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 2o5r-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o5r-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o5r-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o5r-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/2o5r-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o5r-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 ============================================================ 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/2o5r-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o5r-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 459 and 0 Target number of residues in the AU: 459 Target solvent content: 0.6903 Checking the provided sequence file Detected sequence length: 481 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 481 Adjusted target solvent content: 0.68 Input MTZ file: 2o5r-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: 152 Cell parameters: 69.953 69.953 283.945 90.000 90.000 120.000 Input sequence file: 2o5r-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 3848 target number of atoms Had to go as low as 1.05 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: 19.992 3.800 Wilson plot Bfac: 111.33 8487 reflections ( 99.02 % complete ) and 0 restraints for refining 4258 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.3571 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3616 (Rfree = 0.000) for 4258 atoms. Found 23 (23 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 4.08 3.17 Search for helices and strands: 0 residues in 0 chains, 4348 seeds are put forward Round 1: 172 peptides, 31 chains. Longest chain 10 peptides. Score 0.298 Round 2: 230 peptides, 35 chains. Longest chain 13 peptides. Score 0.390 Round 3: 235 peptides, 28 chains. Longest chain 23 peptides. Score 0.466 Round 4: 242 peptides, 28 chains. Longest chain 16 peptides. Score 0.480 Round 5: 249 peptides, 33 chains. Longest chain 18 peptides. Score 0.448 Taking the results from Round 4 Chains 28, Residues 214, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8487 reflections ( 99.02 % complete ) and 8090 restraints for refining 3465 atoms. 7262 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3190 (Rfree = 0.000) for 3465 atoms. Found 19 (19 requested) and removed 24 (9 requested) atoms. Cycle 2: After refmac, R = 0.3053 (Rfree = 0.000) for 3357 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 3: After refmac, R = 0.3083 (Rfree = 0.000) for 3288 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. Cycle 4: After refmac, R = 0.2984 (Rfree = 0.000) for 3252 atoms. Found 18 (18 requested) and removed 21 (9 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2894 (Rfree = 0.000) for 3213 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.94 3.07 Search for helices and strands: 0 residues in 0 chains, 3365 seeds are put forward Round 1: 242 peptides, 35 chains. Longest chain 14 peptides. Score 0.415 Round 2: 282 peptides, 38 chains. Longest chain 19 peptides. Score 0.467 Round 3: 274 peptides, 32 chains. Longest chain 19 peptides. Score 0.504 Round 4: 282 peptides, 37 chains. Longest chain 17 peptides. Score 0.476 Round 5: 278 peptides, 31 chains. Longest chain 19 peptides. Score 0.520 Taking the results from Round 5 Chains 32, Residues 247, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 8487 reflections ( 99.02 % complete ) and 7520 restraints for refining 3479 atoms. 6525 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2917 (Rfree = 0.000) for 3479 atoms. Found 19 (19 requested) and removed 28 (9 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2765 (Rfree = 0.000) for 3412 atoms. Found 19 (19 requested) and removed 37 (9 requested) atoms. Cycle 8: After refmac, R = 0.2555 (Rfree = 0.000) for 3333 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2512 (Rfree = 0.000) for 3305 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. Cycle 10: After refmac, R = 0.2312 (Rfree = 0.000) for 3283 atoms. Found 17 (18 requested) and removed 20 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.97 3.09 Search for helices and strands: 0 residues in 0 chains, 3449 seeds are put forward Round 1: 227 peptides, 35 chains. Longest chain 12 peptides. Score 0.383 Round 2: 249 peptides, 29 chains. Longest chain 17 peptides. Score 0.484 Round 3: 275 peptides, 32 chains. Longest chain 18 peptides. Score 0.506 Round 4: 268 peptides, 33 chains. Longest chain 19 peptides. Score 0.484 Round 5: 272 peptides, 33 chains. Longest chain 16 peptides. Score 0.492 Taking the results from Round 3 Chains 35, Residues 243, Estimated correctness of the model 0.0 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 8487 reflections ( 99.02 % complete ) and 7274 restraints for refining 3480 atoms. 6239 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2899 (Rfree = 0.000) for 3480 atoms. Found 19 (19 requested) and removed 34 (9 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2706 (Rfree = 0.000) for 3404 atoms. Found 19 (19 requested) and removed 29 (9 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2679 (Rfree = 0.000) for 3357 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. Cycle 14: After refmac, R = 0.2537 (Rfree = 0.000) for 3324 atoms. Found 18 (18 requested) and removed 26 (9 requested) atoms. Cycle 15: After refmac, R = 0.2367 (Rfree = 0.000) for 3294 atoms. Found 10 (18 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.97 3.09 Search for helices and strands: 0 residues in 0 chains, 3424 seeds are put forward Round 1: 233 peptides, 35 chains. Longest chain 17 peptides. Score 0.396 Round 2: 274 peptides, 35 chains. Longest chain 19 peptides. Score 0.478 Round 3: 279 peptides, 32 chains. Longest chain 17 peptides. Score 0.513 Round 4: 283 peptides, 35 chains. Longest chain 17 peptides. Score 0.495 Round 5: 277 peptides, 30 chains. Longest chain 26 peptides. Score 0.526 Taking the results from Round 5 Chains 30, Residues 247, Estimated correctness of the model 0.0 % 2 chains (31 residues) have been docked in sequence ------------------------------------------------------ 8487 reflections ( 99.02 % complete ) and 7307 restraints for refining 3479 atoms. 6221 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2768 (Rfree = 0.000) for 3479 atoms. Found 19 (19 requested) and removed 85 (9 requested) atoms. Cycle 17: After refmac, R = 0.2496 (Rfree = 0.000) for 3359 atoms. Found 13 (18 requested) and removed 22 (9 requested) atoms. Cycle 18: After refmac, R = 0.2384 (Rfree = 0.000) for 3332 atoms. Found 12 (18 requested) and removed 14 (9 requested) atoms. Cycle 19: After refmac, R = 0.2349 (Rfree = 0.000) for 3319 atoms. Found 4 (18 requested) and removed 13 (9 requested) atoms. Cycle 20: After refmac, R = 0.2302 (Rfree = 0.000) for 3302 atoms. Found 5 (18 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.96 3.08 Search for helices and strands: 0 residues in 0 chains, 3428 seeds are put forward Round 1: 258 peptides, 40 chains. Longest chain 12 peptides. Score 0.401 Round 2: 269 peptides, 31 chains. Longest chain 26 peptides. Score 0.503 Round 3: 290 peptides, 34 chains. Longest chain 16 peptides. Score 0.516 Round 4: 284 peptides, 37 chains. Longest chain 24 peptides. Score 0.479 Round 5: 280 peptides, 32 chains. Longest chain 19 peptides. Score 0.515 Taking the results from Round 3 Chains 34, Residues 256, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 8487 reflections ( 99.02 % complete ) and 7426 restraints for refining 3480 atoms. 6390 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2752 (Rfree = 0.000) for 3480 atoms. Found 19 (19 requested) and removed 25 (9 requested) atoms. Cycle 22: After refmac, R = 0.2714 (Rfree = 0.000) for 3427 atoms. Found 19 (19 requested) and removed 112 (9 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2712 (Rfree = 0.000) for 3291 atoms. Found 18 (18 requested) and removed 49 (9 requested) atoms. Cycle 24: After refmac, R = 0.2671 (Rfree = 0.000) for 3236 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. Cycle 25: After refmac, R = 0.2570 (Rfree = 0.000) for 3205 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.89 3.03 Search for helices and strands: 0 residues in 0 chains, 3421 seeds are put forward Round 1: 225 peptides, 39 chains. Longest chain 11 peptides. Score 0.340 Round 2: 253 peptides, 31 chains. Longest chain 15 peptides. Score 0.473 Round 3: 266 peptides, 33 chains. Longest chain 18 peptides. Score 0.480 Round 4: 268 peptides, 34 chains. Longest chain 23 peptides. Score 0.475 Round 5: 271 peptides, 30 chains. Longest chain 20 peptides. Score 0.516 Taking the results from Round 5 Chains 31, Residues 241, Estimated correctness of the model 0.0 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 8487 reflections ( 99.02 % complete ) and 7270 restraints for refining 3481 atoms. 6260 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3138 (Rfree = 0.000) for 3481 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Cycle 27: After refmac, R = 0.2706 (Rfree = 0.000) for 3437 atoms. Found 19 (19 requested) and removed 25 (9 requested) atoms. Cycle 28: After refmac, R = 0.2335 (Rfree = 0.000) for 3390 atoms. Found 14 (18 requested) and removed 20 (9 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2601 (Rfree = 0.000) for 3364 atoms. Found 18 (18 requested) and removed 20 (9 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2197 (Rfree = 0.000) for 3348 atoms. Found 9 (18 requested) and removed 20 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.95 3.07 Search for helices and strands: 0 residues in 0 chains, 3467 seeds are put forward Round 1: 223 peptides, 34 chains. Longest chain 12 peptides. Score 0.384 Round 2: 237 peptides, 33 chains. Longest chain 16 peptides. Score 0.423 Round 3: 240 peptides, 31 chains. Longest chain 21 peptides. Score 0.448 Round 4: 240 peptides, 30 chains. Longest chain 20 peptides. Score 0.457 Round 5: 232 peptides, 30 chains. Longest chain 22 peptides. Score 0.442 Taking the results from Round 4 Chains 30, Residues 210, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8487 reflections ( 99.02 % complete ) and 7732 restraints for refining 3480 atoms. 6922 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2901 (Rfree = 0.000) for 3480 atoms. Found 19 (19 requested) and removed 51 (9 requested) atoms. Cycle 32: After refmac, R = 0.2691 (Rfree = 0.000) for 3418 atoms. Found 18 (18 requested) and removed 29 (9 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2558 (Rfree = 0.000) for 3372 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. Cycle 34: After refmac, R = 0.2495 (Rfree = 0.000) for 3348 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. Cycle 35: After refmac, R = 0.2221 (Rfree = 0.000) for 3342 atoms. Found 18 (18 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.92 3.05 Search for helices and strands: 0 residues in 0 chains, 3564 seeds are put forward Round 1: 203 peptides, 35 chains. Longest chain 11 peptides. Score 0.330 Round 2: 235 peptides, 35 chains. Longest chain 19 peptides. Score 0.400 Round 3: 241 peptides, 33 chains. Longest chain 21 peptides. Score 0.431 Round 4: 247 peptides, 31 chains. Longest chain 20 peptides. Score 0.462 Round 5: 256 peptides, 33 chains. Longest chain 24 peptides. Score 0.461 Taking the results from Round 4 Chains 31, Residues 216, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 8487 reflections ( 99.02 % complete ) and 7448 restraints for refining 3481 atoms. 6572 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2869 (Rfree = 0.000) for 3481 atoms. Found 19 (19 requested) and removed 154 (9 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2567 (Rfree = 0.000) for 3290 atoms. Found 18 (18 requested) and removed 17 (9 requested) atoms. Cycle 38: After refmac, R = 0.2245 (Rfree = 0.000) for 3270 atoms. Found 12 (18 requested) and removed 11 (9 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2103 (Rfree = 0.000) for 3262 atoms. Found 12 (17 requested) and removed 15 (8 requested) atoms. Cycle 40: After refmac, R = 0.2023 (Rfree = 0.000) for 3254 atoms. Found 2 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.92 3.05 Search for helices and strands: 0 residues in 0 chains, 3431 seeds are put forward Round 1: 206 peptides, 39 chains. Longest chain 10 peptides. Score 0.296 Round 2: 228 peptides, 33 chains. Longest chain 17 peptides. Score 0.405 Round 3: 261 peptides, 40 chains. Longest chain 19 peptides. Score 0.407 Round 4: 265 peptides, 41 chains. Longest chain 19 peptides. Score 0.406 Round 5: 275 peptides, 36 chains. Longest chain 20 peptides. Score 0.471 Taking the results from Round 5 Chains 38, Residues 239, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 8487 reflections ( 99.02 % complete ) and 7496 restraints for refining 3481 atoms. 6539 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2417 (Rfree = 0.000) for 3481 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. Cycle 42: After refmac, R = 0.2217 (Rfree = 0.000) for 3448 atoms. Found 8 (19 requested) and removed 11 (9 requested) atoms. Cycle 43: After refmac, R = 0.2171 (Rfree = 0.000) for 3435 atoms. Found 8 (18 requested) and removed 10 (9 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.2131 (Rfree = 0.000) for 3431 atoms. Found 4 (18 requested) and removed 9 (9 requested) atoms. Cycle 45: After refmac, R = 0.2133 (Rfree = 0.000) for 3424 atoms. Found 6 (18 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.92 3.05 Search for helices and strands: 0 residues in 0 chains, 3584 seeds are put forward Round 1: 211 peptides, 40 chains. Longest chain 9 peptides. Score 0.298 Round 2: 226 peptides, 34 chains. Longest chain 18 peptides. Score 0.391 Round 3: 234 peptides, 35 chains. Longest chain 18 peptides. Score 0.398 Round 4: 222 peptides, 33 chains. Longest chain 16 peptides. Score 0.392 Round 5: 243 peptides, 34 chains. Longest chain 17 peptides. Score 0.426 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 209, 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 2o5r-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8487 reflections ( 99.02 % complete ) and 7920 restraints for refining 3481 atoms. 7118 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2570 (Rfree = 0.000) for 3481 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2390 (Rfree = 0.000) for 3454 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2365 (Rfree = 0.000) for 3436 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2354 (Rfree = 0.000) for 3424 atoms. Found 0 (18 requested) and removed 6 (9 requested) atoms. Writing output files ... TimeTaking 63.02