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 2hag-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hag-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hag-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hag-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/2hag-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hag-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 22:23:18 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/2hag-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hag-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 323 and 0 Target number of residues in the AU: 323 Target solvent content: 0.6584 Checking the provided sequence file Detected sequence length: 312 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 312 Adjusted target solvent content: 0.67 Input MTZ file: 2hag-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: 96 Cell parameters: 94.680 94.680 114.160 90.000 90.000 90.000 Input sequence file: 2hag-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 2496 target number of atoms Had to go as low as 1.00 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: 29.659 3.800 Wilson plot Bfac: 83.11 5458 reflections ( 99.56 % complete ) and 0 restraints for refining 2750 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.3431 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3241 (Rfree = 0.000) for 2750 atoms. Found 15 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.65 2.88 Search for helices and strands: 0 residues in 0 chains, 2808 seeds are put forward Round 1: 162 peptides, 29 chains. Longest chain 11 peptides. Score 0.341 Round 2: 199 peptides, 25 chains. Longest chain 19 peptides. Score 0.512 Round 3: 214 peptides, 21 chains. Longest chain 28 peptides. Score 0.600 Round 4: 213 peptides, 22 chains. Longest chain 22 peptides. Score 0.586 Round 5: 225 peptides, 22 chains. Longest chain 32 peptides. Score 0.614 Taking the results from Round 5 Chains 22, Residues 203, Estimated correctness of the model 5.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5458 reflections ( 99.56 % complete ) and 4806 restraints for refining 2258 atoms. 4016 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2752 (Rfree = 0.000) for 2258 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 2: After refmac, R = 0.2558 (Rfree = 0.000) for 2230 atoms. Found 8 (12 requested) and removed 11 (6 requested) atoms. Cycle 3: After refmac, R = 0.2490 (Rfree = 0.000) for 2212 atoms. Found 10 (12 requested) and removed 9 (6 requested) atoms. Cycle 4: After refmac, R = 0.2381 (Rfree = 0.000) for 2204 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 5: After refmac, R = 0.2376 (Rfree = 0.000) for 2187 atoms. Found 9 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.71 2.93 Search for helices and strands: 0 residues in 0 chains, 2283 seeds are put forward Round 1: 207 peptides, 24 chains. Longest chain 20 peptides. Score 0.546 Round 2: 206 peptides, 22 chains. Longest chain 21 peptides. Score 0.568 Round 3: 222 peptides, 21 chains. Longest chain 20 peptides. Score 0.619 Round 4: 230 peptides, 19 chains. Longest chain 21 peptides. Score 0.658 Round 5: 229 peptides, 20 chains. Longest chain 29 peptides. Score 0.645 Taking the results from Round 4 Chains 19, Residues 211, Estimated correctness of the model 24.1 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5458 reflections ( 99.56 % complete ) and 4838 restraints for refining 2258 atoms. 4013 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2691 (Rfree = 0.000) for 2258 atoms. Found 12 (12 requested) and removed 6 (6 requested) atoms. Cycle 7: After refmac, R = 0.2521 (Rfree = 0.000) for 2238 atoms. Found 6 (12 requested) and removed 8 (6 requested) atoms. Cycle 8: After refmac, R = 0.2435 (Rfree = 0.000) for 2221 atoms. Found 11 (12 requested) and removed 12 (6 requested) atoms. Cycle 9: After refmac, R = 0.2308 (Rfree = 0.000) for 2211 atoms. Found 9 (12 requested) and removed 11 (6 requested) atoms. Cycle 10: After refmac, R = 0.2245 (Rfree = 0.000) for 2205 atoms. Found 6 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.67 2.90 Search for helices and strands: 0 residues in 0 chains, 2277 seeds are put forward Round 1: 201 peptides, 26 chains. Longest chain 20 peptides. Score 0.505 Round 2: 207 peptides, 20 chains. Longest chain 25 peptides. Score 0.594 Round 3: 207 peptides, 20 chains. Longest chain 25 peptides. Score 0.594 Round 4: 215 peptides, 20 chains. Longest chain 28 peptides. Score 0.614 Round 5: 213 peptides, 22 chains. Longest chain 22 peptides. Score 0.586 Taking the results from Round 4 Chains 21, Residues 195, Estimated correctness of the model 5.3 % 2 chains (43 residues) have been docked in sequence ------------------------------------------------------ 5458 reflections ( 99.56 % complete ) and 4392 restraints for refining 2258 atoms. 3451 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2695 (Rfree = 0.000) for 2258 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 12: After refmac, R = 0.2524 (Rfree = 0.000) for 2228 atoms. Found 7 (12 requested) and removed 9 (6 requested) atoms. Cycle 13: After refmac, R = 0.2507 (Rfree = 0.000) for 2216 atoms. Found 9 (12 requested) and removed 8 (6 requested) atoms. Cycle 14: After refmac, R = 0.2484 (Rfree = 0.000) for 2210 atoms. Found 7 (12 requested) and removed 9 (6 requested) atoms. Cycle 15: After refmac, R = 0.2475 (Rfree = 0.000) for 2202 atoms. Found 7 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.66 2.89 Search for helices and strands: 0 residues in 0 chains, 2271 seeds are put forward Round 1: 178 peptides, 26 chains. Longest chain 14 peptides. Score 0.437 Round 2: 199 peptides, 21 chains. Longest chain 22 peptides. Score 0.562 Round 3: 202 peptides, 22 chains. Longest chain 21 peptides. Score 0.558 Round 4: 208 peptides, 23 chains. Longest chain 24 peptides. Score 0.561 Round 5: 199 peptides, 20 chains. Longest chain 26 peptides. Score 0.574 Taking the results from Round 5 Chains 24, Residues 179, Estimated correctness of the model 0.0 % 3 chains (35 residues) have been docked in sequence ------------------------------------------------------ 5458 reflections ( 99.56 % complete ) and 4624 restraints for refining 2258 atoms. 3789 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2810 (Rfree = 0.000) for 2258 atoms. Found 10 (12 requested) and removed 13 (6 requested) atoms. Cycle 17: After refmac, R = 0.2621 (Rfree = 0.000) for 2246 atoms. Found 5 (12 requested) and removed 12 (6 requested) atoms. Cycle 18: After refmac, R = 0.2543 (Rfree = 0.000) for 2236 atoms. Found 5 (12 requested) and removed 12 (6 requested) atoms. Cycle 19: After refmac, R = 0.2456 (Rfree = 0.000) for 2224 atoms. Found 4 (12 requested) and removed 8 (6 requested) atoms. Cycle 20: After refmac, R = 0.2401 (Rfree = 0.000) for 2218 atoms. Found 3 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.62 2.86 Search for helices and strands: 0 residues in 0 chains, 2283 seeds are put forward Round 1: 176 peptides, 25 chains. Longest chain 16 peptides. Score 0.445 Round 2: 203 peptides, 25 chains. Longest chain 26 peptides. Score 0.523 Round 3: 191 peptides, 26 chains. Longest chain 16 peptides. Score 0.476 Round 4: 189 peptides, 18 chains. Longest chain 19 peptides. Score 0.574 Round 5: 188 peptides, 20 chains. Longest chain 38 peptides. Score 0.546 Taking the results from Round 4 Chains 22, Residues 171, Estimated correctness of the model 0.0 % 3 chains (39 residues) have been docked in sequence ------------------------------------------------------ 5458 reflections ( 99.56 % complete ) and 4631 restraints for refining 2256 atoms. 3810 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3109 (Rfree = 0.000) for 2256 atoms. Found 12 (12 requested) and removed 26 (6 requested) atoms. Cycle 22: After refmac, R = 0.2760 (Rfree = 0.000) for 2212 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. Cycle 23: After refmac, R = 0.2690 (Rfree = 0.000) for 2203 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 24: After refmac, R = 0.2469 (Rfree = 0.000) for 2198 atoms. Found 6 (12 requested) and removed 8 (6 requested) atoms. Cycle 25: After refmac, R = 0.2365 (Rfree = 0.000) for 2195 atoms. Found 0 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.63 2.87 Search for helices and strands: 0 residues in 0 chains, 2259 seeds are put forward Round 1: 180 peptides, 28 chains. Longest chain 20 peptides. Score 0.415 Round 2: 174 peptides, 25 chains. Longest chain 16 peptides. Score 0.438 Round 3: 193 peptides, 21 chains. Longest chain 28 peptides. Score 0.546 Round 4: 181 peptides, 24 chains. Longest chain 22 peptides. Score 0.473 Round 5: 196 peptides, 26 chains. Longest chain 22 peptides. Score 0.490 Taking the results from Round 3 Chains 21, Residues 172, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5458 reflections ( 99.56 % complete ) and 4877 restraints for refining 2258 atoms. 4210 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2667 (Rfree = 0.000) for 2258 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 27: After refmac, R = 0.2665 (Rfree = 0.000) for 2244 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 28: After refmac, R = 0.2384 (Rfree = 0.000) for 2241 atoms. Found 2 (12 requested) and removed 8 (6 requested) atoms. Cycle 29: After refmac, R = 0.2414 (Rfree = 0.000) for 2232 atoms. Found 4 (12 requested) and removed 7 (6 requested) atoms. Cycle 30: After refmac, R = 0.2598 (Rfree = 0.000) for 2228 atoms. Found 4 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.63 2.87 Search for helices and strands: 0 residues in 0 chains, 2299 seeds are put forward Round 1: 157 peptides, 26 chains. Longest chain 14 peptides. Score 0.369 Round 2: 167 peptides, 24 chains. Longest chain 13 peptides. Score 0.431 Round 3: 180 peptides, 25 chains. Longest chain 14 peptides. Score 0.457 Round 4: 181 peptides, 23 chains. Longest chain 16 peptides. Score 0.487 Round 5: 182 peptides, 25 chains. Longest chain 17 peptides. Score 0.463 Taking the results from Round 4 Chains 23, Residues 158, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 5458 reflections ( 99.56 % complete ) and 5181 restraints for refining 2258 atoms. 4537 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3317 (Rfree = 0.000) for 2258 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 32: After refmac, R = 0.2910 (Rfree = 0.000) for 2226 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 33: After refmac, R = 0.2911 (Rfree = 0.000) for 2210 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 34: After refmac, R = 0.2723 (Rfree = 0.000) for 2197 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 35: After refmac, R = 0.2724 (Rfree = 0.000) for 2187 atoms. Found 10 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.66 2.89 Search for helices and strands: 0 residues in 0 chains, 2267 seeds are put forward Round 1: 162 peptides, 30 chains. Longest chain 12 peptides. Score 0.326 Round 2: 169 peptides, 25 chains. Longest chain 11 peptides. Score 0.423 Round 3: 177 peptides, 26 chains. Longest chain 14 peptides. Score 0.434 Round 4: 176 peptides, 27 chains. Longest chain 14 peptides. Score 0.417 Round 5: 185 peptides, 27 chains. Longest chain 12 peptides. Score 0.444 Taking the results from Round 5 Chains 27, Residues 158, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 5458 reflections ( 99.56 % complete ) and 5243 restraints for refining 2258 atoms. 4619 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3052 (Rfree = 0.000) for 2258 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 37: After refmac, R = 0.2834 (Rfree = 0.000) for 2235 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 38: After refmac, R = 0.3051 (Rfree = 0.000) for 2215 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 39: After refmac, R = 0.2695 (Rfree = 0.000) for 2194 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 40: After refmac, R = 0.2531 (Rfree = 0.000) for 2185 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.67 2.90 Search for helices and strands: 0 residues in 0 chains, 2288 seeds are put forward Round 1: 132 peptides, 25 chains. Longest chain 8 peptides. Score 0.296 Round 2: 165 peptides, 26 chains. Longest chain 16 peptides. Score 0.395 Round 3: 167 peptides, 26 chains. Longest chain 19 peptides. Score 0.402 Round 4: 167 peptides, 22 chains. Longest chain 16 peptides. Score 0.459 Round 5: 167 peptides, 23 chains. Longest chain 15 peptides. Score 0.445 Taking the results from Round 4 Chains 22, Residues 145, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5458 reflections ( 99.56 % complete ) and 5273 restraints for refining 2258 atoms. 4715 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2540 (Rfree = 0.000) for 2258 atoms. Found 4 (12 requested) and removed 9 (6 requested) atoms. Cycle 42: After refmac, R = 0.2398 (Rfree = 0.000) for 2244 atoms. Found 8 (12 requested) and removed 8 (6 requested) atoms. Cycle 43: After refmac, R = 0.2322 (Rfree = 0.000) for 2235 atoms. Found 2 (12 requested) and removed 9 (6 requested) atoms. Cycle 44: After refmac, R = 0.2346 (Rfree = 0.000) for 2227 atoms. Found 8 (12 requested) and removed 10 (6 requested) atoms. Cycle 45: After refmac, R = 0.2276 (Rfree = 0.000) for 2223 atoms. Found 8 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.66 2.89 Search for helices and strands: 0 residues in 0 chains, 2292 seeds are put forward Round 1: 149 peptides, 28 chains. Longest chain 8 peptides. Score 0.311 Round 2: 158 peptides, 23 chains. Longest chain 12 peptides. Score 0.417 Round 3: 170 peptides, 24 chains. Longest chain 19 peptides. Score 0.440 Round 4: 164 peptides, 23 chains. Longest chain 19 peptides. Score 0.436 Round 5: 172 peptides, 27 chains. Longest chain 14 peptides. Score 0.404 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 26, Residues 146, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2hag-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5458 reflections ( 99.56 % complete ) and 5156 restraints for refining 2257 atoms. 4556 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2529 (Rfree = 0.000) for 2257 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2372 (Rfree = 0.000) for 2236 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.2321 (Rfree = 0.000) for 2225 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.2298 (Rfree = 0.000) for 2215 atoms. TimeTaking 48.1