Starting phenix.real_space_refine on Wed Mar 4 09:33:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hpn_34934/03_2026/8hpn_34934.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hpn_34934/03_2026/8hpn_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 { model { file = "/net/cci-nas-00/data/ceres_data/8hpn_34934/03_2026/8hpn_34934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hpn_34934/03_2026/8hpn_34934.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hpn_34934/03_2026/8hpn_34934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hpn_34934/03_2026/8hpn_34934.map" } resolution = 4.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ARG:plan': 5, 'GLN:plan1': 2, 'GLU:plan': 2, 'TYR:plan': 2, 'TRP:plan': 1, 'PHE:plan': 1} 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: {'PHE:plan': 3, 'ARG:plan': 4, 'ASP:plan': 2, 'TRP:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} 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: {'ASP:plan': 5, 'ARG:plan': 8, 'PHE:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 4, 'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 1} 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: {'ASP:plan': 3, 'ARG:plan': 8, 'PHE:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 4, 'GLN:plan1': 3, 'TYR:plan': 2} 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: {'GLU:plan': 5, 'ARG:plan': 8, 'ASP:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 3} 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: 3.20, per 1000 atoms: 0.26 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: 1.15 Conformation dependent library (CDL) restraints added in 609.8 milliseconds 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: 0.44 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: 2.22 Time building geometry restraints manager: 1.47 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 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 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: 5.490 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.320 Find NCS groups from input model: 0.150 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.760 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.014 0.001 ARG D 302 TYR 0.120 0.021 TYR E 402 PHE 0.113 0.017 PHE C 234 TRP 0.128 0.017 TRP E 166 HIS 0.011 0.003 HIS D 290 Details of bonding type rmsd covalent geometry : bond 0.01217 (12579) covalent geometry : angle 1.81367 (17252) hydrogen bonds : bond 0.14868 ( 725) hydrogen bonds : angle 8.10798 ( 2043) glycosidic custom : bond 0.02882 ( 1) glycosidic custom : angle 2.03772 ( 3) *********************** 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 : 0.474 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: symmetry clash REVERT: A 139 TYR cc_start: 0.9486 (m-80) cc_final: 0.8928 (m-80) REVERT: A 162 GLN cc_start: 0.9526 (tt0) cc_final: 0.9068 (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: 0.9105 (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: 0.9062 (ttt) REVERT: C 163 ASP cc_start: 0.8276 (m-30) cc_final: 0.7967 (t0) REVERT: C 239 ILE cc_start: 0.8991 (tp) cc_final: 0.8672 (pt) REVERT: D 177 MET cc_start: 0.9143 (mmm) cc_final: 0.8690 (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: 0.8439 (m100) REVERT: E 154 TYR cc_start: 0.8947 (p90) cc_final: 0.8234 (p90) outliers start: 4 outliers final: 0 residues processed: 313 average time/residue: 0.1152 time to fit residues: 51.4141 Evaluate side-chains 204 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.0870 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.0970 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- 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 C 99 GLN C 164 GLN C 218 GLN ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 GLN E 65 ASN E 174 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.063740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.047497 restraints weight = 81763.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.048898 restraints weight = 59663.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.049999 restraints weight = 46516.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.050736 restraints weight = 37999.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.051505 restraints weight = 32506.753| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12580 Z= 0.167 Angle : 0.775 10.618 17255 Z= 0.408 Chirality : 0.048 0.197 2083 Planarity : 0.006 0.056 2235 Dihedral : 8.070 71.445 1908 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.09 % Favored : 95.80 % Rotamer: Outliers : 0.52 % Allowed : 4.33 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.20), residues: 1689 helix: -0.16 (0.17), residues: 868 sheet: -1.03 (0.35), residues: 158 loop : -0.99 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 74 TYR 0.030 0.003 TYR D 13 PHE 0.038 0.003 PHE D 36 TRP 0.041 0.003 TRP E 97 HIS 0.006 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00339 (12579) covalent geometry : angle 0.77469 (17252) hydrogen bonds : bond 0.05090 ( 725) hydrogen bonds : angle 5.79310 ( 2043) glycosidic custom : bond 0.01030 ( 1) glycosidic custom : angle 0.56311 ( 3) *********************** 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 278 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 272 time to evaluate : 0.298 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: 0.9546 (m-80) cc_final: 0.9030 (m-80) REVERT: A 161 ASP cc_start: 0.9364 (m-30) cc_final: 0.8890 (p0) REVERT: A 162 GLN cc_start: 0.9649 (tt0) cc_final: 0.9021 (tp40) REVERT: A 166 LEU cc_start: 0.9815 (mt) cc_final: 0.9608 (mt) REVERT: A 176 LYS cc_start: 0.9538 (tptp) cc_final: 0.9196 (tppt) REVERT: A 198 ASN cc_start: 0.9584 (m110) cc_final: 0.9218 (m110) REVERT: A 201 GLN cc_start: 0.9559 (OUTLIER) cc_final: 0.8965 (mm-40) REVERT: A 260 ASP cc_start: 0.9131 (t0) cc_final: 0.8568 (t0) REVERT: A 261 ASN cc_start: 0.9360 (m-40) cc_final: 0.9099 (m-40) REVERT: B 90 MET cc_start: 0.8221 (mmp) cc_final: 0.7604 (tmm) REVERT: B 118 HIS cc_start: 0.9182 (m-70) cc_final: 0.8852 (m-70) REVERT: B 121 LEU cc_start: 0.9545 (mm) cc_final: 0.8833 (mm) REVERT: B 127 ASN cc_start: 0.9504 (m-40) cc_final: 0.8889 (m110) REVERT: B 168 LEU cc_start: 0.9460 (pt) cc_final: 0.9207 (mm) REVERT: B 203 PHE cc_start: 0.9497 (t80) cc_final: 0.9281 (t80) REVERT: B 205 PHE cc_start: 0.9386 (t80) cc_final: 0.9170 (t80) REVERT: C 163 ASP cc_start: 0.8874 (m-30) cc_final: 0.8248 (t0) REVERT: C 225 GLU cc_start: 0.9664 (mm-30) cc_final: 0.9443 (tm-30) REVERT: C 239 ILE cc_start: 0.9021 (tp) cc_final: 0.8590 (pt) REVERT: C 244 MET cc_start: 0.8485 (tpp) cc_final: 0.7999 (tpt) REVERT: E 91 MET cc_start: 0.8811 (ptp) cc_final: 0.8606 (ptp) REVERT: E 166 TRP cc_start: 0.8436 (m100) cc_final: 0.8235 (m100) outliers start: 6 outliers final: 0 residues processed: 274 average time/residue: 0.0918 time to fit residues: 38.2817 Evaluate side-chains 201 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 65 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 143 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 147 optimal weight: 6.9990 chunk 116 optimal weight: 0.0050 chunk 105 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN D 276 GLN E 137 GLN E 305 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.062631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.046932 restraints weight = 84292.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.048279 restraints weight = 61367.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.049348 restraints weight = 47732.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.050174 restraints weight = 38918.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.050845 restraints weight = 32867.191| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12580 Z= 0.158 Angle : 0.695 7.403 17255 Z= 0.365 Chirality : 0.045 0.202 2083 Planarity : 0.005 0.052 2235 Dihedral : 7.360 78.604 1908 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.44 % Favored : 95.38 % Rotamer: Outliers : 0.26 % Allowed : 3.37 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.20), residues: 1689 helix: 0.25 (0.17), residues: 872 sheet: -1.21 (0.33), residues: 187 loop : -0.97 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 144 TYR 0.021 0.002 TYR E 378 PHE 0.024 0.002 PHE B 116 TRP 0.041 0.002 TRP E 97 HIS 0.006 0.001 HIS C 268 Details of bonding type rmsd covalent geometry : bond 0.00325 (12579) covalent geometry : angle 0.69463 (17252) hydrogen bonds : bond 0.04352 ( 725) hydrogen bonds : angle 5.45713 ( 2043) glycosidic custom : bond 0.00028 ( 1) glycosidic custom : angle 1.23476 ( 3) *********************** 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 253 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 250 time to evaluate : 0.415 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: A 45 TYR cc_start: 0.8727 (t80) cc_final: 0.8343 (t80) REVERT: A 139 TYR cc_start: 0.9560 (m-80) cc_final: 0.9018 (m-80) REVERT: A 150 ASN cc_start: 0.8654 (t0) cc_final: 0.8245 (m-40) REVERT: A 161 ASP cc_start: 0.9355 (m-30) cc_final: 0.9144 (m-30) REVERT: A 162 GLN cc_start: 0.9640 (tt0) cc_final: 0.8902 (tp40) REVERT: A 176 LYS cc_start: 0.9546 (tptp) cc_final: 0.9221 (tppt) REVERT: A 198 ASN cc_start: 0.9601 (m110) cc_final: 0.9237 (m110) REVERT: A 201 GLN cc_start: 0.9531 (OUTLIER) cc_final: 0.8837 (mm-40) REVERT: A 260 ASP cc_start: 0.9138 (t0) cc_final: 0.8680 (t0) REVERT: A 261 ASN cc_start: 0.9376 (m-40) cc_final: 0.9117 (m-40) REVERT: B 58 LYS cc_start: 0.9699 (ptpp) cc_final: 0.9351 (mmtt) REVERT: B 90 MET cc_start: 0.8123 (mmp) cc_final: 0.7623 (tmm) REVERT: B 116 PHE cc_start: 0.7941 (t80) cc_final: 0.7738 (t80) REVERT: B 127 ASN cc_start: 0.9525 (m-40) cc_final: 0.8792 (m110) REVERT: B 128 MET cc_start: 0.9458 (mmt) cc_final: 0.8922 (mmp) REVERT: B 145 TYR cc_start: 0.9369 (m-10) cc_final: 0.8746 (m-80) REVERT: B 168 LEU cc_start: 0.9455 (pt) cc_final: 0.9160 (mm) REVERT: B 203 PHE cc_start: 0.9453 (t80) cc_final: 0.9234 (t80) REVERT: B 205 PHE cc_start: 0.9363 (t80) cc_final: 0.9162 (t80) REVERT: C 163 ASP cc_start: 0.8833 (m-30) cc_final: 0.8415 (p0) REVERT: C 244 MET cc_start: 0.8420 (tpp) cc_final: 0.7898 (tpt) REVERT: D 212 MET cc_start: 0.5981 (tpt) cc_final: 0.5269 (tpt) REVERT: E 40 GLU cc_start: 0.9317 (tt0) cc_final: 0.8803 (tt0) outliers start: 3 outliers final: 0 residues processed: 251 average time/residue: 0.0926 time to fit residues: 35.4628 Evaluate side-chains 195 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 1 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 359 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.063570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.047699 restraints weight = 82022.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.049107 restraints weight = 59471.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.050212 restraints weight = 46036.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.051072 restraints weight = 37354.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.051746 restraints weight = 31463.388| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12580 Z= 0.135 Angle : 0.655 12.047 17255 Z= 0.337 Chirality : 0.044 0.189 2083 Planarity : 0.005 0.055 2235 Dihedral : 7.215 79.228 1908 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.79 % Favored : 96.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.20), residues: 1689 helix: 0.45 (0.18), residues: 876 sheet: -0.98 (0.35), residues: 165 loop : -0.91 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 183 TYR 0.018 0.002 TYR A 41 PHE 0.021 0.001 PHE A 98 TRP 0.034 0.002 TRP E 97 HIS 0.005 0.001 HIS C 268 Details of bonding type rmsd covalent geometry : bond 0.00278 (12579) covalent geometry : angle 0.65464 (17252) hydrogen bonds : bond 0.03933 ( 725) hydrogen bonds : angle 5.23120 ( 2043) glycosidic custom : bond 0.00103 ( 1) glycosidic custom : angle 0.90781 ( 3) *********************** 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 247 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 246 time to evaluate : 0.280 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 45 TYR cc_start: 0.8722 (t80) cc_final: 0.8278 (t80) REVERT: A 139 TYR cc_start: 0.9569 (m-80) cc_final: 0.9194 (m-80) REVERT: A 161 ASP cc_start: 0.9345 (m-30) cc_final: 0.8961 (m-30) REVERT: A 162 GLN cc_start: 0.9618 (tt0) cc_final: 0.8655 (tp40) REVERT: A 176 LYS cc_start: 0.9539 (tptp) cc_final: 0.9230 (tppt) REVERT: A 198 ASN cc_start: 0.9615 (m110) cc_final: 0.9226 (m110) REVERT: A 201 GLN cc_start: 0.9563 (OUTLIER) cc_final: 0.8844 (mm-40) REVERT: A 260 ASP cc_start: 0.9069 (t0) cc_final: 0.8606 (t0) REVERT: A 261 ASN cc_start: 0.9220 (m-40) cc_final: 0.8899 (m-40) REVERT: B 32 LEU cc_start: 0.9636 (mm) cc_final: 0.9313 (mm) REVERT: B 36 LEU cc_start: 0.9567 (mm) cc_final: 0.9025 (mm) REVERT: B 57 TYR cc_start: 0.9006 (m-80) cc_final: 0.8791 (m-80) REVERT: B 58 LYS cc_start: 0.9666 (ptpp) cc_final: 0.9348 (mmtt) REVERT: B 90 MET cc_start: 0.8142 (mmp) cc_final: 0.7679 (tmm) REVERT: B 127 ASN cc_start: 0.9530 (m-40) cc_final: 0.8683 (m110) REVERT: B 128 MET cc_start: 0.9455 (mmt) cc_final: 0.8863 (mmp) REVERT: B 145 TYR cc_start: 0.9362 (m-10) cc_final: 0.8736 (m-80) REVERT: B 168 LEU cc_start: 0.9456 (pt) cc_final: 0.9139 (mm) REVERT: C 163 ASP cc_start: 0.8805 (m-30) cc_final: 0.8114 (t0) REVERT: C 244 MET cc_start: 0.8426 (tpp) cc_final: 0.7969 (tpt) REVERT: D 177 MET cc_start: 0.9152 (mmp) cc_final: 0.8719 (mmp) REVERT: D 212 MET cc_start: 0.6148 (tpt) cc_final: 0.5444 (tpt) REVERT: D 224 ASP cc_start: 0.9588 (t0) cc_final: 0.9189 (p0) REVERT: E 40 GLU cc_start: 0.9102 (tt0) cc_final: 0.8814 (tt0) REVERT: E 91 MET cc_start: 0.8936 (ptp) cc_final: 0.8424 (pmm) REVERT: E 159 MET cc_start: 0.8390 (ppp) cc_final: 0.8131 (ppp) outliers start: 1 outliers final: 0 residues processed: 247 average time/residue: 0.0837 time to fit residues: 32.4982 Evaluate side-chains 190 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 102 optimal weight: 0.6980 chunk 150 optimal weight: 0.5980 chunk 124 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 134 optimal weight: 0.3980 chunk 125 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 157 optimal weight: 20.0000 chunk 165 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 249 ASN ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.061431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.045952 restraints weight = 85930.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.047306 restraints weight = 62205.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.048358 restraints weight = 48166.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.049178 restraints weight = 39132.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.049816 restraints weight = 32984.866| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12580 Z= 0.160 Angle : 0.653 7.783 17255 Z= 0.339 Chirality : 0.044 0.197 2083 Planarity : 0.005 0.051 2235 Dihedral : 7.238 82.435 1908 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.32 % Favored : 95.56 % Rotamer: Outliers : 0.09 % Allowed : 2.60 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.20), residues: 1689 helix: 0.61 (0.18), residues: 875 sheet: -1.06 (0.33), residues: 177 loop : -1.03 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 183 TYR 0.018 0.002 TYR E 333 PHE 0.022 0.002 PHE A 279 TRP 0.040 0.002 TRP E 97 HIS 0.005 0.001 HIS C 268 Details of bonding type rmsd covalent geometry : bond 0.00330 (12579) covalent geometry : angle 0.65293 (17252) hydrogen bonds : bond 0.03820 ( 725) hydrogen bonds : angle 5.18802 ( 2043) glycosidic custom : bond 0.00202 ( 1) glycosidic custom : angle 1.50900 ( 3) *********************** 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 239 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 0.457 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: 0.9573 (m-80) cc_final: 0.9143 (m-80) REVERT: A 161 ASP cc_start: 0.9096 (m-30) cc_final: 0.8616 (p0) REVERT: A 162 GLN cc_start: 0.9554 (tt0) cc_final: 0.8713 (tp40) REVERT: A 176 LYS cc_start: 0.9543 (tptp) cc_final: 0.9228 (tppt) REVERT: A 250 ASP cc_start: 0.9448 (m-30) cc_final: 0.9175 (p0) REVERT: A 260 ASP cc_start: 0.9100 (t0) cc_final: 0.8643 (t0) REVERT: A 261 ASN cc_start: 0.9272 (m-40) cc_final: 0.8988 (m-40) REVERT: A 291 LYS cc_start: 0.9099 (tptt) cc_final: 0.8885 (pttm) REVERT: B 58 LYS cc_start: 0.9669 (ptpp) cc_final: 0.9364 (mmtt) REVERT: B 90 MET cc_start: 0.8189 (mmp) cc_final: 0.7700 (tmm) REVERT: B 127 ASN cc_start: 0.9528 (m-40) cc_final: 0.9071 (m110) REVERT: B 168 LEU cc_start: 0.9418 (pt) cc_final: 0.9108 (mm) REVERT: B 203 PHE cc_start: 0.9245 (t80) cc_final: 0.8986 (t80) REVERT: C 163 ASP cc_start: 0.8931 (m-30) cc_final: 0.8431 (p0) REVERT: C 216 GLU cc_start: 0.9238 (mm-30) cc_final: 0.8632 (mm-30) REVERT: D 86 PHE cc_start: 0.9490 (t80) cc_final: 0.9201 (t80) REVERT: D 212 MET cc_start: 0.6325 (tpt) cc_final: 0.5837 (tpt) REVERT: D 224 ASP cc_start: 0.9547 (t0) cc_final: 0.9118 (p0) REVERT: E 44 PHE cc_start: 0.9154 (m-80) cc_final: 0.8625 (m-80) REVERT: E 91 MET cc_start: 0.9009 (ptp) cc_final: 0.8755 (pmm) REVERT: E 101 PHE cc_start: 0.8936 (m-80) cc_final: 0.8719 (m-80) REVERT: E 159 MET cc_start: 0.8402 (ppp) cc_final: 0.8093 (ppp) outliers start: 1 outliers final: 0 residues processed: 239 average time/residue: 0.0873 time to fit residues: 32.7040 Evaluate side-chains 181 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 168 optimal weight: 0.9990 chunk 166 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 102 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 167 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.063366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.047666 restraints weight = 82345.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.049060 restraints weight = 59775.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.050144 restraints weight = 46325.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.051001 restraints weight = 37625.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.051669 restraints weight = 31678.243| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12580 Z= 0.124 Angle : 0.634 7.274 17255 Z= 0.323 Chirality : 0.044 0.209 2083 Planarity : 0.005 0.051 2235 Dihedral : 7.002 80.730 1908 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.73 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.21), residues: 1689 helix: 0.72 (0.18), residues: 876 sheet: -0.88 (0.34), residues: 177 loop : -0.99 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 183 TYR 0.020 0.002 TYR A 41 PHE 0.025 0.001 PHE A 98 TRP 0.031 0.002 TRP E 97 HIS 0.005 0.001 HIS C 268 Details of bonding type rmsd covalent geometry : bond 0.00259 (12579) covalent geometry : angle 0.63401 (17252) hydrogen bonds : bond 0.03560 ( 725) hydrogen bonds : angle 5.01785 ( 2043) glycosidic custom : bond 0.00911 ( 1) glycosidic custom : angle 1.27535 ( 3) *********************** 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 241 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.462 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 45 TYR cc_start: 0.8734 (t80) cc_final: 0.8297 (t80) REVERT: A 139 TYR cc_start: 0.9556 (m-80) cc_final: 0.9209 (m-80) REVERT: A 162 GLN cc_start: 0.9537 (tt0) cc_final: 0.8903 (tp40) REVERT: A 176 LYS cc_start: 0.9515 (tptp) cc_final: 0.9204 (tppt) REVERT: A 260 ASP cc_start: 0.9028 (t0) cc_final: 0.8583 (t0) REVERT: A 261 ASN cc_start: 0.9244 (m-40) cc_final: 0.8977 (m-40) REVERT: A 291 LYS cc_start: 0.9083 (tptt) cc_final: 0.8877 (pttm) REVERT: B 32 LEU cc_start: 0.9635 (mm) cc_final: 0.9359 (mm) REVERT: B 36 LEU cc_start: 0.9554 (mm) cc_final: 0.8926 (mm) REVERT: B 58 LYS cc_start: 0.9649 (ptpp) cc_final: 0.9327 (mmtt) REVERT: B 90 MET cc_start: 0.8170 (mmp) cc_final: 0.7702 (tmm) REVERT: B 93 TYR cc_start: 0.9352 (t80) cc_final: 0.9141 (t80) REVERT: B 127 ASN cc_start: 0.9490 (m-40) cc_final: 0.8851 (m110) REVERT: B 128 MET cc_start: 0.9493 (mmt) cc_final: 0.8974 (mmt) REVERT: B 168 LEU cc_start: 0.9371 (pt) cc_final: 0.9044 (mm) REVERT: B 203 PHE cc_start: 0.9220 (t80) cc_final: 0.8965 (t80) REVERT: B 207 TRP cc_start: 0.8657 (t60) cc_final: 0.8427 (t60) REVERT: C 163 ASP cc_start: 0.8898 (m-30) cc_final: 0.8326 (p0) REVERT: C 216 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8685 (mp0) REVERT: D 86 PHE cc_start: 0.9462 (t80) cc_final: 0.9198 (t80) REVERT: D 212 MET cc_start: 0.6533 (tpt) cc_final: 0.5884 (tpt) REVERT: D 224 ASP cc_start: 0.9541 (t0) cc_final: 0.9097 (p0) REVERT: D 244 MET cc_start: 0.5016 (tpt) cc_final: 0.4689 (tpp) REVERT: E 40 GLU cc_start: 0.9084 (tt0) cc_final: 0.8795 (tt0) REVERT: E 101 PHE cc_start: 0.8958 (m-80) cc_final: 0.8732 (m-80) REVERT: E 159 MET cc_start: 0.8510 (ppp) cc_final: 0.8163 (ppp) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.0911 time to fit residues: 33.8440 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 : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 55 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 43 optimal weight: 0.3980 chunk 67 optimal weight: 7.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** 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 = 0.3323 r_free = 0.3323 target = 0.062441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.046935 restraints weight = 84306.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.048279 restraints weight = 61314.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.049308 restraints weight = 47657.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.050130 restraints weight = 38872.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.050780 restraints weight = 32823.800| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12580 Z= 0.131 Angle : 0.617 7.179 17255 Z= 0.316 Chirality : 0.043 0.211 2083 Planarity : 0.005 0.051 2235 Dihedral : 6.882 83.648 1908 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.67 % Favored : 96.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.21), residues: 1689 helix: 0.78 (0.18), residues: 878 sheet: -0.92 (0.32), residues: 189 loop : -0.97 (0.27), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 183 TYR 0.016 0.002 TYR A 41 PHE 0.016 0.001 PHE C 160 TRP 0.035 0.002 TRP E 97 HIS 0.005 0.001 HIS C 268 Details of bonding type rmsd covalent geometry : bond 0.00275 (12579) covalent geometry : angle 0.61691 (17252) hydrogen bonds : bond 0.03448 ( 725) hydrogen bonds : angle 4.96411 ( 2043) glycosidic custom : bond 0.00030 ( 1) glycosidic custom : angle 1.25893 ( 3) *********************** 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 232 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.407 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: A 45 TYR cc_start: 0.8730 (t80) cc_final: 0.8305 (t80) REVERT: A 58 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8687 (tm-30) REVERT: A 139 TYR cc_start: 0.9558 (m-80) cc_final: 0.9172 (m-80) REVERT: A 162 GLN cc_start: 0.9566 (tt0) cc_final: 0.8905 (tp40) REVERT: A 176 LYS cc_start: 0.9508 (tptp) cc_final: 0.9199 (tppt) REVERT: A 260 ASP cc_start: 0.9068 (t0) cc_final: 0.8662 (t0) REVERT: A 261 ASN cc_start: 0.9264 (m-40) cc_final: 0.9024 (m-40) REVERT: A 279 PHE cc_start: 0.9684 (t80) cc_final: 0.9477 (t80) REVERT: A 291 LYS cc_start: 0.9194 (tptt) cc_final: 0.8959 (pttm) REVERT: B 32 LEU cc_start: 0.9628 (mm) cc_final: 0.9323 (mm) REVERT: B 36 LEU cc_start: 0.9554 (mm) cc_final: 0.8853 (mm) REVERT: B 57 TYR cc_start: 0.9213 (m-10) cc_final: 0.9002 (m-80) REVERT: B 58 LYS cc_start: 0.9663 (ptpp) cc_final: 0.9327 (mmtt) REVERT: B 90 MET cc_start: 0.8140 (mmp) cc_final: 0.7746 (tmm) REVERT: B 127 ASN cc_start: 0.9486 (m-40) cc_final: 0.8879 (m110) REVERT: B 128 MET cc_start: 0.9561 (mmt) cc_final: 0.9071 (mmt) REVERT: B 162 ARG cc_start: 0.9236 (mtp180) cc_final: 0.9031 (mtp180) REVERT: B 168 LEU cc_start: 0.9377 (pt) cc_final: 0.9021 (mm) REVERT: B 203 PHE cc_start: 0.9227 (t80) cc_final: 0.8971 (t80) REVERT: C 163 ASP cc_start: 0.9008 (m-30) cc_final: 0.8436 (p0) REVERT: D 39 LEU cc_start: 0.9540 (tp) cc_final: 0.9307 (tp) REVERT: D 86 PHE cc_start: 0.9488 (t80) cc_final: 0.9220 (t80) REVERT: D 212 MET cc_start: 0.7612 (tpp) cc_final: 0.7118 (tpp) REVERT: D 224 ASP cc_start: 0.9550 (t0) cc_final: 0.9107 (p0) REVERT: D 244 MET cc_start: 0.4836 (tpt) cc_final: 0.4548 (tpp) REVERT: E 40 GLU cc_start: 0.9103 (tt0) cc_final: 0.8821 (tt0) REVERT: E 101 PHE cc_start: 0.8994 (m-80) cc_final: 0.8788 (m-80) REVERT: E 159 MET cc_start: 0.8516 (ppp) cc_final: 0.8104 (ppp) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.0875 time to fit residues: 31.8913 Evaluate side-chains 178 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 63 optimal weight: 0.9980 chunk 153 optimal weight: 8.9990 chunk 152 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 158 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 73 optimal weight: 0.0980 chunk 157 optimal weight: 20.0000 chunk 95 optimal weight: 8.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.062514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.046713 restraints weight = 82703.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.048074 restraints weight = 60251.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.049111 restraints weight = 46900.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.049873 restraints weight = 38282.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.050577 restraints weight = 32819.675| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12580 Z= 0.128 Angle : 0.618 7.297 17255 Z= 0.314 Chirality : 0.043 0.228 2083 Planarity : 0.005 0.051 2235 Dihedral : 6.769 83.475 1908 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.03 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.21), residues: 1689 helix: 0.82 (0.18), residues: 883 sheet: -0.67 (0.35), residues: 177 loop : -0.88 (0.27), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 183 TYR 0.017 0.002 TYR A 41 PHE 0.016 0.001 PHE A 83 TRP 0.036 0.002 TRP E 97 HIS 0.005 0.001 HIS C 268 Details of bonding type rmsd covalent geometry : bond 0.00272 (12579) covalent geometry : angle 0.61756 (17252) hydrogen bonds : bond 0.03374 ( 725) hydrogen bonds : angle 4.90284 ( 2043) glycosidic custom : bond 0.00174 ( 1) glycosidic custom : angle 1.26575 ( 3) *********************** 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 232 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.556 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: 0.8797 (t80) cc_final: 0.8324 (t80) REVERT: A 58 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8764 (tm-30) REVERT: A 139 TYR cc_start: 0.9564 (m-80) cc_final: 0.9179 (m-80) REVERT: A 162 GLN cc_start: 0.9554 (tt0) cc_final: 0.8878 (tp40) REVERT: A 176 LYS cc_start: 0.9530 (tptp) cc_final: 0.9247 (tppt) REVERT: A 260 ASP cc_start: 0.9083 (t0) cc_final: 0.8669 (t0) REVERT: A 261 ASN cc_start: 0.9298 (m-40) cc_final: 0.9072 (m-40) REVERT: A 291 LYS cc_start: 0.9244 (tptt) cc_final: 0.8988 (pttm) REVERT: B 57 TYR cc_start: 0.9275 (m-10) cc_final: 0.9008 (m-80) REVERT: B 58 LYS cc_start: 0.9675 (ptpp) cc_final: 0.9339 (mmtt) REVERT: B 90 MET cc_start: 0.8123 (mmp) cc_final: 0.7735 (tmm) REVERT: B 127 ASN cc_start: 0.9481 (m-40) cc_final: 0.8888 (m110) REVERT: B 128 MET cc_start: 0.9581 (mmt) cc_final: 0.9070 (mmt) REVERT: B 162 ARG cc_start: 0.9244 (mtp180) cc_final: 0.9028 (mtp180) REVERT: B 168 LEU cc_start: 0.9378 (pt) cc_final: 0.9023 (mm) REVERT: B 203 PHE cc_start: 0.9232 (t80) cc_final: 0.8983 (t80) REVERT: C 163 ASP cc_start: 0.9019 (m-30) cc_final: 0.8445 (p0) REVERT: D 86 PHE cc_start: 0.9512 (t80) cc_final: 0.9246 (t80) REVERT: D 224 ASP cc_start: 0.9550 (t0) cc_final: 0.9109 (p0) REVERT: D 244 MET cc_start: 0.4978 (tpt) cc_final: 0.4643 (tpp) REVERT: E 40 GLU cc_start: 0.9150 (tt0) cc_final: 0.8878 (tt0) REVERT: E 101 PHE cc_start: 0.9030 (m-80) cc_final: 0.8826 (m-80) REVERT: E 159 MET cc_start: 0.8541 (ppp) cc_final: 0.8066 (ppp) REVERT: E 402 TYR cc_start: 0.8804 (t80) cc_final: 0.8540 (t80) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.0840 time to fit residues: 30.9120 Evaluate side-chains 181 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 85 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 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 = 0.3328 r_free = 0.3328 target = 0.062825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.047077 restraints weight = 83655.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.048457 restraints weight = 60622.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.049510 restraints weight = 46901.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.050353 restraints weight = 38154.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.051005 restraints weight = 32122.869| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12580 Z= 0.119 Angle : 0.615 7.215 17255 Z= 0.310 Chirality : 0.043 0.231 2083 Planarity : 0.005 0.052 2235 Dihedral : 6.647 84.394 1908 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.03 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.21), residues: 1689 helix: 0.85 (0.18), residues: 880 sheet: -0.76 (0.34), residues: 189 loop : -0.95 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 183 TYR 0.018 0.002 TYR A 41 PHE 0.025 0.001 PHE A 98 TRP 0.037 0.002 TRP E 97 HIS 0.005 0.001 HIS C 268 Details of bonding type rmsd covalent geometry : bond 0.00256 (12579) covalent geometry : angle 0.61481 (17252) hydrogen bonds : bond 0.03285 ( 725) hydrogen bonds : angle 4.84967 ( 2043) glycosidic custom : bond 0.00200 ( 1) glycosidic custom : angle 1.13148 ( 3) *********************** 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 : 0.472 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: 0.8756 (t80) cc_final: 0.8318 (t80) REVERT: A 58 GLU cc_start: 0.9014 (tm-30) cc_final: 0.8789 (tm-30) REVERT: A 139 TYR cc_start: 0.9554 (m-80) cc_final: 0.9178 (m-80) REVERT: A 162 GLN cc_start: 0.9564 (tt0) cc_final: 0.8862 (tp40) REVERT: A 176 LYS cc_start: 0.9522 (tptp) cc_final: 0.9210 (tppp) REVERT: A 260 ASP cc_start: 0.9063 (t0) cc_final: 0.8695 (t0) REVERT: A 261 ASN cc_start: 0.9292 (m-40) cc_final: 0.9016 (m-40) REVERT: A 291 LYS cc_start: 0.9278 (tptt) cc_final: 0.9021 (pttm) REVERT: B 36 LEU cc_start: 0.9595 (mm) cc_final: 0.8953 (mm) REVERT: B 57 TYR cc_start: 0.9294 (m-10) cc_final: 0.9030 (m-80) REVERT: B 58 LYS cc_start: 0.9678 (ptpp) cc_final: 0.9337 (mmtt) REVERT: B 90 MET cc_start: 0.8148 (mmp) cc_final: 0.7716 (tmm) REVERT: B 127 ASN cc_start: 0.9489 (m-40) cc_final: 0.8902 (m110) REVERT: B 128 MET cc_start: 0.9570 (mmt) cc_final: 0.9065 (mmt) REVERT: B 162 ARG cc_start: 0.9235 (mtp180) cc_final: 0.9017 (mtp180) REVERT: B 168 LEU cc_start: 0.9360 (pt) cc_final: 0.8990 (mm) REVERT: B 203 PHE cc_start: 0.9224 (t80) cc_final: 0.8963 (t80) REVERT: C 163 ASP cc_start: 0.8977 (m-30) cc_final: 0.8372 (p0) REVERT: D 39 LEU cc_start: 0.9533 (tp) cc_final: 0.9330 (tp) REVERT: D 86 PHE cc_start: 0.9527 (t80) cc_final: 0.9256 (t80) REVERT: D 224 ASP cc_start: 0.9542 (t0) cc_final: 0.9112 (p0) REVERT: D 244 MET cc_start: 0.5211 (tpt) cc_final: 0.4866 (tpp) REVERT: E 40 GLU cc_start: 0.9156 (tt0) cc_final: 0.8886 (tt0) REVERT: E 159 MET cc_start: 0.8568 (ppp) cc_final: 0.8072 (ppp) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.0837 time to fit residues: 30.8089 Evaluate side-chains 176 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 73 optimal weight: 7.9990 chunk 146 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 144 optimal weight: 0.0570 chunk 165 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 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 = 0.3329 r_free = 0.3329 target = 0.063052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.047166 restraints weight = 82379.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.048541 restraints weight = 59827.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.049596 restraints weight = 46439.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.050363 restraints weight = 37796.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.051067 restraints weight = 32241.803| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 12580 Z= 0.117 Angle : 0.614 7.233 17255 Z= 0.308 Chirality : 0.043 0.241 2083 Planarity : 0.005 0.052 2235 Dihedral : 6.512 85.328 1908 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.85 % Favored : 96.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.21), residues: 1689 helix: 0.88 (0.18), residues: 886 sheet: -0.70 (0.34), residues: 189 loop : -0.89 (0.27), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 183 TYR 0.018 0.002 TYR A 41 PHE 0.024 0.001 PHE A 279 TRP 0.034 0.002 TRP E 97 HIS 0.005 0.001 HIS C 268 Details of bonding type rmsd covalent geometry : bond 0.00250 (12579) covalent geometry : angle 0.61343 (17252) hydrogen bonds : bond 0.03241 ( 725) hydrogen bonds : angle 4.79405 ( 2043) glycosidic custom : bond 0.00195 ( 1) glycosidic custom : angle 1.17650 ( 3) ********************** 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 235 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.577 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 45 TYR cc_start: 0.8782 (t80) cc_final: 0.8350 (t80) REVERT: A 139 TYR cc_start: 0.9540 (m-80) cc_final: 0.9159 (m-80) REVERT: A 162 GLN cc_start: 0.9552 (tt0) cc_final: 0.8842 (tp40) REVERT: A 168 ILE cc_start: 0.9680 (mm) cc_final: 0.9434 (mm) REVERT: A 229 PHE cc_start: 0.9320 (t80) cc_final: 0.8961 (t80) REVERT: A 233 ASP cc_start: 0.8812 (m-30) cc_final: 0.8525 (m-30) REVERT: A 260 ASP cc_start: 0.9109 (t0) cc_final: 0.8695 (t0) REVERT: A 261 ASN cc_start: 0.9285 (m-40) cc_final: 0.8974 (m-40) REVERT: A 291 LYS cc_start: 0.9313 (tptt) cc_final: 0.9059 (pttm) REVERT: B 36 LEU cc_start: 0.9574 (mm) cc_final: 0.9000 (mm) REVERT: B 37 LYS cc_start: 0.9044 (mtpt) cc_final: 0.8518 (mmmm) REVERT: B 90 MET cc_start: 0.8148 (mmp) cc_final: 0.7720 (tmm) REVERT: B 127 ASN cc_start: 0.9495 (m-40) cc_final: 0.8912 (m110) REVERT: B 128 MET cc_start: 0.9579 (mmt) cc_final: 0.9066 (mmt) REVERT: B 162 ARG cc_start: 0.9208 (mtp180) cc_final: 0.8975 (mtp180) REVERT: B 168 LEU cc_start: 0.9342 (pt) cc_final: 0.8986 (mm) REVERT: B 203 PHE cc_start: 0.9225 (t80) cc_final: 0.8971 (t80) REVERT: C 163 ASP cc_start: 0.8989 (m-30) cc_final: 0.8394 (p0) REVERT: D 39 LEU cc_start: 0.9528 (tp) cc_final: 0.9321 (tp) REVERT: D 86 PHE cc_start: 0.9538 (t80) cc_final: 0.9261 (t80) REVERT: D 224 ASP cc_start: 0.9550 (t0) cc_final: 0.9128 (p0) REVERT: D 244 MET cc_start: 0.5208 (tpt) cc_final: 0.4900 (tpp) REVERT: E 40 GLU cc_start: 0.9162 (tt0) cc_final: 0.8887 (tt0) REVERT: E 159 MET cc_start: 0.8619 (ppp) cc_final: 0.8134 (ppp) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.0842 time to fit residues: 31.4148 Evaluate side-chains 177 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 30 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 150 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 0.0570 chunk 35 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 overall best weight: 1.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 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 = 0.3325 r_free = 0.3325 target = 0.062792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.047108 restraints weight = 82146.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.048467 restraints weight = 59830.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.049515 restraints weight = 46425.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.050258 restraints weight = 37773.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.050929 restraints weight = 32251.069| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12580 Z= 0.120 Angle : 0.613 7.225 17255 Z= 0.308 Chirality : 0.043 0.232 2083 Planarity : 0.005 0.052 2235 Dihedral : 6.462 86.161 1908 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.97 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.21), residues: 1689 helix: 0.84 (0.18), residues: 886 sheet: -0.62 (0.33), residues: 191 loop : -0.84 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 183 TYR 0.017 0.001 TYR A 41 PHE 0.025 0.001 PHE A 98 TRP 0.031 0.002 TRP A 137 HIS 0.006 0.001 HIS C 268 Details of bonding type rmsd covalent geometry : bond 0.00256 (12579) covalent geometry : angle 0.61293 (17252) hydrogen bonds : bond 0.03188 ( 725) hydrogen bonds : angle 4.78358 ( 2043) glycosidic custom : bond 0.00116 ( 1) glycosidic custom : angle 1.20167 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2073.44 seconds wall clock time: 36 minutes 35.23 seconds (2195.23 seconds total)