Starting phenix.real_space_refine on Sat Aug 23 00:41:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jbf_36144/08_2025/8jbf_36144.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jbf_36144/08_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_36144/08_2025/8jbf_36144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jbf_36144/08_2025/8jbf_36144.map" model { file = "/net/cci-nas-00/data/ceres_data/8jbf_36144/08_2025/8jbf_36144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jbf_36144/08_2025/8jbf_36144.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASN:plan1': 2, 'GLN:plan1': 2, 'ARG:plan': 4, 'GLU:plan': 2, 'TYR:plan': 1, 'PHE:plan': 3} 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: {'GLU:plan': 4, 'ASP:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 4} 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, 'ASP:plan': 1, 'ARG: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: {'ARG:plan': 2, 'GLU:plan': 1, '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, 'ASP:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 35 Time building chain proxies: 1.55, per 1000 atoms: 0.18 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: 0.44 Conformation dependent library (CDL) restraints added in 344.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.24 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: 1.18 Time building geometry restraints manager: 0.60 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.180 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.850 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.008 0.001 ARG C 209 TYR 0.048 0.003 TYR B 92 PHE 0.023 0.002 PHE D 151 TRP 0.015 0.002 TRP E 47 HIS 0.008 0.002 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00713 ( 8984) covalent geometry : angle 0.86396 (12223) hydrogen bonds : bond 0.28386 ( 355) hydrogen bonds : angle 10.55425 ( 996) *********************** 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 : 0.208 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: 0.3941 time to fit residues: 95.7433 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 : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.1980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.0370 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 ASN B 316 HIS 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 = 0.3628 r_free = 0.3628 target = 0.125396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.112003 restraints weight = 12849.065| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.98 r_work: 0.3338 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8984 Z= 0.134 Angle : 0.586 9.341 12223 Z= 0.312 Chirality : 0.043 0.222 1396 Planarity : 0.005 0.060 1546 Dihedral : 5.149 43.199 1236 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.61 (0.21), residues: 1126 helix: -2.74 (0.20), residues: 387 sheet: -2.10 (0.28), residues: 261 loop : -2.04 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 49 TYR 0.038 0.002 TYR E 235 PHE 0.013 0.001 PHE B 367 TRP 0.010 0.001 TRP D 211 HIS 0.004 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8984) covalent geometry : angle 0.58607 (12223) hydrogen bonds : bond 0.04544 ( 355) hydrogen bonds : angle 5.44840 ( 996) *********************** 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 246 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 223 time to evaluate : 0.341 Fit side-chains REVERT: B 129 PHE cc_start: 0.7565 (t80) cc_final: 0.7290 (t80) REVERT: B 153 PHE cc_start: 0.8060 (m-80) cc_final: 0.7853 (m-80) REVERT: B 210 LEU cc_start: 0.8385 (mt) cc_final: 0.8096 (mt) REVERT: B 268 THR cc_start: 0.8436 (p) cc_final: 0.8230 (t) REVERT: B 294 LYS cc_start: 0.8305 (mtpt) cc_final: 0.7974 (mtpt) REVERT: D 14 LEU cc_start: 0.7896 (mt) cc_final: 0.7616 (mp) REVERT: D 37 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8257 (mt) REVERT: D 44 GLN cc_start: 0.7946 (mt0) cc_final: 0.7369 (mt0) REVERT: D 46 ARG cc_start: 0.7890 (mpp-170) cc_final: 0.7536 (mpp-170) REVERT: E 4 LEU cc_start: 0.7817 (mt) cc_final: 0.7421 (mt) REVERT: E 59 TYR cc_start: 0.7494 (m-10) cc_final: 0.7216 (m-10) REVERT: E 67 ARG cc_start: 0.8860 (mtm110) cc_final: 0.8534 (mtp180) REVERT: E 83 MET cc_start: 0.8429 (mtt) cc_final: 0.8167 (mtt) REVERT: E 99 SER cc_start: 0.8505 (m) cc_final: 0.8268 (p) REVERT: E 140 MET cc_start: 0.8412 (mmm) cc_final: 0.8165 (mmt) REVERT: E 166 LEU cc_start: 0.8383 (tp) cc_final: 0.8023 (tt) REVERT: E 173 TYR cc_start: 0.8517 (m-10) cc_final: 0.8110 (m-80) REVERT: C 17 LYS cc_start: 0.8302 (mtmt) cc_final: 0.8070 (mtmt) REVERT: C 192 ASP cc_start: 0.8027 (m-30) cc_final: 0.7796 (m-30) REVERT: C 242 SER cc_start: 0.8434 (m) cc_final: 0.8228 (m) REVERT: C 251 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7980 (m) REVERT: C 267 LYS cc_start: 0.8338 (ttmm) cc_final: 0.8053 (ttmt) REVERT: C 356 ARG cc_start: 0.7877 (mtm110) cc_final: 0.7652 (mtm180) outliers start: 23 outliers final: 8 residues processed: 232 average time/residue: 0.3965 time to fit residues: 99.2225 Evaluate side-chains 209 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 199 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 251 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 2 optimal weight: 0.0040 chunk 8 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 5 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 77 optimal weight: 0.0370 chunk 46 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 107 optimal weight: 0.0970 chunk 55 optimal weight: 0.8980 overall best weight: 0.2668 ------------------------------------------------------------------------------- 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 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.127502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.114154 restraints weight = 12779.415| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.97 r_work: 0.3365 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2107 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= 0.106 Angle : 0.535 7.826 12223 Z= 0.282 Chirality : 0.042 0.188 1396 Planarity : 0.004 0.057 1546 Dihedral : 4.655 41.130 1236 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.30 % Allowed : 13.93 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.50 (0.23), residues: 1126 helix: -1.23 (0.25), residues: 383 sheet: -1.76 (0.28), residues: 260 loop : -1.79 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 49 TYR 0.032 0.001 TYR B 315 PHE 0.023 0.001 PHE B 245 TRP 0.010 0.001 TRP D 211 HIS 0.008 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 8984) covalent geometry : angle 0.53522 (12223) hydrogen bonds : bond 0.03585 ( 355) hydrogen bonds : angle 4.65506 ( 996) *********************** 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 237 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 216 time to evaluate : 0.194 Fit side-chains REVERT: B 153 PHE cc_start: 0.8070 (m-80) cc_final: 0.7814 (m-80) REVERT: B 210 LEU cc_start: 0.8369 (mt) cc_final: 0.8085 (mt) REVERT: B 294 LYS cc_start: 0.8223 (mtpt) cc_final: 0.7993 (mtpt) REVERT: D 34 THR cc_start: 0.8351 (m) cc_final: 0.7959 (p) REVERT: D 37 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8306 (mt) REVERT: D 46 ARG cc_start: 0.7768 (mpp-170) cc_final: 0.7444 (mpp-170) REVERT: D 86 THR cc_start: 0.8335 (OUTLIER) cc_final: 0.8100 (p) REVERT: D 212 ASP cc_start: 0.8087 (t0) cc_final: 0.7598 (p0) REVERT: E 4 LEU cc_start: 0.7743 (mt) cc_final: 0.7362 (mt) REVERT: E 23 SER cc_start: 0.8509 (m) cc_final: 0.8284 (p) REVERT: E 59 TYR cc_start: 0.7500 (m-10) cc_final: 0.7173 (m-10) REVERT: E 67 ARG cc_start: 0.8809 (mtm110) cc_final: 0.8448 (mtp180) REVERT: E 83 MET cc_start: 0.8382 (mtt) cc_final: 0.8071 (mtt) REVERT: E 99 SER cc_start: 0.8449 (m) cc_final: 0.8219 (p) REVERT: E 166 LEU cc_start: 0.8497 (tp) cc_final: 0.8124 (tt) REVERT: E 173 TYR cc_start: 0.8472 (m-10) cc_final: 0.8007 (m-80) REVERT: E 192 MET cc_start: 0.8233 (ttp) cc_final: 0.8026 (tmm) REVERT: E 239 PHE cc_start: 0.8509 (m-80) cc_final: 0.8306 (m-80) REVERT: C 17 LYS cc_start: 0.8156 (mtmt) cc_final: 0.7895 (mtmt) REVERT: C 188 LYS cc_start: 0.8484 (mppt) cc_final: 0.8270 (mppt) REVERT: C 241 ASP cc_start: 0.7974 (t0) cc_final: 0.7253 (t0) REVERT: C 245 ASN cc_start: 0.8160 (m-40) cc_final: 0.7889 (m-40) REVERT: C 267 LYS cc_start: 0.8338 (ttmm) cc_final: 0.8080 (ttmt) REVERT: C 314 ASP cc_start: 0.7338 (m-30) cc_final: 0.6841 (m-30) REVERT: C 356 ARG cc_start: 0.7869 (mtm110) cc_final: 0.7649 (mtm180) outliers start: 21 outliers final: 9 residues processed: 224 average time/residue: 0.4091 time to fit residues: 98.6864 Evaluate side-chains 216 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 205 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 303 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 218 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 54 optimal weight: 0.0370 chunk 89 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 78 optimal weight: 0.0870 overall best weight: 0.6838 ------------------------------------------------------------------------------- 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 239 ASN C 238 ASN C 352 GLN C 354 ASN C 359 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.125050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111639 restraints weight = 12980.858| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.99 r_work: 0.3329 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8984 Z= 0.163 Angle : 0.574 7.802 12223 Z= 0.300 Chirality : 0.044 0.209 1396 Planarity : 0.004 0.055 1546 Dihedral : 4.672 35.848 1236 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.40 % Allowed : 14.69 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.01 (0.24), residues: 1126 helix: -0.69 (0.27), residues: 386 sheet: -1.59 (0.29), residues: 265 loop : -1.56 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 219 TYR 0.033 0.002 TYR B 315 PHE 0.012 0.001 PHE D 151 TRP 0.010 0.001 TRP E 47 HIS 0.004 0.001 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 8984) covalent geometry : angle 0.57391 (12223) hydrogen bonds : bond 0.03811 ( 355) hydrogen bonds : angle 4.54761 ( 996) *********************** 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 249 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 218 time to evaluate : 0.220 Fit side-chains REVERT: B 129 PHE cc_start: 0.7656 (t80) cc_final: 0.7381 (t80) REVERT: B 147 LEU cc_start: 0.6499 (OUTLIER) cc_final: 0.5669 (mt) REVERT: B 153 PHE cc_start: 0.8087 (m-80) cc_final: 0.7878 (m-80) REVERT: B 210 LEU cc_start: 0.8429 (mt) cc_final: 0.8123 (mt) REVERT: B 294 LYS cc_start: 0.8266 (mtpt) cc_final: 0.7982 (mtpt) REVERT: D 34 THR cc_start: 0.8344 (m) cc_final: 0.7973 (p) REVERT: D 37 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8398 (mt) REVERT: D 44 GLN cc_start: 0.7968 (mt0) cc_final: 0.7430 (mt0) REVERT: D 46 ARG cc_start: 0.7870 (mpp-170) cc_final: 0.7509 (mpp-170) REVERT: D 86 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.8069 (p) REVERT: E 59 TYR cc_start: 0.7634 (m-10) cc_final: 0.7380 (m-10) REVERT: E 67 ARG cc_start: 0.8807 (mtm110) cc_final: 0.8440 (mtp180) REVERT: E 83 MET cc_start: 0.8383 (mtt) cc_final: 0.8076 (mtt) REVERT: E 99 SER cc_start: 0.8448 (m) cc_final: 0.8200 (p) REVERT: E 166 LEU cc_start: 0.8463 (tp) cc_final: 0.8091 (tt) REVERT: E 173 TYR cc_start: 0.8490 (m-10) cc_final: 0.7927 (m-80) REVERT: C 17 LYS cc_start: 0.8205 (mtmt) cc_final: 0.7959 (mtmt) REVERT: C 46 LYS cc_start: 0.8075 (ttmt) cc_final: 0.7472 (tttt) REVERT: C 188 LYS cc_start: 0.8507 (mppt) cc_final: 0.8293 (mppt) REVERT: C 241 ASP cc_start: 0.8063 (t0) cc_final: 0.7457 (t0) REVERT: C 245 ASN cc_start: 0.8113 (m-40) cc_final: 0.7874 (m-40) REVERT: C 267 LYS cc_start: 0.8393 (ttmm) cc_final: 0.8151 (ttmt) REVERT: C 314 ASP cc_start: 0.7385 (m-30) cc_final: 0.6905 (m-30) REVERT: C 348 ASP cc_start: 0.8214 (t0) cc_final: 0.7741 (t0) REVERT: C 352 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.7650 (mp-120) REVERT: C 356 ARG cc_start: 0.7859 (mtm110) cc_final: 0.7658 (mtm180) outliers start: 31 outliers final: 16 residues processed: 232 average time/residue: 0.4028 time to fit residues: 100.6341 Evaluate side-chains 227 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 207 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 LEU 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 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 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 325 ILE Chi-restraints excluded: chain C residue 352 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 49 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 D 220 GLN D 239 ASN C 238 ASN C 352 GLN 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 = 0.3599 r_free = 0.3599 target = 0.123485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.109975 restraints weight = 12998.830| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.97 r_work: 0.3306 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 8984 Z= 0.241 Angle : 0.626 8.737 12223 Z= 0.327 Chirality : 0.047 0.234 1396 Planarity : 0.005 0.054 1546 Dihedral : 4.915 36.323 1236 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.40 % Allowed : 15.68 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.24), residues: 1126 helix: -0.61 (0.26), residues: 386 sheet: -1.56 (0.28), residues: 276 loop : -1.47 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 32 TYR 0.038 0.002 TYR B 315 PHE 0.016 0.002 PHE D 151 TRP 0.012 0.002 TRP E 47 HIS 0.006 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00562 ( 8984) covalent geometry : angle 0.62600 (12223) hydrogen bonds : bond 0.04123 ( 355) hydrogen bonds : angle 4.64028 ( 996) *********************** 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 248 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 217 time to evaluate : 0.345 Fit side-chains REVERT: B 100 VAL cc_start: 0.8039 (m) cc_final: 0.7602 (t) REVERT: B 129 PHE cc_start: 0.7674 (t80) cc_final: 0.7393 (t80) REVERT: B 147 LEU cc_start: 0.6490 (OUTLIER) cc_final: 0.5638 (mt) REVERT: B 210 LEU cc_start: 0.8441 (mt) cc_final: 0.8167 (mt) REVERT: B 294 LYS cc_start: 0.8361 (mtpt) cc_final: 0.8064 (mtpt) REVERT: D 46 ARG cc_start: 0.7927 (mpp-170) cc_final: 0.7580 (mpp-170) REVERT: D 322 ASP cc_start: 0.7790 (m-30) cc_final: 0.7502 (m-30) REVERT: E 59 TYR cc_start: 0.7768 (m-10) cc_final: 0.7539 (m-10) REVERT: E 67 ARG cc_start: 0.8820 (mtm110) cc_final: 0.8429 (mtp180) REVERT: E 83 MET cc_start: 0.8376 (mtt) cc_final: 0.8063 (mtt) REVERT: E 99 SER cc_start: 0.8435 (m) cc_final: 0.8178 (p) REVERT: E 166 LEU cc_start: 0.8418 (tp) cc_final: 0.8057 (tt) REVERT: C 17 LYS cc_start: 0.8269 (mtmt) cc_final: 0.8069 (mtmt) REVERT: C 188 LYS cc_start: 0.8526 (mppt) cc_final: 0.8320 (mppt) REVERT: C 192 ASP cc_start: 0.7867 (m-30) cc_final: 0.7652 (m-30) REVERT: C 232 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7780 (ptp-110) REVERT: C 241 ASP cc_start: 0.8127 (t0) cc_final: 0.7505 (t0) REVERT: C 245 ASN cc_start: 0.8126 (m-40) cc_final: 0.7895 (m-40) REVERT: C 266 GLU cc_start: 0.7834 (pp20) cc_final: 0.7388 (pp20) REVERT: C 267 LYS cc_start: 0.8401 (ttmm) cc_final: 0.8004 (ttmt) REVERT: C 314 ASP cc_start: 0.7435 (m-30) cc_final: 0.6956 (m-30) outliers start: 31 outliers final: 20 residues processed: 232 average time/residue: 0.3804 time to fit residues: 95.6216 Evaluate side-chains 236 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 214 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 303 ILE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain D residue 37 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 7 SER Chi-restraints excluded: chain E residue 118 THR 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 232 ARG Chi-restraints excluded: chain C residue 243 ILE 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 90 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 238 ASN C 246 ASN C 352 GLN C 359 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.123708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.110247 restraints weight = 12943.550| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.97 r_work: 0.3304 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8984 Z= 0.198 Angle : 0.599 8.705 12223 Z= 0.312 Chirality : 0.046 0.225 1396 Planarity : 0.004 0.052 1546 Dihedral : 4.848 35.687 1236 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.40 % Allowed : 17.00 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.24), residues: 1126 helix: -0.32 (0.27), residues: 386 sheet: -1.41 (0.28), residues: 275 loop : -1.34 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 219 TYR 0.036 0.002 TYR B 315 PHE 0.024 0.002 PHE B 245 TRP 0.011 0.002 TRP E 47 HIS 0.005 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 8984) covalent geometry : angle 0.59905 (12223) hydrogen bonds : bond 0.03887 ( 355) hydrogen bonds : angle 4.55876 ( 996) *********************** 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: 31 poor density : 211 time to evaluate : 0.323 Fit side-chains REVERT: B 129 PHE cc_start: 0.7630 (t80) cc_final: 0.7380 (t80) REVERT: B 147 LEU cc_start: 0.6360 (OUTLIER) cc_final: 0.5481 (mt) REVERT: B 210 LEU cc_start: 0.8459 (mt) cc_final: 0.8177 (mt) REVERT: B 294 LYS cc_start: 0.8351 (mtpt) cc_final: 0.8065 (mtpt) REVERT: D 46 ARG cc_start: 0.7913 (mpp-170) cc_final: 0.7577 (mpp-170) REVERT: D 228 ASP cc_start: 0.7896 (m-30) cc_final: 0.7542 (p0) REVERT: D 251 ARG cc_start: 0.8425 (mtt90) cc_final: 0.8218 (ttm170) REVERT: D 322 ASP cc_start: 0.7786 (m-30) cc_final: 0.7498 (m-30) REVERT: E 7 SER cc_start: 0.8264 (OUTLIER) cc_final: 0.8042 (p) REVERT: E 59 TYR cc_start: 0.7793 (m-10) cc_final: 0.7536 (m-10) REVERT: E 67 ARG cc_start: 0.8827 (mtm110) cc_final: 0.8419 (mtp180) REVERT: E 83 MET cc_start: 0.8344 (mtt) cc_final: 0.8069 (mtt) REVERT: E 99 SER cc_start: 0.8424 (m) cc_final: 0.8173 (p) REVERT: E 166 LEU cc_start: 0.8424 (tp) cc_final: 0.8060 (tt) REVERT: E 192 MET cc_start: 0.8193 (ttp) cc_final: 0.7977 (tmm) REVERT: G 58 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7205 (pm20) REVERT: C 17 LYS cc_start: 0.8202 (mtmt) cc_final: 0.7976 (mtmt) REVERT: C 32 ARG cc_start: 0.8058 (tpp-160) cc_final: 0.7811 (ttm-80) REVERT: C 232 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7832 (ptp-110) REVERT: C 266 GLU cc_start: 0.7848 (pp20) cc_final: 0.7407 (pp20) REVERT: C 267 LYS cc_start: 0.8392 (ttmm) cc_final: 0.8003 (ttmt) REVERT: C 314 ASP cc_start: 0.7450 (m-30) cc_final: 0.6999 (m-30) outliers start: 31 outliers final: 20 residues processed: 228 average time/residue: 0.4032 time to fit residues: 98.9535 Evaluate side-chains 230 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain D residue 37 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 7 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 218 VAL Chi-restraints excluded: chain C residue 232 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 96 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 93 optimal weight: 0.1980 chunk 43 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 ASN D 32 GLN D 220 GLN D 239 ASN C 238 ASN C 352 GLN 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 = 0.3614 r_free = 0.3614 target = 0.124595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.111194 restraints weight = 12905.928| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.96 r_work: 0.3322 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8984 Z= 0.156 Angle : 0.577 8.467 12223 Z= 0.302 Chirality : 0.045 0.199 1396 Planarity : 0.004 0.053 1546 Dihedral : 4.696 34.751 1236 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.07 % Allowed : 18.31 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.24), residues: 1126 helix: -0.10 (0.27), residues: 394 sheet: -1.32 (0.28), residues: 275 loop : -1.34 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 219 TYR 0.035 0.001 TYR B 315 PHE 0.012 0.001 PHE D 151 TRP 0.011 0.001 TRP E 47 HIS 0.004 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 8984) covalent geometry : angle 0.57674 (12223) hydrogen bonds : bond 0.03653 ( 355) hydrogen bonds : angle 4.44530 ( 996) *********************** 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 239 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 211 time to evaluate : 0.258 Fit side-chains REVERT: B 129 PHE cc_start: 0.7628 (t80) cc_final: 0.7415 (t80) REVERT: B 147 LEU cc_start: 0.6196 (OUTLIER) cc_final: 0.5334 (mt) REVERT: B 210 LEU cc_start: 0.8433 (mt) cc_final: 0.8175 (mt) REVERT: B 294 LYS cc_start: 0.8377 (mtpt) cc_final: 0.8046 (mtpt) REVERT: D 34 THR cc_start: 0.8264 (m) cc_final: 0.7877 (p) REVERT: D 46 ARG cc_start: 0.7886 (mpp-170) cc_final: 0.7565 (mpp-170) REVERT: D 86 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8055 (p) REVERT: D 147 SER cc_start: 0.8357 (m) cc_final: 0.8012 (p) REVERT: D 228 ASP cc_start: 0.7879 (m-30) cc_final: 0.7549 (p0) REVERT: D 322 ASP cc_start: 0.7769 (m-30) cc_final: 0.7501 (m-30) REVERT: E 4 LEU cc_start: 0.7821 (mt) cc_final: 0.7319 (mt) REVERT: E 7 SER cc_start: 0.8268 (OUTLIER) cc_final: 0.7897 (p) REVERT: E 59 TYR cc_start: 0.7751 (m-10) cc_final: 0.7540 (m-10) REVERT: E 67 ARG cc_start: 0.8839 (mtm110) cc_final: 0.8433 (mtp180) REVERT: E 83 MET cc_start: 0.8313 (mtt) cc_final: 0.8048 (mtt) REVERT: E 99 SER cc_start: 0.8417 (m) cc_final: 0.8162 (p) REVERT: E 166 LEU cc_start: 0.8505 (tp) cc_final: 0.8143 (tt) REVERT: G 58 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7194 (pm20) REVERT: C 17 LYS cc_start: 0.8148 (mtmt) cc_final: 0.7942 (mtmt) REVERT: C 32 ARG cc_start: 0.8031 (tpp-160) cc_final: 0.7785 (ttm-80) REVERT: C 232 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7830 (ptp-110) REVERT: C 241 ASP cc_start: 0.8157 (t0) cc_final: 0.7716 (t0) REVERT: C 266 GLU cc_start: 0.7817 (pp20) cc_final: 0.7396 (pp20) REVERT: C 267 LYS cc_start: 0.8383 (ttmm) cc_final: 0.7995 (ttmt) REVERT: C 314 ASP cc_start: 0.7450 (m-30) cc_final: 0.6905 (m-30) REVERT: C 352 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7572 (mp-120) outliers start: 28 outliers final: 17 residues processed: 225 average time/residue: 0.4107 time to fit residues: 99.5882 Evaluate side-chains 233 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 VAL 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 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 7 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 232 ARG 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 352 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 15 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 0.1980 chunk 83 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 ASN D 32 GLN D 220 GLN D 239 ASN C 238 ASN C 352 GLN 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 = 0.3617 r_free = 0.3617 target = 0.124787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.111400 restraints weight = 12895.772| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.96 r_work: 0.3322 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8984 Z= 0.148 Angle : 0.575 8.245 12223 Z= 0.300 Chirality : 0.044 0.196 1396 Planarity : 0.004 0.052 1546 Dihedral : 4.638 33.382 1236 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.07 % Allowed : 19.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.25), residues: 1126 helix: 0.08 (0.27), residues: 394 sheet: -1.31 (0.28), residues: 281 loop : -1.20 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 219 TYR 0.035 0.001 TYR B 315 PHE 0.014 0.001 PHE B 163 TRP 0.012 0.001 TRP C 248 HIS 0.004 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8984) covalent geometry : angle 0.57507 (12223) hydrogen bonds : bond 0.03596 ( 355) hydrogen bonds : angle 4.39064 ( 996) *********************** 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 237 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 209 time to evaluate : 0.378 Fit side-chains REVERT: B 129 PHE cc_start: 0.7630 (t80) cc_final: 0.7404 (t80) REVERT: B 147 LEU cc_start: 0.6051 (OUTLIER) cc_final: 0.5173 (mt) REVERT: B 210 LEU cc_start: 0.8435 (mt) cc_final: 0.8177 (mt) REVERT: B 294 LYS cc_start: 0.8339 (mtpt) cc_final: 0.8052 (mtpt) REVERT: D 34 THR cc_start: 0.8281 (m) cc_final: 0.7919 (p) REVERT: D 46 ARG cc_start: 0.7883 (mpp-170) cc_final: 0.7555 (mpp-170) REVERT: D 70 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8242 (pt) REVERT: D 86 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.8037 (p) REVERT: D 147 SER cc_start: 0.8364 (m) cc_final: 0.7944 (p) REVERT: D 228 ASP cc_start: 0.7887 (m-30) cc_final: 0.7548 (p0) REVERT: D 314 ARG cc_start: 0.7979 (ttt180) cc_final: 0.7595 (ttt180) REVERT: D 322 ASP cc_start: 0.7765 (m-30) cc_final: 0.7485 (m-30) REVERT: E 7 SER cc_start: 0.8230 (OUTLIER) cc_final: 0.8014 (p) REVERT: E 59 TYR cc_start: 0.7737 (m-10) cc_final: 0.7503 (m-10) REVERT: E 67 ARG cc_start: 0.8838 (mtm110) cc_final: 0.8434 (mtp180) REVERT: E 83 MET cc_start: 0.8316 (mtt) cc_final: 0.8035 (mtt) REVERT: E 99 SER cc_start: 0.8411 (m) cc_final: 0.8166 (p) REVERT: E 166 LEU cc_start: 0.8472 (tp) cc_final: 0.8123 (tt) REVERT: G 58 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7191 (pm20) REVERT: C 17 LYS cc_start: 0.8072 (mtmt) cc_final: 0.7860 (mtmt) REVERT: C 21 LYS cc_start: 0.8453 (mtpp) cc_final: 0.8246 (mtpp) REVERT: C 32 ARG cc_start: 0.8002 (tpp-160) cc_final: 0.7758 (ttm-80) REVERT: C 188 LYS cc_start: 0.8502 (mppt) cc_final: 0.8288 (mppt) REVERT: C 232 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7841 (ptp-110) REVERT: C 241 ASP cc_start: 0.8099 (t0) cc_final: 0.7707 (t0) REVERT: C 266 GLU cc_start: 0.7816 (pp20) cc_final: 0.7406 (pp20) REVERT: C 267 LYS cc_start: 0.8388 (ttmm) cc_final: 0.7999 (ttmt) REVERT: C 314 ASP cc_start: 0.7431 (m-30) cc_final: 0.6890 (m-30) outliers start: 28 outliers final: 17 residues processed: 224 average time/residue: 0.4332 time to fit residues: 104.3604 Evaluate side-chains 230 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 207 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 THR 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 7 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 232 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 42 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 60 optimal weight: 0.0770 chunk 107 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 52 optimal weight: 0.4980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 ASN D 32 GLN D 220 GLN D 239 ASN C 238 ASN C 352 GLN 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 = 0.3619 r_free = 0.3619 target = 0.124941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.111610 restraints weight = 12860.696| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.96 r_work: 0.3325 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2631 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= 0.148 Angle : 0.581 8.140 12223 Z= 0.302 Chirality : 0.044 0.197 1396 Planarity : 0.004 0.053 1546 Dihedral : 4.558 32.679 1236 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.07 % Allowed : 20.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.25), residues: 1126 helix: 0.22 (0.27), residues: 395 sheet: -1.24 (0.29), residues: 281 loop : -1.13 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 219 TYR 0.035 0.001 TYR B 315 PHE 0.012 0.001 PHE D 151 TRP 0.010 0.001 TRP E 47 HIS 0.004 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 8984) covalent geometry : angle 0.58085 (12223) hydrogen bonds : bond 0.03584 ( 355) hydrogen bonds : angle 4.37653 ( 996) *********************** 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 238 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 0.291 Fit side-chains REVERT: B 129 PHE cc_start: 0.7609 (t80) cc_final: 0.7400 (t80) REVERT: B 147 LEU cc_start: 0.5920 (OUTLIER) cc_final: 0.5045 (mt) REVERT: B 210 LEU cc_start: 0.8449 (mt) cc_final: 0.8182 (mt) REVERT: B 294 LYS cc_start: 0.8318 (mtpt) cc_final: 0.8013 (mtpt) REVERT: D 44 GLN cc_start: 0.8032 (mt0) cc_final: 0.7513 (mt0) REVERT: D 46 ARG cc_start: 0.7871 (mpp-170) cc_final: 0.7558 (mpp-170) REVERT: D 86 THR cc_start: 0.8356 (OUTLIER) cc_final: 0.8040 (p) REVERT: D 147 SER cc_start: 0.8358 (m) cc_final: 0.7944 (p) REVERT: D 228 ASP cc_start: 0.7886 (m-30) cc_final: 0.7513 (p0) REVERT: D 322 ASP cc_start: 0.7766 (m-30) cc_final: 0.7492 (m-30) REVERT: E 7 SER cc_start: 0.8260 (OUTLIER) cc_final: 0.7911 (p) REVERT: E 67 ARG cc_start: 0.8836 (mtm110) cc_final: 0.8441 (mtp180) REVERT: E 83 MET cc_start: 0.8384 (mtt) cc_final: 0.8121 (mtt) REVERT: E 99 SER cc_start: 0.8413 (m) cc_final: 0.8176 (p) REVERT: E 166 LEU cc_start: 0.8468 (tp) cc_final: 0.8125 (tt) REVERT: G 58 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7174 (pm20) REVERT: C 17 LYS cc_start: 0.8053 (mtmt) cc_final: 0.7837 (mtmt) REVERT: C 21 LYS cc_start: 0.8463 (mtpp) cc_final: 0.8259 (ttmm) REVERT: C 32 ARG cc_start: 0.7990 (tpp-160) cc_final: 0.7772 (ttm-80) REVERT: C 188 LYS cc_start: 0.8511 (mppt) cc_final: 0.8293 (mppt) REVERT: C 241 ASP cc_start: 0.8052 (t0) cc_final: 0.7719 (t0) REVERT: C 266 GLU cc_start: 0.7811 (pp20) cc_final: 0.7412 (pp20) REVERT: C 267 LYS cc_start: 0.8404 (ttmm) cc_final: 0.8008 (ttmt) REVERT: C 314 ASP cc_start: 0.7452 (m-30) cc_final: 0.6922 (m-30) REVERT: C 348 ASP cc_start: 0.8193 (t0) cc_final: 0.7681 (t0) REVERT: C 352 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.7625 (mp-120) outliers start: 28 outliers final: 20 residues processed: 224 average time/residue: 0.4094 time to fit residues: 98.7683 Evaluate side-chains 233 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 THR 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 263 THR Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain E residue 7 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 277 ASP Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 352 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 38 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 238 ASN C 245 ASN C 352 GLN 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 = 0.3609 r_free = 0.3609 target = 0.124265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.110894 restraints weight = 12806.532| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.95 r_work: 0.3317 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8984 Z= 0.191 Angle : 0.613 8.545 12223 Z= 0.318 Chirality : 0.046 0.197 1396 Planarity : 0.004 0.052 1546 Dihedral : 4.670 32.613 1236 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.96 % Allowed : 20.61 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.25), residues: 1126 helix: 0.21 (0.27), residues: 395 sheet: -1.31 (0.29), residues: 277 loop : -1.13 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 251 TYR 0.038 0.002 TYR B 315 PHE 0.014 0.002 PHE D 151 TRP 0.011 0.002 TRP C 248 HIS 0.005 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 8984) covalent geometry : angle 0.61294 (12223) hydrogen bonds : bond 0.03760 ( 355) hydrogen bonds : angle 4.41453 ( 996) ********************** 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 239 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 0.281 Fit side-chains REVERT: B 129 PHE cc_start: 0.7625 (t80) cc_final: 0.7414 (t80) REVERT: B 147 LEU cc_start: 0.6021 (OUTLIER) cc_final: 0.5066 (mt) REVERT: B 210 LEU cc_start: 0.8439 (mt) cc_final: 0.8181 (mt) REVERT: B 294 LYS cc_start: 0.8385 (mtpt) cc_final: 0.8065 (mtpt) REVERT: D 34 THR cc_start: 0.8232 (m) cc_final: 0.7893 (p) REVERT: D 46 ARG cc_start: 0.7884 (mpp-170) cc_final: 0.7582 (mpp-170) REVERT: D 147 SER cc_start: 0.8368 (m) cc_final: 0.7943 (p) REVERT: D 228 ASP cc_start: 0.7895 (m-30) cc_final: 0.7580 (p0) REVERT: D 322 ASP cc_start: 0.7768 (m-30) cc_final: 0.7493 (m-30) REVERT: E 7 SER cc_start: 0.8266 (OUTLIER) cc_final: 0.7920 (p) REVERT: E 67 ARG cc_start: 0.8843 (mtm110) cc_final: 0.8446 (mtp180) REVERT: E 83 MET cc_start: 0.8387 (mtt) cc_final: 0.8136 (mtt) REVERT: E 99 SER cc_start: 0.8426 (m) cc_final: 0.8182 (p) REVERT: E 166 LEU cc_start: 0.8470 (tp) cc_final: 0.8128 (tt) REVERT: G 58 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7169 (pm20) REVERT: C 17 LYS cc_start: 0.8047 (mtmt) cc_final: 0.7846 (mtmt) REVERT: C 21 LYS cc_start: 0.8460 (mtpp) cc_final: 0.8247 (mtpp) REVERT: C 32 ARG cc_start: 0.8019 (tpp-160) cc_final: 0.7717 (ttm-80) REVERT: C 266 GLU cc_start: 0.7830 (pp20) cc_final: 0.7435 (pp20) REVERT: C 267 LYS cc_start: 0.8398 (ttmm) cc_final: 0.7993 (ttmt) REVERT: C 314 ASP cc_start: 0.7438 (m-30) cc_final: 0.6908 (m-30) outliers start: 27 outliers final: 19 residues processed: 227 average time/residue: 0.4278 time to fit residues: 104.5545 Evaluate side-chains 232 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 THR 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 7 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 9 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 107 optimal weight: 0.3980 chunk 64 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 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 E 77 ASN C 238 ASN C 354 ASN C 359 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.124782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.111464 restraints weight = 12744.772| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.96 r_work: 0.3323 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8984 Z= 0.161 Angle : 0.599 8.528 12223 Z= 0.310 Chirality : 0.045 0.199 1396 Planarity : 0.004 0.052 1546 Dihedral : 4.635 32.360 1236 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.96 % Allowed : 20.72 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.25), residues: 1126 helix: 0.35 (0.27), residues: 397 sheet: -1.26 (0.29), residues: 278 loop : -1.12 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 219 TYR 0.037 0.001 TYR B 315 PHE 0.013 0.001 PHE C 189 TRP 0.011 0.001 TRP B 151 HIS 0.004 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 8984) covalent geometry : angle 0.59861 (12223) hydrogen bonds : bond 0.03614 ( 355) hydrogen bonds : angle 4.37624 ( 996) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2834.54 seconds wall clock time: 48 minutes 55.10 seconds (2935.10 seconds total)