Starting phenix.real_space_refine on Wed Jul 30 16:46:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hpn_34934/07_2025/8hpn_34934.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hpn_34934/07_2025/8hpn_34934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hpn_34934/07_2025/8hpn_34934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hpn_34934/07_2025/8hpn_34934.map" model { file = "/net/cci-nas-00/data/ceres_data/8hpn_34934/07_2025/8hpn_34934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hpn_34934/07_2025/8hpn_34934.cif" } resolution = 4.55 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= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 23 5.16 5 C 7862 2.51 5 N 2078 2.21 5 O 2360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12329 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2009 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 14, 'TRANS': 269} Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'TRP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 70 Chain: "B" Number of atoms: 1904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1904 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 16, 'TRANS': 248} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2563 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Chain breaks: 2 Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 116 Chain: "D" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2577 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Chain breaks: 2 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 103 Chain: "E" Number of atoms: 3191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3191 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 31, 'TRANS': 404} Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 90 Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.15, per 1000 atoms: 0.74 Number of scatterers: 12329 At special positions: 0 Unit cell: (81.18, 89.38, 167.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 P 6 15.00 O 2360 8.00 N 2078 7.00 C 7862 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 Links applied ALPHA1-1 " GLC G 1 " - " GLC G 2 " Time building additional restraints: 4.22 Conformation dependent library (CDL) restraints added in 1.8 seconds 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3176 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 13 sheets defined 57.1% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 17 through 38 Proline residue: A 30 - end of helix Processing helix chain 'A' and resid 39 through 52 Processing helix chain 'A' and resid 67 through 76 Processing helix chain 'A' and resid 76 through 111 removed outlier: 3.771A pdb=" N ALA A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 128 removed outlier: 4.022A pdb=" N VAL A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) Proline residue: A 125 - end of helix Processing helix chain 'A' and resid 129 through 141 Processing helix chain 'A' and resid 146 through 151 Processing helix chain 'A' and resid 157 through 160 Processing helix chain 'A' and resid 161 through 191 removed outlier: 4.855A pdb=" N TRP A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 193 through 202 removed outlier: 3.927A pdb=" N LEU A 197 " --> pdb=" O PRO A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 219 Proline residue: A 217 - end of helix Processing helix chain 'A' and resid 224 through 236 removed outlier: 3.878A pdb=" N PHE A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ARG A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 246 Processing helix chain 'A' and resid 253 through 264 removed outlier: 3.537A pdb=" N LEU A 262 " --> pdb=" O GLY A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 292 removed outlier: 4.087A pdb=" N ILE A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 37 Proline residue: B 27 - end of helix Processing helix chain 'B' and resid 38 through 42 removed outlier: 3.522A pdb=" N VAL B 42 " --> pdb=" O THR B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 62 Processing helix chain 'B' and resid 64 through 97 removed outlier: 4.063A pdb=" N ALA B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR B 93 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ALA B 94 " --> pdb=" O MET B 90 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 114 removed outlier: 4.453A pdb=" N LEU B 112 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 128 removed outlier: 4.059A pdb=" N LEU B 121 " --> pdb=" O PRO B 117 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N THR B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 137 through 163 Proline residue: B 144 - end of helix Proline residue: B 151 - end of helix Processing helix chain 'B' and resid 166 through 176 removed outlier: 3.552A pdb=" N LYS B 170 " --> pdb=" O TRP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 208 Proline residue: B 189 - end of helix Proline residue: B 193 - end of helix Processing helix chain 'B' and resid 210 through 216 Processing helix chain 'B' and resid 224 through 232 Processing helix chain 'B' and resid 241 through 263 Proline residue: B 255 - end of helix removed outlier: 3.736A pdb=" N ILE B 262 " --> pdb=" O ILE B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 270 removed outlier: 4.131A pdb=" N ILE B 267 " --> pdb=" O PHE B 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 55 removed outlier: 3.668A pdb=" N ASN C 52 " --> pdb=" O SER C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 96 through 108 Proline residue: C 104 - end of helix Processing helix chain 'C' and resid 111 through 127 Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.552A pdb=" N LEU C 139 " --> pdb=" O PRO C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 156 removed outlier: 3.640A pdb=" N ARG C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 169 Processing helix chain 'C' and resid 170 through 188 Processing helix chain 'C' and resid 198 through 206 Processing helix chain 'C' and resid 222 through 229 Processing helix chain 'C' and resid 232 through 239 Processing helix chain 'C' and resid 266 through 276 removed outlier: 4.013A pdb=" N LEU C 272 " --> pdb=" O HIS C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 305 Processing helix chain 'D' and resid 46 through 55 Processing helix chain 'D' and resid 76 through 81 Processing helix chain 'D' and resid 96 through 108 Proline residue: D 104 - end of helix Processing helix chain 'D' and resid 111 through 125 Processing helix chain 'D' and resid 135 through 139 Processing helix chain 'D' and resid 140 through 154 Processing helix chain 'D' and resid 165 through 169 Processing helix chain 'D' and resid 170 through 189 Processing helix chain 'D' and resid 198 through 206 removed outlier: 4.023A pdb=" N THR D 204 " --> pdb=" O THR D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 229 Processing helix chain 'D' and resid 232 through 239 Processing helix chain 'D' and resid 266 through 276 Processing helix chain 'D' and resid 287 through 291 Processing helix chain 'D' and resid 295 through 297 No H-bonds generated for 'chain 'D' and resid 295 through 297' Processing helix chain 'D' and resid 298 through 304 Processing helix chain 'E' and resid 40 through 56 removed outlier: 3.797A pdb=" N PHE E 44 " --> pdb=" O GLU E 40 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLN E 54 " --> pdb=" O ARG E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 83 Processing helix chain 'E' and resid 98 through 105 Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 116 through 121 Processing helix chain 'E' and resid 127 through 135 removed outlier: 3.604A pdb=" N LEU E 131 " --> pdb=" O LEU E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 180 Processing helix chain 'E' and resid 192 through 206 removed outlier: 3.916A pdb=" N VAL E 196 " --> pdb=" O TYR E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 243 removed outlier: 4.764A pdb=" N ALA E 241 " --> pdb=" O ILE E 237 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR E 242 " --> pdb=" O LYS E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 264 Processing helix chain 'E' and resid 275 through 287 removed outlier: 3.556A pdb=" N LYS E 286 " --> pdb=" O GLU E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 Processing helix chain 'E' and resid 305 through 309 removed outlier: 3.548A pdb=" N GLY E 308 " --> pdb=" O ASN E 305 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR E 309 " --> pdb=" O ASP E 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 305 through 309' Processing helix chain 'E' and resid 313 through 327 Processing helix chain 'E' and resid 360 through 372 Processing helix chain 'E' and resid 372 through 382 removed outlier: 4.044A pdb=" N TYR E 378 " --> pdb=" O GLU E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 394 Processing helix chain 'E' and resid 395 through 402 Processing helix chain 'E' and resid 404 through 413 removed outlier: 3.816A pdb=" N THR E 413 " --> pdb=" O ARG E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 436 Processing helix chain 'E' and resid 437 through 441 removed outlier: 3.983A pdb=" N ILE E 441 " --> pdb=" O ILE E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 460 removed outlier: 3.646A pdb=" N ALA E 447 " --> pdb=" O PRO E 443 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP E 448 " --> pdb=" O GLU E 444 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 21 through 31 removed outlier: 6.459A pdb=" N ALA C 23 " --> pdb=" O SER C 12 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N SER C 12 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LYS C 25 " --> pdb=" O THR C 10 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N THR C 10 " --> pdb=" O LYS C 25 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE C 27 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU C 6 " --> pdb=" O ARG C 66 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ARG C 66 " --> pdb=" O LEU C 6 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ARG C 8 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLU C 64 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 82 through 85 removed outlier: 3.710A pdb=" N ASP C 163 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE C 36 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL C 210 " --> pdb=" O PHE C 36 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE C 38 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N MET C 212 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL C 40 " --> pdb=" O MET C 212 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU C 213 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N VAL C 217 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 261 through 264 removed outlier: 3.581A pdb=" N GLY C 261 " --> pdb=" O LEU C 258 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 291 through 293 removed outlier: 4.044A pdb=" N GLU C 366 " --> pdb=" O ALA C 312 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 314 through 317 Processing sheet with id=AA6, first strand: chain 'D' and resid 21 through 24 removed outlier: 6.305A pdb=" N LYS D 11 " --> pdb=" O ALA D 23 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 21 through 24 removed outlier: 6.305A pdb=" N LYS D 11 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL D 9 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SER D 62 " --> pdb=" O VAL D 9 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 83 through 85 removed outlier: 6.662A pdb=" N PHE D 160 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N VAL D 195 " --> pdb=" O PHE D 160 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N MET D 162 " --> pdb=" O VAL D 195 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N PHE D 36 " --> pdb=" O ARG D 208 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N VAL D 210 " --> pdb=" O PHE D 36 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE D 38 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N MET D 212 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL D 40 " --> pdb=" O MET D 212 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL D 209 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE D 220 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL D 211 " --> pdb=" O GLN D 218 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 261 through 264 removed outlier: 3.667A pdb=" N GLY D 261 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 292 through 293 Processing sheet with id=AB2, first strand: chain 'D' and resid 314 through 317 Processing sheet with id=AB3, first strand: chain 'E' and resid 60 through 66 removed outlier: 10.691A pdb=" N VAL E 31 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N VAL E 90 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASN E 33 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ALA E 92 " --> pdb=" O ASN E 33 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N TYR E 35 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLY E 347 " --> pdb=" O THR E 147 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR E 147 " --> pdb=" O GLY E 347 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU E 349 " --> pdb=" O ILE E 145 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 269 through 272 728 hydrogen bonds defined for protein. 2043 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: 4.23 Time building geometry restraints manager: 4.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2097 1.29 - 1.42: 3083 1.42 - 1.55: 7337 1.55 - 1.68: 20 1.68 - 1.82: 42 Bond restraints: 12579 Sorted by residual: bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.85e+01 bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.79e+01 bond pdb=" C LEU A 262 " pdb=" O LEU A 262 " ideal model delta sigma weight residual 1.234 1.173 0.062 8.30e-03 1.45e+04 5.52e+01 bond pdb=" C5 ATP C 501 " pdb=" C6 ATP C 501 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.39e+01 bond pdb=" C5 ATP D 501 " pdb=" C6 ATP D 501 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.36e+01 ... (remaining 12574 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.91: 16635 3.91 - 7.83: 600 7.83 - 11.74: 13 11.74 - 15.65: 0 15.65 - 19.56: 4 Bond angle restraints: 17252 Sorted by residual: angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 120.31 19.56 1.00e+00 1.00e+00 3.83e+02 angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 120.48 19.39 1.00e+00 1.00e+00 3.76e+02 angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 120.52 16.31 1.00e+00 1.00e+00 2.66e+02 angle pdb=" PA ATP D 501 " pdb=" O3A ATP D 501 " pdb=" PB ATP D 501 " ideal model delta sigma weight residual 136.83 120.53 16.30 1.00e+00 1.00e+00 2.66e+02 angle pdb=" C5 ATP C 501 " pdb=" C4 ATP C 501 " pdb=" N3 ATP C 501 " ideal model delta sigma weight residual 126.80 118.63 8.17 1.00e+00 1.00e+00 6.67e+01 ... (remaining 17247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 6924 17.98 - 35.96: 485 35.96 - 53.95: 79 53.95 - 71.93: 29 71.93 - 89.91: 5 Dihedral angle restraints: 7522 sinusoidal: 2608 harmonic: 4914 Sorted by residual: dihedral pdb=" CA ASP E 121 " pdb=" C ASP E 121 " pdb=" N ALA E 122 " pdb=" CA ALA E 122 " ideal model delta harmonic sigma weight residual 180.00 150.34 29.66 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA TRP E 106 " pdb=" C TRP E 106 " pdb=" N ALA E 107 " pdb=" CA ALA E 107 " ideal model delta harmonic sigma weight residual -180.00 -151.24 -28.76 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA ARG D 134 " pdb=" C ARG D 134 " pdb=" N LYS D 135 " pdb=" CA LYS D 135 " ideal model delta harmonic sigma weight residual 180.00 151.26 28.74 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 7519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1319 0.085 - 0.169: 593 0.169 - 0.254: 136 0.254 - 0.338: 28 0.338 - 0.423: 7 Chirality restraints: 2083 Sorted by residual: chirality pdb=" C1 GLC G 1 " pdb=" C2 GLC G 1 " pdb=" O5 GLC G 1 " pdb=" O1 GLC G 2 " both_signs ideal model delta sigma weight residual False 2.40 2.29 0.11 2.00e-02 2.50e+03 2.92e+01 chirality pdb=" CA LEU A 262 " pdb=" N LEU A 262 " pdb=" C LEU A 262 " pdb=" CB LEU A 262 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" CA LYS C 109 " pdb=" N LYS C 109 " pdb=" C LYS C 109 " pdb=" CB LYS C 109 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.33e+00 ... (remaining 2080 not shown) Planarity restraints: 2235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 402 " -0.120 2.00e-02 2.50e+03 6.83e-02 9.33e+01 pdb=" CG TYR E 402 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR E 402 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR E 402 " 0.061 2.00e-02 2.50e+03 pdb=" CE1 TYR E 402 " 0.058 2.00e-02 2.50e+03 pdb=" CE2 TYR E 402 " 0.032 2.00e-02 2.50e+03 pdb=" CZ TYR E 402 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR E 402 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 166 " 0.128 2.00e-02 2.50e+03 5.95e-02 8.85e+01 pdb=" CG TRP E 166 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP E 166 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP E 166 " -0.050 2.00e-02 2.50e+03 pdb=" NE1 TRP E 166 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP E 166 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 166 " -0.060 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 166 " 0.071 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 166 " -0.029 2.00e-02 2.50e+03 pdb=" CH2 TRP E 166 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 234 " -0.113 2.00e-02 2.50e+03 6.91e-02 8.35e+01 pdb=" CG PHE C 234 " 0.088 2.00e-02 2.50e+03 pdb=" CD1 PHE C 234 " 0.059 2.00e-02 2.50e+03 pdb=" CD2 PHE C 234 " 0.068 2.00e-02 2.50e+03 pdb=" CE1 PHE C 234 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE C 234 " -0.024 2.00e-02 2.50e+03 pdb=" CZ PHE C 234 " -0.063 2.00e-02 2.50e+03 ... (remaining 2232 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1278 2.77 - 3.31: 14649 3.31 - 3.84: 21082 3.84 - 4.37: 24636 4.37 - 4.90: 39194 Nonbonded interactions: 100839 Sorted by model distance: nonbonded pdb=" OD2 ASP B 175 " pdb=" OH TYR C 92 " model vdw 2.243 3.040 nonbonded pdb=" OE1 GLN E 150 " pdb=" CE2 TYR E 333 " model vdw 2.302 3.340 nonbonded pdb=" O ASP E 440 " pdb=" OD1 ASP E 440 " model vdw 2.349 3.040 nonbonded pdb=" CD2 LEU A 185 " pdb=" CD1 ILE A 223 " model vdw 2.408 3.880 nonbonded pdb=" O ILE B 132 " pdb=" N LEU B 134 " model vdw 2.424 3.120 ... (remaining 100834 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 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 2 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 124 or (resid 125 through 128 and ( \ name N or name CA or name C or name O or name CB )) or resid 129 through 142 or \ (resid 143 and (name N or name CA or name C or name O or name CB )) or resid 144 \ through 152 or (resid 153 and (name N or name CA or name C or name O or name CB \ )) or resid 154 through 193 or (resid 194 and (name N or name CA or name C or n \ ame O or name CB )) or resid 195 through 204 or (resid 205 and (name N or name C \ A or name C or name O or name CB )) or resid 206 through 261 or (resid 262 and ( \ name N or name CA or name C or name O or name CB )) or resid 263 through 286 or \ (resid 287 and (name N or name CA or name C or name O or name CB )) or resid 288 \ through 313 or (resid 314 and (name N or name CA or name C or name O or name CB \ )) or resid 315 through 376 or (resid 377 and (name N or name CA or name C or n \ ame O or name CB )) or resid 378 through 385 or (resid 386 and (name N or name C \ A or name C or name O or name CB )) or resid 387 or (resid 388 and (name N or na \ me CA or name C or name O or name CB )) or resid 389 through 391 or resid 501)) selection = (chain 'D' and (resid 2 through 50 or (resid 51 through 52 and (name N or name C \ A or name C or name O or name CB )) or resid 53 through 57 or (resid 58 and (nam \ e N or name CA or name C or name O or name CB )) or resid 59 through 77 or (resi \ d 78 and (name N or name CA or name C or name O or name CB )) or resid 79 throug \ h 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 through 117 or (resid 118 and (name N or name CA or name C or name O or n \ ame CB )) or resid 119 through 126 or (resid 127 through 128 and (name N or name \ CA or name C or name O or name CB )) or resid 129 through 137 or (resid 138 and \ (name N or name CA or name C or name O or name CB )) or resid 139 through 174 o \ r (resid 175 through 179 and (name N or name CA or name C or name O or name CB ) \ ) or resid 180 through 195 or (resid 196 and (name N or name CA or name C or nam \ e O or name CB )) or resid 197 through 285 or (resid 286 through 287 and (name N \ or name CA or name C or name O or name CB )) or resid 288 through 289 or (resid \ 290 and (name N or name CA or name C or name O or name CB )) or resid 291 throu \ gh 324 or (resid 325 and (name N or name CA or name C or name O or name CB )) or \ resid 326 through 378 or (resid 379 and (name N or name CA or name C or name O \ or name CB )) or resid 380 or (resid 381 through 383 and (name N or name CA or n \ ame C or name O or name CB )) or resid 384 through 391 or resid 501)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 34.590 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 : 0.012 0.134 12580 Z= 0.749 Angle : 1.814 19.565 17255 Z= 1.224 Chirality : 0.098 0.423 2083 Planarity : 0.013 0.105 2235 Dihedral : 13.611 89.910 4346 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.28 % Favored : 92.48 % Rotamer: Outliers : 0.35 % Allowed : 6.92 % Favored : 92.73 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.18), residues: 1689 helix: -1.78 (0.14), residues: 859 sheet: -1.41 (0.39), residues: 126 loop : -1.56 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.128 0.017 TRP E 166 HIS 0.011 0.003 HIS D 290 PHE 0.113 0.017 PHE C 234 TYR 0.120 0.021 TYR E 402 ARG 0.014 0.001 ARG D 302 Details of bonding type rmsd hydrogen bonds : bond 0.14868 ( 725) hydrogen bonds : angle 8.10798 ( 2043) glycosidic custom : bond 0.02882 ( 1) glycosidic custom : angle 2.03772 ( 3) covalent geometry : bond 0.01217 (12579) covalent geometry : angle 1.81367 (17252) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 310 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 TYR cc_start: 0.9486 (m-80) cc_final: 0.8927 (m-80) REVERT: A 162 GLN cc_start: 0.9526 (tt0) cc_final: 0.9069 (tp40) REVERT: A 166 LEU cc_start: 0.9803 (mt) cc_final: 0.9551 (mt) REVERT: A 176 LYS cc_start: 0.9433 (tptp) cc_final: 0.9090 (tppt) REVERT: A 233 ASP cc_start: 0.8725 (m-30) cc_final: 0.8246 (m-30) REVERT: A 260 ASP cc_start: 0.9013 (t0) cc_final: 0.8443 (t0) REVERT: A 261 ASN cc_start: 0.9085 (m-40) cc_final: 0.8869 (m-40) REVERT: A 289 TYR cc_start: 0.9466 (m-80) cc_final: 0.9217 (m-10) REVERT: A 291 LYS cc_start: 0.8916 (tptt) cc_final: 0.8671 (mmtp) REVERT: B 113 ILE cc_start: 0.9423 (pt) cc_final: 0.9186 (mm) REVERT: B 116 PHE cc_start: 0.8800 (m-80) cc_final: 0.8216 (m-80) REVERT: B 127 ASN cc_start: 0.9537 (m-40) cc_final: 0.9106 (m110) REVERT: B 144 PRO cc_start: 0.9529 (Cg_exo) cc_final: 0.9253 (Cg_endo) REVERT: B 148 PHE cc_start: 0.9528 (m-80) cc_final: 0.9290 (m-80) REVERT: B 174 MET cc_start: 0.9284 (mtp) cc_final: 0.9063 (ttt) REVERT: C 163 ASP cc_start: 0.8276 (m-30) cc_final: 0.7966 (t0) REVERT: C 239 ILE cc_start: 0.8991 (tp) cc_final: 0.8666 (pt) REVERT: D 177 MET cc_start: 0.9143 (mmm) cc_final: 0.8689 (mmp) REVERT: D 269 MET cc_start: 0.8702 (mtt) cc_final: 0.8221 (mmm) REVERT: E 91 MET cc_start: 0.8946 (ptp) cc_final: 0.8689 (ptp) REVERT: E 153 TRP cc_start: 0.8691 (m100) cc_final: 0.8438 (m100) REVERT: E 154 TYR cc_start: 0.8947 (p90) cc_final: 0.8233 (p90) outliers start: 4 outliers final: 0 residues processed: 313 average time/residue: 0.2613 time to fit residues: 115.0005 Evaluate side-chains 203 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 153 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 201 GLN B 72 ASN ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN C 218 GLN ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 GLN ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN E 174 ASN E 305 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.061508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.045799 restraints weight = 84839.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.047160 restraints weight = 61673.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.048206 restraints weight = 47937.901| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12580 Z= 0.192 Angle : 0.780 10.856 17255 Z= 0.415 Chirality : 0.047 0.188 2083 Planarity : 0.006 0.062 2235 Dihedral : 8.119 74.092 1908 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.80 % Favored : 95.09 % Rotamer: Outliers : 0.52 % Allowed : 4.41 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.20), residues: 1689 helix: -0.29 (0.17), residues: 866 sheet: -1.13 (0.34), residues: 158 loop : -1.11 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP E 97 HIS 0.006 0.001 HIS C 94 PHE 0.030 0.003 PHE D 36 TYR 0.029 0.002 TYR D 13 ARG 0.011 0.001 ARG D 183 Details of bonding type rmsd hydrogen bonds : bond 0.05120 ( 725) hydrogen bonds : angle 5.91427 ( 2043) glycosidic custom : bond 0.01364 ( 1) glycosidic custom : angle 1.13626 ( 3) covalent geometry : bond 0.00392 (12579) covalent geometry : angle 0.78018 (17252) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 254 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 TYR cc_start: 0.9559 (m-80) cc_final: 0.9072 (m-80) REVERT: A 150 ASN cc_start: 0.8716 (t0) cc_final: 0.8305 (m-40) REVERT: A 162 GLN cc_start: 0.9642 (tt0) cc_final: 0.8934 (tp40) REVERT: A 166 LEU cc_start: 0.9838 (mt) cc_final: 0.9613 (mt) REVERT: A 176 LYS cc_start: 0.9540 (tptp) cc_final: 0.9210 (tppt) REVERT: A 198 ASN cc_start: 0.9609 (m110) cc_final: 0.9285 (m110) REVERT: A 201 GLN cc_start: 0.9572 (OUTLIER) cc_final: 0.8953 (mm-40) REVERT: A 229 PHE cc_start: 0.9151 (t80) cc_final: 0.8763 (t80) REVERT: A 233 ASP cc_start: 0.8689 (m-30) cc_final: 0.8380 (m-30) REVERT: A 260 ASP cc_start: 0.9164 (t0) cc_final: 0.8628 (t0) REVERT: A 261 ASN cc_start: 0.9380 (m-40) cc_final: 0.9103 (m-40) REVERT: B 90 MET cc_start: 0.8160 (mmp) cc_final: 0.7567 (tmm) REVERT: B 118 HIS cc_start: 0.9179 (m-70) cc_final: 0.8733 (m-70) REVERT: B 121 LEU cc_start: 0.9548 (mm) cc_final: 0.8974 (mm) REVERT: B 127 ASN cc_start: 0.9533 (m-40) cc_final: 0.8950 (m110) REVERT: B 203 PHE cc_start: 0.9516 (t80) cc_final: 0.9259 (t80) REVERT: C 244 MET cc_start: 0.8445 (tpp) cc_final: 0.8038 (tpt) REVERT: D 138 GLN cc_start: 0.8018 (mt0) cc_final: 0.7653 (tm-30) REVERT: E 91 MET cc_start: 0.8877 (ptp) cc_final: 0.8640 (ptp) REVERT: E 166 TRP cc_start: 0.8487 (m100) cc_final: 0.8226 (m100) REVERT: E 262 LEU cc_start: 0.9629 (tp) cc_final: 0.9324 (tp) REVERT: E 272 ASN cc_start: 0.8507 (m-40) cc_final: 0.8295 (m110) outliers start: 6 outliers final: 0 residues processed: 257 average time/residue: 0.2166 time to fit residues: 83.2748 Evaluate side-chains 184 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 150 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 GLN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.062850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.047058 restraints weight = 84305.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.048438 restraints weight = 61369.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.049495 restraints weight = 47690.847| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12580 Z= 0.142 Angle : 0.690 8.326 17255 Z= 0.359 Chirality : 0.045 0.209 2083 Planarity : 0.005 0.055 2235 Dihedral : 7.411 77.343 1908 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.26 % Favored : 95.62 % Rotamer: Outliers : 0.26 % Allowed : 4.15 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.20), residues: 1689 helix: 0.25 (0.17), residues: 873 sheet: -0.62 (0.36), residues: 153 loop : -1.02 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 198 HIS 0.008 0.001 HIS C 268 PHE 0.022 0.002 PHE A 98 TYR 0.018 0.002 TYR E 378 ARG 0.004 0.000 ARG E 74 Details of bonding type rmsd hydrogen bonds : bond 0.04286 ( 725) hydrogen bonds : angle 5.42146 ( 2043) glycosidic custom : bond 0.00421 ( 1) glycosidic custom : angle 1.08557 ( 3) covalent geometry : bond 0.00294 (12579) covalent geometry : angle 0.68975 (17252) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 253 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 TYR cc_start: 0.9578 (m-80) cc_final: 0.9158 (m-80) REVERT: A 150 ASN cc_start: 0.8725 (t0) cc_final: 0.8317 (m-40) REVERT: A 161 ASP cc_start: 0.9400 (m-30) cc_final: 0.9029 (m-30) REVERT: A 162 GLN cc_start: 0.9637 (tt0) cc_final: 0.8681 (tp40) REVERT: A 176 LYS cc_start: 0.9543 (tptp) cc_final: 0.9244 (tppt) REVERT: A 260 ASP cc_start: 0.9114 (t0) cc_final: 0.8663 (t0) REVERT: A 261 ASN cc_start: 0.9379 (m-40) cc_final: 0.9059 (m-40) REVERT: A 291 LYS cc_start: 0.8965 (tptt) cc_final: 0.8764 (pttm) REVERT: B 58 LYS cc_start: 0.9705 (ptpp) cc_final: 0.9359 (mmtt) REVERT: B 90 MET cc_start: 0.8128 (mmp) cc_final: 0.7622 (tmm) REVERT: B 116 PHE cc_start: 0.8105 (t80) cc_final: 0.7865 (t80) REVERT: B 118 HIS cc_start: 0.9211 (m-70) cc_final: 0.8816 (m-70) REVERT: B 127 ASN cc_start: 0.9529 (m-40) cc_final: 0.8741 (m-40) REVERT: B 128 MET cc_start: 0.9454 (mmt) cc_final: 0.8978 (mmm) REVERT: B 145 TYR cc_start: 0.9353 (m-10) cc_final: 0.8792 (m-80) REVERT: B 168 LEU cc_start: 0.9474 (pt) cc_final: 0.9216 (mm) REVERT: B 203 PHE cc_start: 0.9448 (t80) cc_final: 0.8935 (t80) REVERT: C 244 MET cc_start: 0.8472 (tpp) cc_final: 0.7950 (tpt) REVERT: D 212 MET cc_start: 0.7705 (tpp) cc_final: 0.7497 (tpt) REVERT: E 40 GLU cc_start: 0.9381 (tt0) cc_final: 0.8867 (tt0) REVERT: E 91 MET cc_start: 0.8963 (ptp) cc_final: 0.8541 (pmm) outliers start: 3 outliers final: 0 residues processed: 253 average time/residue: 0.2120 time to fit residues: 80.6297 Evaluate side-chains 194 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 71 optimal weight: 4.9990 chunk 63 optimal weight: 0.2980 chunk 58 optimal weight: 0.6980 chunk 78 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 104 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 359 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.063146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.047285 restraints weight = 81742.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.048690 restraints weight = 59141.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.049781 restraints weight = 45689.299| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12580 Z= 0.141 Angle : 0.645 7.169 17255 Z= 0.336 Chirality : 0.044 0.187 2083 Planarity : 0.005 0.052 2235 Dihedral : 7.316 79.922 1908 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.97 % Favored : 95.86 % Rotamer: Outliers : 0.09 % Allowed : 3.11 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.20), residues: 1689 helix: 0.48 (0.17), residues: 876 sheet: -0.98 (0.35), residues: 165 loop : -0.89 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 79 HIS 0.005 0.001 HIS C 268 PHE 0.018 0.001 PHE D 36 TYR 0.018 0.002 TYR A 41 ARG 0.015 0.000 ARG D 183 Details of bonding type rmsd hydrogen bonds : bond 0.03916 ( 725) hydrogen bonds : angle 5.21698 ( 2043) glycosidic custom : bond 0.00425 ( 1) glycosidic custom : angle 1.09367 ( 3) covalent geometry : bond 0.00284 (12579) covalent geometry : angle 0.64452 (17252) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 251 time to evaluate : 3.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 TYR cc_start: 0.9582 (m-80) cc_final: 0.9203 (m-80) REVERT: A 162 GLN cc_start: 0.9532 (tt0) cc_final: 0.8955 (tp-100) REVERT: A 176 LYS cc_start: 0.9537 (tptp) cc_final: 0.9224 (tppt) REVERT: A 260 ASP cc_start: 0.9076 (t0) cc_final: 0.8622 (t0) REVERT: A 261 ASN cc_start: 0.9333 (m-40) cc_final: 0.9025 (m-40) REVERT: A 263 PHE cc_start: 0.9579 (m-80) cc_final: 0.9378 (m-10) REVERT: B 58 LYS cc_start: 0.9668 (ptpp) cc_final: 0.9366 (mmtt) REVERT: B 90 MET cc_start: 0.8103 (mmp) cc_final: 0.7606 (tmm) REVERT: B 118 HIS cc_start: 0.9202 (m-70) cc_final: 0.8915 (m-70) REVERT: B 127 ASN cc_start: 0.9527 (m-40) cc_final: 0.9043 (m110) REVERT: B 145 TYR cc_start: 0.9355 (m-10) cc_final: 0.8776 (m-80) REVERT: B 168 LEU cc_start: 0.9449 (pt) cc_final: 0.9147 (mm) REVERT: B 203 PHE cc_start: 0.9430 (t80) cc_final: 0.8930 (t80) REVERT: C 194 TYR cc_start: 0.8678 (t80) cc_final: 0.8351 (t80) REVERT: C 244 MET cc_start: 0.8509 (tpp) cc_final: 0.8053 (tpt) REVERT: D 86 PHE cc_start: 0.9459 (t80) cc_final: 0.9130 (t80) REVERT: D 138 GLN cc_start: 0.8100 (mp10) cc_final: 0.7369 (pp30) REVERT: D 176 GLN cc_start: 0.9742 (mt0) cc_final: 0.9539 (mt0) REVERT: D 177 MET cc_start: 0.9205 (mmp) cc_final: 0.8745 (mmp) REVERT: D 224 ASP cc_start: 0.9559 (t0) cc_final: 0.9141 (p0) REVERT: E 44 PHE cc_start: 0.9217 (m-80) cc_final: 0.8707 (m-80) REVERT: E 270 GLU cc_start: 0.9282 (pm20) cc_final: 0.8907 (pp20) outliers start: 1 outliers final: 0 residues processed: 251 average time/residue: 0.2601 time to fit residues: 101.3288 Evaluate side-chains 192 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 68 optimal weight: 0.0970 chunk 92 optimal weight: 20.0000 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 145 optimal weight: 0.0000 chunk 59 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 ASN B 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.064044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.048094 restraints weight = 81291.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.049486 restraints weight = 59478.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.050565 restraints weight = 46368.102| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12580 Z= 0.127 Angle : 0.645 7.576 17255 Z= 0.326 Chirality : 0.045 0.241 2083 Planarity : 0.005 0.053 2235 Dihedral : 7.139 79.807 1908 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.91 % Favored : 95.97 % Rotamer: Outliers : 0.09 % Allowed : 2.08 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.21), residues: 1689 helix: 0.66 (0.18), residues: 875 sheet: -0.81 (0.35), residues: 165 loop : -0.93 (0.26), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 198 HIS 0.004 0.001 HIS C 268 PHE 0.027 0.002 PHE B 116 TYR 0.020 0.002 TYR A 41 ARG 0.015 0.000 ARG D 183 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 725) hydrogen bonds : angle 5.04503 ( 2043) glycosidic custom : bond 0.00519 ( 1) glycosidic custom : angle 0.98280 ( 3) covalent geometry : bond 0.00252 (12579) covalent geometry : angle 0.64539 (17252) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 250 time to evaluate : 2.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 TYR cc_start: 0.9556 (m-80) cc_final: 0.9276 (m-80) REVERT: A 162 GLN cc_start: 0.9557 (tt0) cc_final: 0.8989 (tp40) REVERT: A 176 LYS cc_start: 0.9506 (tptp) cc_final: 0.9238 (tppt) REVERT: A 260 ASP cc_start: 0.9012 (t0) cc_final: 0.8593 (t0) REVERT: A 261 ASN cc_start: 0.9129 (m-40) cc_final: 0.8854 (m-40) REVERT: B 32 LEU cc_start: 0.9638 (mm) cc_final: 0.9349 (mm) REVERT: B 36 LEU cc_start: 0.9552 (mm) cc_final: 0.8967 (mm) REVERT: B 58 LYS cc_start: 0.9651 (ptpp) cc_final: 0.9318 (mmtt) REVERT: B 90 MET cc_start: 0.8115 (mmp) cc_final: 0.7640 (tmm) REVERT: B 116 PHE cc_start: 0.8261 (t80) cc_final: 0.8047 (t80) REVERT: B 118 HIS cc_start: 0.9287 (m-70) cc_final: 0.8846 (m-70) REVERT: B 127 ASN cc_start: 0.9531 (m-40) cc_final: 0.9030 (m110) REVERT: B 145 TYR cc_start: 0.9352 (m-10) cc_final: 0.8769 (m-80) REVERT: B 168 LEU cc_start: 0.9438 (pt) cc_final: 0.9121 (mm) REVERT: B 203 PHE cc_start: 0.9414 (t80) cc_final: 0.8963 (t80) REVERT: B 207 TRP cc_start: 0.8622 (t60) cc_final: 0.8394 (t60) REVERT: C 194 TYR cc_start: 0.8699 (t80) cc_final: 0.8318 (t80) REVERT: C 244 MET cc_start: 0.8431 (tpp) cc_final: 0.7981 (tpt) REVERT: D 86 PHE cc_start: 0.9518 (t80) cc_final: 0.9215 (t80) REVERT: D 176 GLN cc_start: 0.9752 (mt0) cc_final: 0.9529 (mt0) REVERT: D 177 MET cc_start: 0.9157 (mmp) cc_final: 0.8795 (mmp) REVERT: D 224 ASP cc_start: 0.9531 (t0) cc_final: 0.9099 (p0) REVERT: E 44 PHE cc_start: 0.9171 (m-80) cc_final: 0.8683 (m-80) REVERT: E 91 MET cc_start: 0.8920 (ptp) cc_final: 0.8712 (pmm) REVERT: E 159 MET cc_start: 0.8345 (ppp) cc_final: 0.8092 (ppp) outliers start: 1 outliers final: 0 residues processed: 250 average time/residue: 0.3624 time to fit residues: 141.3423 Evaluate side-chains 188 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 3.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 42 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 161 optimal weight: 7.9990 chunk 123 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.063053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.047207 restraints weight = 83612.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.048598 restraints weight = 60765.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.049691 restraints weight = 47192.408| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12580 Z= 0.126 Angle : 0.618 7.077 17255 Z= 0.316 Chirality : 0.044 0.202 2083 Planarity : 0.005 0.050 2235 Dihedral : 6.950 81.296 1908 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.79 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.21), residues: 1689 helix: 0.80 (0.18), residues: 875 sheet: -1.01 (0.33), residues: 189 loop : -0.96 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 79 HIS 0.005 0.001 HIS C 268 PHE 0.023 0.001 PHE A 279 TYR 0.016 0.001 TYR E 333 ARG 0.015 0.000 ARG D 183 Details of bonding type rmsd hydrogen bonds : bond 0.03475 ( 725) hydrogen bonds : angle 4.97614 ( 2043) glycosidic custom : bond 0.00241 ( 1) glycosidic custom : angle 1.36488 ( 3) covalent geometry : bond 0.00265 (12579) covalent geometry : angle 0.61743 (17252) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 2.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8763 (tm-30) REVERT: A 139 TYR cc_start: 0.9580 (m-80) cc_final: 0.9277 (m-80) REVERT: A 162 GLN cc_start: 0.9577 (tt0) cc_final: 0.8921 (tp40) REVERT: A 176 LYS cc_start: 0.9548 (tptp) cc_final: 0.9233 (tppt) REVERT: A 260 ASP cc_start: 0.9047 (t0) cc_final: 0.8625 (t0) REVERT: A 261 ASN cc_start: 0.9139 (m-40) cc_final: 0.8908 (m-40) REVERT: A 291 LYS cc_start: 0.9148 (tptt) cc_final: 0.8919 (pttm) REVERT: B 32 LEU cc_start: 0.9654 (mm) cc_final: 0.9345 (mm) REVERT: B 36 LEU cc_start: 0.9629 (mm) cc_final: 0.8990 (mm) REVERT: B 57 TYR cc_start: 0.9251 (m-10) cc_final: 0.9008 (m-80) REVERT: B 58 LYS cc_start: 0.9665 (ptpp) cc_final: 0.9317 (mmtt) REVERT: B 90 MET cc_start: 0.8114 (mmp) cc_final: 0.7674 (tmm) REVERT: B 116 PHE cc_start: 0.8440 (t80) cc_final: 0.8133 (t80) REVERT: B 118 HIS cc_start: 0.9315 (m-70) cc_final: 0.8983 (m-70) REVERT: B 127 ASN cc_start: 0.9523 (m-40) cc_final: 0.9042 (m110) REVERT: B 162 ARG cc_start: 0.9114 (mtp180) cc_final: 0.8854 (mtp180) REVERT: B 168 LEU cc_start: 0.9376 (pt) cc_final: 0.9037 (mm) REVERT: B 203 PHE cc_start: 0.9416 (t80) cc_final: 0.8932 (t80) REVERT: C 194 TYR cc_start: 0.8603 (t80) cc_final: 0.8160 (t80) REVERT: C 216 GLU cc_start: 0.9251 (mm-30) cc_final: 0.8793 (mm-30) REVERT: D 86 PHE cc_start: 0.9510 (t80) cc_final: 0.9219 (t80) REVERT: D 224 ASP cc_start: 0.9544 (t0) cc_final: 0.9115 (p0) REVERT: D 244 MET cc_start: 0.5217 (tpt) cc_final: 0.4791 (tpp) REVERT: E 40 GLU cc_start: 0.9125 (tt0) cc_final: 0.8836 (tt0) REVERT: E 159 MET cc_start: 0.8379 (ppp) cc_final: 0.8093 (ppp) REVERT: E 270 GLU cc_start: 0.9192 (pm20) cc_final: 0.8845 (pp20) REVERT: E 398 PHE cc_start: 0.8049 (t80) cc_final: 0.7786 (t80) REVERT: E 402 TYR cc_start: 0.8889 (t80) cc_final: 0.8521 (t80) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.2957 time to fit residues: 110.9908 Evaluate side-chains 189 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 125 optimal weight: 8.9990 chunk 165 optimal weight: 0.7980 chunk 135 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 82 optimal weight: 20.0000 chunk 155 optimal weight: 0.8980 chunk 127 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 147 optimal weight: 0.0970 chunk 46 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.063965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.047774 restraints weight = 80632.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.049176 restraints weight = 58975.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.050259 restraints weight = 46049.638| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12580 Z= 0.116 Angle : 0.620 7.413 17255 Z= 0.315 Chirality : 0.043 0.219 2083 Planarity : 0.005 0.050 2235 Dihedral : 6.822 80.946 1908 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.73 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.21), residues: 1689 helix: 0.81 (0.18), residues: 874 sheet: -0.89 (0.32), residues: 191 loop : -0.89 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP E 97 HIS 0.005 0.001 HIS C 268 PHE 0.018 0.001 PHE A 83 TYR 0.018 0.002 TYR A 41 ARG 0.007 0.000 ARG D 183 Details of bonding type rmsd hydrogen bonds : bond 0.03429 ( 725) hydrogen bonds : angle 4.90447 ( 2043) glycosidic custom : bond 0.00442 ( 1) glycosidic custom : angle 0.86991 ( 3) covalent geometry : bond 0.00242 (12579) covalent geometry : angle 0.62028 (17252) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8746 (t80) cc_final: 0.8304 (t80) REVERT: A 58 GLU cc_start: 0.9030 (tm-30) cc_final: 0.8804 (tm-30) REVERT: A 139 TYR cc_start: 0.9578 (m-80) cc_final: 0.9331 (m-80) REVERT: A 162 GLN cc_start: 0.9546 (tt0) cc_final: 0.8900 (tp40) REVERT: A 176 LYS cc_start: 0.9548 (tptp) cc_final: 0.9260 (tppt) REVERT: A 260 ASP cc_start: 0.9040 (t0) cc_final: 0.8592 (t0) REVERT: A 261 ASN cc_start: 0.9106 (m-40) cc_final: 0.8852 (m-40) REVERT: A 263 PHE cc_start: 0.9532 (m-80) cc_final: 0.9289 (m-10) REVERT: A 291 LYS cc_start: 0.9163 (tptt) cc_final: 0.8922 (pttm) REVERT: B 32 LEU cc_start: 0.9651 (mm) cc_final: 0.9417 (mm) REVERT: B 36 LEU cc_start: 0.9647 (mm) cc_final: 0.9029 (mm) REVERT: B 57 TYR cc_start: 0.9274 (m-10) cc_final: 0.9019 (m-80) REVERT: B 58 LYS cc_start: 0.9671 (ptpp) cc_final: 0.9330 (mmtt) REVERT: B 90 MET cc_start: 0.8077 (mmp) cc_final: 0.7680 (tmm) REVERT: B 93 TYR cc_start: 0.9374 (t80) cc_final: 0.9167 (t80) REVERT: B 116 PHE cc_start: 0.8515 (t80) cc_final: 0.8205 (t80) REVERT: B 118 HIS cc_start: 0.9340 (m-70) cc_final: 0.8831 (m-70) REVERT: B 127 ASN cc_start: 0.9506 (m-40) cc_final: 0.8862 (m110) REVERT: B 128 MET cc_start: 0.9557 (mmt) cc_final: 0.9055 (mmt) REVERT: B 162 ARG cc_start: 0.9058 (mtp180) cc_final: 0.8765 (mtp180) REVERT: B 168 LEU cc_start: 0.9349 (pt) cc_final: 0.8969 (mm) REVERT: B 203 PHE cc_start: 0.9416 (t80) cc_final: 0.8960 (t80) REVERT: B 239 GLU cc_start: 0.8847 (tp30) cc_final: 0.8625 (tp30) REVERT: C 194 TYR cc_start: 0.8566 (t80) cc_final: 0.8171 (t80) REVERT: C 244 MET cc_start: 0.8514 (tpp) cc_final: 0.8184 (tpt) REVERT: D 39 LEU cc_start: 0.9558 (tp) cc_final: 0.9341 (tp) REVERT: D 86 PHE cc_start: 0.9504 (t80) cc_final: 0.9213 (t80) REVERT: D 138 GLN cc_start: 0.8287 (mp10) cc_final: 0.7578 (pp30) REVERT: D 212 MET cc_start: 0.6200 (tpt) cc_final: 0.5597 (tpt) REVERT: D 224 ASP cc_start: 0.9563 (t0) cc_final: 0.9142 (p0) REVERT: D 244 MET cc_start: 0.4971 (tpt) cc_final: 0.4635 (tpp) REVERT: E 40 GLU cc_start: 0.9173 (tt0) cc_final: 0.8873 (tt0) REVERT: E 159 MET cc_start: 0.8446 (ppp) cc_final: 0.8123 (ppp) REVERT: E 272 ASN cc_start: 0.8831 (m-40) cc_final: 0.8625 (t0) REVERT: E 402 TYR cc_start: 0.8831 (t80) cc_final: 0.8563 (t80) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.2004 time to fit residues: 73.8426 Evaluate side-chains 184 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 99 optimal weight: 0.0000 chunk 161 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 137 optimal weight: 0.4980 chunk 109 optimal weight: 0.3980 chunk 152 optimal weight: 0.0970 chunk 54 optimal weight: 20.0000 chunk 128 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.064683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.048331 restraints weight = 81165.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.049742 restraints weight = 59489.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.050856 restraints weight = 46457.552| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12580 Z= 0.113 Angle : 0.609 7.287 17255 Z= 0.306 Chirality : 0.043 0.220 2083 Planarity : 0.005 0.051 2235 Dihedral : 6.612 82.489 1908 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.79 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.21), residues: 1689 helix: 0.88 (0.18), residues: 878 sheet: -0.76 (0.32), residues: 191 loop : -0.95 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 79 HIS 0.005 0.001 HIS C 268 PHE 0.017 0.001 PHE A 83 TYR 0.016 0.001 TYR A 41 ARG 0.009 0.000 ARG E 227 Details of bonding type rmsd hydrogen bonds : bond 0.03245 ( 725) hydrogen bonds : angle 4.78536 ( 2043) glycosidic custom : bond 0.00426 ( 1) glycosidic custom : angle 0.92324 ( 3) covalent geometry : bond 0.00232 (12579) covalent geometry : angle 0.60880 (17252) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8757 (t80) cc_final: 0.8329 (t80) REVERT: A 58 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8843 (tm-30) REVERT: A 139 TYR cc_start: 0.9574 (m-80) cc_final: 0.9342 (m-80) REVERT: A 162 GLN cc_start: 0.9565 (tt0) cc_final: 0.8894 (tp40) REVERT: A 176 LYS cc_start: 0.9564 (tptp) cc_final: 0.9303 (tppt) REVERT: A 260 ASP cc_start: 0.9033 (t0) cc_final: 0.8678 (t0) REVERT: A 261 ASN cc_start: 0.9095 (m-40) cc_final: 0.8803 (m-40) REVERT: A 263 PHE cc_start: 0.9396 (m-80) cc_final: 0.9114 (m-80) REVERT: A 291 LYS cc_start: 0.9216 (tptt) cc_final: 0.8958 (pttm) REVERT: B 32 LEU cc_start: 0.9653 (mm) cc_final: 0.9330 (mm) REVERT: B 36 LEU cc_start: 0.9627 (mm) cc_final: 0.9012 (mm) REVERT: B 57 TYR cc_start: 0.9283 (m-10) cc_final: 0.9003 (m-80) REVERT: B 58 LYS cc_start: 0.9678 (ptpp) cc_final: 0.9331 (mmtt) REVERT: B 90 MET cc_start: 0.8076 (mmp) cc_final: 0.7728 (tmm) REVERT: B 116 PHE cc_start: 0.8572 (t80) cc_final: 0.8130 (t80) REVERT: B 118 HIS cc_start: 0.9397 (m-70) cc_final: 0.8586 (m-70) REVERT: B 127 ASN cc_start: 0.9507 (m-40) cc_final: 0.8868 (m110) REVERT: B 128 MET cc_start: 0.9551 (mmt) cc_final: 0.9058 (mmt) REVERT: B 162 ARG cc_start: 0.9010 (mtp180) cc_final: 0.8757 (mtp180) REVERT: B 168 LEU cc_start: 0.9313 (pt) cc_final: 0.8908 (mm) REVERT: B 203 PHE cc_start: 0.9403 (t80) cc_final: 0.8955 (t80) REVERT: B 239 GLU cc_start: 0.8812 (tp30) cc_final: 0.8599 (tp30) REVERT: C 194 TYR cc_start: 0.8605 (t80) cc_final: 0.8235 (t80) REVERT: C 244 MET cc_start: 0.8523 (tpp) cc_final: 0.8214 (tpt) REVERT: D 39 LEU cc_start: 0.9544 (tp) cc_final: 0.9331 (tp) REVERT: D 86 PHE cc_start: 0.9521 (t80) cc_final: 0.9223 (t80) REVERT: D 138 GLN cc_start: 0.8235 (mp10) cc_final: 0.7547 (pp30) REVERT: D 212 MET cc_start: 0.5995 (tpt) cc_final: 0.5634 (tpt) REVERT: D 224 ASP cc_start: 0.9569 (t0) cc_final: 0.9151 (p0) REVERT: D 244 MET cc_start: 0.4992 (tpt) cc_final: 0.4566 (tpp) REVERT: E 40 GLU cc_start: 0.9192 (tt0) cc_final: 0.8915 (tt0) REVERT: E 153 TRP cc_start: 0.9003 (m100) cc_final: 0.8785 (m-10) REVERT: E 159 MET cc_start: 0.8480 (ppp) cc_final: 0.8116 (ppp) REVERT: E 402 TYR cc_start: 0.8721 (t80) cc_final: 0.8486 (t80) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.2350 time to fit residues: 87.7448 Evaluate side-chains 184 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 38 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 114 optimal weight: 0.3980 chunk 150 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 17 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 154 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.064416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.048072 restraints weight = 80236.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.049447 restraints weight = 59273.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.050532 restraints weight = 46537.086| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12580 Z= 0.113 Angle : 0.615 7.275 17255 Z= 0.307 Chirality : 0.043 0.229 2083 Planarity : 0.005 0.051 2235 Dihedral : 6.511 83.654 1908 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.55 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.21), residues: 1689 helix: 0.88 (0.18), residues: 878 sheet: -0.76 (0.32), residues: 191 loop : -0.91 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 97 HIS 0.006 0.001 HIS C 268 PHE 0.019 0.001 PHE B 148 TYR 0.015 0.001 TYR A 41 ARG 0.003 0.000 ARG B 162 Details of bonding type rmsd hydrogen bonds : bond 0.03208 ( 725) hydrogen bonds : angle 4.77774 ( 2043) glycosidic custom : bond 0.00170 ( 1) glycosidic custom : angle 0.92516 ( 3) covalent geometry : bond 0.00242 (12579) covalent geometry : angle 0.61461 (17252) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8757 (t80) cc_final: 0.8315 (t80) REVERT: A 58 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8831 (tm-30) REVERT: A 137 TRP cc_start: 0.9427 (m100) cc_final: 0.9215 (m100) REVERT: A 139 TYR cc_start: 0.9569 (m-80) cc_final: 0.9327 (m-80) REVERT: A 162 GLN cc_start: 0.9564 (tt0) cc_final: 0.8906 (tp-100) REVERT: A 260 ASP cc_start: 0.9080 (t0) cc_final: 0.8694 (t0) REVERT: A 261 ASN cc_start: 0.9146 (m-40) cc_final: 0.8876 (m-40) REVERT: A 291 LYS cc_start: 0.9269 (tptt) cc_final: 0.8984 (pttm) REVERT: B 36 LEU cc_start: 0.9615 (mm) cc_final: 0.9037 (mm) REVERT: B 57 TYR cc_start: 0.9296 (m-10) cc_final: 0.9017 (m-80) REVERT: B 58 LYS cc_start: 0.9676 (ptpp) cc_final: 0.9326 (mmtt) REVERT: B 90 MET cc_start: 0.8064 (mmp) cc_final: 0.7743 (tmm) REVERT: B 116 PHE cc_start: 0.8576 (t80) cc_final: 0.8244 (t80) REVERT: B 127 ASN cc_start: 0.9509 (m-40) cc_final: 0.8867 (m110) REVERT: B 128 MET cc_start: 0.9572 (mmt) cc_final: 0.9088 (mmt) REVERT: B 162 ARG cc_start: 0.9012 (mtp180) cc_final: 0.8770 (mtp180) REVERT: B 168 LEU cc_start: 0.9313 (pt) cc_final: 0.8898 (mm) REVERT: B 203 PHE cc_start: 0.9406 (t80) cc_final: 0.8951 (t80) REVERT: C 194 TYR cc_start: 0.8570 (t80) cc_final: 0.8220 (t80) REVERT: C 244 MET cc_start: 0.8520 (tpp) cc_final: 0.8222 (tpt) REVERT: D 39 LEU cc_start: 0.9547 (tp) cc_final: 0.9320 (tp) REVERT: D 86 PHE cc_start: 0.9527 (t80) cc_final: 0.9209 (t80) REVERT: D 138 GLN cc_start: 0.8174 (mp10) cc_final: 0.7591 (pp30) REVERT: D 203 MET cc_start: 0.8406 (ppp) cc_final: 0.8203 (ppp) REVERT: D 212 MET cc_start: 0.5826 (tpt) cc_final: 0.5486 (tpt) REVERT: D 224 ASP cc_start: 0.9542 (t0) cc_final: 0.9121 (p0) REVERT: D 244 MET cc_start: 0.4977 (tpt) cc_final: 0.4559 (tpp) REVERT: E 40 GLU cc_start: 0.9158 (tt0) cc_final: 0.8893 (tt0) REVERT: E 79 ARG cc_start: 0.9079 (ttt180) cc_final: 0.8820 (ttt180) REVERT: E 153 TRP cc_start: 0.9044 (m100) cc_final: 0.8684 (m-10) REVERT: E 159 MET cc_start: 0.8497 (ppp) cc_final: 0.8121 (ppp) REVERT: E 402 TYR cc_start: 0.8682 (t80) cc_final: 0.8447 (t80) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2113 time to fit residues: 72.8632 Evaluate side-chains 183 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 34 optimal weight: 0.9990 chunk 83 optimal weight: 0.0010 chunk 77 optimal weight: 0.0000 chunk 111 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 55 optimal weight: 0.1980 chunk 92 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 127 optimal weight: 4.9990 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.065257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.048660 restraints weight = 78737.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.050066 restraints weight = 57947.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.051170 restraints weight = 45481.464| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12580 Z= 0.118 Angle : 0.635 11.184 17255 Z= 0.317 Chirality : 0.044 0.242 2083 Planarity : 0.005 0.052 2235 Dihedral : 6.455 83.856 1908 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.61 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.21), residues: 1689 helix: 0.88 (0.18), residues: 882 sheet: -0.74 (0.32), residues: 191 loop : -0.93 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 97 HIS 0.009 0.001 HIS D 290 PHE 0.017 0.001 PHE A 83 TYR 0.016 0.001 TYR A 41 ARG 0.003 0.000 ARG B 162 Details of bonding type rmsd hydrogen bonds : bond 0.03226 ( 725) hydrogen bonds : angle 4.73252 ( 2043) glycosidic custom : bond 0.00434 ( 1) glycosidic custom : angle 0.87858 ( 3) covalent geometry : bond 0.00253 (12579) covalent geometry : angle 0.63518 (17252) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.8735 (t80) cc_final: 0.8318 (t80) REVERT: A 137 TRP cc_start: 0.9435 (m100) cc_final: 0.9214 (m100) REVERT: A 139 TYR cc_start: 0.9561 (m-80) cc_final: 0.9324 (m-80) REVERT: A 162 GLN cc_start: 0.9562 (tt0) cc_final: 0.8908 (tp-100) REVERT: A 224 LEU cc_start: 0.8412 (tp) cc_final: 0.8062 (tp) REVERT: A 260 ASP cc_start: 0.9077 (t0) cc_final: 0.8706 (t0) REVERT: A 261 ASN cc_start: 0.9228 (m-40) cc_final: 0.8935 (m-40) REVERT: A 291 LYS cc_start: 0.9281 (tptt) cc_final: 0.9020 (pttm) REVERT: B 36 LEU cc_start: 0.9648 (mm) cc_final: 0.9045 (mm) REVERT: B 57 TYR cc_start: 0.9306 (m-10) cc_final: 0.9052 (m-80) REVERT: B 58 LYS cc_start: 0.9685 (ptpp) cc_final: 0.9341 (mmtt) REVERT: B 90 MET cc_start: 0.8036 (mmp) cc_final: 0.7709 (tmm) REVERT: B 116 PHE cc_start: 0.8629 (t80) cc_final: 0.8403 (t80) REVERT: B 127 ASN cc_start: 0.9519 (m-40) cc_final: 0.8906 (m110) REVERT: B 128 MET cc_start: 0.9568 (mmt) cc_final: 0.9082 (mmt) REVERT: B 162 ARG cc_start: 0.9023 (mtp180) cc_final: 0.8810 (mtp180) REVERT: B 168 LEU cc_start: 0.9299 (pt) cc_final: 0.8878 (mm) REVERT: B 203 PHE cc_start: 0.9393 (t80) cc_final: 0.8952 (t80) REVERT: B 254 ILE cc_start: 0.9666 (tp) cc_final: 0.9401 (pt) REVERT: C 194 TYR cc_start: 0.8543 (t80) cc_final: 0.8288 (t80) REVERT: C 244 MET cc_start: 0.8527 (tpp) cc_final: 0.8228 (tpt) REVERT: D 39 LEU cc_start: 0.9548 (tp) cc_final: 0.9310 (tp) REVERT: D 86 PHE cc_start: 0.9549 (t80) cc_final: 0.9226 (t80) REVERT: D 138 GLN cc_start: 0.8173 (mp10) cc_final: 0.7621 (pp30) REVERT: D 203 MET cc_start: 0.8376 (ppp) cc_final: 0.8048 (ppp) REVERT: D 212 MET cc_start: 0.5872 (tpt) cc_final: 0.5511 (tpt) REVERT: D 224 ASP cc_start: 0.9562 (t0) cc_final: 0.9164 (p0) REVERT: D 244 MET cc_start: 0.5074 (tpt) cc_final: 0.4767 (tpp) REVERT: E 40 GLU cc_start: 0.9195 (tt0) cc_final: 0.8943 (tt0) REVERT: E 79 ARG cc_start: 0.9043 (ttt180) cc_final: 0.8775 (ttt180) REVERT: E 153 TRP cc_start: 0.9003 (m100) cc_final: 0.8648 (m-10) REVERT: E 159 MET cc_start: 0.8520 (ppp) cc_final: 0.8121 (ppp) REVERT: E 402 TYR cc_start: 0.8695 (t80) cc_final: 0.8460 (t80) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.2041 time to fit residues: 73.4105 Evaluate side-chains 184 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 126 optimal weight: 7.9990 chunk 135 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 87 optimal weight: 0.0060 chunk 47 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.064883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.048416 restraints weight = 79880.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.049817 restraints weight = 58872.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.050864 restraints weight = 46161.799| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.5501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12580 Z= 0.114 Angle : 0.622 8.642 17255 Z= 0.310 Chirality : 0.043 0.250 2083 Planarity : 0.005 0.054 2235 Dihedral : 6.368 85.186 1908 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.79 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.21), residues: 1689 helix: 0.88 (0.18), residues: 885 sheet: -0.70 (0.32), residues: 191 loop : -0.91 (0.27), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 207 HIS 0.005 0.001 HIS D 290 PHE 0.017 0.001 PHE B 148 TYR 0.016 0.001 TYR A 41 ARG 0.003 0.000 ARG B 162 Details of bonding type rmsd hydrogen bonds : bond 0.03136 ( 725) hydrogen bonds : angle 4.70844 ( 2043) glycosidic custom : bond 0.00318 ( 1) glycosidic custom : angle 0.96412 ( 3) covalent geometry : bond 0.00244 (12579) covalent geometry : angle 0.62176 (17252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4447.88 seconds wall clock time: 81 minutes 12.57 seconds (4872.57 seconds total)