Starting phenix.real_space_refine on Wed Sep 17 21:04:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e4i_30986/09_2025/7e4i_30986.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e4i_30986/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7e4i_30986/09_2025/7e4i_30986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e4i_30986/09_2025/7e4i_30986.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e4i_30986/09_2025/7e4i_30986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e4i_30986/09_2025/7e4i_30986.map" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.79, per 1000 atoms: 0.25 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: 1.04 Conformation dependent library (CDL) restraints added in 497.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.43 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: 2.05 Time building geometry restraints manager: 1.40 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: 1.510 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.200 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.450 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG C 124 TYR 0.011 0.001 TYR B 164 PHE 0.015 0.001 PHE A 237 TRP 0.008 0.001 TRP A 240 HIS 0.003 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00204 (11565) covalent geometry : angle 0.48279 (15631) hydrogen bonds : bond 0.13602 ( 627) hydrogen bonds : angle 5.13510 ( 1776) *********************** 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 : 0.542 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: 0.1137 time to fit residues: 28.6879 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 : 0.482 ------------------------------------------------------------------------------- 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 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 40.0000 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 overall best weight: 1.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 273 GLN C 285 ASN C 300 ASN D 65 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.193280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3383 r_free = 0.3383 target = 0.119804 restraints weight = 13384.339| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 3.15 r_work: 0.2902 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11565 Z= 0.219 Angle : 0.585 8.590 15631 Z= 0.307 Chirality : 0.044 0.175 1764 Planarity : 0.004 0.044 1988 Dihedral : 5.371 55.733 1528 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.14 % Allowed : 6.96 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.23), residues: 1404 helix: 0.90 (0.25), residues: 464 sheet: 0.57 (0.25), residues: 437 loop : -0.88 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 124 TYR 0.022 0.002 TYR B 164 PHE 0.019 0.002 PHE D 340 TRP 0.011 0.001 TRP A 240 HIS 0.006 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00537 (11565) covalent geometry : angle 0.58518 (15631) hydrogen bonds : bond 0.04717 ( 627) hydrogen bonds : angle 4.46156 ( 1776) *********************** 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 151 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 HIS cc_start: 0.8130 (m170) cc_final: 0.7746 (m170) REVERT: A 298 MET cc_start: 0.9085 (tmm) cc_final: 0.8502 (tmm) REVERT: A 299 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8556 (tp) REVERT: B 17 THR cc_start: 0.7647 (OUTLIER) cc_final: 0.7408 (t) REVERT: B 70 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7651 (pt0) REVERT: B 135 TYR cc_start: 0.9057 (t80) cc_final: 0.8709 (t80) REVERT: D 70 VAL cc_start: 0.6901 (OUTLIER) cc_final: 0.6579 (p) REVERT: D 94 MET cc_start: 0.6573 (mmp) cc_final: 0.5761 (ptm) REVERT: D 186 SER cc_start: 0.5848 (t) cc_final: 0.5611 (m) REVERT: D 369 MET cc_start: 0.4031 (mtt) cc_final: 0.3536 (mmm) outliers start: 27 outliers final: 16 residues processed: 146 average time/residue: 0.1103 time to fit residues: 23.1422 Evaluate side-chains 133 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 299 LEU 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 70 GLU Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain C residue 5 SER 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 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 62 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 89 optimal weight: 0.0980 chunk 50 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 126 optimal weight: 30.0000 chunk 83 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN C 168 ASN C 300 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.194644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.117044 restraints weight = 13378.070| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.21 r_work: 0.3021 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11565 Z= 0.139 Angle : 0.512 6.745 15631 Z= 0.272 Chirality : 0.041 0.162 1764 Planarity : 0.003 0.045 1988 Dihedral : 5.046 49.556 1525 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.37 % Allowed : 8.07 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.23), residues: 1404 helix: 1.18 (0.25), residues: 464 sheet: 0.58 (0.25), residues: 438 loop : -0.84 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 120 TYR 0.017 0.001 TYR B 164 PHE 0.013 0.001 PHE B 44 TRP 0.010 0.001 TRP A 240 HIS 0.006 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00333 (11565) covalent geometry : angle 0.51223 (15631) hydrogen bonds : bond 0.03850 ( 627) hydrogen bonds : angle 4.32340 ( 1776) *********************** 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 148 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 HIS cc_start: 0.8098 (m170) cc_final: 0.7744 (m170) REVERT: A 298 MET cc_start: 0.9114 (tmm) cc_final: 0.8523 (tmm) REVERT: B 17 THR cc_start: 0.7647 (OUTLIER) cc_final: 0.7437 (t) REVERT: B 70 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7619 (pt0) REVERT: B 135 TYR cc_start: 0.9069 (t80) cc_final: 0.8733 (t80) REVERT: C 153 MET cc_start: 0.8382 (mtm) cc_final: 0.7953 (mpp) REVERT: C 271 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8077 (mp) REVERT: D 70 VAL cc_start: 0.6691 (OUTLIER) cc_final: 0.6462 (p) REVERT: D 94 MET cc_start: 0.6551 (mmp) cc_final: 0.5743 (ptm) REVERT: D 369 MET cc_start: 0.3920 (mtt) cc_final: 0.3406 (mmm) outliers start: 30 outliers final: 18 residues processed: 141 average time/residue: 0.1100 time to fit residues: 22.5638 Evaluate side-chains 142 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 160 LEU 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 17 THR Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain C residue 5 SER 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 14 optimal weight: 0.8980 chunk 119 optimal weight: 30.0000 chunk 132 optimal weight: 30.0000 chunk 57 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 137 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.4168 r_free = 0.4168 target = 0.192374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.131753 restraints weight = 13397.292| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.87 r_work: 0.3068 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11565 Z= 0.204 Angle : 0.562 8.559 15631 Z= 0.296 Chirality : 0.042 0.189 1764 Planarity : 0.004 0.048 1988 Dihedral : 5.169 50.097 1523 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.69 % Allowed : 8.94 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.23), residues: 1404 helix: 1.10 (0.25), residues: 465 sheet: 0.52 (0.24), residues: 442 loop : -0.93 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 124 TYR 0.020 0.002 TYR B 164 PHE 0.021 0.002 PHE D 340 TRP 0.011 0.001 TRP C 9 HIS 0.007 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00503 (11565) covalent geometry : angle 0.56162 (15631) hydrogen bonds : bond 0.04348 ( 627) hydrogen bonds : angle 4.39556 ( 1776) *********************** 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 149 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.6840 (mt0) REVERT: A 169 HIS cc_start: 0.8199 (m170) cc_final: 0.7857 (m170) REVERT: A 298 MET cc_start: 0.9052 (tmm) cc_final: 0.8491 (tmm) REVERT: A 323 TRP cc_start: 0.8214 (OUTLIER) cc_final: 0.7946 (m-90) REVERT: B 135 TYR cc_start: 0.9096 (t80) cc_final: 0.8893 (t80) REVERT: C 153 MET cc_start: 0.8552 (mtm) cc_final: 0.8145 (mpp) REVERT: C 271 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8237 (mp) REVERT: D 70 VAL cc_start: 0.6831 (OUTLIER) cc_final: 0.6585 (p) REVERT: D 94 MET cc_start: 0.6577 (mmp) cc_final: 0.5835 (ptm) REVERT: D 272 GLU cc_start: 0.7421 (tp30) cc_final: 0.7189 (tp30) REVERT: D 369 MET cc_start: 0.3955 (mtt) cc_final: 0.3412 (mmm) outliers start: 34 outliers final: 23 residues processed: 141 average time/residue: 0.1128 time to fit residues: 22.9695 Evaluate side-chains 138 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 160 LEU 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 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 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 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 13 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 65 optimal weight: 0.0970 chunk 98 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 30 optimal weight: 0.0980 chunk 90 optimal weight: 10.0000 chunk 5 optimal weight: 0.0270 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 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 = 0.4205 r_free = 0.4205 target = 0.196199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 120)---------------| | r_work = 0.3437 r_free = 0.3437 target = 0.124197 restraints weight = 13335.754| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.98 r_work: 0.2962 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11565 Z= 0.088 Angle : 0.460 6.473 15631 Z= 0.247 Chirality : 0.039 0.149 1764 Planarity : 0.003 0.049 1988 Dihedral : 4.455 51.998 1519 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.06 % Allowed : 9.97 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.23), residues: 1404 helix: 1.49 (0.25), residues: 464 sheet: 0.68 (0.25), residues: 435 loop : -0.80 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 85 TYR 0.022 0.001 TYR A 140 PHE 0.024 0.001 PHE D 340 TRP 0.009 0.001 TRP C 9 HIS 0.006 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00189 (11565) covalent geometry : angle 0.46011 (15631) hydrogen bonds : bond 0.03087 ( 627) hydrogen bonds : angle 4.18106 ( 1776) *********************** 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 149 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.7966 (mmmt) cc_final: 0.7625 (mmtt) REVERT: A 86 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6516 (mt0) REVERT: A 169 HIS cc_start: 0.8034 (m170) cc_final: 0.7658 (m170) REVERT: A 298 MET cc_start: 0.8979 (tmm) cc_final: 0.8461 (tmm) REVERT: A 323 TRP cc_start: 0.8123 (OUTLIER) cc_final: 0.7873 (m-90) REVERT: B 135 TYR cc_start: 0.9054 (t80) cc_final: 0.8732 (t80) REVERT: C 153 MET cc_start: 0.8312 (mtm) cc_final: 0.8048 (mpp) REVERT: D 70 VAL cc_start: 0.6819 (OUTLIER) cc_final: 0.6540 (p) REVERT: D 94 MET cc_start: 0.6608 (mmp) cc_final: 0.5840 (ptm) REVERT: D 272 GLU cc_start: 0.7427 (tp30) cc_final: 0.7177 (tp30) REVERT: D 369 MET cc_start: 0.3954 (mtt) cc_final: 0.3425 (mmm) outliers start: 26 outliers final: 19 residues processed: 143 average time/residue: 0.1049 time to fit residues: 21.4208 Evaluate side-chains 139 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 323 TRP Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 424 ASN Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain B residue 205 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 40 optimal weight: 0.0050 chunk 101 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 overall best weight: 1.3598 ------------------------------------------------------------------------------- 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 = 0.193745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3520 r_free = 0.3520 target = 0.130394 restraints weight = 13430.698| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.77 r_work: 0.2983 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11565 Z= 0.162 Angle : 0.518 7.405 15631 Z= 0.274 Chirality : 0.041 0.173 1764 Planarity : 0.003 0.047 1988 Dihedral : 4.580 51.935 1519 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.53 % Allowed : 10.05 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.23), residues: 1404 helix: 1.44 (0.25), residues: 464 sheet: 0.65 (0.25), residues: 442 loop : -0.80 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 120 TYR 0.018 0.001 TYR B 164 PHE 0.023 0.001 PHE D 340 TRP 0.010 0.001 TRP C 9 HIS 0.006 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00397 (11565) covalent geometry : angle 0.51799 (15631) hydrogen bonds : bond 0.03856 ( 627) hydrogen bonds : angle 4.22510 ( 1776) *********************** 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 150 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.7958 (mmmt) cc_final: 0.7623 (mmtt) REVERT: A 86 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.6755 (mt0) REVERT: A 169 HIS cc_start: 0.8041 (m170) cc_final: 0.7709 (m170) REVERT: A 298 MET cc_start: 0.8979 (tmm) cc_final: 0.8479 (tmm) REVERT: A 323 TRP cc_start: 0.8131 (OUTLIER) cc_final: 0.7883 (m-90) REVERT: C 153 MET cc_start: 0.8414 (mtm) cc_final: 0.8078 (mpp) REVERT: D 70 VAL cc_start: 0.6996 (OUTLIER) cc_final: 0.6735 (p) REVERT: D 94 MET cc_start: 0.6640 (mmp) cc_final: 0.5926 (ptm) REVERT: D 214 GLU cc_start: 0.7151 (tt0) cc_final: 0.6617 (pt0) REVERT: D 272 GLU cc_start: 0.7409 (tp30) cc_final: 0.7178 (tp30) REVERT: D 369 MET cc_start: 0.3997 (mtt) cc_final: 0.3437 (mmm) outliers start: 32 outliers final: 26 residues processed: 143 average time/residue: 0.1116 time to fit residues: 22.8981 Evaluate side-chains 144 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 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 323 TRP 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 54 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 B residue 291 SER 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 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 6 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 106 optimal weight: 20.0000 chunk 127 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 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 = 0.4168 r_free = 0.4168 target = 0.192331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.128790 restraints weight = 13318.954| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.72 r_work: 0.3105 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11565 Z= 0.202 Angle : 0.561 8.793 15631 Z= 0.296 Chirality : 0.043 0.192 1764 Planarity : 0.004 0.047 1988 Dihedral : 4.736 51.694 1519 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.69 % Allowed : 10.76 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.23), residues: 1404 helix: 1.26 (0.25), residues: 469 sheet: 0.66 (0.25), residues: 431 loop : -0.93 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 85 TYR 0.020 0.002 TYR B 164 PHE 0.025 0.002 PHE D 340 TRP 0.011 0.001 TRP C 9 HIS 0.006 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00497 (11565) covalent geometry : angle 0.56108 (15631) hydrogen bonds : bond 0.04251 ( 627) hydrogen bonds : angle 4.31958 ( 1776) *********************** 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 145 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8021 (mmmt) cc_final: 0.7736 (mmtt) REVERT: A 86 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.6852 (mt0) REVERT: A 169 HIS cc_start: 0.8159 (m170) cc_final: 0.7832 (m170) REVERT: A 298 MET cc_start: 0.8983 (tmm) cc_final: 0.8491 (tmm) REVERT: A 323 TRP cc_start: 0.8109 (OUTLIER) cc_final: 0.7841 (m-90) REVERT: C 153 MET cc_start: 0.8531 (mtm) cc_final: 0.8160 (mpp) REVERT: D 70 VAL cc_start: 0.6948 (OUTLIER) cc_final: 0.6721 (p) REVERT: D 94 MET cc_start: 0.6634 (mmp) cc_final: 0.5824 (ptm) REVERT: D 214 GLU cc_start: 0.7209 (tt0) cc_final: 0.6679 (pt0) REVERT: D 369 MET cc_start: 0.4029 (mtt) cc_final: 0.3450 (mmm) outliers start: 34 outliers final: 25 residues processed: 137 average time/residue: 0.1135 time to fit residues: 22.3671 Evaluate side-chains 136 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 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 370 THR Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 54 LEU 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 291 SER Chi-restraints excluded: chain C residue 160 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 19 optimal weight: 0.9990 chunk 132 optimal weight: 30.0000 chunk 50 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 61 optimal weight: 0.3980 chunk 62 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 126 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4192 r_free = 0.4192 target = 0.194779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.3538 r_free = 0.3538 target = 0.131824 restraints weight = 13286.996| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.85 r_work: 0.2984 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11565 Z= 0.110 Angle : 0.485 7.184 15631 Z= 0.258 Chirality : 0.040 0.167 1764 Planarity : 0.003 0.048 1988 Dihedral : 4.459 53.141 1519 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.14 % Allowed : 11.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.23), residues: 1404 helix: 1.52 (0.25), residues: 465 sheet: 0.78 (0.25), residues: 423 loop : -0.84 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 85 TYR 0.015 0.001 TYR A 140 PHE 0.024 0.001 PHE D 340 TRP 0.010 0.001 TRP C 9 HIS 0.006 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00257 (11565) covalent geometry : angle 0.48472 (15631) hydrogen bonds : bond 0.03341 ( 627) hydrogen bonds : angle 4.17752 ( 1776) *********************** 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 142 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.7909 (mmmt) cc_final: 0.7573 (mmtt) REVERT: A 86 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.6654 (mt0) REVERT: A 169 HIS cc_start: 0.8053 (m170) cc_final: 0.7692 (m170) REVERT: A 298 MET cc_start: 0.8980 (tmm) cc_final: 0.8478 (tmm) REVERT: A 323 TRP cc_start: 0.8079 (OUTLIER) cc_final: 0.7819 (m-90) REVERT: C 153 MET cc_start: 0.8371 (mtm) cc_final: 0.8086 (mpp) REVERT: D 70 VAL cc_start: 0.6893 (OUTLIER) cc_final: 0.6645 (p) REVERT: D 94 MET cc_start: 0.6690 (mmp) cc_final: 0.5872 (ptm) REVERT: D 369 MET cc_start: 0.4093 (mtt) cc_final: 0.3500 (mmm) outliers start: 27 outliers final: 23 residues processed: 136 average time/residue: 0.1149 time to fit residues: 22.3833 Evaluate side-chains 139 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 323 TRP 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 479 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 291 SER 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 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 131 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.4187 r_free = 0.4187 target = 0.194248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.133877 restraints weight = 13237.291| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.77 r_work: 0.3136 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11565 Z= 0.144 Angle : 0.520 7.891 15631 Z= 0.272 Chirality : 0.041 0.173 1764 Planarity : 0.003 0.047 1988 Dihedral : 4.467 53.464 1518 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.22 % Allowed : 11.55 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.23), residues: 1404 helix: 1.48 (0.25), residues: 467 sheet: 0.75 (0.25), residues: 425 loop : -0.85 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 85 TYR 0.017 0.001 TYR B 135 PHE 0.026 0.001 PHE D 340 TRP 0.010 0.001 TRP C 9 HIS 0.007 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00350 (11565) covalent geometry : angle 0.52030 (15631) hydrogen bonds : bond 0.03678 ( 627) hydrogen bonds : angle 4.20054 ( 1776) *********************** 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 142 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.7938 (mmmt) cc_final: 0.7614 (mmtt) REVERT: A 86 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.6750 (mt0) REVERT: A 169 HIS cc_start: 0.8172 (m170) cc_final: 0.7862 (m170) REVERT: A 298 MET cc_start: 0.8981 (tmm) cc_final: 0.8523 (tmm) REVERT: C 153 MET cc_start: 0.8440 (mtm) cc_final: 0.8157 (mpp) REVERT: D 70 VAL cc_start: 0.6790 (OUTLIER) cc_final: 0.6552 (p) REVERT: D 94 MET cc_start: 0.6714 (mmp) cc_final: 0.5866 (ptm) REVERT: D 214 GLU cc_start: 0.7360 (tt0) cc_final: 0.6762 (pt0) REVERT: D 369 MET cc_start: 0.3922 (mtt) cc_final: 0.3364 (mmm) outliers start: 28 outliers final: 24 residues processed: 135 average time/residue: 0.1164 time to fit residues: 22.5492 Evaluate side-chains 139 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 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 479 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 291 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 17 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.4169 r_free = 0.4169 target = 0.192468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.139040 restraints weight = 13342.563| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.80 r_work: 0.3103 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11565 Z= 0.184 Angle : 0.556 8.156 15631 Z= 0.290 Chirality : 0.042 0.186 1764 Planarity : 0.004 0.046 1988 Dihedral : 4.616 53.105 1518 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.29 % Allowed : 11.63 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.23), residues: 1404 helix: 1.33 (0.24), residues: 470 sheet: 0.68 (0.25), residues: 431 loop : -0.91 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 85 TYR 0.020 0.002 TYR B 135 PHE 0.026 0.001 PHE D 340 TRP 0.009 0.001 TRP A 240 HIS 0.006 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00452 (11565) covalent geometry : angle 0.55607 (15631) hydrogen bonds : bond 0.04089 ( 627) hydrogen bonds : angle 4.29053 ( 1776) ********************** 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 141 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8045 (mmmt) cc_final: 0.7761 (mmtt) REVERT: A 86 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.6817 (mt0) REVERT: A 169 HIS cc_start: 0.8215 (m170) cc_final: 0.7901 (m170) REVERT: A 298 MET cc_start: 0.9026 (tmm) cc_final: 0.8576 (tmm) REVERT: C 153 MET cc_start: 0.8506 (mtm) cc_final: 0.8161 (mpp) REVERT: D 70 VAL cc_start: 0.6747 (OUTLIER) cc_final: 0.6536 (p) REVERT: D 94 MET cc_start: 0.6694 (mmp) cc_final: 0.5846 (ptm) REVERT: D 214 GLU cc_start: 0.7421 (tt0) cc_final: 0.6819 (pt0) REVERT: D 369 MET cc_start: 0.4013 (mtt) cc_final: 0.3463 (mmm) outliers start: 29 outliers final: 27 residues processed: 133 average time/residue: 0.1198 time to fit residues: 22.7828 Evaluate side-chains 141 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 479 LEU Chi-restraints excluded: chain B residue 54 LEU 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 291 SER Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 160 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 114 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 137 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 = 0.4166 r_free = 0.4166 target = 0.192137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.128965 restraints weight = 13441.172| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.91 r_work: 0.2942 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 11565 Z= 0.235 Angle : 0.601 8.870 15631 Z= 0.313 Chirality : 0.044 0.201 1764 Planarity : 0.004 0.046 1988 Dihedral : 4.798 52.794 1518 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.45 % Allowed : 11.63 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.23), residues: 1404 helix: 1.13 (0.24), residues: 471 sheet: 0.62 (0.25), residues: 430 loop : -0.98 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 85 TYR 0.022 0.002 TYR B 164 PHE 0.026 0.002 PHE D 340 TRP 0.009 0.001 TRP C 9 HIS 0.007 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00579 (11565) covalent geometry : angle 0.60107 (15631) hydrogen bonds : bond 0.04526 ( 627) hydrogen bonds : angle 4.41903 ( 1776) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4240.85 seconds wall clock time: 73 minutes 1.72 seconds (4381.72 seconds total)