Sun 23 Dec 22:22:46 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 1vpz-2.1-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vpz-2.1-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vpz-2.1-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpz-2.1-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/1vpz-2.1-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpz-2.1-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 22:22:54 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/1vpz-2.1-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpz-2.1-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 114 and 0 Target number of residues in the AU: 114 Target solvent content: 0.5492 Checking the provided sequence file Detected sequence length: 73 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 146 Adjusted target solvent content: 0.42 Input MTZ file: 1vpz-2.1-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: 20 Cell parameters: 49.075 56.647 98.468 90.000 90.000 90.000 Input sequence file: 1vpz-2.1-parrot-hancs.fasta_lf Building free atoms model in initial map for 1168 target number of atoms Had to go as low as 0.40 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 1 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: 24.580 2.051 Wilson plot Bfac: 35.03 8798 reflections ( 98.63 % complete ) and 0 restraints for refining 1290 atoms. Observations/parameters ratio is 1.71 ------------------------------------------------------ Starting model: R = 0.3568 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3534 (Rfree = 0.000) for 1290 atoms. Found 18 (41 requested) and removed 49 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.52 2.81 NCS extension: 0 residues added, 1259 seeds are put forward Round 1: 67 peptides, 11 chains. Longest chain 13 peptides. Score 0.455 Round 2: 72 peptides, 9 chains. Longest chain 17 peptides. Score 0.592 Round 3: 74 peptides, 8 chains. Longest chain 23 peptides. Score 0.647 Round 4: 78 peptides, 9 chains. Longest chain 16 peptides. Score 0.643 Round 5: 85 peptides, 6 chains. Longest chain 29 peptides. Score 0.783 Taking the results from Round 5 Chains 7, Residues 79, Estimated correctness of the model 95.3 % 2 chains (51 residues) have been docked in sequence Building loops using Loopy2018 7 chains (79 residues) following loop building 2 chains (51 residues) in sequence following loop building ------------------------------------------------------ 8798 reflections ( 98.63 % complete ) and 2015 restraints for refining 1127 atoms. 1528 conditional restraints added. Observations/parameters ratio is 1.95 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3807 (Rfree = 0.000) for 1127 atoms. Found 23 (35 requested) and removed 20 (17 requested) atoms. Cycle 2: After refmac, R = 0.3582 (Rfree = 0.000) for 1110 atoms. Found 16 (35 requested) and removed 30 (18 requested) atoms. Cycle 3: After refmac, R = 0.3543 (Rfree = 0.000) for 1076 atoms. Found 20 (33 requested) and removed 19 (17 requested) atoms. Cycle 4: After refmac, R = 0.3420 (Rfree = 0.000) for 1061 atoms. Found 18 (32 requested) and removed 24 (17 requested) atoms. Cycle 5: After refmac, R = 0.3177 (Rfree = 0.000) for 1044 atoms. Found 11 (30 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.39 2.66 NCS extension: 20 residues added (2 deleted due to clashes), 1059 seeds are put forward Round 1: 95 peptides, 8 chains. Longest chain 35 peptides. Score 0.783 Round 2: 102 peptides, 6 chains. Longest chain 37 peptides. Score 0.856 Round 3: 96 peptides, 5 chains. Longest chain 30 peptides. Score 0.854 Round 4: 99 peptides, 6 chains. Longest chain 51 peptides. Score 0.845 Round 5: 90 peptides, 6 chains. Longest chain 31 peptides. Score 0.807 Taking the results from Round 2 Chains 7, Residues 96, Estimated correctness of the model 97.8 % 3 chains (83 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 34 B and 38 B 5 chains (98 residues) following loop building 2 chains (86 residues) in sequence following loop building ------------------------------------------------------ 8798 reflections ( 98.63 % complete ) and 1401 restraints for refining 1078 atoms. 689 conditional restraints added. Observations/parameters ratio is 2.04 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3396 (Rfree = 0.000) for 1078 atoms. Found 18 (31 requested) and removed 24 (17 requested) atoms. Cycle 7: After refmac, R = 0.3194 (Rfree = 0.000) for 1069 atoms. Found 12 (30 requested) and removed 17 (17 requested) atoms. Cycle 8: After refmac, R = 0.3081 (Rfree = 0.000) for 1062 atoms. Found 20 (28 requested) and removed 16 (16 requested) atoms. Cycle 9: After refmac, R = 0.2964 (Rfree = 0.000) for 1065 atoms. Found 4 (28 requested) and removed 16 (16 requested) atoms. Cycle 10: After refmac, R = 0.2970 (Rfree = 0.000) for 1043 atoms. Found 10 (27 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.38 2.65 NCS extension: 18 residues added (2 deleted due to clashes), 1057 seeds are put forward Round 1: 106 peptides, 10 chains. Longest chain 27 peptides. Score 0.789 Round 2: 111 peptides, 5 chains. Longest chain 54 peptides. Score 0.898 Round 3: 106 peptides, 5 chains. Longest chain 38 peptides. Score 0.885 Round 4: 105 peptides, 6 chains. Longest chain 30 peptides. Score 0.865 Round 5: 107 peptides, 5 chains. Longest chain 55 peptides. Score 0.888 Taking the results from Round 2 Chains 5, Residues 106, Estimated correctness of the model 98.8 % 3 chains (100 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 38 B and 41 B 4 chains (108 residues) following loop building 2 chains (102 residues) in sequence following loop building ------------------------------------------------------ 8798 reflections ( 98.63 % complete ) and 1194 restraints for refining 1073 atoms. 374 conditional restraints added. Observations/parameters ratio is 2.05 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3052 (Rfree = 0.000) for 1073 atoms. Found 27 (27 requested) and removed 22 (17 requested) atoms. Cycle 12: After refmac, R = 0.2902 (Rfree = 0.000) for 1076 atoms. Found 6 (27 requested) and removed 18 (17 requested) atoms. Cycle 13: After refmac, R = 0.2804 (Rfree = 0.000) for 1058 atoms. Found 7 (25 requested) and removed 16 (16 requested) atoms. Cycle 14: After refmac, R = 0.2726 (Rfree = 0.000) for 1040 atoms. Found 7 (24 requested) and removed 13 (16 requested) atoms. Cycle 15: After refmac, R = 0.2644 (Rfree = 0.000) for 1031 atoms. Found 9 (23 requested) and removed 5 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.37 2.64 NCS extension: 8 residues added (2 deleted due to clashes), 1045 seeds are put forward Round 1: 106 peptides, 3 chains. Longest chain 54 peptides. Score 0.915 Round 2: 109 peptides, 5 chains. Longest chain 55 peptides. Score 0.893 Round 3: 108 peptides, 3 chains. Longest chain 54 peptides. Score 0.920 Round 4: 107 peptides, 3 chains. Longest chain 55 peptides. Score 0.918 Round 5: 111 peptides, 4 chains. Longest chain 41 peptides. Score 0.912 Taking the results from Round 3 Chains 3, Residues 105, Estimated correctness of the model 99.2 % 3 chains (105 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 34 B and 37 B 2 chains (107 residues) following loop building 2 chains (107 residues) in sequence following loop building ------------------------------------------------------ 8798 reflections ( 98.63 % complete ) and 1115 restraints for refining 1057 atoms. 267 conditional restraints added. Observations/parameters ratio is 2.08 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2911 (Rfree = 0.000) for 1057 atoms. Found 19 (23 requested) and removed 20 (16 requested) atoms. Cycle 17: After refmac, R = 0.2717 (Rfree = 0.000) for 1053 atoms. Found 11 (22 requested) and removed 16 (16 requested) atoms. Cycle 18: After refmac, R = 0.2593 (Rfree = 0.000) for 1043 atoms. Found 12 (22 requested) and removed 16 (16 requested) atoms. Cycle 19: After refmac, R = 0.2552 (Rfree = 0.000) for 1037 atoms. Found 6 (21 requested) and removed 16 (16 requested) atoms. Cycle 20: After refmac, R = 0.2486 (Rfree = 0.000) for 1026 atoms. Found 7 (20 requested) and removed 15 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.37 2.64 NCS extension: 6 residues added (1 deleted due to clashes), 1024 seeds are put forward Round 1: 109 peptides, 3 chains. Longest chain 54 peptides. Score 0.922 Round 2: 113 peptides, 5 chains. Longest chain 31 peptides. Score 0.903 Round 3: 114 peptides, 4 chains. Longest chain 56 peptides. Score 0.918 Round 4: 114 peptides, 4 chains. Longest chain 56 peptides. Score 0.918 Round 5: 112 peptides, 5 chains. Longest chain 55 peptides. Score 0.901 Taking the results from Round 1 Chains 3, Residues 106, Estimated correctness of the model 99.3 % 3 chains (106 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 37 B and 40 B 2 chains (108 residues) following loop building 2 chains (108 residues) in sequence following loop building ------------------------------------------------------ 8798 reflections ( 98.63 % complete ) and 1099 restraints for refining 1050 atoms. 240 conditional restraints added. Observations/parameters ratio is 2.09 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2848 (Rfree = 0.000) for 1050 atoms. Found 20 (20 requested) and removed 19 (16 requested) atoms. Cycle 22: After refmac, R = 0.2698 (Rfree = 0.000) for 1047 atoms. Found 13 (19 requested) and removed 16 (16 requested) atoms. Cycle 23: After refmac, R = 0.2630 (Rfree = 0.000) for 1040 atoms. Found 15 (18 requested) and removed 16 (16 requested) atoms. Cycle 24: After refmac, R = 0.2527 (Rfree = 0.000) for 1037 atoms. Found 10 (18 requested) and removed 14 (16 requested) atoms. Cycle 25: After refmac, R = 0.2485 (Rfree = 0.000) for 1032 atoms. Found 7 (17 requested) and removed 4 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.38 2.65 NCS extension: 2 residues added (2 deleted due to clashes), 1037 seeds are put forward Round 1: 106 peptides, 4 chains. Longest chain 28 peptides. Score 0.901 Round 2: 109 peptides, 2 chains. Longest chain 55 peptides. Score 0.935 Round 3: 109 peptides, 3 chains. Longest chain 55 peptides. Score 0.922 Round 4: 109 peptides, 3 chains. Longest chain 55 peptides. Score 0.922 Round 5: 111 peptides, 2 chains. Longest chain 56 peptides. Score 0.938 Taking the results from Round 5 Chains 3, Residues 109, Estimated correctness of the model 99.5 % 2 chains (108 residues) have been docked in sequence Building loops using Loopy2018 3 chains (109 residues) following loop building 2 chains (108 residues) in sequence following loop building ------------------------------------------------------ 8798 reflections ( 98.63 % complete ) and 1102 restraints for refining 1051 atoms. 240 conditional restraints added. Observations/parameters ratio is 2.09 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2792 (Rfree = 0.000) for 1051 atoms. Found 16 (16 requested) and removed 18 (16 requested) atoms. Cycle 27: After refmac, R = 0.2799 (Rfree = 0.000) for 1049 atoms. Found 16 (16 requested) and removed 16 (16 requested) atoms. Cycle 28: After refmac, R = 0.2627 (Rfree = 0.000) for 1049 atoms. Found 11 (16 requested) and removed 16 (16 requested) atoms. Cycle 29: After refmac, R = 0.2579 (Rfree = 0.000) for 1039 atoms. Found 14 (16 requested) and removed 8 (16 requested) atoms. Cycle 30: After refmac, R = 0.2552 (Rfree = 0.000) for 1041 atoms. Found 14 (16 requested) and removed 6 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.37 2.64 NCS extension: 7 residues added (1 deleted due to clashes), 1057 seeds are put forward Round 1: 105 peptides, 3 chains. Longest chain 51 peptides. Score 0.913 Round 2: 108 peptides, 4 chains. Longest chain 31 peptides. Score 0.906 Round 3: 109 peptides, 2 chains. Longest chain 55 peptides. Score 0.935 Round 4: 109 peptides, 7 chains. Longest chain 28 peptides. Score 0.861 Round 5: 113 peptides, 2 chains. Longest chain 58 peptides. Score 0.941 Taking the results from Round 5 Chains 2, Residues 111, Estimated correctness of the model 99.6 % 2 chains (111 residues) have been docked in sequence Building loops using Loopy2018 2 chains (111 residues) following loop building 2 chains (111 residues) in sequence following loop building ------------------------------------------------------ 8798 reflections ( 98.63 % complete ) and 1089 restraints for refining 1071 atoms. 208 conditional restraints added. Observations/parameters ratio is 2.05 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2828 (Rfree = 0.000) for 1071 atoms. Found 17 (17 requested) and removed 19 (17 requested) atoms. Cycle 32: After refmac, R = 0.2664 (Rfree = 0.000) for 1067 atoms. Found 15 (17 requested) and removed 17 (17 requested) atoms. Cycle 33: After refmac, R = 0.2555 (Rfree = 0.000) for 1060 atoms. Found 9 (16 requested) and removed 16 (16 requested) atoms. Cycle 34: After refmac, R = 0.2516 (Rfree = 0.000) for 1052 atoms. Found 12 (16 requested) and removed 16 (16 requested) atoms. Cycle 35: After refmac, R = 0.2448 (Rfree = 0.000) for 1047 atoms. Found 6 (16 requested) and removed 12 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.37 2.64 NCS extension: 0 residues added, 1041 seeds are put forward Round 1: 112 peptides, 3 chains. Longest chain 58 peptides. Score 0.927 Round 2: 115 peptides, 2 chains. Longest chain 60 peptides. Score 0.944 Round 3: 111 peptides, 4 chains. Longest chain 48 peptides. Score 0.912 Round 4: 114 peptides, 3 chains. Longest chain 55 peptides. Score 0.931 Round 5: 113 peptides, 3 chains. Longest chain 55 peptides. Score 0.929 Taking the results from Round 2 Chains 2, Residues 113, Estimated correctness of the model 99.6 % 2 chains (113 residues) have been docked in sequence Building loops using Loopy2018 2 chains (113 residues) following loop building 2 chains (113 residues) in sequence following loop building ------------------------------------------------------ 8798 reflections ( 98.63 % complete ) and 1061 restraints for refining 1066 atoms. 158 conditional restraints added. Observations/parameters ratio is 2.06 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2670 (Rfree = 0.000) for 1066 atoms. Found 16 (16 requested) and removed 17 (16 requested) atoms. Cycle 37: After refmac, R = 0.2530 (Rfree = 0.000) for 1065 atoms. Found 13 (16 requested) and removed 16 (16 requested) atoms. Cycle 38: After refmac, R = 0.2465 (Rfree = 0.000) for 1061 atoms. Found 12 (16 requested) and removed 16 (16 requested) atoms. Cycle 39: After refmac, R = 0.2413 (Rfree = 0.000) for 1056 atoms. Found 11 (16 requested) and removed 16 (16 requested) atoms. Cycle 40: After refmac, R = 0.2416 (Rfree = 0.000) for 1047 atoms. Found 16 (16 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.37 2.64 NCS extension: 4 residues added (0 deleted due to clashes), 1051 seeds are put forward Round 1: 110 peptides, 3 chains. Longest chain 56 peptides. Score 0.924 Round 2: 111 peptides, 3 chains. Longest chain 55 peptides. Score 0.925 Round 3: 109 peptides, 4 chains. Longest chain 45 peptides. Score 0.908 Round 4: 111 peptides, 3 chains. Longest chain 55 peptides. Score 0.925 Round 5: 112 peptides, 2 chains. Longest chain 57 peptides. Score 0.940 Taking the results from Round 5 Chains 2, Residues 110, Estimated correctness of the model 99.6 % 2 chains (110 residues) have been docked in sequence Building loops using Loopy2018 2 chains (110 residues) following loop building 2 chains (110 residues) in sequence following loop building ------------------------------------------------------ 8798 reflections ( 98.63 % complete ) and 1075 restraints for refining 1070 atoms. 199 conditional restraints added. Observations/parameters ratio is 2.06 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2646 (Rfree = 0.000) for 1070 atoms. Found 17 (17 requested) and removed 18 (17 requested) atoms. Cycle 42: After refmac, R = 0.2521 (Rfree = 0.000) for 1067 atoms. Found 15 (17 requested) and removed 17 (17 requested) atoms. Cycle 43: After refmac, R = 0.2438 (Rfree = 0.000) for 1063 atoms. Found 10 (16 requested) and removed 9 (16 requested) atoms. Cycle 44: After refmac, R = 0.2366 (Rfree = 0.000) for 1063 atoms. Found 11 (16 requested) and removed 5 (16 requested) atoms. Cycle 45: After refmac, R = 0.2334 (Rfree = 0.000) for 1065 atoms. Found 8 (17 requested) and removed 6 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.37 2.64 NCS extension: 4 residues added (0 deleted due to clashes), 1071 seeds are put forward Round 1: 110 peptides, 4 chains. Longest chain 31 peptides. Score 0.910 Round 2: 111 peptides, 3 chains. Longest chain 57 peptides. Score 0.925 Round 3: 114 peptides, 5 chains. Longest chain 30 peptides. Score 0.905 Round 4: 114 peptides, 4 chains. Longest chain 42 peptides. Score 0.918 Round 5: 116 peptides, 2 chains. Longest chain 61 peptides. Score 0.946 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 2, Residues 114, Estimated correctness of the model 99.6 % 2 chains (114 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 2 chains (114 residues) following loop building 2 chains (114 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 8798 reflections ( 98.63 % complete ) and 911 restraints for refining 903 atoms. Observations/parameters ratio is 2.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3056 (Rfree = 0.000) for 903 atoms. Found 3 (14 requested) and removed 0 (14 requested) atoms. Cycle 47: After refmac, R = 0.2868 (Rfree = 0.000) for 903 atoms. Found 3 (14 requested) and removed 0 (14 requested) atoms. Cycle 48: After refmac, R = 0.2744 (Rfree = 0.000) for 903 atoms. Found 1 (14 requested) and removed 1 (14 requested) atoms. Cycle 49: After refmac, R = 0.2670 (Rfree = 0.000) for 903 atoms. Found 0 (14 requested) and removed 2 (14 requested) atoms. Writing output files ... TimeTaking 26.75