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 2hag-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hag-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hag-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hag-3.6-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-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hag-3.6-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 19:28:07 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-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hag-3.6-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 328 and 0 Target number of residues in the AU: 328 Target solvent content: 0.6531 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-3.6-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-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2496 target number of atoms Had to go as low as 0.95 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 3.601 Wilson plot Bfac: 79.54 6392 reflections ( 99.59 % complete ) and 0 restraints for refining 2797 atoms. Observations/parameters ratio is 0.57 ------------------------------------------------------ Starting model: R = 0.3320 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3253 (Rfree = 0.000) for 2797 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.56 2.81 Search for helices and strands: 0 residues in 0 chains, 2861 seeds are put forward Round 1: 173 peptides, 26 chains. Longest chain 15 peptides. Score 0.421 Round 2: 211 peptides, 24 chains. Longest chain 22 peptides. Score 0.557 Round 3: 212 peptides, 22 chains. Longest chain 22 peptides. Score 0.583 Round 4: 222 peptides, 24 chains. Longest chain 19 peptides. Score 0.585 Round 5: 224 peptides, 22 chains. Longest chain 27 peptides. Score 0.612 Taking the results from Round 5 Chains 23, Residues 202, Estimated correctness of the model 19.2 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 6392 reflections ( 99.59 % complete ) and 4652 restraints for refining 2263 atoms. 3824 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2661 (Rfree = 0.000) for 2263 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 2: After refmac, R = 0.2573 (Rfree = 0.000) for 2222 atoms. Found 13 (14 requested) and removed 12 (7 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2484 (Rfree = 0.000) for 2206 atoms. Found 14 (14 requested) and removed 12 (7 requested) atoms. Cycle 4: After refmac, R = 0.2396 (Rfree = 0.000) for 2197 atoms. Found 13 (14 requested) and removed 9 (7 requested) atoms. Cycle 5: After refmac, R = 0.2162 (Rfree = 0.000) for 2193 atoms. Found 7 (14 requested) and removed 9 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.57 2.82 Search for helices and strands: 0 residues in 0 chains, 2282 seeds are put forward Round 1: 204 peptides, 24 chains. Longest chain 20 peptides. Score 0.538 Round 2: 218 peptides, 25 chains. Longest chain 18 peptides. Score 0.563 Round 3: 224 peptides, 23 chains. Longest chain 21 peptides. Score 0.601 Round 4: 214 peptides, 23 chains. Longest chain 21 peptides. Score 0.576 Round 5: 222 peptides, 19 chains. Longest chain 26 peptides. Score 0.641 Taking the results from Round 5 Chains 20, Residues 203, Estimated correctness of the model 29.9 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 6392 reflections ( 99.59 % complete ) and 4621 restraints for refining 2263 atoms. 3759 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2549 (Rfree = 0.000) for 2263 atoms. Found 14 (14 requested) and removed 16 (7 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2375 (Rfree = 0.000) for 2235 atoms. Found 9 (14 requested) and removed 7 (7 requested) atoms. Cycle 8: After refmac, R = 0.2326 (Rfree = 0.000) for 2225 atoms. Found 8 (14 requested) and removed 10 (7 requested) atoms. Cycle 9: After refmac, R = 0.2289 (Rfree = 0.000) for 2215 atoms. Found 9 (14 requested) and removed 11 (7 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2267 (Rfree = 0.000) for 2204 atoms. Found 13 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.51 2.77 Search for helices and strands: 0 residues in 0 chains, 2301 seeds are put forward Round 1: 209 peptides, 26 chains. Longest chain 16 peptides. Score 0.527 Round 2: 220 peptides, 21 chains. Longest chain 30 peptides. Score 0.614 Round 3: 221 peptides, 22 chains. Longest chain 27 peptides. Score 0.605 Round 4: 219 peptides, 24 chains. Longest chain 27 peptides. Score 0.577 Round 5: 224 peptides, 23 chains. Longest chain 25 peptides. Score 0.601 Taking the results from Round 2 Chains 21, Residues 199, Estimated correctness of the model 20.0 % 1 chains (29 residues) have been docked in sequence ------------------------------------------------------ 6392 reflections ( 99.59 % complete ) and 4518 restraints for refining 2263 atoms. 3604 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2438 (Rfree = 0.000) for 2263 atoms. Found 14 (14 requested) and removed 17 (7 requested) atoms. Cycle 12: After refmac, R = 0.2234 (Rfree = 0.000) for 2252 atoms. Found 5 (14 requested) and removed 11 (7 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2173 (Rfree = 0.000) for 2238 atoms. Found 4 (14 requested) and removed 11 (7 requested) atoms. Cycle 14: After refmac, R = 0.2138 (Rfree = 0.000) for 2228 atoms. Found 6 (14 requested) and removed 7 (7 requested) atoms. Cycle 15: After refmac, R = 0.2091 (Rfree = 0.000) for 2225 atoms. Found 1 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.55 2.80 Search for helices and strands: 0 residues in 0 chains, 2272 seeds are put forward Round 1: 214 peptides, 25 chains. Longest chain 17 peptides. Score 0.552 Round 2: 238 peptides, 20 chains. Longest chain 46 peptides. Score 0.665 Round 3: 232 peptides, 25 chains. Longest chain 20 peptides. Score 0.598 Round 4: 228 peptides, 22 chains. Longest chain 27 peptides. Score 0.621 Round 5: 227 peptides, 26 chains. Longest chain 23 peptides. Score 0.574 Taking the results from Round 2 Chains 22, Residues 218, Estimated correctness of the model 38.3 % 4 chains (80 residues) have been docked in sequence ------------------------------------------------------ 6392 reflections ( 99.59 % complete ) and 3672 restraints for refining 2263 atoms. 2471 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2592 (Rfree = 0.000) for 2263 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2430 (Rfree = 0.000) for 2250 atoms. Found 5 (14 requested) and removed 9 (7 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2372 (Rfree = 0.000) for 2238 atoms. Found 6 (14 requested) and removed 10 (7 requested) atoms. Cycle 19: After refmac, R = 0.2349 (Rfree = 0.000) for 2233 atoms. Found 9 (14 requested) and removed 10 (7 requested) atoms. Cycle 20: After refmac, R = 0.2348 (Rfree = 0.000) for 2232 atoms. Found 4 (14 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.58 2.83 Search for helices and strands: 0 residues in 0 chains, 2303 seeds are put forward Round 1: 197 peptides, 25 chains. Longest chain 18 peptides. Score 0.506 Round 2: 221 peptides, 23 chains. Longest chain 27 peptides. Score 0.594 Round 3: 210 peptides, 26 chains. Longest chain 31 peptides. Score 0.530 Round 4: 214 peptides, 19 chains. Longest chain 39 peptides. Score 0.622 Round 5: 213 peptides, 22 chains. Longest chain 34 peptides. Score 0.586 Taking the results from Round 4 Chains 24, Residues 195, Estimated correctness of the model 23.0 % 3 chains (57 residues) have been docked in sequence ------------------------------------------------------ 6392 reflections ( 99.59 % complete ) and 4296 restraints for refining 2263 atoms. 3297 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2664 (Rfree = 0.000) for 2263 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2434 (Rfree = 0.000) for 2252 atoms. Found 6 (14 requested) and removed 9 (7 requested) atoms. Cycle 23: After refmac, R = 0.2347 (Rfree = 0.000) for 2239 atoms. Found 6 (14 requested) and removed 12 (7 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2284 (Rfree = 0.000) for 2232 atoms. Found 3 (14 requested) and removed 7 (7 requested) atoms. Cycle 25: After refmac, R = 0.2346 (Rfree = 0.000) for 2225 atoms. Found 5 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.57 2.82 Search for helices and strands: 0 residues in 0 chains, 2297 seeds are put forward Round 1: 191 peptides, 26 chains. Longest chain 18 peptides. Score 0.476 Round 2: 196 peptides, 23 chains. Longest chain 32 peptides. Score 0.529 Round 3: 205 peptides, 25 chains. Longest chain 22 peptides. Score 0.528 Round 4: 203 peptides, 20 chains. Longest chain 23 peptides. Score 0.584 Round 5: 208 peptides, 22 chains. Longest chain 20 peptides. Score 0.573 Taking the results from Round 4 Chains 20, Residues 183, Estimated correctness of the model 8.2 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ 6392 reflections ( 99.59 % complete ) and 4496 restraints for refining 2263 atoms. 3655 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2631 (Rfree = 0.000) for 2263 atoms. Found 14 (14 requested) and removed 11 (7 requested) atoms. Cycle 27: After refmac, R = 0.2369 (Rfree = 0.000) for 2250 atoms. Found 6 (14 requested) and removed 12 (7 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2331 (Rfree = 0.000) for 2236 atoms. Found 12 (14 requested) and removed 10 (7 requested) atoms. Cycle 29: After refmac, R = 0.2237 (Rfree = 0.000) for 2232 atoms. Found 10 (14 requested) and removed 8 (7 requested) atoms. Cycle 30: After refmac, R = 0.2200 (Rfree = 0.000) for 2230 atoms. Found 10 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.56 2.81 Search for helices and strands: 0 residues in 0 chains, 2295 seeds are put forward Round 1: 187 peptides, 26 chains. Longest chain 15 peptides. Score 0.464 Round 2: 187 peptides, 23 chains. Longest chain 23 peptides. Score 0.504 Round 3: 196 peptides, 21 chains. Longest chain 22 peptides. Score 0.554 Round 4: 187 peptides, 23 chains. Longest chain 16 peptides. Score 0.504 Round 5: 191 peptides, 21 chains. Longest chain 27 peptides. Score 0.541 Taking the results from Round 3 Chains 23, Residues 175, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 6392 reflections ( 99.59 % complete ) and 4692 restraints for refining 2263 atoms. 3943 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2515 (Rfree = 0.000) for 2263 atoms. Found 10 (14 requested) and removed 10 (7 requested) atoms. Cycle 32: After refmac, R = 0.2443 (Rfree = 0.000) for 2243 atoms. Found 8 (14 requested) and removed 7 (7 requested) atoms. Cycle 33: After refmac, R = 0.2430 (Rfree = 0.000) for 2237 atoms. Found 9 (14 requested) and removed 10 (7 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.2416 (Rfree = 0.000) for 2231 atoms. Found 11 (14 requested) and removed 8 (7 requested) atoms. Cycle 35: After refmac, R = 0.2291 (Rfree = 0.000) for 2228 atoms. Found 9 (14 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.54 2.80 Search for helices and strands: 0 residues in 0 chains, 2325 seeds are put forward Round 1: 184 peptides, 29 chains. Longest chain 16 peptides. Score 0.414 Round 2: 177 peptides, 23 chains. Longest chain 16 peptides. Score 0.475 Round 3: 186 peptides, 26 chains. Longest chain 13 peptides. Score 0.461 Round 4: 198 peptides, 25 chains. Longest chain 20 peptides. Score 0.509 Round 5: 190 peptides, 25 chains. Longest chain 14 peptides. Score 0.486 Taking the results from Round 4 Chains 25, Residues 173, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6392 reflections ( 99.59 % complete ) and 4898 restraints for refining 2263 atoms. 4231 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2448 (Rfree = 0.000) for 2263 atoms. Found 9 (14 requested) and removed 10 (7 requested) atoms. Cycle 37: After refmac, R = 0.2348 (Rfree = 0.000) for 2253 atoms. Found 10 (14 requested) and removed 7 (7 requested) atoms. Cycle 38: After refmac, R = 0.2366 (Rfree = 0.000) for 2250 atoms. Found 14 (14 requested) and removed 9 (7 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2089 (Rfree = 0.000) for 2248 atoms. Found 2 (14 requested) and removed 10 (7 requested) atoms. Cycle 40: After refmac, R = 0.2205 (Rfree = 0.000) for 2236 atoms. Found 10 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.61 2.85 Search for helices and strands: 0 residues in 0 chains, 2327 seeds are put forward Round 1: 168 peptides, 27 chains. Longest chain 12 peptides. Score 0.391 Round 2: 195 peptides, 27 chains. Longest chain 18 peptides. Score 0.474 Round 3: 201 peptides, 24 chains. Longest chain 20 peptides. Score 0.530 Round 4: 200 peptides, 25 chains. Longest chain 26 peptides. Score 0.515 Round 5: 182 peptides, 24 chains. Longest chain 17 peptides. Score 0.476 Taking the results from Round 3 Chains 24, Residues 177, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 6392 reflections ( 99.59 % complete ) and 4693 restraints for refining 2262 atoms. 3928 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2440 (Rfree = 0.000) for 2262 atoms. Found 12 (14 requested) and removed 10 (7 requested) atoms. Cycle 42: After refmac, R = 0.2390 (Rfree = 0.000) for 2251 atoms. Found 7 (14 requested) and removed 9 (7 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2354 (Rfree = 0.000) for 2245 atoms. Found 8 (14 requested) and removed 7 (7 requested) atoms. Cycle 44: After refmac, R = 0.2312 (Rfree = 0.000) for 2244 atoms. Found 4 (14 requested) and removed 9 (7 requested) atoms. Cycle 45: After refmac, R = 0.2301 (Rfree = 0.000) for 2233 atoms. Found 8 (14 requested) and removed 7 (7 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.55 2.80 Search for helices and strands: 0 residues in 0 chains, 2317 seeds are put forward Round 1: 169 peptides, 24 chains. Longest chain 19 peptides. Score 0.437 Round 2: 185 peptides, 24 chains. Longest chain 20 peptides. Score 0.485 Round 3: 190 peptides, 23 chains. Longest chain 21 peptides. Score 0.513 Round 4: 189 peptides, 24 chains. Longest chain 15 peptides. Score 0.497 Round 5: 182 peptides, 19 chains. Longest chain 26 peptides. Score 0.542 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 163, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2hag-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6392 reflections ( 99.59 % complete ) and 4942 restraints for refining 2262 atoms. 4280 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2434 (Rfree = 0.000) for 2262 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2372 (Rfree = 0.000) for 2242 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 48: After refmac, R = 0.2420 (Rfree = 0.000) for 2234 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Cycle 49: After refmac, R = 0.2442 (Rfree = 0.000) for 2226 atoms. Found 0 (14 requested) and removed 7 (7 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 51.09