Sun 23 Dec 22:23:13 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 1vk3-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vk3-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vk3-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk3-4.0-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/1vk3-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk3-4.0-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 22:23:22 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/1vk3-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk3-4.0-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 408 and 0 Target number of residues in the AU: 408 Target solvent content: 0.6047 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: 1vk3-4.0-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: 1vk3-4.0-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 4.001 Wilson plot Bfac: 54.40 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 4954 reflections ( 97.75 % complete ) and 0 restraints for refining 5440 atoms. Observations/parameters ratio is 0.23 ------------------------------------------------------ Starting model: R = 0.3254 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3150 (Rfree = 0.000) for 5440 atoms. Found 19 (25 requested) and removed 142 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 3.81 Search for helices and strands: 0 residues in 0 chains, 5355 seeds are put forward Round 1: 126 peptides, 30 chains. Longest chain 7 peptides. Score 0.190 Round 2: 181 peptides, 40 chains. Longest chain 8 peptides. Score 0.240 Round 3: 204 peptides, 40 chains. Longest chain 10 peptides. Score 0.314 Round 4: 218 peptides, 44 chains. Longest chain 9 peptides. Score 0.306 Round 5: 220 peptides, 43 chains. Longest chain 10 peptides. Score 0.325 Taking the results from Round 5 Chains 43, Residues 177, Estimated correctness of the model 0.0 % 7 chains (28 residues) have been docked in sequence ------------------------------------------------------ 4954 reflections ( 97.75 % complete ) and 10787 restraints for refining 4443 atoms. 10062 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2950 (Rfree = 0.000) for 4443 atoms. Found 21 (21 requested) and removed 43 (10 requested) atoms. Cycle 2: After refmac, R = 0.2805 (Rfree = 0.000) for 4354 atoms. Found 18 (20 requested) and removed 40 (10 requested) atoms. Cycle 3: After refmac, R = 0.2698 (Rfree = 0.000) for 4289 atoms. Found 20 (20 requested) and removed 25 (10 requested) atoms. Cycle 4: After refmac, R = 0.2621 (Rfree = 0.000) for 4247 atoms. Found 20 (20 requested) and removed 36 (10 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2575 (Rfree = 0.000) for 4208 atoms. Found 20 (20 requested) and removed 26 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.33 3.81 Search for helices and strands: 0 residues in 0 chains, 4346 seeds are put forward Round 1: 165 peptides, 37 chains. Longest chain 7 peptides. Score 0.227 Round 2: 200 peptides, 37 chains. Longest chain 17 peptides. Score 0.342 Round 3: 244 peptides, 43 chains. Longest chain 14 peptides. Score 0.396 Round 4: 249 peptides, 43 chains. Longest chain 12 peptides. Score 0.410 Round 5: 255 peptides, 44 chains. Longest chain 14 peptides. Score 0.415 Taking the results from Round 5 Chains 45, Residues 211, Estimated correctness of the model 0.0 % 5 chains (34 residues) have been docked in sequence ------------------------------------------------------ 4954 reflections ( 97.75 % complete ) and 8933 restraints for refining 3959 atoms. 8032 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2821 (Rfree = 0.000) for 3959 atoms. Found 18 (18 requested) and removed 37 (9 requested) atoms. Cycle 7: After refmac, R = 0.2495 (Rfree = 0.000) for 3911 atoms. Found 18 (18 requested) and removed 29 (9 requested) atoms. Cycle 8: After refmac, R = 0.2283 (Rfree = 0.000) for 3880 atoms. Found 10 (18 requested) and removed 19 (9 requested) atoms. Cycle 9: After refmac, R = 0.2494 (Rfree = 0.000) for 3856 atoms. Found 18 (18 requested) and removed 26 (9 requested) atoms. Cycle 10: After refmac, R = 0.2577 (Rfree = 0.000) for 3841 atoms. Found 18 (18 requested) and removed 33 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.36 3.85 Search for helices and strands: 0 residues in 0 chains, 3947 seeds are put forward Round 1: 199 peptides, 40 chains. Longest chain 10 peptides. Score 0.299 Round 2: 234 peptides, 38 chains. Longest chain 14 peptides. Score 0.429 Round 3: 249 peptides, 40 chains. Longest chain 14 peptides. Score 0.446 Round 4: 245 peptides, 40 chains. Longest chain 12 peptides. Score 0.435 Round 5: 268 peptides, 45 chains. Longest chain 12 peptides. Score 0.439 Taking the results from Round 3 Chains 40, Residues 209, Estimated correctness of the model 0.0 % 8 chains (40 residues) have been docked in sequence ------------------------------------------------------ 4954 reflections ( 97.75 % complete ) and 8812 restraints for refining 3946 atoms. 7921 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2616 (Rfree = 0.000) for 3946 atoms. Found 18 (18 requested) and removed 39 (9 requested) atoms. Cycle 12: After refmac, R = 0.2299 (Rfree = 0.000) for 3906 atoms. Found 18 (18 requested) and removed 33 (9 requested) atoms. Cycle 13: After refmac, R = 0.2336 (Rfree = 0.000) for 3873 atoms. Found 18 (18 requested) and removed 18 (9 requested) atoms. Cycle 14: After refmac, R = 0.2300 (Rfree = 0.000) for 3860 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. Cycle 15: After refmac, R = 0.1733 (Rfree = 0.000) for 3854 atoms. Found 7 (18 requested) and removed 16 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.41 3.90 Search for helices and strands: 0 residues in 0 chains, 3962 seeds are put forward Round 1: 217 peptides, 42 chains. Longest chain 13 peptides. Score 0.329 Round 2: 247 peptides, 42 chains. Longest chain 18 peptides. Score 0.417 Round 3: 258 peptides, 43 chains. Longest chain 13 peptides. Score 0.435 Round 4: 256 peptides, 43 chains. Longest chain 15 peptides. Score 0.430 Round 5: 255 peptides, 39 chains. Longest chain 13 peptides. Score 0.474 Taking the results from Round 5 Chains 40, Residues 216, Estimated correctness of the model 0.0 % 8 chains (45 residues) have been docked in sequence ------------------------------------------------------ 4954 reflections ( 97.75 % complete ) and 9293 restraints for refining 4140 atoms. 8350 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2604 (Rfree = 0.000) for 4140 atoms. Found 19 (19 requested) and removed 39 (9 requested) atoms. Cycle 17: After refmac, R = 0.2332 (Rfree = 0.000) for 4078 atoms. Found 19 (19 requested) and removed 31 (9 requested) atoms. Cycle 18: After refmac, R = 0.2254 (Rfree = 0.000) for 4035 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. Cycle 19: After refmac, R = 0.2364 (Rfree = 0.000) for 4010 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. Cycle 20: After refmac, R = 0.2369 (Rfree = 0.000) for 3991 atoms. Found 19 (19 requested) and removed 18 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.41 3.90 Search for helices and strands: 0 residues in 0 chains, 4091 seeds are put forward Round 1: 209 peptides, 44 chains. Longest chain 12 peptides. Score 0.277 Round 2: 232 peptides, 39 chains. Longest chain 12 peptides. Score 0.411 Round 3: 241 peptides, 40 chains. Longest chain 14 peptides. Score 0.424 Round 4: 242 peptides, 41 chains. Longest chain 15 peptides. Score 0.415 Round 5: 261 peptides, 42 chains. Longest chain 12 peptides. Score 0.455 Taking the results from Round 5 Chains 43, Residues 219, Estimated correctness of the model 0.0 % 4 chains (22 residues) have been docked in sequence ------------------------------------------------------ 4954 reflections ( 97.75 % complete ) and 9309 restraints for refining 4134 atoms. 8427 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2540 (Rfree = 0.000) for 4134 atoms. Found 19 (19 requested) and removed 37 (9 requested) atoms. Cycle 22: After refmac, R = 0.2412 (Rfree = 0.000) for 4078 atoms. Found 19 (19 requested) and removed 35 (9 requested) atoms. Cycle 23: After refmac, R = 0.1939 (Rfree = 0.000) for 4033 atoms. Found 13 (19 requested) and removed 26 (9 requested) atoms. Cycle 24: After refmac, R = 0.1883 (Rfree = 0.000) for 4008 atoms. Found 6 (19 requested) and removed 12 (9 requested) atoms. Cycle 25: After refmac, R = 0.1796 (Rfree = 0.000) for 3999 atoms. Found 10 (19 requested) and removed 15 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.42 3.91 Search for helices and strands: 0 residues in 0 chains, 4114 seeds are put forward Round 1: 199 peptides, 43 chains. Longest chain 8 peptides. Score 0.258 Round 2: 223 peptides, 39 chains. Longest chain 10 peptides. Score 0.385 Round 3: 232 peptides, 42 chains. Longest chain 11 peptides. Score 0.373 Round 4: 226 peptides, 37 chains. Longest chain 12 peptides. Score 0.418 Round 5: 236 peptides, 39 chains. Longest chain 15 peptides. Score 0.422 Taking the results from Round 5 Chains 40, Residues 197, Estimated correctness of the model 0.0 % 5 chains (29 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 4954 reflections ( 97.75 % complete ) and 9601 restraints for refining 4162 atoms. 8781 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2834 (Rfree = 0.000) for 4162 atoms. Found 19 (19 requested) and removed 40 (9 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2626 (Rfree = 0.000) for 4103 atoms. Found 19 (19 requested) and removed 34 (9 requested) atoms. Cycle 28: After refmac, R = 0.2820 (Rfree = 0.000) for 4065 atoms. Found 19 (19 requested) and removed 36 (9 requested) atoms. Cycle 29: After refmac, R = 0.2610 (Rfree = 0.000) for 4023 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 30: After refmac, R = 0.2648 (Rfree = 0.000) for 4005 atoms. Found 19 (19 requested) and removed 23 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.39 3.88 Search for helices and strands: 0 residues in 0 chains, 4100 seeds are put forward Round 1: 192 peptides, 39 chains. Longest chain 9 peptides. Score 0.290 Round 2: 198 peptides, 35 chains. Longest chain 16 peptides. Score 0.362 Round 3: 217 peptides, 38 chains. Longest chain 13 peptides. Score 0.380 Round 4: 225 peptides, 39 chains. Longest chain 22 peptides. Score 0.391 Round 5: 226 peptides, 39 chains. Longest chain 14 peptides. Score 0.394 Taking the results from Round 5 Chains 40, Residues 187, Estimated correctness of the model 0.0 % 5 chains (30 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDBFailed to save intermediate PDB 4954 reflections ( 97.75 % complete ) and 9241 restraints for refining 4095 atoms. 8445 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2743 (Rfree = 0.000) for 4095 atoms. Found 19 (19 requested) and removed 37 (9 requested) atoms. Cycle 32: After refmac, R = 0.2535 (Rfree = 0.000) for 4055 atoms. Found 19 (19 requested) and removed 32 (9 requested) atoms. Cycle 33: After refmac, R = 0.2283 (Rfree = 0.000) for 4025 atoms. Found 10 (19 requested) and removed 21 (9 requested) atoms. Cycle 34: After refmac, R = 0.1603 (Rfree = 0.000) for 4004 atoms. Found 7 (19 requested) and removed 12 (9 requested) atoms. Cycle 35: After refmac, R = 0.2191 (Rfree = 0.000) for 3991 atoms. Found 18 (18 requested) and removed 22 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.40 3.89 Search for helices and strands: 0 residues in 0 chains, 4085 seeds are put forward Round 1: 185 peptides, 39 chains. Longest chain 14 peptides. Score 0.267 Round 2: 199 peptides, 35 chains. Longest chain 11 peptides. Score 0.365 Round 3: 202 peptides, 34 chains. Longest chain 14 peptides. Score 0.387 Round 4: 210 peptides, 37 chains. Longest chain 17 peptides. Score 0.372 Round 5: 218 peptides, 35 chains. Longest chain 22 peptides. Score 0.420 Taking the results from Round 5 Chains 37, Residues 183, Estimated correctness of the model 0.0 % 5 chains (36 residues) have been docked in sequence ------------------------------------------------------ 4954 reflections ( 97.75 % complete ) and 9450 restraints for refining 4152 atoms. 8636 conditional restraints added. Observations/parameters ratio is 0.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2909 (Rfree = 0.000) for 4152 atoms. Found 19 (19 requested) and removed 46 (9 requested) atoms. Cycle 37: After refmac, R = 0.2701 (Rfree = 0.000) for 4101 atoms. Found 19 (19 requested) and removed 35 (9 requested) atoms. Cycle 38: After refmac, R = 0.2546 (Rfree = 0.000) for 4064 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 39: After refmac, R = 0.1916 (Rfree = 0.000) for 4051 atoms. Found 8 (19 requested) and removed 12 (9 requested) atoms. Cycle 40: After refmac, R = 0.1729 (Rfree = 0.000) for 4035 atoms. Found 10 (19 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.41 3.90 Search for helices and strands: 0 residues in 0 chains, 4106 seeds are put forward Round 1: 162 peptides, 34 chains. Longest chain 10 peptides. Score 0.260 Round 2: 175 peptides, 34 chains. Longest chain 10 peptides. Score 0.303 Round 3: 182 peptides, 33 chains. Longest chain 12 peptides. Score 0.339 Round 4: 180 peptides, 33 chains. Longest chain 9 peptides. Score 0.333 Round 5: 178 peptides, 33 chains. Longest chain 10 peptides. Score 0.326 Taking the results from Round 3 Chains 33, Residues 149, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4954 reflections ( 97.75 % complete ) and 9384 restraints for refining 3984 atoms. 8803 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2608 (Rfree = 0.000) for 3984 atoms. Found 18 (18 requested) and removed 27 (9 requested) atoms. Cycle 42: After refmac, R = 0.2438 (Rfree = 0.000) for 3960 atoms. Found 18 (18 requested) and removed 30 (9 requested) atoms. Cycle 43: After refmac, R = 0.1694 (Rfree = 0.000) for 3942 atoms. Found 10 (18 requested) and removed 17 (9 requested) atoms. Cycle 44: After refmac, R = 0.1504 (Rfree = 0.000) for 3933 atoms. Found 10 (18 requested) and removed 16 (9 requested) atoms. Cycle 45: After refmac, R = 0.1432 (Rfree = 0.000) for 3925 atoms. Found 12 (18 requested) and removed 14 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.44 3.94 Search for helices and strands: 0 residues in 0 chains, 4001 seeds are put forward Round 1: 132 peptides, 29 chains. Longest chain 7 peptides. Score 0.228 Round 2: 154 peptides, 31 chains. Longest chain 8 peptides. Score 0.276 Round 3: 164 peptides, 31 chains. Longest chain 9 peptides. Score 0.309 Round 4: 164 peptides, 32 chains. Longest chain 9 peptides. Score 0.295 Round 5: 162 peptides, 30 chains. Longest chain 9 peptides. Score 0.317 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 132, 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 1vk3-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. Failed to save intermediate PDB 4954 reflections ( 97.75 % complete ) and 9274 restraints for refining 3903 atoms. 8776 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2306 (Rfree = 0.000) for 3903 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2150 (Rfree = 0.000) for 3880 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1957 (Rfree = 0.000) for 3860 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2071 (Rfree = 0.000) for 3842 atoms. TimeTaking 57.17