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 2prv-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2prv-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2prv-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prv-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/2prv-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prv-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 23 Dec 22:23:20 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/2prv-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prv-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 194 and 0 Target number of residues in the AU: 194 Target solvent content: 0.6591 Checking the provided sequence file Detected sequence length: 153 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 306 Adjusted target solvent content: 0.46 Input MTZ file: 2prv-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: 1 Cell parameters: 40.107 45.170 48.067 84.512 67.558 73.075 Input sequence file: 2prv-3.8-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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 44.420 3.800 Wilson plot Bfac: 83.18 2868 reflections ( 97.72 % complete ) and 0 restraints for refining 2709 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3839 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3429 (Rfree = 0.000) for 2709 atoms. Found 9 (14 requested) and removed 93 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.51 3.70 Search for helices and strands: 0 residues in 0 chains, 2648 seeds are put forward NCS extension: 0 residues added, 2648 seeds are put forward Round 1: 57 peptides, 13 chains. Longest chain 6 peptides. Score 0.205 Round 2: 78 peptides, 17 chains. Longest chain 7 peptides. Score 0.235 Round 3: 68 peptides, 14 chains. Longest chain 7 peptides. Score 0.252 Round 4: 72 peptides, 13 chains. Longest chain 11 peptides. Score 0.306 Round 5: 65 peptides, 13 chains. Longest chain 8 peptides. Score 0.260 Taking the results from Round 4 Chains 13, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2868 reflections ( 97.72 % complete ) and 5445 restraints for refining 2214 atoms. 5222 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3174 (Rfree = 0.000) for 2214 atoms. Found 12 (12 requested) and removed 22 (6 requested) atoms. Cycle 2: After refmac, R = 0.2698 (Rfree = 0.000) for 2194 atoms. Found 6 (12 requested) and removed 12 (6 requested) atoms. Cycle 3: After refmac, R = 0.2005 (Rfree = 0.000) for 2178 atoms. Found 6 (12 requested) and removed 12 (6 requested) atoms. Cycle 4: After refmac, R = 0.1812 (Rfree = 0.000) for 2162 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. Cycle 5: After refmac, R = 0.1825 (Rfree = 0.000) for 2154 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.54 3.73 Search for helices and strands: 0 residues in 0 chains, 2189 seeds are put forward NCS extension: 0 residues added, 2189 seeds are put forward Round 1: 62 peptides, 15 chains. Longest chain 5 peptides. Score 0.181 Round 2: 96 peptides, 21 chains. Longest chain 12 peptides. Score 0.243 Round 3: 103 peptides, 21 chains. Longest chain 10 peptides. Score 0.285 Round 4: 100 peptides, 19 chains. Longest chain 11 peptides. Score 0.318 Round 5: 96 peptides, 19 chains. Longest chain 11 peptides. Score 0.294 Taking the results from Round 4 Chains 19, Residues 81, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 2868 reflections ( 97.72 % complete ) and 4893 restraints for refining 2106 atoms. 4581 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1932 (Rfree = 0.000) for 2106 atoms. Found 9 (11 requested) and removed 12 (5 requested) atoms. Cycle 7: After refmac, R = 0.1805 (Rfree = 0.000) for 2097 atoms. Found 2 (11 requested) and removed 7 (5 requested) atoms. Cycle 8: After refmac, R = 0.1734 (Rfree = 0.000) for 2090 atoms. Found 1 (11 requested) and removed 6 (5 requested) atoms. Cycle 9: After refmac, R = 0.1611 (Rfree = 0.000) for 2081 atoms. Found 1 (11 requested) and removed 9 (5 requested) atoms. Cycle 10: After refmac, R = 0.1476 (Rfree = 0.000) for 2071 atoms. Found 2 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.51 3.70 Search for helices and strands: 0 residues in 0 chains, 2119 seeds are put forward NCS extension: 0 residues added, 2119 seeds are put forward Round 1: 85 peptides, 19 chains. Longest chain 8 peptides. Score 0.226 Round 2: 98 peptides, 20 chains. Longest chain 7 peptides. Score 0.281 Round 3: 95 peptides, 17 chains. Longest chain 10 peptides. Score 0.338 Round 4: 85 peptides, 16 chains. Longest chain 7 peptides. Score 0.305 Round 5: 90 peptides, 17 chains. Longest chain 8 peptides. Score 0.309 Taking the results from Round 3 Chains 17, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2868 reflections ( 97.72 % complete ) and 4929 restraints for refining 2114 atoms. 4634 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1834 (Rfree = 0.000) for 2114 atoms. Found 4 (11 requested) and removed 13 (5 requested) atoms. Cycle 12: After refmac, R = 0.1712 (Rfree = 0.000) for 2101 atoms. Found 4 (11 requested) and removed 7 (5 requested) atoms. Cycle 13: After refmac, R = 0.1691 (Rfree = 0.000) for 2097 atoms. Found 2 (11 requested) and removed 6 (5 requested) atoms. Cycle 14: After refmac, R = 0.1704 (Rfree = 0.000) for 2092 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 15: After refmac, R = 0.1678 (Rfree = 0.000) for 2086 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 3.77 Search for helices and strands: 0 residues in 0 chains, 2116 seeds are put forward NCS extension: 0 residues added, 2116 seeds are put forward Round 1: 95 peptides, 20 chains. Longest chain 7 peptides. Score 0.263 Round 2: 112 peptides, 22 chains. Longest chain 12 peptides. Score 0.313 Round 3: 121 peptides, 23 chains. Longest chain 10 peptides. Score 0.340 Round 4: 116 peptides, 23 chains. Longest chain 9 peptides. Score 0.312 Round 5: 101 peptides, 18 chains. Longest chain 10 peptides. Score 0.348 Taking the results from Round 5 Chains 18, Residues 83, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2868 reflections ( 97.72 % complete ) and 5187 restraints for refining 2214 atoms. 4873 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2040 (Rfree = 0.000) for 2214 atoms. Found 10 (12 requested) and removed 18 (6 requested) atoms. Cycle 17: After refmac, R = 0.1895 (Rfree = 0.000) for 2202 atoms. Found 5 (12 requested) and removed 9 (6 requested) atoms. Cycle 18: After refmac, R = 0.1854 (Rfree = 0.000) for 2197 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 19: After refmac, R = 0.1832 (Rfree = 0.000) for 2190 atoms. Found 1 (12 requested) and removed 8 (6 requested) atoms. Cycle 20: After refmac, R = 0.1809 (Rfree = 0.000) for 2183 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.58 3.78 Search for helices and strands: 0 residues in 0 chains, 2201 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 2204 seeds are put forward Round 1: 101 peptides, 22 chains. Longest chain 12 peptides. Score 0.249 Round 2: 103 peptides, 21 chains. Longest chain 7 peptides. Score 0.285 Round 3: 113 peptides, 22 chains. Longest chain 10 peptides. Score 0.319 Round 4: 110 peptides, 19 chains. Longest chain 11 peptides. Score 0.374 Round 5: 99 peptides, 19 chains. Longest chain 10 peptides. Score 0.312 Taking the results from Round 4 Chains 19, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2868 reflections ( 97.72 % complete ) and 5051 restraints for refining 2214 atoms. 4706 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2246 (Rfree = 0.000) for 2214 atoms. Found 3 (12 requested) and removed 9 (6 requested) atoms. Cycle 22: After refmac, R = 0.2015 (Rfree = 0.000) for 2202 atoms. Found 8 (12 requested) and removed 9 (6 requested) atoms. Cycle 23: After refmac, R = 0.1906 (Rfree = 0.000) for 2198 atoms. Found 2 (12 requested) and removed 8 (6 requested) atoms. Cycle 24: After refmac, R = 0.1944 (Rfree = 0.000) for 2190 atoms. Found 4 (12 requested) and removed 8 (6 requested) atoms. Cycle 25: After refmac, R = 0.1993 (Rfree = 0.000) for 2180 atoms. Found 4 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.60 3.80 Search for helices and strands: 0 residues in 0 chains, 2231 seeds are put forward NCS extension: 6 residues added (1 deleted due to clashes), 2237 seeds are put forward Round 1: 100 peptides, 22 chains. Longest chain 7 peptides. Score 0.242 Round 2: 105 peptides, 22 chains. Longest chain 7 peptides. Score 0.273 Round 3: 110 peptides, 20 chains. Longest chain 10 peptides. Score 0.350 Round 4: 99 peptides, 19 chains. Longest chain 9 peptides. Score 0.312 Round 5: 108 peptides, 20 chains. Longest chain 10 peptides. Score 0.339 Taking the results from Round 3 Chains 20, Residues 90, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2868 reflections ( 97.72 % complete ) and 5117 restraints for refining 2214 atoms. 4777 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1791 (Rfree = 0.000) for 2214 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. Cycle 27: After refmac, R = 0.1567 (Rfree = 0.000) for 2201 atoms. Found 2 (12 requested) and removed 6 (6 requested) atoms. Cycle 28: After refmac, R = 0.1572 (Rfree = 0.000) for 2190 atoms. Found 0 (12 requested) and removed 7 (6 requested) atoms. Cycle 29: After refmac, R = 0.1459 (Rfree = 0.000) for 2180 atoms. Found 0 (12 requested) and removed 7 (6 requested) atoms. Cycle 30: After refmac, R = 0.1523 (Rfree = 0.000) for 2173 atoms. Found 1 (11 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.57 3.77 Search for helices and strands: 0 residues in 0 chains, 2214 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 2217 seeds are put forward Round 1: 78 peptides, 18 chains. Longest chain 6 peptides. Score 0.207 Round 2: 105 peptides, 20 chains. Longest chain 8 peptides. Score 0.322 Round 3: 99 peptides, 19 chains. Longest chain 8 peptides. Score 0.312 Round 4: 102 peptides, 19 chains. Longest chain 9 peptides. Score 0.329 Round 5: 99 peptides, 18 chains. Longest chain 10 peptides. Score 0.337 Taking the results from Round 5 Chains 18, Residues 81, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2868 reflections ( 97.72 % complete ) and 5060 restraints for refining 2206 atoms. 4754 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2207 (Rfree = 0.000) for 2206 atoms. Found 8 (12 requested) and removed 13 (6 requested) atoms. Cycle 32: After refmac, R = 0.1999 (Rfree = 0.000) for 2190 atoms. Found 8 (12 requested) and removed 10 (6 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2127 (Rfree = 0.000) for 2183 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 34: After refmac, R = 0.1389 (Rfree = 0.000) for 2177 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 35: After refmac, R = 0.1317 (Rfree = 0.000) for 2168 atoms. Found 3 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.55 3.74 Search for helices and strands: 0 residues in 0 chains, 2207 seeds are put forward NCS extension: 0 residues added, 2207 seeds are put forward Round 1: 72 peptides, 15 chains. Longest chain 6 peptides. Score 0.250 Round 2: 85 peptides, 18 chains. Longest chain 8 peptides. Score 0.253 Round 3: 96 peptides, 17 chains. Longest chain 10 peptides. Score 0.344 Round 4: 84 peptides, 17 chains. Longest chain 8 peptides. Score 0.273 Round 5: 84 peptides, 16 chains. Longest chain 8 peptides. Score 0.299 Taking the results from Round 3 Chains 17, Residues 79, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2868 reflections ( 97.72 % complete ) and 4998 restraints for refining 2185 atoms. 4699 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1895 (Rfree = 0.000) for 2185 atoms. Found 9 (12 requested) and removed 9 (6 requested) atoms. Cycle 37: After refmac, R = 0.2114 (Rfree = 0.000) for 2175 atoms. Found 11 (12 requested) and removed 9 (6 requested) atoms. Cycle 38: After refmac, R = 0.1915 (Rfree = 0.000) for 2174 atoms. Found 8 (11 requested) and removed 9 (5 requested) atoms. Cycle 39: After refmac, R = 0.1931 (Rfree = 0.000) for 2167 atoms. Found 10 (11 requested) and removed 10 (5 requested) atoms. Cycle 40: After refmac, R = 0.1988 (Rfree = 0.000) for 2163 atoms. Found 11 (11 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.59 3.79 Search for helices and strands: 0 residues in 0 chains, 2221 seeds are put forward NCS extension: 0 residues added, 2221 seeds are put forward Round 1: 58 peptides, 13 chains. Longest chain 6 peptides. Score 0.212 Round 2: 69 peptides, 15 chains. Longest chain 7 peptides. Score 0.230 Round 3: 69 peptides, 14 chains. Longest chain 7 peptides. Score 0.259 Round 4: 65 peptides, 13 chains. Longest chain 7 peptides. Score 0.260 Round 5: 60 peptides, 11 chains. Longest chain 9 peptides. Score 0.285 Taking the results from Round 5 Chains 11, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2868 reflections ( 97.72 % complete ) and 5191 restraints for refining 2184 atoms. 5006 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1836 (Rfree = 0.000) for 2184 atoms. Found 8 (12 requested) and removed 9 (6 requested) atoms. Cycle 42: After refmac, R = 0.1898 (Rfree = 0.000) for 2178 atoms. Found 10 (12 requested) and removed 11 (6 requested) atoms. Cycle 43: After refmac, R = 0.1925 (Rfree = 0.000) for 2174 atoms. Found 8 (11 requested) and removed 9 (5 requested) atoms. Cycle 44: After refmac, R = 0.1884 (Rfree = 0.000) for 2169 atoms. Found 10 (11 requested) and removed 8 (5 requested) atoms. Cycle 45: After refmac, R = 0.1805 (Rfree = 0.000) for 2168 atoms. Found 6 (11 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.53 3.72 Search for helices and strands: 0 residues in 0 chains, 2215 seeds are put forward NCS extension: 0 residues added, 2215 seeds are put forward Round 1: 45 peptides, 11 chains. Longest chain 5 peptides. Score 0.175 Round 2: 56 peptides, 12 chains. Longest chain 7 peptides. Score 0.228 Round 3: 62 peptides, 12 chains. Longest chain 9 peptides. Score 0.269 Round 4: 64 peptides, 13 chains. Longest chain 9 peptides. Score 0.254 Round 5: 61 peptides, 11 chains. Longest chain 9 peptides. Score 0.292 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 50, 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 2prv-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2868 reflections ( 97.72 % complete ) and 4821 restraints for refining 2119 atoms. 4632 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1906 (Rfree = 0.000) for 2119 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.1883 (Rfree = 0.000) for 2108 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.1951 (Rfree = 0.000) for 2101 atoms. Found 0 (11 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.1795 (Rfree = 0.000) for 2094 atoms. TimeTaking 33.25