Mon 24 Dec 00:34:38 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 1vr5-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vr5-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vr5-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr5-3.6-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/1vr5-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr5-3.6-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 00:34:42 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/1vr5-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr5-3.6-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 1020 and 0 Target number of residues in the AU: 1020 Target solvent content: 0.6477 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: 1vr5-3.6-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: 18 Cell parameters: 140.030 96.640 115.780 90.000 90.000 90.000 Input sequence file: 1vr5-3.6-parrot-mrncs.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 3.600 Wilson plot Bfac: 76.58 18746 reflections ( 99.62 % complete ) and 0 restraints for refining 9712 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3194 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2801 (Rfree = 0.000) for 9712 atoms. Found 62 (62 requested) and removed 42 (31 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.49 2.97 Search for helices and strands: 0 residues in 0 chains, 9901 seeds are put forward NCS extension: 0 residues added, 9901 seeds are put forward Round 1: 634 peptides, 92 chains. Longest chain 17 peptides. Score 0.470 Round 2: 746 peptides, 88 chains. Longest chain 22 peptides. Score 0.584 Round 3: 798 peptides, 84 chains. Longest chain 33 peptides. Score 0.637 Round 4: 811 peptides, 71 chains. Longest chain 41 peptides. Score 0.688 Round 5: 827 peptides, 73 chains. Longest chain 45 peptides. Score 0.692 Taking the results from Round 5 Chains 80, Residues 754, Estimated correctness of the model 47.1 % 9 chains (196 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 18746 reflections ( 99.62 % complete ) and 14900 restraints for refining 8137 atoms. 11074 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2457 (Rfree = 0.000) for 8137 atoms. Found 52 (52 requested) and removed 62 (26 requested) atoms. Cycle 2: After refmac, R = 0.2234 (Rfree = 0.000) for 8007 atoms. Found 38 (52 requested) and removed 40 (26 requested) atoms. Cycle 3: After refmac, R = 0.2156 (Rfree = 0.000) for 7956 atoms. Found 24 (51 requested) and removed 40 (25 requested) atoms. Cycle 4: After refmac, R = 0.2063 (Rfree = 0.000) for 7905 atoms. Found 18 (50 requested) and removed 36 (25 requested) atoms. Cycle 5: After refmac, R = 0.2025 (Rfree = 0.000) for 7865 atoms. Found 16 (50 requested) and removed 30 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.50 2.97 Search for helices and strands: 0 residues in 0 chains, 8084 seeds are put forward NCS extension: 27 residues added (9 deleted due to clashes), 8111 seeds are put forward Round 1: 746 peptides, 94 chains. Longest chain 19 peptides. Score 0.562 Round 2: 809 peptides, 80 chains. Longest chain 32 peptides. Score 0.658 Round 3: 812 peptides, 79 chains. Longest chain 33 peptides. Score 0.663 Round 4: 807 peptides, 75 chains. Longest chain 35 peptides. Score 0.673 Round 5: 793 peptides, 74 chains. Longest chain 29 peptides. Score 0.666 Taking the results from Round 4 Chains 87, Residues 732, Estimated correctness of the model 41.0 % 11 chains (195 residues) have been docked in sequence ------------------------------------------------------ 18746 reflections ( 99.62 % complete ) and 14706 restraints for refining 7933 atoms. 10974 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2447 (Rfree = 0.000) for 7933 atoms. Found 50 (50 requested) and removed 65 (25 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2218 (Rfree = 0.000) for 7860 atoms. Found 31 (50 requested) and removed 37 (25 requested) atoms. Cycle 8: After refmac, R = 0.2123 (Rfree = 0.000) for 7837 atoms. Found 29 (50 requested) and removed 28 (25 requested) atoms. Cycle 9: After refmac, R = 0.2083 (Rfree = 0.000) for 7826 atoms. Found 17 (50 requested) and removed 29 (25 requested) atoms. Cycle 10: After refmac, R = 0.2047 (Rfree = 0.000) for 7808 atoms. Found 20 (50 requested) and removed 27 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.46 2.94 Search for helices and strands: 0 residues in 0 chains, 8046 seeds are put forward NCS extension: 42 residues added (2 deleted due to clashes), 8088 seeds are put forward Round 1: 725 peptides, 96 chains. Longest chain 23 peptides. Score 0.536 Round 2: 785 peptides, 77 chains. Longest chain 28 peptides. Score 0.651 Round 3: 799 peptides, 74 chains. Longest chain 31 peptides. Score 0.670 Round 4: 783 peptides, 74 chains. Longest chain 33 peptides. Score 0.660 Round 5: 810 peptides, 72 chains. Longest chain 45 peptides. Score 0.684 Taking the results from Round 5 Chains 84, Residues 738, Estimated correctness of the model 44.6 % 11 chains (158 residues) have been docked in sequence ------------------------------------------------------ 18746 reflections ( 99.62 % complete ) and 15092 restraints for refining 7934 atoms. 11549 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2427 (Rfree = 0.000) for 7934 atoms. Found 50 (50 requested) and removed 47 (25 requested) atoms. Cycle 12: After refmac, R = 0.2109 (Rfree = 0.000) for 7869 atoms. Found 33 (50 requested) and removed 38 (25 requested) atoms. Cycle 13: After refmac, R = 0.1961 (Rfree = 0.000) for 7845 atoms. Found 27 (50 requested) and removed 36 (25 requested) atoms. Cycle 14: After refmac, R = 0.1891 (Rfree = 0.000) for 7823 atoms. Found 16 (50 requested) and removed 34 (25 requested) atoms. Cycle 15: After refmac, R = 0.1842 (Rfree = 0.000) for 7798 atoms. Found 9 (50 requested) and removed 25 (25 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 2.93 Search for helices and strands: 0 residues in 0 chains, 8031 seeds are put forward NCS extension: 28 residues added (8 deleted due to clashes), 8059 seeds are put forward Round 1: 716 peptides, 88 chains. Longest chain 30 peptides. Score 0.559 Round 2: 778 peptides, 81 chains. Longest chain 33 peptides. Score 0.633 Round 3: 783 peptides, 75 chains. Longest chain 40 peptides. Score 0.656 Round 4: 793 peptides, 79 chains. Longest chain 30 peptides. Score 0.650 Round 5: 803 peptides, 79 chains. Longest chain 44 peptides. Score 0.657 Taking the results from Round 5 Chains 86, Residues 724, Estimated correctness of the model 35.6 % 8 chains (138 residues) have been docked in sequence ------------------------------------------------------ 18746 reflections ( 99.62 % complete ) and 15354 restraints for refining 7933 atoms. 11925 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2368 (Rfree = 0.000) for 7933 atoms. Found 50 (50 requested) and removed 53 (25 requested) atoms. Cycle 17: After refmac, R = 0.2131 (Rfree = 0.000) for 7858 atoms. Found 24 (50 requested) and removed 33 (25 requested) atoms. Cycle 18: After refmac, R = 0.2025 (Rfree = 0.000) for 7820 atoms. Found 17 (50 requested) and removed 30 (25 requested) atoms. Cycle 19: After refmac, R = 0.2004 (Rfree = 0.000) for 7790 atoms. Found 13 (50 requested) and removed 30 (25 requested) atoms. Cycle 20: After refmac, R = 0.2002 (Rfree = 0.000) for 7758 atoms. Found 13 (49 requested) and removed 31 (24 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.45 2.93 Search for helices and strands: 0 residues in 0 chains, 7969 seeds are put forward NCS extension: 17 residues added (7 deleted due to clashes), 7986 seeds are put forward Round 1: 722 peptides, 94 chains. Longest chain 21 peptides. Score 0.541 Round 2: 768 peptides, 82 chains. Longest chain 31 peptides. Score 0.622 Round 3: 754 peptides, 83 chains. Longest chain 27 peptides. Score 0.608 Round 4: 800 peptides, 85 chains. Longest chain 36 peptides. Score 0.635 Round 5: 779 peptides, 76 chains. Longest chain 28 peptides. Score 0.650 Taking the results from Round 5 Chains 86, Residues 703, Estimated correctness of the model 33.2 % 8 chains (95 residues) have been docked in sequence ------------------------------------------------------ 18746 reflections ( 99.62 % complete ) and 16123 restraints for refining 7932 atoms. 13027 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2317 (Rfree = 0.000) for 7932 atoms. Found 50 (50 requested) and removed 36 (25 requested) atoms. Cycle 22: After refmac, R = 0.2111 (Rfree = 0.000) for 7890 atoms. Found 20 (50 requested) and removed 34 (25 requested) atoms. Cycle 23: After refmac, R = 0.2006 (Rfree = 0.000) for 7861 atoms. Found 12 (50 requested) and removed 28 (25 requested) atoms. Cycle 24: After refmac, R = 0.1964 (Rfree = 0.000) for 7841 atoms. Found 9 (50 requested) and removed 29 (25 requested) atoms. Cycle 25: After refmac, R = 0.1929 (Rfree = 0.000) for 7816 atoms. Found 12 (50 requested) and removed 27 (25 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.48 2.96 Search for helices and strands: 0 residues in 0 chains, 8053 seeds are put forward NCS extension: 26 residues added (3 deleted due to clashes), 8079 seeds are put forward Round 1: 694 peptides, 97 chains. Longest chain 31 peptides. Score 0.505 Round 2: 726 peptides, 78 chains. Longest chain 32 peptides. Score 0.604 Round 3: 745 peptides, 82 chains. Longest chain 34 peptides. Score 0.605 Round 4: 758 peptides, 79 chains. Longest chain 42 peptides. Score 0.625 Round 5: 745 peptides, 74 chains. Longest chain 40 peptides. Score 0.633 Taking the results from Round 5 Chains 85, Residues 671, Estimated correctness of the model 27.1 % 11 chains (149 residues) have been docked in sequence ------------------------------------------------------ 18746 reflections ( 99.62 % complete ) and 15717 restraints for refining 7934 atoms. 12487 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2375 (Rfree = 0.000) for 7934 atoms. Found 50 (50 requested) and removed 45 (25 requested) atoms. Cycle 27: After refmac, R = 0.2166 (Rfree = 0.000) for 7894 atoms. Found 22 (50 requested) and removed 28 (25 requested) atoms. Cycle 28: After refmac, R = 0.2062 (Rfree = 0.000) for 7860 atoms. Found 10 (50 requested) and removed 29 (25 requested) atoms. Cycle 29: After refmac, R = 0.1989 (Rfree = 0.000) for 7828 atoms. Found 8 (50 requested) and removed 29 (25 requested) atoms. Cycle 30: After refmac, R = 0.1933 (Rfree = 0.000) for 7799 atoms. Found 13 (50 requested) and removed 25 (25 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.49 2.97 Search for helices and strands: 0 residues in 0 chains, 8027 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 8048 seeds are put forward Round 1: 674 peptides, 91 chains. Longest chain 26 peptides. Score 0.511 Round 2: 731 peptides, 81 chains. Longest chain 36 peptides. Score 0.597 Round 3: 722 peptides, 80 chains. Longest chain 30 peptides. Score 0.594 Round 4: 759 peptides, 74 chains. Longest chain 36 peptides. Score 0.643 Round 5: 734 peptides, 74 chains. Longest chain 33 peptides. Score 0.625 Taking the results from Round 4 Chains 84, Residues 685, Estimated correctness of the model 30.7 % 8 chains (117 residues) have been docked in sequence ------------------------------------------------------ 18746 reflections ( 99.62 % complete ) and 15908 restraints for refining 7934 atoms. 12738 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2314 (Rfree = 0.000) for 7934 atoms. Found 42 (50 requested) and removed 51 (25 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2111 (Rfree = 0.000) for 7903 atoms. Found 17 (50 requested) and removed 34 (25 requested) atoms. Cycle 33: After refmac, R = 0.2033 (Rfree = 0.000) for 7881 atoms. Found 11 (50 requested) and removed 29 (25 requested) atoms. Cycle 34: After refmac, R = 0.1985 (Rfree = 0.000) for 7856 atoms. Found 9 (50 requested) and removed 26 (25 requested) atoms. Cycle 35: After refmac, R = 0.1985 (Rfree = 0.000) for 7835 atoms. Found 3 (50 requested) and removed 26 (25 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.47 2.95 Search for helices and strands: 0 residues in 0 chains, 8043 seeds are put forward NCS extension: 36 residues added (10 deleted due to clashes), 8079 seeds are put forward Round 1: 665 peptides, 95 chains. Longest chain 20 peptides. Score 0.486 Round 2: 705 peptides, 80 chains. Longest chain 31 peptides. Score 0.580 Round 3: 702 peptides, 75 chains. Longest chain 36 peptides. Score 0.597 Round 4: 714 peptides, 81 chains. Longest chain 33 peptides. Score 0.584 Round 5: 689 peptides, 80 chains. Longest chain 26 peptides. Score 0.567 Taking the results from Round 3 Chains 83, Residues 627, Estimated correctness of the model 13.5 % 8 chains (128 residues) have been docked in sequence ------------------------------------------------------ 18746 reflections ( 99.62 % complete ) and 16079 restraints for refining 7934 atoms. 13112 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2199 (Rfree = 0.000) for 7934 atoms. Found 40 (50 requested) and removed 39 (25 requested) atoms. Cycle 37: After refmac, R = 0.2034 (Rfree = 0.000) for 7897 atoms. Found 22 (50 requested) and removed 32 (25 requested) atoms. Cycle 38: After refmac, R = 0.2053 (Rfree = 0.000) for 7869 atoms. Found 22 (50 requested) and removed 29 (25 requested) atoms. Cycle 39: After refmac, R = 0.1972 (Rfree = 0.000) for 7852 atoms. Found 19 (50 requested) and removed 28 (25 requested) atoms. Cycle 40: After refmac, R = 0.1949 (Rfree = 0.000) for 7832 atoms. Found 12 (50 requested) and removed 28 (25 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 2.96 Search for helices and strands: 0 residues in 0 chains, 8064 seeds are put forward NCS extension: 22 residues added (4 deleted due to clashes), 8086 seeds are put forward Round 1: 640 peptides, 95 chains. Longest chain 19 peptides. Score 0.463 Round 2: 680 peptides, 83 chains. Longest chain 26 peptides. Score 0.548 Round 3: 679 peptides, 81 chains. Longest chain 36 peptides. Score 0.555 Round 4: 679 peptides, 84 chains. Longest chain 27 peptides. Score 0.543 Round 5: 693 peptides, 81 chains. Longest chain 36 peptides. Score 0.567 Taking the results from Round 5 Chains 89, Residues 612, Estimated correctness of the model 1.3 % 6 chains (64 residues) have been docked in sequence ------------------------------------------------------ 18746 reflections ( 99.62 % complete ) and 16873 restraints for refining 7934 atoms. 14254 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2243 (Rfree = 0.000) for 7934 atoms. Found 41 (50 requested) and removed 38 (25 requested) atoms. Cycle 42: After refmac, R = 0.2012 (Rfree = 0.000) for 7902 atoms. Found 29 (50 requested) and removed 30 (25 requested) atoms. Cycle 43: After refmac, R = 0.1961 (Rfree = 0.000) for 7889 atoms. Found 14 (50 requested) and removed 30 (25 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1948 (Rfree = 0.000) for 7864 atoms. Found 30 (50 requested) and removed 29 (25 requested) atoms. Cycle 45: After refmac, R = 0.1889 (Rfree = 0.000) for 7857 atoms. Found 15 (50 requested) and removed 31 (25 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.49 2.97 Search for helices and strands: 0 residues in 0 chains, 8057 seeds are put forward NCS extension: 23 residues added (9 deleted due to clashes), 8080 seeds are put forward Round 1: 598 peptides, 87 chains. Longest chain 26 peptides. Score 0.457 Round 2: 680 peptides, 85 chains. Longest chain 44 peptides. Score 0.540 Round 3: 652 peptides, 78 chains. Longest chain 33 peptides. Score 0.544 Round 4: 674 peptides, 77 chains. Longest chain 26 peptides. Score 0.567 Round 5: 658 peptides, 73 chains. Longest chain 31 peptides. Score 0.569 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 77, Residues 585, Estimated correctness of the model 2.2 % 5 chains (72 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 1vr5-3_warpNtrace.pdb as input Building loops using Loopy2018 77 chains (585 residues) following loop building 5 chains (72 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 18746 reflections ( 99.62 % complete ) and 16876 restraints for refining 7934 atoms. 14296 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2202 (Rfree = 0.000) for 7934 atoms. Found 0 (50 requested) and removed 25 (25 requested) atoms. Cycle 47: After refmac, R = 0.2055 (Rfree = 0.000) for 7887 atoms. Found 0 (50 requested) and removed 25 (25 requested) atoms. Cycle 48: After refmac, R = 0.2048 (Rfree = 0.000) for 7858 atoms. Found 0 (50 requested) and removed 9 (25 requested) atoms. Cycle 49: After refmac, R = 0.2000 (Rfree = 0.000) for 7845 atoms. TimeTaking 89.02