null Tue 25 Dec 20:46:15 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vll-3.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vll-3.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vll-3.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vll-3.0-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vll-3.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vll-3.0-parrot-noncs ############### 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 ============================================================ Tue 25 Dec 20:46:41 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/noncs/ArpWArp/wArpResults/WorkingDir/1vll-3.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vll-3.0-parrot-noncs/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-noncs.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-noncs.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 5896 atoms. Observations/parameters ratio is 0.63 ------------------------------------------------------ Starting model: R = 0.3562 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3280 (Rfree = 0.000) for 5896 atoms. Found 43 (63 requested) and removed 60 (31 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.41 3.46 Search for helices and strands: 0 residues in 0 chains, 5999 seeds are put forward NCS extension: 0 residues added, 5999 seeds are put forward Round 1: 285 peptides, 57 chains. Longest chain 13 peptides. Score 0.314 Round 2: 352 peptides, 49 chains. Longest chain 16 peptides. Score 0.533 Round 3: 353 peptides, 51 chains. Longest chain 19 peptides. Score 0.518 Round 4: 386 peptides, 51 chains. Longest chain 22 peptides. Score 0.579 Round 5: 366 peptides, 53 chains. Longest chain 22 peptides. Score 0.526 Taking the results from Round 4 Chains 55, Residues 335, Estimated correctness of the model 47.2 % 6 chains (44 residues) have been docked in sequence ------------------------------------------------------ 14887 reflections ( 99.98 % complete ) and 10971 restraints for refining 4905 atoms. 9564 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2893 (Rfree = 0.000) for 4905 atoms. Found 19 (52 requested) and removed 43 (26 requested) atoms. Cycle 2: After refmac, R = 0.3086 (Rfree = 0.000) for 4825 atoms. Found 29 (52 requested) and removed 48 (26 requested) atoms. Cycle 3: After refmac, R = 0.2943 (Rfree = 0.000) for 4784 atoms. Found 22 (51 requested) and removed 52 (25 requested) atoms. Cycle 4: After refmac, R = 0.3027 (Rfree = 0.000) for 4729 atoms. Found 51 (51 requested) and removed 43 (25 requested) atoms. Cycle 5: After refmac, R = 0.2883 (Rfree = 0.000) for 4711 atoms. Found 33 (51 requested) and removed 42 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.39 3.44 Search for helices and strands: 0 residues in 0 chains, 4894 seeds are put forward NCS extension: 30 residues added (3 deleted due to clashes), 4924 seeds are put forward Round 1: 314 peptides, 57 chains. Longest chain 13 peptides. Score 0.382 Round 2: 363 peptides, 56 chains. Longest chain 29 peptides. Score 0.495 Round 3: 376 peptides, 48 chains. Longest chain 32 peptides. Score 0.585 Round 4: 379 peptides, 47 chains. Longest chain 24 peptides. Score 0.598 Round 5: 373 peptides, 47 chains. Longest chain 23 peptides. Score 0.587 Taking the results from Round 4 Chains 51, Residues 332, Estimated correctness of the model 51.5 % 6 chains (48 residues) have been docked in sequence ------------------------------------------------------ 14887 reflections ( 99.98 % complete ) and 10821 restraints for refining 4905 atoms. 9382 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3065 (Rfree = 0.000) for 4905 atoms. Found 19 (52 requested) and removed 58 (26 requested) atoms. Cycle 7: After refmac, R = 0.2829 (Rfree = 0.000) for 4849 atoms. Found 31 (52 requested) and removed 43 (26 requested) atoms. Cycle 8: After refmac, R = 0.2583 (Rfree = 0.000) for 4809 atoms. Found 9 (52 requested) and removed 37 (26 requested) atoms. Cycle 9: After refmac, R = 0.2644 (Rfree = 0.000) for 4769 atoms. Found 16 (51 requested) and removed 29 (25 requested) atoms. Cycle 10: After refmac, R = 0.2682 (Rfree = 0.000) for 4749 atoms. Found 26 (51 requested) and removed 39 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.41 3.46 Search for helices and strands: 0 residues in 0 chains, 4930 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 4956 seeds are put forward Round 1: 311 peptides, 51 chains. Longest chain 18 peptides. Score 0.432 Round 2: 361 peptides, 44 chains. Longest chain 30 peptides. Score 0.590 Round 3: 348 peptides, 43 chains. Longest chain 30 peptides. Score 0.575 Round 4: 377 peptides, 45 chains. Longest chain 34 peptides. Score 0.610 Round 5: 379 peptides, 42 chains. Longest chain 40 peptides. Score 0.635 Taking the results from Round 5 Chains 46, Residues 337, Estimated correctness of the model 59.3 % 7 chains (115 residues) have been docked in sequence ------------------------------------------------------ 14887 reflections ( 99.98 % complete ) and 9751 restraints for refining 4903 atoms. 7997 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2694 (Rfree = 0.000) for 4903 atoms. Found 31 (52 requested) and removed 42 (26 requested) atoms. Cycle 12: After refmac, R = 0.2445 (Rfree = 0.000) for 4882 atoms. Found 7 (52 requested) and removed 34 (26 requested) atoms. Cycle 13: After refmac, R = 0.2351 (Rfree = 0.000) for 4842 atoms. Found 4 (52 requested) and removed 26 (26 requested) atoms. Cycle 14: After refmac, R = 0.2298 (Rfree = 0.000) for 4818 atoms. Found 4 (51 requested) and removed 25 (25 requested) atoms. Cycle 15: After refmac, R = 0.2420 (Rfree = 0.000) for 4792 atoms. Found 11 (51 requested) and removed 27 (25 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.37 3.42 Search for helices and strands: 0 residues in 0 chains, 4926 seeds are put forward NCS extension: 32 residues added (6 deleted due to clashes), 4958 seeds are put forward Round 1: 336 peptides, 50 chains. Longest chain 29 peptides. Score 0.494 Round 2: 355 peptides, 45 chains. Longest chain 35 peptides. Score 0.572 Round 3: 379 peptides, 44 chains. Longest chain 34 peptides. Score 0.620 Round 4: 372 peptides, 42 chains. Longest chain 35 peptides. Score 0.624 Round 5: 345 peptides, 45 chains. Longest chain 27 peptides. Score 0.554 Taking the results from Round 4 Chains 46, Residues 330, Estimated correctness of the model 57.1 % 6 chains (85 residues) have been docked in sequence ------------------------------------------------------ 14887 reflections ( 99.98 % complete ) and 10205 restraints for refining 4903 atoms. 8630 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2681 (Rfree = 0.000) for 4903 atoms. Found 12 (52 requested) and removed 48 (26 requested) atoms. Cycle 17: After refmac, R = 0.2545 (Rfree = 0.000) for 4849 atoms. Found 31 (52 requested) and removed 36 (26 requested) atoms. Cycle 18: After refmac, R = 0.2596 (Rfree = 0.000) for 4838 atoms. Found 25 (52 requested) and removed 34 (26 requested) atoms. Cycle 19: After refmac, R = 0.2464 (Rfree = 0.000) for 4812 atoms. Found 7 (52 requested) and removed 33 (26 requested) atoms. Cycle 20: After refmac, R = 0.2638 (Rfree = 0.000) for 4773 atoms. Found 30 (51 requested) and removed 39 (25 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.41 3.46 Search for helices and strands: 0 residues in 0 chains, 4928 seeds are put forward NCS extension: 44 residues added (13 deleted due to clashes), 4972 seeds are put forward Round 1: 330 peptides, 49 chains. Longest chain 16 peptides. Score 0.490 Round 2: 364 peptides, 48 chains. Longest chain 25 peptides. Score 0.564 Round 3: 367 peptides, 44 chains. Longest chain 22 peptides. Score 0.600 Round 4: 366 peptides, 48 chains. Longest chain 28 peptides. Score 0.567 Round 5: 373 peptides, 41 chains. Longest chain 31 peptides. Score 0.633 Taking the results from Round 5 Chains 43, Residues 332, Estimated correctness of the model 58.9 % 4 chains (54 residues) have been docked in sequence ------------------------------------------------------ 14887 reflections ( 99.98 % complete ) and 10421 restraints for refining 4904 atoms. 8945 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3109 (Rfree = 0.000) for 4904 atoms. Found 36 (52 requested) and removed 57 (26 requested) atoms. Cycle 22: After refmac, R = 0.2947 (Rfree = 0.000) for 4850 atoms. Found 34 (52 requested) and removed 37 (26 requested) atoms. Cycle 23: After refmac, R = 0.2848 (Rfree = 0.000) for 4811 atoms. Found 33 (52 requested) and removed 41 (26 requested) atoms. Cycle 24: After refmac, R = 0.2867 (Rfree = 0.000) for 4788 atoms. Found 33 (51 requested) and removed 32 (25 requested) atoms. Cycle 25: After refmac, R = 0.2883 (Rfree = 0.000) for 4765 atoms. Found 27 (51 requested) and removed 36 (25 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.41 3.46 Search for helices and strands: 0 residues in 0 chains, 4985 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 5013 seeds are put forward Round 1: 304 peptides, 53 chains. Longest chain 16 peptides. Score 0.398 Round 2: 329 peptides, 46 chains. Longest chain 19 peptides. Score 0.515 Round 3: 344 peptides, 45 chains. Longest chain 22 peptides. Score 0.552 Round 4: 344 peptides, 46 chains. Longest chain 15 peptides. Score 0.543 Round 5: 347 peptides, 43 chains. Longest chain 21 peptides. Score 0.574 Taking the results from Round 5 Chains 45, Residues 304, Estimated correctness of the model 46.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 14887 reflections ( 99.98 % complete ) and 10785 restraints for refining 4903 atoms. 9560 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2949 (Rfree = 0.000) for 4903 atoms. Found 39 (52 requested) and removed 56 (26 requested) atoms. Cycle 27: After refmac, R = 0.2828 (Rfree = 0.000) for 4861 atoms. Found 40 (52 requested) and removed 41 (26 requested) atoms. Cycle 28: After refmac, R = 0.2870 (Rfree = 0.000) for 4835 atoms. Found 51 (52 requested) and removed 41 (26 requested) atoms. Cycle 29: After refmac, R = 0.2276 (Rfree = 0.000) for 4829 atoms. Found 13 (52 requested) and removed 30 (26 requested) atoms. Cycle 30: After refmac, R = 0.1983 (Rfree = 0.000) for 4804 atoms. Found 12 (51 requested) and removed 26 (25 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.35 3.39 Search for helices and strands: 0 residues in 0 chains, 4991 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 5003 seeds are put forward Round 1: 290 peptides, 50 chains. Longest chain 21 peptides. Score 0.395 Round 2: 328 peptides, 46 chains. Longest chain 22 peptides. Score 0.513 Round 3: 327 peptides, 48 chains. Longest chain 20 peptides. Score 0.493 Round 4: 330 peptides, 42 chains. Longest chain 22 peptides. Score 0.551 Round 5: 328 peptides, 41 chains. Longest chain 17 peptides. Score 0.556 Taking the results from Round 5 Chains 46, Residues 287, Estimated correctness of the model 41.8 % 6 chains (54 residues) have been docked in sequence ------------------------------------------------------ 14887 reflections ( 99.98 % complete ) and 10562 restraints for refining 4905 atoms. 9279 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2413 (Rfree = 0.000) for 4905 atoms. Found 22 (52 requested) and removed 41 (26 requested) atoms. Cycle 32: After refmac, R = 0.2240 (Rfree = 0.000) for 4876 atoms. Found 9 (52 requested) and removed 32 (26 requested) atoms. Cycle 33: After refmac, R = 0.2278 (Rfree = 0.000) for 4849 atoms. Found 16 (52 requested) and removed 34 (26 requested) atoms. Cycle 34: After refmac, R = 0.2140 (Rfree = 0.000) for 4825 atoms. Found 1 (52 requested) and removed 26 (26 requested) atoms. Cycle 35: After refmac, R = 0.2064 (Rfree = 0.000) for 4796 atoms. Found 5 (51 requested) and removed 25 (25 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 3.43 Search for helices and strands: 0 residues in 0 chains, 4920 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 4938 seeds are put forward Round 1: 300 peptides, 50 chains. Longest chain 23 peptides. Score 0.418 Round 2: 319 peptides, 44 chains. Longest chain 20 peptides. Score 0.513 Round 3: 334 peptides, 46 chains. Longest chain 22 peptides. Score 0.525 Round 4: 310 peptides, 43 chains. Longest chain 19 peptides. Score 0.504 Round 5: 332 peptides, 45 chains. Longest chain 22 peptides. Score 0.529 Taking the results from Round 5 Chains 48, Residues 287, Estimated correctness of the model 35.1 % 5 chains (63 residues) have been docked in sequence ------------------------------------------------------ 14887 reflections ( 99.98 % complete ) and 10328 restraints for refining 4905 atoms. 8998 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2876 (Rfree = 0.000) for 4905 atoms. Found 50 (52 requested) and removed 46 (26 requested) atoms. Cycle 37: After refmac, R = 0.2861 (Rfree = 0.000) for 4891 atoms. Found 52 (52 requested) and removed 42 (26 requested) atoms. Cycle 38: After refmac, R = 0.2782 (Rfree = 0.000) for 4882 atoms. Found 52 (52 requested) and removed 37 (26 requested) atoms. Cycle 39: After refmac, R = 0.2522 (Rfree = 0.000) for 4886 atoms. Found 31 (52 requested) and removed 38 (26 requested) atoms. Cycle 40: After refmac, R = 0.2266 (Rfree = 0.000) for 4875 atoms. Found 11 (52 requested) and removed 31 (26 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.41 3.46 Search for helices and strands: 0 residues in 0 chains, 4998 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 5018 seeds are put forward Round 1: 266 peptides, 48 chains. Longest chain 12 peptides. Score 0.360 Round 2: 315 peptides, 45 chains. Longest chain 21 peptides. Score 0.496 Round 3: 303 peptides, 49 chains. Longest chain 14 peptides. Score 0.434 Round 4: 301 peptides, 42 chains. Longest chain 22 peptides. Score 0.495 Round 5: 299 peptides, 46 chains. Longest chain 18 peptides. Score 0.454 Taking the results from Round 2 Chains 49, Residues 270, Estimated correctness of the model 26.6 % 4 chains (31 residues) have been docked in sequence ------------------------------------------------------ 14887 reflections ( 99.98 % complete ) and 10921 restraints for refining 4905 atoms. 9807 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2898 (Rfree = 0.000) for 4905 atoms. Found 51 (52 requested) and removed 44 (26 requested) atoms. Cycle 42: After refmac, R = 0.2816 (Rfree = 0.000) for 4881 atoms. Found 44 (52 requested) and removed 42 (26 requested) atoms. Cycle 43: After refmac, R = 0.2821 (Rfree = 0.000) for 4863 atoms. Found 41 (52 requested) and removed 37 (26 requested) atoms. Cycle 44: After refmac, R = 0.2781 (Rfree = 0.000) for 4854 atoms. Found 34 (52 requested) and removed 37 (26 requested) atoms. Cycle 45: After refmac, R = 0.2679 (Rfree = 0.000) for 4840 atoms. Found 29 (52 requested) and removed 37 (26 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.40 3.45 Search for helices and strands: 0 residues in 0 chains, 4962 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 4978 seeds are put forward Round 1: 227 peptides, 43 chains. Longest chain 10 peptides. Score 0.317 Round 2: 256 peptides, 39 chains. Longest chain 13 peptides. Score 0.427 Round 3: 261 peptides, 41 chains. Longest chain 14 peptides. Score 0.419 Round 4: 271 peptides, 36 chains. Longest chain 16 peptides. Score 0.489 Round 5: 268 peptides, 38 chains. Longest chain 20 peptides. Score 0.463 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 40, Residues 235, Estimated correctness of the model 24.7 % 5 chains (43 residues) have been docked in sequence Sequence coverage is 18 % Consider running further cycles of model building using 1vll-3_warpNtrace.pdb as input Building loops using Loopy2018 40 chains (235 residues) following loop building 5 chains (43 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14887 reflections ( 99.98 % complete ) and 10580 restraints for refining 4905 atoms. 9529 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2936 (Rfree = 0.000) for 4905 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Cycle 47: After refmac, R = 0.2591 (Rfree = 0.000) for 4860 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Cycle 48: After refmac, R = 0.2725 (Rfree = 0.000) for 4814 atoms. Found 0 (52 requested) and removed 26 (26 requested) atoms. Cycle 49: After refmac, R = 0.2431 (Rfree = 0.000) for 4778 atoms. Found 0 (51 requested) and removed 25 (25 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 22:08:45 GMT 2018 Job finished. TimeTaking 82.5 Used memory is bytes: 6469872