Mon 24 Dec 01:08:02 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 1vr5-3.4-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vr5-3.4-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vr5-3.4-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr5-3.4-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/1vr5-3.4-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr5-3.4-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 01:08:07 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/1vr5-3.4-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr5-3.4-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 1039 and 0 Target number of residues in the AU: 1039 Target solvent content: 0.6411 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: 1vr5-3.4-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: 1vr5-3.4-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 3.400 Wilson plot Bfac: 72.71 22185 reflections ( 99.66 % complete ) and 0 restraints for refining 9646 atoms. Observations/parameters ratio is 0.57 ------------------------------------------------------ Starting model: R = 0.3112 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2959 (Rfree = 0.000) for 9646 atoms. Found 72 (72 requested) and removed 49 (36 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.36 2.85 Search for helices and strands: 0 residues in 0 chains, 9868 seeds are put forward NCS extension: 0 residues added, 9868 seeds are put forward Round 1: 653 peptides, 105 chains. Longest chain 18 peptides. Score 0.432 Round 2: 753 peptides, 92 chains. Longest chain 25 peptides. Score 0.575 Round 3: 779 peptides, 85 chains. Longest chain 25 peptides. Score 0.620 Round 4: 796 peptides, 78 chains. Longest chain 53 peptides. Score 0.656 Round 5: 829 peptides, 79 chains. Longest chain 54 peptides. Score 0.674 Taking the results from Round 5 Chains 86, Residues 750, Estimated correctness of the model 50.9 % 10 chains (179 residues) have been docked in sequence ------------------------------------------------------ 22185 reflections ( 99.66 % complete ) and 15104 restraints for refining 8220 atoms. 11347 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2775 (Rfree = 0.000) for 8220 atoms. Found 62 (62 requested) and removed 68 (31 requested) atoms. Cycle 2: After refmac, R = 0.2396 (Rfree = 0.000) for 8095 atoms. Found 52 (62 requested) and removed 49 (31 requested) atoms. Cycle 3: After refmac, R = 0.2283 (Rfree = 0.000) for 8035 atoms. Found 42 (61 requested) and removed 43 (30 requested) atoms. Cycle 4: After refmac, R = 0.2151 (Rfree = 0.000) for 8004 atoms. Found 23 (60 requested) and removed 36 (30 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2094 (Rfree = 0.000) for 7971 atoms. Found 36 (60 requested) and removed 42 (30 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 2.84 Search for helices and strands: 0 residues in 0 chains, 8197 seeds are put forward NCS extension: 14 residues added (20 deleted due to clashes), 8211 seeds are put forward Round 1: 776 peptides, 92 chains. Longest chain 29 peptides. Score 0.593 Round 2: 811 peptides, 81 chains. Longest chain 51 peptides. Score 0.656 Round 3: 820 peptides, 78 chains. Longest chain 54 peptides. Score 0.672 Round 4: 816 peptides, 76 chains. Longest chain 45 peptides. Score 0.675 Round 5: 814 peptides, 81 chains. Longest chain 31 peptides. Score 0.658 Taking the results from Round 4 Chains 84, Residues 740, Estimated correctness of the model 51.2 % 15 chains (214 residues) have been docked in sequence ------------------------------------------------------ 22185 reflections ( 99.66 % complete ) and 14463 restraints for refining 7957 atoms. 10586 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2614 (Rfree = 0.000) for 7957 atoms. Found 60 (60 requested) and removed 59 (30 requested) atoms. Cycle 7: After refmac, R = 0.2310 (Rfree = 0.000) for 7887 atoms. Found 43 (60 requested) and removed 36 (30 requested) atoms. Cycle 8: After refmac, R = 0.2205 (Rfree = 0.000) for 7876 atoms. Found 18 (59 requested) and removed 36 (29 requested) atoms. Cycle 9: After refmac, R = 0.2177 (Rfree = 0.000) for 7838 atoms. Found 30 (59 requested) and removed 33 (29 requested) atoms. Cycle 10: After refmac, R = 0.2111 (Rfree = 0.000) for 7813 atoms. Found 23 (59 requested) and removed 31 (29 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.33 2.83 Search for helices and strands: 0 residues in 0 chains, 8038 seeds are put forward NCS extension: 15 residues added (15 deleted due to clashes), 8053 seeds are put forward Round 1: 776 peptides, 88 chains. Longest chain 36 peptides. Score 0.607 Round 2: 819 peptides, 76 chains. Longest chain 44 peptides. Score 0.677 Round 3: 821 peptides, 77 chains. Longest chain 35 peptides. Score 0.675 Round 4: 832 peptides, 73 chains. Longest chain 32 peptides. Score 0.695 Round 5: 832 peptides, 78 chains. Longest chain 43 peptides. Score 0.680 Taking the results from Round 4 Chains 77, Residues 759, Estimated correctness of the model 56.6 % 11 chains (209 residues) have been docked in sequence ------------------------------------------------------ 22185 reflections ( 99.66 % complete ) and 14497 restraints for refining 7957 atoms. 10610 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2501 (Rfree = 0.000) for 7957 atoms. Found 60 (60 requested) and removed 43 (30 requested) atoms. Cycle 12: After refmac, R = 0.2320 (Rfree = 0.000) for 7902 atoms. Found 45 (60 requested) and removed 36 (30 requested) atoms. Cycle 13: After refmac, R = 0.2214 (Rfree = 0.000) for 7893 atoms. Found 24 (59 requested) and removed 34 (29 requested) atoms. Cycle 14: After refmac, R = 0.2135 (Rfree = 0.000) for 7870 atoms. Found 17 (59 requested) and removed 31 (29 requested) atoms. Cycle 15: After refmac, R = 0.2109 (Rfree = 0.000) for 7844 atoms. Found 28 (59 requested) and removed 32 (29 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.33 2.83 Search for helices and strands: 0 residues in 0 chains, 8063 seeds are put forward NCS extension: 15 residues added (8 deleted due to clashes), 8078 seeds are put forward Round 1: 763 peptides, 85 chains. Longest chain 29 peptides. Score 0.608 Round 2: 811 peptides, 78 chains. Longest chain 33 peptides. Score 0.666 Round 3: 853 peptides, 72 chains. Longest chain 51 peptides. Score 0.711 Round 4: 830 peptides, 72 chains. Longest chain 37 peptides. Score 0.697 Round 5: 854 peptides, 75 chains. Longest chain 55 peptides. Score 0.702 Taking the results from Round 3 Chains 81, Residues 781, Estimated correctness of the model 60.7 % 11 chains (225 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 63 A and 66 A 80 chains (782 residues) following loop building 10 chains (227 residues) in sequence following loop building ------------------------------------------------------ 22185 reflections ( 99.66 % complete ) and 14367 restraints for refining 7957 atoms. 10420 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2421 (Rfree = 0.000) for 7957 atoms. Found 60 (60 requested) and removed 49 (30 requested) atoms. Cycle 17: After refmac, R = 0.2199 (Rfree = 0.000) for 7921 atoms. Found 30 (59 requested) and removed 39 (30 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2149 (Rfree = 0.000) for 7888 atoms. Found 19 (57 requested) and removed 34 (29 requested) atoms. Cycle 19: After refmac, R = 0.2114 (Rfree = 0.000) for 7859 atoms. Found 20 (55 requested) and removed 31 (29 requested) atoms. Cycle 20: After refmac, R = 0.2062 (Rfree = 0.000) for 7838 atoms. Found 16 (54 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.38 2.87 Search for helices and strands: 0 residues in 0 chains, 8038 seeds are put forward NCS extension: 44 residues added (9 deleted due to clashes), 8082 seeds are put forward Round 1: 788 peptides, 94 chains. Longest chain 23 peptides. Score 0.595 Round 2: 830 peptides, 76 chains. Longest chain 37 peptides. Score 0.684 Round 3: 818 peptides, 77 chains. Longest chain 54 peptides. Score 0.674 Round 4: 803 peptides, 77 chains. Longest chain 42 peptides. Score 0.664 Round 5: 832 peptides, 77 chains. Longest chain 48 peptides. Score 0.683 Taking the results from Round 2 Chains 83, Residues 754, Estimated correctness of the model 53.7 % 14 chains (226 residues) have been docked in sequence ------------------------------------------------------ 22185 reflections ( 99.66 % complete ) and 14463 restraints for refining 7957 atoms. 10459 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2378 (Rfree = 0.000) for 7957 atoms. Found 54 (54 requested) and removed 52 (30 requested) atoms. Cycle 22: After refmac, R = 0.2207 (Rfree = 0.000) for 7912 atoms. Found 36 (54 requested) and removed 35 (30 requested) atoms. Cycle 23: After refmac, R = 0.2132 (Rfree = 0.000) for 7898 atoms. Found 25 (53 requested) and removed 32 (29 requested) atoms. Cycle 24: After refmac, R = 0.2080 (Rfree = 0.000) for 7872 atoms. Found 25 (53 requested) and removed 35 (29 requested) atoms. Cycle 25: After refmac, R = 0.2011 (Rfree = 0.000) for 7851 atoms. Found 14 (53 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 2.82 Search for helices and strands: 0 residues in 0 chains, 8054 seeds are put forward NCS extension: 18 residues added (19 deleted due to clashes), 8072 seeds are put forward Round 1: 734 peptides, 96 chains. Longest chain 28 peptides. Score 0.544 Round 2: 795 peptides, 77 chains. Longest chain 37 peptides. Score 0.658 Round 3: 776 peptides, 84 chains. Longest chain 32 peptides. Score 0.621 Round 4: 803 peptides, 76 chains. Longest chain 40 peptides. Score 0.667 Round 5: 803 peptides, 75 chains. Longest chain 46 peptides. Score 0.670 Taking the results from Round 5 Chains 87, Residues 728, Estimated correctness of the model 49.8 % 15 chains (256 residues) have been docked in sequence ------------------------------------------------------ 22185 reflections ( 99.66 % complete ) and 14352 restraints for refining 7958 atoms. 10333 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2458 (Rfree = 0.000) for 7958 atoms. Found 54 (54 requested) and removed 60 (30 requested) atoms. Cycle 27: After refmac, R = 0.2267 (Rfree = 0.000) for 7910 atoms. Found 37 (54 requested) and removed 35 (30 requested) atoms. Cycle 28: After refmac, R = 0.2191 (Rfree = 0.000) for 7892 atoms. Found 33 (53 requested) and removed 32 (29 requested) atoms. Cycle 29: After refmac, R = 0.2141 (Rfree = 0.000) for 7882 atoms. Found 18 (53 requested) and removed 30 (29 requested) atoms. Cycle 30: After refmac, R = 0.2104 (Rfree = 0.000) for 7855 atoms. Found 21 (53 requested) and removed 32 (29 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.34 2.84 Search for helices and strands: 0 residues in 0 chains, 8028 seeds are put forward NCS extension: 24 residues added (14 deleted due to clashes), 8052 seeds are put forward Round 1: 751 peptides, 90 chains. Longest chain 25 peptides. Score 0.580 Round 2: 775 peptides, 79 chains. Longest chain 31 peptides. Score 0.637 Round 3: 788 peptides, 81 chains. Longest chain 36 peptides. Score 0.640 Round 4: 808 peptides, 79 chains. Longest chain 46 peptides. Score 0.660 Round 5: 773 peptides, 80 chains. Longest chain 27 peptides. Score 0.633 Taking the results from Round 4 Chains 86, Residues 729, Estimated correctness of the model 47.0 % 10 chains (172 residues) have been docked in sequence ------------------------------------------------------ 22185 reflections ( 99.66 % complete ) and 15006 restraints for refining 7958 atoms. 11383 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2448 (Rfree = 0.000) for 7958 atoms. Found 54 (54 requested) and removed 55 (30 requested) atoms. Cycle 32: After refmac, R = 0.2271 (Rfree = 0.000) for 7923 atoms. Found 30 (54 requested) and removed 39 (30 requested) atoms. Cycle 33: After refmac, R = 0.2193 (Rfree = 0.000) for 7900 atoms. Found 28 (53 requested) and removed 32 (29 requested) atoms. Cycle 34: After refmac, R = 0.2126 (Rfree = 0.000) for 7885 atoms. Found 21 (53 requested) and removed 31 (29 requested) atoms. Cycle 35: After refmac, R = 0.2120 (Rfree = 0.000) for 7867 atoms. Found 23 (53 requested) and removed 32 (29 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 2.85 Search for helices and strands: 0 residues in 0 chains, 8067 seeds are put forward NCS extension: 43 residues added (16 deleted due to clashes), 8110 seeds are put forward Round 1: 698 peptides, 84 chains. Longest chain 27 peptides. Score 0.560 Round 2: 778 peptides, 67 chains. Longest chain 51 peptides. Score 0.679 Round 3: 773 peptides, 72 chains. Longest chain 37 peptides. Score 0.659 Round 4: 766 peptides, 75 chains. Longest chain 51 peptides. Score 0.645 Round 5: 780 peptides, 73 chains. Longest chain 39 peptides. Score 0.661 Taking the results from Round 2 Chains 78, Residues 711, Estimated correctness of the model 52.3 % 11 chains (205 residues) have been docked in sequence ------------------------------------------------------ 22185 reflections ( 99.66 % complete ) and 14717 restraints for refining 7957 atoms. 11016 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2378 (Rfree = 0.000) for 7957 atoms. Found 54 (54 requested) and removed 55 (30 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2259 (Rfree = 0.000) for 7928 atoms. Found 32 (54 requested) and removed 35 (30 requested) atoms. Cycle 38: After refmac, R = 0.2161 (Rfree = 0.000) for 7915 atoms. Found 27 (53 requested) and removed 30 (29 requested) atoms. Cycle 39: After refmac, R = 0.2117 (Rfree = 0.000) for 7899 atoms. Found 29 (53 requested) and removed 29 (29 requested) atoms. Cycle 40: After refmac, R = 0.2091 (Rfree = 0.000) for 7891 atoms. Found 15 (53 requested) and removed 30 (29 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.35 2.85 Search for helices and strands: 0 residues in 0 chains, 8082 seeds are put forward NCS extension: 40 residues added (13 deleted due to clashes), 8122 seeds are put forward Round 1: 684 peptides, 87 chains. Longest chain 29 peptides. Score 0.536 Round 2: 732 peptides, 78 chains. Longest chain 46 peptides. Score 0.609 Round 3: 726 peptides, 79 chains. Longest chain 28 peptides. Score 0.601 Round 4: 741 peptides, 73 chains. Longest chain 43 peptides. Score 0.633 Round 5: 740 peptides, 77 chains. Longest chain 29 peptides. Score 0.619 Taking the results from Round 4 Chains 79, Residues 668, Estimated correctness of the model 39.1 % 7 chains (111 residues) have been docked in sequence ------------------------------------------------------ 22185 reflections ( 99.66 % complete ) and 15997 restraints for refining 7956 atoms. 12856 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2346 (Rfree = 0.000) for 7956 atoms. Found 54 (54 requested) and removed 43 (30 requested) atoms. Cycle 42: After refmac, R = 0.2243 (Rfree = 0.000) for 7943 atoms. Found 35 (54 requested) and removed 33 (30 requested) atoms. Cycle 43: After refmac, R = 0.2184 (Rfree = 0.000) for 7934 atoms. Found 36 (53 requested) and removed 31 (29 requested) atoms. Cycle 44: After refmac, R = 0.2111 (Rfree = 0.000) for 7924 atoms. Found 24 (53 requested) and removed 29 (29 requested) atoms. Cycle 45: After refmac, R = 0.2111 (Rfree = 0.000) for 7912 atoms. Found 43 (53 requested) and removed 30 (29 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 2.83 Search for helices and strands: 0 residues in 0 chains, 8132 seeds are put forward NCS extension: 21 residues added (2 deleted due to clashes), 8153 seeds are put forward Round 1: 649 peptides, 89 chains. Longest chain 27 peptides. Score 0.496 Round 2: 699 peptides, 75 chains. Longest chain 28 peptides. Score 0.594 Round 3: 708 peptides, 78 chains. Longest chain 29 peptides. Score 0.590 Round 4: 731 peptides, 77 chains. Longest chain 26 peptides. Score 0.612 Round 5: 745 peptides, 77 chains. Longest chain 26 peptides. Score 0.622 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 83, Residues 668, Estimated correctness of the model 35.7 % 10 chains (129 residues) have been docked in sequence Sequence coverage is 19 % Consider running further cycles of model building using 1vr5-3_warpNtrace.pdb as input Building loops using Loopy2018 83 chains (668 residues) following loop building 10 chains (129 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 22185 reflections ( 99.66 % complete ) and 15946 restraints for refining 7958 atoms. 12727 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2378 (Rfree = 0.000) for 7958 atoms. Found 0 (54 requested) and removed 30 (30 requested) atoms. Cycle 47: After refmac, R = 0.2280 (Rfree = 0.000) for 7898 atoms. Found 0 (53 requested) and removed 21 (29 requested) atoms. Cycle 48: After refmac, R = 0.2255 (Rfree = 0.000) for 7860 atoms. Found 0 (53 requested) and removed 17 (29 requested) atoms. Cycle 49: After refmac, R = 0.2222 (Rfree = 0.000) for 7834 atoms. TimeTaking 90.58