Starting phenix.real_space_refine on Thu Jul 31 07:15:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pdy_20319/07_2025/6pdy_20319_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pdy_20319/07_2025/6pdy_20319.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pdy_20319/07_2025/6pdy_20319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pdy_20319/07_2025/6pdy_20319.map" model { file = "/net/cci-nas-00/data/ceres_data/6pdy_20319/07_2025/6pdy_20319_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pdy_20319/07_2025/6pdy_20319_neut_trim.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.058 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: 8 Type Number sf(0) Gaussians P 10 5.49 5 Mg 4 5.21 5 S 59 5.16 5 Be 4 3.05 5 C 8216 2.51 5 N 2330 2.21 5 O 2461 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13096 Number of models: 1 Model: "" Number of chains: 12 Chain: "F" Number of atoms: 1831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1831 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 15, 'TRANS': 220} Chain breaks: 2 Chain: "A" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2048 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 245} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2209 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 15, 'TRANS': 266} Chain breaks: 1 Chain: "C" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2327 Classifications: {'peptide': 298} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 280} Chain breaks: 1 Chain: "D" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2293 Classifications: {'peptide': 293} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 275} Chain breaks: 1 Chain: "E" Number of atoms: 2183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2183 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 15, 'TRANS': 263} Chain breaks: 1 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.97, per 1000 atoms: 0.68 Number of scatterers: 13096 At special positions: 0 Unit cell: (85.779, 138.729, 136.611, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 59 16.00 P 10 15.00 Mg 4 11.99 F 12 9.00 O 2461 8.00 N 2330 7.00 C 8216 6.00 Be 4 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.67 Conformation dependent library (CDL) restraints added in 1.8 seconds 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3072 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 8 sheets defined 51.3% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'F' and resid 90 through 96 Processing helix chain 'F' and resid 97 through 99 No H-bonds generated for 'chain 'F' and resid 97 through 99' Processing helix chain 'F' and resid 109 through 113 removed outlier: 3.616A pdb=" N ILE F 113 " --> pdb=" O PHE F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 127 Processing helix chain 'F' and resid 127 through 132 Processing helix chain 'F' and resid 133 through 137 Processing helix chain 'F' and resid 158 through 171 removed outlier: 3.706A pdb=" N ALA F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N HIS F 169 " --> pdb=" O LYS F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 184 Processing helix chain 'F' and resid 189 through 205 removed outlier: 3.656A pdb=" N PHE F 199 " --> pdb=" O VAL F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 240 removed outlier: 3.795A pdb=" N MET F 238 " --> pdb=" O LYS F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 275 Processing helix chain 'F' and resid 288 through 299 removed outlier: 3.717A pdb=" N ARG F 292 " --> pdb=" O GLU F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 316 removed outlier: 4.046A pdb=" N THR F 316 " --> pdb=" O ILE F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 327 Processing helix chain 'F' and resid 336 through 342 Processing helix chain 'A' and resid 49 through 64 Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.817A pdb=" N GLN A 95 " --> pdb=" O GLU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.823A pdb=" N VAL A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 118 through 127 Processing helix chain 'A' and resid 127 through 132 removed outlier: 3.594A pdb=" N LEU A 131 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 170 Processing helix chain 'A' and resid 192 through 205 removed outlier: 3.661A pdb=" N PHE A 199 " --> pdb=" O VAL A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 240 Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 286 through 298 Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 320 through 344 Proline residue: A 335 - end of helix Processing helix chain 'B' and resid 45 through 65 removed outlier: 3.524A pdb=" N ILE B 65 " --> pdb=" O ARG B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 98 removed outlier: 3.671A pdb=" N ALA B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 127 removed outlier: 3.820A pdb=" N LYS B 124 " --> pdb=" O ILE B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 removed outlier: 3.848A pdb=" N LEU B 131 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR B 132 " --> pdb=" O ILE B 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 127 through 132' Processing helix chain 'B' and resid 133 through 138 removed outlier: 3.736A pdb=" N LEU B 136 " --> pdb=" O MET B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 171 removed outlier: 3.542A pdb=" N ALA B 164 " --> pdb=" O LYS B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 205 removed outlier: 3.509A pdb=" N VAL B 195 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE B 199 " --> pdb=" O VAL B 195 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS B 203 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B 204 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 205 " --> pdb=" O LEU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 242 removed outlier: 4.012A pdb=" N VAL B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP B 242 " --> pdb=" O MET B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 274 removed outlier: 3.914A pdb=" N ARG B 274 " --> pdb=" O GLU B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 removed outlier: 3.543A pdb=" N GLU B 295 " --> pdb=" O ARG B 291 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 316 removed outlier: 4.523A pdb=" N ILE B 312 " --> pdb=" O ASP B 308 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR B 316 " --> pdb=" O ILE B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 339 Proline residue: B 335 - end of helix Processing helix chain 'B' and resid 340 through 345 removed outlier: 3.728A pdb=" N ARG B 344 " --> pdb=" O ILE B 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 64 removed outlier: 3.825A pdb=" N ARG C 50 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN C 64 " --> pdb=" O ILE C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 95 removed outlier: 3.810A pdb=" N GLN C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 100 Processing helix chain 'C' and resid 102 through 106 removed outlier: 4.113A pdb=" N ILE C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 125 Processing helix chain 'C' and resid 127 through 132 Processing helix chain 'C' and resid 133 through 138 removed outlier: 3.745A pdb=" N LEU C 136 " --> pdb=" O MET C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 170 removed outlier: 3.524A pdb=" N LYS C 165 " --> pdb=" O THR C 161 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA C 166 " --> pdb=" O MET C 162 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL C 167 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 184 removed outlier: 3.952A pdb=" N LEU C 183 " --> pdb=" O HIS C 179 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR C 184 " --> pdb=" O ILE C 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 179 through 184' Processing helix chain 'C' and resid 192 through 205 removed outlier: 3.905A pdb=" N PHE C 199 " --> pdb=" O VAL C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 242 removed outlier: 3.903A pdb=" N VAL C 233 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS C 234 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET C 238 " --> pdb=" O LYS C 234 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU C 240 " --> pdb=" O GLU C 236 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP C 242 " --> pdb=" O MET C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 268 removed outlier: 3.571A pdb=" N ASP C 267 " --> pdb=" O ARG C 264 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE C 268 " --> pdb=" O ILE C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 268' Processing helix chain 'C' and resid 269 through 274 Processing helix chain 'C' and resid 286 through 298 Processing helix chain 'C' and resid 308 through 316 removed outlier: 3.902A pdb=" N ILE C 312 " --> pdb=" O ASP C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 331 removed outlier: 4.012A pdb=" N GLU C 326 " --> pdb=" O SER C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 344 Processing helix chain 'D' and resid 43 through 64 removed outlier: 3.686A pdb=" N ILE D 60 " --> pdb=" O ASN D 56 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN D 64 " --> pdb=" O ILE D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 98 removed outlier: 3.879A pdb=" N GLN D 95 " --> pdb=" O GLU D 91 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL D 96 " --> pdb=" O TYR D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 113 removed outlier: 3.505A pdb=" N ASP D 112 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE D 113 " --> pdb=" O PHE D 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 109 through 113' Processing helix chain 'D' and resid 121 through 126 removed outlier: 3.868A pdb=" N THR D 126 " --> pdb=" O GLU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 168 Processing helix chain 'D' and resid 179 through 183 Processing helix chain 'D' and resid 189 through 205 removed outlier: 3.571A pdb=" N VAL D 195 " --> pdb=" O SER D 191 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS D 203 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 219 removed outlier: 4.257A pdb=" N VAL D 218 " --> pdb=" O GLU D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 231 Processing helix chain 'D' and resid 236 through 241 Processing helix chain 'D' and resid 271 through 276 removed outlier: 3.578A pdb=" N ARG D 275 " --> pdb=" O ALA D 271 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET D 276 " --> pdb=" O ILE D 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 271 through 276' Processing helix chain 'D' and resid 288 through 298 removed outlier: 3.512A pdb=" N GLU D 295 " --> pdb=" O ARG D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 317 removed outlier: 3.773A pdb=" N ILE D 312 " --> pdb=" O ASP D 308 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA D 317 " --> pdb=" O ALA D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 342 removed outlier: 4.034A pdb=" N ALA D 334 " --> pdb=" O ASP D 330 " (cutoff:3.500A) Proline residue: D 335 - end of helix Processing helix chain 'E' and resid 45 through 64 removed outlier: 4.219A pdb=" N GLN E 64 " --> pdb=" O ILE E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 98 removed outlier: 3.798A pdb=" N VAL E 96 " --> pdb=" O TYR E 92 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU E 98 " --> pdb=" O ASN E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 116 through 126 removed outlier: 3.554A pdb=" N GLU E 121 " --> pdb=" O ASP E 117 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU E 122 " --> pdb=" O ASP E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 140 removed outlier: 4.136A pdb=" N HIS E 139 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 170 Processing helix chain 'E' and resid 179 through 183 Processing helix chain 'E' and resid 191 through 205 removed outlier: 3.667A pdb=" N PHE E 199 " --> pdb=" O VAL E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 219 removed outlier: 3.805A pdb=" N VAL E 218 " --> pdb=" O GLU E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 242 removed outlier: 3.620A pdb=" N VAL E 233 " --> pdb=" O ALA E 229 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS E 234 " --> pdb=" O SER E 230 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA E 235 " --> pdb=" O GLY E 231 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU E 236 " --> pdb=" O MET E 232 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP E 242 " --> pdb=" O MET E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 247 removed outlier: 3.646A pdb=" N SER E 246 " --> pdb=" O GLY E 243 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR E 247 " --> pdb=" O LEU E 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 243 through 247' Processing helix chain 'E' and resid 286 through 298 removed outlier: 3.505A pdb=" N LEU E 298 " --> pdb=" O LEU E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 316 removed outlier: 3.904A pdb=" N ILE E 312 " --> pdb=" O ASP E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 331 removed outlier: 3.903A pdb=" N LYS E 325 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU E 326 " --> pdb=" O SER E 322 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG E 329 " --> pdb=" O LYS E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 340 removed outlier: 4.342A pdb=" N GLU E 338 " --> pdb=" O ALA E 334 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR E 339 " --> pdb=" O PRO E 335 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE E 340 " --> pdb=" O MET E 336 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 176 through 177 removed outlier: 6.872A pdb=" N ILE F 176 " --> pdb=" O PHE F 211 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ASP F 213 " --> pdb=" O ILE F 176 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE F 210 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ALA F 261 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE F 212 " --> pdb=" O ALA F 261 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL F 150 " --> pdb=" O GLY F 260 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N THR F 262 " --> pdb=" O VAL F 150 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU F 152 " --> pdb=" O THR F 262 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLY F 149 " --> pdb=" O LYS F 278 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N PHE F 280 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LEU F 151 " --> pdb=" O PHE F 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 151 removed outlier: 6.500A pdb=" N VAL A 150 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA A 261 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 175 removed outlier: 6.090A pdb=" N SER A 174 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N SER A 208 " --> pdb=" O VAL A 257 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 176 through 177 removed outlier: 6.778A pdb=" N ILE B 176 " --> pdb=" O PHE B 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 261 through 262 removed outlier: 8.434A pdb=" N THR C 262 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU C 152 " --> pdb=" O THR C 262 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 176 through 177 removed outlier: 6.555A pdb=" N ILE C 176 " --> pdb=" O PHE C 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 174 through 177 removed outlier: 3.550A pdb=" N ILE D 209 " --> pdb=" O SER D 174 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER D 208 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU D 259 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE D 210 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ALA D 261 " --> pdb=" O ILE D 210 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE D 212 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS D 278 " --> pdb=" O GLY D 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 176 through 177 removed outlier: 7.150A pdb=" N ILE E 176 " --> pdb=" O PHE E 211 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N ASP E 213 " --> pdb=" O ILE E 176 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE E 210 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ALA E 261 " --> pdb=" O ILE E 210 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE E 212 " --> pdb=" O ALA E 261 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS E 278 " --> pdb=" O GLY E 149 " (cutoff:3.500A) 436 hydrogen bonds defined for protein. 1221 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: 3.43 Time building geometry restraints manager: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3422 1.33 - 1.45: 2082 1.45 - 1.57: 7689 1.57 - 1.69: 15 1.69 - 1.81: 106 Bond restraints: 13314 Sorted by residual: bond pdb=" F2 BEF A 502 " pdb="BE BEF A 502 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" F2 BEF C 502 " pdb="BE BEF C 502 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" F2 BEF B 502 " pdb="BE BEF B 502 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.83e+01 bond pdb=" F2 BEF E 501 " pdb="BE BEF E 501 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" F3 BEF E 501 " pdb="BE BEF E 501 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 13309 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 17706 2.56 - 5.12: 263 5.12 - 7.67: 41 7.67 - 10.23: 4 10.23 - 12.79: 4 Bond angle restraints: 18018 Sorted by residual: angle pdb=" C ILE B 340 " pdb=" N ARG B 341 " pdb=" CA ARG B 341 " ideal model delta sigma weight residual 120.28 126.72 -6.44 1.44e+00 4.82e-01 2.00e+01 angle pdb=" C ILE C 215 " pdb=" CA ILE C 215 " pdb=" CB ILE C 215 " ideal model delta sigma weight residual 111.29 104.19 7.10 1.64e+00 3.72e-01 1.87e+01 angle pdb=" F2 BEF B 502 " pdb="BE BEF B 502 " pdb=" F3 BEF B 502 " ideal model delta sigma weight residual 119.96 107.17 12.79 3.00e+00 1.11e-01 1.82e+01 angle pdb=" F2 BEF E 501 " pdb="BE BEF E 501 " pdb=" F3 BEF E 501 " ideal model delta sigma weight residual 119.96 107.23 12.73 3.00e+00 1.11e-01 1.80e+01 angle pdb=" F2 BEF C 502 " pdb="BE BEF C 502 " pdb=" F3 BEF C 502 " ideal model delta sigma weight residual 119.96 107.28 12.68 3.00e+00 1.11e-01 1.79e+01 ... (remaining 18013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 8128 35.89 - 71.77: 41 71.77 - 107.66: 4 107.66 - 143.54: 4 143.54 - 179.43: 1 Dihedral angle restraints: 8178 sinusoidal: 3421 harmonic: 4757 Sorted by residual: dihedral pdb=" CA GLN B 206 " pdb=" C GLN B 206 " pdb=" N PRO B 207 " pdb=" CA PRO B 207 " ideal model delta harmonic sigma weight residual 180.00 137.20 42.80 0 5.00e+00 4.00e-02 7.33e+01 dihedral pdb=" CA TYR B 129 " pdb=" C TYR B 129 " pdb=" N PRO B 130 " pdb=" CA PRO B 130 " ideal model delta harmonic sigma weight residual 180.00 140.75 39.25 0 5.00e+00 4.00e-02 6.16e+01 dihedral pdb=" CA TYR D 129 " pdb=" C TYR D 129 " pdb=" N PRO D 130 " pdb=" CA PRO D 130 " ideal model delta harmonic sigma weight residual 180.00 141.41 38.59 0 5.00e+00 4.00e-02 5.96e+01 ... (remaining 8175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1782 0.065 - 0.129: 240 0.129 - 0.194: 17 0.194 - 0.259: 0 0.259 - 0.323: 3 Chirality restraints: 2042 Sorted by residual: chirality pdb=" CA HIS B 343 " pdb=" N HIS B 343 " pdb=" C HIS B 343 " pdb=" CB HIS B 343 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA GLU C 214 " pdb=" N GLU C 214 " pdb=" C GLU C 214 " pdb=" CB GLU C 214 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA ILE C 212 " pdb=" N ILE C 212 " pdb=" C ILE C 212 " pdb=" CB ILE C 212 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 2039 not shown) Planarity restraints: 2325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 129 " 0.071 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO B 130 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO B 130 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 130 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 129 " 0.070 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO D 130 " -0.185 5.00e-02 4.00e+02 pdb=" CA PRO D 130 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO D 130 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 106 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO F 107 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO F 107 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 107 " -0.035 5.00e-02 4.00e+02 ... (remaining 2322 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.11: 14 2.11 - 2.81: 3822 2.81 - 3.51: 19814 3.51 - 4.20: 30643 4.20 - 4.90: 51753 Nonbonded interactions: 106046 Sorted by model distance: nonbonded pdb=" OD2 ASP C 213 " pdb="MG MG C 503 " model vdw 1.416 2.170 nonbonded pdb="BE BEF B 502 " pdb="MG MG B 503 " model vdw 1.762 1.550 nonbonded pdb=" OD2 ASP D 213 " pdb="MG MG D 502 " model vdw 2.017 2.170 nonbonded pdb=" OG1 THR B 161 " pdb="MG MG B 503 " model vdw 2.033 2.170 nonbonded pdb=" OD1 ASP D 213 " pdb="MG MG D 502 " model vdw 2.051 2.170 ... (remaining 106041 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 'A' and (resid 48 through 64 or resid 87 through 342)) selection = (chain 'B' and (resid 48 through 64 or resid 87 through 132 or resid 145 through \ 220 or (resid 228 through 229 and (name N or name CA or name C or name O or nam \ e CB )) or resid 230 through 243 or resid 252 through 342)) selection = (chain 'C' and (resid 48 through 64 or resid 87 through 132 or resid 145 through \ 220 or (resid 228 through 229 and (name N or name CA or name C or name O or nam \ e CB )) or resid 230 through 243 or resid 252 through 342)) selection = (chain 'D' and (resid 48 through 132 or resid 145 through 220 or (resid 228 thro \ ugh 229 and (name N or name CA or name C or name O or name CB )) or resid 230 th \ rough 243 or resid 252 through 342)) selection = (chain 'E' and (resid 48 through 64 or resid 87 through 132 or resid 145 through \ 220 or (resid 228 through 229 and (name N or name CA or name C or name O or nam \ e CB )) or resid 230 through 243 or resid 252 through 342)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.680 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 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 : 0.004 0.086 13314 Z= 0.205 Angle : 0.799 12.789 18018 Z= 0.448 Chirality : 0.045 0.323 2042 Planarity : 0.006 0.108 2325 Dihedral : 11.278 179.426 5106 Min Nonbonded Distance : 1.416 Molprobity Statistics. All-atom Clashscore : 47.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.82 % Favored : 89.12 % Rotamer: Outliers : 0.65 % Allowed : 1.73 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.29 (0.18), residues: 1618 helix: -2.43 (0.15), residues: 713 sheet: -3.16 (0.37), residues: 148 loop : -3.17 (0.21), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 241 HIS 0.006 0.001 HIS B 343 PHE 0.012 0.001 PHE E 307 TYR 0.016 0.001 TYR D 129 ARG 0.005 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.21384 ( 436) hydrogen bonds : angle 7.92071 ( 1221) covalent geometry : bond 0.00370 (13314) covalent geometry : angle 0.79888 (18018) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 360 time to evaluate : 1.462 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: 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: F 169 HIS cc_start: 0.8237 (t-90) cc_final: 0.7984 (t-90) REVERT: F 177 ASN cc_start: 0.8411 (t0) cc_final: 0.7954 (t0) REVERT: F 178 LEU cc_start: 0.8702 (tp) cc_final: 0.8301 (tp) REVERT: F 192 ASN cc_start: 0.8378 (t0) cc_final: 0.6520 (t0) REVERT: F 336 MET cc_start: 0.7759 (tpt) cc_final: 0.7465 (tpp) REVERT: A 94 ASN cc_start: 0.7473 (m-40) cc_final: 0.7081 (m-40) REVERT: A 201 LEU cc_start: 0.9051 (tp) cc_final: 0.8664 (pp) REVERT: B 54 GLN cc_start: 0.8921 (mt0) cc_final: 0.8261 (mm-40) REVERT: B 188 TYR cc_start: 0.7606 (t80) cc_final: 0.7405 (t80) REVERT: B 333 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8358 (mtm) REVERT: C 122 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7845 (mt-10) REVERT: D 242 ASP cc_start: 0.7615 (p0) cc_final: 0.7287 (t0) REVERT: E 237 PHE cc_start: 0.9008 (t80) cc_final: 0.8783 (t80) outliers start: 9 outliers final: 6 residues processed: 367 average time/residue: 0.3490 time to fit residues: 168.5338 Evaluate side-chains 212 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 205 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 215 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 6.9990 chunk 123 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 83 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 127 optimal weight: 0.3980 chunk 49 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 148 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 ASN B 177 ASN B 192 ASN B 289 GLN B 342 GLN C 94 ASN C 289 GLN D 46 ASN D 139 HIS D 206 GLN D 248 ASN D 342 GLN E 54 GLN E 95 GLN E 179 HIS E 192 ASN ** E 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.126509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.097307 restraints weight = 36165.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.098437 restraints weight = 24703.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.099128 restraints weight = 18095.521| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13314 Z= 0.171 Angle : 0.883 12.203 18018 Z= 0.424 Chirality : 0.051 0.241 2042 Planarity : 0.007 0.102 2325 Dihedral : 9.776 159.491 1888 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.20 % Favored : 89.74 % Rotamer: Outliers : 2.31 % Allowed : 9.73 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.19), residues: 1618 helix: -1.57 (0.17), residues: 737 sheet: -2.69 (0.38), residues: 139 loop : -2.89 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 241 HIS 0.013 0.002 HIS E 179 PHE 0.019 0.002 PHE A 211 TYR 0.023 0.002 TYR D 339 ARG 0.015 0.001 ARG E 62 Details of bonding type rmsd hydrogen bonds : bond 0.04341 ( 436) hydrogen bonds : angle 5.27869 ( 1221) covalent geometry : bond 0.00387 (13314) covalent geometry : angle 0.88333 (18018) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 239 time to evaluate : 1.456 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 92 TYR cc_start: 0.9030 (m-80) cc_final: 0.8661 (m-80) REVERT: F 169 HIS cc_start: 0.8160 (t-90) cc_final: 0.7907 (t-90) REVERT: F 177 ASN cc_start: 0.8439 (t0) cc_final: 0.7880 (t0) REVERT: F 178 LEU cc_start: 0.8713 (tp) cc_final: 0.8367 (tp) REVERT: F 239 THR cc_start: 0.8382 (m) cc_final: 0.8137 (m) REVERT: A 165 LYS cc_start: 0.8120 (tttt) cc_final: 0.7580 (tttm) REVERT: A 201 LEU cc_start: 0.9179 (tp) cc_final: 0.8914 (pp) REVERT: A 262 THR cc_start: 0.7947 (t) cc_final: 0.7727 (t) REVERT: C 122 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7874 (mt-10) REVERT: D 52 LYS cc_start: 0.9433 (mmmt) cc_final: 0.8868 (mmtm) REVERT: E 113 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8292 (mt) outliers start: 32 outliers final: 17 residues processed: 261 average time/residue: 0.2563 time to fit residues: 95.3810 Evaluate side-chains 215 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 176 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 10 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 162 optimal weight: 10.0000 chunk 2 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 17 optimal weight: 30.0000 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN B 177 ASN ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN C 254 ASN D 179 HIS ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.125072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.095242 restraints weight = 36699.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.096392 restraints weight = 25403.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.098264 restraints weight = 18420.039| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13314 Z= 0.166 Angle : 0.824 13.058 18018 Z= 0.391 Chirality : 0.048 0.215 2042 Planarity : 0.007 0.098 2325 Dihedral : 8.870 141.011 1871 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 2.52 % Allowed : 13.33 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.19), residues: 1618 helix: -1.18 (0.18), residues: 735 sheet: -2.12 (0.41), residues: 141 loop : -2.70 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 241 HIS 0.007 0.001 HIS F 179 PHE 0.022 0.002 PHE A 175 TYR 0.021 0.002 TYR B 129 ARG 0.013 0.001 ARG E 62 Details of bonding type rmsd hydrogen bonds : bond 0.03998 ( 436) hydrogen bonds : angle 5.00428 ( 1221) covalent geometry : bond 0.00381 (13314) covalent geometry : angle 0.82395 (18018) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 214 time to evaluate : 1.572 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: symmetry clash revert: symmetry clash REVERT: F 177 ASN cc_start: 0.8366 (t0) cc_final: 0.7720 (t0) REVERT: F 178 LEU cc_start: 0.8683 (tp) cc_final: 0.8338 (tp) REVERT: F 276 MET cc_start: 0.8783 (tpp) cc_final: 0.8379 (tpp) REVERT: A 165 LYS cc_start: 0.7989 (tttt) cc_final: 0.7395 (tttm) REVERT: A 175 PHE cc_start: 0.6327 (t80) cc_final: 0.5834 (t80) REVERT: A 201 LEU cc_start: 0.9159 (tp) cc_final: 0.8886 (pp) REVERT: A 211 PHE cc_start: 0.8674 (t80) cc_final: 0.8153 (t80) REVERT: A 213 ASP cc_start: 0.7311 (t0) cc_final: 0.7064 (t0) REVERT: A 262 THR cc_start: 0.8009 (t) cc_final: 0.7789 (t) REVERT: D 98 LEU cc_start: 0.8679 (tp) cc_final: 0.8272 (tp) outliers start: 35 outliers final: 16 residues processed: 238 average time/residue: 0.2642 time to fit residues: 89.7623 Evaluate side-chains 202 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain E residue 176 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 3 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 111 optimal weight: 0.0370 chunk 72 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 chunk 156 optimal weight: 2.9990 overall best weight: 0.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN B 177 ASN B 179 HIS ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 248 ASN ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.125283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.095261 restraints weight = 36123.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.097219 restraints weight = 24704.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.098061 restraints weight = 17549.216| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13314 Z= 0.158 Angle : 0.812 12.945 18018 Z= 0.384 Chirality : 0.048 0.220 2042 Planarity : 0.006 0.095 2325 Dihedral : 8.693 123.431 1871 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 2.81 % Allowed : 14.77 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.20), residues: 1618 helix: -0.97 (0.18), residues: 745 sheet: -1.78 (0.43), residues: 139 loop : -2.61 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 241 HIS 0.009 0.001 HIS F 179 PHE 0.017 0.002 PHE A 175 TYR 0.017 0.002 TYR D 339 ARG 0.008 0.001 ARG E 62 Details of bonding type rmsd hydrogen bonds : bond 0.03709 ( 436) hydrogen bonds : angle 4.92083 ( 1221) covalent geometry : bond 0.00355 (13314) covalent geometry : angle 0.81244 (18018) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 200 time to evaluate : 1.449 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: symmetry clash revert: symmetry clash REVERT: F 177 ASN cc_start: 0.8373 (t0) cc_final: 0.7677 (t0) REVERT: F 178 LEU cc_start: 0.8731 (tp) cc_final: 0.8410 (tp) REVERT: F 239 THR cc_start: 0.7811 (m) cc_final: 0.7251 (m) REVERT: F 276 MET cc_start: 0.8783 (tpp) cc_final: 0.8473 (tpp) REVERT: F 280 PHE cc_start: 0.6895 (m-10) cc_final: 0.6686 (m-80) REVERT: A 94 ASN cc_start: 0.7365 (m-40) cc_final: 0.7130 (t0) REVERT: A 201 LEU cc_start: 0.9160 (tp) cc_final: 0.8902 (pp) REVERT: A 262 THR cc_start: 0.8181 (t) cc_final: 0.7964 (t) REVERT: A 319 MET cc_start: 0.7774 (mpp) cc_final: 0.7485 (ptp) REVERT: C 227 HIS cc_start: 0.6678 (t-90) cc_final: 0.6278 (t-90) REVERT: D 98 LEU cc_start: 0.8753 (tp) cc_final: 0.8342 (tp) REVERT: E 238 MET cc_start: 0.7709 (ptt) cc_final: 0.7380 (ptt) outliers start: 39 outliers final: 23 residues processed: 227 average time/residue: 0.2600 time to fit residues: 83.8492 Evaluate side-chains 204 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 192 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 237 PHE Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 323 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 99 optimal weight: 0.0270 chunk 57 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 121 optimal weight: 0.4980 chunk 20 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 103 optimal weight: 0.4980 overall best weight: 1.0240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN B 135 HIS B 177 ASN ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN E 95 GLN ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.124942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.096262 restraints weight = 36540.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.096829 restraints weight = 26072.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.097191 restraints weight = 18942.270| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13314 Z= 0.155 Angle : 0.808 13.851 18018 Z= 0.383 Chirality : 0.047 0.217 2042 Planarity : 0.006 0.095 2325 Dihedral : 8.495 122.933 1871 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 2.74 % Allowed : 16.14 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.20), residues: 1618 helix: -0.84 (0.18), residues: 751 sheet: -1.59 (0.44), residues: 139 loop : -2.52 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 241 HIS 0.010 0.001 HIS F 179 PHE 0.025 0.002 PHE A 175 TYR 0.028 0.002 TYR A 129 ARG 0.007 0.000 ARG B 275 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 436) hydrogen bonds : angle 4.89091 ( 1221) covalent geometry : bond 0.00353 (13314) covalent geometry : angle 0.80750 (18018) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 1.527 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: symmetry clash REVERT: F 177 ASN cc_start: 0.8322 (t0) cc_final: 0.7588 (t0) REVERT: F 178 LEU cc_start: 0.8702 (tp) cc_final: 0.8391 (tp) REVERT: A 201 LEU cc_start: 0.9156 (tp) cc_final: 0.8921 (pp) REVERT: C 227 HIS cc_start: 0.6578 (t-90) cc_final: 0.6172 (t-90) REVERT: D 98 LEU cc_start: 0.8833 (tp) cc_final: 0.8428 (tp) REVERT: E 113 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8363 (mt) REVERT: E 238 MET cc_start: 0.7684 (ptt) cc_final: 0.7368 (ptt) REVERT: E 319 MET cc_start: 0.6367 (mtm) cc_final: 0.5610 (mtt) outliers start: 38 outliers final: 22 residues processed: 226 average time/residue: 0.2482 time to fit residues: 81.0552 Evaluate side-chains 206 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 192 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 237 PHE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 176 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 155 optimal weight: 0.0670 chunk 150 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 135 HIS ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN B 177 ASN C 64 GLN C 94 ASN ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.124913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.095153 restraints weight = 36935.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.096346 restraints weight = 26317.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.097007 restraints weight = 18915.294| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13314 Z= 0.162 Angle : 0.817 14.792 18018 Z= 0.390 Chirality : 0.047 0.244 2042 Planarity : 0.006 0.094 2325 Dihedral : 8.349 120.150 1871 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 2.95 % Allowed : 17.29 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.20), residues: 1618 helix: -0.74 (0.18), residues: 749 sheet: -1.61 (0.44), residues: 139 loop : -2.44 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 241 HIS 0.012 0.001 HIS F 179 PHE 0.019 0.002 PHE A 175 TYR 0.025 0.002 TYR B 92 ARG 0.007 0.000 ARG B 275 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 436) hydrogen bonds : angle 4.89637 ( 1221) covalent geometry : bond 0.00373 (13314) covalent geometry : angle 0.81737 (18018) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 1.469 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: symmetry clash revert: symmetry clash REVERT: F 119 ILE cc_start: 0.8242 (mm) cc_final: 0.7785 (mp) REVERT: F 177 ASN cc_start: 0.8298 (t0) cc_final: 0.7575 (t0) REVERT: F 178 LEU cc_start: 0.8675 (tp) cc_final: 0.8378 (tp) REVERT: F 239 THR cc_start: 0.7607 (m) cc_final: 0.7322 (m) REVERT: F 280 PHE cc_start: 0.7257 (m-10) cc_final: 0.6807 (m-80) REVERT: A 165 LYS cc_start: 0.8031 (tttt) cc_final: 0.7354 (tttm) REVERT: A 201 LEU cc_start: 0.9181 (tp) cc_final: 0.8926 (pp) REVERT: B 58 ARG cc_start: 0.7944 (ttm110) cc_final: 0.7546 (tpp-160) REVERT: D 98 LEU cc_start: 0.8799 (tp) cc_final: 0.8396 (tp) REVERT: E 113 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8350 (mt) outliers start: 41 outliers final: 25 residues processed: 217 average time/residue: 0.2592 time to fit residues: 80.2853 Evaluate side-chains 202 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 237 PHE Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 323 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 39 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 111 optimal weight: 0.0270 chunk 124 optimal weight: 2.9990 chunk 138 optimal weight: 0.0040 overall best weight: 0.9652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 ASN ** 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 = 0.4085 r_free = 0.4085 target = 0.125705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.096029 restraints weight = 36666.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.097351 restraints weight = 25815.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.098110 restraints weight = 18250.136| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13314 Z= 0.153 Angle : 0.816 16.642 18018 Z= 0.389 Chirality : 0.047 0.242 2042 Planarity : 0.006 0.093 2325 Dihedral : 8.208 119.500 1871 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.37 % Favored : 88.63 % Rotamer: Outliers : 3.10 % Allowed : 18.16 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.21), residues: 1618 helix: -0.67 (0.19), residues: 750 sheet: -1.70 (0.43), residues: 139 loop : -2.35 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 241 HIS 0.014 0.001 HIS F 179 PHE 0.012 0.001 PHE A 211 TYR 0.020 0.002 TYR A 153 ARG 0.006 0.000 ARG D 50 Details of bonding type rmsd hydrogen bonds : bond 0.03447 ( 436) hydrogen bonds : angle 4.83528 ( 1221) covalent geometry : bond 0.00349 (13314) covalent geometry : angle 0.81569 (18018) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 182 time to evaluate : 1.632 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: F 177 ASN cc_start: 0.8278 (t0) cc_final: 0.7539 (t0) REVERT: F 178 LEU cc_start: 0.8687 (tp) cc_final: 0.8383 (tp) REVERT: F 280 PHE cc_start: 0.7191 (m-10) cc_final: 0.6828 (m-10) REVERT: A 165 LYS cc_start: 0.8034 (tttt) cc_final: 0.7350 (tttm) REVERT: A 201 LEU cc_start: 0.9187 (tp) cc_final: 0.8928 (pp) REVERT: B 58 ARG cc_start: 0.7962 (ttm110) cc_final: 0.7541 (tpp-160) REVERT: D 98 LEU cc_start: 0.8852 (tp) cc_final: 0.8470 (tp) REVERT: E 113 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8344 (mt) REVERT: E 238 MET cc_start: 0.7671 (ptt) cc_final: 0.7378 (ptt) outliers start: 43 outliers final: 26 residues processed: 214 average time/residue: 0.2584 time to fit residues: 80.2075 Evaluate side-chains 202 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 237 PHE Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 176 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 32 optimal weight: 9.9990 chunk 151 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 22 optimal weight: 40.0000 chunk 100 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 83 optimal weight: 0.4980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 169 HIS ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 HIS B 177 ASN ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.124503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.094330 restraints weight = 36643.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.095176 restraints weight = 25782.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.095643 restraints weight = 18800.486| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13314 Z= 0.178 Angle : 0.852 17.031 18018 Z= 0.403 Chirality : 0.048 0.295 2042 Planarity : 0.006 0.094 2325 Dihedral : 8.229 118.369 1871 Min Nonbonded Distance : 1.672 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.05 % Favored : 87.95 % Rotamer: Outliers : 3.39 % Allowed : 18.37 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.21), residues: 1618 helix: -0.72 (0.18), residues: 758 sheet: -1.88 (0.43), residues: 142 loop : -2.32 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 241 HIS 0.004 0.001 HIS F 179 PHE 0.025 0.002 PHE A 211 TYR 0.041 0.002 TYR A 153 ARG 0.012 0.001 ARG F 275 Details of bonding type rmsd hydrogen bonds : bond 0.03550 ( 436) hydrogen bonds : angle 4.85759 ( 1221) covalent geometry : bond 0.00411 (13314) covalent geometry : angle 0.85218 (18018) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 182 time to evaluate : 1.407 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 177 ASN cc_start: 0.8295 (t0) cc_final: 0.7552 (t0) REVERT: F 178 LEU cc_start: 0.8708 (tp) cc_final: 0.8393 (tp) REVERT: F 280 PHE cc_start: 0.7363 (m-10) cc_final: 0.6957 (m-80) REVERT: A 100 VAL cc_start: 0.8593 (OUTLIER) cc_final: 0.8322 (m) REVERT: A 165 LYS cc_start: 0.8080 (tttt) cc_final: 0.7359 (tttm) REVERT: A 201 LEU cc_start: 0.9207 (tp) cc_final: 0.8944 (pp) REVERT: A 211 PHE cc_start: 0.8318 (t80) cc_final: 0.8079 (t80) REVERT: B 58 ARG cc_start: 0.8061 (ttm110) cc_final: 0.7611 (tpp-160) REVERT: B 232 MET cc_start: 0.8497 (ptp) cc_final: 0.8287 (ptp) REVERT: B 244 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8679 (mm) REVERT: D 98 LEU cc_start: 0.8798 (tp) cc_final: 0.8393 (tp) REVERT: E 92 TYR cc_start: 0.8511 (m-10) cc_final: 0.8300 (m-80) REVERT: E 113 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8362 (mt) outliers start: 47 outliers final: 30 residues processed: 216 average time/residue: 0.2644 time to fit residues: 81.9446 Evaluate side-chains 211 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 192 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 237 PHE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 323 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 27 optimal weight: 6.9990 chunk 150 optimal weight: 0.1980 chunk 133 optimal weight: 0.3980 chunk 31 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 115 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS ** E 254 ASN ** 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 = 0.4086 r_free = 0.4086 target = 0.125821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.096554 restraints weight = 36490.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.097125 restraints weight = 27175.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.097779 restraints weight = 19377.656| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13314 Z= 0.143 Angle : 0.870 20.345 18018 Z= 0.407 Chirality : 0.048 0.248 2042 Planarity : 0.006 0.091 2325 Dihedral : 8.133 116.693 1871 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 2.81 % Allowed : 19.52 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.21), residues: 1618 helix: -0.62 (0.19), residues: 749 sheet: -1.80 (0.44), residues: 130 loop : -2.34 (0.23), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 241 HIS 0.003 0.001 HIS D 343 PHE 0.019 0.001 PHE A 211 TYR 0.030 0.001 TYR A 153 ARG 0.008 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.03499 ( 436) hydrogen bonds : angle 4.81718 ( 1221) covalent geometry : bond 0.00323 (13314) covalent geometry : angle 0.87040 (18018) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 202 time to evaluate : 1.456 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: F 280 PHE cc_start: 0.6968 (m-10) cc_final: 0.6613 (m-80) REVERT: A 100 VAL cc_start: 0.8560 (OUTLIER) cc_final: 0.8285 (m) REVERT: A 165 LYS cc_start: 0.8003 (tttt) cc_final: 0.7302 (tttm) REVERT: A 201 LEU cc_start: 0.9133 (tp) cc_final: 0.8908 (pp) REVERT: A 211 PHE cc_start: 0.8220 (t80) cc_final: 0.7998 (t80) REVERT: A 276 MET cc_start: 0.5491 (ppp) cc_final: 0.5246 (pmm) REVERT: B 58 ARG cc_start: 0.7947 (ttm110) cc_final: 0.7512 (tpp-160) REVERT: B 244 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8647 (mm) REVERT: B 276 MET cc_start: 0.7303 (mtp) cc_final: 0.7063 (mtm) REVERT: C 56 ASN cc_start: 0.7791 (m-40) cc_final: 0.7293 (m-40) REVERT: D 98 LEU cc_start: 0.8721 (tp) cc_final: 0.8324 (tp) REVERT: D 196 ARG cc_start: 0.8190 (ptm-80) cc_final: 0.7954 (ttp80) REVERT: D 232 MET cc_start: 0.8180 (mtm) cc_final: 0.7881 (mtm) outliers start: 39 outliers final: 27 residues processed: 231 average time/residue: 0.2660 time to fit residues: 87.8595 Evaluate side-chains 213 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 184 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 192 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 237 PHE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 176 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 59 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 141 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 65 optimal weight: 0.9980 chunk 134 optimal weight: 0.0270 chunk 116 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN B 192 ASN ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 HIS E 206 GLN E 254 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.126477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.096592 restraints weight = 36526.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.097744 restraints weight = 26054.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.098473 restraints weight = 18874.854| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13314 Z= 0.146 Angle : 0.891 19.581 18018 Z= 0.415 Chirality : 0.048 0.242 2042 Planarity : 0.006 0.090 2325 Dihedral : 8.066 115.558 1871 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 2.38 % Allowed : 20.39 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.21), residues: 1618 helix: -0.63 (0.19), residues: 759 sheet: -1.73 (0.45), residues: 130 loop : -2.41 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 241 HIS 0.004 0.001 HIS D 343 PHE 0.014 0.001 PHE A 211 TYR 0.018 0.001 TYR A 153 ARG 0.011 0.001 ARG C 59 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 436) hydrogen bonds : angle 4.83550 ( 1221) covalent geometry : bond 0.00332 (13314) covalent geometry : angle 0.89145 (18018) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 1.687 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: F 276 MET cc_start: 0.8414 (tpp) cc_final: 0.8099 (tpt) REVERT: F 280 PHE cc_start: 0.7144 (m-10) cc_final: 0.6744 (m-80) REVERT: A 100 VAL cc_start: 0.8582 (OUTLIER) cc_final: 0.8320 (m) REVERT: A 165 LYS cc_start: 0.8031 (tttt) cc_final: 0.7301 (tttm) REVERT: A 201 LEU cc_start: 0.9166 (tp) cc_final: 0.8923 (pp) REVERT: A 211 PHE cc_start: 0.8255 (t80) cc_final: 0.8022 (t80) REVERT: A 276 MET cc_start: 0.5494 (ppp) cc_final: 0.5234 (pmm) REVERT: B 58 ARG cc_start: 0.7951 (ttm110) cc_final: 0.7523 (tpp-160) REVERT: B 136 LEU cc_start: 0.7995 (pp) cc_final: 0.7621 (mp) REVERT: B 244 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8658 (mm) REVERT: B 276 MET cc_start: 0.7296 (mtp) cc_final: 0.7094 (mtm) REVERT: C 227 HIS cc_start: 0.6866 (t-90) cc_final: 0.6638 (t-90) REVERT: D 98 LEU cc_start: 0.8722 (tp) cc_final: 0.8332 (tp) REVERT: D 196 ARG cc_start: 0.8195 (ptm-80) cc_final: 0.7910 (ttp80) outliers start: 33 outliers final: 27 residues processed: 219 average time/residue: 0.2560 time to fit residues: 81.1623 Evaluate side-chains 210 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 192 ASN Chi-restraints excluded: chain F residue 237 PHE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 179 HIS Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 323 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 77 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 29 optimal weight: 0.0030 chunk 107 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 137 optimal weight: 7.9990 chunk 76 optimal weight: 0.1980 chunk 41 optimal weight: 0.2980 chunk 101 optimal weight: 4.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 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 = 0.4112 r_free = 0.4112 target = 0.127315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.097421 restraints weight = 36734.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.098520 restraints weight = 26057.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.099805 restraints weight = 19260.332| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13314 Z= 0.142 Angle : 0.886 20.755 18018 Z= 0.412 Chirality : 0.047 0.294 2042 Planarity : 0.006 0.088 2325 Dihedral : 7.941 114.101 1871 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 2.31 % Allowed : 20.89 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 3.16 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.21), residues: 1618 helix: -0.51 (0.19), residues: 753 sheet: -1.66 (0.45), residues: 130 loop : -2.40 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 241 HIS 0.004 0.001 HIS E 169 PHE 0.012 0.001 PHE F 110 TYR 0.020 0.001 TYR C 188 ARG 0.012 0.001 ARG E 48 Details of bonding type rmsd hydrogen bonds : bond 0.03517 ( 436) hydrogen bonds : angle 4.83408 ( 1221) covalent geometry : bond 0.00317 (13314) covalent geometry : angle 0.88590 (18018) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4271.67 seconds wall clock time: 74 minutes 49.61 seconds (4489.61 seconds total)