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 1vk3-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vk3-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vk3-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk3-3.8-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/1vk3-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk3-3.8-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 22:23:15 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/1vk3-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk3-3.8-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 417 and 0 Target number of residues in the AU: 417 Target solvent content: 0.5960 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: 1vk3-3.8-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: 19 Cell parameters: 59.785 72.683 128.550 90.000 90.000 90.000 Input sequence file: 1vk3-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 4920 target number of atoms Had to go as low as 0.60 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 3.800 Wilson plot Bfac: 50.72 5773 reflections ( 98.00 % complete ) and 0 restraints for refining 5448 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3223 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3078 (Rfree = 0.000) for 5448 atoms. Found 24 (29 requested) and removed 170 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.20 3.66 Search for helices and strands: 0 residues in 0 chains, 5340 seeds are put forward Round 1: 130 peptides, 30 chains. Longest chain 6 peptides. Score 0.205 Round 2: 184 peptides, 39 chains. Longest chain 8 peptides. Score 0.264 Round 3: 228 peptides, 43 chains. Longest chain 9 peptides. Score 0.349 Round 4: 234 peptides, 44 chains. Longest chain 15 peptides. Score 0.354 Round 5: 241 peptides, 43 chains. Longest chain 9 peptides. Score 0.387 Taking the results from Round 5 Chains 43, Residues 198, Estimated correctness of the model 0.0 % 8 chains (33 residues) have been docked in sequence ------------------------------------------------------ 5773 reflections ( 98.00 % complete ) and 10446 restraints for refining 4449 atoms. 9632 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2830 (Rfree = 0.000) for 4449 atoms. Found 24 (24 requested) and removed 52 (12 requested) atoms. Cycle 2: After refmac, R = 0.2819 (Rfree = 0.000) for 4372 atoms. Found 24 (24 requested) and removed 47 (12 requested) atoms. Cycle 3: After refmac, R = 0.2493 (Rfree = 0.000) for 4315 atoms. Found 23 (23 requested) and removed 29 (11 requested) atoms. Cycle 4: After refmac, R = 0.2750 (Rfree = 0.000) for 4290 atoms. Found 23 (23 requested) and removed 30 (11 requested) atoms. Cycle 5: After refmac, R = 0.2091 (Rfree = 0.000) for 4259 atoms. Found 16 (23 requested) and removed 18 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.27 3.74 Search for helices and strands: 0 residues in 0 chains, 4382 seeds are put forward Round 1: 207 peptides, 45 chains. Longest chain 8 peptides. Score 0.257 Round 2: 264 peptides, 53 chains. Longest chain 11 peptides. Score 0.331 Round 3: 275 peptides, 52 chains. Longest chain 13 peptides. Score 0.375 Round 4: 285 peptides, 47 chains. Longest chain 14 peptides. Score 0.461 Round 5: 253 peptides, 45 chains. Longest chain 14 peptides. Score 0.397 Taking the results from Round 4 Chains 50, Residues 238, Estimated correctness of the model 0.0 % 9 chains (54 residues) have been docked in sequence ------------------------------------------------------ 5773 reflections ( 98.00 % complete ) and 9558 restraints for refining 4294 atoms. 8502 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2735 (Rfree = 0.000) for 4294 atoms. Found 23 (23 requested) and removed 49 (11 requested) atoms. Cycle 7: After refmac, R = 0.2636 (Rfree = 0.000) for 4225 atoms. Found 23 (23 requested) and removed 35 (11 requested) atoms. Cycle 8: After refmac, R = 0.2488 (Rfree = 0.000) for 4181 atoms. Found 18 (23 requested) and removed 32 (11 requested) atoms. Cycle 9: After refmac, R = 0.2357 (Rfree = 0.000) for 4151 atoms. Found 4 (22 requested) and removed 22 (11 requested) atoms. Cycle 10: After refmac, R = 0.2263 (Rfree = 0.000) for 4126 atoms. Found 9 (22 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.26 3.73 Search for helices and strands: 0 residues in 0 chains, 4250 seeds are put forward Round 1: 231 peptides, 46 chains. Longest chain 11 peptides. Score 0.320 Round 2: 263 peptides, 47 chains. Longest chain 16 peptides. Score 0.401 Round 3: 277 peptides, 50 chains. Longest chain 11 peptides. Score 0.405 Round 4: 271 peptides, 48 chains. Longest chain 18 peptides. Score 0.412 Round 5: 284 peptides, 50 chains. Longest chain 14 peptides. Score 0.424 Taking the results from Round 5 Chains 50, Residues 234, Estimated correctness of the model 0.0 % 6 chains (32 residues) have been docked in sequence ------------------------------------------------------ 5773 reflections ( 98.00 % complete ) and 9867 restraints for refining 4349 atoms. 8905 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2736 (Rfree = 0.000) for 4349 atoms. Found 23 (23 requested) and removed 42 (11 requested) atoms. Cycle 12: After refmac, R = 0.2514 (Rfree = 0.000) for 4304 atoms. Found 23 (23 requested) and removed 41 (11 requested) atoms. Cycle 13: After refmac, R = 0.2129 (Rfree = 0.000) for 4267 atoms. Found 11 (23 requested) and removed 16 (11 requested) atoms. Cycle 14: After refmac, R = 0.2094 (Rfree = 0.000) for 4254 atoms. Found 9 (23 requested) and removed 19 (11 requested) atoms. Cycle 15: After refmac, R = 0.2137 (Rfree = 0.000) for 4239 atoms. Found 6 (23 requested) and removed 18 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 3.73 Search for helices and strands: 0 residues in 0 chains, 4335 seeds are put forward Round 1: 231 peptides, 51 chains. Longest chain 8 peptides. Score 0.255 Round 2: 226 peptides, 42 chains. Longest chain 13 peptides. Score 0.356 Round 3: 239 peptides, 40 chains. Longest chain 19 peptides. Score 0.418 Round 4: 241 peptides, 42 chains. Longest chain 12 peptides. Score 0.400 Round 5: 260 peptides, 46 chains. Longest chain 13 peptides. Score 0.405 Taking the results from Round 3 Chains 43, Residues 199, Estimated correctness of the model 0.0 % 5 chains (28 residues) have been docked in sequence ------------------------------------------------------ 5773 reflections ( 98.00 % complete ) and 10301 restraints for refining 4383 atoms. 9485 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2392 (Rfree = 0.000) for 4383 atoms. Found 22 (24 requested) and removed 28 (12 requested) atoms. Cycle 17: After refmac, R = 0.2297 (Rfree = 0.000) for 4356 atoms. Found 18 (24 requested) and removed 25 (12 requested) atoms. Cycle 18: After refmac, R = 0.1942 (Rfree = 0.000) for 4338 atoms. Found 3 (23 requested) and removed 19 (11 requested) atoms. Cycle 19: After refmac, R = 0.1892 (Rfree = 0.000) for 4317 atoms. Found 5 (23 requested) and removed 16 (11 requested) atoms. Cycle 20: After refmac, R = 0.1947 (Rfree = 0.000) for 4303 atoms. Found 5 (23 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.25 3.72 Search for helices and strands: 0 residues in 0 chains, 4415 seeds are put forward Round 1: 212 peptides, 45 chains. Longest chain 8 peptides. Score 0.274 Round 2: 230 peptides, 42 chains. Longest chain 14 peptides. Score 0.368 Round 3: 231 peptides, 40 chains. Longest chain 14 peptides. Score 0.396 Round 4: 248 peptides, 41 chains. Longest chain 14 peptides. Score 0.431 Round 5: 238 peptides, 39 chains. Longest chain 13 peptides. Score 0.428 Taking the results from Round 4 Chains 42, Residues 207, Estimated correctness of the model 0.0 % 8 chains (42 residues) have been docked in sequence ------------------------------------------------------ 5773 reflections ( 98.00 % complete ) and 10126 restraints for refining 4435 atoms. 9233 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2338 (Rfree = 0.000) for 4435 atoms. Found 24 (24 requested) and removed 42 (12 requested) atoms. Cycle 22: After refmac, R = 0.2365 (Rfree = 0.000) for 4400 atoms. Found 24 (24 requested) and removed 43 (12 requested) atoms. Cycle 23: After refmac, R = 0.1971 (Rfree = 0.000) for 4373 atoms. Found 9 (24 requested) and removed 31 (12 requested) atoms. Cycle 24: After refmac, R = 0.1875 (Rfree = 0.000) for 4346 atoms. Found 9 (23 requested) and removed 20 (11 requested) atoms. Cycle 25: After refmac, R = 0.1916 (Rfree = 0.000) for 4329 atoms. Found 8 (23 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.28 3.75 Search for helices and strands: 0 residues in 0 chains, 4434 seeds are put forward Round 1: 211 peptides, 46 chains. Longest chain 10 peptides. Score 0.257 Round 2: 244 peptides, 44 chains. Longest chain 11 peptides. Score 0.384 Round 3: 256 peptides, 43 chains. Longest chain 12 peptides. Score 0.430 Round 4: 249 peptides, 44 chains. Longest chain 11 peptides. Score 0.398 Round 5: 245 peptides, 40 chains. Longest chain 11 peptides. Score 0.435 Taking the results from Round 5 Chains 40, Residues 205, Estimated correctness of the model 0.0 % 4 chains (23 residues) have been docked in sequence ------------------------------------------------------ 5773 reflections ( 98.00 % complete ) and 10446 restraints for refining 4450 atoms. 9616 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2506 (Rfree = 0.000) for 4450 atoms. Found 24 (24 requested) and removed 35 (12 requested) atoms. Cycle 27: After refmac, R = 0.2243 (Rfree = 0.000) for 4422 atoms. Found 24 (24 requested) and removed 38 (12 requested) atoms. Cycle 28: After refmac, R = 0.1757 (Rfree = 0.000) for 4389 atoms. Found 6 (24 requested) and removed 19 (12 requested) atoms. Cycle 29: After refmac, R = 0.1636 (Rfree = 0.000) for 4369 atoms. Found 5 (24 requested) and removed 14 (12 requested) atoms. Cycle 30: After refmac, R = 0.1680 (Rfree = 0.000) for 4356 atoms. Found 0 (23 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.22 3.69 Search for helices and strands: 0 residues in 0 chains, 4452 seeds are put forward Round 1: 177 peptides, 38 chains. Longest chain 7 peptides. Score 0.254 Round 2: 209 peptides, 41 chains. Longest chain 10 peptides. Score 0.317 Round 3: 212 peptides, 38 chains. Longest chain 10 peptides. Score 0.365 Round 4: 224 peptides, 42 chains. Longest chain 12 peptides. Score 0.350 Round 5: 209 peptides, 39 chains. Longest chain 9 peptides. Score 0.343 Taking the results from Round 3 Chains 38, Residues 174, Estimated correctness of the model 0.0 % 4 chains (18 residues) have been docked in sequence ------------------------------------------------------ 5773 reflections ( 98.00 % complete ) and 10685 restraints for refining 4450 atoms. 9985 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2197 (Rfree = 0.000) for 4450 atoms. Found 24 (24 requested) and removed 39 (12 requested) atoms. Cycle 32: After refmac, R = 0.2113 (Rfree = 0.000) for 4422 atoms. Found 24 (24 requested) and removed 31 (12 requested) atoms. Cycle 33: After refmac, R = 0.1801 (Rfree = 0.000) for 4406 atoms. Found 13 (24 requested) and removed 22 (12 requested) atoms. Cycle 34: After refmac, R = 0.1760 (Rfree = 0.000) for 4392 atoms. Found 5 (24 requested) and removed 19 (12 requested) atoms. Cycle 35: After refmac, R = 0.1757 (Rfree = 0.000) for 4374 atoms. Found 7 (24 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.24 3.71 Search for helices and strands: 0 residues in 0 chains, 4496 seeds are put forward Round 1: 174 peptides, 37 chains. Longest chain 7 peptides. Score 0.258 Round 2: 196 peptides, 39 chains. Longest chain 7 peptides. Score 0.302 Round 3: 214 peptides, 41 chains. Longest chain 10 peptides. Score 0.332 Round 4: 204 peptides, 38 chains. Longest chain 12 peptides. Score 0.341 Round 5: 212 peptides, 38 chains. Longest chain 11 peptides. Score 0.365 Taking the results from Round 5 Chains 38, Residues 174, Estimated correctness of the model 0.0 % 7 chains (34 residues) have been docked in sequence ------------------------------------------------------ 5773 reflections ( 98.00 % complete ) and 10504 restraints for refining 4443 atoms. 9787 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1928 (Rfree = 0.000) for 4443 atoms. Found 20 (24 requested) and removed 27 (12 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2038 (Rfree = 0.000) for 4428 atoms. Found 24 (24 requested) and removed 36 (12 requested) atoms. Cycle 38: After refmac, R = 0.1629 (Rfree = 0.000) for 4408 atoms. Found 8 (24 requested) and removed 20 (12 requested) atoms. Cycle 39: After refmac, R = 0.1594 (Rfree = 0.000) for 4391 atoms. Found 9 (24 requested) and removed 18 (12 requested) atoms. Cycle 40: After refmac, R = 0.1633 (Rfree = 0.000) for 4381 atoms. Found 8 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.25 3.72 Search for helices and strands: 0 residues in 0 chains, 4474 seeds are put forward Round 1: 166 peptides, 36 chains. Longest chain 8 peptides. Score 0.245 Round 2: 190 peptides, 37 chains. Longest chain 10 peptides. Score 0.310 Round 3: 186 peptides, 33 chains. Longest chain 11 peptides. Score 0.352 Round 4: 182 peptides, 32 chains. Longest chain 10 peptides. Score 0.353 Round 5: 175 peptides, 32 chains. Longest chain 11 peptides. Score 0.331 Taking the results from Round 4 Chains 32, Residues 150, Estimated correctness of the model 0.0 % 5 chains (25 residues) have been docked in sequence ------------------------------------------------------ 5773 reflections ( 98.00 % complete ) and 10604 restraints for refining 4450 atoms. 9977 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2143 (Rfree = 0.000) for 4450 atoms. Found 24 (24 requested) and removed 26 (12 requested) atoms. Cycle 42: After refmac, R = 0.2115 (Rfree = 0.000) for 4430 atoms. Found 24 (24 requested) and removed 29 (12 requested) atoms. Cycle 43: After refmac, R = 0.2085 (Rfree = 0.000) for 4417 atoms. Found 24 (24 requested) and removed 33 (12 requested) atoms. Cycle 44: After refmac, R = 0.1561 (Rfree = 0.000) for 4401 atoms. Found 15 (24 requested) and removed 16 (12 requested) atoms. Cycle 45: After refmac, R = 0.1631 (Rfree = 0.000) for 4398 atoms. Found 10 (24 requested) and removed 20 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.23 3.70 Search for helices and strands: 0 residues in 0 chains, 4509 seeds are put forward Round 1: 142 peptides, 30 chains. Longest chain 8 peptides. Score 0.249 Round 2: 162 peptides, 30 chains. Longest chain 9 peptides. Score 0.317 Round 3: 148 peptides, 29 chains. Longest chain 9 peptides. Score 0.284 Round 4: 170 peptides, 30 chains. Longest chain 9 peptides. Score 0.342 Round 5: 157 peptides, 27 chains. Longest chain 10 peptides. Score 0.343 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 130, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence Sequence coverage is 5 % Consider running further cycles of model building using 1vk3-3_warpNtrace.pdb as input Building loops using Loopy2018 27 chains (130 residues) following loop building 2 chains (7 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5773 reflections ( 98.00 % complete ) and 10859 restraints for refining 4419 atoms. 10352 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2011 (Rfree = 0.000) for 4419 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.1800 (Rfree = 0.000) for 4398 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.1701 (Rfree = 0.000) for 4382 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.1764 (Rfree = 0.000) for 4369 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Writing output files ... TimeTaking 59.5