5 chains (29 residues) have been docked in sequence ------------------------------------------------------ 10439 reflections ( 98.84 % complete ) and 18172 restraints for refining 7716 atoms. 16735 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1925 (Rfree = 0.000) for 7716 atoms. Found 36 (36 requested) and removed 53 (18 requested) atoms. Cycle 32: After refmac, R = 0.1870 (Rfree = 0.000) for 7659 atoms. Found 36 (36 requested) and removed 49 (18 requested) atoms. Cycle 33: After refmac, R = 0.1734 (Rfree = 0.000) for 7620 atoms. Found 36 (36 requested) and removed 55 (18 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1775 (Rfree = 0.000) for 7568 atoms. Found 36 (36 requested) and removed 37 (18 requested) atoms. Cycle 35: After refmac, R = 0.1695 (Rfree = 0.000) for 7541 atoms. Found 35 (35 requested) and removed 48 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.80 3.65 Search for helices and strands: 0 residues in 0 chains, 7784 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 7799 seeds are put forward Round 1: 349 peptides, 74 chains. Longest chain 9 peptides. Score 0.253 Round 2: 430 peptides, 80 chains. Longest chain 10 peptides. Score 0.335 Round 3: 449 peptides, 82 chains. Longest chain 11 peptides. Score 0.349 Round 4: 415 peptides, 73 chains. Longest chain 10 peptides. Score 0.356 Round 5: 419 peptides, 70 chains. Longest chain 13 peptides. Score 0.380 Taking the results from Round 5 Chains 70, Residues 349, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 10439 reflections ( 98.84 % complete ) and 18330 restraints for refining 7715 atoms. 16981 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1902 (Rfree = 0.000) for 7715 atoms. Found 36 (36 requested) and removed 121 (18 requested) atoms. Cycle 37: After refmac, R = 0.1820 (Rfree = 0.000) for 7579 atoms. Found 36 (36 requested) and removed 67 (18 requested) atoms. Cycle 38: After refmac, R = 0.1862 (Rfree = 0.000) for 7528 atoms. Found 35 (35 requested) and removed 56 (17 requested) atoms. Cycle 39: After refmac, R = 0.1904 (Rfree = 0.000) for 7486 atoms. Found 35 (35 requested) and removed 67 (17 requested) atoms. Cycle 40: After refmac, R = 0.1873 (Rfree = 0.000) for 7440 atoms. Found 35 (35 requested) and removed 48 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.80 3.65 Search for helices and strands: 0 residues in 0 chains, 7689 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 7706 seeds are put forward Round 1: 347 peptides, 77 chains. Longest chain 10 peptides. Score 0.230 Round 2: 391 peptides, 75 chains. Longest chain 11 peptides. Score 0.310 Round 3: 386 peptides, 67 chains. Longest chain 13 peptides. Score 0.352 Round 4: 390 peptides, 70 chains. Longest chain 12 peptides. Score 0.339 Round 5: 406 peptides, 68 chains. Longest chain 14 peptides. Score 0.374 Taking the results from Round 5 Chains 68, Residues 338, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence ------------------------------------------------------ 10439 reflections ( 98.84 % complete ) and 17767 restraints for refining 7547 atoms. 16462 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1872 (Rfree = 0.000) for 7547 atoms. Found 35 (35 requested) and removed 49 (17 requested) atoms. Cycle 42: After refmac, R = 0.1867 (Rfree = 0.000) for 7495 atoms. Found 35 (35 requested) and removed 39 (17 requested) atoms. Cycle 43: After refmac, R = 0.1896 (Rfree = 0.000) for 7470 atoms. Found 35 (35 requested) and removed 40 (17 requested) atoms. Cycle 44: After refmac, R = 0.1835 (Rfree = 0.000) for 7446 atoms. Found 35 (35 requested) and removed 32 (17 requested) atoms. Cycle 45: After refmac, R = 0.1923 (Rfree = 0.000) for 7425 atoms. Found 35 (35 requested) and removed 43 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.81 3.66 Search for helices and strands: 0 residues in 0 chains, 7677 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 7699 seeds are put forward Round 1: 286 peptides, 60 chains. Longest chain 9 peptides. Score 0.247 Round 2: 331 peptides, 67 chains. Longest chain 10 peptides. Score 0.271 Round 3: 361 peptides, 68 chains. Longest chain 13 peptides. Score 0.310 Round 4: 338 peptides, 59 chains. Longest chain 11 peptides. Score 0.334 Round 5: 340 peptides, 59 chains. Longest chain 11 peptides. Score 0.337 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 59, Residues 281, Estimated correctness of the model 0.0 % 2 chains (8 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 1vm8-4_warpNtrace.pdb as input Building loops using Loopy2018 59 chains (281 residues) following loop building 2 chains (8 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10439 reflections ( 98.84 % complete ) and 17894 restraints for refining 7503 atoms. 16812 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2025 (Rfree = 0.000) for 7503 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.2007 (Rfree = 0.000) for 7445 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 48: After refmac, R = 0.1983 (Rfree = 0.000) for 7393 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 49: After refmac, R = 0.2017 (Rfree = 0.000) for 7353 atoms. TimeTaking 91.28