Mon 24 Dec 07:26:23 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 1vr5-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vr5-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vr5-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr5-4.0-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/1vr5-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr5-4.0-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 ============================================================ Mon 24 Dec 07:26:28 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/1vr5-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr5-4.0-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 971 and 0 Target number of residues in the AU: 971 Target solvent content: 0.6646 Checking the provided sequence file Detected sequence length: 547 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 1094 Adjusted target solvent content: 0.62 Input MTZ file: 1vr5-4.0-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: 18 Cell parameters: 140.030 96.640 115.780 90.000 90.000 90.000 Input sequence file: 1vr5-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 8752 target number of atoms Had to go as low as 0.95 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: 115.780 4.000 Wilson plot Bfac: 88.19 13747 reflections ( 99.52 % complete ) and 0 restraints for refining 9721 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3348 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3095 (Rfree = 0.000) for 9721 atoms. Found 46 (46 requested) and removed 48 (23 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.77 3.20 Search for helices and strands: 0 residues in 0 chains, 9876 seeds are put forward NCS extension: 0 residues added, 9876 seeds are put forward Round 1: 518 peptides, 92 chains. Longest chain 14 peptides. Score 0.350 Round 2: 660 peptides, 88 chains. Longest chain 19 peptides. Score 0.511 Round 3: 689 peptides, 86 chains. Longest chain 26 peptides. Score 0.544 Round 4: 682 peptides, 79 chains. Longest chain 29 peptides. Score 0.565 Round 5: 705 peptides, 82 chains. Longest chain 24 peptides. Score 0.573 Taking the results from Round 5 Chains 85, Residues 623, Estimated correctness of the model 0.0 % 7 chains (79 residues) have been docked in sequence ------------------------------------------------------ 13747 reflections ( 99.52 % complete ) and 16712 restraints for refining 7900 atoms. 14006 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2390 (Rfree = 0.000) for 7900 atoms. Found 33 (37 requested) and removed 38 (18 requested) atoms. Cycle 2: After refmac, R = 0.2139 (Rfree = 0.000) for 7767 atoms. Found 19 (37 requested) and removed 34 (18 requested) atoms. Cycle 3: After refmac, R = 0.2041 (Rfree = 0.000) for 7692 atoms. Found 15 (36 requested) and removed 30 (18 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.1940 (Rfree = 0.000) for 7650 atoms. Found 11 (36 requested) and removed 25 (18 requested) atoms. Cycle 5: After refmac, R = 0.1951 (Rfree = 0.000) for 7615 atoms. Found 19 (36 requested) and removed 22 (18 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.73 3.17 Search for helices and strands: 0 residues in 0 chains, 7885 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 7906 seeds are put forward Round 1: 632 peptides, 92 chains. Longest chain 17 peptides. Score 0.468 Round 2: 680 peptides, 78 chains. Longest chain 28 peptides. Score 0.568 Round 3: 662 peptides, 84 chains. Longest chain 21 peptides. Score 0.529 Round 4: 669 peptides, 77 chains. Longest chain 22 peptides. Score 0.562 Round 5: 680 peptides, 76 chains. Longest chain 22 peptides. Score 0.575 Taking the results from Round 5 Chains 79, Residues 604, Estimated correctness of the model 0.0 % 4 chains (62 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 13747 reflections ( 99.52 % complete ) and 16964 restraints for refining 7903 atoms. 14366 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2223 (Rfree = 0.000) for 7903 atoms. Found 32 (37 requested) and removed 40 (18 requested) atoms. Cycle 7: After refmac, R = 0.2054 (Rfree = 0.000) for 7821 atoms. Found 26 (37 requested) and removed 32 (18 requested) atoms. Cycle 8: After refmac, R = 0.2026 (Rfree = 0.000) for 7788 atoms. Found 20 (37 requested) and removed 34 (18 requested) atoms. Cycle 9: After refmac, R = 0.1992 (Rfree = 0.000) for 7738 atoms. Found 27 (36 requested) and removed 34 (18 requested) atoms. Cycle 10: After refmac, R = 0.1966 (Rfree = 0.000) for 7701 atoms. Found 34 (36 requested) and removed 47 (18 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.74 3.18 Search for helices and strands: 0 residues in 0 chains, 7902 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 7918 seeds are put forward Round 1: 616 peptides, 97 chains. Longest chain 16 peptides. Score 0.430 Round 2: 670 peptides, 91 chains. Longest chain 19 peptides. Score 0.507 Round 3: 676 peptides, 80 chains. Longest chain 21 peptides. Score 0.557 Round 4: 699 peptides, 83 chains. Longest chain 24 peptides. Score 0.564 Round 5: 706 peptides, 80 chains. Longest chain 23 peptides. Score 0.581 Taking the results from Round 5 Chains 81, Residues 626, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 13747 reflections ( 99.52 % complete ) and 17221 restraints for refining 7901 atoms. 14742 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2192 (Rfree = 0.000) for 7901 atoms. Found 32 (37 requested) and removed 32 (18 requested) atoms. Cycle 12: After refmac, R = 0.2054 (Rfree = 0.000) for 7808 atoms. Found 36 (37 requested) and removed 33 (18 requested) atoms. Cycle 13: After refmac, R = 0.1980 (Rfree = 0.000) for 7765 atoms. Found 34 (37 requested) and removed 28 (18 requested) atoms. Cycle 14: After refmac, R = 0.1925 (Rfree = 0.000) for 7742 atoms. Found 30 (36 requested) and removed 28 (18 requested) atoms. Cycle 15: After refmac, R = 0.1926 (Rfree = 0.000) for 7720 atoms. Found 36 (36 requested) and removed 31 (18 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.74 3.18 Search for helices and strands: 0 residues in 0 chains, 8076 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 8096 seeds are put forward Round 1: 602 peptides, 103 chains. Longest chain 14 peptides. Score 0.389 Round 2: 661 peptides, 87 chains. Longest chain 22 peptides. Score 0.516 Round 3: 671 peptides, 87 chains. Longest chain 17 peptides. Score 0.525 Round 4: 688 peptides, 83 chains. Longest chain 28 peptides. Score 0.555 Round 5: 675 peptides, 84 chains. Longest chain 29 peptides. Score 0.540 Taking the results from Round 4 Chains 87, Residues 605, Estimated correctness of the model 0.0 % 5 chains (40 residues) have been docked in sequence ------------------------------------------------------ 13747 reflections ( 99.52 % complete ) and 17212 restraints for refining 7899 atoms. 14722 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2314 (Rfree = 0.000) for 7899 atoms. Found 37 (37 requested) and removed 44 (18 requested) atoms. Cycle 17: After refmac, R = 0.2075 (Rfree = 0.000) for 7801 atoms. Found 37 (37 requested) and removed 30 (18 requested) atoms. Cycle 18: After refmac, R = 0.2072 (Rfree = 0.000) for 7738 atoms. Found 37 (37 requested) and removed 31 (18 requested) atoms. Cycle 19: After refmac, R = 0.2035 (Rfree = 0.000) for 7695 atoms. Found 36 (36 requested) and removed 25 (18 requested) atoms. Cycle 20: After refmac, R = 0.1933 (Rfree = 0.000) for 7679 atoms. Found 30 (36 requested) and removed 28 (18 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.71 3.15 Search for helices and strands: 0 residues in 0 chains, 7986 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 8012 seeds are put forward Round 1: 591 peptides, 98 chains. Longest chain 15 peptides. Score 0.401 Round 2: 665 peptides, 86 chains. Longest chain 20 peptides. Score 0.523 Round 3: 660 peptides, 78 chains. Longest chain 30 peptides. Score 0.551 Round 4: 688 peptides, 86 chains. Longest chain 20 peptides. Score 0.543 Round 5: 677 peptides, 89 chains. Longest chain 18 peptides. Score 0.522 Taking the results from Round 3 Chains 80, Residues 582, Estimated correctness of the model 0.0 % 6 chains (62 residues) have been docked in sequence ------------------------------------------------------ 13747 reflections ( 99.52 % complete ) and 16889 restraints for refining 7902 atoms. 14379 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2078 (Rfree = 0.000) for 7902 atoms. Found 37 (37 requested) and removed 45 (18 requested) atoms. Cycle 22: After refmac, R = 0.2094 (Rfree = 0.000) for 7827 atoms. Found 37 (37 requested) and removed 30 (18 requested) atoms. Cycle 23: After refmac, R = 0.1983 (Rfree = 0.000) for 7806 atoms. Found 37 (37 requested) and removed 45 (18 requested) atoms. Cycle 24: After refmac, R = 0.1870 (Rfree = 0.000) for 7782 atoms. Found 27 (37 requested) and removed 34 (18 requested) atoms. Cycle 25: After refmac, R = 0.1877 (Rfree = 0.000) for 7755 atoms. Found 31 (36 requested) and removed 41 (18 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.71 3.15 Search for helices and strands: 0 residues in 0 chains, 8040 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 8058 seeds are put forward Round 1: 573 peptides, 99 chains. Longest chain 13 peptides. Score 0.377 Round 2: 616 peptides, 87 chains. Longest chain 23 peptides. Score 0.474 Round 3: 628 peptides, 88 chains. Longest chain 19 peptides. Score 0.481 Round 4: 625 peptides, 85 chains. Longest chain 24 peptides. Score 0.491 Round 5: 629 peptides, 86 chains. Longest chain 20 peptides. Score 0.490 Taking the results from Round 4 Chains 89, Residues 540, Estimated correctness of the model 0.0 % 3 chains (30 residues) have been docked in sequence ------------------------------------------------------ 13747 reflections ( 99.52 % complete ) and 17532 restraints for refining 7902 atoms. 15329 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2048 (Rfree = 0.000) for 7902 atoms. Found 37 (37 requested) and removed 44 (18 requested) atoms. Cycle 27: After refmac, R = 0.1902 (Rfree = 0.000) for 7826 atoms. Found 29 (37 requested) and removed 34 (18 requested) atoms. Cycle 28: After refmac, R = 0.1864 (Rfree = 0.000) for 7796 atoms. Found 37 (37 requested) and removed 31 (18 requested) atoms. Cycle 29: After refmac, R = 0.1829 (Rfree = 0.000) for 7781 atoms. Found 37 (37 requested) and removed 36 (18 requested) atoms. Cycle 30: After refmac, R = 0.1800 (Rfree = 0.000) for 7773 atoms. Found 36 (36 requested) and removed 41 (18 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.72 3.16 Search for helices and strands: 0 residues in 0 chains, 8044 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 8066 seeds are put forward Round 1: 505 peptides, 90 chains. Longest chain 13 peptides. Score 0.346 Round 2: 599 peptides, 89 chains. Longest chain 23 peptides. Score 0.449 Round 3: 607 peptides, 91 chains. Longest chain 21 peptides. Score 0.448 Round 4: 618 peptides, 88 chains. Longest chain 18 peptides. Score 0.472 Round 5: 622 peptides, 82 chains. Longest chain 28 peptides. Score 0.501 Taking the results from Round 5 Chains 88, Residues 540, Estimated correctness of the model 0.0 % 9 chains (90 residues) have been docked in sequence ------------------------------------------------------ 13747 reflections ( 99.52 % complete ) and 16957 restraints for refining 7902 atoms. 14533 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2131 (Rfree = 0.000) for 7902 atoms. Found 37 (37 requested) and removed 46 (18 requested) atoms. Cycle 32: After refmac, R = 0.1991 (Rfree = 0.000) for 7832 atoms. Found 35 (37 requested) and removed 34 (18 requested) atoms. Cycle 33: After refmac, R = 0.1902 (Rfree = 0.000) for 7813 atoms. Found 35 (37 requested) and removed 45 (18 requested) atoms. Cycle 34: After refmac, R = 0.1774 (Rfree = 0.000) for 7792 atoms. Found 21 (37 requested) and removed 32 (18 requested) atoms. Cycle 35: After refmac, R = 0.1789 (Rfree = 0.000) for 7771 atoms. Found 26 (36 requested) and removed 25 (18 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.77 3.20 Search for helices and strands: 0 residues in 0 chains, 7993 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 8017 seeds are put forward Round 1: 529 peptides, 92 chains. Longest chain 13 peptides. Score 0.362 Round 2: 599 peptides, 88 chains. Longest chain 27 peptides. Score 0.453 Round 3: 596 peptides, 83 chains. Longest chain 20 peptides. Score 0.472 Round 4: 601 peptides, 78 chains. Longest chain 20 peptides. Score 0.498 Round 5: 634 peptides, 87 chains. Longest chain 18 peptides. Score 0.491 Taking the results from Round 4 Chains 81, Residues 523, Estimated correctness of the model 0.0 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 13747 reflections ( 99.52 % complete ) and 17666 restraints for refining 7902 atoms. 15534 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2219 (Rfree = 0.000) for 7902 atoms. Found 37 (37 requested) and removed 37 (18 requested) atoms. Cycle 37: After refmac, R = 0.2010 (Rfree = 0.000) for 7865 atoms. Found 31 (37 requested) and removed 38 (18 requested) atoms. Cycle 38: After refmac, R = 0.2075 (Rfree = 0.000) for 7841 atoms. Found 37 (37 requested) and removed 50 (18 requested) atoms. Cycle 39: After refmac, R = 0.1997 (Rfree = 0.000) for 7820 atoms. Found 37 (37 requested) and removed 34 (18 requested) atoms. Cycle 40: After refmac, R = 0.1875 (Rfree = 0.000) for 7812 atoms. Found 18 (37 requested) and removed 45 (18 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.79 3.22 Search for helices and strands: 0 residues in 0 chains, 8025 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 8040 seeds are put forward Round 1: 508 peptides, 93 chains. Longest chain 13 peptides. Score 0.334 Round 2: 563 peptides, 80 chains. Longest chain 16 peptides. Score 0.453 Round 3: 569 peptides, 84 chains. Longest chain 21 peptides. Score 0.441 Round 4: 578 peptides, 82 chains. Longest chain 19 peptides. Score 0.459 Round 5: 560 peptides, 78 chains. Longest chain 19 peptides. Score 0.459 Taking the results from Round 5 Chains 78, Residues 482, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 13747 reflections ( 99.52 % complete ) and 18169 restraints for refining 7900 atoms. 16277 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2298 (Rfree = 0.000) for 7900 atoms. Found 33 (37 requested) and removed 30 (18 requested) atoms. Cycle 42: After refmac, R = 0.2107 (Rfree = 0.000) for 7856 atoms. Found 30 (37 requested) and removed 33 (18 requested) atoms. Cycle 43: After refmac, R = 0.2066 (Rfree = 0.000) for 7820 atoms. Found 36 (37 requested) and removed 35 (18 requested) atoms. Cycle 44: After refmac, R = 0.1955 (Rfree = 0.000) for 7809 atoms. Found 37 (37 requested) and removed 21 (18 requested) atoms. Cycle 45: After refmac, R = 0.1983 (Rfree = 0.000) for 7807 atoms. Found 31 (37 requested) and removed 34 (18 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.69 3.13 Search for helices and strands: 0 residues in 0 chains, 8007 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 8024 seeds are put forward Round 1: 445 peptides, 84 chains. Longest chain 11 peptides. Score 0.306 Round 2: 493 peptides, 78 chains. Longest chain 13 peptides. Score 0.390 Round 3: 507 peptides, 74 chains. Longest chain 15 peptides. Score 0.424 Round 4: 524 peptides, 76 chains. Longest chain 18 peptides. Score 0.432 Round 5: 517 peptides, 74 chains. Longest chain 16 peptides. Score 0.434 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 75, Residues 443, Estimated correctness of the model 0.0 % 3 chains (16 residues) have been docked in sequence Sequence coverage is 3 % Consider running further cycles of model building using 1vr5-4_warpNtrace.pdb as input Building loops using Loopy2018 75 chains (443 residues) following loop building 3 chains (16 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 13747 reflections ( 99.52 % complete ) and 18530 restraints for refining 7901 atoms. 16780 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2406 (Rfree = 0.000) for 7901 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 47: After refmac, R = 0.2204 (Rfree = 0.000) for 7829 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 48: After refmac, R = 0.2078 (Rfree = 0.000) for 7780 atoms. Found 0 (37 requested) and removed 18 (18 requested) atoms. Cycle 49: After refmac, R = 0.2112 (Rfree = 0.000) for 7731 atoms. TimeTaking 90.22