null Sun 23 Dec 23:50:02 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vkh-3.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vkh-3.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vkh-3.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkh-3.6-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vkh-3.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkh-3.6-parrot-mrncs ############### 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 23:50:07 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/mrncs/ArpWArp/wArpResults/WorkingDir/1vkh-3.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkh-3.6-parrot-mrncs/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 369 and 0 Target number of residues in the AU: 369 Target solvent content: 0.6036 Checking the provided sequence file Detected sequence length: 273 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 546 Adjusted target solvent content: 0.41 Input MTZ file: 1vkh-3.6-parrot-mrncs.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: 4 Cell parameters: 41.965 85.956 70.476 90.000 97.713 90.000 Input sequence file: 1vkh-3.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 4368 target number of atoms Had to go as low as 0.65 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 19.289 3.600 Wilson plot Bfac: 53.96 5789 reflections ( 99.30 % complete ) and 0 restraints for refining 4831 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3205 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3068 (Rfree = 0.000) for 4831 atoms. Found 30 (30 requested) and removed 66 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.18 3.59 Search for helices and strands: 0 residues in 0 chains, 4923 seeds are put forward NCS extension: 0 residues added, 4923 seeds are put forward Round 1: 164 peptides, 34 chains. Longest chain 7 peptides. Score 0.274 Round 2: 219 peptides, 39 chains. Longest chain 13 peptides. Score 0.390 Round 3: 240 peptides, 39 chains. Longest chain 13 peptides. Score 0.454 Round 4: 233 peptides, 40 chains. Longest chain 13 peptides. Score 0.420 Round 5: 241 peptides, 41 chains. Longest chain 21 peptides. Score 0.431 Taking the results from Round 3 Chains 39, Residues 201, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5789 reflections ( 99.30 % complete ) and 9158 restraints for refining 3960 atoms. 8393 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2434 (Rfree = 0.000) for 3960 atoms. Found 25 (25 requested) and removed 31 (12 requested) atoms. Cycle 2: After refmac, R = 0.2310 (Rfree = 0.000) for 3915 atoms. Found 25 (25 requested) and removed 23 (12 requested) atoms. Cycle 3: After refmac, R = 0.2267 (Rfree = 0.000) for 3896 atoms. Found 25 (25 requested) and removed 22 (12 requested) atoms. Cycle 4: After refmac, R = 0.2308 (Rfree = 0.000) for 3886 atoms. Found 25 (25 requested) and removed 24 (12 requested) atoms. Cycle 5: After refmac, R = 0.1798 (Rfree = 0.000) for 3877 atoms. Found 16 (24 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.20 3.61 Search for helices and strands: 0 residues in 0 chains, 4058 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 4073 seeds are put forward Round 1: 222 peptides, 49 chains. Longest chain 10 peptides. Score 0.260 Round 2: 266 peptides, 49 chains. Longest chain 11 peptides. Score 0.404 Round 3: 271 peptides, 48 chains. Longest chain 15 peptides. Score 0.432 Round 4: 282 peptides, 47 chains. Longest chain 19 peptides. Score 0.476 Round 5: 279 peptides, 42 chains. Longest chain 14 peptides. Score 0.527 Taking the results from Round 5 Chains 42, Residues 237, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5789 reflections ( 99.30 % complete ) and 9371 restraints for refining 3960 atoms. 8465 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2356 (Rfree = 0.000) for 3960 atoms. Found 25 (25 requested) and removed 28 (12 requested) atoms. Cycle 7: After refmac, R = 0.2283 (Rfree = 0.000) for 3930 atoms. Found 25 (25 requested) and removed 23 (12 requested) atoms. Cycle 8: After refmac, R = 0.2142 (Rfree = 0.000) for 3924 atoms. Found 23 (25 requested) and removed 22 (12 requested) atoms. Cycle 9: After refmac, R = 0.1800 (Rfree = 0.000) for 3918 atoms. Found 9 (25 requested) and removed 19 (12 requested) atoms. Cycle 10: After refmac, R = 0.1698 (Rfree = 0.000) for 3905 atoms. Found 4 (25 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.23 3.65 Search for helices and strands: 0 residues in 0 chains, 4043 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 4059 seeds are put forward Round 1: 220 peptides, 44 chains. Longest chain 10 peptides. Score 0.324 Round 2: 247 peptides, 39 chains. Longest chain 13 peptides. Score 0.475 Round 3: 247 peptides, 40 chains. Longest chain 13 peptides. Score 0.462 Round 4: 241 peptides, 38 chains. Longest chain 14 peptides. Score 0.470 Round 5: 264 peptides, 39 chains. Longest chain 21 peptides. Score 0.522 Taking the results from Round 5 Chains 39, Residues 225, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5789 reflections ( 99.30 % complete ) and 9317 restraints for refining 3960 atoms. 8456 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2241 (Rfree = 0.000) for 3960 atoms. Found 25 (25 requested) and removed 29 (12 requested) atoms. Cycle 12: After refmac, R = 0.2338 (Rfree = 0.000) for 3944 atoms. Found 25 (25 requested) and removed 33 (12 requested) atoms. Cycle 13: After refmac, R = 0.2319 (Rfree = 0.000) for 3927 atoms. Found 25 (25 requested) and removed 28 (12 requested) atoms. Cycle 14: After refmac, R = 0.1777 (Rfree = 0.000) for 3916 atoms. Found 13 (25 requested) and removed 13 (12 requested) atoms. Cycle 15: After refmac, R = 0.1608 (Rfree = 0.000) for 3911 atoms. Found 4 (25 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.21 3.62 Search for helices and strands: 0 residues in 0 chains, 4063 seeds are put forward NCS extension: 40 residues added (0 deleted due to clashes), 4103 seeds are put forward Round 1: 223 peptides, 47 chains. Longest chain 11 peptides. Score 0.292 Round 2: 275 peptides, 46 chains. Longest chain 19 peptides. Score 0.468 Round 3: 272 peptides, 49 chains. Longest chain 20 peptides. Score 0.422 Round 4: 277 peptides, 43 chains. Longest chain 14 peptides. Score 0.510 Round 5: 263 peptides, 42 chains. Longest chain 16 peptides. Score 0.483 Taking the results from Round 4 Chains 43, Residues 234, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5789 reflections ( 99.30 % complete ) and 9311 restraints for refining 3959 atoms. 8418 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2179 (Rfree = 0.000) for 3959 atoms. Found 16 (25 requested) and removed 24 (12 requested) atoms. Cycle 17: After refmac, R = 0.2102 (Rfree = 0.000) for 3939 atoms. Found 25 (25 requested) and removed 25 (12 requested) atoms. Cycle 18: After refmac, R = 0.2132 (Rfree = 0.000) for 3934 atoms. Found 25 (25 requested) and removed 15 (12 requested) atoms. Cycle 19: After refmac, R = 0.2190 (Rfree = 0.000) for 3941 atoms. Found 25 (25 requested) and removed 20 (12 requested) atoms. Cycle 20: After refmac, R = 0.2169 (Rfree = 0.000) for 3944 atoms. Found 25 (25 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.17 3.58 Search for helices and strands: 0 residues in 0 chains, 4114 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 4129 seeds are put forward Round 1: 193 peptides, 36 chains. Longest chain 13 peptides. Score 0.346 Round 2: 209 peptides, 37 chains. Longest chain 10 peptides. Score 0.385 Round 3: 208 peptides, 35 chains. Longest chain 12 peptides. Score 0.409 Round 4: 231 peptides, 32 chains. Longest chain 25 peptides. Score 0.516 Round 5: 227 peptides, 39 chains. Longest chain 15 peptides. Score 0.415 Taking the results from Round 4 Chains 32, Residues 199, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 5789 reflections ( 99.30 % complete ) and 9236 restraints for refining 3960 atoms. 8448 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2189 (Rfree = 0.000) for 3960 atoms. Found 25 (25 requested) and removed 24 (12 requested) atoms. Cycle 22: After refmac, R = 0.2286 (Rfree = 0.000) for 3946 atoms. Found 25 (25 requested) and removed 22 (12 requested) atoms. Cycle 23: After refmac, R = 0.1691 (Rfree = 0.000) for 3941 atoms. Found 6 (25 requested) and removed 17 (12 requested) atoms. Cycle 24: After refmac, R = 0.1541 (Rfree = 0.000) for 3927 atoms. Found 5 (25 requested) and removed 15 (12 requested) atoms. Cycle 25: After refmac, R = 0.1493 (Rfree = 0.000) for 3914 atoms. Found 1 (25 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.22 3.63 Search for helices and strands: 0 residues in 0 chains, 4040 seeds are put forward NCS extension: 31 residues added (3 deleted due to clashes), 4071 seeds are put forward Round 1: 189 peptides, 39 chains. Longest chain 11 peptides. Score 0.289 Round 2: 234 peptides, 42 chains. Longest chain 11 peptides. Score 0.396 Round 3: 226 peptides, 38 chains. Longest chain 13 peptides. Score 0.425 Round 4: 231 peptides, 37 chains. Longest chain 13 peptides. Score 0.453 Round 5: 229 peptides, 37 chains. Longest chain 18 peptides. Score 0.447 Taking the results from Round 4 Chains 37, Residues 194, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5789 reflections ( 99.30 % complete ) and 9371 restraints for refining 3960 atoms. 8632 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1982 (Rfree = 0.000) for 3960 atoms. Found 24 (25 requested) and removed 19 (12 requested) atoms. Cycle 27: After refmac, R = 0.2155 (Rfree = 0.000) for 3950 atoms. Found 25 (25 requested) and removed 19 (12 requested) atoms. Cycle 28: After refmac, R = 0.2155 (Rfree = 0.000) for 3949 atoms. Found 25 (25 requested) and removed 25 (12 requested) atoms. Cycle 29: After refmac, R = 0.1509 (Rfree = 0.000) for 3945 atoms. Found 17 (25 requested) and removed 16 (12 requested) atoms. Cycle 30: After refmac, R = 0.1363 (Rfree = 0.000) for 3944 atoms. Found 10 (25 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.20 3.61 Search for helices and strands: 0 residues in 0 chains, 4099 seeds are put forward NCS extension: 15 residues added (1 deleted due to clashes), 4114 seeds are put forward Round 1: 190 peptides, 40 chains. Longest chain 11 peptides. Score 0.278 Round 2: 218 peptides, 40 chains. Longest chain 10 peptides. Score 0.373 Round 3: 229 peptides, 39 chains. Longest chain 18 peptides. Score 0.421 Round 4: 227 peptides, 38 chains. Longest chain 11 peptides. Score 0.428 Round 5: 226 peptides, 37 chains. Longest chain 23 peptides. Score 0.438 Taking the results from Round 5 Chains 38, Residues 189, Estimated correctness of the model 0.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 5789 reflections ( 99.30 % complete ) and 9198 restraints for refining 3960 atoms. 8390 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2042 (Rfree = 0.000) for 3960 atoms. Found 25 (25 requested) and removed 22 (12 requested) atoms. Cycle 32: After refmac, R = 0.2048 (Rfree = 0.000) for 3943 atoms. Found 25 (25 requested) and removed 19 (12 requested) atoms. Cycle 33: After refmac, R = 0.2085 (Rfree = 0.000) for 3940 atoms. Found 25 (25 requested) and removed 23 (12 requested) atoms. Cycle 34: After refmac, R = 0.1883 (Rfree = 0.000) for 3936 atoms. Found 25 (25 requested) and removed 22 (12 requested) atoms. Cycle 35: After refmac, R = 0.1910 (Rfree = 0.000) for 3935 atoms. Found 25 (25 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.17 3.58 Search for helices and strands: 0 residues in 0 chains, 4096 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 4122 seeds are put forward Round 1: 178 peptides, 38 chains. Longest chain 9 peptides. Score 0.265 Round 2: 191 peptides, 35 chains. Longest chain 10 peptides. Score 0.354 Round 3: 185 peptides, 34 chains. Longest chain 10 peptides. Score 0.348 Round 4: 193 peptides, 33 chains. Longest chain 10 peptides. Score 0.389 Round 5: 201 peptides, 33 chains. Longest chain 11 peptides. Score 0.415 Taking the results from Round 5 Chains 33, Residues 168, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5789 reflections ( 99.30 % complete ) and 9511 restraints for refining 3960 atoms. 8872 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2070 (Rfree = 0.000) for 3960 atoms. Found 25 (25 requested) and removed 25 (12 requested) atoms. Cycle 37: After refmac, R = 0.2118 (Rfree = 0.000) for 3946 atoms. Found 25 (25 requested) and removed 21 (12 requested) atoms. Cycle 38: After refmac, R = 0.2099 (Rfree = 0.000) for 3940 atoms. Found 25 (25 requested) and removed 24 (12 requested) atoms. Cycle 39: After refmac, R = 0.2197 (Rfree = 0.000) for 3927 atoms. Found 25 (25 requested) and removed 20 (12 requested) atoms. Cycle 40: After refmac, R = 0.2066 (Rfree = 0.000) for 3914 atoms. Found 25 (25 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.22 3.63 Search for helices and strands: 0 residues in 0 chains, 4068 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 4081 seeds are put forward Round 1: 145 peptides, 32 chains. Longest chain 9 peptides. Score 0.234 Round 2: 170 peptides, 36 chains. Longest chain 8 peptides. Score 0.266 Round 3: 182 peptides, 35 chains. Longest chain 11 peptides. Score 0.323 Round 4: 174 peptides, 31 chains. Longest chain 13 peptides. Score 0.355 Round 5: 171 peptides, 27 chains. Longest chain 14 peptides. Score 0.403 Taking the results from Round 5 Chains 27, Residues 144, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5789 reflections ( 99.30 % complete ) and 9535 restraints for refining 3901 atoms. 8986 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2154 (Rfree = 0.000) for 3901 atoms. Found 25 (25 requested) and removed 25 (12 requested) atoms. Cycle 42: After refmac, R = 0.2297 (Rfree = 0.000) for 3895 atoms. Found 25 (25 requested) and removed 19 (12 requested) atoms. Cycle 43: After refmac, R = 0.2111 (Rfree = 0.000) for 3896 atoms. Found 25 (25 requested) and removed 20 (12 requested) atoms. Cycle 44: After refmac, R = 0.1560 (Rfree = 0.000) for 3897 atoms. Found 7 (25 requested) and removed 17 (12 requested) atoms. Cycle 45: After refmac, R = 0.1447 (Rfree = 0.000) for 3886 atoms. Found 11 (24 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.19 3.60 Search for helices and strands: 0 residues in 0 chains, 4025 seeds are put forward NCS extension: 12 residues added (2 deleted due to clashes), 4037 seeds are put forward Round 1: 124 peptides, 27 chains. Longest chain 7 peptides. Score 0.234 Round 2: 132 peptides, 26 chains. Longest chain 8 peptides. Score 0.281 Round 3: 148 peptides, 26 chains. Longest chain 14 peptides. Score 0.340 Round 4: 150 peptides, 27 chains. Longest chain 11 peptides. Score 0.331 Round 5: 154 peptides, 27 chains. Longest chain 11 peptides. Score 0.346 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 127, 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 1vkh-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5789 reflections ( 99.30 % complete ) and 9479 restraints for refining 3853 atoms. 8998 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2163 (Rfree = 0.000) for 3853 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2158 (Rfree = 0.000) for 3830 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.2271 (Rfree = 0.000) for 3812 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.1596 (Rfree = 0.000) for 3794 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:38:33 GMT 2018 Job finished. TimeTaking 48.53 Used memory is bytes: 7808976