null Sun 23 Dec 22:23:10 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 1vpy-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vpy-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vpy-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpy-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/1vpy-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpy-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 22:23:19 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/1vpy-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpy-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 248 and 0 Target number of residues in the AU: 248 Target solvent content: 0.6590 Checking the provided sequence file Detected sequence length: 289 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 289 Adjusted target solvent content: 0.60 Input MTZ file: 1vpy-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: 170 Cell parameters: 114.136 114.136 52.333 90.000 90.000 120.000 Input sequence file: 1vpy-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2312 target number of atoms Had to go as low as 0.90 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: 98.845 4.000 Wilson plot Bfac: 84.12 3395 reflections ( 99.65 % complete ) and 0 restraints for refining 2567 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3208 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3229 (Rfree = 0.000) for 2567 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.85 3.36 Search for helices and strands: 0 residues in 0 chains, 2621 seeds are put forward Round 1: 117 peptides, 19 chains. Longest chain 10 peptides. Score 0.372 Round 2: 143 peptides, 16 chains. Longest chain 20 peptides. Score 0.530 Round 3: 150 peptides, 15 chains. Longest chain 29 peptides. Score 0.570 Round 4: 151 peptides, 15 chains. Longest chain 34 peptides. Score 0.574 Round 5: 151 peptides, 12 chains. Longest chain 37 peptides. Score 0.620 Taking the results from Round 5 Chains 15, Residues 139, Estimated correctness of the model 0.0 % 2 chains (39 residues) have been docked in sequence ------------------------------------------------------ 3395 reflections ( 99.65 % complete ) and 4455 restraints for refining 2087 atoms. 3747 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2547 (Rfree = 0.000) for 2087 atoms. Found 9 (9 requested) and removed 14 (4 requested) atoms. Cycle 2: After refmac, R = 0.2627 (Rfree = 0.000) for 2036 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 3: After refmac, R = 0.2346 (Rfree = 0.000) for 2003 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. Cycle 4: After refmac, R = 0.2386 (Rfree = 0.000) for 1979 atoms. Found 7 (9 requested) and removed 19 (4 requested) atoms. Cycle 5: After refmac, R = 0.2253 (Rfree = 0.000) for 1950 atoms. Found 9 (9 requested) and removed 13 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.72 3.25 Search for helices and strands: 0 residues in 0 chains, 2012 seeds are put forward Round 1: 127 peptides, 18 chains. Longest chain 15 peptides. Score 0.433 Round 2: 154 peptides, 19 chains. Longest chain 18 peptides. Score 0.519 Round 3: 159 peptides, 21 chains. Longest chain 15 peptides. Score 0.504 Round 4: 163 peptides, 20 chains. Longest chain 25 peptides. Score 0.535 Round 5: 160 peptides, 18 chains. Longest chain 20 peptides. Score 0.556 Taking the results from Round 5 Chains 18, Residues 142, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3395 reflections ( 99.65 % complete ) and 4774 restraints for refining 2088 atoms. 4224 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2431 (Rfree = 0.000) for 2088 atoms. Found 9 (9 requested) and removed 19 (4 requested) atoms. Cycle 7: After refmac, R = 0.2394 (Rfree = 0.000) for 2065 atoms. Found 9 (9 requested) and removed 43 (4 requested) atoms. Cycle 8: After refmac, R = 0.2406 (Rfree = 0.000) for 2025 atoms. Found 9 (9 requested) and removed 26 (4 requested) atoms. Cycle 9: After refmac, R = 0.2171 (Rfree = 0.000) for 1998 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 10: After refmac, R = 0.2110 (Rfree = 0.000) for 1992 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.74 3.27 Search for helices and strands: 0 residues in 0 chains, 2061 seeds are put forward Round 1: 151 peptides, 22 chains. Longest chain 12 peptides. Score 0.457 Round 2: 168 peptides, 21 chains. Longest chain 15 peptides. Score 0.536 Round 3: 177 peptides, 21 chains. Longest chain 17 peptides. Score 0.567 Round 4: 157 peptides, 20 chains. Longest chain 18 peptides. Score 0.513 Round 5: 145 peptides, 17 chains. Longest chain 18 peptides. Score 0.520 Taking the results from Round 3 Chains 21, Residues 156, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3395 reflections ( 99.65 % complete ) and 4779 restraints for refining 2088 atoms. 4176 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2330 (Rfree = 0.000) for 2088 atoms. Found 9 (9 requested) and removed 11 (4 requested) atoms. Cycle 12: After refmac, R = 0.2300 (Rfree = 0.000) for 2069 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 13: After refmac, R = 0.2298 (Rfree = 0.000) for 2064 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 14: After refmac, R = 0.1872 (Rfree = 0.000) for 2060 atoms. Found 5 (9 requested) and removed 8 (4 requested) atoms. Cycle 15: After refmac, R = 0.2130 (Rfree = 0.000) for 2054 atoms. Found 6 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.77 3.29 Search for helices and strands: 0 residues in 0 chains, 2124 seeds are put forward Round 1: 133 peptides, 21 chains. Longest chain 16 peptides. Score 0.402 Round 2: 153 peptides, 18 chains. Longest chain 20 peptides. Score 0.532 Round 3: 157 peptides, 20 chains. Longest chain 17 peptides. Score 0.513 Round 4: 164 peptides, 18 chains. Longest chain 20 peptides. Score 0.570 Round 5: 158 peptides, 18 chains. Longest chain 18 peptides. Score 0.550 Taking the results from Round 4 Chains 18, Residues 146, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3395 reflections ( 99.65 % complete ) and 4734 restraints for refining 2088 atoms. 4137 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2383 (Rfree = 0.000) for 2088 atoms. Found 9 (9 requested) and removed 20 (4 requested) atoms. Cycle 17: After refmac, R = 0.2599 (Rfree = 0.000) for 2060 atoms. Found 8 (9 requested) and removed 103 (4 requested) atoms. Cycle 18: After refmac, R = 0.2116 (Rfree = 0.000) for 1957 atoms. Found 4 (9 requested) and removed 7 (4 requested) atoms. Cycle 19: After refmac, R = 0.2125 (Rfree = 0.000) for 1949 atoms. Found 2 (9 requested) and removed 6 (4 requested) atoms. Cycle 20: After refmac, R = 0.1939 (Rfree = 0.000) for 1943 atoms. Found 1 (9 requested) and removed 7 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.78 3.30 Search for helices and strands: 0 residues in 0 chains, 2026 seeds are put forward Round 1: 129 peptides, 18 chains. Longest chain 17 peptides. Score 0.442 Round 2: 151 peptides, 20 chains. Longest chain 24 peptides. Score 0.491 Round 3: 131 peptides, 18 chains. Longest chain 20 peptides. Score 0.450 Round 4: 142 peptides, 20 chains. Longest chain 20 peptides. Score 0.457 Round 5: 148 peptides, 17 chains. Longest chain 19 peptides. Score 0.531 Taking the results from Round 5 Chains 17, Residues 131, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3395 reflections ( 99.65 % complete ) and 4879 restraints for refining 2088 atoms. 4372 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2865 (Rfree = 0.000) for 2088 atoms. Found 9 (9 requested) and removed 25 (4 requested) atoms. Cycle 22: After refmac, R = 0.2208 (Rfree = 0.000) for 2066 atoms. Found 8 (9 requested) and removed 8 (4 requested) atoms. Cycle 23: After refmac, R = 0.2099 (Rfree = 0.000) for 2063 atoms. Found 2 (9 requested) and removed 6 (4 requested) atoms. Cycle 24: After refmac, R = 0.2549 (Rfree = 0.000) for 2057 atoms. Found 6 (9 requested) and removed 16 (4 requested) atoms. Cycle 25: After refmac, R = 0.2456 (Rfree = 0.000) for 2046 atoms. Found 2 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.79 3.31 Search for helices and strands: 0 residues in 0 chains, 2108 seeds are put forward Round 1: 124 peptides, 23 chains. Longest chain 9 peptides. Score 0.325 Round 2: 139 peptides, 20 chains. Longest chain 18 peptides. Score 0.445 Round 3: 141 peptides, 20 chains. Longest chain 13 peptides. Score 0.453 Round 4: 154 peptides, 19 chains. Longest chain 19 peptides. Score 0.519 Round 5: 140 peptides, 18 chains. Longest chain 18 peptides. Score 0.485 Taking the results from Round 4 Chains 19, Residues 135, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3395 reflections ( 99.65 % complete ) and 4780 restraints for refining 2088 atoms. 4259 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2800 (Rfree = 0.000) for 2088 atoms. Found 8 (9 requested) and removed 10 (4 requested) atoms. Cycle 27: After refmac, R = 0.2305 (Rfree = 0.000) for 2077 atoms. Found 8 (9 requested) and removed 17 (4 requested) atoms. Cycle 28: After refmac, R = 0.2588 (Rfree = 0.000) for 2066 atoms. Found 5 (9 requested) and removed 7 (4 requested) atoms. Cycle 29: After refmac, R = 0.2587 (Rfree = 0.000) for 2063 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. Cycle 30: After refmac, R = 0.2860 (Rfree = 0.000) for 2058 atoms. Found 6 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.74 3.27 Search for helices and strands: 0 residues in 0 chains, 2133 seeds are put forward Round 1: 118 peptides, 20 chains. Longest chain 15 peptides. Score 0.357 Round 2: 131 peptides, 20 chains. Longest chain 16 peptides. Score 0.413 Round 3: 129 peptides, 19 chains. Longest chain 17 peptides. Score 0.423 Round 4: 119 peptides, 16 chains. Longest chain 15 peptides. Score 0.438 Round 5: 117 peptides, 15 chains. Longest chain 16 peptides. Score 0.449 Taking the results from Round 5 Chains 15, Residues 102, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3395 reflections ( 99.65 % complete ) and 4934 restraints for refining 2088 atoms. 4541 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2696 (Rfree = 0.000) for 2088 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 32: After refmac, R = 0.2690 (Rfree = 0.000) for 2079 atoms. Found 5 (9 requested) and removed 10 (4 requested) atoms. Cycle 33: After refmac, R = 0.2739 (Rfree = 0.000) for 2071 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 34: After refmac, R = 0.2605 (Rfree = 0.000) for 2068 atoms. Found 3 (9 requested) and removed 5 (4 requested) atoms. Cycle 35: After refmac, R = 0.2605 (Rfree = 0.000) for 2066 atoms. Found 1 (9 requested) and removed 5 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.78 3.30 Search for helices and strands: 0 residues in 0 chains, 2122 seeds are put forward Round 1: 117 peptides, 21 chains. Longest chain 13 peptides. Score 0.333 Round 2: 129 peptides, 18 chains. Longest chain 19 peptides. Score 0.442 Round 3: 135 peptides, 20 chains. Longest chain 19 peptides. Score 0.429 Round 4: 140 peptides, 19 chains. Longest chain 17 peptides. Score 0.467 Round 5: 143 peptides, 22 chains. Longest chain 17 peptides. Score 0.425 Taking the results from Round 4 Chains 19, Residues 121, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3395 reflections ( 99.65 % complete ) and 4818 restraints for refining 2088 atoms. 4353 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2948 (Rfree = 0.000) for 2088 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 37: After refmac, R = 0.2827 (Rfree = 0.000) for 2082 atoms. Found 8 (9 requested) and removed 9 (4 requested) atoms. Cycle 38: After refmac, R = 0.2296 (Rfree = 0.000) for 2077 atoms. Found 2 (9 requested) and removed 7 (4 requested) atoms. Cycle 39: After refmac, R = 0.2069 (Rfree = 0.000) for 2072 atoms. Found 0 (9 requested) and removed 6 (4 requested) atoms. Cycle 40: After refmac, R = 0.2144 (Rfree = 0.000) for 2066 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.77 3.29 Search for helices and strands: 0 residues in 0 chains, 2125 seeds are put forward Round 1: 125 peptides, 24 chains. Longest chain 12 peptides. Score 0.310 Round 2: 129 peptides, 21 chains. Longest chain 11 peptides. Score 0.386 Round 3: 130 peptides, 20 chains. Longest chain 15 peptides. Score 0.409 Round 4: 132 peptides, 19 chains. Longest chain 14 peptides. Score 0.435 Round 5: 123 peptides, 18 chains. Longest chain 15 peptides. Score 0.417 Taking the results from Round 4 Chains 19, Residues 113, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3395 reflections ( 99.65 % complete ) and 4877 restraints for refining 2088 atoms. 4444 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3094 (Rfree = 0.000) for 2088 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. Cycle 42: After refmac, R = 0.2277 (Rfree = 0.000) for 2082 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. Cycle 43: After refmac, R = 0.2425 (Rfree = 0.000) for 2076 atoms. Found 1 (9 requested) and removed 6 (4 requested) atoms. Cycle 44: After refmac, R = 0.2294 (Rfree = 0.000) for 2066 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 45: After refmac, R = 0.2250 (Rfree = 0.000) for 2060 atoms. Found 2 (9 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.79 3.31 Search for helices and strands: 0 residues in 0 chains, 2129 seeds are put forward Round 1: 109 peptides, 21 chains. Longest chain 9 peptides. Score 0.295 Round 2: 116 peptides, 20 chains. Longest chain 15 peptides. Score 0.348 Round 3: 128 peptides, 22 chains. Longest chain 10 peptides. Score 0.362 Round 4: 117 peptides, 18 chains. Longest chain 12 peptides. Score 0.392 Round 5: 115 peptides, 16 chains. Longest chain 15 peptides. Score 0.422 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 99, 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 1vpy-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3395 reflections ( 99.65 % complete ) and 5021 restraints for refining 2088 atoms. 4641 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2477 (Rfree = 0.000) for 2088 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2176 (Rfree = 0.000) for 2082 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2115 (Rfree = 0.000) for 2076 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2056 (Rfree = 0.000) for 2070 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:08:19 GMT 2018 Job finished. TimeTaking 45.16 Used memory is bytes: 22494176