Sun 30 Dec 03:45:07 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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vpy-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vpy-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpy-3.8-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-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpy-3.8-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 30 Dec 03:46:18 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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vpy-3.8-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 256 and 0 Target number of residues in the AU: 256 Target solvent content: 0.6480 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-3.8-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-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2312 target number of atoms Had to go as low as 0.85 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 3.800 Wilson plot Bfac: 76.69 3942 reflections ( 99.70 % complete ) and 0 restraints for refining 2574 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3147 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3185 (Rfree = 0.000) for 2574 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.62 3.16 Search for helices and strands: 0 residues in 0 chains, 2613 seeds are put forward Round 1: 125 peptides, 23 chains. Longest chain 10 peptides. Score 0.330 Round 2: 154 peptides, 18 chains. Longest chain 25 peptides. Score 0.536 Round 3: 139 peptides, 16 chains. Longest chain 21 peptides. Score 0.515 Round 4: 151 peptides, 17 chains. Longest chain 18 peptides. Score 0.541 Round 5: 151 peptides, 16 chains. Longest chain 18 peptides. Score 0.558 Taking the results from Round 5 Chains 16, Residues 135, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3942 reflections ( 99.70 % complete ) and 4882 restraints for refining 2090 atoms. 4358 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2670 (Rfree = 0.000) for 2090 atoms. Found 10 (11 requested) and removed 28 (5 requested) atoms. Cycle 2: After refmac, R = 0.2455 (Rfree = 0.000) for 2049 atoms. Found 10 (11 requested) and removed 9 (5 requested) atoms. Cycle 3: After refmac, R = 0.2270 (Rfree = 0.000) for 2037 atoms. Found 6 (11 requested) and removed 12 (5 requested) atoms. Cycle 4: After refmac, R = 0.2390 (Rfree = 0.000) for 2022 atoms. Found 8 (11 requested) and removed 9 (5 requested) atoms. Cycle 5: After refmac, R = 0.2318 (Rfree = 0.000) for 2016 atoms. Found 6 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.58 3.13 Search for helices and strands: 0 residues in 0 chains, 2100 seeds are put forward Round 1: 143 peptides, 22 chains. Longest chain 18 peptides. Score 0.425 Round 2: 161 peptides, 21 chains. Longest chain 14 peptides. Score 0.511 Round 3: 152 peptides, 18 chains. Longest chain 20 peptides. Score 0.529 Round 4: 155 peptides, 17 chains. Longest chain 21 peptides. Score 0.555 Round 5: 152 peptides, 19 chains. Longest chain 21 peptides. Score 0.512 Taking the results from Round 4 Chains 19, Residues 138, Estimated correctness of the model 0.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 3942 reflections ( 99.70 % complete ) and 4578 restraints for refining 2091 atoms. 3966 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2496 (Rfree = 0.000) for 2091 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 7: After refmac, R = 0.2205 (Rfree = 0.000) for 2063 atoms. Found 4 (11 requested) and removed 19 (5 requested) atoms. Cycle 8: After refmac, R = 0.2109 (Rfree = 0.000) for 2034 atoms. Found 4 (11 requested) and removed 11 (5 requested) atoms. Cycle 9: After refmac, R = 0.2160 (Rfree = 0.000) for 2020 atoms. Found 3 (11 requested) and removed 11 (5 requested) atoms. Cycle 10: After refmac, R = 0.2119 (Rfree = 0.000) for 2006 atoms. Found 3 (11 requested) and removed 14 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.61 3.15 Search for helices and strands: 0 residues in 0 chains, 2094 seeds are put forward Round 1: 138 peptides, 22 chains. Longest chain 11 peptides. Score 0.405 Round 2: 158 peptides, 22 chains. Longest chain 21 peptides. Score 0.484 Round 3: 154 peptides, 19 chains. Longest chain 21 peptides. Score 0.519 Round 4: 143 peptides, 18 chains. Longest chain 13 peptides. Score 0.496 Round 5: 155 peptides, 22 chains. Longest chain 15 peptides. Score 0.472 Taking the results from Round 3 Chains 20, Residues 135, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3942 reflections ( 99.70 % complete ) and 4580 restraints for refining 2046 atoms. 4040 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2364 (Rfree = 0.000) for 2046 atoms. Found 11 (11 requested) and removed 18 (5 requested) atoms. Cycle 12: After refmac, R = 0.2469 (Rfree = 0.000) for 2027 atoms. Found 7 (11 requested) and removed 10 (5 requested) atoms. Cycle 13: After refmac, R = 0.2108 (Rfree = 0.000) for 2013 atoms. Found 9 (11 requested) and removed 17 (5 requested) atoms. Cycle 14: After refmac, R = 0.2229 (Rfree = 0.000) for 1999 atoms. Found 9 (11 requested) and removed 7 (5 requested) atoms. Cycle 15: After refmac, R = 0.2193 (Rfree = 0.000) for 1997 atoms. Found 4 (11 requested) and removed 13 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.59 3.14 Search for helices and strands: 0 residues in 0 chains, 2063 seeds are put forward Round 1: 138 peptides, 22 chains. Longest chain 18 peptides. Score 0.405 Round 2: 160 peptides, 18 chains. Longest chain 30 peptides. Score 0.556 Round 3: 153 peptides, 19 chains. Longest chain 27 peptides. Score 0.516 Round 4: 148 peptides, 19 chains. Longest chain 27 peptides. Score 0.497 Round 5: 160 peptides, 17 chains. Longest chain 27 peptides. Score 0.572 Taking the results from Round 5 Chains 19, Residues 143, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3942 reflections ( 99.70 % complete ) and 4706 restraints for refining 2090 atoms. 4111 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2376 (Rfree = 0.000) for 2090 atoms. Found 11 (11 requested) and removed 12 (5 requested) atoms. Cycle 17: After refmac, R = 0.2261 (Rfree = 0.000) for 2075 atoms. Found 6 (11 requested) and removed 8 (5 requested) atoms. Cycle 18: After refmac, R = 0.2199 (Rfree = 0.000) for 2066 atoms. Found 6 (11 requested) and removed 7 (5 requested) atoms. Cycle 19: After refmac, R = 0.2134 (Rfree = 0.000) for 2062 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 20: After refmac, R = 0.2117 (Rfree = 0.000) for 2053 atoms. Found 2 (11 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.57 3.12 TimeTaking 2880.32