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 2p4o-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p4o-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p4o-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4o-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/2p4o-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4o-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 22:23:14 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/2p4o-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p4o-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 190 and 0 Target number of residues in the AU: 190 Target solvent content: 0.6723 Checking the provided sequence file Detected sequence length: 306 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 306 Adjusted target solvent content: 0.47 Input MTZ file: 2p4o-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: 94 Cell parameters: 91.400 91.400 75.131 90.000 90.000 90.000 Input sequence file: 2p4o-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2448 target number of atoms Had to go as low as 0.70 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: 29.686 4.000 Wilson plot Bfac: 93.12 2946 reflections ( 99.63 % complete ) and 0 restraints for refining 2702 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3640 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3656 (Rfree = 0.000) for 2702 atoms. Found 12 (12 requested) and removed 25 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.83 3.99 Search for helices and strands: 0 residues in 0 chains, 2709 seeds are put forward Round 1: 83 peptides, 18 chains. Longest chain 10 peptides. Score 0.239 Round 2: 108 peptides, 21 chains. Longest chain 12 peptides. Score 0.312 Round 3: 128 peptides, 24 chains. Longest chain 11 peptides. Score 0.352 Round 4: 140 peptides, 24 chains. Longest chain 10 peptides. Score 0.414 Round 5: 137 peptides, 24 chains. Longest chain 15 peptides. Score 0.399 Taking the results from Round 4 Chains 24, Residues 116, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 2946 reflections ( 99.63 % complete ) and 5380 restraints for refining 2211 atoms. 4918 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3114 (Rfree = 0.000) for 2211 atoms. Found 10 (10 requested) and removed 21 (5 requested) atoms. Cycle 2: After refmac, R = 0.3113 (Rfree = 0.000) for 2168 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. Cycle 3: After refmac, R = 0.2906 (Rfree = 0.000) for 2142 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 4: After refmac, R = 0.2800 (Rfree = 0.000) for 2126 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 5: After refmac, R = 0.2691 (Rfree = 0.000) for 2107 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.95 4.11 Search for helices and strands: 0 residues in 0 chains, 2184 seeds are put forward Round 1: 125 peptides, 27 chains. Longest chain 9 peptides. Score 0.267 Round 2: 145 peptides, 24 chains. Longest chain 15 peptides. Score 0.439 Round 3: 147 peptides, 21 chains. Longest chain 18 peptides. Score 0.509 Round 4: 154 peptides, 23 chains. Longest chain 14 peptides. Score 0.501 Round 5: 145 peptides, 19 chains. Longest chain 18 peptides. Score 0.539 Taking the results from Round 5 Chains 19, Residues 126, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2946 reflections ( 99.63 % complete ) and 5161 restraints for refining 2167 atoms. 4676 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2806 (Rfree = 0.000) for 2167 atoms. Found 10 (10 requested) and removed 23 (5 requested) atoms. Cycle 7: After refmac, R = 0.2655 (Rfree = 0.000) for 2127 atoms. Found 10 (10 requested) and removed 23 (5 requested) atoms. Cycle 8: After refmac, R = 0.2228 (Rfree = 0.000) for 2102 atoms. Found 7 (10 requested) and removed 11 (5 requested) atoms. Cycle 9: After refmac, R = 0.2553 (Rfree = 0.000) for 2089 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 10: After refmac, R = 0.2383 (Rfree = 0.000) for 2081 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.88 4.04 Search for helices and strands: 0 residues in 0 chains, 2117 seeds are put forward Round 1: 118 peptides, 22 chains. Longest chain 12 peptides. Score 0.344 Round 2: 127 peptides, 19 chains. Longest chain 16 peptides. Score 0.457 Round 3: 130 peptides, 20 chains. Longest chain 12 peptides. Score 0.451 Round 4: 135 peptides, 22 chains. Longest chain 12 peptides. Score 0.432 Round 5: 141 peptides, 25 chains. Longest chain 11 peptides. Score 0.398 Taking the results from Round 2 Chains 20, Residues 108, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 2946 reflections ( 99.63 % complete ) and 5098 restraints for refining 2131 atoms. 4646 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2494 (Rfree = 0.000) for 2131 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 12: After refmac, R = 0.2562 (Rfree = 0.000) for 2101 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 13: After refmac, R = 0.2397 (Rfree = 0.000) for 2088 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 14: After refmac, R = 0.2517 (Rfree = 0.000) for 2065 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 15: After refmac, R = 0.1825 (Rfree = 0.000) for 2047 atoms. Found 2 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.84 4.00 Search for helices and strands: 0 residues in 0 chains, 2067 seeds are put forward Round 1: 101 peptides, 21 chains. Longest chain 8 peptides. Score 0.272 Round 2: 118 peptides, 20 chains. Longest chain 12 peptides. Score 0.390 Round 3: 121 peptides, 21 chains. Longest chain 16 peptides. Score 0.383 Round 4: 127 peptides, 21 chains. Longest chain 11 peptides. Score 0.414 Round 5: 122 peptides, 19 chains. Longest chain 13 peptides. Score 0.433 Taking the results from Round 5 Chains 19, Residues 103, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2946 reflections ( 99.63 % complete ) and 5017 restraints for refining 2118 atoms. 4624 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2076 (Rfree = 0.000) for 2118 atoms. Found 5 (10 requested) and removed 23 (5 requested) atoms. Cycle 17: After refmac, R = 0.2454 (Rfree = 0.000) for 2086 atoms. Found 9 (9 requested) and removed 20 (4 requested) atoms. Cycle 18: After refmac, R = 0.2338 (Rfree = 0.000) for 2065 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 19: After refmac, R = 0.2357 (Rfree = 0.000) for 2045 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 20: After refmac, R = 0.2308 (Rfree = 0.000) for 2025 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.83 3.99 Search for helices and strands: 0 residues in 0 chains, 2089 seeds are put forward Round 1: 105 peptides, 20 chains. Longest chain 10 peptides. Score 0.319 Round 2: 117 peptides, 17 chains. Longest chain 10 peptides. Score 0.452 Round 3: 114 peptides, 18 chains. Longest chain 10 peptides. Score 0.415 Round 4: 125 peptides, 19 chains. Longest chain 11 peptides. Score 0.448 Round 5: 127 peptides, 18 chains. Longest chain 11 peptides. Score 0.479 Taking the results from Round 5 Chains 18, Residues 109, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2946 reflections ( 99.63 % complete ) and 4613 restraints for refining 2039 atoms. 4195 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2483 (Rfree = 0.000) for 2039 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 22: After refmac, R = 0.2327 (Rfree = 0.000) for 2014 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 23: After refmac, R = 0.2425 (Rfree = 0.000) for 1996 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 24: After refmac, R = 0.2246 (Rfree = 0.000) for 1986 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 25: After refmac, R = 0.2228 (Rfree = 0.000) for 1978 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.80 3.96 Search for helices and strands: 0 residues in 0 chains, 2045 seeds are put forward Round 1: 77 peptides, 16 chains. Longest chain 7 peptides. Score 0.254 Round 2: 85 peptides, 15 chains. Longest chain 12 peptides. Score 0.329 Round 3: 107 peptides, 18 chains. Longest chain 12 peptides. Score 0.378 Round 4: 114 peptides, 19 chains. Longest chain 11 peptides. Score 0.392 Round 5: 111 peptides, 19 chains. Longest chain 12 peptides. Score 0.376 Taking the results from Round 4 Chains 19, Residues 95, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2946 reflections ( 99.63 % complete ) and 4648 restraints for refining 1993 atoms. 4287 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2338 (Rfree = 0.000) for 1993 atoms. Found 9 (9 requested) and removed 18 (4 requested) atoms. Cycle 27: After refmac, R = 0.2272 (Rfree = 0.000) for 1978 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 28: After refmac, R = 0.2126 (Rfree = 0.000) for 1964 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 29: After refmac, R = 0.2371 (Rfree = 0.000) for 1950 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 30: After refmac, R = 0.2341 (Rfree = 0.000) for 1941 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.78 3.93 Search for helices and strands: 0 residues in 0 chains, 2005 seeds are put forward Round 1: 91 peptides, 21 chains. Longest chain 6 peptides. Score 0.211 Round 2: 105 peptides, 20 chains. Longest chain 9 peptides. Score 0.319 Round 3: 99 peptides, 19 chains. Longest chain 7 peptides. Score 0.310 Round 4: 105 peptides, 19 chains. Longest chain 12 peptides. Score 0.343 Round 5: 109 peptides, 18 chains. Longest chain 11 peptides. Score 0.389 Taking the results from Round 5 Chains 18, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2946 reflections ( 99.63 % complete ) and 4774 restraints for refining 2043 atoms. 4428 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2479 (Rfree = 0.000) for 2043 atoms. Found 9 (9 requested) and removed 19 (4 requested) atoms. Cycle 32: After refmac, R = 0.2158 (Rfree = 0.000) for 2018 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 33: After refmac, R = 0.2413 (Rfree = 0.000) for 2002 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.2365 (Rfree = 0.000) for 1988 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 35: After refmac, R = 0.2286 (Rfree = 0.000) for 1980 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.95 4.11 Search for helices and strands: 0 residues in 0 chains, 2035 seeds are put forward Round 1: 81 peptides, 17 chains. Longest chain 11 peptides. Score 0.253 Round 2: 100 peptides, 18 chains. Longest chain 14 peptides. Score 0.340 Round 3: 96 peptides, 16 chains. Longest chain 11 peptides. Score 0.366 Round 4: 104 peptides, 16 chains. Longest chain 14 peptides. Score 0.409 Round 5: 111 peptides, 18 chains. Longest chain 12 peptides. Score 0.399 Taking the results from Round 4 Chains 16, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2946 reflections ( 99.63 % complete ) and 4558 restraints for refining 1952 atoms. 4222 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2399 (Rfree = 0.000) for 1952 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 37: After refmac, R = 0.2215 (Rfree = 0.000) for 1945 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 38: After refmac, R = 0.2176 (Rfree = 0.000) for 1934 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 39: After refmac, R = 0.2310 (Rfree = 0.000) for 1926 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 40: After refmac, R = 0.2197 (Rfree = 0.000) for 1922 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.89 4.05 Search for helices and strands: 0 residues in 0 chains, 1978 seeds are put forward Round 1: 86 peptides, 18 chains. Longest chain 9 peptides. Score 0.258 Round 2: 105 peptides, 19 chains. Longest chain 10 peptides. Score 0.343 Round 3: 114 peptides, 18 chains. Longest chain 14 peptides. Score 0.415 Round 4: 102 peptides, 18 chains. Longest chain 12 peptides. Score 0.351 Round 5: 110 peptides, 17 chains. Longest chain 14 peptides. Score 0.417 Taking the results from Round 5 Chains 17, Residues 93, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2946 reflections ( 99.63 % complete ) and 4642 restraints for refining 1981 atoms. 4287 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2464 (Rfree = 0.000) for 1981 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 42: After refmac, R = 0.2203 (Rfree = 0.000) for 1965 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 43: After refmac, R = 0.2082 (Rfree = 0.000) for 1956 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 44: After refmac, R = 0.2276 (Rfree = 0.000) for 1950 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 45: After refmac, R = 0.2117 (Rfree = 0.000) for 1941 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.87 4.03 Search for helices and strands: 0 residues in 0 chains, 1993 seeds are put forward Round 1: 76 peptides, 17 chains. Longest chain 7 peptides. Score 0.221 Round 2: 85 peptides, 17 chains. Longest chain 9 peptides. Score 0.277 Round 3: 91 peptides, 17 chains. Longest chain 10 peptides. Score 0.313 Round 4: 79 peptides, 15 chains. Longest chain 8 peptides. Score 0.293 Round 5: 93 peptides, 18 chains. Longest chain 9 peptides. Score 0.300 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 17, Residues 74, 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 2p4o-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2946 reflections ( 99.63 % complete ) and 4509 restraints for refining 1947 atoms. 4230 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2311 (Rfree = 0.000) for 1947 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2359 (Rfree = 0.000) for 1931 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2386 (Rfree = 0.000) for 1922 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2418 (Rfree = 0.000) for 1908 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Writing output files ... TimeTaking 43.13