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 1vll-3.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vll-3.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vll-3.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vll-3.0-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/1vll-3.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vll-3.0-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 22:23:09 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/1vll-3.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vll-3.0-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 445 and 0 Target number of residues in the AU: 445 Target solvent content: 0.6617 Checking the provided sequence file Detected sequence length: 334 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 668 Adjusted target solvent content: 0.49 Input MTZ file: 1vll-3.0-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: 19 Cell parameters: 57.294 93.405 133.015 90.000 90.000 90.000 Input sequence file: 1vll-3.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 5344 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: 76.441 3.000 Wilson plot Bfac: 85.98 14887 reflections ( 99.98 % complete ) and 0 restraints for refining 5965 atoms. Observations/parameters ratio is 0.62 ------------------------------------------------------ Starting model: R = 0.3401 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2882 (Rfree = 0.000) for 5965 atoms. Found 24 (64 requested) and removed 48 (32 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.41 3.46 Search for helices and strands: 0 residues in 0 chains, 6092 seeds are put forward NCS extension: 0 residues added, 6092 seeds are put forward Round 1: 342 peptides, 60 chains. Longest chain 14 peptides. Score 0.416 Round 2: 402 peptides, 53 chains. Longest chain 23 peptides. Score 0.591 Round 3: 410 peptides, 51 chains. Longest chain 23 peptides. Score 0.619 Round 4: 430 peptides, 47 chains. Longest chain 25 peptides. Score 0.676 Round 5: 411 peptides, 51 chains. Longest chain 23 peptides. Score 0.621 Taking the results from Round 4 Chains 52, Residues 383, Estimated correctness of the model 67.3 % 7 chains (87 residues) have been docked in sequence ------------------------------------------------------ 14887 reflections ( 99.98 % complete ) and 10104 restraints for refining 4905 atoms. 8329 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3003 (Rfree = 0.000) for 4905 atoms. Found 20 (52 requested) and removed 63 (26 requested) atoms. Cycle 2: After refmac, R = 0.2852 (Rfree = 0.000) for 4777 atoms. Found 19 (52 requested) and removed 45 (26 requested) atoms. Cycle 3: After refmac, R = 0.2813 (Rfree = 0.000) for 4731 atoms. Found 12 (51 requested) and removed 39 (25 requested) atoms. Cycle 4: After refmac, R = 0.2815 (Rfree = 0.000) for 4682 atoms. Found 18 (50 requested) and removed 40 (25 requested) atoms. Cycle 5: After refmac, R = 0.2924 (Rfree = 0.000) for 4625 atoms. Found 25 (50 requested) and removed 39 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.39 3.44 Search for helices and strands: 0 residues in 0 chains, 4785 seeds are put forward NCS extension: 12 residues added (5 deleted due to clashes), 4797 seeds are put forward Round 1: 375 peptides, 60 chains. Longest chain 26 peptides. Score 0.484 Round 2: 415 peptides, 56 chains. Longest chain 28 peptides. Score 0.590 Round 3: 420 peptides, 50 chains. Longest chain 28 peptides. Score 0.642 Round 4: 402 peptides, 45 chains. Longest chain 29 peptides. Score 0.649 Round 5: 413 peptides, 49 chains. Longest chain 25 peptides. Score 0.638 Taking the results from Round 4 Chains 48, Residues 357, Estimated correctness of the model 62.1 % 6 chains (75 residues) have been docked in sequence ------------------------------------------------------ 14887 reflections ( 99.98 % complete ) and 10223 restraints for refining 4903 atoms. 8561 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2766 (Rfree = 0.000) for 4903 atoms. Found 10 (52 requested) and removed 64 (26 requested) atoms. Cycle 7: After refmac, R = 0.2880 (Rfree = 0.000) for 4821 atoms. Found 32 (52 requested) and removed 56 (26 requested) atoms. Cycle 8: After refmac, R = 0.2845 (Rfree = 0.000) for 4774 atoms. Found 37 (51 requested) and removed 54 (25 requested) atoms. Cycle 9: After refmac, R = 0.2820 (Rfree = 0.000) for 4740 atoms. Found 37 (51 requested) and removed 43 (25 requested) atoms. Cycle 10: After refmac, R = 0.2745 (Rfree = 0.000) for 4721 atoms. Found 46 (51 requested) and removed 34 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.38 3.43 Search for helices and strands: 0 residues in 0 chains, 4930 seeds are put forward NCS extension: 19 residues added (8 deleted due to clashes), 4949 seeds are put forward Round 1: 338 peptides, 49 chains. Longest chain 17 peptides. Score 0.506 Round 2: 384 peptides, 47 chains. Longest chain 21 peptides. Score 0.606 Round 3: 407 peptides, 47 chains. Longest chain 23 peptides. Score 0.643 Round 4: 401 peptides, 41 chains. Longest chain 22 peptides. Score 0.675 Round 5: 391 peptides, 41 chains. Longest chain 29 peptides. Score 0.660 Taking the results from Round 4 Chains 48, Residues 360, Estimated correctness of the model 67.1 % 6 chains (58 residues) have been docked in sequence ------------------------------------------------------ 14887 reflections ( 99.98 % complete ) and 10527 restraints for refining 4905 atoms. 8970 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3005 (Rfree = 0.000) for 4905 atoms. Found 23 (52 requested) and removed 81 (26 requested) atoms. Cycle 12: After refmac, R = 0.2693 (Rfree = 0.000) for 4817 atoms. Found 25 (52 requested) and removed 45 (26 requested) atoms. Cycle 13: After refmac, R = 0.2582 (Rfree = 0.000) for 4780 atoms. Found 23 (51 requested) and removed 36 (25 requested) atoms. Cycle 14: After refmac, R = 0.2496 (Rfree = 0.000) for 4759 atoms. Found 21 (51 requested) and removed 35 (25 requested) atoms. Cycle 15: After refmac, R = 0.2411 (Rfree = 0.000) for 4731 atoms. Found 14 (51 requested) and removed 31 (25 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.40 3.45 Search for helices and strands: 0 residues in 0 chains, 4932 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 4954 seeds are put forward Round 1: 346 peptides, 54 chains. Longest chain 16 peptides. Score 0.478 Round 2: 390 peptides, 45 chains. Longest chain 24 peptides. Score 0.630 Round 3: 379 peptides, 49 chains. Longest chain 21 peptides. Score 0.582 Round 4: 397 peptides, 42 chains. Longest chain 32 peptides. Score 0.662 Round 5: 388 peptides, 48 chains. Longest chain 18 peptides. Score 0.605 Taking the results from Round 4 Chains 46, Residues 355, Estimated correctness of the model 64.7 % 8 chains (95 residues) have been docked in sequence ------------------------------------------------------ 14887 reflections ( 99.98 % complete ) and 10029 restraints for refining 4904 atoms. 8313 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2913 (Rfree = 0.000) for 4904 atoms. Found 33 (52 requested) and removed 64 (26 requested) atoms. Cycle 17: After refmac, R = 0.2751 (Rfree = 0.000) for 4834 atoms. Found 33 (52 requested) and removed 39 (26 requested) atoms. Cycle 18: After refmac, R = 0.2654 (Rfree = 0.000) for 4813 atoms. Found 28 (52 requested) and removed 40 (26 requested) atoms. Cycle 19: After refmac, R = 0.2789 (Rfree = 0.000) for 4796 atoms. Found 30 (51 requested) and removed 42 (25 requested) atoms. Cycle 20: After refmac, R = 0.2737 (Rfree = 0.000) for 4775 atoms. Found 37 (51 requested) and removed 38 (25 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.44 Search for helices and strands: 0 residues in 0 chains, 4963 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 4983 seeds are put forward Round 1: 321 peptides, 49 chains. Longest chain 22 peptides. Score 0.472 Round 2: 373 peptides, 48 chains. Longest chain 30 peptides. Score 0.580 Round 3: 377 peptides, 49 chains. Longest chain 24 peptides. Score 0.579 Round 4: 380 peptides, 47 chains. Longest chain 33 peptides. Score 0.599 Round 5: 384 peptides, 47 chains. Longest chain 29 peptides. Score 0.606 Taking the results from Round 5 Chains 47, Residues 337, Estimated correctness of the model 53.2 % 4 chains (54 residues) have been docked in sequence ------------------------------------------------------ 14887 reflections ( 99.98 % complete ) and 10472 restraints for refining 4904 atoms. 8991 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2860 (Rfree = 0.000) for 4904 atoms. Found 28 (52 requested) and removed 47 (26 requested) atoms. Cycle 22: After refmac, R = 0.2559 (Rfree = 0.000) for 4858 atoms. Found 27 (52 requested) and removed 36 (26 requested) atoms. Cycle 23: After refmac, R = 0.2530 (Rfree = 0.000) for 4833 atoms. Found 19 (52 requested) and removed 39 (26 requested) atoms. Cycle 24: After refmac, R = 0.2055 (Rfree = 0.000) for 4802 atoms. Found 9 (51 requested) and removed 28 (25 requested) atoms. Cycle 25: After refmac, R = 0.2006 (Rfree = 0.000) for 4778 atoms. Found 7 (51 requested) and removed 29 (25 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.38 3.43 Search for helices and strands: 0 residues in 0 chains, 4941 seeds are put forward NCS extension: 19 residues added (10 deleted due to clashes), 4960 seeds are put forward Round 1: 304 peptides, 45 chains. Longest chain 23 peptides. Score 0.473 Round 2: 340 peptides, 44 chains. Longest chain 26 peptides. Score 0.553 Round 3: 350 peptides, 46 chains. Longest chain 20 peptides. Score 0.555 Round 4: 342 peptides, 44 chains. Longest chain 18 peptides. Score 0.556 Round 5: 353 peptides, 46 chains. Longest chain 18 peptides. Score 0.560 Taking the results from Round 5 Chains 48, Residues 307, Estimated correctness of the model 42.7 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 14887 reflections ( 99.98 % complete ) and 10966 restraints for refining 4905 atoms. 9707 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2852 (Rfree = 0.000) for 4905 atoms. Found 41 (52 requested) and removed 38 (26 requested) atoms. Cycle 27: After refmac, R = 0.2841 (Rfree = 0.000) for 4895 atoms. Found 44 (52 requested) and removed 36 (26 requested) atoms. Cycle 28: After refmac, R = 0.2865 (Rfree = 0.000) for 4883 atoms. Found 52 (52 requested) and removed 45 (26 requested) atoms. Cycle 29: After refmac, R = 0.2821 (Rfree = 0.000) for 4870 atoms. Found 47 (52 requested) and removed 36 (26 requested) atoms. Cycle 30: After refmac, R = 0.2694 (Rfree = 0.000) for 4863 atoms. Found 51 (52 requested) and removed 37 (26 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.42 3.47 Search for helices and strands: 0 residues in 0 chains, 5060 seeds are put forward NCS extension: 12 residues added (3 deleted due to clashes), 5072 seeds are put forward Round 1: 297 peptides, 51 chains. Longest chain 23 peptides. Score 0.401 Round 2: 332 peptides, 48 chains. Longest chain 30 peptides. Score 0.503 Round 3: 335 peptides, 47 chains. Longest chain 28 peptides. Score 0.518 Round 4: 336 peptides, 50 chains. Longest chain 15 peptides. Score 0.494 Round 5: 361 peptides, 54 chains. Longest chain 24 peptides. Score 0.508 Taking the results from Round 3 Chains 48, Residues 288, Estimated correctness of the model 32.3 % 6 chains (62 residues) have been docked in sequence ------------------------------------------------------ 14887 reflections ( 99.98 % complete ) and 10444 restraints for refining 4904 atoms. 9114 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2801 (Rfree = 0.000) for 4904 atoms. Found 52 (52 requested) and removed 44 (26 requested) atoms. Cycle 32: After refmac, R = 0.2547 (Rfree = 0.000) for 4888 atoms. Found 47 (52 requested) and removed 37 (26 requested) atoms. Cycle 33: After refmac, R = 0.2255 (Rfree = 0.000) for 4877 atoms. Found 35 (52 requested) and removed 32 (26 requested) atoms. Cycle 34: After refmac, R = 0.2310 (Rfree = 0.000) for 4874 atoms. Found 39 (52 requested) and removed 28 (26 requested) atoms. Cycle 35: After refmac, R = 0.1889 (Rfree = 0.000) for 4882 atoms. Found 6 (52 requested) and removed 28 (26 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.37 3.42 Search for helices and strands: 0 residues in 0 chains, 5000 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 5030 seeds are put forward Round 1: 295 peptides, 52 chains. Longest chain 17 peptides. Score 0.387 Round 2: 331 peptides, 46 chains. Longest chain 24 peptides. Score 0.519 Round 3: 346 peptides, 48 chains. Longest chain 24 peptides. Score 0.530 Round 4: 328 peptides, 41 chains. Longest chain 22 peptides. Score 0.556 Round 5: 333 peptides, 43 chains. Longest chain 22 peptides. Score 0.548 Taking the results from Round 4 Chains 41, Residues 287, Estimated correctness of the model 41.8 % 5 chains (44 residues) have been docked in sequence ------------------------------------------------------ 14887 reflections ( 99.98 % complete ) and 10792 restraints for refining 4905 atoms. 9553 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2410 (Rfree = 0.000) for 4905 atoms. Found 17 (52 requested) and removed 34 (26 requested) atoms. Cycle 37: After refmac, R = 0.2214 (Rfree = 0.000) for 4878 atoms. Found 21 (52 requested) and removed 34 (26 requested) atoms. Cycle 38: After refmac, R = 0.2250 (Rfree = 0.000) for 4860 atoms. Found 32 (52 requested) and removed 27 (26 requested) atoms. Cycle 39: After refmac, R = 0.2228 (Rfree = 0.000) for 4858 atoms. Found 26 (52 requested) and removed 34 (26 requested) atoms. Cycle 40: After refmac, R = 0.2365 (Rfree = 0.000) for 4840 atoms. Found 44 (52 requested) and removed 28 (26 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.36 3.41 Search for helices and strands: 0 residues in 0 chains, 5027 seeds are put forward NCS extension: 20 residues added (5 deleted due to clashes), 5047 seeds are put forward Round 1: 253 peptides, 46 chains. Longest chain 15 peptides. Score 0.349 Round 2: 288 peptides, 43 chains. Longest chain 24 peptides. Score 0.458 Round 3: 293 peptides, 43 chains. Longest chain 14 peptides. Score 0.469 Round 4: 309 peptides, 43 chains. Longest chain 23 peptides. Score 0.502 Round 5: 317 peptides, 42 chains. Longest chain 23 peptides. Score 0.526 Taking the results from Round 5 Chains 43, Residues 275, Estimated correctness of the model 34.4 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 14887 reflections ( 99.98 % complete ) and 11043 restraints for refining 4905 atoms. 9944 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2395 (Rfree = 0.000) for 4905 atoms. Found 25 (52 requested) and removed 35 (26 requested) atoms. Cycle 42: After refmac, R = 0.2391 (Rfree = 0.000) for 4878 atoms. Found 32 (52 requested) and removed 29 (26 requested) atoms. Cycle 43: After refmac, R = 0.2155 (Rfree = 0.000) for 4873 atoms. Found 19 (52 requested) and removed 29 (26 requested) atoms. Cycle 44: After refmac, R = 0.2069 (Rfree = 0.000) for 4858 atoms. Found 16 (52 requested) and removed 31 (26 requested) atoms. Cycle 45: After refmac, R = 0.2149 (Rfree = 0.000) for 4837 atoms. Found 35 (52 requested) and removed 29 (26 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.35 3.39 Search for helices and strands: 0 residues in 0 chains, 5014 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 5039 seeds are put forward Round 1: 244 peptides, 44 chains. Longest chain 23 peptides. Score 0.348 Round 2: 283 peptides, 44 chains. Longest chain 16 peptides. Score 0.438 Round 3: 281 peptides, 42 chains. Longest chain 17 peptides. Score 0.453 Round 4: 289 peptides, 45 chains. Longest chain 17 peptides. Score 0.441 Round 5: 276 peptides, 41 chains. Longest chain 16 peptides. Score 0.452 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 42, Residues 239, Estimated correctness of the model 14.7 % 2 chains (21 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 1vll-3_warpNtrace.pdb as input Building loops using Loopy2018 42 chains (239 residues) following loop building 2 chains (21 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14887 reflections ( 99.98 % complete ) and 11069 restraints for refining 4905 atoms. 10095 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2201 (Rfree = 0.000) for 4905 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Cycle 47: After refmac, R = 0.1971 (Rfree = 0.000) for 4866 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Cycle 48: After refmac, R = 0.1902 (Rfree = 0.000) for 4837 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Cycle 49: After refmac, R = 0.1933 (Rfree = 0.000) for 4809 atoms. Found 0 (51 requested) and removed 25 (25 requested) atoms. Writing output files ... TimeTaking 71.3