null Sun 23 Dec 22:22:52 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 2huh-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2huh-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2huh-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2huh-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/2huh-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2huh-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 22:23:00 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/2huh-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2huh-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 99 and 0 Target number of residues in the AU: 99 Target solvent content: 0.6537 Checking the provided sequence file Detected sequence length: 147 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 147 Adjusted target solvent content: 0.49 Input MTZ file: 2huh-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: 43.026 43.026 167.168 90.000 90.000 90.000 Input sequence file: 2huh-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1176 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: 41.792 3.601 Wilson plot Bfac: 78.45 2104 reflections ( 99.67 % complete ) and 0 restraints for refining 1296 atoms. Observations/parameters ratio is 0.41 ------------------------------------------------------ Starting model: R = 0.3577 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3027 (Rfree = 0.000) for 1296 atoms. Found 8 (8 requested) and removed 19 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.53 3.58 Search for helices and strands: 0 residues in 0 chains, 1304 seeds are put forward Round 1: 75 peptides, 15 chains. Longest chain 9 peptides. Score 0.337 Round 2: 98 peptides, 16 chains. Longest chain 10 peptides. Score 0.518 Round 3: 85 peptides, 12 chains. Longest chain 16 peptides. Score 0.555 Round 4: 87 peptides, 13 chains. Longest chain 12 peptides. Score 0.534 Round 5: 91 peptides, 9 chains. Longest chain 17 peptides. Score 0.696 Taking the results from Round 5 Chains 9, Residues 82, Estimated correctness of the model 48.3 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2104 reflections ( 99.67 % complete ) and 2278 restraints for refining 1065 atoms. 1939 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2568 (Rfree = 0.000) for 1065 atoms. Found 3 (6 requested) and removed 12 (3 requested) atoms. Cycle 2: After refmac, R = 0.2375 (Rfree = 0.000) for 1046 atoms. Found 1 (6 requested) and removed 6 (3 requested) atoms. Cycle 3: After refmac, R = 0.2247 (Rfree = 0.000) for 1037 atoms. Found 2 (6 requested) and removed 8 (3 requested) atoms. Cycle 4: After refmac, R = 0.2194 (Rfree = 0.000) for 1029 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. Cycle 5: After refmac, R = 0.2137 (Rfree = 0.000) for 1026 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.58 3.63 Search for helices and strands: 0 residues in 0 chains, 1057 seeds are put forward Round 1: 83 peptides, 16 chains. Longest chain 10 peptides. Score 0.377 Round 2: 89 peptides, 14 chains. Longest chain 13 peptides. Score 0.514 Round 3: 82 peptides, 10 chains. Longest chain 20 peptides. Score 0.602 Round 4: 84 peptides, 11 chains. Longest chain 13 peptides. Score 0.583 Round 5: 86 peptides, 12 chains. Longest chain 13 peptides. Score 0.563 Taking the results from Round 3 Chains 10, Residues 72, Estimated correctness of the model 15.4 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 2104 reflections ( 99.67 % complete ) and 2220 restraints for refining 1066 atoms. 1866 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2564 (Rfree = 0.000) for 1066 atoms. Found 4 (6 requested) and removed 21 (3 requested) atoms. Cycle 7: After refmac, R = 0.2353 (Rfree = 0.000) for 1042 atoms. Found 3 (6 requested) and removed 6 (3 requested) atoms. Cycle 8: After refmac, R = 0.2225 (Rfree = 0.000) for 1036 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. Cycle 9: After refmac, R = 0.2226 (Rfree = 0.000) for 1030 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. Cycle 10: After refmac, R = 0.2128 (Rfree = 0.000) for 1026 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.58 3.63 Search for helices and strands: 0 residues in 0 chains, 1047 seeds are put forward Round 1: 88 peptides, 17 chains. Longest chain 8 peptides. Score 0.385 Round 2: 96 peptides, 14 chains. Longest chain 21 peptides. Score 0.573 Round 3: 91 peptides, 16 chains. Longest chain 12 peptides. Score 0.455 Round 4: 99 peptides, 12 chains. Longest chain 18 peptides. Score 0.659 Round 5: 94 peptides, 12 chains. Longest chain 18 peptides. Score 0.624 Taking the results from Round 4 Chains 12, Residues 87, Estimated correctness of the model 36.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2104 reflections ( 99.67 % complete ) and 2316 restraints for refining 1066 atoms. 1980 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2510 (Rfree = 0.000) for 1066 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. Cycle 12: After refmac, R = 0.2451 (Rfree = 0.000) for 1063 atoms. Found 2 (6 requested) and removed 7 (3 requested) atoms. Cycle 13: After refmac, R = 0.2308 (Rfree = 0.000) for 1056 atoms. Found 1 (6 requested) and removed 6 (3 requested) atoms. Cycle 14: After refmac, R = 0.2308 (Rfree = 0.000) for 1051 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 15: After refmac, R = 0.2200 (Rfree = 0.000) for 1050 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.55 3.60 Search for helices and strands: 0 residues in 0 chains, 1080 seeds are put forward Round 1: 93 peptides, 18 chains. Longest chain 11 peptides. Score 0.393 Round 2: 103 peptides, 15 chains. Longest chain 13 peptides. Score 0.593 Round 3: 93 peptides, 15 chains. Longest chain 12 peptides. Score 0.512 Round 4: 100 peptides, 16 chains. Longest chain 13 peptides. Score 0.535 Round 5: 93 peptides, 13 chains. Longest chain 19 peptides. Score 0.583 Taking the results from Round 2 Chains 15, Residues 88, Estimated correctness of the model 11.8 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 2104 reflections ( 99.67 % complete ) and 2266 restraints for refining 1066 atoms. 1899 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2445 (Rfree = 0.000) for 1066 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 17: After refmac, R = 0.2209 (Rfree = 0.000) for 1058 atoms. Found 4 (6 requested) and removed 5 (3 requested) atoms. Cycle 18: After refmac, R = 0.2232 (Rfree = 0.000) for 1055 atoms. Found 0 (6 requested) and removed 5 (3 requested) atoms. Cycle 19: After refmac, R = 0.2105 (Rfree = 0.000) for 1049 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 20: After refmac, R = 0.2049 (Rfree = 0.000) for 1047 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.55 3.60 Search for helices and strands: 0 residues in 0 chains, 1069 seeds are put forward Round 1: 73 peptides, 15 chains. Longest chain 11 peptides. Score 0.315 Round 2: 76 peptides, 13 chains. Longest chain 12 peptides. Score 0.434 Round 3: 83 peptides, 13 chains. Longest chain 13 peptides. Score 0.499 Round 4: 83 peptides, 13 chains. Longest chain 13 peptides. Score 0.499 Round 5: 81 peptides, 14 chains. Longest chain 15 peptides. Score 0.441 Taking the results from Round 4 Chains 13, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2104 reflections ( 99.67 % complete ) and 2473 restraints for refining 1065 atoms. 2206 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2355 (Rfree = 0.000) for 1065 atoms. Found 2 (6 requested) and removed 6 (3 requested) atoms. Cycle 22: After refmac, R = 0.2332 (Rfree = 0.000) for 1055 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 23: After refmac, R = 0.2165 (Rfree = 0.000) for 1056 atoms. Found 0 (6 requested) and removed 4 (3 requested) atoms. Cycle 24: After refmac, R = 0.2296 (Rfree = 0.000) for 1051 atoms. Found 5 (6 requested) and removed 5 (3 requested) atoms. Cycle 25: After refmac, R = 0.1988 (Rfree = 0.000) for 1050 atoms. Found 2 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.57 3.62 Search for helices and strands: 0 residues in 0 chains, 1076 seeds are put forward Round 1: 69 peptides, 12 chains. Longest chain 9 peptides. Score 0.407 Round 2: 77 peptides, 12 chains. Longest chain 11 peptides. Score 0.484 Round 3: 73 peptides, 12 chains. Longest chain 9 peptides. Score 0.446 Round 4: 82 peptides, 12 chains. Longest chain 16 peptides. Score 0.529 Round 5: 75 peptides, 12 chains. Longest chain 13 peptides. Score 0.466 Taking the results from Round 4 Chains 12, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2104 reflections ( 99.67 % complete ) and 2403 restraints for refining 1066 atoms. 2135 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2259 (Rfree = 0.000) for 1066 atoms. Found 5 (6 requested) and removed 3 (3 requested) atoms. Cycle 27: After refmac, R = 0.2101 (Rfree = 0.000) for 1065 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 28: After refmac, R = 0.2125 (Rfree = 0.000) for 1062 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 29: After refmac, R = 0.2145 (Rfree = 0.000) for 1062 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 30: After refmac, R = 0.2254 (Rfree = 0.000) for 1060 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.54 3.59 Search for helices and strands: 0 residues in 0 chains, 1090 seeds are put forward Round 1: 54 peptides, 11 chains. Longest chain 9 peptides. Score 0.290 Round 2: 68 peptides, 11 chains. Longest chain 15 peptides. Score 0.440 Round 3: 65 peptides, 11 chains. Longest chain 9 peptides. Score 0.410 Round 4: 75 peptides, 13 chains. Longest chain 9 peptides. Score 0.424 Round 5: 67 peptides, 12 chains. Longest chain 16 peptides. Score 0.386 Taking the results from Round 2 Chains 11, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2104 reflections ( 99.67 % complete ) and 2590 restraints for refining 1066 atoms. 2373 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2391 (Rfree = 0.000) for 1066 atoms. Found 6 (6 requested) and removed 18 (3 requested) atoms. Cycle 32: After refmac, R = 0.2344 (Rfree = 0.000) for 1053 atoms. Found 4 (6 requested) and removed 10 (3 requested) atoms. Cycle 33: After refmac, R = 0.2328 (Rfree = 0.000) for 1046 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 34: After refmac, R = 0.2478 (Rfree = 0.000) for 1041 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. Cycle 35: After refmac, R = 0.2255 (Rfree = 0.000) for 1031 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.58 3.63 Search for helices and strands: 0 residues in 0 chains, 1057 seeds are put forward Round 1: 62 peptides, 14 chains. Longest chain 7 peptides. Score 0.238 Round 2: 71 peptides, 11 chains. Longest chain 11 peptides. Score 0.469 Round 3: 65 peptides, 11 chains. Longest chain 12 peptides. Score 0.410 Round 4: 76 peptides, 12 chains. Longest chain 11 peptides. Score 0.475 Round 5: 71 peptides, 12 chains. Longest chain 11 peptides. Score 0.427 Taking the results from Round 4 Chains 12, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2104 reflections ( 99.67 % complete ) and 2424 restraints for refining 1066 atoms. 2180 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2442 (Rfree = 0.000) for 1066 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. Cycle 37: After refmac, R = 0.2305 (Rfree = 0.000) for 1055 atoms. Found 5 (6 requested) and removed 4 (3 requested) atoms. Cycle 38: After refmac, R = 0.2220 (Rfree = 0.000) for 1054 atoms. Found 1 (6 requested) and removed 7 (3 requested) atoms. Cycle 39: After refmac, R = 0.2204 (Rfree = 0.000) for 1045 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 40: After refmac, R = 0.2163 (Rfree = 0.000) for 1044 atoms. Found 3 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.56 3.61 Search for helices and strands: 0 residues in 0 chains, 1053 seeds are put forward Round 1: 52 peptides, 10 chains. Longest chain 9 peptides. Score 0.315 Round 2: 62 peptides, 11 chains. Longest chain 14 peptides. Score 0.378 Round 3: 54 peptides, 9 chains. Longest chain 11 peptides. Score 0.385 Round 4: 52 peptides, 9 chains. Longest chain 11 peptides. Score 0.364 Round 5: 56 peptides, 10 chains. Longest chain 10 peptides. Score 0.360 Taking the results from Round 3 Chains 9, Residues 45, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2104 reflections ( 99.67 % complete ) and 2533 restraints for refining 1066 atoms. 2362 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2282 (Rfree = 0.000) for 1066 atoms. Found 5 (6 requested) and removed 7 (3 requested) atoms. Cycle 42: After refmac, R = 0.2325 (Rfree = 0.000) for 1061 atoms. Found 4 (6 requested) and removed 5 (3 requested) atoms. Cycle 43: After refmac, R = 0.2452 (Rfree = 0.000) for 1057 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 44: After refmac, R = 0.2226 (Rfree = 0.000) for 1056 atoms. Found 5 (6 requested) and removed 6 (3 requested) atoms. Cycle 45: After refmac, R = 0.1727 (Rfree = 0.000) for 1054 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.52 3.57 Search for helices and strands: 0 residues in 0 chains, 1068 seeds are put forward Round 1: 55 peptides, 11 chains. Longest chain 10 peptides. Score 0.301 Round 2: 58 peptides, 10 chains. Longest chain 11 peptides. Score 0.382 Round 3: 62 peptides, 10 chains. Longest chain 14 peptides. Score 0.423 Round 4: 62 peptides, 12 chains. Longest chain 9 peptides. Score 0.332 Round 5: 66 peptides, 11 chains. Longest chain 16 peptides. Score 0.420 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 52, 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 2huh-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2104 reflections ( 99.67 % complete ) and 2556 restraints for refining 1066 atoms. 2358 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2128 (Rfree = 0.000) for 1066 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.1943 (Rfree = 0.000) for 1059 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.1978 (Rfree = 0.000) for 1056 atoms. Found 0 (6 requested) and removed 1 (3 requested) atoms. Cycle 49: After refmac, R = 0.1777 (Rfree = 0.000) for 1055 atoms. Found 0 (6 requested) and removed 2 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:47:21 GMT 2018 Job finished. TimeTaking 24.47 Used memory is bytes: 7959272