Mon 24 Dec 01:10:46 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vll-3.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vll-3.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vll-3.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vll-3.0-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vll-3.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vll-3.0-parrot-mrncs ############### 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 ============================================================ Mon 24 Dec 01:10:50 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vll-3.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vll-3.0-parrot-mrncs/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-mrncs.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-mrncs.fasta_lf Building free atoms model in initial map for 5344 target number of atoms Had to go as low as 0.70 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 5878 atoms. Observations/parameters ratio is 0.63 ------------------------------------------------------ Starting model: R = 0.3422 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2774 (Rfree = 0.000) for 5878 atoms. Found 26 (63 requested) and removed 50 (31 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.39 3.44 Search for helices and strands: 0 residues in 0 chains, 6002 seeds are put forward NCS extension: 0 residues added, 6002 seeds are put forward Round 1: 370 peptides, 56 chains. Longest chain 18 peptides. Score 0.509 Round 2: 410 peptides, 53 chains. Longest chain 18 peptides. Score 0.604 Round 3: 434 peptides, 49 chains. Longest chain 23 peptides. Score 0.669 Round 4: 444 peptides, 50 chains. Longest chain 32 peptides. Score 0.677 Round 5: 448 peptides, 47 chains. Longest chain 29 peptides. Score 0.701 Taking the results from Round 5 Chains 52, Residues 401, Estimated correctness of the model 71.8 % 8 chains (80 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 71 A and 81 A 50 chains (405 residues) following loop building 7 chains (89 residues) in sequence following loop building ------------------------------------------------------ 14887 reflections ( 99.98 % complete ) and 9942 restraints for refining 4905 atoms. 8105 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2924 (Rfree = 0.000) for 4905 atoms. Found 24 (52 requested) and removed 63 (26 requested) atoms. Cycle 2: After refmac, R = 0.2729 (Rfree = 0.000) for 4808 atoms. Found 13 (51 requested) and removed 31 (26 requested) atoms. Cycle 3: After refmac, R = 0.2620 (Rfree = 0.000) for 4758 atoms. Found 10 (49 requested) and removed 31 (25 requested) atoms. Cycle 4: After refmac, R = 0.2647 (Rfree = 0.000) for 4722 atoms. Found 6 (48 requested) and removed 30 (25 requested) atoms. Cycle 5: After refmac, R = 0.2657 (Rfree = 0.000) for 4679 atoms. Found 22 (46 requested) and removed 38 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.36 3.41 Search for helices and strands: 0 residues in 0 chains, 4862 seeds are put forward NCS extension: 32 residues added (14 deleted due to clashes), 4894 seeds are put forward Round 1: 382 peptides, 52 chains. Longest chain 19 peptides. Score 0.564 Round 2: 434 peptides, 52 chains. Longest chain 22 peptides. Score 0.649 Round 3: 458 peptides, 44 chains. Longest chain 26 peptides. Score 0.731 Round 4: 442 peptides, 43 chains. Longest chain 50 peptides. Score 0.717 Round 5: 437 peptides, 44 chains. Longest chain 34 peptides. Score 0.705 Taking the results from Round 3 Chains 51, Residues 414, Estimated correctness of the model 76.7 % 8 chains (109 residues) have been docked in sequence Building loops using Loopy2018 51 chains (414 residues) following loop building 8 chains (109 residues) in sequence following loop building ------------------------------------------------------ 14887 reflections ( 99.98 % complete ) and 9695 restraints for refining 4904 atoms. 7684 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2833 (Rfree = 0.000) for 4904 atoms. Found 38 (47 requested) and removed 46 (26 requested) atoms. Cycle 7: After refmac, R = 0.2589 (Rfree = 0.000) for 4871 atoms. Found 11 (46 requested) and removed 31 (26 requested) atoms. Cycle 8: After refmac, R = 0.2558 (Rfree = 0.000) for 4837 atoms. Found 10 (45 requested) and removed 27 (26 requested) atoms. Cycle 9: After refmac, R = 0.2497 (Rfree = 0.000) for 4812 atoms. Found 10 (43 requested) and removed 33 (25 requested) atoms. Cycle 10: After refmac, R = 0.2556 (Rfree = 0.000) for 4777 atoms. Found 6 (42 requested) and removed 33 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.38 3.43 Search for helices and strands: 0 residues in 0 chains, 4934 seeds are put forward NCS extension: 23 residues added (4 deleted due to clashes), 4957 seeds are put forward Round 1: 397 peptides, 52 chains. Longest chain 33 peptides. Score 0.590 Round 2: 435 peptides, 51 chains. Longest chain 21 peptides. Score 0.657 Round 3: 438 peptides, 47 chains. Longest chain 36 peptides. Score 0.687 Round 4: 437 peptides, 47 chains. Longest chain 44 peptides. Score 0.686 Round 5: 427 peptides, 44 chains. Longest chain 43 peptides. Score 0.691 Taking the results from Round 5 Chains 50, Residues 383, Estimated correctness of the model 70.0 % 9 chains (154 residues) have been docked in sequence ------------------------------------------------------ 14887 reflections ( 99.98 % complete ) and 9382 restraints for refining 4905 atoms. 7327 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2886 (Rfree = 0.000) for 4905 atoms. Found 15 (42 requested) and removed 72 (26 requested) atoms. Cycle 12: After refmac, R = 0.2664 (Rfree = 0.000) for 4828 atoms. Found 15 (42 requested) and removed 37 (26 requested) atoms. Cycle 13: After refmac, R = 0.2460 (Rfree = 0.000) for 4783 atoms. Found 8 (41 requested) and removed 34 (25 requested) atoms. Cycle 14: After refmac, R = 0.2362 (Rfree = 0.000) for 4749 atoms. Found 13 (41 requested) and removed 29 (25 requested) atoms. Cycle 15: After refmac, R = 0.2322 (Rfree = 0.000) for 4727 atoms. Found 12 (41 requested) and removed 32 (25 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.38 3.43 Search for helices and strands: 0 residues in 0 chains, 4860 seeds are put forward NCS extension: 32 residues added (10 deleted due to clashes), 4892 seeds are put forward Round 1: 374 peptides, 53 chains. Longest chain 26 peptides. Score 0.541 Round 2: 414 peptides, 51 chains. Longest chain 32 peptides. Score 0.625 Round 3: 414 peptides, 50 chains. Longest chain 26 peptides. Score 0.632 Round 4: 436 peptides, 52 chains. Longest chain 29 peptides. Score 0.652 Round 5: 441 peptides, 46 chains. Longest chain 26 peptides. Score 0.698 Taking the results from Round 5 Chains 48, Residues 395, Estimated correctness of the model 71.2 % 7 chains (62 residues) have been docked in sequence ------------------------------------------------------ 14887 reflections ( 99.98 % complete ) and 10214 restraints for refining 4900 atoms. 8481 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2677 (Rfree = 0.000) for 4900 atoms. Found 28 (42 requested) and removed 39 (26 requested) atoms. Cycle 17: After refmac, R = 0.2571 (Rfree = 0.000) for 4874 atoms. Found 9 (42 requested) and removed 38 (26 requested) atoms. Cycle 18: After refmac, R = 0.2493 (Rfree = 0.000) for 4833 atoms. Found 12 (42 requested) and removed 31 (26 requested) atoms. Cycle 19: After refmac, R = 0.2579 (Rfree = 0.000) for 4801 atoms. Found 13 (41 requested) and removed 34 (25 requested) atoms. Cycle 20: After refmac, R = 0.2596 (Rfree = 0.000) for 4771 atoms. Found 20 (41 requested) and removed 37 (25 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.44 Search for helices and strands: 0 residues in 0 chains, 4914 seeds are put forward NCS extension: 33 residues added (4 deleted due to clashes), 4947 seeds are put forward Round 1: 368 peptides, 60 chains. Longest chain 15 peptides. Score 0.470 Round 2: 417 peptides, 53 chains. Longest chain 22 peptides. Score 0.616 Round 3: 438 peptides, 52 chains. Longest chain 34 peptides. Score 0.655 Round 4: 419 peptides, 51 chains. Longest chain 35 peptides. Score 0.633 Round 5: 417 peptides, 49 chains. Longest chain 35 peptides. Score 0.644 Taking the results from Round 3 Chains 53, Residues 386, Estimated correctness of the model 63.3 % 4 chains (29 residues) have been docked in sequence ------------------------------------------------------ 14887 reflections ( 99.98 % complete ) and 10327 restraints for refining 4903 atoms. 8730 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2605 (Rfree = 0.000) for 4903 atoms. Found 12 (42 requested) and removed 37 (26 requested) atoms. Cycle 22: After refmac, R = 0.2408 (Rfree = 0.000) for 4865 atoms. Found 10 (42 requested) and removed 33 (26 requested) atoms. Cycle 23: After refmac, R = 0.2386 (Rfree = 0.000) for 4831 atoms. Found 4 (42 requested) and removed 29 (26 requested) atoms. Cycle 24: After refmac, R = 0.2330 (Rfree = 0.000) for 4804 atoms. Found 3 (41 requested) and removed 26 (25 requested) atoms. Cycle 25: After refmac, R = 0.2287 (Rfree = 0.000) for 4773 atoms. Found 6 (41 requested) and removed 25 (25 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.37 3.42 Search for helices and strands: 0 residues in 0 chains, 4917 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 4933 seeds are put forward Round 1: 330 peptides, 55 chains. Longest chain 15 peptides. Score 0.436 Round 2: 375 peptides, 53 chains. Longest chain 15 peptides. Score 0.543 Round 3: 392 peptides, 54 chains. Longest chain 23 peptides. Score 0.566 Round 4: 392 peptides, 53 chains. Longest chain 23 peptides. Score 0.574 Round 5: 382 peptides, 46 chains. Longest chain 25 peptides. Score 0.610 Taking the results from Round 5 Chains 48, Residues 336, Estimated correctness of the model 54.1 % 3 chains (35 residues) have been docked in sequence ------------------------------------------------------ 14887 reflections ( 99.98 % complete ) and 10501 restraints for refining 4905 atoms. 9067 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2616 (Rfree = 0.000) for 4905 atoms. Found 11 (42 requested) and removed 36 (26 requested) atoms. Cycle 27: After refmac, R = 0.2651 (Rfree = 0.000) for 4869 atoms. Found 31 (42 requested) and removed 34 (26 requested) atoms. Cycle 28: After refmac, R = 0.2829 (Rfree = 0.000) for 4855 atoms. Found 42 (42 requested) and removed 40 (26 requested) atoms. Cycle 29: After refmac, R = 0.2765 (Rfree = 0.000) for 4851 atoms. Found 32 (42 requested) and removed 39 (26 requested) atoms. Cycle 30: After refmac, R = 0.2398 (Rfree = 0.000) for 4826 atoms. Found 11 (42 requested) and removed 35 (26 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.41 3.46 Search for helices and strands: 0 residues in 0 chains, 4981 seeds are put forward NCS extension: 19 residues added (4 deleted due to clashes), 5000 seeds are put forward Round 1: 300 peptides, 50 chains. Longest chain 16 peptides. Score 0.418 Round 2: 348 peptides, 51 chains. Longest chain 22 peptides. Score 0.509 Round 3: 348 peptides, 50 chains. Longest chain 19 peptides. Score 0.517 Round 4: 351 peptides, 50 chains. Longest chain 20 peptides. Score 0.523 Round 5: 375 peptides, 55 chains. Longest chain 20 peptides. Score 0.527 Taking the results from Round 5 Chains 57, Residues 320, Estimated correctness of the model 34.6 % 5 chains (30 residues) have been docked in sequence ------------------------------------------------------ 14887 reflections ( 99.98 % complete ) and 10898 restraints for refining 4904 atoms. 9578 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2816 (Rfree = 0.000) for 4904 atoms. Found 32 (42 requested) and removed 45 (26 requested) atoms. Cycle 32: After refmac, R = 0.2636 (Rfree = 0.000) for 4881 atoms. Found 40 (42 requested) and removed 34 (26 requested) atoms. Cycle 33: After refmac, R = 0.2535 (Rfree = 0.000) for 4871 atoms. Found 32 (42 requested) and removed 31 (26 requested) atoms. Cycle 34: After refmac, R = 0.2202 (Rfree = 0.000) for 4864 atoms. Found 11 (42 requested) and removed 27 (26 requested) atoms. Cycle 35: After refmac, R = 0.2069 (Rfree = 0.000) for 4840 atoms. Found 10 (42 requested) and removed 28 (26 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.39 3.44 Search for helices and strands: 0 residues in 0 chains, 4975 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 4993 seeds are put forward Round 1: 285 peptides, 54 chains. Longest chain 14 peptides. Score 0.344 Round 2: 345 peptides, 52 chains. Longest chain 15 peptides. Score 0.494 Round 3: 323 peptides, 45 chains. Longest chain 16 peptides. Score 0.512 Round 4: 320 peptides, 44 chains. Longest chain 26 peptides. Score 0.515 Round 5: 300 peptides, 47 chains. Longest chain 17 peptides. Score 0.446 Taking the results from Round 4 Chains 46, Residues 276, Estimated correctness of the model 31.6 % 5 chains (49 residues) have been docked in sequence ------------------------------------------------------ 14887 reflections ( 99.98 % complete ) and 10885 restraints for refining 4904 atoms. 9669 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2793 (Rfree = 0.000) for 4904 atoms. Found 33 (42 requested) and removed 46 (26 requested) atoms. Cycle 37: After refmac, R = 0.2793 (Rfree = 0.000) for 4865 atoms. Found 42 (42 requested) and removed 36 (26 requested) atoms. Cycle 38: After refmac, R = 0.2872 (Rfree = 0.000) for 4854 atoms. Found 42 (42 requested) and removed 37 (26 requested) atoms. Cycle 39: After refmac, R = 0.2831 (Rfree = 0.000) for 4846 atoms. Found 42 (42 requested) and removed 39 (26 requested) atoms. Cycle 40: After refmac, R = 0.2706 (Rfree = 0.000) for 4836 atoms. Found 42 (42 requested) and removed 34 (26 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.42 3.47 Search for helices and strands: 0 residues in 0 chains, 4992 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 5006 seeds are put forward Round 1: 218 peptides, 34 chains. Longest chain 16 peptides. Score 0.391 Round 2: 250 peptides, 35 chains. Longest chain 18 peptides. Score 0.454 Round 3: 262 peptides, 36 chains. Longest chain 18 peptides. Score 0.470 Round 4: 268 peptides, 37 chains. Longest chain 18 peptides. Score 0.473 Round 5: 282 peptides, 40 chains. Longest chain 18 peptides. Score 0.474 Taking the results from Round 5 Chains 40, Residues 242, Estimated correctness of the model 20.6 % 3 chains (20 residues) have been docked in sequence ------------------------------------------------------ 14887 reflections ( 99.98 % complete ) and 10787 restraints for refining 4891 atoms. 9807 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2535 (Rfree = 0.000) for 4891 atoms. Found 37 (42 requested) and removed 39 (26 requested) atoms. Cycle 42: After refmac, R = 0.2666 (Rfree = 0.000) for 4878 atoms. Found 42 (42 requested) and removed 41 (26 requested) atoms. Cycle 43: After refmac, R = 0.2551 (Rfree = 0.000) for 4875 atoms. Found 40 (42 requested) and removed 33 (26 requested) atoms. Cycle 44: After refmac, R = 0.2472 (Rfree = 0.000) for 4874 atoms. Found 42 (42 requested) and removed 34 (26 requested) atoms. Cycle 45: After refmac, R = 0.2466 (Rfree = 0.000) for 4878 atoms. Found 34 (42 requested) and removed 31 (26 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.40 3.45 Search for helices and strands: 0 residues in 0 chains, 5035 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 5049 seeds are put forward Round 1: 207 peptides, 39 chains. Longest chain 15 peptides. Score 0.310 Round 2: 261 peptides, 45 chains. Longest chain 15 peptides. Score 0.378 Round 3: 244 peptides, 38 chains. Longest chain 17 peptides. Score 0.410 Round 4: 249 peptides, 37 chains. Longest chain 18 peptides. Score 0.432 Round 5: 247 peptides, 40 chains. Longest chain 17 peptides. Score 0.397 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 37, Residues 212, Estimated correctness of the model 8.6 % 3 chains (24 residues) have been docked in sequence Sequence coverage is 11 % Consider running further cycles of model building using 1vll-3_warpNtrace.pdb as input Building loops using Loopy2018 37 chains (212 residues) following loop building 3 chains (24 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 14887 reflections ( 99.98 % complete ) and 11106 restraints for refining 4905 atoms. 10227 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2938 (Rfree = 0.000) for 4905 atoms. Found 0 (42 requested) and removed 26 (26 requested) atoms. Cycle 47: After refmac, R = 0.2590 (Rfree = 0.000) for 4862 atoms. Found 0 (42 requested) and removed 26 (26 requested) atoms. Cycle 48: After refmac, R = 0.2938 (Rfree = 0.000) for 4829 atoms. Found 0 (42 requested) and removed 26 (26 requested) atoms. Cycle 49: After refmac, R = 0.2723 (Rfree = 0.000) for 4792 atoms. TimeTaking 52.83