Starting phenix.real_space_refine on Tue Jul 29 12:28:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e4i_30986/07_2025/7e4i_30986.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e4i_30986/07_2025/7e4i_30986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e4i_30986/07_2025/7e4i_30986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e4i_30986/07_2025/7e4i_30986.map" model { file = "/net/cci-nas-00/data/ceres_data/7e4i_30986/07_2025/7e4i_30986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e4i_30986/07_2025/7e4i_30986.cif" } resolution = 3.05 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= 0.116 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 47 5.16 5 C 7240 2.51 5 N 1932 2.21 5 O 2117 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11336 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3494 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 17, 'TRANS': 421} Chain breaks: 2 Chain: "B" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2536 Classifications: {'peptide': 317} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 307} Chain: "C" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2344 Classifications: {'peptide': 291} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 284} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2378 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Chain: "E" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 317 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "F" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 267 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Time building chain proxies: 7.30, per 1000 atoms: 0.64 Number of scatterers: 11336 At special positions: 0 Unit cell: (123.918, 113.048, 115.222, 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 47 16.00 O 2117 8.00 N 1932 7.00 C 7240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.94 Conformation dependent library (CDL) restraints added in 1.6 seconds 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2680 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 8 sheets defined 38.5% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 43 through 56 removed outlier: 4.030A pdb=" N ALA A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 78 Processing helix chain 'A' and resid 198 through 201 Processing helix chain 'A' and resid 263 through 268 removed outlier: 3.764A pdb=" N SER A 268 " --> pdb=" O GLY A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 348 removed outlier: 3.750A pdb=" N GLN A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 356 removed outlier: 3.571A pdb=" N LYS A 356 " --> pdb=" O ILE A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 404 removed outlier: 4.174A pdb=" N GLU A 404 " --> pdb=" O LYS A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 434 Processing helix chain 'B' and resid 14 through 18 Processing helix chain 'B' and resid 30 through 37 removed outlier: 3.733A pdb=" N ALA B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 95 Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 119 through 123 removed outlier: 3.948A pdb=" N ASN B 123 " --> pdb=" O ARG B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 152 Processing helix chain 'B' and resid 157 through 168 removed outlier: 3.509A pdb=" N LEU B 161 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP B 168 " --> pdb=" O TYR B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 182 Processing helix chain 'B' and resid 184 through 192 removed outlier: 3.742A pdb=" N GLU B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 191 " --> pdb=" O GLN B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 225 removed outlier: 3.639A pdb=" N VAL B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LYS B 218 " --> pdb=" O LYS B 214 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N SER B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 234 Processing helix chain 'B' and resid 239 through 243 removed outlier: 3.930A pdb=" N GLY B 243 " --> pdb=" O SER B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 273 removed outlier: 3.725A pdb=" N ASN B 253 " --> pdb=" O HIS B 249 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN B 254 " --> pdb=" O ASN B 250 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN B 267 " --> pdb=" O GLU B 263 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 297 Processing helix chain 'B' and resid 303 through 312 Processing helix chain 'B' and resid 313 through 325 removed outlier: 3.620A pdb=" N VAL B 317 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN B 318 " --> pdb=" O LYS B 314 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA B 320 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 30 removed outlier: 3.669A pdb=" N ILE C 23 " --> pdb=" O SER C 19 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C 24 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 42 removed outlier: 3.760A pdb=" N SER C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET C 40 " --> pdb=" O GLU C 36 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 55 removed outlier: 4.001A pdb=" N LEU C 54 " --> pdb=" O ASN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 83 removed outlier: 3.505A pdb=" N LYS C 83 " --> pdb=" O GLN C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 107 through 132 removed outlier: 3.601A pdb=" N GLU C 111 " --> pdb=" O ASP C 107 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ARG C 124 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR C 126 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 138 Processing helix chain 'C' and resid 140 through 149 removed outlier: 3.954A pdb=" N LEU C 144 " --> pdb=" O TYR C 140 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE C 145 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER C 146 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS C 147 " --> pdb=" O LYS C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 154 removed outlier: 3.608A pdb=" N TRP C 154 " --> pdb=" O PHE C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 168 removed outlier: 3.867A pdb=" N LEU C 159 " --> pdb=" O TYR C 155 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN C 168 " --> pdb=" O GLN C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 208 through 241 removed outlier: 4.155A pdb=" N GLY C 212 " --> pdb=" O ASN C 208 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C 223 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP C 226 " --> pdb=" O ASN C 222 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 263 removed outlier: 3.555A pdb=" N PHE C 255 " --> pdb=" O SER C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 280 removed outlier: 4.180A pdb=" N ILE C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR C 278 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 Processing helix chain 'C' and resid 308 through 312 Processing helix chain 'C' and resid 314 through 327 removed outlier: 3.526A pdb=" N TYR C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 56 Processing helix chain 'D' and resid 62 through 66 removed outlier: 3.879A pdb=" N LEU D 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 72 Processing helix chain 'D' and resid 364 through 373 Processing helix chain 'E' and resid 14 through 49 Proline residue: E 39 - end of helix Processing helix chain 'F' and resid 30 through 51 Processing helix chain 'F' and resid 51 through 58 removed outlier: 3.837A pdb=" N ASP F 55 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA F 58 " --> pdb=" O MET F 54 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 37 removed outlier: 5.042A pdb=" N VAL A 31 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N VAL A 112 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLY A 33 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N GLN A 114 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL A 35 " --> pdb=" O GLN A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 132 removed outlier: 3.780A pdb=" N ASP A 136 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ILE A 168 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN A 196 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 180 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE A 414 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 464 through 466 removed outlier: 7.092A pdb=" N ALA A 465 " --> pdb=" O TYR B 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 41 through 43 removed outlier: 6.282A pdb=" N TYR B 60 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU B 116 " --> pdb=" O TYR B 60 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LEU B 62 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 45 through 46 removed outlier: 3.576A pdb=" N THR B 45 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 67 through 69 Processing sheet with id=AA7, first strand: chain 'C' and resid 46 through 47 removed outlier: 5.921A pdb=" N VAL C 6 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 83 through 93 removed outlier: 6.839A pdb=" N PHE D 98 " --> pdb=" O PHE D 92 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N CYS D 165 " --> pdb=" O ASN D 184 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR D 194 " --> pdb=" O PRO D 185 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL D 205 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU D 209 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL D 267 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N GLY D 83 " --> pdb=" O CYS D 355 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU D 357 " --> pdb=" O GLY D 83 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG D 85 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N PHE D 359 " --> pdb=" O ARG D 85 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASP D 87 " --> pdb=" O PHE D 359 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR D 361 " --> pdb=" O ASP D 87 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASN D 89 " --> pdb=" O THR D 361 " (cutoff:3.500A) 627 hydrogen bonds defined for protein. 1776 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: 3.72 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3662 1.34 - 1.46: 2389 1.46 - 1.58: 5443 1.58 - 1.69: 0 1.69 - 1.81: 71 Bond restraints: 11565 Sorted by residual: bond pdb=" CG PRO B 19 " pdb=" CD PRO B 19 " ideal model delta sigma weight residual 1.512 1.488 0.024 2.70e-02 1.37e+03 8.19e-01 bond pdb=" CB PRO B 129 " pdb=" CG PRO B 129 " ideal model delta sigma weight residual 1.506 1.477 0.029 3.90e-02 6.57e+02 5.66e-01 bond pdb=" CA PRO B 302 " pdb=" C PRO B 302 " ideal model delta sigma weight residual 1.527 1.519 0.008 1.07e-02 8.73e+03 5.33e-01 bond pdb=" C LEU C 60 " pdb=" N PRO C 61 " ideal model delta sigma weight residual 1.334 1.351 -0.017 2.34e-02 1.83e+03 5.09e-01 bond pdb=" CA ILE A 117 " pdb=" C ILE A 117 " ideal model delta sigma weight residual 1.517 1.527 -0.010 1.49e-02 4.50e+03 4.55e-01 ... (remaining 11560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 15289 1.32 - 2.64: 274 2.64 - 3.96: 54 3.96 - 5.28: 11 5.28 - 6.61: 3 Bond angle restraints: 15631 Sorted by residual: angle pdb=" N ILE B 154 " pdb=" CA ILE B 154 " pdb=" C ILE B 154 " ideal model delta sigma weight residual 113.20 109.44 3.76 9.60e-01 1.09e+00 1.53e+01 angle pdb=" N THR A 294 " pdb=" CA THR A 294 " pdb=" C THR A 294 " ideal model delta sigma weight residual 114.56 110.03 4.53 1.27e+00 6.20e-01 1.27e+01 angle pdb=" C ASP A 53 " pdb=" N THR A 54 " pdb=" CA THR A 54 " ideal model delta sigma weight residual 122.53 116.79 5.74 1.92e+00 2.71e-01 8.94e+00 angle pdb=" CA THR A 294 " pdb=" C THR A 294 " pdb=" N LYS A 295 " ideal model delta sigma weight residual 119.26 116.73 2.53 1.14e+00 7.69e-01 4.94e+00 angle pdb=" CA LEU C 60 " pdb=" C LEU C 60 " pdb=" N PRO C 61 " ideal model delta sigma weight residual 118.44 121.74 -3.30 1.59e+00 3.96e-01 4.30e+00 ... (remaining 15626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 6610 16.48 - 32.97: 247 32.97 - 49.45: 52 49.45 - 65.93: 15 65.93 - 82.41: 4 Dihedral angle restraints: 6928 sinusoidal: 2786 harmonic: 4142 Sorted by residual: dihedral pdb=" CA LYS C 59 " pdb=" C LYS C 59 " pdb=" N LEU C 60 " pdb=" CA LEU C 60 " ideal model delta harmonic sigma weight residual -180.00 -158.47 -21.53 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA ASN D 95 " pdb=" C ASN D 95 " pdb=" N PRO D 96 " pdb=" CA PRO D 96 " ideal model delta harmonic sigma weight residual 180.00 160.20 19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA TRP A 197 " pdb=" C TRP A 197 " pdb=" N ASN A 198 " pdb=" CA ASN A 198 " ideal model delta harmonic sigma weight residual 180.00 -162.75 -17.25 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 6925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1041 0.028 - 0.057: 508 0.057 - 0.085: 122 0.085 - 0.113: 76 0.113 - 0.142: 17 Chirality restraints: 1764 Sorted by residual: chirality pdb=" CA ILE D 256 " pdb=" N ILE D 256 " pdb=" C ILE D 256 " pdb=" CB ILE D 256 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA LEU C 60 " pdb=" N LEU C 60 " pdb=" C LEU C 60 " pdb=" CB LEU C 60 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA ILE C 64 " pdb=" N ILE C 64 " pdb=" C ILE C 64 " pdb=" CB ILE C 64 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 1761 not shown) Planarity restraints: 1988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 206 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO D 207 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 207 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 207 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 52 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" C ASP A 52 " -0.022 2.00e-02 2.50e+03 pdb=" O ASP A 52 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP A 53 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 258 " 0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO A 259 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 259 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 259 " 0.016 5.00e-02 4.00e+02 ... (remaining 1985 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1081 2.75 - 3.29: 10493 3.29 - 3.82: 17349 3.82 - 4.36: 21160 4.36 - 4.90: 37928 Nonbonded interactions: 88011 Sorted by model distance: nonbonded pdb=" OD2 ASP A 288 " pdb=" OG1 THR A 294 " model vdw 2.212 3.040 nonbonded pdb=" OG SER B 184 " pdb=" OE2 GLU B 301 " model vdw 2.241 3.040 nonbonded pdb=" OG SER D 93 " pdb=" O PRO D 96 " model vdw 2.248 3.040 nonbonded pdb=" OG SER A 344 " pdb=" O SER A 348 " model vdw 2.259 3.040 nonbonded pdb=" O SER A 253 " pdb=" OH TYR A 262 " model vdw 2.292 3.040 ... (remaining 88006 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: 1.360 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: 0.000 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 29.760 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 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 : 0.002 0.029 11565 Z= 0.101 Angle : 0.483 6.606 15631 Z= 0.271 Chirality : 0.039 0.142 1764 Planarity : 0.003 0.043 1988 Dihedral : 9.900 82.414 4248 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.42 % Allowed : 4.59 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.19 (0.23), residues: 1404 helix: 0.78 (0.26), residues: 450 sheet: 0.50 (0.25), residues: 442 loop : -0.68 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 240 HIS 0.003 0.001 HIS A 310 PHE 0.015 0.001 PHE A 237 TYR 0.011 0.001 TYR B 164 ARG 0.002 0.000 ARG C 124 Details of bonding type rmsd hydrogen bonds : bond 0.13602 ( 627) hydrogen bonds : angle 5.13510 ( 1776) covalent geometry : bond 0.00204 (11565) covalent geometry : angle 0.48279 (15631) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 HIS cc_start: 0.7573 (m170) cc_final: 0.7272 (m170) REVERT: A 456 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7342 (mt-10) REVERT: B 17 THR cc_start: 0.7884 (OUTLIER) cc_final: 0.7625 (t) REVERT: B 135 TYR cc_start: 0.8707 (t80) cc_final: 0.8463 (t80) REVERT: B 168 ASP cc_start: 0.8219 (p0) cc_final: 0.7997 (p0) REVERT: B 205 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7554 (tp) REVERT: B 251 SER cc_start: 0.8721 (t) cc_final: 0.8461 (t) REVERT: D 94 MET cc_start: 0.6368 (mmp) cc_final: 0.5866 (ptm) REVERT: D 186 SER cc_start: 0.6028 (t) cc_final: 0.5788 (m) REVERT: D 267 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.8023 (m) REVERT: D 369 MET cc_start: 0.4132 (mtt) cc_final: 0.3512 (mmm) outliers start: 18 outliers final: 6 residues processed: 176 average time/residue: 0.2403 time to fit residues: 60.3306 Evaluate side-chains 132 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 424 ASN Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 339 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 30.0000 chunk 105 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 108 optimal weight: 20.0000 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 126 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 159 ASN C 168 ASN C 285 ASN C 300 ASN D 65 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.195475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 117)---------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122242 restraints weight = 13243.368| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.07 r_work: 0.3087 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11565 Z= 0.137 Angle : 0.513 6.462 15631 Z= 0.271 Chirality : 0.041 0.150 1764 Planarity : 0.003 0.044 1988 Dihedral : 5.108 55.386 1528 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.74 % Allowed : 7.59 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.44 (0.23), residues: 1404 helix: 1.18 (0.25), residues: 458 sheet: 0.63 (0.25), residues: 435 loop : -0.75 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 240 HIS 0.005 0.001 HIS A 238 PHE 0.019 0.001 PHE D 340 TYR 0.018 0.001 TYR A 140 ARG 0.002 0.000 ARG C 124 Details of bonding type rmsd hydrogen bonds : bond 0.04054 ( 627) hydrogen bonds : angle 4.30933 ( 1776) covalent geometry : bond 0.00322 (11565) covalent geometry : angle 0.51277 (15631) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8038 (mmmt) cc_final: 0.7676 (mmtt) REVERT: A 169 HIS cc_start: 0.8090 (m170) cc_final: 0.7685 (m170) REVERT: A 298 MET cc_start: 0.9073 (tmm) cc_final: 0.8417 (tmm) REVERT: B 17 THR cc_start: 0.7716 (OUTLIER) cc_final: 0.7499 (t) REVERT: B 135 TYR cc_start: 0.9064 (t80) cc_final: 0.8733 (t80) REVERT: B 205 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7136 (tp) REVERT: B 242 GLN cc_start: 0.8500 (mt0) cc_final: 0.8300 (mt0) REVERT: C 153 MET cc_start: 0.8315 (mtm) cc_final: 0.7938 (mpp) REVERT: D 94 MET cc_start: 0.6565 (mmp) cc_final: 0.5748 (ptm) REVERT: D 186 SER cc_start: 0.5853 (t) cc_final: 0.5619 (m) REVERT: D 369 MET cc_start: 0.4020 (mtt) cc_final: 0.3534 (mmm) outliers start: 22 outliers final: 13 residues processed: 141 average time/residue: 0.2407 time to fit residues: 48.7595 Evaluate side-chains 131 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 424 ASN Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 339 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 55 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 138 optimal weight: 20.0000 chunk 98 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 57 optimal weight: 0.0570 chunk 82 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 124 optimal weight: 8.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.195557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.134017 restraints weight = 13402.784| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.79 r_work: 0.3146 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11565 Z= 0.126 Angle : 0.495 6.659 15631 Z= 0.263 Chirality : 0.040 0.157 1764 Planarity : 0.003 0.044 1988 Dihedral : 4.867 50.924 1524 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.98 % Allowed : 8.07 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.55 (0.23), residues: 1404 helix: 1.30 (0.25), residues: 464 sheet: 0.70 (0.25), residues: 428 loop : -0.73 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 240 HIS 0.005 0.001 HIS A 310 PHE 0.012 0.001 PHE A 237 TYR 0.023 0.001 TYR A 140 ARG 0.002 0.000 ARG C 124 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 627) hydrogen bonds : angle 4.23252 ( 1776) covalent geometry : bond 0.00297 (11565) covalent geometry : angle 0.49527 (15631) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.7949 (mmmt) cc_final: 0.7642 (mmtt) REVERT: A 169 HIS cc_start: 0.8135 (m170) cc_final: 0.7763 (m170) REVERT: A 298 MET cc_start: 0.9010 (tmm) cc_final: 0.8362 (tmm) REVERT: B 17 THR cc_start: 0.7838 (OUTLIER) cc_final: 0.7622 (t) REVERT: B 135 TYR cc_start: 0.9049 (t80) cc_final: 0.8762 (t80) REVERT: C 153 MET cc_start: 0.8525 (mtm) cc_final: 0.8200 (mpp) REVERT: C 271 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8177 (mp) REVERT: D 70 VAL cc_start: 0.6798 (OUTLIER) cc_final: 0.6550 (p) REVERT: D 94 MET cc_start: 0.6567 (mmp) cc_final: 0.5858 (ptm) REVERT: D 369 MET cc_start: 0.3990 (mtt) cc_final: 0.3434 (mmm) outliers start: 25 outliers final: 18 residues processed: 141 average time/residue: 0.2320 time to fit residues: 47.5698 Evaluate side-chains 140 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 424 ASN Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 339 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 127 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 0.0770 chunk 48 optimal weight: 1.9990 chunk 120 optimal weight: 30.0000 chunk 74 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN C 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.193818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 127)---------------| | r_work = 0.3365 r_free = 0.3365 target = 0.119517 restraints weight = 13334.152| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 3.17 r_work: 0.2930 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11565 Z= 0.168 Angle : 0.531 7.579 15631 Z= 0.281 Chirality : 0.041 0.177 1764 Planarity : 0.003 0.046 1988 Dihedral : 4.830 50.361 1522 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.53 % Allowed : 8.47 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.52 (0.23), residues: 1404 helix: 1.30 (0.25), residues: 464 sheet: 0.66 (0.25), residues: 431 loop : -0.76 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 240 HIS 0.006 0.001 HIS A 238 PHE 0.021 0.001 PHE D 340 TYR 0.019 0.001 TYR B 164 ARG 0.003 0.000 ARG C 305 Details of bonding type rmsd hydrogen bonds : bond 0.04014 ( 627) hydrogen bonds : angle 4.29242 ( 1776) covalent geometry : bond 0.00411 (11565) covalent geometry : angle 0.53107 (15631) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 2.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 HIS cc_start: 0.8068 (m170) cc_final: 0.7698 (m170) REVERT: A 298 MET cc_start: 0.9067 (tmm) cc_final: 0.8498 (tmm) REVERT: A 323 TRP cc_start: 0.8219 (OUTLIER) cc_final: 0.7952 (m-90) REVERT: B 17 THR cc_start: 0.7665 (OUTLIER) cc_final: 0.7453 (t) REVERT: B 70 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7606 (pt0) REVERT: B 135 TYR cc_start: 0.9069 (t80) cc_final: 0.8757 (t80) REVERT: B 205 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6851 (tp) REVERT: C 153 MET cc_start: 0.8333 (mtm) cc_final: 0.7925 (mpp) REVERT: C 271 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8109 (mp) REVERT: D 70 VAL cc_start: 0.6718 (OUTLIER) cc_final: 0.6466 (p) REVERT: D 94 MET cc_start: 0.6645 (mmp) cc_final: 0.5834 (ptm) REVERT: D 272 GLU cc_start: 0.7416 (tp30) cc_final: 0.7171 (tp30) REVERT: D 369 MET cc_start: 0.3930 (mtt) cc_final: 0.3413 (mmm) outliers start: 32 outliers final: 19 residues processed: 143 average time/residue: 0.3314 time to fit residues: 67.8463 Evaluate side-chains 141 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 339 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 104 optimal weight: 0.0470 chunk 133 optimal weight: 10.0000 chunk 79 optimal weight: 0.2980 chunk 124 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 138 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.195026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.131386 restraints weight = 13218.888| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.77 r_work: 0.2986 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11565 Z= 0.128 Angle : 0.491 6.901 15631 Z= 0.262 Chirality : 0.040 0.167 1764 Planarity : 0.003 0.046 1988 Dihedral : 4.580 51.863 1520 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.29 % Allowed : 9.57 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.64 (0.23), residues: 1404 helix: 1.44 (0.25), residues: 464 sheet: 0.73 (0.25), residues: 428 loop : -0.74 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 240 HIS 0.006 0.001 HIS A 310 PHE 0.022 0.001 PHE D 340 TYR 0.016 0.001 TYR B 164 ARG 0.002 0.000 ARG D 85 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 627) hydrogen bonds : angle 4.20995 ( 1776) covalent geometry : bond 0.00306 (11565) covalent geometry : angle 0.49135 (15631) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 2.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.7951 (mmmt) cc_final: 0.7613 (mmtt) REVERT: A 86 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6730 (mt0) REVERT: A 144 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7456 (tp30) REVERT: A 169 HIS cc_start: 0.8014 (m170) cc_final: 0.7639 (m170) REVERT: A 298 MET cc_start: 0.9003 (tmm) cc_final: 0.8413 (tmm) REVERT: B 70 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7500 (pt0) REVERT: B 135 TYR cc_start: 0.9016 (t80) cc_final: 0.8698 (t80) REVERT: C 153 MET cc_start: 0.8453 (mtm) cc_final: 0.8102 (mpp) REVERT: C 271 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8076 (mp) REVERT: D 70 VAL cc_start: 0.6779 (OUTLIER) cc_final: 0.6534 (p) REVERT: D 94 MET cc_start: 0.6575 (mmp) cc_final: 0.5849 (ptm) REVERT: D 272 GLU cc_start: 0.7425 (tp30) cc_final: 0.7180 (tp30) REVERT: D 369 MET cc_start: 0.4031 (mtt) cc_final: 0.3463 (mmm) outliers start: 29 outliers final: 20 residues processed: 139 average time/residue: 0.3045 time to fit residues: 62.7778 Evaluate side-chains 140 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 424 ASN Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 339 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 8 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 128 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 42 optimal weight: 0.1980 chunk 2 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 134 optimal weight: 30.0000 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 ASN C 277 GLN C 300 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.190466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3480 r_free = 0.3480 target = 0.127419 restraints weight = 13462.403| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.74 r_work: 0.2915 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 11565 Z= 0.327 Angle : 0.666 10.966 15631 Z= 0.348 Chirality : 0.047 0.232 1764 Planarity : 0.005 0.052 1988 Dihedral : 5.118 50.040 1519 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.69 % Allowed : 10.13 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.15 (0.23), residues: 1404 helix: 0.91 (0.24), residues: 470 sheet: 0.60 (0.25), residues: 420 loop : -1.02 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 9 HIS 0.008 0.001 HIS A 238 PHE 0.023 0.002 PHE D 340 TYR 0.024 0.002 TYR B 164 ARG 0.004 0.001 ARG A 157 Details of bonding type rmsd hydrogen bonds : bond 0.05264 ( 627) hydrogen bonds : angle 4.53037 ( 1776) covalent geometry : bond 0.00809 (11565) covalent geometry : angle 0.66606 (15631) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.6889 (mt0) REVERT: A 144 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7646 (tp30) REVERT: A 169 HIS cc_start: 0.8138 (m170) cc_final: 0.7808 (m170) REVERT: A 298 MET cc_start: 0.8992 (tmm) cc_final: 0.8580 (tmm) REVERT: B 205 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7106 (tp) REVERT: C 271 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8136 (mp) REVERT: D 70 VAL cc_start: 0.7049 (OUTLIER) cc_final: 0.6830 (p) REVERT: D 94 MET cc_start: 0.6467 (mmp) cc_final: 0.5791 (ptm) REVERT: D 369 MET cc_start: 0.4036 (mtt) cc_final: 0.3432 (mmm) outliers start: 34 outliers final: 23 residues processed: 141 average time/residue: 0.2251 time to fit residues: 46.2865 Evaluate side-chains 133 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 339 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 130 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 134 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 131 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.194631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 114)---------------| | r_work = 0.3392 r_free = 0.3392 target = 0.121728 restraints weight = 13428.863| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.15 r_work: 0.2923 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11565 Z= 0.120 Angle : 0.499 7.105 15631 Z= 0.266 Chirality : 0.040 0.168 1764 Planarity : 0.003 0.048 1988 Dihedral : 4.646 52.439 1519 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.45 % Allowed : 11.23 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.48 (0.23), residues: 1404 helix: 1.31 (0.25), residues: 467 sheet: 0.71 (0.25), residues: 417 loop : -0.88 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 9 HIS 0.006 0.001 HIS A 310 PHE 0.022 0.001 PHE D 340 TYR 0.015 0.001 TYR B 164 ARG 0.002 0.000 ARG B 120 Details of bonding type rmsd hydrogen bonds : bond 0.03520 ( 627) hydrogen bonds : angle 4.27547 ( 1776) covalent geometry : bond 0.00282 (11565) covalent geometry : angle 0.49850 (15631) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.7971 (mmmt) cc_final: 0.7606 (mmtt) REVERT: A 86 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.6694 (mt0) REVERT: A 169 HIS cc_start: 0.8081 (m170) cc_final: 0.7690 (m170) REVERT: A 298 MET cc_start: 0.9036 (tmm) cc_final: 0.8560 (tmm) REVERT: B 135 TYR cc_start: 0.8852 (t80) cc_final: 0.8642 (t80) REVERT: C 153 MET cc_start: 0.8318 (mtm) cc_final: 0.7947 (mpp) REVERT: C 271 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8096 (mp) REVERT: D 70 VAL cc_start: 0.6775 (OUTLIER) cc_final: 0.6560 (p) REVERT: D 94 MET cc_start: 0.6737 (mmp) cc_final: 0.5851 (ptm) REVERT: D 369 MET cc_start: 0.3980 (mtt) cc_final: 0.3425 (mmm) outliers start: 31 outliers final: 25 residues processed: 138 average time/residue: 0.3819 time to fit residues: 78.0037 Evaluate side-chains 139 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 424 ASN Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 339 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 108 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 3 optimal weight: 0.1980 chunk 113 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 42 optimal weight: 0.0570 chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 overall best weight: 1.2504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.193725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 120)---------------| | r_work = 0.3471 r_free = 0.3471 target = 0.125795 restraints weight = 13371.826| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.04 r_work: 0.3121 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11565 Z= 0.154 Angle : 0.525 7.228 15631 Z= 0.278 Chirality : 0.041 0.186 1764 Planarity : 0.003 0.048 1988 Dihedral : 4.631 52.531 1519 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.37 % Allowed : 11.23 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.48 (0.23), residues: 1404 helix: 1.34 (0.25), residues: 469 sheet: 0.69 (0.25), residues: 418 loop : -0.91 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 9 HIS 0.007 0.001 HIS A 310 PHE 0.024 0.001 PHE D 340 TYR 0.017 0.001 TYR B 164 ARG 0.003 0.000 ARG D 85 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 627) hydrogen bonds : angle 4.27101 ( 1776) covalent geometry : bond 0.00375 (11565) covalent geometry : angle 0.52468 (15631) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8059 (mmmt) cc_final: 0.7726 (mmtt) REVERT: A 86 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.6832 (mt0) REVERT: A 169 HIS cc_start: 0.8134 (m170) cc_final: 0.7803 (m170) REVERT: A 298 MET cc_start: 0.8978 (tmm) cc_final: 0.8516 (tmm) REVERT: A 405 LYS cc_start: 0.8325 (mmmm) cc_final: 0.7988 (mmmt) REVERT: C 153 MET cc_start: 0.8447 (mtm) cc_final: 0.8101 (mpp) REVERT: C 271 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8163 (mp) REVERT: D 70 VAL cc_start: 0.6792 (OUTLIER) cc_final: 0.6578 (p) REVERT: D 94 MET cc_start: 0.6724 (mmp) cc_final: 0.5859 (ptm) REVERT: D 369 MET cc_start: 0.3992 (mtt) cc_final: 0.3437 (mmm) outliers start: 30 outliers final: 26 residues processed: 136 average time/residue: 0.2386 time to fit residues: 47.0472 Evaluate side-chains 142 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 424 ASN Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 339 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 0.6980 chunk 105 optimal weight: 9.9990 chunk 5 optimal weight: 0.3980 chunk 117 optimal weight: 40.0000 chunk 102 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 116 optimal weight: 9.9990 chunk 103 optimal weight: 0.0270 chunk 115 optimal weight: 20.0000 chunk 95 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.195867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.118752 restraints weight = 13451.043| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.23 r_work: 0.2941 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11565 Z= 0.094 Angle : 0.474 7.237 15631 Z= 0.253 Chirality : 0.040 0.177 1764 Planarity : 0.003 0.048 1988 Dihedral : 4.402 54.219 1519 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.29 % Allowed : 11.39 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.70 (0.23), residues: 1404 helix: 1.61 (0.25), residues: 464 sheet: 0.78 (0.25), residues: 414 loop : -0.80 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 9 HIS 0.006 0.001 HIS A 310 PHE 0.025 0.001 PHE D 340 TYR 0.011 0.001 TYR B 164 ARG 0.003 0.000 ARG D 85 Details of bonding type rmsd hydrogen bonds : bond 0.03133 ( 627) hydrogen bonds : angle 4.14879 ( 1776) covalent geometry : bond 0.00208 (11565) covalent geometry : angle 0.47449 (15631) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.7951 (mmmt) cc_final: 0.7587 (mmtt) REVERT: A 86 GLN cc_start: 0.7337 (OUTLIER) cc_final: 0.6560 (mt0) REVERT: A 169 HIS cc_start: 0.8030 (m170) cc_final: 0.7641 (m170) REVERT: A 298 MET cc_start: 0.9005 (tmm) cc_final: 0.8478 (tmm) REVERT: A 405 LYS cc_start: 0.8356 (mmmm) cc_final: 0.7970 (mmmt) REVERT: B 135 TYR cc_start: 0.8821 (t80) cc_final: 0.8491 (t80) REVERT: C 153 MET cc_start: 0.8253 (mtm) cc_final: 0.7962 (mpp) REVERT: D 70 VAL cc_start: 0.6634 (OUTLIER) cc_final: 0.6423 (p) REVERT: D 94 MET cc_start: 0.6754 (mmp) cc_final: 0.5865 (ptm) REVERT: D 369 MET cc_start: 0.3900 (mtt) cc_final: 0.3372 (mmm) outliers start: 29 outliers final: 23 residues processed: 136 average time/residue: 0.2450 time to fit residues: 47.6293 Evaluate side-chains 138 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 424 ASN Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 339 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 0.0010 chunk 119 optimal weight: 7.9990 chunk 54 optimal weight: 0.5980 chunk 105 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 chunk 75 optimal weight: 0.0050 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 overall best weight: 0.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.196663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.119159 restraints weight = 13288.974| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.11 r_work: 0.2942 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11565 Z= 0.089 Angle : 0.466 8.440 15631 Z= 0.246 Chirality : 0.039 0.167 1764 Planarity : 0.003 0.048 1988 Dihedral : 4.223 55.239 1518 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.90 % Allowed : 11.63 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.92 (0.23), residues: 1404 helix: 1.82 (0.25), residues: 460 sheet: 0.87 (0.25), residues: 416 loop : -0.66 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 9 HIS 0.006 0.001 HIS A 310 PHE 0.026 0.001 PHE D 340 TYR 0.011 0.001 TYR B 164 ARG 0.003 0.000 ARG A 275 Details of bonding type rmsd hydrogen bonds : bond 0.02953 ( 627) hydrogen bonds : angle 4.05056 ( 1776) covalent geometry : bond 0.00199 (11565) covalent geometry : angle 0.46647 (15631) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.6446 (mt0) REVERT: A 169 HIS cc_start: 0.7979 (m170) cc_final: 0.7567 (m170) REVERT: A 298 MET cc_start: 0.9008 (tmm) cc_final: 0.8431 (tmm) REVERT: B 135 TYR cc_start: 0.8760 (t80) cc_final: 0.8412 (t80) REVERT: B 189 MET cc_start: 0.9177 (mmt) cc_final: 0.8965 (mmt) REVERT: D 70 VAL cc_start: 0.6583 (OUTLIER) cc_final: 0.6342 (p) REVERT: D 94 MET cc_start: 0.6785 (mmp) cc_final: 0.5897 (ptm) REVERT: D 369 MET cc_start: 0.4012 (mtt) cc_final: 0.3516 (mmm) outliers start: 24 outliers final: 21 residues processed: 134 average time/residue: 0.2649 time to fit residues: 51.2585 Evaluate side-chains 139 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 424 ASN Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 339 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 7 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 ASN C 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.190780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.112422 restraints weight = 13315.157| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.32 r_work: 0.2940 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 11565 Z= 0.265 Angle : 0.616 9.804 15631 Z= 0.319 Chirality : 0.045 0.202 1764 Planarity : 0.004 0.045 1988 Dihedral : 4.703 53.203 1518 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.45 % Allowed : 11.39 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.48 (0.23), residues: 1404 helix: 1.29 (0.24), residues: 466 sheet: 0.80 (0.25), residues: 413 loop : -0.95 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 9 HIS 0.007 0.001 HIS A 310 PHE 0.026 0.002 PHE D 340 TYR 0.024 0.002 TYR C 260 ARG 0.003 0.001 ARG C 124 Details of bonding type rmsd hydrogen bonds : bond 0.04606 ( 627) hydrogen bonds : angle 4.35231 ( 1776) covalent geometry : bond 0.00658 (11565) covalent geometry : angle 0.61590 (15631) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9177.37 seconds wall clock time: 166 minutes 44.87 seconds (10004.87 seconds total)