Tue 25 Dec 19:27:57 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 2gvk-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gvk-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gvk-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvk-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/2gvk-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvk-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 ============================================================ Tue 25 Dec 19:28:06 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/2gvk-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gvk-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 265 and 0 Target number of residues in the AU: 265 Target solvent content: 0.6590 Checking the provided sequence file Detected sequence length: 317 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 317 Adjusted target solvent content: 0.59 Input MTZ file: 2gvk-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: 182 Cell parameters: 109.180 109.180 122.210 90.000 90.000 120.000 Input sequence file: 2gvk-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2536 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: 29.072 4.001 Wilson plot Bfac: 84.22 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 3957 reflections ( 99.47 % complete ) and 0 restraints for refining 2808 atoms. Observations/parameters ratio is 0.35 ------------------------------------------------------ Starting model: R = 0.3496 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3395 (Rfree = 0.000) for 2808 atoms. Found 13 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.84 3.40 Search for helices and strands: 0 residues in 0 chains, 2846 seeds are put forward Round 1: 132 peptides, 24 chains. Longest chain 17 peptides. Score 0.334 Round 2: 165 peptides, 23 chains. Longest chain 21 peptides. Score 0.478 Round 3: 179 peptides, 24 chains. Longest chain 23 peptides. Score 0.511 Round 4: 185 peptides, 21 chains. Longest chain 25 peptides. Score 0.574 Round 5: 185 peptides, 24 chains. Longest chain 27 peptides. Score 0.531 Taking the results from Round 4 Chains 22, Residues 164, Estimated correctness of the model 0.0 % 2 chains (25 residues) have been docked in sequence ------------------------------------------------------ 3957 reflections ( 99.47 % complete ) and 4950 restraints for refining 2288 atoms. 4224 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2922 (Rfree = 0.000) for 2288 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 2: After refmac, R = 0.2781 (Rfree = 0.000) for 2229 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 3: After refmac, R = 0.2566 (Rfree = 0.000) for 2197 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 4: After refmac, R = 0.2289 (Rfree = 0.000) for 2167 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 5: After refmac, R = 0.2297 (Rfree = 0.000) for 2159 atoms. Found 10 (10 requested) and removed 18 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.70 3.28 Search for helices and strands: 0 residues in 0 chains, 2234 seeds are put forward Round 1: 161 peptides, 23 chains. Longest chain 16 peptides. Score 0.464 Round 2: 170 peptides, 23 chains. Longest chain 20 peptides. Score 0.496 Round 3: 179 peptides, 22 chains. Longest chain 26 peptides. Score 0.541 Round 4: 172 peptides, 21 chains. Longest chain 16 peptides. Score 0.533 Round 5: 163 peptides, 21 chains. Longest chain 17 peptides. Score 0.503 Taking the results from Round 3 Chains 22, Residues 157, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3957 reflections ( 99.47 % complete ) and 5106 restraints for refining 2254 atoms. 4482 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2855 (Rfree = 0.000) for 2254 atoms. Found 10 (10 requested) and removed 20 (5 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2364 (Rfree = 0.000) for 2223 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 8: After refmac, R = 0.2179 (Rfree = 0.000) for 2212 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2165 (Rfree = 0.000) for 2194 atoms. Found 10 (10 requested) and removed 20 (5 requested) atoms. Cycle 10: After refmac, R = 0.2178 (Rfree = 0.000) for 2172 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.73 3.30 Search for helices and strands: 0 residues in 0 chains, 2264 seeds are put forward Round 1: 151 peptides, 27 chains. Longest chain 11 peptides. Score 0.358 Round 2: 178 peptides, 22 chains. Longest chain 22 peptides. Score 0.538 Round 3: 187 peptides, 22 chains. Longest chain 19 peptides. Score 0.566 Round 4: 186 peptides, 22 chains. Longest chain 16 peptides. Score 0.563 Round 5: 186 peptides, 21 chains. Longest chain 27 peptides. Score 0.577 Taking the results from Round 5 Chains 21, Residues 165, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3957 reflections ( 99.47 % complete ) and 5088 restraints for refining 2290 atoms. 4410 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2558 (Rfree = 0.000) for 2290 atoms. Found 10 (10 requested) and removed 19 (5 requested) atoms. Cycle 12: After refmac, R = 0.2328 (Rfree = 0.000) for 2244 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2260 (Rfree = 0.000) for 2220 atoms. Found 6 (10 requested) and removed 11 (5 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2232 (Rfree = 0.000) for 2208 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 15: After refmac, R = 0.2231 (Rfree = 0.000) for 2197 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.74 3.31 Search for helices and strands: 0 residues in 0 chains, 2293 seeds are put forward Round 1: 179 peptides, 26 chains. Longest chain 16 peptides. Score 0.480 Round 2: 190 peptides, 24 chains. Longest chain 17 peptides. Score 0.547 Round 3: 185 peptides, 26 chains. Longest chain 15 peptides. Score 0.501 Round 4: 179 peptides, 19 chains. Longest chain 23 peptides. Score 0.585 Round 5: 190 peptides, 25 chains. Longest chain 19 peptides. Score 0.533 Taking the results from Round 4 Chains 20, Residues 160, Estimated correctness of the model 0.0 % 2 chains (32 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3957 reflections ( 99.47 % complete ) and 4645 restraints for refining 2288 atoms. 3893 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2587 (Rfree = 0.000) for 2288 atoms. Found 9 (10 requested) and removed 29 (5 requested) atoms. Cycle 17: After refmac, R = 0.2424 (Rfree = 0.000) for 2233 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2447 (Rfree = 0.000) for 2211 atoms. Found 10 (10 requested) and removed 15 (5 requested) atoms. Cycle 19: After refmac, R = 0.2257 (Rfree = 0.000) for 2200 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 20: After refmac, R = 0.2287 (Rfree = 0.000) for 2189 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.70 3.28 Search for helices and strands: 0 residues in 0 chains, 2274 seeds are put forward Round 1: 157 peptides, 26 chains. Longest chain 14 peptides. Score 0.399 Round 2: 167 peptides, 25 chains. Longest chain 11 peptides. Score 0.453 Round 3: 159 peptides, 26 chains. Longest chain 13 peptides. Score 0.407 Round 4: 165 peptides, 25 chains. Longest chain 14 peptides. Score 0.446 Round 5: 159 peptides, 22 chains. Longest chain 14 peptides. Score 0.473 Taking the results from Round 5 Chains 24, Residues 137, Estimated correctness of the model 0.0 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 3957 reflections ( 99.47 % complete ) and 5070 restraints for refining 2290 atoms. 4459 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2435 (Rfree = 0.000) for 2290 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2253 (Rfree = 0.000) for 2268 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 23: After refmac, R = 0.2190 (Rfree = 0.000) for 2251 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 24: After refmac, R = 0.2137 (Rfree = 0.000) for 2236 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Cycle 25: After refmac, R = 0.2097 (Rfree = 0.000) for 2232 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.73 3.30 Search for helices and strands: 0 residues in 0 chains, 2323 seeds are put forward Round 1: 133 peptides, 25 chains. Longest chain 10 peptides. Score 0.319 Round 2: 159 peptides, 23 chains. Longest chain 29 peptides. Score 0.457 Round 3: 151 peptides, 21 chains. Longest chain 25 peptides. Score 0.461 Round 4: 161 peptides, 26 chains. Longest chain 12 peptides. Score 0.415 Round 5: 159 peptides, 19 chains. Longest chain 18 peptides. Score 0.521 Taking the results from Round 5 Chains 20, Residues 140, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 3957 reflections ( 99.47 % complete ) and 5024 restraints for refining 2290 atoms. 4397 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2436 (Rfree = 0.000) for 2290 atoms. Found 10 (10 requested) and removed 17 (5 requested) atoms. Cycle 27: After refmac, R = 0.2301 (Rfree = 0.000) for 2262 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2222 (Rfree = 0.000) for 2241 atoms. Found 7 (10 requested) and removed 14 (5 requested) atoms. Cycle 29: After refmac, R = 0.2151 (Rfree = 0.000) for 2221 atoms. Found 10 (10 requested) and removed 10 (5 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2086 (Rfree = 0.000) for 2213 atoms. Found 8 (10 requested) and removed 12 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.69 3.27 Search for helices and strands: 0 residues in 0 chains, 2280 seeds are put forward Round 1: 132 peptides, 23 chains. Longest chain 11 peptides. Score 0.352 Round 2: 155 peptides, 27 chains. Longest chain 9 peptides. Score 0.374 Round 3: 160 peptides, 23 chains. Longest chain 16 peptides. Score 0.460 Round 4: 171 peptides, 27 chains. Longest chain 13 peptides. Score 0.436 Round 5: 165 peptides, 25 chains. Longest chain 11 peptides. Score 0.446 Taking the results from Round 3 Chains 23, Residues 137, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3957 reflections ( 99.47 % complete ) and 5336 restraints for refining 2290 atoms. 4811 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2324 (Rfree = 0.000) for 2290 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2358 (Rfree = 0.000) for 2267 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 33: After refmac, R = 0.2211 (Rfree = 0.000) for 2251 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 34: After refmac, R = 0.2167 (Rfree = 0.000) for 2239 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 35: After refmac, R = 0.1841 (Rfree = 0.000) for 2225 atoms. Found 2 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.77 3.34 Search for helices and strands: 0 residues in 0 chains, 2320 seeds are put forward Round 1: 146 peptides, 30 chains. Longest chain 9 peptides. Score 0.284 Round 2: 165 peptides, 27 chains. Longest chain 15 peptides. Score 0.413 Round 3: 153 peptides, 24 chains. Longest chain 14 peptides. Score 0.418 Round 4: 148 peptides, 24 chains. Longest chain 13 peptides. Score 0.399 Round 5: 164 peptides, 22 chains. Longest chain 18 peptides. Score 0.491 Taking the results from Round 5 Chains 22, Residues 142, Estimated correctness of the model 0.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 3957 reflections ( 99.47 % complete ) and 5107 restraints for refining 2290 atoms. 4507 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2522 (Rfree = 0.000) for 2290 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 37: After refmac, R = 0.2270 (Rfree = 0.000) for 2261 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.2175 (Rfree = 0.000) for 2247 atoms. Found 8 (10 requested) and removed 7 (5 requested) atoms. Cycle 39: After refmac, R = 0.2136 (Rfree = 0.000) for 2233 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 40: After refmac, R = 0.2189 (Rfree = 0.000) for 2223 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.75 3.32 Search for helices and strands: 0 residues in 0 chains, 2304 seeds are put forward Round 1: 117 peptides, 24 chains. Longest chain 8 peptides. Score 0.268 Round 2: 148 peptides, 25 chains. Longest chain 14 peptides. Score 0.381 Round 3: 142 peptides, 22 chains. Longest chain 16 peptides. Score 0.410 Round 4: 150 peptides, 23 chains. Longest chain 17 peptides. Score 0.423 Round 5: 152 peptides, 25 chains. Longest chain 10 peptides. Score 0.397 Taking the results from Round 4 Chains 23, Residues 127, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 3957 reflections ( 99.47 % complete ) and 5001 restraints for refining 2290 atoms. 4435 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2446 (Rfree = 0.000) for 2290 atoms. Found 10 (10 requested) and removed 39 (5 requested) atoms. Cycle 42: After refmac, R = 0.2232 (Rfree = 0.000) for 2242 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 43: After refmac, R = 0.2168 (Rfree = 0.000) for 2227 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 44: After refmac, R = 0.2177 (Rfree = 0.000) for 2211 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 45: After refmac, R = 0.2247 (Rfree = 0.000) for 2201 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.74 3.31 Search for helices and strands: 0 residues in 0 chains, 2282 seeds are put forward Round 1: 124 peptides, 23 chains. Longest chain 11 peptides. Score 0.318 Round 2: 149 peptides, 26 chains. Longest chain 16 peptides. Score 0.368 Round 3: 143 peptides, 23 chains. Longest chain 9 peptides. Score 0.396 Round 4: 143 peptides, 25 chains. Longest chain 10 peptides. Score 0.361 Round 5: 153 peptides, 25 chains. Longest chain 15 peptides. Score 0.401 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 128, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2gvk-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3957 reflections ( 99.47 % complete ) and 5067 restraints for refining 2290 atoms. 4534 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2307 (Rfree = 0.000) for 2290 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2227 (Rfree = 0.000) for 2264 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2197 (Rfree = 0.000) for 2246 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.2170 (Rfree = 0.000) for 2225 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:23:09 GMT 2018 Job finished. TimeTaking 55.2