null Sun 23 Dec 22:23:05 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 2hti-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hti-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hti-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hti-3.2-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/2hti-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hti-3.2-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 22:23:13 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/2hti-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hti-3.2-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 126 and 0 Target number of residues in the AU: 126 Target solvent content: 0.6490 Checking the provided sequence file Detected sequence length: 185 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 185 Adjusted target solvent content: 0.48 Input MTZ file: 2hti-3.2-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: 178 Cell parameters: 72.007 72.007 129.790 90.000 90.000 120.000 Input sequence file: 2hti-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1480 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 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 Loops will be built when appropriate and at the last cycle Resolution range: 28.784 3.200 Wilson plot Bfac: 77.32 3622 reflections ( 99.37 % complete ) and 0 restraints for refining 1634 atoms. Observations/parameters ratio is 0.55 ------------------------------------------------------ Starting model: R = 0.3415 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2955 (Rfree = 0.000) for 1634 atoms. Found 10 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.42 3.51 Search for helices and strands: 0 residues in 0 chains, 1655 seeds are put forward Round 1: 72 peptides, 9 chains. Longest chain 14 peptides. Score 0.502 Round 2: 90 peptides, 10 chains. Longest chain 15 peptides. Score 0.594 Round 3: 102 peptides, 11 chains. Longest chain 20 peptides. Score 0.638 Round 4: 103 peptides, 9 chains. Longest chain 20 peptides. Score 0.695 Round 5: 107 peptides, 7 chains. Longest chain 27 peptides. Score 0.758 Taking the results from Round 5 Chains 7, Residues 100, Estimated correctness of the model 76.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3622 reflections ( 99.37 % complete ) and 2433 restraints for refining 1127 atoms. 2040 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3061 (Rfree = 0.000) for 1127 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 2: After refmac, R = 0.2945 (Rfree = 0.000) for 1104 atoms. Found 7 (10 requested) and removed 12 (5 requested) atoms. Cycle 3: After refmac, R = 0.3183 (Rfree = 0.000) for 1087 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 4: After refmac, R = 0.2957 (Rfree = 0.000) for 1065 atoms. Found 6 (8 requested) and removed 9 (4 requested) atoms. Cycle 5: After refmac, R = 0.2861 (Rfree = 0.000) for 1052 atoms. Found 6 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.38 3.47 Search for helices and strands: 0 residues in 0 chains, 1090 seeds are put forward Round 1: 107 peptides, 10 chains. Longest chain 20 peptides. Score 0.691 Round 2: 109 peptides, 11 chains. Longest chain 23 peptides. Score 0.677 Round 3: 100 peptides, 11 chains. Longest chain 20 peptides. Score 0.627 Round 4: 96 peptides, 10 chains. Longest chain 23 peptides. Score 0.631 Round 5: 98 peptides, 8 chains. Longest chain 26 peptides. Score 0.694 Taking the results from Round 5 Chains 9, Residues 90, Estimated correctness of the model 63.9 % 3 chains (56 residues) have been docked in sequence ------------------------------------------------------ 3622 reflections ( 99.37 % complete ) and 1892 restraints for refining 1117 atoms. 1330 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3129 (Rfree = 0.000) for 1117 atoms. Found 9 (9 requested) and removed 20 (5 requested) atoms. Cycle 7: After refmac, R = 0.2946 (Rfree = 0.000) for 1086 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 8: After refmac, R = 0.2654 (Rfree = 0.000) for 1065 atoms. Found 7 (8 requested) and removed 8 (4 requested) atoms. Cycle 9: After refmac, R = 0.2561 (Rfree = 0.000) for 1051 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 10: After refmac, R = 0.2593 (Rfree = 0.000) for 1047 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.39 3.48 Search for helices and strands: 0 residues in 0 chains, 1063 seeds are put forward Round 1: 101 peptides, 11 chains. Longest chain 18 peptides. Score 0.633 Round 2: 109 peptides, 8 chains. Longest chain 29 peptides. Score 0.745 Round 3: 107 peptides, 9 chains. Longest chain 30 peptides. Score 0.714 Round 4: 112 peptides, 8 chains. Longest chain 31 peptides. Score 0.758 Round 5: 102 peptides, 10 chains. Longest chain 23 peptides. Score 0.664 Taking the results from Round 4 Chains 10, Residues 104, Estimated correctness of the model 76.5 % 2 chains (45 residues) have been docked in sequence Building loops using Loopy2018 10 chains (104 residues) following loop building 2 chains (45 residues) in sequence following loop building ------------------------------------------------------ 3622 reflections ( 99.37 % complete ) and 1902 restraints for refining 1145 atoms. 1315 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3186 (Rfree = 0.000) for 1145 atoms. Found 9 (9 requested) and removed 26 (5 requested) atoms. Cycle 12: After refmac, R = 0.3110 (Rfree = 0.000) for 1109 atoms. Found 9 (9 requested) and removed 16 (5 requested) atoms. Cycle 13: After refmac, R = 0.2896 (Rfree = 0.000) for 1093 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 14: After refmac, R = 0.3101 (Rfree = 0.000) for 1081 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 15: After refmac, R = 0.2892 (Rfree = 0.000) for 1069 atoms. Found 5 (7 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.32 3.41 Search for helices and strands: 0 residues in 0 chains, 1108 seeds are put forward Round 1: 96 peptides, 10 chains. Longest chain 18 peptides. Score 0.631 Round 2: 106 peptides, 8 chains. Longest chain 29 peptides. Score 0.732 Round 3: 106 peptides, 9 chains. Longest chain 27 peptides. Score 0.709 Round 4: 110 peptides, 6 chains. Longest chain 36 peptides. Score 0.790 Round 5: 108 peptides, 8 chains. Longest chain 28 peptides. Score 0.741 Taking the results from Round 4 Chains 6, Residues 104, Estimated correctness of the model 81.9 % 3 chains (80 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 A and 52 A 5 chains (107 residues) following loop building 2 chains (83 residues) in sequence following loop building ------------------------------------------------------ 3622 reflections ( 99.37 % complete ) and 1563 restraints for refining 1169 atoms. 796 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3034 (Rfree = 0.000) for 1169 atoms. Found 8 (8 requested) and removed 27 (5 requested) atoms. Cycle 17: After refmac, R = 0.2880 (Rfree = 0.000) for 1141 atoms. Found 8 (8 requested) and removed 15 (5 requested) atoms. Cycle 18: After refmac, R = 0.2800 (Rfree = 0.000) for 1124 atoms. Found 7 (8 requested) and removed 10 (5 requested) atoms. Cycle 19: After refmac, R = 0.2687 (Rfree = 0.000) for 1109 atoms. Found 5 (7 requested) and removed 11 (5 requested) atoms. Cycle 20: After refmac, R = 0.2588 (Rfree = 0.000) for 1099 atoms. Found 6 (6 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.41 3.50 Search for helices and strands: 0 residues in 0 chains, 1140 seeds are put forward Round 1: 104 peptides, 9 chains. Longest chain 34 peptides. Score 0.700 Round 2: 107 peptides, 7 chains. Longest chain 35 peptides. Score 0.758 Round 3: 114 peptides, 10 chains. Longest chain 44 peptides. Score 0.724 Round 4: 111 peptides, 7 chains. Longest chain 51 peptides. Score 0.774 Round 5: 106 peptides, 6 chains. Longest chain 46 peptides. Score 0.775 Taking the results from Round 5 Chains 7, Residues 100, Estimated correctness of the model 79.4 % 3 chains (67 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 54 A and 64 A 5 chains (104 residues) following loop building 2 chains (76 residues) in sequence following loop building ------------------------------------------------------ 3622 reflections ( 99.37 % complete ) and 1651 restraints for refining 1172 atoms. 946 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2884 (Rfree = 0.000) for 1172 atoms. Found 7 (7 requested) and removed 30 (5 requested) atoms. Cycle 22: After refmac, R = 0.2700 (Rfree = 0.000) for 1141 atoms. Found 7 (7 requested) and removed 12 (5 requested) atoms. Cycle 23: After refmac, R = 0.2662 (Rfree = 0.000) for 1127 atoms. Found 7 (7 requested) and removed 8 (5 requested) atoms. Cycle 24: After refmac, R = 0.2820 (Rfree = 0.000) for 1118 atoms. Found 6 (6 requested) and removed 10 (5 requested) atoms. Cycle 25: After refmac, R = 0.2574 (Rfree = 0.000) for 1104 atoms. Found 6 (6 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.37 3.46 Search for helices and strands: 0 residues in 0 chains, 1133 seeds are put forward Round 1: 99 peptides, 7 chains. Longest chain 32 peptides. Score 0.723 Round 2: 96 peptides, 8 chains. Longest chain 33 peptides. Score 0.684 Round 3: 104 peptides, 7 chains. Longest chain 34 peptides. Score 0.746 Round 4: 103 peptides, 6 chains. Longest chain 32 peptides. Score 0.763 Round 5: 104 peptides, 7 chains. Longest chain 32 peptides. Score 0.746 Taking the results from Round 4 Chains 9, Residues 97, Estimated correctness of the model 77.4 % 3 chains (68 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 47 A and 52 A 7 chains (99 residues) following loop building 2 chains (72 residues) in sequence following loop building ------------------------------------------------------ 3622 reflections ( 99.37 % complete ) and 1674 restraints for refining 1171 atoms. 998 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3186 (Rfree = 0.000) for 1171 atoms. Found 6 (6 requested) and removed 27 (5 requested) atoms. Cycle 27: After refmac, R = 0.2879 (Rfree = 0.000) for 1144 atoms. Found 6 (6 requested) and removed 13 (5 requested) atoms. Cycle 28: After refmac, R = 0.2813 (Rfree = 0.000) for 1117 atoms. Found 6 (6 requested) and removed 10 (5 requested) atoms. Cycle 29: After refmac, R = 0.2565 (Rfree = 0.000) for 1107 atoms. Found 5 (5 requested) and removed 13 (4 requested) atoms. Cycle 30: After refmac, R = 0.2753 (Rfree = 0.000) for 1092 atoms. Found 5 (5 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.49 Search for helices and strands: 0 residues in 0 chains, 1139 seeds are put forward Round 1: 90 peptides, 10 chains. Longest chain 19 peptides. Score 0.594 Round 2: 114 peptides, 9 chains. Longest chain 31 peptides. Score 0.745 Round 3: 101 peptides, 9 chains. Longest chain 34 peptides. Score 0.684 Round 4: 108 peptides, 10 chains. Longest chain 27 peptides. Score 0.696 Round 5: 108 peptides, 8 chains. Longest chain 34 peptides. Score 0.741 Taking the results from Round 2 Chains 10, Residues 105, Estimated correctness of the model 74.1 % 3 chains (70 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 A and 52 A 9 chains (108 residues) following loop building 2 chains (73 residues) in sequence following loop building ------------------------------------------------------ 3622 reflections ( 99.37 % complete ) and 1650 restraints for refining 1176 atoms. 917 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3014 (Rfree = 0.000) for 1176 atoms. Found 5 (5 requested) and removed 23 (5 requested) atoms. Cycle 32: After refmac, R = 0.2616 (Rfree = 0.000) for 1152 atoms. Found 5 (5 requested) and removed 16 (5 requested) atoms. Cycle 33: After refmac, R = 0.2519 (Rfree = 0.000) for 1133 atoms. Found 5 (5 requested) and removed 12 (5 requested) atoms. Cycle 34: After refmac, R = 0.2156 (Rfree = 0.000) for 1118 atoms. Found 0 (5 requested) and removed 7 (5 requested) atoms. Cycle 35: After refmac, R = 0.2388 (Rfree = 0.000) for 1107 atoms. Found 4 (4 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.36 3.45 Search for helices and strands: 0 residues in 0 chains, 1144 seeds are put forward Round 1: 97 peptides, 10 chains. Longest chain 21 peptides. Score 0.637 Round 2: 98 peptides, 6 chains. Longest chain 34 peptides. Score 0.742 Round 3: 98 peptides, 8 chains. Longest chain 18 peptides. Score 0.694 Round 4: 102 peptides, 6 chains. Longest chain 57 peptides. Score 0.759 Round 5: 104 peptides, 5 chains. Longest chain 32 peptides. Score 0.788 Taking the results from Round 5 Chains 7, Residues 99, Estimated correctness of the model 81.6 % 3 chains (71 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 49 A and 52 A 5 chains (100 residues) following loop building 2 chains (73 residues) in sequence following loop building ------------------------------------------------------ 3622 reflections ( 99.37 % complete ) and 1782 restraints for refining 1187 atoms. 1084 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3376 (Rfree = 0.000) for 1187 atoms. Found 5 (5 requested) and removed 32 (5 requested) atoms. Cycle 37: After refmac, R = 0.2745 (Rfree = 0.000) for 1149 atoms. Found 5 (5 requested) and removed 15 (5 requested) atoms. Cycle 38: After refmac, R = 0.2769 (Rfree = 0.000) for 1134 atoms. Found 5 (5 requested) and removed 16 (5 requested) atoms. Cycle 39: After refmac, R = 0.2813 (Rfree = 0.000) for 1121 atoms. Found 5 (5 requested) and removed 10 (5 requested) atoms. Cycle 40: After refmac, R = 0.2676 (Rfree = 0.000) for 1106 atoms. Found 5 (5 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 3.40 Search for helices and strands: 0 residues in 0 chains, 1129 seeds are put forward Round 1: 103 peptides, 9 chains. Longest chain 19 peptides. Score 0.695 Round 2: 104 peptides, 6 chains. Longest chain 30 peptides. Score 0.767 Round 3: 108 peptides, 8 chains. Longest chain 29 peptides. Score 0.741 Round 4: 113 peptides, 8 chains. Longest chain 30 peptides. Score 0.762 Round 5: 102 peptides, 9 chains. Longest chain 19 peptides. Score 0.690 Taking the results from Round 2 Chains 7, Residues 98, Estimated correctness of the model 78.1 % 3 chains (71 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 44 A and 51 A 6 chains (104 residues) following loop building 2 chains (77 residues) in sequence following loop building ------------------------------------------------------ 3622 reflections ( 99.37 % complete ) and 1554 restraints for refining 1161 atoms. 817 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2708 (Rfree = 0.000) for 1161 atoms. Found 4 (5 requested) and removed 21 (5 requested) atoms. Cycle 42: After refmac, R = 0.2470 (Rfree = 0.000) for 1135 atoms. Found 5 (5 requested) and removed 9 (5 requested) atoms. Cycle 43: After refmac, R = 0.2374 (Rfree = 0.000) for 1130 atoms. Found 5 (5 requested) and removed 9 (5 requested) atoms. Cycle 44: After refmac, R = 0.2411 (Rfree = 0.000) for 1121 atoms. Found 5 (5 requested) and removed 9 (5 requested) atoms. Cycle 45: After refmac, R = 0.2239 (Rfree = 0.000) for 1110 atoms. Found 2 (5 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.36 3.45 Search for helices and strands: 0 residues in 0 chains, 1139 seeds are put forward Round 1: 102 peptides, 8 chains. Longest chain 28 peptides. Score 0.714 Round 2: 104 peptides, 7 chains. Longest chain 22 peptides. Score 0.746 Round 3: 111 peptides, 6 chains. Longest chain 37 peptides. Score 0.794 Round 4: 101 peptides, 8 chains. Longest chain 20 peptides. Score 0.709 Round 5: 105 peptides, 5 chains. Longest chain 29 peptides. Score 0.792 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 105, Estimated correctness of the model 82.5 % 3 chains (80 residues) have been docked in sequence Sequence coverage is 75 % Consider running further cycles of model building using 2hti-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 49 A and 52 A 5 chains (107 residues) following loop building 2 chains (82 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3622 reflections ( 99.37 % complete ) and 1606 restraints for refining 1187 atoms. 842 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3129 (Rfree = 0.000) for 1187 atoms. Found 0 (5 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2632 (Rfree = 0.000) for 1178 atoms. Found 0 (5 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2488 (Rfree = 0.000) for 1169 atoms. Found 0 (5 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2496 (Rfree = 0.000) for 1156 atoms. Found 0 (5 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:54:28 GMT 2018 Job finished. TimeTaking 31.39 Used memory is bytes: 11582536