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 2eth-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2eth-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2eth-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2eth-3.4-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/2eth-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2eth-3.4-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/2eth-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2eth-3.4-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 243 and 0 Target number of residues in the AU: 243 Target solvent content: 0.6505 Checking the provided sequence file Detected sequence length: 154 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 308 Adjusted target solvent content: 0.56 Input MTZ file: 2eth-3.4-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: 5 Cell parameters: 98.852 58.439 80.432 90.000 125.913 90.000 Input sequence file: 2eth-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2464 target number of atoms Had to go as low as 0.80 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: 65.143 3.400 Wilson plot Bfac: 78.41 5128 reflections ( 98.18 % complete ) and 0 restraints for refining 2739 atoms. Observations/parameters ratio is 0.47 ------------------------------------------------------ Starting model: R = 0.3341 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3305 (Rfree = 0.000) for 2739 atoms. Found 20 (20 requested) and removed 11 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.47 3.20 Search for helices and strands: 0 residues in 0 chains, 2812 seeds are put forward NCS extension: 0 residues added, 2812 seeds are put forward Round 1: 109 peptides, 19 chains. Longest chain 11 peptides. Score 0.341 Round 2: 143 peptides, 20 chains. Longest chain 25 peptides. Score 0.470 Round 3: 153 peptides, 24 chains. Longest chain 11 peptides. Score 0.439 Round 4: 165 peptides, 20 chains. Longest chain 24 peptides. Score 0.553 Round 5: 159 peptides, 19 chains. Longest chain 28 peptides. Score 0.548 Taking the results from Round 4 Chains 20, Residues 145, Estimated correctness of the model 12.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5128 reflections ( 98.18 % complete ) and 5009 restraints for refining 2181 atoms. 4449 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2713 (Rfree = 0.000) for 2181 atoms. Found 16 (16 requested) and removed 11 (8 requested) atoms. Cycle 2: After refmac, R = 0.2657 (Rfree = 0.000) for 2145 atoms. Found 14 (16 requested) and removed 13 (8 requested) atoms. Cycle 3: After refmac, R = 0.2565 (Rfree = 0.000) for 2130 atoms. Found 9 (16 requested) and removed 9 (8 requested) atoms. Cycle 4: After refmac, R = 0.2477 (Rfree = 0.000) for 2127 atoms. Found 10 (16 requested) and removed 13 (8 requested) atoms. Cycle 5: After refmac, R = 0.2393 (Rfree = 0.000) for 2117 atoms. Found 3 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.47 3.20 Search for helices and strands: 0 residues in 0 chains, 2220 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 2249 seeds are put forward Round 1: 150 peptides, 21 chains. Longest chain 13 peptides. Score 0.480 Round 2: 161 peptides, 21 chains. Longest chain 22 peptides. Score 0.522 Round 3: 153 peptides, 20 chains. Longest chain 20 peptides. Score 0.509 Round 4: 168 peptides, 20 chains. Longest chain 19 peptides. Score 0.564 Round 5: 159 peptides, 19 chains. Longest chain 16 peptides. Score 0.548 Taking the results from Round 4 Chains 21, Residues 148, Estimated correctness of the model 16.5 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 5128 reflections ( 98.18 % complete ) and 4911 restraints for refining 2181 atoms. 4302 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2518 (Rfree = 0.000) for 2181 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 7: After refmac, R = 0.2471 (Rfree = 0.000) for 2168 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 8: After refmac, R = 0.2465 (Rfree = 0.000) for 2161 atoms. Found 11 (16 requested) and removed 10 (8 requested) atoms. Cycle 9: After refmac, R = 0.2361 (Rfree = 0.000) for 2157 atoms. Found 13 (16 requested) and removed 9 (8 requested) atoms. Cycle 10: After refmac, R = 0.2314 (Rfree = 0.000) for 2157 atoms. Found 10 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.49 3.22 Search for helices and strands: 0 residues in 0 chains, 2261 seeds are put forward NCS extension: 8 residues added (0 deleted due to clashes), 2269 seeds are put forward Round 1: 161 peptides, 22 chains. Longest chain 16 peptides. Score 0.505 Round 2: 169 peptides, 22 chains. Longest chain 15 peptides. Score 0.535 Round 3: 169 peptides, 21 chains. Longest chain 17 peptides. Score 0.551 Round 4: 184 peptides, 21 chains. Longest chain 18 peptides. Score 0.602 Round 5: 184 peptides, 20 chains. Longest chain 36 peptides. Score 0.616 Taking the results from Round 5 Chains 20, Residues 164, Estimated correctness of the model 33.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5128 reflections ( 98.18 % complete ) and 4972 restraints for refining 2228 atoms. 4336 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2524 (Rfree = 0.000) for 2228 atoms. Found 10 (16 requested) and removed 16 (8 requested) atoms. Cycle 12: After refmac, R = 0.2436 (Rfree = 0.000) for 2213 atoms. Found 10 (16 requested) and removed 11 (8 requested) atoms. Cycle 13: After refmac, R = 0.2455 (Rfree = 0.000) for 2204 atoms. Found 11 (16 requested) and removed 12 (8 requested) atoms. Cycle 14: After refmac, R = 0.2337 (Rfree = 0.000) for 2201 atoms. Found 12 (16 requested) and removed 10 (8 requested) atoms. Cycle 15: After refmac, R = 0.2355 (Rfree = 0.000) for 2199 atoms. Found 5 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.54 3.27 Search for helices and strands: 0 residues in 0 chains, 2288 seeds are put forward NCS extension: 21 residues added (5 deleted due to clashes), 2309 seeds are put forward Round 1: 147 peptides, 24 chains. Longest chain 14 peptides. Score 0.413 Round 2: 158 peptides, 18 chains. Longest chain 18 peptides. Score 0.561 Round 3: 159 peptides, 21 chains. Longest chain 17 peptides. Score 0.515 Round 4: 155 peptides, 20 chains. Longest chain 21 peptides. Score 0.517 Round 5: 152 peptides, 21 chains. Longest chain 15 peptides. Score 0.488 Taking the results from Round 2 Chains 18, Residues 140, Estimated correctness of the model 15.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5128 reflections ( 98.18 % complete ) and 5073 restraints for refining 2232 atoms. 4531 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2424 (Rfree = 0.000) for 2232 atoms. Found 14 (16 requested) and removed 11 (8 requested) atoms. Cycle 17: After refmac, R = 0.3048 (Rfree = 0.000) for 2229 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 18: After refmac, R = 0.2247 (Rfree = 0.000) for 2227 atoms. Found 4 (16 requested) and removed 11 (8 requested) atoms. Cycle 19: After refmac, R = 0.2345 (Rfree = 0.000) for 2217 atoms. Found 16 (16 requested) and removed 14 (8 requested) atoms. Cycle 20: After refmac, R = 0.2267 (Rfree = 0.000) for 2214 atoms. Found 12 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.52 3.25 Search for helices and strands: 0 residues in 0 chains, 2317 seeds are put forward NCS extension: 12 residues added (6 deleted due to clashes), 2329 seeds are put forward Round 1: 129 peptides, 21 chains. Longest chain 13 peptides. Score 0.393 Round 2: 150 peptides, 22 chains. Longest chain 21 peptides. Score 0.462 Round 3: 152 peptides, 22 chains. Longest chain 17 peptides. Score 0.470 Round 4: 152 peptides, 20 chains. Longest chain 16 peptides. Score 0.505 Round 5: 151 peptides, 21 chains. Longest chain 20 peptides. Score 0.484 Taking the results from Round 4 Chains 20, Residues 132, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5128 reflections ( 98.18 % complete ) and 5173 restraints for refining 2241 atoms. 4665 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2394 (Rfree = 0.000) for 2241 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. Cycle 22: After refmac, R = 0.2218 (Rfree = 0.000) for 2239 atoms. Found 14 (16 requested) and removed 11 (8 requested) atoms. Cycle 23: After refmac, R = 0.2312 (Rfree = 0.000) for 2233 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. Cycle 24: After refmac, R = 0.2302 (Rfree = 0.000) for 2233 atoms. Found 16 (16 requested) and removed 9 (8 requested) atoms. Cycle 25: After refmac, R = 0.2804 (Rfree = 0.000) for 2237 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.56 3.29 Search for helices and strands: 0 residues in 0 chains, 2329 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 2349 seeds are put forward Round 1: 113 peptides, 21 chains. Longest chain 11 peptides. Score 0.319 Round 2: 127 peptides, 18 chains. Longest chain 15 peptides. Score 0.442 Round 3: 135 peptides, 20 chains. Longest chain 15 peptides. Score 0.437 Round 4: 135 peptides, 19 chains. Longest chain 14 peptides. Score 0.456 Round 5: 139 peptides, 20 chains. Longest chain 12 peptides. Score 0.454 Taking the results from Round 4 Chains 19, Residues 116, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5128 reflections ( 98.18 % complete ) and 5088 restraints for refining 2219 atoms. 4643 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2525 (Rfree = 0.000) for 2219 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 27: After refmac, R = 0.3001 (Rfree = 0.000) for 2207 atoms. Found 16 (16 requested) and removed 56 (8 requested) atoms. Cycle 28: After refmac, R = 0.2273 (Rfree = 0.000) for 2156 atoms. Found 13 (16 requested) and removed 8 (8 requested) atoms. Cycle 29: After refmac, R = 0.2718 (Rfree = 0.000) for 2155 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 30: After refmac, R = 0.2468 (Rfree = 0.000) for 2152 atoms. Found 16 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.59 3.31 Search for helices and strands: 0 residues in 0 chains, 2261 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2274 seeds are put forward Round 1: 115 peptides, 23 chains. Longest chain 11 peptides. Score 0.287 Round 2: 134 peptides, 23 chains. Longest chain 13 peptides. Score 0.376 Round 3: 138 peptides, 22 chains. Longest chain 14 peptides. Score 0.413 Round 4: 132 peptides, 20 chains. Longest chain 14 peptides. Score 0.425 Round 5: 138 peptides, 21 chains. Longest chain 14 peptides. Score 0.431 Taking the results from Round 5 Chains 21, Residues 117, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5128 reflections ( 98.18 % complete ) and 5138 restraints for refining 2215 atoms. 4691 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2542 (Rfree = 0.000) for 2215 atoms. Found 16 (16 requested) and removed 16 (8 requested) atoms. Cycle 32: After refmac, R = 0.2477 (Rfree = 0.000) for 2206 atoms. Found 9 (16 requested) and removed 9 (8 requested) atoms. Cycle 33: After refmac, R = 0.2482 (Rfree = 0.000) for 2202 atoms. Found 13 (16 requested) and removed 20 (8 requested) atoms. Cycle 34: After refmac, R = 0.2192 (Rfree = 0.000) for 2180 atoms. Found 6 (16 requested) and removed 8 (8 requested) atoms. Cycle 35: After refmac, R = 0.1973 (Rfree = 0.000) for 2174 atoms. Found 3 (16 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.50 3.23 Search for helices and strands: 0 residues in 0 chains, 2286 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 2292 seeds are put forward Round 1: 121 peptides, 23 chains. Longest chain 9 peptides. Score 0.316 Round 2: 141 peptides, 26 chains. Longest chain 9 peptides. Score 0.349 Round 3: 137 peptides, 20 chains. Longest chain 17 peptides. Score 0.446 Round 4: 134 peptides, 20 chains. Longest chain 17 peptides. Score 0.433 Round 5: 140 peptides, 18 chains. Longest chain 17 peptides. Score 0.494 Taking the results from Round 5 Chains 18, Residues 122, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5128 reflections ( 98.18 % complete ) and 5088 restraints for refining 2241 atoms. 4618 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2212 (Rfree = 0.000) for 2241 atoms. Found 11 (16 requested) and removed 10 (8 requested) atoms. Cycle 37: After refmac, R = 0.2171 (Rfree = 0.000) for 2238 atoms. Found 8 (16 requested) and removed 9 (8 requested) atoms. Cycle 38: After refmac, R = 0.1994 (Rfree = 0.000) for 2233 atoms. Found 6 (16 requested) and removed 11 (8 requested) atoms. Cycle 39: After refmac, R = 0.2028 (Rfree = 0.000) for 2224 atoms. Found 8 (16 requested) and removed 8 (8 requested) atoms. Cycle 40: After refmac, R = 0.2047 (Rfree = 0.000) for 2219 atoms. Found 10 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.51 3.24 Search for helices and strands: 0 residues in 0 chains, 2323 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 2341 seeds are put forward Round 1: 117 peptides, 22 chains. Longest chain 16 peptides. Score 0.317 Round 2: 138 peptides, 23 chains. Longest chain 16 peptides. Score 0.394 Round 3: 151 peptides, 24 chains. Longest chain 17 peptides. Score 0.430 Round 4: 153 peptides, 23 chains. Longest chain 17 peptides. Score 0.456 Round 5: 146 peptides, 21 chains. Longest chain 17 peptides. Score 0.464 Taking the results from Round 5 Chains 21, Residues 125, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5128 reflections ( 98.18 % complete ) and 5145 restraints for refining 2240 atoms. 4666 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2235 (Rfree = 0.000) for 2240 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.2188 (Rfree = 0.000) for 2221 atoms. Found 4 (16 requested) and removed 10 (8 requested) atoms. Cycle 43: After refmac, R = 0.2053 (Rfree = 0.000) for 2212 atoms. Found 6 (16 requested) and removed 10 (8 requested) atoms. Cycle 44: After refmac, R = 0.2035 (Rfree = 0.000) for 2200 atoms. Found 7 (16 requested) and removed 8 (8 requested) atoms. Cycle 45: After refmac, R = 0.2013 (Rfree = 0.000) for 2198 atoms. Found 7 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.46 3.19 Search for helices and strands: 0 residues in 0 chains, 2299 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 2317 seeds are put forward Round 1: 108 peptides, 21 chains. Longest chain 8 peptides. Score 0.295 Round 2: 107 peptides, 19 chains. Longest chain 12 peptides. Score 0.332 Round 3: 106 peptides, 19 chains. Longest chain 9 peptides. Score 0.327 Round 4: 121 peptides, 22 chains. Longest chain 12 peptides. Score 0.336 Round 5: 124 peptides, 22 chains. Longest chain 13 peptides. Score 0.350 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 22, Residues 102, 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 2eth-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5128 reflections ( 98.18 % complete ) and 5396 restraints for refining 2240 atoms. 5010 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2240 (Rfree = 0.000) for 2240 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2150 (Rfree = 0.000) for 2226 atoms. Found 0 (16 requested) and removed 6 (8 requested) atoms. Cycle 48: After refmac, R = 0.2142 (Rfree = 0.000) for 2217 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2103 (Rfree = 0.000) for 2206 atoms. TimeTaking 47.1