Sun 23 Dec 22:22:43 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-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hti-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hti-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hti-4.0-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-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hti-4.0-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 22:22:53 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-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hti-4.0-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 120 and 0 Target number of residues in the AU: 120 Target solvent content: 0.6657 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-4.0-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-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1480 target number of atoms Had to go as low as 0.45 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 4.000 Wilson plot Bfac: 87.30 1908 reflections ( 99.22 % complete ) and 0 restraints for refining 1630 atoms. Observations/parameters ratio is 0.29 ------------------------------------------------------ Starting model: R = 0.3409 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3855 (Rfree = 0.000) for 1630 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.84 3.94 Search for helices and strands: 0 residues in 0 chains, 1648 seeds are put forward Round 1: 41 peptides, 9 chains. Longest chain 6 peptides. Score 0.224 Round 2: 48 peptides, 7 chains. Longest chain 11 peptides. Score 0.381 Round 3: 48 peptides, 7 chains. Longest chain 9 peptides. Score 0.381 Round 4: 62 peptides, 7 chains. Longest chain 19 peptides. Score 0.497 Round 5: 64 peptides, 8 chains. Longest chain 17 peptides. Score 0.476 Taking the results from Round 4 Chains 7, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1908 reflections ( 99.22 % complete ) and 3110 restraints for refining 1228 atoms. 2897 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3585 (Rfree = 0.000) for 1228 atoms. Found 5 (5 requested) and removed 12 (2 requested) atoms. Cycle 2: After refmac, R = 0.3597 (Rfree = 0.000) for 1176 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 3: After refmac, R = 0.3446 (Rfree = 0.000) for 1151 atoms. Found 5 (5 requested) and removed 9 (2 requested) atoms. Cycle 4: After refmac, R = 0.3586 (Rfree = 0.000) for 1128 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 5: After refmac, R = 0.3557 (Rfree = 0.000) for 1113 atoms. Found 5 (5 requested) and removed 11 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.69 3.79 Search for helices and strands: 0 residues in 0 chains, 1141 seeds are put forward Round 1: 58 peptides, 11 chains. Longest chain 10 peptides. Score 0.309 Round 2: 66 peptides, 11 chains. Longest chain 12 peptides. Score 0.381 Round 3: 78 peptides, 12 chains. Longest chain 14 peptides. Score 0.444 Round 4: 74 peptides, 10 chains. Longest chain 15 peptides. Score 0.483 Round 5: 72 peptides, 10 chains. Longest chain 15 peptides. Score 0.467 Taking the results from Round 4 Chains 10, Residues 64, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 1908 reflections ( 99.22 % complete ) and 2279 restraints for refining 1048 atoms. 1971 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3141 (Rfree = 0.000) for 1048 atoms. Found 4 (4 requested) and removed 23 (2 requested) atoms. Cycle 7: After refmac, R = 0.2812 (Rfree = 0.000) for 1008 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. Cycle 8: After refmac, R = 0.3160 (Rfree = 0.000) for 995 atoms. Found 2 (4 requested) and removed 11 (2 requested) atoms. Cycle 9: After refmac, R = 0.2790 (Rfree = 0.000) for 971 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. Cycle 10: After refmac, R = 0.2720 (Rfree = 0.000) for 959 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.69 3.79 Search for helices and strands: 0 residues in 0 chains, 1018 seeds are put forward Round 1: 62 peptides, 11 chains. Longest chain 12 peptides. Score 0.346 Round 2: 71 peptides, 11 chains. Longest chain 12 peptides. Score 0.423 Round 3: 76 peptides, 12 chains. Longest chain 15 peptides. Score 0.428 Round 4: 82 peptides, 10 chains. Longest chain 17 peptides. Score 0.541 Round 5: 71 peptides, 8 chains. Longest chain 17 peptides. Score 0.529 Taking the results from Round 4 Chains 10, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1908 reflections ( 99.22 % complete ) and 2231 restraints for refining 1010 atoms. 1953 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3044 (Rfree = 0.000) for 1010 atoms. Found 4 (4 requested) and removed 9 (2 requested) atoms. Cycle 12: After refmac, R = 0.2880 (Rfree = 0.000) for 989 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. Cycle 13: After refmac, R = 0.2817 (Rfree = 0.000) for 971 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 14: After refmac, R = 0.2826 (Rfree = 0.000) for 961 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 15: After refmac, R = 0.2754 (Rfree = 0.000) for 952 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.73 3.83 Search for helices and strands: 0 residues in 0 chains, 1006 seeds are put forward Round 1: 64 peptides, 12 chains. Longest chain 10 peptides. Score 0.325 Round 2: 70 peptides, 12 chains. Longest chain 11 peptides. Score 0.378 Round 3: 79 peptides, 11 chains. Longest chain 11 peptides. Score 0.486 Round 4: 70 peptides, 11 chains. Longest chain 10 peptides. Score 0.415 Round 5: 76 peptides, 10 chains. Longest chain 13 peptides. Score 0.498 Taking the results from Round 5 Chains 10, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1908 reflections ( 99.22 % complete ) and 2240 restraints for refining 1014 atoms. 1986 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2737 (Rfree = 0.000) for 1014 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. Cycle 17: After refmac, R = 0.2634 (Rfree = 0.000) for 998 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 18: After refmac, R = 0.2636 (Rfree = 0.000) for 986 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 19: After refmac, R = 0.2613 (Rfree = 0.000) for 974 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. Cycle 20: After refmac, R = 0.2526 (Rfree = 0.000) for 965 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.73 3.83 Search for helices and strands: 0 residues in 0 chains, 1024 seeds are put forward Round 1: 59 peptides, 10 chains. Longest chain 13 peptides. Score 0.358 Round 2: 69 peptides, 12 chains. Longest chain 9 peptides. Score 0.369 Round 3: 79 peptides, 11 chains. Longest chain 17 peptides. Score 0.486 Round 4: 65 peptides, 11 chains. Longest chain 9 peptides. Score 0.372 Round 5: 71 peptides, 10 chains. Longest chain 14 peptides. Score 0.459 Taking the results from Round 3 Chains 11, Residues 68, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1908 reflections ( 99.22 % complete ) and 2137 restraints for refining 1003 atoms. 1876 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2760 (Rfree = 0.000) for 1003 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. Cycle 22: After refmac, R = 0.2712 (Rfree = 0.000) for 990 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. Cycle 23: After refmac, R = 0.3320 (Rfree = 0.000) for 979 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 24: After refmac, R = 0.2626 (Rfree = 0.000) for 974 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 25: After refmac, R = 0.2736 (Rfree = 0.000) for 974 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.76 3.86 Search for helices and strands: 0 residues in 0 chains, 1023 seeds are put forward Round 1: 65 peptides, 12 chains. Longest chain 9 peptides. Score 0.334 Round 2: 70 peptides, 10 chains. Longest chain 20 peptides. Score 0.451 Round 3: 74 peptides, 11 chains. Longest chain 10 peptides. Score 0.448 Round 4: 73 peptides, 10 chains. Longest chain 14 peptides. Score 0.475 Round 5: 83 peptides, 11 chains. Longest chain 16 peptides. Score 0.516 Taking the results from Round 5 Chains 11, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1908 reflections ( 99.22 % complete ) and 2148 restraints for refining 1009 atoms. 1871 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3225 (Rfree = 0.000) for 1009 atoms. Found 4 (4 requested) and removed 14 (2 requested) atoms. Cycle 27: After refmac, R = 0.3070 (Rfree = 0.000) for 994 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. Cycle 28: After refmac, R = 0.2859 (Rfree = 0.000) for 987 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 29: After refmac, R = 0.2418 (Rfree = 0.000) for 979 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 30: After refmac, R = 0.2807 (Rfree = 0.000) for 976 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.83 3.93 Search for helices and strands: 0 residues in 0 chains, 1017 seeds are put forward Round 1: 67 peptides, 13 chains. Longest chain 8 peptides. Score 0.313 Round 2: 68 peptides, 10 chains. Longest chain 12 peptides. Score 0.435 Round 3: 75 peptides, 11 chains. Longest chain 13 peptides. Score 0.455 Round 4: 74 peptides, 11 chains. Longest chain 9 peptides. Score 0.448 Round 5: 76 peptides, 9 chains. Longest chain 13 peptides. Score 0.531 Taking the results from Round 5 Chains 9, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1908 reflections ( 99.22 % complete ) and 2384 restraints for refining 1058 atoms. 2125 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3362 (Rfree = 0.000) for 1058 atoms. Found 5 (5 requested) and removed 17 (2 requested) atoms. Cycle 32: After refmac, R = 0.2930 (Rfree = 0.000) for 1038 atoms. Found 4 (4 requested) and removed 11 (2 requested) atoms. Cycle 33: After refmac, R = 0.2849 (Rfree = 0.000) for 1030 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. Cycle 34: After refmac, R = 0.2983 (Rfree = 0.000) for 1021 atoms. Found 4 (4 requested) and removed 9 (2 requested) atoms. Cycle 35: After refmac, R = 0.2690 (Rfree = 0.000) for 1012 atoms. Found 2 (4 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.76 3.86 Search for helices and strands: 0 residues in 0 chains, 1049 seeds are put forward Round 1: 51 peptides, 11 chains. Longest chain 6 peptides. Score 0.241 Round 2: 58 peptides, 12 chains. Longest chain 8 peptides. Score 0.269 Round 3: 54 peptides, 10 chains. Longest chain 9 peptides. Score 0.312 Round 4: 63 peptides, 12 chains. Longest chain 10 peptides. Score 0.316 Round 5: 58 peptides, 10 chains. Longest chain 10 peptides. Score 0.349 Taking the results from Round 5 Chains 10, Residues 48, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1908 reflections ( 99.22 % complete ) and 2388 restraints for refining 1037 atoms. 2206 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3253 (Rfree = 0.000) for 1037 atoms. Found 4 (4 requested) and removed 16 (2 requested) atoms. Cycle 37: After refmac, R = 0.3004 (Rfree = 0.000) for 1019 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. Cycle 38: After refmac, R = 0.2482 (Rfree = 0.000) for 1005 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. Cycle 39: After refmac, R = 0.2946 (Rfree = 0.000) for 1003 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 40: After refmac, R = 0.2978 (Rfree = 0.000) for 994 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.77 3.87 Search for helices and strands: 0 residues in 0 chains, 1045 seeds are put forward Round 1: 46 peptides, 10 chains. Longest chain 7 peptides. Score 0.233 Round 2: 42 peptides, 9 chains. Longest chain 6 peptides. Score 0.235 Round 3: 50 peptides, 10 chains. Longest chain 8 peptides. Score 0.273 Round 4: 50 peptides, 10 chains. Longest chain 7 peptides. Score 0.273 Round 5: 40 peptides, 8 chains. Longest chain 6 peptides. Score 0.259 Taking the results from Round 4 Chains 10, Residues 40, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1908 reflections ( 99.22 % complete ) and 2221 restraints for refining 978 atoms. 2071 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3181 (Rfree = 0.000) for 978 atoms. Found 4 (4 requested) and removed 10 (2 requested) atoms. Cycle 42: After refmac, R = 0.3100 (Rfree = 0.000) for 963 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. Cycle 43: After refmac, R = 0.2979 (Rfree = 0.000) for 956 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 44: After refmac, R = 0.3133 (Rfree = 0.000) for 955 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. Cycle 45: After refmac, R = 0.2627 (Rfree = 0.000) for 945 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.77 3.87 Search for helices and strands: 0 residues in 0 chains, 995 seeds are put forward Round 1: 42 peptides, 10 chains. Longest chain 5 peptides. Score 0.189 Round 2: 53 peptides, 11 chains. Longest chain 9 peptides. Score 0.261 Round 3: 53 peptides, 12 chains. Longest chain 6 peptides. Score 0.219 Round 4: 56 peptides, 11 chains. Longest chain 9 peptides. Score 0.290 Round 5: 52 peptides, 11 chains. Longest chain 8 peptides. Score 0.251 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 45, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2hti-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1908 reflections ( 99.22 % complete ) and 2193 restraints for refining 964 atoms. 2024 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2691 (Rfree = 0.000) for 964 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2588 (Rfree = 0.000) for 960 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2524 (Rfree = 0.000) for 956 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2364 (Rfree = 0.000) for 952 atoms. TimeTaking 26.47