null Mon 24 Dec 07:47:30 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 1vr5-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vr5-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vr5-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr5-3.8-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/1vr5-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr5-3.8-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 07:47:34 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/1vr5-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vr5-3.8-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 995 and 0 Target number of residues in the AU: 995 Target solvent content: 0.6563 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: 1vr5-3.8-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: 1vr5-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 8752 target number of atoms Had to go as low as 0.90 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 3.800 Wilson plot Bfac: 82.25 15989 reflections ( 99.57 % complete ) and 0 restraints for refining 9676 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3298 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2982 (Rfree = 0.000) for 9676 atoms. Found 53 (53 requested) and removed 48 (26 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.64 3.09 Search for helices and strands: 0 residues in 0 chains, 9854 seeds are put forward NCS extension: 0 residues added, 9854 seeds are put forward Round 1: 584 peptides, 98 chains. Longest chain 16 peptides. Score 0.393 Round 2: 726 peptides, 86 chains. Longest chain 26 peptides. Score 0.575 Round 3: 745 peptides, 91 chains. Longest chain 25 peptides. Score 0.572 Round 4: 739 peptides, 79 chains. Longest chain 24 peptides. Score 0.611 Round 5: 752 peptides, 78 chains. Longest chain 23 peptides. Score 0.624 Taking the results from Round 5 Chains 87, Residues 674, Estimated correctness of the model 9.7 % 7 chains (75 residues) have been docked in sequence ------------------------------------------------------ 15989 reflections ( 99.57 % complete ) and 16225 restraints for refining 7913 atoms. 13345 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2420 (Rfree = 0.000) for 7913 atoms. Found 43 (43 requested) and removed 49 (21 requested) atoms. Cycle 2: After refmac, R = 0.2251 (Rfree = 0.000) for 7771 atoms. Found 33 (43 requested) and removed 36 (21 requested) atoms. Cycle 3: After refmac, R = 0.2116 (Rfree = 0.000) for 7711 atoms. Found 32 (42 requested) and removed 38 (21 requested) atoms. Cycle 4: After refmac, R = 0.2006 (Rfree = 0.000) for 7676 atoms. Found 26 (42 requested) and removed 30 (21 requested) atoms. Cycle 5: After refmac, R = 0.1961 (Rfree = 0.000) for 7642 atoms. Found 28 (42 requested) and removed 32 (21 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.59 3.05 Search for helices and strands: 0 residues in 0 chains, 7995 seeds are put forward NCS extension: 17 residues added (9 deleted due to clashes), 8012 seeds are put forward Round 1: 700 peptides, 97 chains. Longest chain 19 peptides. Score 0.510 Round 2: 736 peptides, 91 chains. Longest chain 21 peptides. Score 0.565 Round 3: 779 peptides, 87 chains. Longest chain 27 peptides. Score 0.613 Round 4: 747 peptides, 73 chains. Longest chain 25 peptides. Score 0.638 Round 5: 757 peptides, 77 chains. Longest chain 33 peptides. Score 0.631 Taking the results from Round 4 Chains 79, Residues 674, Estimated correctness of the model 15.8 % 6 chains (75 residues) have been docked in sequence ------------------------------------------------------ 15989 reflections ( 99.57 % complete ) and 16265 restraints for refining 7911 atoms. 13333 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2354 (Rfree = 0.000) for 7911 atoms. Found 43 (43 requested) and removed 67 (21 requested) atoms. Cycle 7: After refmac, R = 0.2112 (Rfree = 0.000) for 7840 atoms. Found 38 (43 requested) and removed 45 (21 requested) atoms. Cycle 8: After refmac, R = 0.2042 (Rfree = 0.000) for 7805 atoms. Found 26 (43 requested) and removed 37 (21 requested) atoms. Cycle 9: After refmac, R = 0.1953 (Rfree = 0.000) for 7771 atoms. Found 31 (42 requested) and removed 36 (21 requested) atoms. Cycle 10: After refmac, R = 0.1925 (Rfree = 0.000) for 7752 atoms. Found 28 (42 requested) and removed 35 (21 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.59 3.05 Search for helices and strands: 0 residues in 0 chains, 7975 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 7994 seeds are put forward Round 1: 687 peptides, 92 chains. Longest chain 22 peptides. Score 0.519 Round 2: 770 peptides, 83 chains. Longest chain 36 peptides. Score 0.620 Round 3: 774 peptides, 82 chains. Longest chain 34 peptides. Score 0.626 Round 4: 755 peptides, 81 chains. Longest chain 26 peptides. Score 0.616 Round 5: 781 peptides, 76 chains. Longest chain 29 peptides. Score 0.652 Taking the results from Round 5 Chains 87, Residues 705, Estimated correctness of the model 21.6 % 10 chains (116 residues) have been docked in sequence ------------------------------------------------------ 15989 reflections ( 99.57 % complete ) and 15791 restraints for refining 7915 atoms. 12540 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2317 (Rfree = 0.000) for 7915 atoms. Found 37 (43 requested) and removed 42 (21 requested) atoms. Cycle 12: After refmac, R = 0.2094 (Rfree = 0.000) for 7864 atoms. Found 12 (43 requested) and removed 34 (21 requested) atoms. Cycle 13: After refmac, R = 0.2074 (Rfree = 0.000) for 7822 atoms. Found 22 (43 requested) and removed 35 (21 requested) atoms. Cycle 14: After refmac, R = 0.2019 (Rfree = 0.000) for 7797 atoms. Found 28 (42 requested) and removed 28 (21 requested) atoms. Cycle 15: After refmac, R = 0.1970 (Rfree = 0.000) for 7786 atoms. Found 19 (42 requested) and removed 31 (21 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.62 3.08 Search for helices and strands: 0 residues in 0 chains, 8010 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 8038 seeds are put forward Round 1: 687 peptides, 92 chains. Longest chain 27 peptides. Score 0.519 Round 2: 737 peptides, 89 chains. Longest chain 23 peptides. Score 0.573 Round 3: 725 peptides, 81 chains. Longest chain 28 peptides. Score 0.593 Round 4: 741 peptides, 74 chains. Longest chain 28 peptides. Score 0.630 Round 5: 741 peptides, 72 chains. Longest chain 32 peptides. Score 0.637 Taking the results from Round 5 Chains 83, Residues 669, Estimated correctness of the model 15.3 % 12 chains (177 residues) have been docked in sequence ------------------------------------------------------ 15989 reflections ( 99.57 % complete ) and 15035 restraints for refining 7915 atoms. 11642 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2365 (Rfree = 0.000) for 7915 atoms. Found 43 (43 requested) and removed 53 (21 requested) atoms. Cycle 17: After refmac, R = 0.2257 (Rfree = 0.000) for 7836 atoms. Found 33 (43 requested) and removed 33 (21 requested) atoms. Cycle 18: After refmac, R = 0.2257 (Rfree = 0.000) for 7796 atoms. Found 39 (43 requested) and removed 35 (21 requested) atoms. Cycle 19: After refmac, R = 0.2112 (Rfree = 0.000) for 7763 atoms. Found 25 (42 requested) and removed 38 (21 requested) atoms. Cycle 20: After refmac, R = 0.2099 (Rfree = 0.000) for 7716 atoms. Found 23 (42 requested) and removed 29 (21 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.58 3.04 Search for helices and strands: 0 residues in 0 chains, 7990 seeds are put forward NCS extension: 20 residues added (3 deleted due to clashes), 8010 seeds are put forward Round 1: 667 peptides, 103 chains. Longest chain 18 peptides. Score 0.455 Round 2: 743 peptides, 93 chains. Longest chain 34 peptides. Score 0.563 Round 3: 725 peptides, 92 chains. Longest chain 25 peptides. Score 0.552 Round 4: 729 peptides, 86 chains. Longest chain 27 peptides. Score 0.578 Round 5: 720 peptides, 92 chains. Longest chain 40 peptides. Score 0.547 Taking the results from Round 4 Chains 87, Residues 643, Estimated correctness of the model 0.0 % 2 chains (39 residues) have been docked in sequence ------------------------------------------------------ 15989 reflections ( 99.57 % complete ) and 16925 restraints for refining 7913 atoms. 14259 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2387 (Rfree = 0.000) for 7913 atoms. Found 43 (43 requested) and removed 44 (21 requested) atoms. Cycle 22: After refmac, R = 0.2158 (Rfree = 0.000) for 7841 atoms. Found 41 (43 requested) and removed 39 (21 requested) atoms. Cycle 23: After refmac, R = 0.2053 (Rfree = 0.000) for 7789 atoms. Found 40 (43 requested) and removed 43 (21 requested) atoms. Cycle 24: After refmac, R = 0.2068 (Rfree = 0.000) for 7754 atoms. Found 37 (42 requested) and removed 43 (21 requested) atoms. Cycle 25: After refmac, R = 0.2011 (Rfree = 0.000) for 7708 atoms. Found 35 (42 requested) and removed 45 (21 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.59 3.05 Search for helices and strands: 0 residues in 0 chains, 8036 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 8061 seeds are put forward Round 1: 616 peptides, 107 chains. Longest chain 15 peptides. Score 0.386 Round 2: 676 peptides, 91 chains. Longest chain 27 peptides. Score 0.513 Round 3: 693 peptides, 95 chains. Longest chain 17 peptides. Score 0.512 Round 4: 698 peptides, 89 chains. Longest chain 20 peptides. Score 0.540 Round 5: 699 peptides, 87 chains. Longest chain 26 peptides. Score 0.549 Taking the results from Round 5 Chains 91, Residues 612, Estimated correctness of the model 0.0 % 8 chains (98 residues) have been docked in sequence ------------------------------------------------------ 15989 reflections ( 99.57 % complete ) and 16418 restraints for refining 7914 atoms. 13662 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2378 (Rfree = 0.000) for 7914 atoms. Found 43 (43 requested) and removed 41 (21 requested) atoms. Cycle 27: After refmac, R = 0.2218 (Rfree = 0.000) for 7854 atoms. Found 43 (43 requested) and removed 32 (21 requested) atoms. Cycle 28: After refmac, R = 0.2156 (Rfree = 0.000) for 7806 atoms. Found 43 (43 requested) and removed 34 (21 requested) atoms. Cycle 29: After refmac, R = 0.2059 (Rfree = 0.000) for 7784 atoms. Found 41 (42 requested) and removed 35 (21 requested) atoms. Cycle 30: After refmac, R = 0.2052 (Rfree = 0.000) for 7761 atoms. Found 42 (42 requested) and removed 32 (21 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.59 3.05 Search for helices and strands: 0 residues in 0 chains, 8029 seeds are put forward NCS extension: 34 residues added (2 deleted due to clashes), 8063 seeds are put forward Round 1: 615 peptides, 99 chains. Longest chain 16 peptides. Score 0.421 Round 2: 670 peptides, 93 chains. Longest chain 23 peptides. Score 0.499 Round 3: 683 peptides, 93 chains. Longest chain 22 peptides. Score 0.511 Round 4: 700 peptides, 95 chains. Longest chain 26 peptides. Score 0.518 Round 5: 697 peptides, 89 chains. Longest chain 21 peptides. Score 0.539 Taking the results from Round 5 Chains 92, Residues 608, Estimated correctness of the model 0.0 % 3 chains (28 residues) have been docked in sequence ------------------------------------------------------ 15989 reflections ( 99.57 % complete ) and 17297 restraints for refining 7914 atoms. 14837 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2154 (Rfree = 0.000) for 7914 atoms. Found 43 (43 requested) and removed 27 (21 requested) atoms. Cycle 32: After refmac, R = 0.2032 (Rfree = 0.000) for 7897 atoms. Found 31 (43 requested) and removed 29 (21 requested) atoms. Cycle 33: After refmac, R = 0.1965 (Rfree = 0.000) for 7873 atoms. Found 39 (43 requested) and removed 29 (21 requested) atoms. Cycle 34: After refmac, R = 0.1928 (Rfree = 0.000) for 7851 atoms. Found 43 (43 requested) and removed 35 (21 requested) atoms. Cycle 35: After refmac, R = 0.1880 (Rfree = 0.000) for 7837 atoms. Found 32 (43 requested) and removed 27 (21 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.59 3.05 Search for helices and strands: 0 residues in 0 chains, 8070 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 8104 seeds are put forward Round 1: 594 peptides, 99 chains. Longest chain 21 peptides. Score 0.399 Round 2: 641 peptides, 94 chains. Longest chain 18 peptides. Score 0.468 Round 3: 654 peptides, 85 chains. Longest chain 22 peptides. Score 0.517 Round 4: 664 peptides, 82 chains. Longest chain 21 peptides. Score 0.538 Round 5: 665 peptides, 84 chains. Longest chain 24 peptides. Score 0.531 Taking the results from Round 4 Chains 87, Residues 582, Estimated correctness of the model 0.0 % 6 chains (50 residues) have been docked in sequence ------------------------------------------------------ 15989 reflections ( 99.57 % complete ) and 17076 restraints for refining 7916 atoms. 14641 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1999 (Rfree = 0.000) for 7916 atoms. Found 31 (43 requested) and removed 32 (21 requested) atoms. Cycle 37: After refmac, R = 0.1833 (Rfree = 0.000) for 7875 atoms. Found 24 (43 requested) and removed 29 (21 requested) atoms. Cycle 38: After refmac, R = 0.1778 (Rfree = 0.000) for 7851 atoms. Found 16 (43 requested) and removed 25 (21 requested) atoms. Cycle 39: After refmac, R = 0.1763 (Rfree = 0.000) for 7833 atoms. Found 23 (43 requested) and removed 36 (21 requested) atoms. Cycle 40: After refmac, R = 0.1783 (Rfree = 0.000) for 7814 atoms. Found 27 (43 requested) and removed 25 (21 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.60 3.06 Search for helices and strands: 0 residues in 0 chains, 8140 seeds are put forward NCS extension: 38 residues added (1 deleted due to clashes), 8178 seeds are put forward Round 1: 566 peptides, 103 chains. Longest chain 14 peptides. Score 0.351 Round 2: 619 peptides, 94 chains. Longest chain 26 peptides. Score 0.447 Round 3: 628 peptides, 93 chains. Longest chain 22 peptides. Score 0.460 Round 4: 649 peptides, 87 chains. Longest chain 21 peptides. Score 0.505 Round 5: 629 peptides, 90 chains. Longest chain 19 peptides. Score 0.473 Taking the results from Round 4 Chains 90, Residues 562, Estimated correctness of the model 0.0 % 5 chains (48 residues) have been docked in sequence ------------------------------------------------------ 15989 reflections ( 99.57 % complete ) and 17420 restraints for refining 7915 atoms. 15086 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2044 (Rfree = 0.000) for 7915 atoms. Found 37 (43 requested) and removed 45 (21 requested) atoms. Cycle 42: After refmac, R = 0.1849 (Rfree = 0.000) for 7881 atoms. Found 14 (43 requested) and removed 29 (21 requested) atoms. Cycle 43: After refmac, R = 0.1778 (Rfree = 0.000) for 7849 atoms. Found 5 (43 requested) and removed 26 (21 requested) atoms. Cycle 44: After refmac, R = 0.1742 (Rfree = 0.000) for 7820 atoms. Found 13 (43 requested) and removed 24 (21 requested) atoms. Cycle 45: After refmac, R = 0.1701 (Rfree = 0.000) for 7805 atoms. Found 8 (42 requested) and removed 22 (21 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.63 3.08 Search for helices and strands: 0 residues in 0 chains, 8031 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 8052 seeds are put forward Round 1: 533 peptides, 92 chains. Longest chain 14 peptides. Score 0.367 Round 2: 565 peptides, 81 chains. Longest chain 14 peptides. Score 0.451 Round 3: 572 peptides, 80 chains. Longest chain 20 peptides. Score 0.462 Round 4: 580 peptides, 81 chains. Longest chain 15 peptides. Score 0.465 Round 5: 590 peptides, 84 chains. Longest chain 17 peptides. Score 0.462 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 83, Residues 499, Estimated correctness of the model 0.0 % 5 chains (46 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 1vr5-3_warpNtrace.pdb as input Building loops using Loopy2018 83 chains (499 residues) following loop building 5 chains (46 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 15989 reflections ( 99.57 % complete ) and 17750 restraints for refining 7914 atoms. 15649 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2026 (Rfree = 0.000) for 7914 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 47: After refmac, R = 0.1866 (Rfree = 0.000) for 7861 atoms. Found 0 (43 requested) and removed 21 (21 requested) atoms. Cycle 48: After refmac, R = 0.1780 (Rfree = 0.000) for 7822 atoms. Found 0 (43 requested) and removed 20 (21 requested) atoms. Cycle 49: After refmac, R = 0.1754 (Rfree = 0.000) for 7796 atoms. Found 0 (42 requested) and removed 8 (21 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:27:57 GMT 2018 Job finished. TimeTaking 100.46 Used memory is bytes: 25638360