Sun 23 Dec 22:23:02 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-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hti-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hti-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hti-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/2hti-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hti-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 22:23:12 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-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hti-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 123 and 0 Target number of residues in the AU: 123 Target solvent content: 0.6573 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-3.4-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: 178 Cell parameters: 72.007 72.007 129.790 90.000 90.000 120.000 Input sequence file: 2hti-3.4-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 3.400 Wilson plot Bfac: 83.07 3043 reflections ( 99.31 % complete ) and 0 restraints for refining 1635 atoms. Observations/parameters ratio is 0.47 ------------------------------------------------------ Starting model: R = 0.3331 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3853 (Rfree = 0.000) for 1635 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.56 3.66 Search for helices and strands: 0 residues in 0 chains, 1649 seeds are put forward Round 1: 61 peptides, 10 chains. Longest chain 11 peptides. Score 0.376 Round 2: 81 peptides, 10 chains. Longest chain 15 peptides. Score 0.534 Round 3: 77 peptides, 9 chains. Longest chain 15 peptides. Score 0.538 Round 4: 80 peptides, 8 chains. Longest chain 17 peptides. Score 0.590 Round 5: 95 peptides, 8 chains. Longest chain 18 peptides. Score 0.678 Taking the results from Round 5 Chains 8, Residues 87, Estimated correctness of the model 52.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3043 reflections ( 99.31 % complete ) and 2583 restraints for refining 1146 atoms. 2243 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3847 (Rfree = 0.000) for 1146 atoms. Found 8 (8 requested) and removed 22 (4 requested) atoms. Cycle 2: After refmac, R = 0.3912 (Rfree = 0.000) for 1081 atoms. Found 5 (8 requested) and removed 20 (4 requested) atoms. Cycle 3: After refmac, R = 0.3598 (Rfree = 0.000) for 1050 atoms. Found 5 (8 requested) and removed 12 (4 requested) atoms. Cycle 4: After refmac, R = 0.3611 (Rfree = 0.000) for 1029 atoms. Found 6 (7 requested) and removed 8 (3 requested) atoms. Cycle 5: After refmac, R = 0.3506 (Rfree = 0.000) for 1020 atoms. Found 6 (7 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.57 3.67 Search for helices and strands: 0 residues in 0 chains, 1056 seeds are put forward Round 1: 71 peptides, 8 chains. Longest chain 13 peptides. Score 0.529 Round 2: 92 peptides, 10 chains. Longest chain 25 peptides. Score 0.607 Round 3: 102 peptides, 9 chains. Longest chain 25 peptides. Score 0.690 Round 4: 93 peptides, 7 chains. Longest chain 30 peptides. Score 0.694 Round 5: 84 peptides, 7 chains. Longest chain 28 peptides. Score 0.645 Taking the results from Round 4 Chains 7, Residues 86, Estimated correctness of the model 56.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3043 reflections ( 99.31 % complete ) and 2147 restraints for refining 1001 atoms. 1810 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3224 (Rfree = 0.000) for 1001 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 7: After refmac, R = 0.3170 (Rfree = 0.000) for 991 atoms. Found 5 (7 requested) and removed 9 (3 requested) atoms. Cycle 8: After refmac, R = 0.2993 (Rfree = 0.000) for 979 atoms. Found 4 (7 requested) and removed 11 (3 requested) atoms. Cycle 9: After refmac, R = 0.2888 (Rfree = 0.000) for 967 atoms. Found 6 (7 requested) and removed 6 (3 requested) atoms. Cycle 10: After refmac, R = 0.2805 (Rfree = 0.000) for 965 atoms. Found 4 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.49 3.58 Search for helices and strands: 0 residues in 0 chains, 1018 seeds are put forward Round 1: 85 peptides, 10 chains. Longest chain 19 peptides. Score 0.561 Round 2: 92 peptides, 9 chains. Longest chain 28 peptides. Score 0.635 Round 3: 95 peptides, 10 chains. Longest chain 25 peptides. Score 0.625 Round 4: 102 peptides, 10 chains. Longest chain 27 peptides. Score 0.664 Round 5: 91 peptides, 10 chains. Longest chain 21 peptides. Score 0.600 Taking the results from Round 4 Chains 11, Residues 92, Estimated correctness of the model 48.2 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3043 reflections ( 99.31 % complete ) and 1941 restraints for refining 1013 atoms. 1532 conditional restraints added. Observations/parameters ratio is 0.75 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3186 (Rfree = 0.000) for 1013 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 12: After refmac, R = 0.3187 (Rfree = 0.000) for 1000 atoms. Found 6 (7 requested) and removed 8 (3 requested) atoms. Cycle 13: After refmac, R = 0.2934 (Rfree = 0.000) for 987 atoms. Found 5 (7 requested) and removed 7 (3 requested) atoms. Cycle 14: After refmac, R = 0.2925 (Rfree = 0.000) for 971 atoms. Found 5 (7 requested) and removed 7 (3 requested) atoms. Cycle 15: After refmac, R = 0.3017 (Rfree = 0.000) for 958 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.58 3.68 Search for helices and strands: 0 residues in 0 chains, 1011 seeds are put forward Round 1: 84 peptides, 11 chains. Longest chain 18 peptides. Score 0.523 Round 2: 98 peptides, 9 chains. Longest chain 32 peptides. Score 0.669 Round 3: 98 peptides, 8 chains. Longest chain 29 peptides. Score 0.694 Round 4: 93 peptides, 10 chains. Longest chain 23 peptides. Score 0.613 Round 5: 98 peptides, 9 chains. Longest chain 29 peptides. Score 0.669 Taking the results from Round 3 Chains 8, Residues 90, Estimated correctness of the model 56.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3043 reflections ( 99.31 % complete ) and 2049 restraints for refining 1001 atoms. 1697 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3385 (Rfree = 0.000) for 1001 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 17: After refmac, R = 0.3270 (Rfree = 0.000) for 991 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 18: After refmac, R = 0.3180 (Rfree = 0.000) for 981 atoms. Found 3 (7 requested) and removed 3 (3 requested) atoms. Cycle 19: After refmac, R = 0.2890 (Rfree = 0.000) for 976 atoms. Found 6 (7 requested) and removed 5 (3 requested) atoms. Cycle 20: After refmac, R = 0.3106 (Rfree = 0.000) for 972 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.52 3.62 Search for helices and strands: 0 residues in 0 chains, 1028 seeds are put forward Round 1: 84 peptides, 12 chains. Longest chain 24 peptides. Score 0.490 Round 2: 90 peptides, 11 chains. Longest chain 23 peptides. Score 0.564 Round 3: 96 peptides, 11 chains. Longest chain 22 peptides. Score 0.603 Round 4: 99 peptides, 11 chains. Longest chain 24 peptides. Score 0.621 Round 5: 103 peptides, 10 chains. Longest chain 25 peptides. Score 0.670 Taking the results from Round 5 Chains 10, Residues 93, Estimated correctness of the model 49.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3043 reflections ( 99.31 % complete ) and 2277 restraints for refining 1088 atoms. 1915 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3431 (Rfree = 0.000) for 1088 atoms. Found 8 (8 requested) and removed 22 (4 requested) atoms. Cycle 22: After refmac, R = 0.3453 (Rfree = 0.000) for 1067 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 23: After refmac, R = 0.3266 (Rfree = 0.000) for 1058 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 24: After refmac, R = 0.3135 (Rfree = 0.000) for 1049 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 25: After refmac, R = 0.3249 (Rfree = 0.000) for 1044 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.54 3.64 Search for helices and strands: 0 residues in 0 chains, 1096 seeds are put forward Round 1: 79 peptides, 13 chains. Longest chain 14 peptides. Score 0.417 Round 2: 93 peptides, 14 chains. Longest chain 14 peptides. Score 0.491 Round 3: 99 peptides, 13 chains. Longest chain 14 peptides. Score 0.564 Round 4: 97 peptides, 12 chains. Longest chain 15 peptides. Score 0.580 Round 5: 95 peptides, 12 chains. Longest chain 14 peptides. Score 0.567 Taking the results from Round 4 Chains 13, Residues 85, Estimated correctness of the model 22.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3043 reflections ( 99.31 % complete ) and 2292 restraints for refining 1145 atoms. 1918 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3334 (Rfree = 0.000) for 1145 atoms. Found 8 (8 requested) and removed 22 (4 requested) atoms. Cycle 27: After refmac, R = 0.3031 (Rfree = 0.000) for 1120 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 28: After refmac, R = 0.3187 (Rfree = 0.000) for 1103 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 29: After refmac, R = 0.2946 (Rfree = 0.000) for 1087 atoms. Found 6 (8 requested) and removed 11 (4 requested) atoms. Cycle 30: After refmac, R = 0.3029 (Rfree = 0.000) for 1071 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.56 3.66 Search for helices and strands: 0 residues in 0 chains, 1109 seeds are put forward Round 1: 70 peptides, 10 chains. Longest chain 11 peptides. Score 0.451 Round 2: 78 peptides, 11 chains. Longest chain 11 peptides. Score 0.479 Round 3: 88 peptides, 13 chains. Longest chain 13 peptides. Score 0.487 Round 4: 83 peptides, 13 chains. Longest chain 12 peptides. Score 0.449 Round 5: 83 peptides, 12 chains. Longest chain 13 peptides. Score 0.483 Taking the results from Round 3 Chains 13, Residues 75, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3043 reflections ( 99.31 % complete ) and 2423 restraints for refining 1095 atoms. 2136 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3186 (Rfree = 0.000) for 1095 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 32: After refmac, R = 0.3104 (Rfree = 0.000) for 1085 atoms. Found 8 (8 requested) and removed 16 (4 requested) atoms. Cycle 33: After refmac, R = 0.2984 (Rfree = 0.000) for 1073 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 34: After refmac, R = 0.2946 (Rfree = 0.000) for 1071 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 35: After refmac, R = 0.2984 (Rfree = 0.000) for 1066 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.49 3.58 Search for helices and strands: 0 residues in 0 chains, 1116 seeds are put forward Round 1: 74 peptides, 13 chains. Longest chain 12 peptides. Score 0.375 Round 2: 78 peptides, 12 chains. Longest chain 13 peptides. Score 0.444 Round 3: 81 peptides, 11 chains. Longest chain 13 peptides. Score 0.501 Round 4: 80 peptides, 10 chains. Longest chain 13 peptides. Score 0.527 Round 5: 72 peptides, 9 chains. Longest chain 13 peptides. Score 0.502 Taking the results from Round 4 Chains 10, Residues 70, Estimated correctness of the model 3.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3043 reflections ( 99.31 % complete ) and 2443 restraints for refining 1112 atoms. 2173 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3065 (Rfree = 0.000) for 1112 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 37: After refmac, R = 0.3023 (Rfree = 0.000) for 1100 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 38: After refmac, R = 0.2902 (Rfree = 0.000) for 1094 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 39: After refmac, R = 0.2441 (Rfree = 0.000) for 1090 atoms. Found 8 (8 requested) and removed 5 (4 requested) atoms. Cycle 40: After refmac, R = 0.2360 (Rfree = 0.000) for 1091 atoms. Found 7 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.53 3.63 Search for helices and strands: 0 residues in 0 chains, 1127 seeds are put forward Round 1: 78 peptides, 14 chains. Longest chain 12 peptides. Score 0.373 Round 2: 93 peptides, 15 chains. Longest chain 21 peptides. Score 0.459 Round 3: 94 peptides, 14 chains. Longest chain 15 peptides. Score 0.499 Round 4: 83 peptides, 13 chains. Longest chain 10 peptides. Score 0.449 Round 5: 87 peptides, 13 chains. Longest chain 12 peptides. Score 0.479 Taking the results from Round 3 Chains 14, Residues 80, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3043 reflections ( 99.31 % complete ) and 2231 restraints for refining 1119 atoms. 1894 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3071 (Rfree = 0.000) for 1119 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. Cycle 42: After refmac, R = 0.2921 (Rfree = 0.000) for 1103 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 43: After refmac, R = 0.2842 (Rfree = 0.000) for 1102 atoms. Found 8 (8 requested) and removed 15 (4 requested) atoms. Cycle 44: After refmac, R = 0.2700 (Rfree = 0.000) for 1084 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 45: After refmac, R = 0.2859 (Rfree = 0.000) for 1073 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.49 3.58 Search for helices and strands: 0 residues in 0 chains, 1137 seeds are put forward Round 1: 65 peptides, 10 chains. Longest chain 10 peptides. Score 0.410 Round 2: 76 peptides, 11 chains. Longest chain 17 peptides. Score 0.463 Round 3: 84 peptides, 11 chains. Longest chain 16 peptides. Score 0.523 Round 4: 79 peptides, 10 chains. Longest chain 17 peptides. Score 0.520 Round 5: 79 peptides, 9 chains. Longest chain 17 peptides. Score 0.552 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 9, Residues 70, Estimated correctness of the model 12.2 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2hti-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3043 reflections ( 99.31 % complete ) and 2265 restraints for refining 1084 atoms. 1994 conditional restraints added. Observations/parameters ratio is 0.70 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2902 (Rfree = 0.000) for 1084 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.3038 (Rfree = 0.000) for 1074 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2996 (Rfree = 0.000) for 1067 atoms. Found 0 (8 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.3115 (Rfree = 0.000) for 1059 atoms. TimeTaking 28.85