Starting phenix.real_space_refine on Sat Apr 6 19:21:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jbf_36144/04_2024/8jbf_36144.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jbf_36144/04_2024/8jbf_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jbf_36144/04_2024/8jbf_36144.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jbf_36144/04_2024/8jbf_36144.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jbf_36144/04_2024/8jbf_36144.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jbf_36144/04_2024/8jbf_36144.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 37 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5622 2.51 5 N 1489 2.21 5 O 1615 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 66": "OD1" <-> "OD2" Residue "D TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 154": "OD1" <-> "OD2" Residue "D ASP 205": "OD1" <-> "OD2" Residue "D ASP 228": "OD1" <-> "OD2" Residue "D PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 298": "OD1" <-> "OD2" Residue "D ASP 312": "OD1" <-> "OD2" Residue "D PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "A PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 9": "OD1" <-> "OD2" Residue "C ASP 26": "OD1" <-> "OD2" Residue "C ASP 42": "OD1" <-> "OD2" Residue "C ASP 200": "OD1" <-> "OD2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 226": "OD1" <-> "OD2" Residue "C ASP 229": "OD1" <-> "OD2" Residue "C ASP 239": "OD1" <-> "OD2" Residue "C PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C ASP 298": "OD1" <-> "OD2" Residue "C TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8784 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2194 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 11, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 67 Chain: "D" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2542 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "E" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1751 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "G" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 406 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 58 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1833 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Time building chain proxies: 4.98, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 3.28 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.00 Creating SS restraints... Processing helix chain 'B' and resid 81 through 100 removed outlier: 3.599A pdb=" N ALA B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 87 " --> pdb=" O TRP B 83 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 121 through 137 Processing helix chain 'B' and resid 140 through 145 removed outlier: 3.679A pdb=" N ILE B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 162 removed outlier: 3.649A pdb=" N PHE B 160 " --> pdb=" O ASN B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 186 removed outlier: 3.650A pdb=" N VAL B 169 " --> pdb=" O PRO B 165 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET B 176 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 220 removed outlier: 3.815A pdb=" N LYS B 201 " --> pdb=" O ALA B 197 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER B 206 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Proline residue: B 217 - end of helix Processing helix chain 'B' and resid 240 through 248 removed outlier: 3.938A pdb=" N THR B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS B 248 " --> pdb=" O HIS B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 253 removed outlier: 3.646A pdb=" N ILE B 252 " --> pdb=" O HIS B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 276 removed outlier: 3.570A pdb=" N TYR B 267 " --> pdb=" O MET B 263 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR B 268 " --> pdb=" O GLY B 264 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TRP B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY B 276 " --> pdb=" O ILE B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 295 Processing helix chain 'B' and resid 296 through 307 removed outlier: 3.583A pdb=" N VAL B 305 " --> pdb=" O MET B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 324 Processing helix chain 'B' and resid 325 through 332 removed outlier: 3.839A pdb=" N ARG B 330 " --> pdb=" O GLN B 327 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP B 331 " --> pdb=" O LEU B 328 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS B 332 " --> pdb=" O ASN B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 348 removed outlier: 3.539A pdb=" N ALA B 345 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 360 removed outlier: 3.756A pdb=" N ILE B 354 " --> pdb=" O MET B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 369 removed outlier: 3.614A pdb=" N ARG B 364 " --> pdb=" O ASN B 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 24 removed outlier: 3.845A pdb=" N GLU D 10 " --> pdb=" O GLN D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.928A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.802A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 19 removed outlier: 3.686A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.731A pdb=" N TYR G 40 " --> pdb=" O ASP G 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 26 removed outlier: 3.803A pdb=" N LYS C 21 " --> pdb=" O LYS C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 32 Processing helix chain 'C' and resid 45 through 50 removed outlier: 3.842A pdb=" N VAL C 50 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 214 removed outlier: 3.677A pdb=" N GLN C 213 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 245 removed outlier: 3.513A pdb=" N ALA C 236 " --> pdb=" O ARG C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 269 removed outlier: 3.819A pdb=" N LYS C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 279 removed outlier: 4.545A pdb=" N TYR C 278 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 removed outlier: 4.213A pdb=" N ALA C 283 " --> pdb=" O PRO C 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 280 through 283' Processing helix chain 'C' and resid 298 through 319 removed outlier: 3.694A pdb=" N THR C 302 " --> pdb=" O ASP C 298 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE C 307 " --> pdb=" O ARG C 303 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER C 316 " --> pdb=" O PHE C 312 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA C 318 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 358 Processing sheet with id=AA1, first strand: chain 'B' and resid 223 through 224 removed outlier: 3.884A pdb=" N VAL B 235 " --> pdb=" O LYS B 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 47 through 51 removed outlier: 6.542A pdb=" N ILE D 338 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR D 50 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU D 336 " --> pdb=" O THR D 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 58 through 63 removed outlier: 3.615A pdb=" N ALA D 60 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER D 74 " --> pdb=" O LYS D 78 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU D 79 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA D 92 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE D 81 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 100 through 105 removed outlier: 6.722A pdb=" N GLY D 115 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N CYS D 103 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA D 113 " --> pdb=" O CYS D 103 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N TYR D 105 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N TYR D 111 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY D 116 " --> pdb=" O ILE D 120 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ILE D 120 " --> pdb=" O GLY D 116 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG D 137 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 146 through 153 removed outlier: 6.816A pdb=" N GLN D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE D 157 " --> pdb=" O TRP D 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 187 through 192 removed outlier: 3.537A pdb=" N GLN D 220 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASP D 212 " --> pdb=" O CYS D 218 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N CYS D 218 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 229 through 234 removed outlier: 3.546A pdb=" N SER D 245 " --> pdb=" O THR D 249 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N CYS D 250 " --> pdb=" O THR D 263 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR D 263 " --> pdb=" O CYS D 250 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU D 252 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN D 259 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 273 through 278 removed outlier: 3.546A pdb=" N SER D 275 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY D 306 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASP D 298 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG D 304 " --> pdb=" O ASP D 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.569A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG E 18 " --> pdb=" O MET E 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.540A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 92 through 94 Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 Processing sheet with id=AB4, first strand: chain 'E' and resid 155 through 160 removed outlier: 3.559A pdb=" N THR E 215 " --> pdb=" O SER E 204 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 194 through 195 removed outlier: 5.704A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 184 through 191 removed outlier: 4.253A pdb=" N VAL C 201 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N GLY C 40 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA C 220 " --> pdb=" O ARG C 35 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE C 221 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N PHE C 257 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE C 223 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASN C 259 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL C 225 " --> pdb=" O ASN C 259 " (cutoff:3.500A) 355 hydrogen bonds defined for protein. 996 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.50 Time building geometry restraints manager: 3.59 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: 99.72 - 107.39: 324 107.39 - 115.05: 5210 115.05 - 122.72: 5729 122.72 - 130.39: 909 130.39 - 138.06: 51 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 2.440 nonbonded pdb=" OH TYR B 92 " pdb=" O LEU B 339 " model vdw 2.224 2.440 nonbonded pdb=" OG1 THR D 274 " pdb=" O VAL D 315 " model vdw 2.296 2.440 nonbonded pdb=" O VAL C 29 " pdb=" OG1 THR C 33 " model vdw 2.303 2.440 nonbonded pdb=" O SER D 67 " pdb=" OG SER D 67 " model vdw 2.307 2.440 ... (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 ========== 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 3.890 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.080 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:11.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.010 ------------------------------------------------------------------------------- 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= 0.466 Angle : 0.864 16.646 12223 Z= 0.465 Chirality : 0.058 0.309 1396 Planarity : 0.007 0.070 1546 Dihedral : 12.834 89.951 3108 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.22 % Allowed : 5.26 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.19 (0.18), residues: 1126 helix: -4.74 (0.09), residues: 378 sheet: -2.56 (0.28), residues: 257 loop : -2.62 (0.23), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 47 HIS 0.008 0.002 HIS C 324 PHE 0.023 0.002 PHE D 151 TYR 0.048 0.003 TYR B 92 ARG 0.008 0.001 ARG C 209 *********************** 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 fitting. rotamer outliers: 2 poor density : 223 time to evaluate : 0.929 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: 0.9596 time to fit residues: 233.1862 Evaluate side-chains 206 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 0.3980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 HIS B 142 ASN D 32 GLN D 176 GLN D 220 GLN D 239 ASN D 340 ASN E 3 GLN E 142 GLN E 179 GLN C 28 GLN ** C 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN C 245 ASN C 246 ASN C 338 ASN C 352 GLN C 354 ASN C 359 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1439 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= 0.232 Angle : 0.593 9.864 12223 Z= 0.314 Chirality : 0.044 0.233 1396 Planarity : 0.005 0.056 1546 Dihedral : 5.185 41.203 1236 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.85 % Allowed : 10.75 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.21), residues: 1126 helix: -2.76 (0.20), residues: 387 sheet: -2.09 (0.28), residues: 260 loop : -1.98 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 47 HIS 0.004 0.001 HIS C 197 PHE 0.013 0.001 PHE B 367 TYR 0.039 0.002 TYR E 235 ARG 0.009 0.000 ARG D 49 *********************** 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 245 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 219 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: B 100 VAL cc_start: 0.7900 (m) cc_final: 0.7478 (t) REVERT: B 153 PHE cc_start: 0.7955 (m-80) cc_final: 0.7681 (m-80) REVERT: B 210 LEU cc_start: 0.8119 (mt) cc_final: 0.7867 (mt) REVERT: B 294 LYS cc_start: 0.8079 (mtpt) cc_final: 0.7842 (mtpt) REVERT: D 14 LEU cc_start: 0.7952 (mt) cc_final: 0.7678 (mp) REVERT: D 37 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8125 (mt) REVERT: E 4 LEU cc_start: 0.7552 (mt) cc_final: 0.7257 (mt) REVERT: E 59 TYR cc_start: 0.7015 (m-10) cc_final: 0.6721 (m-10) REVERT: E 67 ARG cc_start: 0.8754 (mtm110) cc_final: 0.8496 (mtm-85) REVERT: E 83 MET cc_start: 0.8170 (mtt) cc_final: 0.7928 (mtt) REVERT: E 93 MET cc_start: 0.7679 (ttp) cc_final: 0.7469 (ttp) REVERT: E 140 MET cc_start: 0.8282 (mmm) cc_final: 0.8060 (mmt) REVERT: E 166 LEU cc_start: 0.8250 (tp) cc_final: 0.7902 (tt) REVERT: E 173 TYR cc_start: 0.8331 (m-10) cc_final: 0.7844 (m-80) REVERT: E 190 TYR cc_start: 0.8245 (p90) cc_final: 0.8013 (p90) REVERT: C 15 ARG cc_start: 0.8320 (ttt90) cc_final: 0.8040 (ttt180) REVERT: C 17 LYS cc_start: 0.7774 (mtmt) cc_final: 0.7548 (mtmt) REVERT: C 251 THR cc_start: 0.7952 (OUTLIER) cc_final: 0.7711 (m) REVERT: C 267 LYS cc_start: 0.8217 (ttmm) cc_final: 0.7930 (ttmt) REVERT: C 340 ARG cc_start: 0.7672 (tpp-160) cc_final: 0.7166 (mmt180) REVERT: C 345 ASP cc_start: 0.7605 (m-30) cc_final: 0.7397 (m-30) outliers start: 26 outliers final: 8 residues processed: 229 average time/residue: 1.0699 time to fit residues: 263.3639 Evaluate side-chains 206 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 196 time to evaluate : 1.359 ------------------------------------------------------------------------------- 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 130 ASP Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 251 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 0.0970 chunk 68 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 0.0870 chunk 99 optimal weight: 0.7980 overall best weight: 0.5156 ------------------------------------------------------------------------------- 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 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 GLN D 239 ASN E 167 HIS E 194 ASN ** C 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN C 245 ASN C 246 ASN C 352 GLN C 354 ASN C 359 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8984 Z= 0.194 Angle : 0.551 8.729 12223 Z= 0.289 Chirality : 0.042 0.204 1396 Planarity : 0.004 0.057 1546 Dihedral : 4.794 39.624 1236 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.96 % Allowed : 13.60 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.23), residues: 1126 helix: -1.42 (0.25), residues: 388 sheet: -1.73 (0.29), residues: 248 loop : -1.72 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 211 HIS 0.009 0.001 HIS E 167 PHE 0.022 0.001 PHE B 245 TYR 0.032 0.001 TYR B 315 ARG 0.006 0.000 ARG D 49 *********************** 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 fitting. rotamer outliers: 27 poor density : 210 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: B 87 LEU cc_start: 0.8463 (mt) cc_final: 0.8201 (mm) REVERT: B 100 VAL cc_start: 0.7829 (m) cc_final: 0.7412 (t) REVERT: B 210 LEU cc_start: 0.8126 (mt) cc_final: 0.7880 (mt) REVERT: B 294 LYS cc_start: 0.8031 (mtpt) cc_final: 0.7824 (mtpt) REVERT: D 37 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8221 (mt) REVERT: E 59 TYR cc_start: 0.7066 (m-10) cc_final: 0.6836 (m-10) REVERT: E 67 ARG cc_start: 0.8722 (mtm110) cc_final: 0.8433 (mtp180) REVERT: E 83 MET cc_start: 0.8122 (mtt) cc_final: 0.7907 (mtt) REVERT: E 93 MET cc_start: 0.7686 (ttp) cc_final: 0.7481 (ttp) REVERT: E 166 LEU cc_start: 0.8233 (tp) cc_final: 0.7880 (tt) REVERT: E 173 TYR cc_start: 0.8244 (m-10) cc_final: 0.7639 (m-80) REVERT: E 190 TYR cc_start: 0.8318 (p90) cc_final: 0.8116 (p90) REVERT: E 192 MET cc_start: 0.7832 (ttp) cc_final: 0.7611 (tmm) REVERT: C 17 LYS cc_start: 0.7709 (mtmt) cc_final: 0.7489 (mtmt) REVERT: C 267 LYS cc_start: 0.8211 (ttmm) cc_final: 0.7968 (ttmt) REVERT: C 314 ASP cc_start: 0.6849 (m-30) cc_final: 0.6367 (m-30) REVERT: C 340 ARG cc_start: 0.7696 (tpp-160) cc_final: 0.7460 (mmp80) REVERT: C 352 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7232 (mp-120) outliers start: 27 outliers final: 14 residues processed: 223 average time/residue: 1.0110 time to fit residues: 242.9660 Evaluate side-chains 214 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 198 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain 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 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 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 352 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.8980 chunk 52 optimal weight: 0.0060 chunk 11 optimal weight: 0.0170 chunk 48 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 101 optimal weight: 0.0770 chunk 107 optimal weight: 0.6980 chunk 96 optimal weight: 0.0270 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 0.4980 chunk 60 optimal weight: 0.8980 overall best weight: 0.1250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 ASN B 218 GLN D 119 ASN D 220 GLN D 239 ASN C 204 GLN C 216 ASN C 238 ASN C 245 ASN C 352 GLN C 359 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8984 Z= 0.122 Angle : 0.504 7.464 12223 Z= 0.263 Chirality : 0.041 0.167 1396 Planarity : 0.004 0.056 1546 Dihedral : 4.368 33.507 1236 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.74 % Allowed : 15.68 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.24), residues: 1126 helix: -0.65 (0.27), residues: 392 sheet: -1.48 (0.28), residues: 281 loop : -1.47 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 211 HIS 0.003 0.000 HIS C 324 PHE 0.010 0.001 PHE B 78 TYR 0.031 0.001 TYR B 315 ARG 0.007 0.000 ARG D 219 *********************** 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 236 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 211 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: B 92 TYR cc_start: 0.7510 (m-80) cc_final: 0.7242 (m-80) REVERT: B 98 VAL cc_start: 0.7235 (p) cc_final: 0.6906 (p) REVERT: B 147 LEU cc_start: 0.5875 (OUTLIER) cc_final: 0.5258 (mt) REVERT: B 210 LEU cc_start: 0.8129 (mt) cc_final: 0.7865 (mt) REVERT: D 34 THR cc_start: 0.8288 (m) cc_final: 0.7983 (p) REVERT: D 37 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8227 (mt) REVERT: E 67 ARG cc_start: 0.8709 (mtm110) cc_final: 0.8429 (mtp180) REVERT: E 83 MET cc_start: 0.8073 (mtt) cc_final: 0.7855 (mtt) REVERT: E 93 MET cc_start: 0.7626 (ttp) cc_final: 0.7415 (ttp) REVERT: E 166 LEU cc_start: 0.8278 (tp) cc_final: 0.7907 (tt) REVERT: E 173 TYR cc_start: 0.8219 (m-10) cc_final: 0.7669 (m-80) REVERT: C 17 LYS cc_start: 0.7590 (mtmt) cc_final: 0.7357 (mtmt) REVERT: C 192 ASP cc_start: 0.7415 (m-30) cc_final: 0.7121 (m-30) REVERT: C 194 VAL cc_start: 0.7862 (t) cc_final: 0.7332 (p) REVERT: C 241 ASP cc_start: 0.7824 (t0) cc_final: 0.7117 (t0) REVERT: C 245 ASN cc_start: 0.7874 (m-40) cc_final: 0.7668 (m-40) REVERT: C 267 LYS cc_start: 0.8179 (ttmm) cc_final: 0.7938 (ttmt) REVERT: C 314 ASP cc_start: 0.6799 (m-30) cc_final: 0.6361 (m-30) REVERT: C 340 ARG cc_start: 0.7639 (tpp-160) cc_final: 0.7251 (mmt180) outliers start: 25 outliers final: 10 residues processed: 220 average time/residue: 0.9314 time to fit residues: 222.0344 Evaluate side-chains 208 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 196 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 262 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 0.0070 chunk 44 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 27 optimal weight: 0.0670 chunk 36 optimal weight: 0.4980 chunk 21 optimal weight: 0.0980 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 ASN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 ASN C 238 ASN C 246 ASN C 359 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2517 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= 0.143 Angle : 0.517 6.856 12223 Z= 0.268 Chirality : 0.041 0.164 1396 Planarity : 0.004 0.054 1546 Dihedral : 4.227 31.998 1236 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.85 % Allowed : 17.43 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.25), residues: 1126 helix: -0.16 (0.27), residues: 393 sheet: -1.25 (0.28), residues: 283 loop : -1.28 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 248 HIS 0.003 0.001 HIS C 324 PHE 0.011 0.001 PHE C 189 TYR 0.026 0.001 TYR E 235 ARG 0.009 0.000 ARG C 32 *********************** 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 234 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 208 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: B 147 LEU cc_start: 0.5521 (OUTLIER) cc_final: 0.4871 (mt) REVERT: B 210 LEU cc_start: 0.8124 (mt) cc_final: 0.7876 (mt) REVERT: B 315 TYR cc_start: 0.7788 (t80) cc_final: 0.7243 (t80) REVERT: D 34 THR cc_start: 0.8277 (m) cc_final: 0.8051 (p) REVERT: D 37 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.7896 (mt) REVERT: E 67 ARG cc_start: 0.8706 (mtm110) cc_final: 0.8424 (mtp180) REVERT: E 83 MET cc_start: 0.8146 (mtt) cc_final: 0.7906 (mtt) REVERT: E 140 MET cc_start: 0.8580 (mmm) cc_final: 0.8101 (mmt) REVERT: E 173 TYR cc_start: 0.8304 (m-10) cc_final: 0.7709 (m-80) REVERT: C 241 ASP cc_start: 0.7604 (t0) cc_final: 0.6848 (t0) REVERT: C 245 ASN cc_start: 0.7862 (m-40) cc_final: 0.7622 (m-40) REVERT: C 267 LYS cc_start: 0.8183 (ttmm) cc_final: 0.7942 (ttmt) REVERT: C 314 ASP cc_start: 0.6796 (m-30) cc_final: 0.6375 (m-30) REVERT: C 340 ARG cc_start: 0.7674 (tpp-160) cc_final: 0.7287 (mmt180) outliers start: 26 outliers final: 13 residues processed: 219 average time/residue: 0.9466 time to fit residues: 224.9340 Evaluate side-chains 214 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 199 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 LEU 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 112 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 277 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 0.0970 chunk 56 optimal weight: 0.9980 chunk 103 optimal weight: 0.1980 chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 ASN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN D 239 ASN C 216 ASN C 238 ASN C 359 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8984 Z= 0.181 Angle : 0.530 7.535 12223 Z= 0.274 Chirality : 0.042 0.170 1396 Planarity : 0.004 0.054 1546 Dihedral : 4.309 31.011 1236 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.07 % Allowed : 18.97 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.25), residues: 1126 helix: 0.11 (0.27), residues: 395 sheet: -1.04 (0.29), residues: 281 loop : -1.23 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 47 HIS 0.003 0.001 HIS C 324 PHE 0.026 0.001 PHE B 245 TYR 0.026 0.001 TYR E 235 ARG 0.007 0.000 ARG D 219 *********************** 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 238 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 210 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: B 92 TYR cc_start: 0.7707 (m-80) cc_final: 0.7406 (m-80) REVERT: B 147 LEU cc_start: 0.5321 (OUTLIER) cc_final: 0.4647 (mt) REVERT: B 210 LEU cc_start: 0.8147 (mt) cc_final: 0.7903 (mt) REVERT: B 268 THR cc_start: 0.8211 (p) cc_final: 0.7977 (t) REVERT: B 315 TYR cc_start: 0.7778 (t80) cc_final: 0.7411 (t80) REVERT: D 34 THR cc_start: 0.8260 (m) cc_final: 0.8030 (p) REVERT: E 7 SER cc_start: 0.7905 (t) cc_final: 0.7697 (p) REVERT: E 67 ARG cc_start: 0.8703 (mtm110) cc_final: 0.8414 (mtp180) REVERT: E 83 MET cc_start: 0.8143 (mtt) cc_final: 0.7890 (mtt) REVERT: E 140 MET cc_start: 0.8590 (mmm) cc_final: 0.8135 (mmt) REVERT: E 166 LEU cc_start: 0.8312 (tp) cc_final: 0.7931 (tt) REVERT: E 173 TYR cc_start: 0.8227 (m-10) cc_final: 0.8026 (m-80) REVERT: E 192 MET cc_start: 0.7786 (ttp) cc_final: 0.7577 (tmm) REVERT: C 241 ASP cc_start: 0.7627 (t0) cc_final: 0.6874 (t0) REVERT: C 245 ASN cc_start: 0.7830 (m-40) cc_final: 0.7603 (m-40) REVERT: C 266 GLU cc_start: 0.7341 (pp20) cc_final: 0.6983 (pp20) REVERT: C 267 LYS cc_start: 0.8152 (ttmm) cc_final: 0.7619 (ttmt) REVERT: C 314 ASP cc_start: 0.6838 (m-30) cc_final: 0.6429 (m-30) REVERT: C 340 ARG cc_start: 0.7690 (tpp-160) cc_final: 0.7464 (mmp80) outliers start: 28 outliers final: 15 residues processed: 227 average time/residue: 0.9538 time to fit residues: 234.2888 Evaluate side-chains 221 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 205 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 LEU 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 112 VAL 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 E residue 118 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 325 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 ASN B 161 GLN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 ASN C 216 ASN C 238 ASN C 354 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8984 Z= 0.243 Angle : 0.564 8.200 12223 Z= 0.291 Chirality : 0.044 0.182 1396 Planarity : 0.004 0.054 1546 Dihedral : 4.508 32.493 1236 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.74 % Allowed : 20.29 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.25), residues: 1126 helix: 0.26 (0.28), residues: 395 sheet: -0.91 (0.30), residues: 269 loop : -1.15 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 47 HIS 0.004 0.001 HIS B 248 PHE 0.011 0.001 PHE D 234 TYR 0.027 0.002 TYR E 235 ARG 0.006 0.000 ARG D 219 *********************** 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 228 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 203 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: B 92 TYR cc_start: 0.7808 (m-80) cc_final: 0.7502 (m-80) REVERT: B 147 LEU cc_start: 0.5538 (OUTLIER) cc_final: 0.4850 (mt) REVERT: B 210 LEU cc_start: 0.8169 (mt) cc_final: 0.7938 (mt) REVERT: E 67 ARG cc_start: 0.8706 (mtm110) cc_final: 0.8403 (mtp180) REVERT: E 83 MET cc_start: 0.8148 (mtt) cc_final: 0.7905 (mtt) REVERT: E 140 MET cc_start: 0.8591 (mmm) cc_final: 0.8167 (mmt) REVERT: E 166 LEU cc_start: 0.8347 (tp) cc_final: 0.7996 (tt) REVERT: E 192 MET cc_start: 0.7821 (ttp) cc_final: 0.7620 (tmm) REVERT: C 10 LYS cc_start: 0.8238 (mtmm) cc_final: 0.7913 (mtmm) REVERT: C 241 ASP cc_start: 0.7699 (t0) cc_final: 0.7437 (t0) REVERT: C 266 GLU cc_start: 0.7393 (pp20) cc_final: 0.7066 (pp20) REVERT: C 267 LYS cc_start: 0.8203 (ttmm) cc_final: 0.7778 (ttmt) REVERT: C 314 ASP cc_start: 0.6900 (m-30) cc_final: 0.6502 (m-30) REVERT: C 340 ARG cc_start: 0.7721 (tpp-160) cc_final: 0.7483 (mmp80) outliers start: 25 outliers final: 17 residues processed: 216 average time/residue: 1.0518 time to fit residues: 244.5581 Evaluate side-chains 213 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 195 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 LEU 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 112 VAL Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 325 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 0.2980 chunk 9 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 chunk 97 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 ASN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 GLN D 239 ASN C 216 ASN C 238 ASN C 245 ASN C 354 ASN C 359 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2571 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= 0.224 Angle : 0.556 8.254 12223 Z= 0.287 Chirality : 0.044 0.182 1396 Planarity : 0.004 0.053 1546 Dihedral : 4.486 31.796 1236 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.63 % Allowed : 20.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.25), residues: 1126 helix: 0.36 (0.28), residues: 395 sheet: -0.85 (0.30), residues: 273 loop : -1.10 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 47 HIS 0.003 0.001 HIS C 324 PHE 0.011 0.001 PHE D 234 TYR 0.032 0.001 TYR B 315 ARG 0.006 0.000 ARG D 219 *********************** 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 220 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 196 time to evaluate : 1.056 Fit side-chains revert: symmetry clash REVERT: B 92 TYR cc_start: 0.7761 (m-80) cc_final: 0.7518 (m-80) REVERT: B 147 LEU cc_start: 0.5454 (OUTLIER) cc_final: 0.4946 (mp) REVERT: B 210 LEU cc_start: 0.8146 (mt) cc_final: 0.7918 (mt) REVERT: B 300 MET cc_start: 0.7539 (tmm) cc_final: 0.7335 (tmt) REVERT: E 67 ARG cc_start: 0.8711 (mtm110) cc_final: 0.8394 (mtp180) REVERT: E 83 MET cc_start: 0.8114 (mtt) cc_final: 0.7909 (mtt) REVERT: E 140 MET cc_start: 0.8575 (mmm) cc_final: 0.8181 (mmt) REVERT: E 166 LEU cc_start: 0.8332 (tp) cc_final: 0.7989 (tt) REVERT: C 10 LYS cc_start: 0.8225 (mtmm) cc_final: 0.7889 (mtmm) REVERT: C 266 GLU cc_start: 0.7407 (pp20) cc_final: 0.7068 (pp20) REVERT: C 267 LYS cc_start: 0.8199 (ttmm) cc_final: 0.7803 (ttmt) REVERT: C 314 ASP cc_start: 0.6884 (m-30) cc_final: 0.6376 (m-30) REVERT: C 340 ARG cc_start: 0.7710 (tpp-160) cc_final: 0.7480 (mmp80) outliers start: 24 outliers final: 14 residues processed: 208 average time/residue: 1.0268 time to fit residues: 230.1708 Evaluate side-chains 206 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 191 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 325 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 0.0470 chunk 90 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 ASN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 GLN D 239 ASN ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN C 245 ASN C 354 ASN C 359 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8984 Z= 0.223 Angle : 0.559 8.230 12223 Z= 0.288 Chirality : 0.043 0.177 1396 Planarity : 0.004 0.053 1546 Dihedral : 4.467 32.062 1236 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.30 % Allowed : 21.60 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.25), residues: 1126 helix: 0.48 (0.28), residues: 395 sheet: -0.78 (0.30), residues: 273 loop : -1.05 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 47 HIS 0.004 0.001 HIS C 324 PHE 0.012 0.001 PHE D 234 TYR 0.034 0.001 TYR B 315 ARG 0.006 0.000 ARG D 219 *********************** 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 221 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 200 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: B 92 TYR cc_start: 0.7784 (m-80) cc_final: 0.7511 (m-80) REVERT: B 147 LEU cc_start: 0.5370 (OUTLIER) cc_final: 0.4808 (mp) REVERT: B 210 LEU cc_start: 0.8144 (mt) cc_final: 0.7911 (mt) REVERT: E 67 ARG cc_start: 0.8712 (mtm110) cc_final: 0.8397 (mtp180) REVERT: E 83 MET cc_start: 0.8109 (mtt) cc_final: 0.7904 (mtt) REVERT: E 140 MET cc_start: 0.8551 (mmm) cc_final: 0.8159 (mmt) REVERT: E 166 LEU cc_start: 0.8276 (tp) cc_final: 0.7934 (tt) REVERT: C 232 ARG cc_start: 0.7868 (ptm160) cc_final: 0.7520 (ptp-110) REVERT: C 266 GLU cc_start: 0.7437 (pp20) cc_final: 0.7083 (pp20) REVERT: C 267 LYS cc_start: 0.8210 (ttmm) cc_final: 0.7802 (ttmt) REVERT: C 314 ASP cc_start: 0.6901 (m-30) cc_final: 0.6400 (m-30) REVERT: C 340 ARG cc_start: 0.7711 (tpp-160) cc_final: 0.7481 (mmp80) outliers start: 21 outliers final: 16 residues processed: 210 average time/residue: 1.0154 time to fit residues: 229.7502 Evaluate side-chains 209 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 192 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 294 CYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 357 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 88 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 26 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 ASN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 GLN D 239 ASN ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN C 238 ASN C 245 ASN C 354 ASN C 359 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8984 Z= 0.221 Angle : 0.572 8.275 12223 Z= 0.292 Chirality : 0.044 0.177 1396 Planarity : 0.004 0.053 1546 Dihedral : 4.464 31.515 1236 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.19 % Allowed : 22.37 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.25), residues: 1126 helix: 0.58 (0.28), residues: 389 sheet: -0.72 (0.30), residues: 271 loop : -0.99 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 47 HIS 0.004 0.001 HIS D 142 PHE 0.012 0.001 PHE D 234 TYR 0.034 0.001 TYR B 315 ARG 0.006 0.000 ARG D 219 ********************** 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 217 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 197 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: B 92 TYR cc_start: 0.7708 (m-80) cc_final: 0.7376 (m-80) REVERT: B 147 LEU cc_start: 0.5350 (OUTLIER) cc_final: 0.4835 (mp) REVERT: B 210 LEU cc_start: 0.8142 (mt) cc_final: 0.7910 (mt) REVERT: E 67 ARG cc_start: 0.8716 (mtm110) cc_final: 0.8400 (mtp180) REVERT: E 83 MET cc_start: 0.8104 (mtt) cc_final: 0.7867 (mtt) REVERT: E 140 MET cc_start: 0.8541 (mmm) cc_final: 0.8154 (mmt) REVERT: E 166 LEU cc_start: 0.8276 (tp) cc_final: 0.7931 (tt) REVERT: C 15 ARG cc_start: 0.8320 (ttt90) cc_final: 0.8010 (ttt180) REVERT: C 232 ARG cc_start: 0.7877 (ptm160) cc_final: 0.7538 (ptp-110) REVERT: C 266 GLU cc_start: 0.7469 (pp20) cc_final: 0.7083 (pp20) REVERT: C 267 LYS cc_start: 0.8232 (ttmm) cc_final: 0.7876 (ttmt) REVERT: C 314 ASP cc_start: 0.6864 (m-30) cc_final: 0.6378 (m-30) REVERT: C 340 ARG cc_start: 0.7709 (tpp-160) cc_final: 0.7480 (mmp80) outliers start: 20 outliers final: 17 residues processed: 205 average time/residue: 1.0553 time to fit residues: 232.5480 Evaluate side-chains 211 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 193 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 32 ARG Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 357 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.5980 chunk 13 optimal weight: 0.0170 chunk 24 optimal weight: 0.3980 chunk 88 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 ASN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 GLN D 239 ASN ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN C 245 ASN 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 = 0.3649 r_free = 0.3649 target = 0.127136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.113962 restraints weight = 12785.058| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.93 r_work: 0.3365 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8984 Z= 0.178 Angle : 0.552 7.862 12223 Z= 0.282 Chirality : 0.043 0.162 1396 Planarity : 0.004 0.053 1546 Dihedral : 4.358 31.471 1236 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.08 % Allowed : 22.48 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.26), residues: 1126 helix: 0.79 (0.28), residues: 386 sheet: -0.70 (0.30), residues: 273 loop : -1.00 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 47 HIS 0.003 0.001 HIS C 324 PHE 0.012 0.001 PHE B 163 TYR 0.032 0.001 TYR B 315 ARG 0.006 0.000 ARG D 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4127.08 seconds wall clock time: 74 minutes 11.81 seconds (4451.81 seconds total)