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 1vky-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vky-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vky-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vky-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/1vky-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vky-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 22:23:07 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/1vky-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vky-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 759 and 0 Target number of residues in the AU: 759 Target solvent content: 0.5743 Checking the provided sequence file Detected sequence length: 347 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 694 Adjusted target solvent content: 0.61 Input MTZ file: 1vky-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: 23 Cell parameters: 119.363 122.591 131.880 90.000 90.000 90.000 Input sequence file: 1vky-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 5552 target number of atoms Had to go as low as 0.75 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: 41.380 3.200 Wilson plot Bfac: 43.08 16292 reflections ( 99.71 % complete ) and 0 restraints for refining 6162 atoms. Observations/parameters ratio is 0.66 ------------------------------------------------------ Starting model: R = 0.3105 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2275 (Rfree = 0.000) for 6162 atoms. Found 54 (55 requested) and removed 57 (27 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.90 2.50 Search for helices and strands: 0 residues in 0 chains, 6276 seeds are put forward NCS extension: 0 residues added, 6276 seeds are put forward Round 1: 375 peptides, 57 chains. Longest chain 17 peptides. Score 0.443 Round 2: 419 peptides, 50 chains. Longest chain 42 peptides. Score 0.556 Round 3: 436 peptides, 49 chains. Longest chain 24 peptides. Score 0.585 Round 4: 435 peptides, 47 chains. Longest chain 22 peptides. Score 0.595 Round 5: 440 peptides, 45 chains. Longest chain 47 peptides. Score 0.614 Taking the results from Round 5 Chains 46, Residues 395, Estimated correctness of the model 44.8 % 4 chains (93 residues) have been docked in sequence ------------------------------------------------------ 16292 reflections ( 99.71 % complete ) and 9739 restraints for refining 5067 atoms. 7776 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2704 (Rfree = 0.000) for 5067 atoms. Found 45 (45 requested) and removed 50 (22 requested) atoms. Cycle 2: After refmac, R = 0.2487 (Rfree = 0.000) for 5023 atoms. Found 41 (45 requested) and removed 30 (22 requested) atoms. Cycle 3: After refmac, R = 0.2352 (Rfree = 0.000) for 5009 atoms. Found 20 (45 requested) and removed 23 (22 requested) atoms. Cycle 4: After refmac, R = 0.2306 (Rfree = 0.000) for 4990 atoms. Found 23 (44 requested) and removed 22 (22 requested) atoms. Cycle 5: After refmac, R = 0.2271 (Rfree = 0.000) for 4986 atoms. Found 22 (44 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.88 2.48 Search for helices and strands: 0 residues in 0 chains, 5111 seeds are put forward NCS extension: 49 residues added (15 deleted due to clashes), 5160 seeds are put forward Round 1: 417 peptides, 54 chains. Longest chain 46 peptides. Score 0.527 Round 2: 419 peptides, 45 chains. Longest chain 35 peptides. Score 0.587 Round 3: 436 peptides, 46 chains. Longest chain 34 peptides. Score 0.603 Round 4: 430 peptides, 42 chains. Longest chain 38 peptides. Score 0.619 Round 5: 432 peptides, 44 chains. Longest chain 48 peptides. Score 0.609 Taking the results from Round 4 Chains 48, Residues 388, Estimated correctness of the model 46.1 % 6 chains (104 residues) have been docked in sequence ------------------------------------------------------ 16292 reflections ( 99.71 % complete ) and 9706 restraints for refining 5068 atoms. 7751 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2654 (Rfree = 0.000) for 5068 atoms. Found 45 (45 requested) and removed 42 (22 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2471 (Rfree = 0.000) for 5044 atoms. Found 31 (45 requested) and removed 30 (22 requested) atoms. Cycle 8: After refmac, R = 0.2391 (Rfree = 0.000) for 5019 atoms. Found 29 (45 requested) and removed 28 (22 requested) atoms. Cycle 9: After refmac, R = 0.2321 (Rfree = 0.000) for 5004 atoms. Found 15 (45 requested) and removed 27 (22 requested) atoms. Cycle 10: After refmac, R = 0.2283 (Rfree = 0.000) for 4979 atoms. Found 17 (44 requested) and removed 26 (22 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.91 2.51 Search for helices and strands: 0 residues in 0 chains, 5114 seeds are put forward NCS extension: 16 residues added (37 deleted due to clashes), 5130 seeds are put forward Round 1: 393 peptides, 47 chains. Longest chain 22 peptides. Score 0.539 Round 2: 424 peptides, 44 chains. Longest chain 29 peptides. Score 0.599 Round 3: 441 peptides, 42 chains. Longest chain 42 peptides. Score 0.632 Round 4: 439 peptides, 46 chains. Longest chain 51 peptides. Score 0.606 Round 5: 446 peptides, 47 chains. Longest chain 28 peptides. Score 0.609 Taking the results from Round 3 Chains 42, Residues 399, Estimated correctness of the model 49.4 % 5 chains (113 residues) have been docked in sequence ------------------------------------------------------ 16292 reflections ( 99.71 % complete ) and 9505 restraints for refining 5067 atoms. 7453 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2669 (Rfree = 0.000) for 5067 atoms. Found 45 (45 requested) and removed 50 (22 requested) atoms. Cycle 12: After refmac, R = 0.2492 (Rfree = 0.000) for 5039 atoms. Found 37 (45 requested) and removed 32 (22 requested) atoms. Cycle 13: After refmac, R = 0.2396 (Rfree = 0.000) for 5032 atoms. Found 25 (45 requested) and removed 27 (22 requested) atoms. Cycle 14: After refmac, R = 0.2338 (Rfree = 0.000) for 5024 atoms. Found 22 (45 requested) and removed 25 (22 requested) atoms. Cycle 15: After refmac, R = 0.2314 (Rfree = 0.000) for 5014 atoms. Found 15 (45 requested) and removed 26 (22 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.88 2.48 Search for helices and strands: 0 residues in 0 chains, 5108 seeds are put forward NCS extension: 41 residues added (3 deleted due to clashes), 5149 seeds are put forward Round 1: 408 peptides, 47 chains. Longest chain 26 peptides. Score 0.560 Round 2: 426 peptides, 44 chains. Longest chain 45 peptides. Score 0.602 Round 3: 455 peptides, 46 chains. Longest chain 39 peptides. Score 0.626 Round 4: 440 peptides, 40 chains. Longest chain 47 peptides. Score 0.642 Round 5: 442 peptides, 46 chains. Longest chain 38 peptides. Score 0.610 Taking the results from Round 4 Chains 43, Residues 400, Estimated correctness of the model 51.9 % 9 chains (166 residues) have been docked in sequence ------------------------------------------------------ 16292 reflections ( 99.71 % complete ) and 8945 restraints for refining 5068 atoms. 6643 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2729 (Rfree = 0.000) for 5068 atoms. Found 45 (45 requested) and removed 48 (22 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2568 (Rfree = 0.000) for 5030 atoms. Found 39 (45 requested) and removed 44 (22 requested) atoms. Cycle 18: After refmac, R = 0.2467 (Rfree = 0.000) for 5009 atoms. Found 19 (45 requested) and removed 27 (22 requested) atoms. Cycle 19: After refmac, R = 0.2413 (Rfree = 0.000) for 4990 atoms. Found 14 (44 requested) and removed 24 (22 requested) atoms. Cycle 20: After refmac, R = 0.2392 (Rfree = 0.000) for 4969 atoms. Found 13 (44 requested) and removed 23 (22 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.90 2.50 Search for helices and strands: 0 residues in 0 chains, 5072 seeds are put forward NCS extension: 38 residues added (26 deleted due to clashes), 5110 seeds are put forward Round 1: 400 peptides, 45 chains. Longest chain 25 peptides. Score 0.561 Round 2: 441 peptides, 47 chains. Longest chain 24 peptides. Score 0.603 Round 3: 450 peptides, 49 chains. Longest chain 45 peptides. Score 0.603 Round 4: 451 peptides, 45 chains. Longest chain 32 peptides. Score 0.627 Round 5: 442 peptides, 48 chains. Longest chain 40 peptides. Score 0.598 Taking the results from Round 4 Chains 45, Residues 406, Estimated correctness of the model 48.1 % 5 chains (123 residues) have been docked in sequence ------------------------------------------------------ 16292 reflections ( 99.71 % complete ) and 9419 restraints for refining 5068 atoms. 7290 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2717 (Rfree = 0.000) for 5068 atoms. Found 45 (45 requested) and removed 49 (22 requested) atoms. Cycle 22: After refmac, R = 0.2539 (Rfree = 0.000) for 5035 atoms. Found 42 (45 requested) and removed 35 (22 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2431 (Rfree = 0.000) for 5028 atoms. Found 24 (45 requested) and removed 24 (22 requested) atoms. Cycle 24: After refmac, R = 0.2372 (Rfree = 0.000) for 5016 atoms. Found 21 (45 requested) and removed 24 (22 requested) atoms. Cycle 25: After refmac, R = 0.2319 (Rfree = 0.000) for 5007 atoms. Found 17 (44 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.92 2.52 Search for helices and strands: 0 residues in 0 chains, 5136 seeds are put forward NCS extension: 37 residues added (9 deleted due to clashes), 5173 seeds are put forward Round 1: 391 peptides, 50 chains. Longest chain 24 peptides. Score 0.516 Round 2: 418 peptides, 46 chains. Longest chain 37 peptides. Score 0.579 Round 3: 425 peptides, 44 chains. Longest chain 30 peptides. Score 0.601 Round 4: 433 peptides, 50 chains. Longest chain 22 peptides. Score 0.575 Round 5: 432 peptides, 44 chains. Longest chain 39 peptides. Score 0.609 Taking the results from Round 5 Chains 45, Residues 388, Estimated correctness of the model 43.5 % 4 chains (76 residues) have been docked in sequence ------------------------------------------------------ 16292 reflections ( 99.71 % complete ) and 10070 restraints for refining 5067 atoms. 8222 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2614 (Rfree = 0.000) for 5067 atoms. Found 45 (45 requested) and removed 40 (22 requested) atoms. Cycle 27: After refmac, R = 0.2435 (Rfree = 0.000) for 5061 atoms. Found 21 (45 requested) and removed 27 (22 requested) atoms. Cycle 28: After refmac, R = 0.2379 (Rfree = 0.000) for 5044 atoms. Found 24 (45 requested) and removed 23 (22 requested) atoms. Cycle 29: After refmac, R = 0.2343 (Rfree = 0.000) for 5039 atoms. Found 14 (45 requested) and removed 22 (22 requested) atoms. Cycle 30: After refmac, R = 0.2308 (Rfree = 0.000) for 5025 atoms. Found 20 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.92 2.52 Search for helices and strands: 0 residues in 0 chains, 5137 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 5156 seeds are put forward Round 1: 386 peptides, 54 chains. Longest chain 22 peptides. Score 0.481 Round 2: 430 peptides, 52 chains. Longest chain 23 peptides. Score 0.558 Round 3: 449 peptides, 51 chains. Longest chain 24 peptides. Score 0.589 Round 4: 438 peptides, 48 chains. Longest chain 27 peptides. Score 0.593 Round 5: 424 peptides, 48 chains. Longest chain 26 peptides. Score 0.575 Taking the results from Round 4 Chains 51, Residues 390, Estimated correctness of the model 39.2 % 3 chains (51 residues) have been docked in sequence ------------------------------------------------------ 16292 reflections ( 99.71 % complete ) and 10396 restraints for refining 5068 atoms. 8639 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2577 (Rfree = 0.000) for 5068 atoms. Found 45 (45 requested) and removed 31 (22 requested) atoms. Cycle 32: After refmac, R = 0.2417 (Rfree = 0.000) for 5069 atoms. Found 25 (45 requested) and removed 22 (22 requested) atoms. Cycle 33: After refmac, R = 0.2340 (Rfree = 0.000) for 5064 atoms. Found 18 (45 requested) and removed 23 (22 requested) atoms. Cycle 34: After refmac, R = 0.2364 (Rfree = 0.000) for 5054 atoms. Found 14 (45 requested) and removed 23 (22 requested) atoms. Cycle 35: After refmac, R = 0.2309 (Rfree = 0.000) for 5041 atoms. Found 9 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.92 2.52 Search for helices and strands: 0 residues in 0 chains, 5138 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 5158 seeds are put forward Round 1: 390 peptides, 49 chains. Longest chain 22 peptides. Score 0.521 Round 2: 426 peptides, 48 chains. Longest chain 31 peptides. Score 0.578 Round 3: 426 peptides, 48 chains. Longest chain 21 peptides. Score 0.578 Round 4: 419 peptides, 48 chains. Longest chain 31 peptides. Score 0.568 Round 5: 416 peptides, 52 chains. Longest chain 20 peptides. Score 0.539 Taking the results from Round 3 Chains 54, Residues 378, Estimated correctness of the model 35.0 % 6 chains (76 residues) have been docked in sequence ------------------------------------------------------ 16292 reflections ( 99.71 % complete ) and 10183 restraints for refining 5067 atoms. 8417 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2586 (Rfree = 0.000) for 5067 atoms. Found 45 (45 requested) and removed 25 (22 requested) atoms. Cycle 37: After refmac, R = 0.2411 (Rfree = 0.000) for 5068 atoms. Found 31 (45 requested) and removed 28 (22 requested) atoms. Cycle 38: After refmac, R = 0.2392 (Rfree = 0.000) for 5053 atoms. Found 24 (45 requested) and removed 22 (22 requested) atoms. Cycle 39: After refmac, R = 0.2338 (Rfree = 0.000) for 5044 atoms. Found 21 (45 requested) and removed 23 (22 requested) atoms. Cycle 40: After refmac, R = 0.2257 (Rfree = 0.000) for 5034 atoms. Found 15 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.91 2.51 Search for helices and strands: 0 residues in 0 chains, 5131 seeds are put forward NCS extension: 31 residues added (3 deleted due to clashes), 5162 seeds are put forward Round 1: 395 peptides, 52 chains. Longest chain 21 peptides. Score 0.509 Round 2: 418 peptides, 46 chains. Longest chain 22 peptides. Score 0.579 Round 3: 427 peptides, 48 chains. Longest chain 23 peptides. Score 0.579 Round 4: 421 peptides, 42 chains. Longest chain 31 peptides. Score 0.608 Round 5: 418 peptides, 46 chains. Longest chain 35 peptides. Score 0.579 Taking the results from Round 4 Chains 46, Residues 379, Estimated correctness of the model 43.2 % 7 chains (93 residues) have been docked in sequence ------------------------------------------------------ 16292 reflections ( 99.71 % complete ) and 10055 restraints for refining 5068 atoms. 8232 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2497 (Rfree = 0.000) for 5068 atoms. Found 45 (45 requested) and removed 29 (22 requested) atoms. Cycle 42: After refmac, R = 0.2318 (Rfree = 0.000) for 5064 atoms. Found 30 (45 requested) and removed 23 (22 requested) atoms. Cycle 43: After refmac, R = 0.2228 (Rfree = 0.000) for 5060 atoms. Found 14 (45 requested) and removed 22 (22 requested) atoms. Cycle 44: After refmac, R = 0.2194 (Rfree = 0.000) for 5044 atoms. Found 22 (45 requested) and removed 22 (22 requested) atoms. Cycle 45: After refmac, R = 0.2149 (Rfree = 0.000) for 5039 atoms. Found 10 (45 requested) and removed 22 (22 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.90 2.50 Search for helices and strands: 0 residues in 0 chains, 5124 seeds are put forward NCS extension: 41 residues added (2 deleted due to clashes), 5165 seeds are put forward Round 1: 366 peptides, 44 chains. Longest chain 26 peptides. Score 0.520 Round 2: 408 peptides, 42 chains. Longest chain 38 peptides. Score 0.591 Round 3: 402 peptides, 44 chains. Longest chain 27 peptides. Score 0.571 Round 4: 399 peptides, 45 chains. Longest chain 27 peptides. Score 0.560 Round 5: 400 peptides, 41 chains. Longest chain 24 peptides. Score 0.587 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 46, Residues 366, Estimated correctness of the model 38.6 % 6 chains (110 residues) have been docked in sequence Sequence coverage is 29 % Consider running further cycles of model building using 1vky-3_warpNtrace.pdb as input Building loops using Loopy2018 46 chains (366 residues) following loop building 6 chains (110 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16292 reflections ( 99.71 % complete ) and 9870 restraints for refining 5068 atoms. 7991 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2451 (Rfree = 0.000) for 5068 atoms. Found 0 (45 requested) and removed 17 (22 requested) atoms. Cycle 47: After refmac, R = 0.2339 (Rfree = 0.000) for 5037 atoms. Found 0 (45 requested) and removed 9 (22 requested) atoms. Cycle 48: After refmac, R = 0.2300 (Rfree = 0.000) for 5018 atoms. Found 0 (45 requested) and removed 5 (22 requested) atoms. Cycle 49: After refmac, R = 0.2260 (Rfree = 0.000) for 5013 atoms. TimeTaking 77.53