Sun 23 Dec 22:22:53 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 2hhz-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hhz-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hhz-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hhz-3.6-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/2hhz-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hhz-3.6-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 22:23:03 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/2hhz-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hhz-3.6-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 95 and 0 Target number of residues in the AU: 95 Target solvent content: 0.6511 Checking the provided sequence file Detected sequence length: 150 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 150 Adjusted target solvent content: 0.45 Input MTZ file: 2hhz-3.6-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: 96 Cell parameters: 71.030 71.030 58.410 90.000 90.000 90.000 Input sequence file: 2hhz-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1200 target number of atoms Had to go as low as 0.75 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: 50.226 3.601 Wilson plot Bfac: 76.65 1924 reflections ( 99.48 % complete ) and 0 restraints for refining 1331 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3438 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3169 (Rfree = 0.000) for 1331 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.51 3.75 Search for helices and strands: 0 residues in 0 chains, 1354 seeds are put forward Round 1: 64 peptides, 12 chains. Longest chain 8 peptides. Score 0.361 Round 2: 79 peptides, 13 chains. Longest chain 9 peptides. Score 0.474 Round 3: 76 peptides, 12 chains. Longest chain 13 peptides. Score 0.486 Round 4: 80 peptides, 13 chains. Longest chain 9 peptides. Score 0.483 Round 5: 76 peptides, 12 chains. Longest chain 10 peptides. Score 0.486 Taking the results from Round 5 Chains 12, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1924 reflections ( 99.48 % complete ) and 2554 restraints for refining 1088 atoms. 2310 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2557 (Rfree = 0.000) for 1088 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 2: After refmac, R = 0.2324 (Rfree = 0.000) for 1068 atoms. Found 5 (6 requested) and removed 6 (3 requested) atoms. Cycle 3: After refmac, R = 0.2383 (Rfree = 0.000) for 1054 atoms. Found 4 (6 requested) and removed 5 (3 requested) atoms. Cycle 4: After refmac, R = 0.2399 (Rfree = 0.000) for 1048 atoms. Found 4 (6 requested) and removed 5 (3 requested) atoms. Cycle 5: After refmac, R = 0.2252 (Rfree = 0.000) for 1039 atoms. Found 1 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 3.70 Search for helices and strands: 0 residues in 0 chains, 1065 seeds are put forward Round 1: 57 peptides, 10 chains. Longest chain 12 peptides. Score 0.379 Round 2: 70 peptides, 11 chains. Longest chain 12 peptides. Score 0.470 Round 3: 73 peptides, 13 chains. Longest chain 13 peptides. Score 0.413 Round 4: 82 peptides, 11 chains. Longest chain 17 peptides. Score 0.580 Round 5: 79 peptides, 11 chains. Longest chain 15 peptides. Score 0.554 Taking the results from Round 4 Chains 11, Residues 71, Estimated correctness of the model 6.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1924 reflections ( 99.48 % complete ) and 2223 restraints for refining 1009 atoms. 1950 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2804 (Rfree = 0.000) for 1009 atoms. Found 6 (6 requested) and removed 21 (3 requested) atoms. Cycle 7: After refmac, R = 0.2302 (Rfree = 0.000) for 989 atoms. Found 3 (6 requested) and removed 6 (3 requested) atoms. Cycle 8: After refmac, R = 0.2187 (Rfree = 0.000) for 981 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Cycle 9: After refmac, R = 0.2058 (Rfree = 0.000) for 977 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 10: After refmac, R = 0.2040 (Rfree = 0.000) for 972 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.44 3.68 Search for helices and strands: 0 residues in 0 chains, 1001 seeds are put forward Round 1: 65 peptides, 12 chains. Longest chain 9 peptides. Score 0.372 Round 2: 76 peptides, 12 chains. Longest chain 21 peptides. Score 0.486 Round 3: 70 peptides, 10 chains. Longest chain 17 peptides. Score 0.513 Round 4: 82 peptides, 12 chains. Longest chain 14 peptides. Score 0.542 Round 5: 82 peptides, 11 chains. Longest chain 20 peptides. Score 0.580 Taking the results from Round 5 Chains 11, Residues 71, Estimated correctness of the model 6.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1924 reflections ( 99.48 % complete ) and 2185 restraints for refining 1017 atoms. 1912 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2225 (Rfree = 0.000) for 1017 atoms. Found 1 (6 requested) and removed 9 (3 requested) atoms. Cycle 12: After refmac, R = 0.2026 (Rfree = 0.000) for 1003 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Cycle 13: After refmac, R = 0.1972 (Rfree = 0.000) for 998 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. Cycle 14: After refmac, R = 0.2008 (Rfree = 0.000) for 993 atoms. Found 3 (6 requested) and removed 10 (3 requested) atoms. Cycle 15: After refmac, R = 0.2041 (Rfree = 0.000) for 986 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.54 3.78 Search for helices and strands: 0 residues in 0 chains, 1019 seeds are put forward Round 1: 65 peptides, 13 chains. Longest chain 9 peptides. Score 0.325 Round 2: 61 peptides, 10 chains. Longest chain 10 peptides. Score 0.422 Round 3: 75 peptides, 10 chains. Longest chain 15 peptides. Score 0.558 Round 4: 68 peptides, 10 chains. Longest chain 11 peptides. Score 0.494 Round 5: 73 peptides, 10 chains. Longest chain 12 peptides. Score 0.540 Taking the results from Round 3 Chains 10, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1924 reflections ( 99.48 % complete ) and 2293 restraints for refining 1024 atoms. 2043 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2207 (Rfree = 0.000) for 1024 atoms. Found 3 (6 requested) and removed 7 (3 requested) atoms. Cycle 17: After refmac, R = 0.2104 (Rfree = 0.000) for 1017 atoms. Found 3 (6 requested) and removed 6 (3 requested) atoms. Cycle 18: After refmac, R = 0.2249 (Rfree = 0.000) for 1013 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 19: After refmac, R = 0.2151 (Rfree = 0.000) for 1009 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 20: After refmac, R = 0.2126 (Rfree = 0.000) for 1006 atoms. Found 2 (6 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.57 3.82 Search for helices and strands: 0 residues in 0 chains, 1034 seeds are put forward Round 1: 68 peptides, 14 chains. Longest chain 8 peptides. Score 0.312 Round 2: 74 peptides, 12 chains. Longest chain 9 peptides. Score 0.467 Round 3: 61 peptides, 12 chains. Longest chain 11 peptides. Score 0.327 Round 4: 63 peptides, 12 chains. Longest chain 10 peptides. Score 0.350 Round 5: 70 peptides, 12 chains. Longest chain 11 peptides. Score 0.426 Taking the results from Round 2 Chains 12, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1924 reflections ( 99.48 % complete ) and 2376 restraints for refining 1039 atoms. 2140 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2374 (Rfree = 0.000) for 1039 atoms. Found 6 (6 requested) and removed 12 (3 requested) atoms. Cycle 22: After refmac, R = 0.2230 (Rfree = 0.000) for 1028 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 23: After refmac, R = 0.1990 (Rfree = 0.000) for 1015 atoms. Found 5 (6 requested) and removed 5 (3 requested) atoms. Cycle 24: After refmac, R = 0.2148 (Rfree = 0.000) for 1013 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 25: After refmac, R = 0.2074 (Rfree = 0.000) for 1012 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.47 3.71 Search for helices and strands: 0 residues in 0 chains, 1044 seeds are put forward Round 1: 55 peptides, 13 chains. Longest chain 6 peptides. Score 0.205 Round 2: 63 peptides, 11 chains. Longest chain 13 peptides. Score 0.397 Round 3: 64 peptides, 11 chains. Longest chain 13 peptides. Score 0.408 Round 4: 67 peptides, 11 chains. Longest chain 10 peptides. Score 0.440 Round 5: 63 peptides, 11 chains. Longest chain 9 peptides. Score 0.397 Taking the results from Round 4 Chains 11, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1924 reflections ( 99.48 % complete ) and 2358 restraints for refining 1049 atoms. 2145 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2328 (Rfree = 0.000) for 1049 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 27: After refmac, R = 0.2194 (Rfree = 0.000) for 1044 atoms. Found 5 (6 requested) and removed 4 (3 requested) atoms. Cycle 28: After refmac, R = 0.2028 (Rfree = 0.000) for 1043 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 29: After refmac, R = 0.2100 (Rfree = 0.000) for 1043 atoms. Found 4 (6 requested) and removed 4 (3 requested) atoms. Cycle 30: After refmac, R = 0.1976 (Rfree = 0.000) for 1040 atoms. Found 5 (6 requested) and removed 18 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.45 3.69 Search for helices and strands: 0 residues in 0 chains, 1069 seeds are put forward Round 1: 56 peptides, 13 chains. Longest chain 6 peptides. Score 0.217 Round 2: 62 peptides, 11 chains. Longest chain 9 peptides. Score 0.386 Round 3: 65 peptides, 13 chains. Longest chain 8 peptides. Score 0.325 Round 4: 70 peptides, 13 chains. Longest chain 8 peptides. Score 0.381 Round 5: 73 peptides, 14 chains. Longest chain 9 peptides. Score 0.368 Taking the results from Round 2 Chains 11, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1924 reflections ( 99.48 % complete ) and 2403 restraints for refining 1045 atoms. 2210 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1959 (Rfree = 0.000) for 1045 atoms. Found 3 (6 requested) and removed 20 (3 requested) atoms. Cycle 32: After refmac, R = 0.2111 (Rfree = 0.000) for 1024 atoms. Found 5 (6 requested) and removed 10 (3 requested) atoms. Cycle 33: After refmac, R = 0.1783 (Rfree = 0.000) for 1019 atoms. Found 4 (6 requested) and removed 6 (3 requested) atoms. Cycle 34: After refmac, R = 0.1791 (Rfree = 0.000) for 1017 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 35: After refmac, R = 0.1372 (Rfree = 0.000) for 1016 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.48 3.72 Search for helices and strands: 0 residues in 0 chains, 1039 seeds are put forward Round 1: 57 peptides, 11 chains. Longest chain 10 peptides. Score 0.330 Round 2: 60 peptides, 11 chains. Longest chain 8 peptides. Score 0.364 Round 3: 61 peptides, 10 chains. Longest chain 12 peptides. Score 0.422 Round 4: 60 peptides, 11 chains. Longest chain 8 peptides. Score 0.364 Round 5: 68 peptides, 12 chains. Longest chain 9 peptides. Score 0.405 Taking the results from Round 3 Chains 10, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1924 reflections ( 99.48 % complete ) and 2457 restraints for refining 1062 atoms. 2263 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2124 (Rfree = 0.000) for 1062 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 37: After refmac, R = 0.2342 (Rfree = 0.000) for 1057 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. Cycle 38: After refmac, R = 0.2139 (Rfree = 0.000) for 1047 atoms. Found 2 (6 requested) and removed 9 (3 requested) atoms. Cycle 39: After refmac, R = 0.1917 (Rfree = 0.000) for 1037 atoms. Found 1 (6 requested) and removed 9 (3 requested) atoms. Cycle 40: After refmac, R = 0.1944 (Rfree = 0.000) for 1023 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.45 3.69 Search for helices and strands: 0 residues in 0 chains, 1049 seeds are put forward Round 1: 44 peptides, 9 chains. Longest chain 6 peptides. Score 0.275 Round 2: 62 peptides, 12 chains. Longest chain 7 peptides. Score 0.339 Round 3: 64 peptides, 12 chains. Longest chain 10 peptides. Score 0.361 Round 4: 58 peptides, 10 chains. Longest chain 9 peptides. Score 0.390 Round 5: 53 peptides, 10 chains. Longest chain 8 peptides. Score 0.333 Taking the results from Round 4 Chains 10, Residues 48, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1924 reflections ( 99.48 % complete ) and 2405 restraints for refining 1054 atoms. 2223 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2589 (Rfree = 0.000) for 1054 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 42: After refmac, R = 0.2369 (Rfree = 0.000) for 1048 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 43: After refmac, R = 0.2084 (Rfree = 0.000) for 1046 atoms. Found 6 (6 requested) and removed 11 (3 requested) atoms. Cycle 44: After refmac, R = 0.2317 (Rfree = 0.000) for 1040 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. Cycle 45: After refmac, R = 0.1900 (Rfree = 0.000) for 1031 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.44 3.68 Search for helices and strands: 0 residues in 0 chains, 1056 seeds are put forward Round 1: 50 peptides, 11 chains. Longest chain 6 peptides. Score 0.245 Round 2: 56 peptides, 10 chains. Longest chain 9 peptides. Score 0.367 Round 3: 62 peptides, 8 chains. Longest chain 13 peptides. Score 0.522 Round 4: 60 peptides, 9 chains. Longest chain 10 peptides. Score 0.458 Round 5: 59 peptides, 11 chains. Longest chain 7 peptides. Score 0.353 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 54, 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 2hhz-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1924 reflections ( 99.48 % complete ) and 2309 restraints for refining 1030 atoms. 2101 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1973 (Rfree = 0.000) for 1030 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.1895 (Rfree = 0.000) for 1025 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1845 (Rfree = 0.000) for 1020 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.1856 (Rfree = 0.000) for 1015 atoms. TimeTaking 24.05