Starting phenix.real_space_refine on Mon May 12 07:27:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jbf_36144/05_2025/8jbf_36144.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jbf_36144/05_2025/8jbf_36144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jbf_36144/05_2025/8jbf_36144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jbf_36144/05_2025/8jbf_36144.map" model { file = "/net/cci-nas-00/data/ceres_data/8jbf_36144/05_2025/8jbf_36144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jbf_36144/05_2025/8jbf_36144.cif" } resolution = 3.0 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 37 atoms to isotropic. 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 58 5.16 5 C 5622 2.51 5 N 1489 2.21 5 O 1615 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8784 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2194 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 11, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 67 Chain: "D" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2542 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "E" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1751 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "G" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 406 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 58 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1833 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Time building chain proxies: 5.11, per 1000 atoms: 0.58 Number of scatterers: 8784 At special positions: 0 Unit cell: (117.42, 116.39, 106.09, 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 58 16.00 O 1615 8.00 N 1489 7.00 C 5622 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: 1.94 Conformation dependent library (CDL) restraints added in 983.0 milliseconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2146 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 15 sheets defined 35.3% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'B' and resid 81 through 100 removed outlier: 3.599A pdb=" N ALA B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 87 " --> pdb=" O TRP B 83 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 121 through 137 Processing helix chain 'B' and resid 140 through 145 removed outlier: 3.679A pdb=" N ILE B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 162 removed outlier: 3.649A pdb=" N PHE B 160 " --> pdb=" O ASN B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 186 removed outlier: 3.650A pdb=" N VAL B 169 " --> pdb=" O PRO B 165 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET B 176 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 220 removed outlier: 3.815A pdb=" N LYS B 201 " --> pdb=" O ALA B 197 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER B 206 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Proline residue: B 217 - end of helix Processing helix chain 'B' and resid 240 through 248 removed outlier: 3.938A pdb=" N THR B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS B 248 " --> pdb=" O HIS B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 253 removed outlier: 3.646A pdb=" N ILE B 252 " --> pdb=" O HIS B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 276 removed outlier: 3.570A pdb=" N TYR B 267 " --> pdb=" O MET B 263 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR B 268 " --> pdb=" O GLY B 264 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TRP B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY B 276 " --> pdb=" O ILE B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 295 Processing helix chain 'B' and resid 296 through 307 removed outlier: 3.583A pdb=" N VAL B 305 " --> pdb=" O MET B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 324 Processing helix chain 'B' and resid 325 through 332 removed outlier: 3.839A pdb=" N ARG B 330 " --> pdb=" O GLN B 327 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP B 331 " --> pdb=" O LEU B 328 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS B 332 " --> pdb=" O ASN B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 348 removed outlier: 3.539A pdb=" N ALA B 345 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 360 removed outlier: 3.756A pdb=" N ILE B 354 " --> pdb=" O MET B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 369 removed outlier: 3.614A pdb=" N ARG B 364 " --> pdb=" O ASN B 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 24 removed outlier: 3.845A pdb=" N GLU D 10 " --> pdb=" O GLN D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.928A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.802A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 19 removed outlier: 3.686A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.731A pdb=" N TYR G 40 " --> pdb=" O ASP G 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 26 removed outlier: 3.803A pdb=" N LYS C 21 " --> pdb=" O LYS C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 32 Processing helix chain 'C' and resid 45 through 50 removed outlier: 3.842A pdb=" N VAL C 50 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 214 removed outlier: 3.677A pdb=" N GLN C 213 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 245 removed outlier: 3.513A pdb=" N ALA C 236 " --> pdb=" O ARG C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 269 removed outlier: 3.819A pdb=" N LYS C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 279 removed outlier: 4.545A pdb=" N TYR C 278 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 removed outlier: 4.213A pdb=" N ALA C 283 " --> pdb=" O PRO C 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 280 through 283' Processing helix chain 'C' and resid 298 through 319 removed outlier: 3.694A pdb=" N THR C 302 " --> pdb=" O ASP C 298 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE C 307 " --> pdb=" O ARG C 303 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER C 316 " --> pdb=" O PHE C 312 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA C 318 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 358 Processing sheet with id=AA1, first strand: chain 'B' and resid 223 through 224 removed outlier: 3.884A pdb=" N VAL B 235 " --> pdb=" O LYS B 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 47 through 51 removed outlier: 6.542A pdb=" N ILE D 338 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR D 50 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU D 336 " --> pdb=" O THR D 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 58 through 63 removed outlier: 3.615A pdb=" N ALA D 60 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER D 74 " --> pdb=" O LYS D 78 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU D 79 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA D 92 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE D 81 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 100 through 105 removed outlier: 6.722A pdb=" N GLY D 115 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N CYS D 103 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA D 113 " --> pdb=" O CYS D 103 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N TYR D 105 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N TYR D 111 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY D 116 " --> pdb=" O ILE D 120 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ILE D 120 " --> pdb=" O GLY D 116 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG D 137 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 146 through 153 removed outlier: 6.816A pdb=" N GLN D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE D 157 " --> pdb=" O TRP D 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 187 through 192 removed outlier: 3.537A pdb=" N GLN D 220 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASP D 212 " --> pdb=" O CYS D 218 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N CYS D 218 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 229 through 234 removed outlier: 3.546A pdb=" N SER D 245 " --> pdb=" O THR D 249 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N CYS D 250 " --> pdb=" O THR D 263 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR D 263 " --> pdb=" O CYS D 250 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU D 252 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN D 259 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 273 through 278 removed outlier: 3.546A pdb=" N SER D 275 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY D 306 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASP D 298 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG D 304 " --> pdb=" O ASP D 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.569A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG E 18 " --> pdb=" O MET E 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.540A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 92 through 94 Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 Processing sheet with id=AB4, first strand: chain 'E' and resid 155 through 160 removed outlier: 3.559A pdb=" N THR E 215 " --> pdb=" O SER E 204 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 194 through 195 removed outlier: 5.704A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 184 through 191 removed outlier: 4.253A pdb=" N VAL C 201 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N GLY C 40 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA C 220 " --> pdb=" O ARG C 35 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE C 221 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N PHE C 257 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE C 223 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASN C 259 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL C 225 " --> pdb=" O ASN C 259 " (cutoff:3.500A) 355 hydrogen bonds defined for protein. 996 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: 2.46 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2782 1.34 - 1.46: 1882 1.46 - 1.57: 4233 1.57 - 1.69: 0 1.69 - 1.81: 87 Bond restraints: 8984 Sorted by residual: bond pdb=" C ASP E 74 " pdb=" N PRO E 75 " ideal model delta sigma weight residual 1.335 1.373 -0.037 1.30e-02 5.92e+03 8.28e+00 bond pdb=" CB CYS D 103 " pdb=" SG CYS D 103 " ideal model delta sigma weight residual 1.808 1.758 0.050 3.30e-02 9.18e+02 2.28e+00 bond pdb=" CB PRO B 259 " pdb=" CG PRO B 259 " ideal model delta sigma weight residual 1.492 1.419 0.073 5.00e-02 4.00e+02 2.12e+00 bond pdb=" N PHE B 78 " pdb=" CA PHE B 78 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.95e-02 2.63e+03 2.09e+00 bond pdb=" CG1 ILE D 81 " pdb=" CD1 ILE D 81 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.82e+00 ... (remaining 8979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 12111 3.33 - 6.66: 96 6.66 - 9.99: 14 9.99 - 13.32: 1 13.32 - 16.65: 1 Bond angle restraints: 12223 Sorted by residual: angle pdb=" C ASP D 195 " pdb=" N THR D 196 " pdb=" CA THR D 196 " ideal model delta sigma weight residual 121.54 130.05 -8.51 1.91e+00 2.74e-01 1.99e+01 angle pdb=" C GLN B 77 " pdb=" N PHE B 78 " pdb=" CA PHE B 78 " ideal model delta sigma weight residual 124.82 132.59 -7.77 1.78e+00 3.16e-01 1.90e+01 angle pdb=" CA TYR E 235 " pdb=" CB TYR E 235 " pdb=" CG TYR E 235 " ideal model delta sigma weight residual 113.90 106.13 7.77 1.80e+00 3.09e-01 1.86e+01 angle pdb=" N TYR E 235 " pdb=" CA TYR E 235 " pdb=" C TYR E 235 " ideal model delta sigma weight residual 109.81 117.99 -8.18 2.21e+00 2.05e-01 1.37e+01 angle pdb=" C LEU B 147 " pdb=" N HIS B 148 " pdb=" CA HIS B 148 " ideal model delta sigma weight residual 121.54 128.24 -6.70 1.91e+00 2.74e-01 1.23e+01 ... (remaining 12218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4842 17.99 - 35.98: 347 35.98 - 53.97: 55 53.97 - 71.96: 6 71.96 - 89.95: 4 Dihedral angle restraints: 5254 sinusoidal: 1926 harmonic: 3328 Sorted by residual: dihedral pdb=" CA HIS B 148 " pdb=" C HIS B 148 " pdb=" N SER B 149 " pdb=" CA SER B 149 " ideal model delta harmonic sigma weight residual -180.00 -126.17 -53.83 0 5.00e+00 4.00e-02 1.16e+02 dihedral pdb=" CA MET B 306 " pdb=" C MET B 306 " pdb=" N THR B 307 " pdb=" CA THR B 307 " ideal model delta harmonic sigma weight residual 180.00 155.41 24.59 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA GLN D 75 " pdb=" C GLN D 75 " pdb=" N ASP D 76 " pdb=" CA ASP D 76 " ideal model delta harmonic sigma weight residual 180.00 157.72 22.28 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 5251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1057 0.062 - 0.124: 290 0.124 - 0.185: 40 0.185 - 0.247: 8 0.247 - 0.309: 1 Chirality restraints: 1396 Sorted by residual: chirality pdb=" CA TYR E 235 " pdb=" N TYR E 235 " pdb=" C TYR E 235 " pdb=" CB TYR E 235 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CB VAL C 218 " pdb=" CA VAL C 218 " pdb=" CG1 VAL C 218 " pdb=" CG2 VAL C 218 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA PHE B 164 " pdb=" N PHE B 164 " pdb=" C PHE B 164 " pdb=" CB PHE B 164 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1393 not shown) Planarity restraints: 1546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 92 " 0.015 2.00e-02 2.50e+03 2.10e-02 8.79e+00 pdb=" CG TYR B 92 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR B 92 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR B 92 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR B 92 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR B 92 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 92 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 92 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 227 " 0.046 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO B 228 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO B 228 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 228 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 235 " -0.047 5.00e-02 4.00e+02 7.03e-02 7.92e+00 pdb=" N PRO E 236 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO E 236 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 236 " -0.040 5.00e-02 4.00e+02 ... (remaining 1543 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1295 2.75 - 3.29: 7880 3.29 - 3.83: 14744 3.83 - 4.36: 18062 4.36 - 4.90: 30997 Nonbonded interactions: 72978 Sorted by model distance: nonbonded pdb=" OG SER D 245 " pdb=" OD1 ASP D 247 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR B 92 " pdb=" O LEU B 339 " model vdw 2.224 3.040 nonbonded pdb=" OG1 THR D 274 " pdb=" O VAL D 315 " model vdw 2.296 3.040 nonbonded pdb=" O VAL C 29 " pdb=" OG1 THR C 33 " model vdw 2.303 3.040 nonbonded pdb=" O SER D 67 " pdb=" OG SER D 67 " model vdw 2.307 3.040 ... (remaining 72973 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.510 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 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 : 0.007 0.073 8984 Z= 0.310 Angle : 0.864 16.646 12223 Z= 0.465 Chirality : 0.058 0.309 1396 Planarity : 0.007 0.070 1546 Dihedral : 12.834 89.951 3108 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.22 % Allowed : 5.26 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -5.19 (0.18), residues: 1126 helix: -4.74 (0.09), residues: 378 sheet: -2.56 (0.28), residues: 257 loop : -2.62 (0.23), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 47 HIS 0.008 0.002 HIS C 324 PHE 0.023 0.002 PHE D 151 TYR 0.048 0.003 TYR B 92 ARG 0.008 0.001 ARG C 209 Details of bonding type rmsd hydrogen bonds : bond 0.28386 ( 355) hydrogen bonds : angle 10.55425 ( 996) covalent geometry : bond 0.00713 ( 8984) covalent geometry : angle 0.86396 (12223) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 223 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: B 129 PHE cc_start: 0.7010 (t80) cc_final: 0.6801 (t80) REVERT: B 153 PHE cc_start: 0.7989 (m-80) cc_final: 0.7754 (m-80) REVERT: B 210 LEU cc_start: 0.7914 (mt) cc_final: 0.7629 (mt) REVERT: B 245 PHE cc_start: 0.7890 (t80) cc_final: 0.7609 (t80) REVERT: B 294 LYS cc_start: 0.8144 (mtpt) cc_final: 0.7922 (mtpt) REVERT: D 14 LEU cc_start: 0.8262 (mt) cc_final: 0.8056 (mp) REVERT: D 17 GLN cc_start: 0.7847 (tm-30) cc_final: 0.7561 (tm-30) REVERT: D 189 SER cc_start: 0.8294 (t) cc_final: 0.8065 (p) REVERT: D 196 THR cc_start: 0.8491 (t) cc_final: 0.8154 (m) REVERT: D 322 ASP cc_start: 0.7078 (m-30) cc_final: 0.6875 (m-30) REVERT: E 4 LEU cc_start: 0.7598 (mt) cc_final: 0.7330 (mt) REVERT: E 67 ARG cc_start: 0.8803 (mtm110) cc_final: 0.8580 (mtp180) REVERT: E 79 LEU cc_start: 0.7733 (tp) cc_final: 0.7409 (tp) REVERT: E 83 MET cc_start: 0.8080 (mtt) cc_final: 0.7872 (mtt) REVERT: E 93 MET cc_start: 0.7655 (ttp) cc_final: 0.7424 (ttp) REVERT: E 99 SER cc_start: 0.8172 (m) cc_final: 0.7901 (p) REVERT: E 166 LEU cc_start: 0.8393 (tp) cc_final: 0.8055 (tt) REVERT: E 194 ASN cc_start: 0.8796 (m-40) cc_final: 0.8557 (m110) REVERT: C 8 GLU cc_start: 0.6470 (tp30) cc_final: 0.6229 (tp30) REVERT: C 17 LYS cc_start: 0.7873 (mtmt) cc_final: 0.7490 (mtmt) REVERT: C 46 LYS cc_start: 0.7601 (ttpp) cc_final: 0.7195 (tttt) REVERT: C 195 ASN cc_start: 0.7575 (m-40) cc_final: 0.7305 (m-40) REVERT: C 200 ASP cc_start: 0.7088 (t0) cc_final: 0.6770 (t0) REVERT: C 251 THR cc_start: 0.7973 (m) cc_final: 0.7729 (m) REVERT: C 267 LYS cc_start: 0.8169 (ttmm) cc_final: 0.7909 (ttmt) REVERT: C 340 ARG cc_start: 0.7886 (tpp-160) cc_final: 0.7566 (mtp85) REVERT: C 356 ARG cc_start: 0.7042 (mtm110) cc_final: 0.6786 (mtm180) outliers start: 2 outliers final: 0 residues processed: 225 average time/residue: 0.9031 time to fit residues: 220.0223 Evaluate side-chains 206 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.0970 chunk 56 optimal weight: 0.0970 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 HIS B 142 ASN D 32 GLN D 176 GLN D 220 GLN D 239 ASN D 340 ASN E 3 GLN E 142 GLN E 179 GLN C 28 GLN ** C 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN C 245 ASN C 246 ASN C 338 ASN C 354 ASN C 359 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.124656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111367 restraints weight = 12736.069| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.96 r_work: 0.3330 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 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 : 0.003 0.035 8984 Z= 0.150 Angle : 0.599 9.956 12223 Z= 0.318 Chirality : 0.044 0.233 1396 Planarity : 0.005 0.060 1546 Dihedral : 5.222 43.344 1236 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.52 % Allowed : 10.20 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.64 (0.21), residues: 1126 helix: -2.77 (0.20), residues: 386 sheet: -2.11 (0.28), residues: 261 loop : -2.07 (0.25), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.005 0.001 HIS C 197 PHE 0.013 0.001 PHE B 367 TYR 0.039 0.002 TYR E 235 ARG 0.007 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.04890 ( 355) hydrogen bonds : angle 5.54587 ( 996) covalent geometry : bond 0.00325 ( 8984) covalent geometry : angle 0.59866 (12223) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 228 time to evaluate : 0.943 Fit side-chains REVERT: B 130 SER cc_start: 0.8100 (p) cc_final: 0.7867 (p) REVERT: B 153 PHE cc_start: 0.8066 (m-80) cc_final: 0.7858 (m-80) REVERT: B 210 LEU cc_start: 0.8391 (mt) cc_final: 0.8100 (mt) REVERT: B 268 THR cc_start: 0.8453 (p) cc_final: 0.8226 (t) REVERT: B 294 LYS cc_start: 0.8320 (mtpt) cc_final: 0.8056 (mtpt) REVERT: B 296 LYS cc_start: 0.8252 (ttpt) cc_final: 0.7853 (ttpp) REVERT: B 341 SER cc_start: 0.8588 (p) cc_final: 0.8358 (p) REVERT: D 14 LEU cc_start: 0.7975 (mt) cc_final: 0.7701 (mp) REVERT: D 17 GLN cc_start: 0.7484 (tm-30) cc_final: 0.7280 (tm-30) REVERT: D 22 ARG cc_start: 0.8116 (mtt180) cc_final: 0.7872 (mtt180) REVERT: D 37 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8282 (mt) REVERT: D 44 GLN cc_start: 0.7960 (mt0) cc_final: 0.7371 (mt0) REVERT: D 46 ARG cc_start: 0.7888 (mpp-170) cc_final: 0.7539 (mpp-170) REVERT: E 4 LEU cc_start: 0.7835 (mt) cc_final: 0.7449 (mt) REVERT: E 59 TYR cc_start: 0.7510 (m-10) cc_final: 0.7233 (m-10) REVERT: E 67 ARG cc_start: 0.8884 (mtm110) cc_final: 0.8540 (mtp180) REVERT: E 83 MET cc_start: 0.8439 (mtt) cc_final: 0.8151 (mtt) REVERT: E 93 MET cc_start: 0.8419 (ttp) cc_final: 0.8216 (ttp) REVERT: E 95 TYR cc_start: 0.8477 (m-80) cc_final: 0.8235 (m-80) REVERT: E 99 SER cc_start: 0.8508 (m) cc_final: 0.8264 (p) REVERT: E 140 MET cc_start: 0.8415 (mmm) cc_final: 0.8176 (mmt) REVERT: E 166 LEU cc_start: 0.8387 (tp) cc_final: 0.8027 (tt) REVERT: E 173 TYR cc_start: 0.8517 (m-10) cc_final: 0.8102 (m-80) REVERT: E 190 TYR cc_start: 0.8259 (p90) cc_final: 0.8019 (p90) REVERT: C 17 LYS cc_start: 0.8309 (mtmt) cc_final: 0.8077 (mtmt) REVERT: C 192 ASP cc_start: 0.7980 (m-30) cc_final: 0.7757 (m-30) REVERT: C 267 LYS cc_start: 0.8383 (ttmm) cc_final: 0.8092 (ttmt) REVERT: C 356 ARG cc_start: 0.7883 (mtm110) cc_final: 0.7655 (mtm180) outliers start: 23 outliers final: 8 residues processed: 236 average time/residue: 0.9649 time to fit residues: 246.3554 Evaluate side-chains 208 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 199 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain C residue 218 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 106 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 107 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 ASN D 75 GLN D 220 GLN D 239 ASN E 167 HIS ** C 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN C 238 ASN C 245 ASN C 246 ASN C 352 GLN C 354 ASN C 359 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.125408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.112295 restraints weight = 12851.512| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.88 r_work: 0.3338 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 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 : 0.003 0.028 8984 Z= 0.149 Angle : 0.569 8.888 12223 Z= 0.299 Chirality : 0.044 0.214 1396 Planarity : 0.005 0.056 1546 Dihedral : 4.908 42.080 1236 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.85 % Allowed : 13.16 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.60 (0.23), residues: 1126 helix: -1.38 (0.25), residues: 382 sheet: -1.81 (0.29), residues: 246 loop : -1.82 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 47 HIS 0.008 0.001 HIS E 167 PHE 0.022 0.001 PHE B 245 TYR 0.034 0.002 TYR B 315 ARG 0.008 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.04076 ( 355) hydrogen bonds : angle 4.85303 ( 996) covalent geometry : bond 0.00336 ( 8984) covalent geometry : angle 0.56909 (12223) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 0.913 Fit side-chains REVERT: B 87 LEU cc_start: 0.8426 (mt) cc_final: 0.8194 (mm) REVERT: B 153 PHE cc_start: 0.8056 (m-80) cc_final: 0.7803 (m-80) REVERT: B 210 LEU cc_start: 0.8411 (mt) cc_final: 0.8131 (mt) REVERT: B 294 LYS cc_start: 0.8307 (mtpt) cc_final: 0.8044 (mtpt) REVERT: B 296 LYS cc_start: 0.8223 (ttpt) cc_final: 0.8013 (ttpp) REVERT: D 17 GLN cc_start: 0.7401 (tm-30) cc_final: 0.7199 (tm-30) REVERT: D 37 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8357 (mt) REVERT: D 46 ARG cc_start: 0.7804 (mpp-170) cc_final: 0.7476 (mpp-170) REVERT: D 49 ARG cc_start: 0.8505 (mmt-90) cc_final: 0.8256 (mmt180) REVERT: D 86 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8217 (p) REVERT: E 4 LEU cc_start: 0.7778 (mt) cc_final: 0.7409 (mt) REVERT: E 59 TYR cc_start: 0.7585 (m-10) cc_final: 0.7311 (m-10) REVERT: E 67 ARG cc_start: 0.8844 (mtm110) cc_final: 0.8480 (mtp180) REVERT: E 83 MET cc_start: 0.8432 (mtt) cc_final: 0.8110 (mtt) REVERT: E 99 SER cc_start: 0.8442 (m) cc_final: 0.8216 (p) REVERT: E 166 LEU cc_start: 0.8518 (tp) cc_final: 0.8151 (tt) REVERT: E 173 TYR cc_start: 0.8507 (m-10) cc_final: 0.8060 (m-80) REVERT: E 192 MET cc_start: 0.8199 (ttp) cc_final: 0.7976 (tmm) REVERT: C 17 LYS cc_start: 0.8245 (mtmt) cc_final: 0.8026 (mtmt) REVERT: C 267 LYS cc_start: 0.8377 (ttmm) cc_final: 0.8120 (ttmt) REVERT: C 314 ASP cc_start: 0.7401 (m-30) cc_final: 0.6874 (m-30) REVERT: C 352 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7622 (mp-120) outliers start: 26 outliers final: 12 residues processed: 221 average time/residue: 0.9801 time to fit residues: 233.6337 Evaluate side-chains 218 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 203 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 352 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 43 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 78 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 ASN D 220 GLN D 230 ASN D 239 ASN C 204 GLN C 216 ASN C 238 ASN C 245 ASN C 352 GLN C 354 ASN C 359 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.124861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111590 restraints weight = 12834.916| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.96 r_work: 0.3327 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8984 Z= 0.158 Angle : 0.571 8.687 12223 Z= 0.299 Chirality : 0.044 0.217 1396 Planarity : 0.004 0.054 1546 Dihedral : 4.789 40.337 1236 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.40 % Allowed : 14.58 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.10 (0.24), residues: 1126 helix: -0.75 (0.27), residues: 383 sheet: -1.70 (0.29), residues: 257 loop : -1.60 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.003 0.001 HIS C 324 PHE 0.013 0.001 PHE D 151 TYR 0.035 0.002 TYR B 315 ARG 0.008 0.000 ARG D 219 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 355) hydrogen bonds : angle 4.65737 ( 996) covalent geometry : bond 0.00362 ( 8984) covalent geometry : angle 0.57090 (12223) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 0.957 Fit side-chains REVERT: B 129 PHE cc_start: 0.7648 (t80) cc_final: 0.7363 (t80) REVERT: B 210 LEU cc_start: 0.8425 (mt) cc_final: 0.8135 (mt) REVERT: B 294 LYS cc_start: 0.8325 (mtpt) cc_final: 0.8028 (mtpt) REVERT: D 46 ARG cc_start: 0.7836 (mpp-170) cc_final: 0.7531 (mpp-170) REVERT: D 86 THR cc_start: 0.8492 (OUTLIER) cc_final: 0.8173 (p) REVERT: D 285 LEU cc_start: 0.8546 (tp) cc_final: 0.8303 (tt) REVERT: D 322 ASP cc_start: 0.7770 (m-30) cc_final: 0.7460 (m-30) REVERT: E 59 TYR cc_start: 0.7654 (m-10) cc_final: 0.7364 (m-10) REVERT: E 67 ARG cc_start: 0.8826 (mtm110) cc_final: 0.8454 (mtp180) REVERT: E 83 MET cc_start: 0.8437 (mtt) cc_final: 0.8121 (mtt) REVERT: E 99 SER cc_start: 0.8457 (m) cc_final: 0.8200 (p) REVERT: E 166 LEU cc_start: 0.8491 (tp) cc_final: 0.8121 (tt) REVERT: E 173 TYR cc_start: 0.8494 (m-10) cc_final: 0.7964 (m-80) REVERT: C 17 LYS cc_start: 0.8256 (mtmt) cc_final: 0.7999 (mtmt) REVERT: C 32 ARG cc_start: 0.8013 (mtt90) cc_final: 0.7803 (ttm-80) REVERT: C 188 LYS cc_start: 0.8512 (mppt) cc_final: 0.8299 (mppt) REVERT: C 267 LYS cc_start: 0.8397 (ttmm) cc_final: 0.8150 (ttmt) REVERT: C 314 ASP cc_start: 0.7399 (m-30) cc_final: 0.6909 (m-30) outliers start: 31 outliers final: 16 residues processed: 221 average time/residue: 0.8977 time to fit residues: 215.1043 Evaluate side-chains 223 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 206 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 325 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 100 optimal weight: 0.0670 chunk 85 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 88 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 104 optimal weight: 0.0050 overall best weight: 0.2732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 ASN B 218 GLN D 220 GLN D 239 ASN E 194 ASN C 238 ASN C 245 ASN C 352 GLN C 354 ASN C 359 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.126725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.113435 restraints weight = 12863.319| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.97 r_work: 0.3356 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8984 Z= 0.103 Angle : 0.526 7.479 12223 Z= 0.275 Chirality : 0.042 0.182 1396 Planarity : 0.004 0.055 1546 Dihedral : 4.492 39.340 1236 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.85 % Allowed : 15.57 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.64 (0.24), residues: 1126 helix: -0.21 (0.27), residues: 387 sheet: -1.33 (0.29), residues: 267 loop : -1.56 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 248 HIS 0.003 0.001 HIS C 324 PHE 0.010 0.001 PHE C 189 TYR 0.031 0.001 TYR B 315 ARG 0.008 0.000 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03298 ( 355) hydrogen bonds : angle 4.35576 ( 996) covalent geometry : bond 0.00228 ( 8984) covalent geometry : angle 0.52607 (12223) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 221 time to evaluate : 0.995 Fit side-chains REVERT: B 98 VAL cc_start: 0.7590 (OUTLIER) cc_final: 0.7346 (p) REVERT: B 129 PHE cc_start: 0.7634 (t80) cc_final: 0.7408 (t80) REVERT: B 210 LEU cc_start: 0.8397 (mt) cc_final: 0.8108 (mt) REVERT: B 294 LYS cc_start: 0.8276 (mtpt) cc_final: 0.8026 (mtpt) REVERT: B 296 LYS cc_start: 0.8132 (ttpt) cc_final: 0.7799 (ttpp) REVERT: B 315 TYR cc_start: 0.8153 (t80) cc_final: 0.7664 (t80) REVERT: D 34 THR cc_start: 0.8341 (m) cc_final: 0.7922 (p) REVERT: D 46 ARG cc_start: 0.7780 (mpp-170) cc_final: 0.7493 (mpp-170) REVERT: D 86 THR cc_start: 0.8306 (OUTLIER) cc_final: 0.8085 (p) REVERT: D 147 SER cc_start: 0.8316 (m) cc_final: 0.7973 (p) REVERT: D 228 ASP cc_start: 0.7841 (m-30) cc_final: 0.7526 (p0) REVERT: D 314 ARG cc_start: 0.7969 (ttt180) cc_final: 0.7725 (ttt180) REVERT: D 322 ASP cc_start: 0.7749 (m-30) cc_final: 0.7466 (m-30) REVERT: E 59 TYR cc_start: 0.7580 (m-10) cc_final: 0.7314 (m-10) REVERT: E 67 ARG cc_start: 0.8802 (mtm110) cc_final: 0.8441 (mtp180) REVERT: E 83 MET cc_start: 0.8298 (mtt) cc_final: 0.8005 (mtt) REVERT: E 99 SER cc_start: 0.8431 (m) cc_final: 0.8186 (p) REVERT: E 166 LEU cc_start: 0.8395 (tp) cc_final: 0.8022 (tt) REVERT: E 173 TYR cc_start: 0.8543 (m-10) cc_final: 0.8051 (m-80) REVERT: C 50 VAL cc_start: 0.7574 (m) cc_final: 0.7367 (m) REVERT: C 188 LYS cc_start: 0.8495 (mppt) cc_final: 0.8269 (mppt) REVERT: C 191 VAL cc_start: 0.7739 (m) cc_final: 0.7423 (t) REVERT: C 194 VAL cc_start: 0.7969 (t) cc_final: 0.7350 (p) REVERT: C 241 ASP cc_start: 0.8039 (t0) cc_final: 0.7372 (t0) REVERT: C 245 ASN cc_start: 0.8107 (m-40) cc_final: 0.7897 (m-40) REVERT: C 267 LYS cc_start: 0.8391 (ttmm) cc_final: 0.8110 (ttmt) REVERT: C 314 ASP cc_start: 0.7381 (m-30) cc_final: 0.6910 (m-30) outliers start: 26 outliers final: 14 residues processed: 234 average time/residue: 0.9373 time to fit residues: 237.9972 Evaluate side-chains 228 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 212 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 325 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 82 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 ASN B 161 GLN B 218 GLN D 239 ASN E 77 ASN C 238 ASN C 352 GLN C 354 ASN C 359 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.124558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.111186 restraints weight = 12679.286| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.95 r_work: 0.3324 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8984 Z= 0.182 Angle : 0.588 8.330 12223 Z= 0.306 Chirality : 0.045 0.209 1396 Planarity : 0.004 0.053 1546 Dihedral : 4.686 34.695 1236 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.96 % Allowed : 16.89 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.45 (0.24), residues: 1126 helix: -0.10 (0.27), residues: 389 sheet: -1.36 (0.29), residues: 270 loop : -1.30 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 47 HIS 0.004 0.001 HIS D 142 PHE 0.013 0.002 PHE D 151 TYR 0.034 0.002 TYR B 315 ARG 0.008 0.001 ARG D 219 Details of bonding type rmsd hydrogen bonds : bond 0.03785 ( 355) hydrogen bonds : angle 4.46020 ( 996) covalent geometry : bond 0.00423 ( 8984) covalent geometry : angle 0.58832 (12223) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 0.992 Fit side-chains REVERT: B 100 VAL cc_start: 0.7950 (m) cc_final: 0.7531 (t) REVERT: B 129 PHE cc_start: 0.7621 (t80) cc_final: 0.7378 (t80) REVERT: B 147 LEU cc_start: 0.6329 (OUTLIER) cc_final: 0.5637 (mt) REVERT: B 210 LEU cc_start: 0.8411 (mt) cc_final: 0.8151 (mt) REVERT: B 221 TYR cc_start: 0.8736 (m-80) cc_final: 0.8480 (m-80) REVERT: B 294 LYS cc_start: 0.8342 (mtpt) cc_final: 0.8036 (mtpt) REVERT: B 296 LYS cc_start: 0.8186 (ttpt) cc_final: 0.7819 (ttpp) REVERT: D 46 ARG cc_start: 0.7898 (mpp-170) cc_final: 0.7565 (mpp-170) REVERT: D 86 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.8014 (p) REVERT: D 147 SER cc_start: 0.8363 (m) cc_final: 0.7979 (p) REVERT: D 228 ASP cc_start: 0.7888 (m-30) cc_final: 0.7550 (p0) REVERT: D 322 ASP cc_start: 0.7745 (m-30) cc_final: 0.7461 (m-30) REVERT: E 7 SER cc_start: 0.8237 (t) cc_final: 0.8008 (p) REVERT: E 59 TYR cc_start: 0.7719 (m-10) cc_final: 0.7469 (m-10) REVERT: E 67 ARG cc_start: 0.8833 (mtm110) cc_final: 0.8446 (mtp180) REVERT: E 83 MET cc_start: 0.8373 (mtt) cc_final: 0.8062 (mtt) REVERT: E 99 SER cc_start: 0.8417 (m) cc_final: 0.8167 (p) REVERT: E 166 LEU cc_start: 0.8419 (tp) cc_final: 0.8049 (tt) REVERT: E 192 MET cc_start: 0.8170 (ttp) cc_final: 0.7937 (tmm) REVERT: C 17 LYS cc_start: 0.8204 (mtmt) cc_final: 0.7978 (mtmt) REVERT: C 46 LYS cc_start: 0.8054 (ttmt) cc_final: 0.7596 (tttt) REVERT: C 188 LYS cc_start: 0.8513 (mppt) cc_final: 0.8301 (mppt) REVERT: C 200 ASP cc_start: 0.7982 (t0) cc_final: 0.7543 (t0) REVERT: C 241 ASP cc_start: 0.8096 (t0) cc_final: 0.7762 (t0) REVERT: C 266 GLU cc_start: 0.7793 (pp20) cc_final: 0.7357 (pp20) REVERT: C 267 LYS cc_start: 0.8399 (ttmm) cc_final: 0.7986 (ttmt) REVERT: C 314 ASP cc_start: 0.7445 (m-30) cc_final: 0.6986 (m-30) REVERT: C 340 ARG cc_start: 0.8141 (mmm160) cc_final: 0.7881 (mmt180) REVERT: C 348 ASP cc_start: 0.8207 (t0) cc_final: 0.7742 (t0) REVERT: C 352 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.7691 (mp-120) outliers start: 27 outliers final: 16 residues processed: 232 average time/residue: 0.9419 time to fit residues: 235.6583 Evaluate side-chains 226 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 207 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 352 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 90 optimal weight: 0.0970 chunk 52 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 0.0050 chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 ASN D 220 GLN D 239 ASN C 216 ASN C 238 ASN C 245 ASN C 352 GLN C 354 ASN C 359 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.125673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.112365 restraints weight = 12928.971| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.97 r_work: 0.3337 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8984 Z= 0.132 Angle : 0.561 7.971 12223 Z= 0.292 Chirality : 0.044 0.190 1396 Planarity : 0.004 0.054 1546 Dihedral : 4.547 34.092 1236 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.85 % Allowed : 18.20 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.19 (0.25), residues: 1126 helix: 0.19 (0.28), residues: 389 sheet: -1.24 (0.29), residues: 270 loop : -1.22 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 151 HIS 0.003 0.001 HIS C 324 PHE 0.011 0.001 PHE D 151 TYR 0.034 0.001 TYR B 315 ARG 0.008 0.001 ARG D 219 Details of bonding type rmsd hydrogen bonds : bond 0.03490 ( 355) hydrogen bonds : angle 4.35723 ( 996) covalent geometry : bond 0.00301 ( 8984) covalent geometry : angle 0.56111 (12223) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 0.836 Fit side-chains REVERT: B 129 PHE cc_start: 0.7614 (t80) cc_final: 0.7403 (t80) REVERT: B 147 LEU cc_start: 0.5923 (OUTLIER) cc_final: 0.5172 (mt) REVERT: B 210 LEU cc_start: 0.8420 (mt) cc_final: 0.8154 (mt) REVERT: B 221 TYR cc_start: 0.8704 (m-80) cc_final: 0.8453 (m-80) REVERT: B 294 LYS cc_start: 0.8314 (mtpt) cc_final: 0.8020 (mtpt) REVERT: B 296 LYS cc_start: 0.8170 (ttpt) cc_final: 0.7792 (ttpp) REVERT: D 46 ARG cc_start: 0.7852 (mpp-170) cc_final: 0.7537 (mpp-170) REVERT: D 86 THR cc_start: 0.8294 (OUTLIER) cc_final: 0.7990 (p) REVERT: D 147 SER cc_start: 0.8338 (m) cc_final: 0.7977 (p) REVERT: D 228 ASP cc_start: 0.7899 (m-30) cc_final: 0.7580 (p0) REVERT: D 322 ASP cc_start: 0.7770 (m-30) cc_final: 0.7499 (m-30) REVERT: E 7 SER cc_start: 0.8243 (t) cc_final: 0.8018 (p) REVERT: E 67 ARG cc_start: 0.8800 (mtm110) cc_final: 0.8413 (mtp180) REVERT: E 79 LEU cc_start: 0.7328 (tp) cc_final: 0.7023 (mp) REVERT: E 83 MET cc_start: 0.8371 (mtt) cc_final: 0.8104 (mtt) REVERT: E 99 SER cc_start: 0.8413 (m) cc_final: 0.8171 (p) REVERT: E 166 LEU cc_start: 0.8504 (tp) cc_final: 0.8129 (tt) REVERT: E 173 TYR cc_start: 0.8456 (m-10) cc_final: 0.7850 (m-80) REVERT: E 192 MET cc_start: 0.8158 (ttp) cc_final: 0.7947 (tmm) REVERT: G 58 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7242 (pm20) REVERT: C 17 LYS cc_start: 0.8118 (mtmt) cc_final: 0.7898 (mtmt) REVERT: C 188 LYS cc_start: 0.8512 (mppt) cc_final: 0.8293 (mppt) REVERT: C 241 ASP cc_start: 0.7996 (t0) cc_final: 0.7642 (t0) REVERT: C 266 GLU cc_start: 0.7772 (pp20) cc_final: 0.7355 (pp20) REVERT: C 267 LYS cc_start: 0.8375 (ttmm) cc_final: 0.7978 (ttmt) REVERT: C 314 ASP cc_start: 0.7465 (m-30) cc_final: 0.7023 (m-30) REVERT: C 340 ARG cc_start: 0.8102 (mmm160) cc_final: 0.7876 (mmt180) outliers start: 26 outliers final: 17 residues processed: 240 average time/residue: 0.9195 time to fit residues: 239.0210 Evaluate side-chains 244 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 224 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 335 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 28 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 102 optimal weight: 0.0770 chunk 94 optimal weight: 1.9990 chunk 107 optimal weight: 0.0270 chunk 73 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 97 optimal weight: 0.0770 chunk 25 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 overall best weight: 0.3354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 ASN B 218 GLN D 239 ASN E 77 ASN C 238 ASN C 245 ASN C 354 ASN C 359 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.126134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.113273 restraints weight = 13081.699| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.87 r_work: 0.3356 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8984 Z= 0.112 Angle : 0.547 7.464 12223 Z= 0.285 Chirality : 0.043 0.172 1396 Planarity : 0.004 0.053 1546 Dihedral : 4.384 31.232 1236 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.41 % Allowed : 19.41 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.97 (0.25), residues: 1126 helix: 0.39 (0.28), residues: 395 sheet: -1.04 (0.30), residues: 263 loop : -1.20 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 151 HIS 0.003 0.001 HIS C 324 PHE 0.012 0.001 PHE C 189 TYR 0.032 0.001 TYR B 315 ARG 0.008 0.001 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 355) hydrogen bonds : angle 4.23494 ( 996) covalent geometry : bond 0.00253 ( 8984) covalent geometry : angle 0.54741 (12223) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 226 time to evaluate : 0.900 Fit side-chains REVERT: B 210 LEU cc_start: 0.8337 (mt) cc_final: 0.8088 (mt) REVERT: B 268 THR cc_start: 0.8549 (t) cc_final: 0.8306 (p) REVERT: B 294 LYS cc_start: 0.8272 (mtpt) cc_final: 0.8040 (mtpt) REVERT: B 296 LYS cc_start: 0.8134 (ttpt) cc_final: 0.7792 (ttpp) REVERT: B 315 TYR cc_start: 0.8185 (t80) cc_final: 0.7604 (t80) REVERT: D 46 ARG cc_start: 0.7784 (mpp-170) cc_final: 0.7497 (mpp-170) REVERT: D 86 THR cc_start: 0.8244 (OUTLIER) cc_final: 0.8034 (p) REVERT: D 228 ASP cc_start: 0.7841 (m-30) cc_final: 0.7571 (p0) REVERT: D 322 ASP cc_start: 0.7739 (m-30) cc_final: 0.7452 (m-30) REVERT: E 7 SER cc_start: 0.8265 (t) cc_final: 0.8062 (p) REVERT: E 67 ARG cc_start: 0.8836 (mtm110) cc_final: 0.8466 (mtp180) REVERT: E 79 LEU cc_start: 0.7321 (tp) cc_final: 0.7037 (mp) REVERT: E 99 SER cc_start: 0.8363 (m) cc_final: 0.8147 (p) REVERT: E 166 LEU cc_start: 0.8500 (tp) cc_final: 0.8137 (tt) REVERT: E 173 TYR cc_start: 0.8451 (m-10) cc_final: 0.7852 (m-80) REVERT: C 17 LYS cc_start: 0.8054 (mtmt) cc_final: 0.7844 (mtmt) REVERT: C 46 LYS cc_start: 0.7924 (ttpt) cc_final: 0.7652 (tttt) REVERT: C 188 LYS cc_start: 0.8474 (mppt) cc_final: 0.8270 (mppt) REVERT: C 241 ASP cc_start: 0.8015 (t0) cc_final: 0.7712 (t0) REVERT: C 266 GLU cc_start: 0.7811 (pp20) cc_final: 0.7438 (pp20) REVERT: C 267 LYS cc_start: 0.8358 (ttmm) cc_final: 0.7897 (ttmt) REVERT: C 301 VAL cc_start: 0.6734 (p) cc_final: 0.6420 (t) REVERT: C 314 ASP cc_start: 0.7418 (m-30) cc_final: 0.6896 (m-30) outliers start: 22 outliers final: 18 residues processed: 238 average time/residue: 0.8823 time to fit residues: 227.5375 Evaluate side-chains 236 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 217 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 335 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.8980 chunk 62 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 58 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 108 optimal weight: 0.1980 chunk 77 optimal weight: 0.0170 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 ASN B 218 GLN D 239 ASN C 238 ASN C 245 ASN C 354 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.126888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.113501 restraints weight = 12981.406| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.98 r_work: 0.3354 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8984 Z= 0.123 Angle : 0.561 7.331 12223 Z= 0.292 Chirality : 0.043 0.185 1396 Planarity : 0.004 0.053 1546 Dihedral : 4.365 30.245 1236 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.41 % Allowed : 19.96 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.25), residues: 1126 helix: 0.53 (0.28), residues: 395 sheet: -0.95 (0.30), residues: 261 loop : -1.14 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 151 HIS 0.003 0.001 HIS C 324 PHE 0.010 0.001 PHE C 189 TYR 0.033 0.001 TYR B 315 ARG 0.009 0.001 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03271 ( 355) hydrogen bonds : angle 4.19570 ( 996) covalent geometry : bond 0.00280 ( 8984) covalent geometry : angle 0.56092 (12223) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 226 time to evaluate : 1.022 Fit side-chains REVERT: B 210 LEU cc_start: 0.8339 (mt) cc_final: 0.8083 (mt) REVERT: B 268 THR cc_start: 0.8581 (t) cc_final: 0.8313 (p) REVERT: B 294 LYS cc_start: 0.8226 (mtpt) cc_final: 0.7993 (mtpt) REVERT: B 296 LYS cc_start: 0.8159 (ttpt) cc_final: 0.7767 (ttpp) REVERT: D 34 THR cc_start: 0.8248 (m) cc_final: 0.7917 (p) REVERT: D 46 ARG cc_start: 0.7819 (mpp-170) cc_final: 0.7512 (mpp-170) REVERT: D 86 THR cc_start: 0.8234 (OUTLIER) cc_final: 0.7994 (p) REVERT: D 228 ASP cc_start: 0.7887 (m-30) cc_final: 0.7563 (p0) REVERT: D 322 ASP cc_start: 0.7756 (m-30) cc_final: 0.7501 (m-30) REVERT: E 7 SER cc_start: 0.8213 (t) cc_final: 0.7988 (p) REVERT: E 67 ARG cc_start: 0.8835 (mtm110) cc_final: 0.8453 (mtp180) REVERT: E 99 SER cc_start: 0.8398 (m) cc_final: 0.8151 (p) REVERT: E 166 LEU cc_start: 0.8472 (tp) cc_final: 0.8111 (tt) REVERT: E 173 TYR cc_start: 0.8543 (m-10) cc_final: 0.8021 (m-80) REVERT: C 17 LYS cc_start: 0.7999 (mtmt) cc_final: 0.7797 (mtmt) REVERT: C 188 LYS cc_start: 0.8508 (mppt) cc_final: 0.8296 (mppt) REVERT: C 241 ASP cc_start: 0.7928 (t0) cc_final: 0.7588 (t0) REVERT: C 266 GLU cc_start: 0.7776 (pp20) cc_final: 0.7384 (pp20) REVERT: C 267 LYS cc_start: 0.8353 (ttmm) cc_final: 0.7882 (ttmt) REVERT: C 314 ASP cc_start: 0.7393 (m-30) cc_final: 0.6879 (m-30) outliers start: 22 outliers final: 18 residues processed: 236 average time/residue: 0.9211 time to fit residues: 234.8119 Evaluate side-chains 242 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 223 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 335 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 17 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 ASN D 220 GLN D 239 ASN E 77 ASN C 216 ASN C 245 ASN C 354 ASN C 359 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.125346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.111985 restraints weight = 12876.550| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.97 r_work: 0.3331 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8984 Z= 0.171 Angle : 0.600 8.063 12223 Z= 0.312 Chirality : 0.045 0.180 1396 Planarity : 0.004 0.053 1546 Dihedral : 4.548 30.502 1236 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.63 % Allowed : 19.96 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.86 (0.25), residues: 1126 helix: 0.50 (0.27), residues: 395 sheet: -1.18 (0.29), residues: 273 loop : -0.99 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 47 HIS 0.005 0.001 HIS D 142 PHE 0.012 0.002 PHE D 151 TYR 0.037 0.002 TYR B 315 ARG 0.009 0.001 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 355) hydrogen bonds : angle 4.28576 ( 996) covalent geometry : bond 0.00398 ( 8984) covalent geometry : angle 0.60007 (12223) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 221 time to evaluate : 0.972 Fit side-chains REVERT: B 210 LEU cc_start: 0.8379 (mt) cc_final: 0.8111 (mt) REVERT: B 221 TYR cc_start: 0.8694 (m-80) cc_final: 0.8419 (m-80) REVERT: B 294 LYS cc_start: 0.8261 (mtpt) cc_final: 0.7994 (mtpt) REVERT: B 296 LYS cc_start: 0.8181 (ttpt) cc_final: 0.7788 (ttpp) REVERT: D 34 THR cc_start: 0.8226 (m) cc_final: 0.7902 (p) REVERT: D 46 ARG cc_start: 0.7855 (mpp-170) cc_final: 0.7548 (mpp-170) REVERT: D 86 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.7922 (p) REVERT: D 228 ASP cc_start: 0.7899 (m-30) cc_final: 0.7548 (p0) REVERT: D 322 ASP cc_start: 0.7757 (m-30) cc_final: 0.7509 (m-30) REVERT: E 7 SER cc_start: 0.8218 (t) cc_final: 0.7978 (p) REVERT: E 67 ARG cc_start: 0.8868 (mtm110) cc_final: 0.8481 (mtp180) REVERT: E 93 MET cc_start: 0.8484 (ttp) cc_final: 0.8232 (ttp) REVERT: E 99 SER cc_start: 0.8407 (m) cc_final: 0.8141 (p) REVERT: E 166 LEU cc_start: 0.8474 (tp) cc_final: 0.8121 (tt) REVERT: E 173 TYR cc_start: 0.8565 (m-10) cc_final: 0.7969 (m-80) REVERT: C 241 ASP cc_start: 0.7970 (t0) cc_final: 0.7718 (t0) REVERT: C 266 GLU cc_start: 0.7841 (pp20) cc_final: 0.7435 (pp20) REVERT: C 267 LYS cc_start: 0.8390 (ttmm) cc_final: 0.8077 (ttmm) REVERT: C 314 ASP cc_start: 0.7425 (m-30) cc_final: 0.6916 (m-30) outliers start: 24 outliers final: 21 residues processed: 231 average time/residue: 0.9159 time to fit residues: 228.8898 Evaluate side-chains 241 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 219 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 357 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 60 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 20 optimal weight: 0.0070 chunk 74 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 ASN D 220 GLN E 77 ASN C 216 ASN C 238 ASN C 245 ASN C 354 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.125922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.112543 restraints weight = 13012.909| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.98 r_work: 0.3342 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8984 Z= 0.149 Angle : 0.589 8.186 12223 Z= 0.306 Chirality : 0.044 0.181 1396 Planarity : 0.004 0.053 1546 Dihedral : 4.509 30.333 1236 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.52 % Allowed : 20.83 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.76 (0.25), residues: 1126 helix: 0.63 (0.27), residues: 394 sheet: -1.11 (0.29), residues: 271 loop : -0.99 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.004 0.001 HIS D 142 PHE 0.012 0.001 PHE D 151 TYR 0.036 0.002 TYR B 315 ARG 0.009 0.001 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 355) hydrogen bonds : angle 4.26515 ( 996) covalent geometry : bond 0.00346 ( 8984) covalent geometry : angle 0.58862 (12223) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6621.42 seconds wall clock time: 114 minutes 31.75 seconds (6871.75 seconds total)