Sun 23 Dec 22:22:49 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vr5-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vr5-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vr5-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr5-3.4-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/1vr5-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr5-3.4-parrot-hancs ############### 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 ============================================================ Sun 23 Dec 22:22:58 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/hancs/ArpWArp/wArpResults/WorkingDir/1vr5-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vr5-3.4-parrot-hancs/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-hancs.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-hancs.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 9644 atoms. Observations/parameters ratio is 0.58 ------------------------------------------------------ Starting model: R = 0.3100 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2925 (Rfree = 0.000) for 9644 atoms. Found 72 (72 requested) and removed 58 (36 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 2.83 Search for helices and strands: 0 residues in 0 chains, 9852 seeds are put forward NCS extension: 0 residues added, 9852 seeds are put forward Round 1: 702 peptides, 111 chains. Longest chain 18 peptides. Score 0.455 Round 2: 772 peptides, 87 chains. Longest chain 22 peptides. Score 0.608 Round 3: 791 peptides, 86 chains. Longest chain 22 peptides. Score 0.625 Round 4: 807 peptides, 74 chains. Longest chain 44 peptides. Score 0.676 Round 5: 833 peptides, 92 chains. Longest chain 29 peptides. Score 0.635 Taking the results from Round 4 Chains 80, Residues 733, Estimated correctness of the model 51.5 % 11 chains (266 residues) have been docked in sequence ------------------------------------------------------ 22185 reflections ( 99.66 % complete ) and 15570 restraints for refining 8574 atoms. 11473 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2491 (Rfree = 0.000) for 8574 atoms. Found 64 (64 requested) and removed 77 (32 requested) atoms. Cycle 2: After refmac, R = 0.2344 (Rfree = 0.000) for 8430 atoms. Found 56 (64 requested) and removed 58 (32 requested) atoms. Cycle 3: After refmac, R = 0.2194 (Rfree = 0.000) for 8382 atoms. Found 32 (63 requested) and removed 42 (31 requested) atoms. Cycle 4: After refmac, R = 0.2180 (Rfree = 0.000) for 8338 atoms. Found 26 (63 requested) and removed 41 (31 requested) atoms. Cycle 5: After refmac, R = 0.2147 (Rfree = 0.000) for 8299 atoms. Found 35 (62 requested) and removed 36 (31 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.32 2.82 Search for helices and strands: 0 residues in 0 chains, 8498 seeds are put forward NCS extension: 28 residues added (9 deleted due to clashes), 8526 seeds are put forward Round 1: 742 peptides, 90 chains. Longest chain 31 peptides. Score 0.573 Round 2: 811 peptides, 84 chains. Longest chain 45 peptides. Score 0.646 Round 3: 834 peptides, 77 chains. Longest chain 41 peptides. Score 0.684 Round 4: 828 peptides, 85 chains. Longest chain 41 peptides. Score 0.655 Round 5: 824 peptides, 83 chains. Longest chain 56 peptides. Score 0.658 Taking the results from Round 3 Chains 85, Residues 757, Estimated correctness of the model 53.7 % 12 chains (226 residues) have been docked in sequence ------------------------------------------------------ 22185 reflections ( 99.66 % complete ) and 14069 restraints for refining 7957 atoms. 10097 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2413 (Rfree = 0.000) for 7957 atoms. Found 60 (60 requested) and removed 55 (30 requested) atoms. Cycle 7: After refmac, R = 0.2250 (Rfree = 0.000) for 7901 atoms. Found 45 (60 requested) and removed 40 (30 requested) atoms. Cycle 8: After refmac, R = 0.2119 (Rfree = 0.000) for 7874 atoms. Found 36 (59 requested) and removed 33 (29 requested) atoms. Cycle 9: After refmac, R = 0.2048 (Rfree = 0.000) for 7859 atoms. Found 30 (59 requested) and removed 34 (29 requested) atoms. Cycle 10: After refmac, R = 0.1965 (Rfree = 0.000) for 7842 atoms. Found 22 (59 requested) and removed 31 (29 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.31 2.81 Search for helices and strands: 0 residues in 0 chains, 8037 seeds are put forward NCS extension: 27 residues added (11 deleted due to clashes), 8064 seeds are put forward Round 1: 787 peptides, 88 chains. Longest chain 25 peptides. Score 0.615 Round 2: 841 peptides, 77 chains. Longest chain 35 peptides. Score 0.688 Round 3: 846 peptides, 80 chains. Longest chain 30 peptides. Score 0.682 Round 4: 843 peptides, 79 chains. Longest chain 33 peptides. Score 0.684 Round 5: 848 peptides, 82 chains. Longest chain 41 peptides. Score 0.678 Taking the results from Round 2 Chains 83, Residues 764, Estimated correctness of the model 54.7 % 14 chains (255 residues) have been docked in sequence ------------------------------------------------------ 22185 reflections ( 99.66 % complete ) and 13792 restraints for refining 7958 atoms. 9666 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2316 (Rfree = 0.000) for 7958 atoms. Found 60 (60 requested) and removed 65 (30 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 12: After refmac, R = 0.2158 (Rfree = 0.000) for 7916 atoms. Found 37 (60 requested) and removed 46 (30 requested) atoms. Cycle 13: After refmac, R = 0.2127 (Rfree = 0.000) for 7891 atoms. Found 26 (59 requested) and removed 32 (29 requested) atoms. Cycle 14: After refmac, R = 0.2044 (Rfree = 0.000) for 7877 atoms. Found 19 (59 requested) and removed 32 (29 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2003 (Rfree = 0.000) for 7848 atoms. Found 16 (59 requested) and removed 33 (29 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.31 2.81 Search for helices and strands: 0 residues in 0 chains, 8049 seeds are put forward NCS extension: 10 residues added (11 deleted due to clashes), 8059 seeds are put forward Round 1: 763 peptides, 89 chains. Longest chain 35 peptides. Score 0.594 Round 2: 820 peptides, 77 chains. Longest chain 36 peptides. Score 0.675 Round 3: 805 peptides, 76 chains. Longest chain 27 peptides. Score 0.668 Round 4: 827 peptides, 76 chains. Longest chain 33 peptides. Score 0.682 Round 5: 809 peptides, 72 chains. Longest chain 47 peptides. Score 0.683 Taking the results from Round 5 Chains 86, Residues 737, Estimated correctness of the model 53.4 % 15 chains (247 residues) have been docked in sequence ------------------------------------------------------ 22185 reflections ( 99.66 % complete ) and 14263 restraints for refining 7957 atoms. 10329 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2435 (Rfree = 0.000) for 7957 atoms. Found 60 (60 requested) and removed 56 (30 requested) atoms. Cycle 17: After refmac, R = 0.2197 (Rfree = 0.000) for 7923 atoms. Found 32 (60 requested) and removed 30 (30 requested) atoms. Cycle 18: After refmac, R = 0.2180 (Rfree = 0.000) for 7910 atoms. Found 29 (59 requested) and removed 41 (29 requested) atoms. Cycle 19: After refmac, R = 0.2058 (Rfree = 0.000) for 7888 atoms. Found 20 (59 requested) and removed 32 (29 requested) atoms. Cycle 20: After refmac, R = 0.2030 (Rfree = 0.000) for 7874 atoms. Found 15 (59 requested) and removed 31 (29 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.33 2.83 Search for helices and strands: 0 residues in 0 chains, 8069 seeds are put forward NCS extension: 55 residues added (3 deleted due to clashes), 8124 seeds are put forward Round 1: 753 peptides, 83 chains. Longest chain 26 peptides. Score 0.607 Round 2: 812 peptides, 78 chains. Longest chain 32 peptides. Score 0.666 Round 3: 816 peptides, 80 chains. Longest chain 34 peptides. Score 0.663 Round 4: 805 peptides, 83 chains. Longest chain 31 peptides. Score 0.645 Round 5: 821 peptides, 75 chains. Longest chain 46 peptides. Score 0.682 Taking the results from Round 5 Chains 88, Residues 746, Estimated correctness of the model 53.1 % 13 chains (219 residues) have been docked in sequence ------------------------------------------------------ 22185 reflections ( 99.66 % complete ) and 14415 restraints for refining 7958 atoms. 10583 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2418 (Rfree = 0.000) for 7958 atoms. Found 57 (60 requested) and removed 48 (30 requested) atoms. Cycle 22: After refmac, R = 0.2215 (Rfree = 0.000) for 7923 atoms. Found 27 (60 requested) and removed 45 (30 requested) atoms. Cycle 23: After refmac, R = 0.2132 (Rfree = 0.000) for 7882 atoms. Found 16 (59 requested) and removed 36 (29 requested) atoms. Cycle 24: After refmac, R = 0.2117 (Rfree = 0.000) for 7852 atoms. Found 17 (59 requested) and removed 33 (29 requested) atoms. Cycle 25: After refmac, R = 0.2058 (Rfree = 0.000) for 7829 atoms. Found 17 (59 requested) and removed 31 (29 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.33 2.83 Search for helices and strands: 0 residues in 0 chains, 8040 seeds are put forward NCS extension: 19 residues added (14 deleted due to clashes), 8059 seeds are put forward Round 1: 732 peptides, 86 chains. Longest chain 25 peptides. Score 0.580 Round 2: 777 peptides, 82 chains. Longest chain 36 peptides. Score 0.629 Round 3: 793 peptides, 82 chains. Longest chain 35 peptides. Score 0.640 Round 4: 781 peptides, 80 chains. Longest chain 35 peptides. Score 0.638 Round 5: 795 peptides, 69 chains. Longest chain 43 peptides. Score 0.684 Taking the results from Round 5 Chains 76, Residues 726, Estimated correctness of the model 53.7 % 14 chains (187 residues) have been docked in sequence ------------------------------------------------------ 22185 reflections ( 99.66 % complete ) and 14920 restraints for refining 7957 atoms. 11274 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2436 (Rfree = 0.000) for 7957 atoms. Found 60 (60 requested) and removed 45 (30 requested) atoms. Cycle 27: After refmac, R = 0.2220 (Rfree = 0.000) for 7939 atoms. Found 24 (60 requested) and removed 35 (30 requested) atoms. Cycle 28: After refmac, R = 0.2171 (Rfree = 0.000) for 7916 atoms. Found 27 (59 requested) and removed 34 (29 requested) atoms. Cycle 29: After refmac, R = 0.2120 (Rfree = 0.000) for 7895 atoms. Found 27 (59 requested) and removed 31 (29 requested) atoms. Cycle 30: After refmac, R = 0.2071 (Rfree = 0.000) for 7883 atoms. Found 14 (59 requested) and removed 30 (29 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.34 2.84 Search for helices and strands: 0 residues in 0 chains, 8084 seeds are put forward NCS extension: 10 residues added (10 deleted due to clashes), 8094 seeds are put forward Round 1: 765 peptides, 96 chains. Longest chain 28 peptides. Score 0.570 Round 2: 793 peptides, 80 chains. Longest chain 35 peptides. Score 0.647 Round 3: 787 peptides, 79 chains. Longest chain 57 peptides. Score 0.646 Round 4: 775 peptides, 75 chains. Longest chain 29 peptides. Score 0.651 Round 5: 784 peptides, 78 chains. Longest chain 34 peptides. Score 0.647 Taking the results from Round 4 Chains 84, Residues 700, Estimated correctness of the model 44.4 % 8 chains (126 residues) have been docked in sequence ------------------------------------------------------ 22185 reflections ( 99.66 % complete ) and 15689 restraints for refining 7957 atoms. 12379 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2343 (Rfree = 0.000) for 7957 atoms. Found 60 (60 requested) and removed 44 (30 requested) atoms. Cycle 32: After refmac, R = 0.2233 (Rfree = 0.000) for 7943 atoms. Found 26 (60 requested) and removed 33 (30 requested) atoms. Cycle 33: After refmac, R = 0.2210 (Rfree = 0.000) for 7922 atoms. Found 28 (59 requested) and removed 29 (29 requested) atoms. Cycle 34: After refmac, R = 0.2159 (Rfree = 0.000) for 7916 atoms. Found 21 (59 requested) and removed 30 (29 requested) atoms. Cycle 35: After refmac, R = 0.2141 (Rfree = 0.000) for 7901 atoms. Found 27 (59 requested) and removed 29 (29 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 2.85 Search for helices and strands: 0 residues in 0 chains, 8104 seeds are put forward NCS extension: 16 residues added (4 deleted due to clashes), 8120 seeds are put forward Round 1: 708 peptides, 87 chains. Longest chain 27 peptides. Score 0.556 Round 2: 735 peptides, 81 chains. Longest chain 31 peptides. Score 0.601 Round 3: 755 peptides, 74 chains. Longest chain 50 peptides. Score 0.640 Round 4: 715 peptides, 71 chains. Longest chain 56 peptides. Score 0.621 Round 5: 734 peptides, 79 chains. Longest chain 24 peptides. Score 0.607 Taking the results from Round 3 Chains 79, Residues 681, Estimated correctness of the model 41.2 % 6 chains (81 residues) have been docked in sequence ------------------------------------------------------ 22185 reflections ( 99.66 % complete ) and 16504 restraints for refining 7958 atoms. 13524 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2294 (Rfree = 0.000) for 7958 atoms. Found 60 (60 requested) and removed 40 (30 requested) atoms. Cycle 37: After refmac, R = 0.2174 (Rfree = 0.000) for 7948 atoms. Found 22 (60 requested) and removed 34 (30 requested) atoms. Cycle 38: After refmac, R = 0.2171 (Rfree = 0.000) for 7922 atoms. Found 27 (59 requested) and removed 33 (29 requested) atoms. Cycle 39: After refmac, R = 0.2156 (Rfree = 0.000) for 7905 atoms. Found 37 (59 requested) and removed 32 (29 requested) atoms. Cycle 40: After refmac, R = 0.2023 (Rfree = 0.000) for 7901 atoms. Found 21 (59 requested) and removed 30 (29 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.36 2.85 Search for helices and strands: 0 residues in 0 chains, 8070 seeds are put forward NCS extension: 25 residues added (11 deleted due to clashes), 8095 seeds are put forward Round 1: 653 peptides, 90 chains. Longest chain 24 peptides. Score 0.496 Round 2: 717 peptides, 80 chains. Longest chain 50 peptides. Score 0.590 Round 3: 743 peptides, 83 chains. Longest chain 36 peptides. Score 0.600 Round 4: 715 peptides, 77 chains. Longest chain 27 peptides. Score 0.600 Round 5: 719 peptides, 77 chains. Longest chain 30 peptides. Score 0.603 Taking the results from Round 5 Chains 80, Residues 642, Estimated correctness of the model 29.7 % 10 chains (158 residues) have been docked in sequence ------------------------------------------------------ 22185 reflections ( 99.66 % complete ) and 15891 restraints for refining 7957 atoms. 12718 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2729 (Rfree = 0.000) for 7957 atoms. Found 60 (60 requested) and removed 72 (30 requested) atoms. Cycle 42: After refmac, R = 0.2265 (Rfree = 0.000) for 7917 atoms. Found 51 (59 requested) and removed 37 (29 requested) atoms. Cycle 43: After refmac, R = 0.2268 (Rfree = 0.000) for 7915 atoms. Found 41 (59 requested) and removed 40 (29 requested) atoms. Cycle 44: After refmac, R = 0.2036 (Rfree = 0.000) for 7902 atoms. Found 26 (59 requested) and removed 34 (29 requested) atoms. Cycle 45: After refmac, R = 0.1908 (Rfree = 0.000) for 7884 atoms. Found 16 (59 requested) and removed 35 (29 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.37 2.86 Search for helices and strands: 0 residues in 0 chains, 8101 seeds are put forward NCS extension: 21 residues added (8 deleted due to clashes), 8122 seeds are put forward Round 1: 662 peptides, 98 chains. Longest chain 30 peptides. Score 0.471 Round 2: 716 peptides, 79 chains. Longest chain 51 peptides. Score 0.593 Round 3: 742 peptides, 76 chains. Longest chain 35 peptides. Score 0.624 Round 4: 741 peptides, 80 chains. Longest chain 55 peptides. Score 0.609 Round 5: 738 peptides, 78 chains. Longest chain 35 peptides. Score 0.614 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 83, Residues 666, Estimated correctness of the model 36.3 % 9 chains (157 residues) have been docked in sequence Sequence coverage is 23 % Consider running further cycles of model building using 1vr5-3_warpNtrace.pdb as input Building loops using Loopy2018 83 chains (666 residues) following loop building 9 chains (157 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 22185 reflections ( 99.66 % complete ) and 15519 restraints for refining 7958 atoms. 12253 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2680 (Rfree = 0.000) for 7958 atoms. Found 0 (60 requested) and removed 30 (30 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2184 (Rfree = 0.000) for 7886 atoms. Found 0 (59 requested) and removed 29 (29 requested) atoms. Cycle 48: After refmac, R = 0.2123 (Rfree = 0.000) for 7832 atoms. Found 0 (59 requested) and removed 29 (29 requested) atoms. Cycle 49: After refmac, R = 0.2012 (Rfree = 0.000) for 7793 atoms. TimeTaking 114.82