Starting phenix.real_space_refine on Sat Dec 28 05:30:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y3g_33594/12_2024/7y3g_33594.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y3g_33594/12_2024/7y3g_33594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y3g_33594/12_2024/7y3g_33594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y3g_33594/12_2024/7y3g_33594.map" model { file = "/net/cci-nas-00/data/ceres_data/7y3g_33594/12_2024/7y3g_33594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y3g_33594/12_2024/7y3g_33594.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 4981 2.51 5 N 1368 2.21 5 O 1463 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7864 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1832 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 6, 'TRANS': 213} Chain breaks: 5 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2035 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain breaks: 1 Time building chain proxies: 4.89, per 1000 atoms: 0.62 Number of scatterers: 7864 At special positions: 0 Unit cell: (78, 101.25, 133.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1463 8.00 N 1368 7.00 C 4981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 181 " - pdb=" SG CYS R 188 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 1.0 seconds 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1886 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 10 sheets defined 41.4% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 11 through 38 removed outlier: 3.635A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.895A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 Processing helix chain 'A' and resid 314 through 318 removed outlier: 3.501A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 350 removed outlier: 4.324A pdb=" N LYS A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N PHE A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.962A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.660A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.640A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.743A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.795A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.753A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 72 removed outlier: 3.868A pdb=" N ILE R 49 " --> pdb=" O ASN R 45 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU R 61 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN R 72 " --> pdb=" O ILE R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 103 removed outlier: 3.757A pdb=" N PHE R 101 " --> pdb=" O LEU R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 144 Processing helix chain 'R' and resid 145 through 148 removed outlier: 4.126A pdb=" N TYR R 148 " --> pdb=" O ALA R 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 145 through 148' Processing helix chain 'R' and resid 153 through 174 removed outlier: 4.287A pdb=" N VAL R 159 " --> pdb=" O THR R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 177 No H-bonds generated for 'chain 'R' and resid 175 through 177' Processing helix chain 'R' and resid 180 through 184 removed outlier: 4.386A pdb=" N ARG R 183 " --> pdb=" O ASN R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 194 through 206 removed outlier: 4.293A pdb=" N VAL R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N PHE R 206 " --> pdb=" O LEU R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 236 removed outlier: 3.679A pdb=" N ILE R 223 " --> pdb=" O GLN R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 247 through 263 Processing helix chain 'R' and resid 264 through 272 Processing helix chain 'R' and resid 280 through 303 removed outlier: 4.145A pdb=" N TYR R 284 " --> pdb=" O SER R 280 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA R 285 " --> pdb=" O ILE R 281 " (cutoff:3.500A) Proline residue: R 289 - end of helix Proline residue: R 298 - end of helix removed outlier: 3.899A pdb=" N TYR R 301 " --> pdb=" O ASN R 297 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE R 303 " --> pdb=" O VAL R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 311 removed outlier: 3.700A pdb=" N GLN R 309 " --> pdb=" O ASN R 305 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA R 311 " --> pdb=" O GLU R 307 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.559A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 9.475A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.519A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.920A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.060A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.899A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.938A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.764A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.646A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.516A pdb=" N LEU N 20 " --> pdb=" O LEU N 81 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR N 80 " --> pdb=" O SER N 71 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.860A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 362 hydrogen bonds defined for protein. 1041 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2572 1.34 - 1.46: 1316 1.46 - 1.57: 4056 1.57 - 1.69: 0 1.69 - 1.81: 73 Bond restraints: 8017 Sorted by residual: bond pdb=" CA LYS A 53 " pdb=" C LYS A 53 " ideal model delta sigma weight residual 1.525 1.498 0.027 1.02e-02 9.61e+03 7.15e+00 bond pdb=" CA THR A 55 " pdb=" C THR A 55 " ideal model delta sigma weight residual 1.524 1.495 0.029 1.24e-02 6.50e+03 5.61e+00 bond pdb=" C THR A 55 " pdb=" N ILE A 56 " ideal model delta sigma weight residual 1.335 1.315 0.020 1.10e-02 8.26e+03 3.32e+00 bond pdb=" N THR A 55 " pdb=" CA THR A 55 " ideal model delta sigma weight residual 1.459 1.440 0.019 1.17e-02 7.31e+03 2.72e+00 bond pdb=" N ILE A 56 " pdb=" CA ILE A 56 " ideal model delta sigma weight residual 1.458 1.437 0.021 1.41e-02 5.03e+03 2.25e+00 ... (remaining 8012 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 10622 1.81 - 3.62: 186 3.62 - 5.43: 38 5.43 - 7.24: 14 7.24 - 9.06: 3 Bond angle restraints: 10863 Sorted by residual: angle pdb=" N LYS A 58 " pdb=" CA LYS A 58 " pdb=" C LYS A 58 " ideal model delta sigma weight residual 113.20 106.54 6.66 1.36e+00 5.41e-01 2.40e+01 angle pdb=" C ARG A 336 " pdb=" N ALA A 337 " pdb=" CA ALA A 337 " ideal model delta sigma weight residual 121.54 127.97 -6.43 1.91e+00 2.74e-01 1.13e+01 angle pdb=" N ASN G 24 " pdb=" CA ASN G 24 " pdb=" C ASN G 24 " ideal model delta sigma weight residual 107.73 112.68 -4.95 1.80e+00 3.09e-01 7.56e+00 angle pdb=" CA VAL R 204 " pdb=" C VAL R 204 " pdb=" N SER R 205 " ideal model delta sigma weight residual 116.60 120.56 -3.96 1.45e+00 4.76e-01 7.46e+00 angle pdb=" CB GLN A 29 " pdb=" CG GLN A 29 " pdb=" CD GLN A 29 " ideal model delta sigma weight residual 112.60 117.11 -4.51 1.70e+00 3.46e-01 7.05e+00 ... (remaining 10858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 4133 17.78 - 35.56: 487 35.56 - 53.35: 132 53.35 - 71.13: 23 71.13 - 88.91: 5 Dihedral angle restraints: 4780 sinusoidal: 1867 harmonic: 2913 Sorted by residual: dihedral pdb=" CA VAL R 190 " pdb=" C VAL R 190 " pdb=" N VAL R 191 " pdb=" CA VAL R 191 " ideal model delta harmonic sigma weight residual 180.00 159.78 20.22 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA ASN R 100 " pdb=" C ASN R 100 " pdb=" N PHE R 101 " pdb=" CA PHE R 101 " ideal model delta harmonic sigma weight residual 180.00 163.69 16.31 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA ASP B 303 " pdb=" CB ASP B 303 " pdb=" CG ASP B 303 " pdb=" OD1 ASP B 303 " ideal model delta sinusoidal sigma weight residual -30.00 -86.06 56.06 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 4777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 814 0.038 - 0.076: 314 0.076 - 0.114: 95 0.114 - 0.152: 16 0.152 - 0.190: 2 Chirality restraints: 1241 Sorted by residual: chirality pdb=" CA ASN G 24 " pdb=" N ASN G 24 " pdb=" C ASN G 24 " pdb=" CB ASN G 24 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.02e-01 chirality pdb=" CB VAL A 57 " pdb=" CA VAL A 57 " pdb=" CG1 VAL A 57 " pdb=" CG2 VAL A 57 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CA MET R 265 " pdb=" N MET R 265 " pdb=" C MET R 265 " pdb=" CB MET R 265 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 1238 not shown) Planarity restraints: 1381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.077 5.00e-02 4.00e+02 1.17e-01 2.17e+01 pdb=" N PRO G 49 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 337 " 0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C ALA A 337 " -0.060 2.00e-02 2.50e+03 pdb=" O ALA A 337 " 0.022 2.00e-02 2.50e+03 pdb=" N LYS A 338 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN G 59 " 0.045 5.00e-02 4.00e+02 6.90e-02 7.62e+00 pdb=" N PRO G 60 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " 0.038 5.00e-02 4.00e+02 ... (remaining 1378 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 69 2.60 - 3.18: 6334 3.18 - 3.75: 11446 3.75 - 4.33: 15167 4.33 - 4.90: 26473 Nonbonded interactions: 59489 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.029 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.046 3.040 nonbonded pdb=" OD1 ASN R 198 " pdb=" OG SER R 271 " model vdw 2.151 3.040 nonbonded pdb=" NH2 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.222 3.120 nonbonded pdb=" O TYR A 318 " pdb=" NH1 ARG A 336 " model vdw 2.336 3.120 ... (remaining 59484 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 19.820 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 36.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8017 Z= 0.283 Angle : 0.663 9.056 10863 Z= 0.358 Chirality : 0.044 0.190 1241 Planarity : 0.006 0.117 1381 Dihedral : 16.443 88.910 2891 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.04 % Allowed : 30.09 % Favored : 66.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.27), residues: 979 helix: 1.79 (0.29), residues: 364 sheet: 0.32 (0.32), residues: 246 loop : -1.17 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 47 HIS 0.006 0.001 HIS A 357 PHE 0.021 0.002 PHE N 108 TYR 0.013 0.001 TYR N 60 ARG 0.016 0.001 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.903 Fit side-chains REVERT: A 34 LYS cc_start: 0.8228 (ttmm) cc_final: 0.8003 (ttmm) REVERT: A 308 ILE cc_start: 0.7008 (OUTLIER) cc_final: 0.6720 (tt) REVERT: B 229 ILE cc_start: 0.8121 (pt) cc_final: 0.7770 (mt) REVERT: B 274 THR cc_start: 0.8519 (m) cc_final: 0.8319 (m) REVERT: N 81 LEU cc_start: 0.8638 (tm) cc_final: 0.8390 (tt) REVERT: R 265 MET cc_start: 0.8546 (mpp) cc_final: 0.8305 (mmp) outliers start: 26 outliers final: 19 residues processed: 194 average time/residue: 1.2223 time to fit residues: 250.6691 Evaluate side-chains 197 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain R residue 105 TYR Chi-restraints excluded: chain R residue 149 HIS Chi-restraints excluded: chain R residue 154 VAL Chi-restraints excluded: chain R residue 189 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 41 optimal weight: 0.0170 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 0.0020 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 overall best weight: 0.4426 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN B 16 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN R 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8017 Z= 0.190 Angle : 0.540 7.343 10863 Z= 0.285 Chirality : 0.042 0.201 1241 Planarity : 0.005 0.080 1381 Dihedral : 6.047 58.108 1120 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.68 % Allowed : 25.53 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.27), residues: 979 helix: 2.00 (0.29), residues: 369 sheet: 0.53 (0.32), residues: 248 loop : -1.11 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE N 108 TYR 0.016 0.001 TYR R 148 ARG 0.006 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 0.896 Fit side-chains REVERT: A 44 LEU cc_start: 0.8811 (tp) cc_final: 0.8541 (tp) REVERT: A 235 ILE cc_start: 0.8267 (tp) cc_final: 0.8067 (tt) REVERT: B 72 SER cc_start: 0.8528 (m) cc_final: 0.8282 (p) REVERT: B 134 ARG cc_start: 0.6819 (ptp90) cc_final: 0.6489 (ptp90) REVERT: R 105 TYR cc_start: 0.6020 (OUTLIER) cc_final: 0.5812 (t80) REVERT: R 163 MET cc_start: 0.7386 (tmm) cc_final: 0.7109 (tmm) REVERT: R 265 MET cc_start: 0.8433 (tpp) cc_final: 0.8139 (mmt) outliers start: 40 outliers final: 18 residues processed: 199 average time/residue: 1.2494 time to fit residues: 262.9915 Evaluate side-chains 180 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain R residue 105 TYR Chi-restraints excluded: chain R residue 149 HIS Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 235 HIS Chi-restraints excluded: chain R residue 291 THR Chi-restraints excluded: chain R residue 296 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 60 optimal weight: 0.1980 chunk 24 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN B 16 ASN B 183 HIS B 237 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 297 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8017 Z= 0.245 Angle : 0.555 8.060 10863 Z= 0.292 Chirality : 0.042 0.149 1241 Planarity : 0.005 0.066 1381 Dihedral : 5.418 56.130 1103 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.80 % Allowed : 23.89 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.27), residues: 979 helix: 2.03 (0.29), residues: 369 sheet: 0.73 (0.33), residues: 234 loop : -1.19 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.015 0.002 PHE N 108 TYR 0.020 0.001 TYR R 148 ARG 0.010 0.001 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 182 time to evaluate : 0.886 Fit side-chains REVERT: A 44 LEU cc_start: 0.8791 (tp) cc_final: 0.8535 (tp) REVERT: B 134 ARG cc_start: 0.6869 (ptp90) cc_final: 0.6543 (ptp90) REVERT: B 156 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.8043 (mt0) REVERT: B 229 ILE cc_start: 0.8133 (pt) cc_final: 0.7798 (mt) REVERT: B 234 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.8394 (m-80) REVERT: R 265 MET cc_start: 0.8376 (tpp) cc_final: 0.8123 (mmt) outliers start: 41 outliers final: 20 residues processed: 207 average time/residue: 1.2079 time to fit residues: 264.4771 Evaluate side-chains 195 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 149 HIS Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain R residue 235 HIS Chi-restraints excluded: chain R residue 291 THR Chi-restraints excluded: chain R residue 295 ILE Chi-restraints excluded: chain R residue 296 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 0.4980 chunk 67 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 9 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 78 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN B 183 HIS B 237 ASN R 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8017 Z= 0.191 Angle : 0.522 7.516 10863 Z= 0.273 Chirality : 0.041 0.132 1241 Planarity : 0.004 0.056 1381 Dihedral : 4.377 52.722 1095 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.33 % Allowed : 25.64 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.27), residues: 979 helix: 1.99 (0.29), residues: 374 sheet: 0.78 (0.33), residues: 234 loop : -1.19 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.012 0.001 PHE B 199 TYR 0.024 0.001 TYR R 148 ARG 0.009 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.935 Fit side-chains REVERT: A 44 LEU cc_start: 0.8752 (tp) cc_final: 0.8527 (tp) REVERT: B 49 ARG cc_start: 0.8704 (mmt-90) cc_final: 0.8470 (mmt-90) REVERT: B 72 SER cc_start: 0.8531 (OUTLIER) cc_final: 0.8262 (p) REVERT: B 229 ILE cc_start: 0.8133 (pt) cc_final: 0.7804 (mt) REVERT: B 234 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8460 (m-80) REVERT: G 24 ASN cc_start: 0.8450 (p0) cc_final: 0.8224 (p0) REVERT: R 162 VAL cc_start: 0.8413 (p) cc_final: 0.8172 (m) REVERT: R 177 MET cc_start: 0.7534 (ppp) cc_final: 0.6871 (ppp) REVERT: R 270 TYR cc_start: 0.8490 (t80) cc_final: 0.8238 (t80) outliers start: 37 outliers final: 17 residues processed: 192 average time/residue: 1.2609 time to fit residues: 256.2121 Evaluate side-chains 188 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 235 HIS Chi-restraints excluded: chain R residue 291 THR Chi-restraints excluded: chain R residue 295 ILE Chi-restraints excluded: chain R residue 296 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 70 optimal weight: 0.0970 chunk 39 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 220 HIS B 237 ASN R 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8017 Z= 0.268 Angle : 0.560 8.307 10863 Z= 0.293 Chirality : 0.043 0.132 1241 Planarity : 0.004 0.052 1381 Dihedral : 4.421 52.643 1091 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.68 % Allowed : 24.36 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.27), residues: 979 helix: 1.81 (0.28), residues: 378 sheet: 0.79 (0.32), residues: 234 loop : -1.22 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.006 0.001 HIS A 357 PHE 0.014 0.002 PHE B 199 TYR 0.024 0.001 TYR R 148 ARG 0.009 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 0.881 Fit side-chains REVERT: A 44 LEU cc_start: 0.8797 (tp) cc_final: 0.8521 (tp) REVERT: A 314 GLU cc_start: 0.7426 (tm-30) cc_final: 0.7144 (tm-30) REVERT: B 49 ARG cc_start: 0.8713 (mmt-90) cc_final: 0.8471 (mmt-90) REVERT: B 72 SER cc_start: 0.8520 (OUTLIER) cc_final: 0.8245 (p) REVERT: B 137 ARG cc_start: 0.7650 (ttm110) cc_final: 0.7390 (ttm-80) REVERT: B 229 ILE cc_start: 0.8183 (pt) cc_final: 0.7950 (mt) REVERT: B 234 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8394 (m-80) REVERT: G 24 ASN cc_start: 0.8357 (p0) cc_final: 0.8147 (p0) REVERT: R 156 PHE cc_start: 0.7990 (t80) cc_final: 0.7732 (t80) REVERT: R 162 VAL cc_start: 0.8424 (p) cc_final: 0.8188 (m) REVERT: R 177 MET cc_start: 0.7458 (ppp) cc_final: 0.6928 (ppp) outliers start: 40 outliers final: 24 residues processed: 207 average time/residue: 1.1854 time to fit residues: 260.4695 Evaluate side-chains 207 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 149 HIS Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 233 LEU Chi-restraints excluded: chain R residue 235 HIS Chi-restraints excluded: chain R residue 291 THR Chi-restraints excluded: chain R residue 292 TYR Chi-restraints excluded: chain R residue 295 ILE Chi-restraints excluded: chain R residue 296 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 78 optimal weight: 0.0470 chunk 43 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 31 optimal weight: 0.0770 chunk 49 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 16 ASN B 237 ASN R 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8017 Z= 0.182 Angle : 0.533 8.355 10863 Z= 0.274 Chirality : 0.041 0.130 1241 Planarity : 0.004 0.047 1381 Dihedral : 4.250 52.151 1091 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.33 % Allowed : 24.94 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.27), residues: 979 helix: 2.01 (0.29), residues: 374 sheet: 0.71 (0.32), residues: 243 loop : -1.19 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.012 0.001 PHE B 199 TYR 0.024 0.001 TYR R 148 ARG 0.009 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 0.869 Fit side-chains REVERT: A 44 LEU cc_start: 0.8755 (tp) cc_final: 0.8512 (tp) REVERT: A 209 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7251 (mt-10) REVERT: A 314 GLU cc_start: 0.7405 (tm-30) cc_final: 0.7066 (tm-30) REVERT: B 49 ARG cc_start: 0.8714 (mmt-90) cc_final: 0.8481 (mmt-90) REVERT: B 72 SER cc_start: 0.8523 (m) cc_final: 0.8273 (p) REVERT: B 137 ARG cc_start: 0.7612 (ttm110) cc_final: 0.7361 (ttm-80) REVERT: B 205 ASP cc_start: 0.7894 (p0) cc_final: 0.7661 (p0) REVERT: B 229 ILE cc_start: 0.8124 (pt) cc_final: 0.7848 (mt) REVERT: B 234 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8424 (m-80) REVERT: R 156 PHE cc_start: 0.7899 (t80) cc_final: 0.7657 (t80) REVERT: R 177 MET cc_start: 0.7464 (ppp) cc_final: 0.6859 (ppp) REVERT: R 270 TYR cc_start: 0.8582 (t80) cc_final: 0.8358 (t80) outliers start: 37 outliers final: 22 residues processed: 209 average time/residue: 1.1359 time to fit residues: 251.9966 Evaluate side-chains 199 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 149 HIS Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 235 HIS Chi-restraints excluded: chain R residue 291 THR Chi-restraints excluded: chain R residue 292 TYR Chi-restraints excluded: chain R residue 295 ILE Chi-restraints excluded: chain R residue 296 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 57 optimal weight: 0.1980 chunk 43 optimal weight: 0.0670 chunk 58 optimal weight: 2.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 220 HIS B 16 ASN B 237 ASN G 24 ASN R 297 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 8017 Z= 0.215 Angle : 0.554 8.231 10863 Z= 0.285 Chirality : 0.042 0.131 1241 Planarity : 0.004 0.045 1381 Dihedral : 4.290 52.303 1091 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.86 % Allowed : 26.81 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.27), residues: 979 helix: 1.98 (0.29), residues: 373 sheet: 0.82 (0.32), residues: 234 loop : -1.16 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.013 0.001 PHE B 199 TYR 0.026 0.001 TYR R 148 ARG 0.010 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.920 Fit side-chains REVERT: A 44 LEU cc_start: 0.8773 (tp) cc_final: 0.8519 (tp) REVERT: A 209 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7259 (mt-10) REVERT: A 232 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.6518 (ptp-170) REVERT: A 314 GLU cc_start: 0.7400 (tm-30) cc_final: 0.7070 (tm-30) REVERT: B 49 ARG cc_start: 0.8711 (mmt-90) cc_final: 0.8479 (mmt-90) REVERT: B 72 SER cc_start: 0.8531 (OUTLIER) cc_final: 0.8259 (p) REVERT: B 137 ARG cc_start: 0.7614 (ttm110) cc_final: 0.7375 (ttm-80) REVERT: B 234 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8442 (m-80) REVERT: N 108 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.8051 (m-80) REVERT: R 156 PHE cc_start: 0.7902 (t80) cc_final: 0.7639 (t80) REVERT: R 177 MET cc_start: 0.7432 (OUTLIER) cc_final: 0.6854 (ppp) REVERT: R 270 TYR cc_start: 0.8614 (t80) cc_final: 0.8377 (t80) outliers start: 33 outliers final: 24 residues processed: 202 average time/residue: 1.2030 time to fit residues: 257.3633 Evaluate side-chains 209 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 149 HIS Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 177 MET Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 235 HIS Chi-restraints excluded: chain R residue 291 THR Chi-restraints excluded: chain R residue 292 TYR Chi-restraints excluded: chain R residue 295 ILE Chi-restraints excluded: chain R residue 296 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 0.0060 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 220 HIS B 16 ASN B 237 ASN G 24 ASN R 297 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8017 Z= 0.229 Angle : 0.562 7.804 10863 Z= 0.290 Chirality : 0.042 0.152 1241 Planarity : 0.004 0.044 1381 Dihedral : 4.324 52.146 1091 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.57 % Allowed : 26.46 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.27), residues: 979 helix: 1.99 (0.29), residues: 373 sheet: 0.84 (0.32), residues: 234 loop : -1.15 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.001 PHE R 206 TYR 0.025 0.001 TYR R 148 ARG 0.009 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 0.830 Fit side-chains REVERT: A 44 LEU cc_start: 0.8783 (tp) cc_final: 0.8519 (tp) REVERT: A 209 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7259 (mt-10) REVERT: A 232 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.6475 (ptp-170) REVERT: A 314 GLU cc_start: 0.7429 (tm-30) cc_final: 0.7096 (tm-30) REVERT: B 49 ARG cc_start: 0.8708 (mmt-90) cc_final: 0.8476 (mmt-90) REVERT: B 72 SER cc_start: 0.8533 (OUTLIER) cc_final: 0.8264 (p) REVERT: B 137 ARG cc_start: 0.7635 (ttm110) cc_final: 0.7398 (ttm-80) REVERT: B 205 ASP cc_start: 0.7910 (p0) cc_final: 0.7696 (p0) REVERT: B 234 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.8456 (m-80) REVERT: B 304 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7672 (ttp-170) REVERT: N 108 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.8133 (m-80) REVERT: R 156 PHE cc_start: 0.7934 (t80) cc_final: 0.7676 (t80) REVERT: R 162 VAL cc_start: 0.8410 (p) cc_final: 0.8180 (m) REVERT: R 177 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.6852 (ppp) REVERT: R 270 TYR cc_start: 0.8590 (t80) cc_final: 0.8381 (t80) outliers start: 39 outliers final: 25 residues processed: 202 average time/residue: 1.1979 time to fit residues: 256.1143 Evaluate side-chains 205 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 149 HIS Chi-restraints excluded: chain R residue 151 GLU Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 177 MET Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 235 HIS Chi-restraints excluded: chain R residue 291 THR Chi-restraints excluded: chain R residue 292 TYR Chi-restraints excluded: chain R residue 295 ILE Chi-restraints excluded: chain R residue 296 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 220 HIS B 16 ASN B 237 ASN G 24 ASN R 297 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8017 Z= 0.260 Angle : 0.575 8.139 10863 Z= 0.298 Chirality : 0.043 0.148 1241 Planarity : 0.004 0.045 1381 Dihedral : 4.397 52.083 1091 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.33 % Allowed : 27.05 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.27), residues: 979 helix: 1.92 (0.29), residues: 374 sheet: 0.84 (0.33), residues: 234 loop : -1.20 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.006 0.001 HIS A 357 PHE 0.014 0.002 PHE B 199 TYR 0.025 0.001 TYR R 148 ARG 0.009 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 0.834 Fit side-chains REVERT: A 44 LEU cc_start: 0.8799 (tp) cc_final: 0.8524 (tp) REVERT: A 232 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.6411 (ptp-170) REVERT: A 314 GLU cc_start: 0.7426 (tm-30) cc_final: 0.7104 (tm-30) REVERT: B 49 ARG cc_start: 0.8717 (mmt-90) cc_final: 0.8460 (mmt-90) REVERT: B 72 SER cc_start: 0.8541 (OUTLIER) cc_final: 0.8265 (p) REVERT: B 137 ARG cc_start: 0.7639 (ttm110) cc_final: 0.7404 (ttm-80) REVERT: B 205 ASP cc_start: 0.7937 (p0) cc_final: 0.7709 (p0) REVERT: B 234 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8416 (m-80) REVERT: N 108 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.8144 (m-80) REVERT: R 156 PHE cc_start: 0.7907 (t80) cc_final: 0.7650 (t80) REVERT: R 162 VAL cc_start: 0.8415 (p) cc_final: 0.8183 (m) REVERT: R 177 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.6865 (ppp) REVERT: R 265 MET cc_start: 0.8474 (mpp) cc_final: 0.8125 (mmt) outliers start: 37 outliers final: 26 residues processed: 201 average time/residue: 1.1498 time to fit residues: 244.8561 Evaluate side-chains 209 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 149 HIS Chi-restraints excluded: chain R residue 151 GLU Chi-restraints excluded: chain R residue 160 MET Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 177 MET Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 235 HIS Chi-restraints excluded: chain R residue 291 THR Chi-restraints excluded: chain R residue 292 TYR Chi-restraints excluded: chain R residue 295 ILE Chi-restraints excluded: chain R residue 296 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.0570 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 64 optimal weight: 0.0670 chunk 97 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 47 optimal weight: 0.0970 chunk 61 optimal weight: 0.3980 overall best weight: 0.2234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 16 ASN B 237 ASN G 24 ASN R 297 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 8017 Z= 0.157 Angle : 0.530 8.421 10863 Z= 0.272 Chirality : 0.041 0.198 1241 Planarity : 0.004 0.042 1381 Dihedral : 4.121 51.826 1091 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.04 % Allowed : 28.10 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.27), residues: 979 helix: 2.13 (0.29), residues: 370 sheet: 0.86 (0.33), residues: 233 loop : -0.99 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.003 0.000 HIS A 220 PHE 0.009 0.001 PHE B 199 TYR 0.026 0.001 TYR R 148 ARG 0.009 0.000 ARG A 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 0.981 Fit side-chains REVERT: A 44 LEU cc_start: 0.8700 (tp) cc_final: 0.8500 (tp) REVERT: A 209 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7223 (mt-10) REVERT: A 314 GLU cc_start: 0.7392 (tm-30) cc_final: 0.7055 (tm-30) REVERT: B 49 ARG cc_start: 0.8707 (mmt-90) cc_final: 0.8467 (mmt-90) REVERT: B 72 SER cc_start: 0.8506 (m) cc_final: 0.8278 (p) REVERT: B 137 ARG cc_start: 0.7574 (ttm110) cc_final: 0.7358 (ttm-80) REVERT: B 234 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8455 (m-80) REVERT: B 304 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7724 (ttt180) REVERT: N 108 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.8058 (m-80) REVERT: R 162 VAL cc_start: 0.8415 (p) cc_final: 0.8194 (m) REVERT: R 177 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.6774 (ppp) REVERT: R 265 MET cc_start: 0.8500 (mpp) cc_final: 0.8251 (mmp) outliers start: 26 outliers final: 13 residues processed: 190 average time/residue: 1.1982 time to fit residues: 240.8656 Evaluate side-chains 184 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain R residue 149 HIS Chi-restraints excluded: chain R residue 177 MET Chi-restraints excluded: chain R residue 235 HIS Chi-restraints excluded: chain R residue 291 THR Chi-restraints excluded: chain R residue 292 TYR Chi-restraints excluded: chain R residue 295 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.0170 chunk 68 optimal weight: 0.9980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN B 16 ASN R 198 ASN R 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.135189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.117402 restraints weight = 11026.741| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.14 r_work: 0.3494 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8017 Z= 0.211 Angle : 0.566 8.317 10863 Z= 0.289 Chirality : 0.043 0.201 1241 Planarity : 0.004 0.044 1381 Dihedral : 4.180 52.080 1090 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.58 % Allowed : 28.69 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.27), residues: 979 helix: 2.08 (0.29), residues: 371 sheet: 0.80 (0.33), residues: 235 loop : -1.08 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.013 0.001 PHE B 199 TYR 0.025 0.001 TYR R 148 ARG 0.009 0.000 ARG A 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4185.04 seconds wall clock time: 75 minutes 11.18 seconds (4511.18 seconds total)