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 1vk3-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vk3-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vk3-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk3-3.6-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/1vk3-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk3-3.6-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 19:28:12 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/1vk3-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk3-3.6-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 434 and 0 Target number of residues in the AU: 434 Target solvent content: 0.5795 Checking the provided sequence file Detected sequence length: 615 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 615 Adjusted target solvent content: 0.40 Input MTZ file: 1vk3-3.6-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: 19 Cell parameters: 59.785 72.683 128.550 90.000 90.000 90.000 Input sequence file: 1vk3-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 4920 target number of atoms Had to go as low as 0.55 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: 30.186 3.600 Wilson plot Bfac: 44.72 Failed to save intermediate PDB 6777 reflections ( 98.22 % complete ) and 0 restraints for refining 5436 atoms. Observations/parameters ratio is 0.31 ------------------------------------------------------ Starting model: R = 0.3198 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2876 (Rfree = 0.000) for 5436 atoms. Found 32 (34 requested) and removed 57 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.05 3.49 Search for helices and strands: 0 residues in 0 chains, 5518 seeds are put forward Round 1: 177 peptides, 37 chains. Longest chain 9 peptides. Score 0.268 Round 2: 223 peptides, 43 chains. Longest chain 10 peptides. Score 0.334 Round 3: 254 peptides, 44 chains. Longest chain 14 peptides. Score 0.412 Round 4: 275 peptides, 47 chains. Longest chain 17 peptides. Score 0.435 Round 5: 277 peptides, 46 chains. Longest chain 18 peptides. Score 0.451 Taking the results from Round 5 Chains 46, Residues 231, Estimated correctness of the model 0.0 % 5 chains (36 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6777 reflections ( 98.22 % complete ) and 10301 restraints for refining 4460 atoms. 9319 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2538 (Rfree = 0.000) for 4460 atoms. Found 22 (28 requested) and removed 34 (14 requested) atoms. Cycle 2: After refmac, R = 0.2528 (Rfree = 0.000) for 4371 atoms. Found 27 (28 requested) and removed 28 (14 requested) atoms. Cycle 3: After refmac, R = 0.2472 (Rfree = 0.000) for 4333 atoms. Found 28 (28 requested) and removed 32 (14 requested) atoms. Cycle 4: After refmac, R = 0.2416 (Rfree = 0.000) for 4296 atoms. Found 23 (27 requested) and removed 24 (13 requested) atoms. Cycle 5: After refmac, R = 0.2343 (Rfree = 0.000) for 4278 atoms. Found 27 (27 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.14 3.59 Search for helices and strands: 0 residues in 0 chains, 4415 seeds are put forward Round 1: 192 peptides, 38 chains. Longest chain 11 peptides. Score 0.303 Round 2: 251 peptides, 46 chains. Longest chain 10 peptides. Score 0.379 Round 3: 265 peptides, 45 chains. Longest chain 15 peptides. Score 0.431 Round 4: 260 peptides, 41 chains. Longest chain 16 peptides. Score 0.464 Round 5: 263 peptides, 41 chains. Longest chain 20 peptides. Score 0.472 Taking the results from Round 5 Chains 41, Residues 222, Estimated correctness of the model 0.0 % 11 chains (57 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6777 reflections ( 98.22 % complete ) and 9374 restraints for refining 4161 atoms. 8406 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2351 (Rfree = 0.000) for 4161 atoms. Found 18 (26 requested) and removed 31 (13 requested) atoms. Cycle 7: After refmac, R = 0.2265 (Rfree = 0.000) for 4123 atoms. Found 26 (26 requested) and removed 36 (13 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.1851 (Rfree = 0.000) for 4093 atoms. Found 10 (26 requested) and removed 18 (13 requested) atoms. Cycle 9: After refmac, R = 0.1929 (Rfree = 0.000) for 4073 atoms. Found 15 (26 requested) and removed 17 (13 requested) atoms. Cycle 10: After refmac, R = 0.1745 (Rfree = 0.000) for 4064 atoms. Found 12 (26 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.11 3.56 Search for helices and strands: 0 residues in 0 chains, 4191 seeds are put forward Round 1: 270 peptides, 53 chains. Longest chain 14 peptides. Score 0.349 Round 2: 291 peptides, 46 chains. Longest chain 14 peptides. Score 0.488 Round 3: 288 peptides, 45 chains. Longest chain 16 peptides. Score 0.491 Round 4: 299 peptides, 51 chains. Longest chain 14 peptides. Score 0.453 Round 5: 276 peptides, 42 chains. Longest chain 15 peptides. Score 0.494 Taking the results from Round 5 Chains 42, Residues 234, Estimated correctness of the model 0.0 % 5 chains (28 residues) have been docked in sequence ------------------------------------------------------ 6777 reflections ( 98.22 % complete ) and 9505 restraints for refining 4171 atoms. 8545 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2277 (Rfree = 0.000) for 4171 atoms. Found 20 (26 requested) and removed 34 (13 requested) atoms. Cycle 12: After refmac, R = 0.2221 (Rfree = 0.000) for 4136 atoms. Found 21 (26 requested) and removed 26 (13 requested) atoms. Cycle 13: After refmac, R = 0.2181 (Rfree = 0.000) for 4119 atoms. Found 23 (26 requested) and removed 24 (13 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2016 (Rfree = 0.000) for 4114 atoms. Found 17 (26 requested) and removed 19 (13 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2080 (Rfree = 0.000) for 4105 atoms. Found 26 (26 requested) and removed 18 (13 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.10 3.55 Search for helices and strands: 0 residues in 0 chains, 4240 seeds are put forward Round 1: 255 peptides, 46 chains. Longest chain 13 peptides. Score 0.391 Round 2: 279 peptides, 49 chains. Longest chain 20 peptides. Score 0.422 Round 3: 279 peptides, 46 chains. Longest chain 14 peptides. Score 0.457 Round 4: 270 peptides, 42 chains. Longest chain 16 peptides. Score 0.478 Round 5: 267 peptides, 43 chains. Longest chain 11 peptides. Score 0.459 Taking the results from Round 4 Chains 42, Residues 228, Estimated correctness of the model 0.0 % 4 chains (26 residues) have been docked in sequence ------------------------------------------------------ 6777 reflections ( 98.22 % complete ) and 9888 restraints for refining 4280 atoms. 8961 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2437 (Rfree = 0.000) for 4280 atoms. Found 27 (27 requested) and removed 48 (13 requested) atoms. Cycle 17: After refmac, R = 0.2268 (Rfree = 0.000) for 4237 atoms. Found 27 (27 requested) and removed 31 (13 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2147 (Rfree = 0.000) for 4221 atoms. Found 27 (27 requested) and removed 21 (13 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2084 (Rfree = 0.000) for 4221 atoms. Found 15 (27 requested) and removed 21 (13 requested) atoms. Cycle 20: After refmac, R = 0.1772 (Rfree = 0.000) for 4207 atoms. Found 12 (27 requested) and removed 17 (13 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.12 3.57 Search for helices and strands: 0 residues in 0 chains, 4352 seeds are put forward Round 1: 219 peptides, 45 chains. Longest chain 9 peptides. Score 0.296 Round 2: 251 peptides, 40 chains. Longest chain 14 peptides. Score 0.451 Round 3: 249 peptides, 40 chains. Longest chain 18 peptides. Score 0.446 Round 4: 261 peptides, 42 chains. Longest chain 10 peptides. Score 0.455 Round 5: 255 peptides, 41 chains. Longest chain 19 peptides. Score 0.450 Taking the results from Round 4 Chains 42, Residues 219, Estimated correctness of the model 0.0 % 6 chains (34 residues) have been docked in sequence ------------------------------------------------------ 6777 reflections ( 98.22 % complete ) and 10039 restraints for refining 4366 atoms. 9124 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2216 (Rfree = 0.000) for 4366 atoms. Found 18 (28 requested) and removed 37 (14 requested) atoms. Cycle 22: After refmac, R = 0.2194 (Rfree = 0.000) for 4326 atoms. Found 27 (27 requested) and removed 34 (13 requested) atoms. Cycle 23: After refmac, R = 0.1874 (Rfree = 0.000) for 4310 atoms. Found 7 (27 requested) and removed 21 (13 requested) atoms. Cycle 24: After refmac, R = 0.1828 (Rfree = 0.000) for 4290 atoms. Found 11 (27 requested) and removed 20 (13 requested) atoms. Cycle 25: After refmac, R = 0.1907 (Rfree = 0.000) for 4278 atoms. Found 14 (27 requested) and removed 19 (13 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.10 3.55 Search for helices and strands: 0 residues in 0 chains, 4383 seeds are put forward Round 1: 218 peptides, 47 chains. Longest chain 9 peptides. Score 0.266 Round 2: 250 peptides, 46 chains. Longest chain 11 peptides. Score 0.376 Round 3: 246 peptides, 38 chains. Longest chain 18 peptides. Score 0.461 Round 4: 250 peptides, 41 chains. Longest chain 16 peptides. Score 0.437 Round 5: 232 peptides, 36 chains. Longest chain 14 peptides. Score 0.447 Taking the results from Round 3 Chains 38, Residues 208, Estimated correctness of the model 0.0 % 4 chains (24 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6777 reflections ( 98.22 % complete ) and 10025 restraints for refining 4360 atoms. 9161 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2007 (Rfree = 0.000) for 4360 atoms. Found 16 (27 requested) and removed 33 (13 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.1846 (Rfree = 0.000) for 4331 atoms. Found 12 (27 requested) and removed 22 (13 requested) atoms. Cycle 28: After refmac, R = 0.1784 (Rfree = 0.000) for 4315 atoms. Found 7 (27 requested) and removed 19 (13 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1733 (Rfree = 0.000) for 4300 atoms. Found 4 (27 requested) and removed 19 (13 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1737 (Rfree = 0.000) for 4282 atoms. Found 6 (27 requested) and removed 25 (13 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.08 3.53 Search for helices and strands: 0 residues in 0 chains, 4388 seeds are put forward Round 1: 216 peptides, 46 chains. Longest chain 9 peptides. Score 0.273 Round 2: 238 peptides, 44 chains. Longest chain 11 peptides. Score 0.366 Round 3: 224 peptides, 40 chains. Longest chain 12 peptides. Score 0.375 Round 4: 236 peptides, 42 chains. Longest chain 17 peptides. Score 0.385 Round 5: 245 peptides, 45 chains. Longest chain 12 peptides. Score 0.374 Taking the results from Round 4 Chains 43, Residues 194, Estimated correctness of the model 0.0 % 8 chains (37 residues) have been docked in sequence ------------------------------------------------------ 6777 reflections ( 98.22 % complete ) and 10323 restraints for refining 4460 atoms. 9512 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2182 (Rfree = 0.000) for 4460 atoms. Found 24 (28 requested) and removed 36 (14 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2016 (Rfree = 0.000) for 4437 atoms. Found 17 (28 requested) and removed 31 (14 requested) atoms. Cycle 33: After refmac, R = 0.1919 (Rfree = 0.000) for 4414 atoms. Found 15 (28 requested) and removed 22 (14 requested) atoms. Cycle 34: After refmac, R = 0.1844 (Rfree = 0.000) for 4403 atoms. Found 13 (28 requested) and removed 21 (14 requested) atoms. Cycle 35: After refmac, R = 0.1762 (Rfree = 0.000) for 4393 atoms. Found 9 (28 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.09 3.54 Search for helices and strands: 0 residues in 0 chains, 4518 seeds are put forward Round 1: 207 peptides, 43 chains. Longest chain 8 peptides. Score 0.284 Round 2: 227 peptides, 41 chains. Longest chain 12 peptides. Score 0.371 Round 3: 231 peptides, 43 chains. Longest chain 10 peptides. Score 0.358 Round 4: 223 peptides, 35 chains. Longest chain 14 peptides. Score 0.435 Round 5: 208 peptides, 36 chains. Longest chain 12 peptides. Score 0.379 Taking the results from Round 4 Chains 35, Residues 188, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6777 reflections ( 98.22 % complete ) and 10493 restraints for refining 4459 atoms. 9745 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2023 (Rfree = 0.000) for 4459 atoms. Found 21 (28 requested) and removed 29 (14 requested) atoms. Cycle 37: After refmac, R = 0.1870 (Rfree = 0.000) for 4438 atoms. Found 16 (28 requested) and removed 23 (14 requested) atoms. Cycle 38: After refmac, R = 0.1896 (Rfree = 0.000) for 4422 atoms. Found 27 (28 requested) and removed 22 (14 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1845 (Rfree = 0.000) for 4421 atoms. Found 22 (28 requested) and removed 22 (14 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1584 (Rfree = 0.000) for 4415 atoms. Found 9 (28 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.06 3.50 Search for helices and strands: 0 residues in 0 chains, 4525 seeds are put forward Round 1: 181 peptides, 39 chains. Longest chain 10 peptides. Score 0.254 Round 2: 199 peptides, 37 chains. Longest chain 10 peptides. Score 0.339 Round 3: 212 peptides, 37 chains. Longest chain 13 peptides. Score 0.378 Round 4: 212 peptides, 40 chains. Longest chain 10 peptides. Score 0.339 Round 5: 207 peptides, 38 chains. Longest chain 11 peptides. Score 0.350 Taking the results from Round 3 Chains 37, Residues 175, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6777 reflections ( 98.22 % complete ) and 10519 restraints for refining 4429 atoms. 9841 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1847 (Rfree = 0.000) for 4429 atoms. Found 17 (28 requested) and removed 31 (14 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.1856 (Rfree = 0.000) for 4404 atoms. Found 27 (28 requested) and removed 24 (14 requested) atoms. Cycle 43: After refmac, R = 0.1678 (Rfree = 0.000) for 4400 atoms. Found 9 (28 requested) and removed 19 (14 requested) atoms. Cycle 44: After refmac, R = 0.1671 (Rfree = 0.000) for 4385 atoms. Found 8 (28 requested) and removed 19 (14 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1583 (Rfree = 0.000) for 4370 atoms. Found 1 (28 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.10 3.55 Search for helices and strands: 0 residues in 0 chains, 4468 seeds are put forward Round 1: 166 peptides, 36 chains. Longest chain 8 peptides. Score 0.245 Round 2: 165 peptides, 32 chains. Longest chain 11 peptides. Score 0.298 Round 3: 180 peptides, 32 chains. Longest chain 16 peptides. Score 0.346 Round 4: 184 peptides, 32 chains. Longest chain 14 peptides. Score 0.359 Round 5: 188 peptides, 30 chains. Longest chain 22 peptides. Score 0.397 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 158, Estimated correctness of the model 0.0 % 3 chains (12 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 1vk3-3_warpNtrace.pdb as input Building loops using Loopy2018 30 chains (158 residues) following loop building 3 chains (12 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6777 reflections ( 98.22 % complete ) and 10620 restraints for refining 4452 atoms. 9994 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1996 (Rfree = 0.000) for 4452 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2127 (Rfree = 0.000) for 4424 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.2040 (Rfree = 0.000) for 4405 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.2019 (Rfree = 0.000) for 4388 atoms. Found 0 (28 requested) and removed 14 (14 requested) atoms. Writing output files ... Failed to save intermediate PDB Normal termination of warpNtrace TimeTaking 78.05