Starting phenix.real_space_refine on Sat Sep 12 02:47:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pdy_20319/09_2026/6pdy_20319_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pdy_20319/09_2026/6pdy_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_20319/09_2026/6pdy_20319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pdy_20319/09_2026/6pdy_20319.map" model { file = "/net/cci-nas-00/data/ceres_data/6pdy_20319/09_2026/6pdy_20319_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pdy_20319/09_2026/6pdy_20319_neut_trim.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: 3.06, per 1000 atoms: 0.23 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: 1.10 Conformation dependent library (CDL) restraints added in 578.5 milliseconds 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: 0.31 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: 1.62 Time building geometry restraints manager: 1.45 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: 1.000 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.610 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.005 0.000 ARG A 290 TYR 0.016 0.001 TYR D 129 PHE 0.012 0.001 PHE E 307 TRP 0.035 0.002 TRP D 241 HIS 0.006 0.001 HIS B 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.21 (13314) covalent geometry : angle 0.79888 / 0.45 (18018) hydrogen bonds : bond 0.21384 / 14.61 ( 436) hydrogen bonds : angle 7.92071 / 5.93 ( 1221) *********************** 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 : 0.414 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: symmetry clash REVERT: F 169 HIS cc_start: 0.8237 (t-90) cc_final: 0.7985 (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: 0.8303 (tp) REVERT: F 192 ASN cc_start: 0.8378 (t0) cc_final: 0.6518 (t0) REVERT: F 336 MET cc_start: 0.7759 (tpt) cc_final: 0.7465 (tpp) REVERT: A 94 ASN cc_start: 0.7472 (m-40) cc_final: 0.7085 (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: 0.8260 (mm-40) REVERT: B 188 TYR cc_start: 0.7606 (t80) cc_final: 0.7402 (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: 0.7846 (mt-10) REVERT: D 242 ASP cc_start: 0.7615 (p0) cc_final: 0.7298 (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: 0.1451 time to fit residues: 70.8696 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 : 0.500 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.1980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN B 192 ASN B 289 GLN C 94 ASN C 289 GLN D 46 ASN ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 ASN D 342 GLN E 54 GLN E 95 GLN E 179 HIS E 192 ASN ** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.126183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.096878 restraints weight = 36390.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.098431 restraints weight = 23506.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.099417 restraints weight = 16975.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.099659 restraints weight = 16584.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.099888 restraints weight = 14693.452| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13314 Z= 0.173 Angle : 0.865 11.782 18018 Z= 0.416 Chirality : 0.049 0.233 2042 Planarity : 0.007 0.101 2325 Dihedral : 9.798 162.017 1888 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.32 % Favored : 89.68 % Rotamer: Outliers : 2.31 % Allowed : 9.80 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.45 (0.19), residues: 1618 helix: -1.56 (0.17), residues: 734 sheet: -2.67 (0.37), residues: 159 loop : -2.94 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 62 TYR 0.025 0.002 TYR D 339 PHE 0.017 0.002 PHE A 211 TRP 0.030 0.002 TRP D 241 HIS 0.013 0.002 HIS E 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (13314) covalent geometry : angle 0.86487 / 0.42 (18018) hydrogen bonds : bond 0.04601 / 3.19 ( 436) hydrogen bonds : angle 5.34731 / 3.79 ( 1221) *********************** 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 270 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 238 time to evaluate : 0.406 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: F 92 TYR cc_start: 0.8949 (m-80) cc_final: 0.8609 (m-80) REVERT: F 177 ASN cc_start: 0.8409 (t0) cc_final: 0.7856 (t0) REVERT: F 178 LEU cc_start: 0.8684 (tp) cc_final: 0.8335 (tp) REVERT: A 165 LYS cc_start: 0.8077 (tttt) cc_final: 0.7844 (tttm) REVERT: A 201 LEU cc_start: 0.9158 (tp) cc_final: 0.8790 (pp) REVERT: A 263 ASN cc_start: 0.7700 (p0) cc_final: 0.7434 (p0) REVERT: B 238 MET cc_start: 0.6539 (mtt) cc_final: 0.6287 (mtt) REVERT: C 122 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7847 (mt-10) REVERT: C 227 HIS cc_start: 0.6744 (t-90) cc_final: 0.6265 (t-90) REVERT: D 52 LYS cc_start: 0.9217 (mmtm) cc_final: 0.8735 (mmtm) outliers start: 32 outliers final: 16 residues processed: 258 average time/residue: 0.1046 time to fit residues: 38.9507 Evaluate side-chains 214 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 198 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 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 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 112 optimal weight: 0.2980 chunk 153 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 76 optimal weight: 0.0370 chunk 3 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 overall best weight: 1.2462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 ASN A 279 GLN B 177 ASN ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 ASN E 206 GLN E 254 ASN 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 = 0.124872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.094637 restraints weight = 36747.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.096843 restraints weight = 23733.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.098333 restraints weight = 17866.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.098685 restraints weight = 14619.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.098814 restraints weight = 13500.056| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3400 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= 0.179 Angle : 0.840 13.636 18018 Z= 0.400 Chirality : 0.049 0.215 2042 Planarity : 0.007 0.098 2325 Dihedral : 8.942 144.428 1871 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.32 % Favored : 89.68 % Rotamer: Outliers : 2.45 % Allowed : 13.54 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.19), residues: 1618 helix: -1.27 (0.18), residues: 739 sheet: -2.33 (0.40), residues: 141 loop : -2.76 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 62 TYR 0.027 0.002 TYR D 339 PHE 0.021 0.002 PHE A 175 TRP 0.023 0.002 TRP D 241 HIS 0.006 0.001 HIS F 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (13314) covalent geometry : angle 0.84036 / 0.40 (18018) hydrogen bonds : bond 0.04019 / 2.80 ( 436) hydrogen bonds : angle 5.12703 / 3.62 ( 1221) *********************** 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 251 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 217 time to evaluate : 0.580 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: F 177 ASN cc_start: 0.8435 (t0) cc_final: 0.7821 (t0) REVERT: F 178 LEU cc_start: 0.8697 (tp) cc_final: 0.8346 (tp) REVERT: F 276 MET cc_start: 0.8778 (tpp) cc_final: 0.8449 (tpp) REVERT: A 175 PHE cc_start: 0.6654 (t80) cc_final: 0.6176 (t80) REVERT: A 201 LEU cc_start: 0.9214 (tp) cc_final: 0.8932 (pp) REVERT: A 203 LYS cc_start: 0.9526 (pttt) cc_final: 0.9289 (pttm) REVERT: A 211 PHE cc_start: 0.8749 (t80) cc_final: 0.8384 (t80) outliers start: 34 outliers final: 17 residues processed: 244 average time/residue: 0.1158 time to fit residues: 41.0551 Evaluate side-chains 202 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 208 SER 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 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 212 ILE Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 338 GLU 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 37 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 131 optimal weight: 0.0970 chunk 90 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 138 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 55.906 > 50:) chunk 124 optimal weight: 4.9990 chunk 151 optimal weight: 0.3980 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN B 177 ASN B 179 HIS ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 248 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.125370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.095389 restraints weight = 36790.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.097362 restraints weight = 25079.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.099201 restraints weight = 17619.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.099288 restraints weight = 16077.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.099241 restraints weight = 14428.029| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13314 Z= 0.160 Angle : 0.821 12.796 18018 Z= 0.388 Chirality : 0.048 0.220 2042 Planarity : 0.006 0.095 2325 Dihedral : 8.729 127.364 1871 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 2.81 % Allowed : 15.13 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.20), residues: 1618 helix: -1.10 (0.18), residues: 743 sheet: -2.00 (0.42), residues: 140 loop : -2.67 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 62 TYR 0.025 0.002 TYR D 339 PHE 0.017 0.002 PHE A 175 TRP 0.021 0.002 TRP D 241 HIS 0.009 0.001 HIS F 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (13314) covalent geometry : angle 0.82140 / 0.39 (18018) hydrogen bonds : bond 0.03819 / 2.63 ( 436) hydrogen bonds : angle 5.03002 / 3.55 ( 1221) *********************** 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 247 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 0.377 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: F 177 ASN cc_start: 0.8396 (t0) cc_final: 0.7725 (t0) REVERT: F 178 LEU cc_start: 0.8721 (tp) cc_final: 0.8392 (tp) REVERT: F 276 MET cc_start: 0.8673 (tpp) cc_final: 0.8076 (tpp) REVERT: A 94 ASN cc_start: 0.7383 (m-40) cc_final: 0.7090 (t0) REVERT: A 179 HIS cc_start: 0.6817 (m-70) cc_final: 0.6413 (m-70) REVERT: A 201 LEU cc_start: 0.9173 (tp) cc_final: 0.8923 (pp) REVERT: A 211 PHE cc_start: 0.8608 (t80) cc_final: 0.8408 (t80) REVERT: A 319 MET cc_start: 0.7835 (mpp) cc_final: 0.7500 (ptp) REVERT: C 205 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8788 (pp) REVERT: D 98 LEU cc_start: 0.8650 (pp) cc_final: 0.8438 (tp) REVERT: E 113 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8341 (mt) REVERT: E 193 LYS cc_start: 0.8441 (mttp) cc_final: 0.7958 (mtmt) REVERT: E 238 MET cc_start: 0.7717 (ptt) cc_final: 0.7388 (ptt) outliers start: 39 outliers final: 21 residues processed: 234 average time/residue: 0.1231 time to fit residues: 41.1263 Evaluate side-chains 207 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 95 GLN 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 212 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 113 ILE 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 0 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 152 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 HIS ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 ASN E 95 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.121249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.090529 restraints weight = 36645.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.090619 restraints weight = 27610.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.091344 restraints weight = 21079.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.092395 restraints weight = 19269.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.092393 restraints weight = 17067.229| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 13314 Z= 0.265 Angle : 0.884 13.506 18018 Z= 0.425 Chirality : 0.050 0.214 2042 Planarity : 0.007 0.101 2325 Dihedral : 8.838 128.887 1871 Min Nonbonded Distance : 1.597 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.05 % Favored : 87.95 % Rotamer: Outliers : 3.31 % Allowed : 16.28 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.20), residues: 1618 helix: -1.18 (0.18), residues: 753 sheet: -1.99 (0.43), residues: 143 loop : -2.57 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 58 TYR 0.018 0.002 TYR C 153 PHE 0.027 0.002 PHE A 175 TRP 0.021 0.002 TRP D 241 HIS 0.011 0.001 HIS F 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.27 (13314) covalent geometry : angle 0.88441 / 0.42 (18018) hydrogen bonds : bond 0.03910 / 2.65 ( 436) hydrogen bonds : angle 5.20438 / 3.66 ( 1221) *********************** 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: 46 poor density : 187 time to evaluate : 0.397 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: F 119 ILE cc_start: 0.8439 (mm) cc_final: 0.8095 (mp) REVERT: F 177 ASN cc_start: 0.8449 (t0) cc_final: 0.7814 (t0) REVERT: F 178 LEU cc_start: 0.8771 (tp) cc_final: 0.8414 (tp) REVERT: F 194 ILE cc_start: 0.9276 (mt) cc_final: 0.9043 (mm) REVERT: F 280 PHE cc_start: 0.7515 (m-10) cc_final: 0.7208 (m-80) REVERT: A 94 ASN cc_start: 0.7516 (m-40) cc_final: 0.7258 (t0) REVERT: A 201 LEU cc_start: 0.9281 (tp) cc_final: 0.8991 (pp) REVERT: D 119 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8505 (mp) REVERT: E 113 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8422 (mt) REVERT: E 238 MET cc_start: 0.7929 (ptt) cc_final: 0.7692 (ptt) REVERT: E 319 MET cc_start: 0.6660 (mtm) cc_final: 0.5914 (mtt) outliers start: 46 outliers final: 30 residues processed: 219 average time/residue: 0.1228 time to fit residues: 38.6267 Evaluate side-chains 206 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 179 HIS 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 90 ASN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 301 THR 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 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 232 MET Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 323 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 35 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 122 optimal weight: 0.2980 chunk 33 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 162 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 135 HIS F 179 HIS ** 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 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.124066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.093727 restraints weight = 36428.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.094829 restraints weight = 24922.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.096376 restraints weight = 18687.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.096557 restraints weight = 15998.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.096709 restraints weight = 14729.155| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13314 Z= 0.150 Angle : 0.825 15.429 18018 Z= 0.395 Chirality : 0.047 0.243 2042 Planarity : 0.006 0.096 2325 Dihedral : 8.520 123.853 1871 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 3.03 % Allowed : 17.51 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.20), residues: 1618 helix: -0.97 (0.18), residues: 754 sheet: -1.91 (0.43), residues: 142 loop : -2.45 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 255 TYR 0.020 0.002 TYR B 92 PHE 0.015 0.002 PHE A 175 TRP 0.018 0.001 TRP D 241 HIS 0.019 0.001 HIS F 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (13314) covalent geometry : angle 0.82526 / 0.39 (18018) hydrogen bonds : bond 0.03610 / 2.47 ( 436) hydrogen bonds : angle 5.04119 / 3.52 ( 1221) *********************** 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 239 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 197 time to evaluate : 0.492 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 119 ILE cc_start: 0.8400 (mm) cc_final: 0.8041 (mp) REVERT: F 177 ASN cc_start: 0.8416 (t0) cc_final: 0.7704 (t0) REVERT: F 280 PHE cc_start: 0.7541 (m-10) cc_final: 0.7233 (m-80) REVERT: A 162 MET cc_start: 0.7502 (ptm) cc_final: 0.7245 (ptm) REVERT: A 165 LYS cc_start: 0.8176 (tttt) cc_final: 0.7506 (tttm) REVERT: A 201 LEU cc_start: 0.9260 (tp) cc_final: 0.8950 (pp) REVERT: A 336 MET cc_start: 0.7959 (tpt) cc_final: 0.7736 (mmm) REVERT: B 190 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7489 (t0) REVERT: C 205 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8787 (pp) REVERT: D 98 LEU cc_start: 0.8812 (tp) cc_final: 0.8319 (tp) REVERT: E 113 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8444 (mt) REVERT: E 133 MET cc_start: 0.8454 (ppp) cc_final: 0.8166 (ppp) REVERT: E 193 LYS cc_start: 0.8378 (mttp) cc_final: 0.7913 (mtmt) REVERT: E 238 MET cc_start: 0.7831 (ptt) cc_final: 0.7548 (ptt) outliers start: 42 outliers final: 23 residues processed: 224 average time/residue: 0.1334 time to fit residues: 42.4906 Evaluate side-chains 201 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 240 LEU Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 190 ASP 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 212 ILE Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 176 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 21 optimal weight: 10.0000 chunk 155 optimal weight: 0.2980 chunk 141 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 179 HIS ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN C 64 GLN ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 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 = 0.4023 r_free = 0.4023 target = 0.121936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.092587 restraints weight = 36439.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.091593 restraints weight = 29215.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.092512 restraints weight = 22142.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.092932 restraints weight = 19362.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.093149 restraints weight = 17982.737| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13314 Z= 0.229 Angle : 0.868 15.714 18018 Z= 0.418 Chirality : 0.049 0.252 2042 Planarity : 0.007 0.098 2325 Dihedral : 8.551 122.196 1871 Min Nonbonded Distance : 1.584 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.99 % Favored : 88.01 % Rotamer: Outliers : 3.46 % Allowed : 18.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.20), residues: 1618 helix: -1.05 (0.18), residues: 762 sheet: -1.95 (0.44), residues: 138 loop : -2.44 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 255 TYR 0.033 0.002 TYR A 153 PHE 0.013 0.002 PHE A 175 TRP 0.013 0.002 TRP D 241 HIS 0.007 0.001 HIS F 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.23 (13314) covalent geometry : angle 0.86792 / 0.42 (18018) hydrogen bonds : bond 0.03804 / 2.56 ( 436) hydrogen bonds : angle 5.13671 / 3.59 ( 1221) *********************** 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: 48 poor density : 177 time to evaluate : 0.564 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: 0.8329 (t0) cc_final: 0.7638 (t0) REVERT: F 178 LEU cc_start: 0.8681 (tp) cc_final: 0.8395 (tp) REVERT: A 165 LYS cc_start: 0.8143 (tttt) cc_final: 0.7475 (tttm) REVERT: A 201 LEU cc_start: 0.9216 (tp) cc_final: 0.8933 (pp) REVERT: B 58 ARG cc_start: 0.8106 (ttm110) cc_final: 0.7655 (tpp-160) REVERT: B 190 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7583 (t0) REVERT: B 232 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8267 (ptp) REVERT: C 205 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8809 (pp) REVERT: D 98 LEU cc_start: 0.8772 (tp) cc_final: 0.8273 (tp) REVERT: E 113 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8440 (mt) REVERT: E 133 MET cc_start: 0.8569 (ppp) cc_final: 0.8222 (ppp) REVERT: E 238 MET cc_start: 0.7853 (ptt) cc_final: 0.7605 (ptt) outliers start: 48 outliers final: 31 residues processed: 215 average time/residue: 0.1234 time to fit residues: 38.3076 Evaluate side-chains 203 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 F residue 240 LEU Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 90 ASN 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 255 ARG Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 232 MET 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 C residue 232 MET Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 323 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 57 optimal weight: 0.9980 chunk 147 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 55 optimal weight: 0.4980 chunk 89 optimal weight: 0.5980 chunk 148 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 87 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 ASN ** 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 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 HIS D 227 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.124764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.095472 restraints weight = 36360.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.096161 restraints weight = 26116.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.096717 restraints weight = 19759.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.097421 restraints weight = 18566.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.097384 restraints weight = 16635.409| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13314 Z= 0.148 Angle : 0.848 15.944 18018 Z= 0.404 Chirality : 0.048 0.258 2042 Planarity : 0.006 0.094 2325 Dihedral : 8.330 118.133 1871 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 3.17 % Allowed : 18.88 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.20), residues: 1618 helix: -0.85 (0.18), residues: 753 sheet: -2.09 (0.43), residues: 143 loop : -2.39 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 59 TYR 0.037 0.002 TYR A 153 PHE 0.012 0.001 PHE C 175 TRP 0.017 0.001 TRP D 241 HIS 0.005 0.001 HIS F 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (13314) covalent geometry : angle 0.84795 / 0.40 (18018) hydrogen bonds : bond 0.03648 / 2.44 ( 436) hydrogen bonds : angle 4.95219 / 3.47 ( 1221) *********************** 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 234 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 190 time to evaluate : 0.441 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 119 ILE cc_start: 0.8176 (mm) cc_final: 0.7973 (mp) REVERT: F 177 ASN cc_start: 0.8264 (t0) cc_final: 0.7516 (t0) REVERT: F 178 LEU cc_start: 0.8603 (tp) cc_final: 0.8272 (tp) REVERT: A 95 GLN cc_start: 0.6907 (OUTLIER) cc_final: 0.6389 (mt0) REVERT: A 100 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8249 (m) REVERT: A 165 LYS cc_start: 0.8148 (tttt) cc_final: 0.7470 (tttm) REVERT: A 201 LEU cc_start: 0.9198 (tp) cc_final: 0.8898 (pp) REVERT: B 54 GLN cc_start: 0.9126 (mt0) cc_final: 0.8799 (mm-40) REVERT: B 58 ARG cc_start: 0.7973 (ttm110) cc_final: 0.7529 (tpp-160) REVERT: B 190 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7372 (t0) REVERT: C 205 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8758 (pp) REVERT: D 98 LEU cc_start: 0.8810 (tp) cc_final: 0.8329 (tp) REVERT: E 113 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8372 (mt) REVERT: E 133 MET cc_start: 0.8439 (ppp) cc_final: 0.8067 (ppp) REVERT: E 238 MET cc_start: 0.7748 (ptt) cc_final: 0.7414 (ptt) outliers start: 44 outliers final: 26 residues processed: 221 average time/residue: 0.1233 time to fit residues: 39.2769 Evaluate side-chains 208 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 240 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 255 ARG 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 190 ASP 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 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 212 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 178 LEU 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 39 optimal weight: 0.1980 chunk 159 optimal weight: 20.0000 chunk 120 optimal weight: 2.9990 chunk 32 optimal weight: 30.0000 chunk 90 optimal weight: 0.7980 chunk 83 optimal weight: 0.0270 chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 169 HIS ** 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 263 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 = 0.4070 r_free = 0.4070 target = 0.124736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.096041 restraints weight = 36846.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.095742 restraints weight = 25932.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.096506 restraints weight = 20495.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.096766 restraints weight = 18949.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.096944 restraints weight = 18408.234| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13314 Z= 0.155 Angle : 0.850 16.419 18018 Z= 0.404 Chirality : 0.047 0.254 2042 Planarity : 0.006 0.094 2325 Dihedral : 8.277 119.598 1871 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.62 % Favored : 88.38 % Rotamer: Outliers : 2.74 % Allowed : 19.67 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.20), residues: 1618 helix: -0.80 (0.19), residues: 755 sheet: -2.14 (0.43), residues: 136 loop : -2.36 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 275 TYR 0.035 0.002 TYR A 153 PHE 0.019 0.002 PHE A 280 TRP 0.014 0.001 TRP D 241 HIS 0.009 0.001 HIS F 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (13314) covalent geometry : angle 0.84997 / 0.40 (18018) hydrogen bonds : bond 0.03606 / 2.41 ( 436) hydrogen bonds : angle 4.93341 / 3.46 ( 1221) *********************** 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 227 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 0.533 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 119 ILE cc_start: 0.8243 (mm) cc_final: 0.8009 (mp) REVERT: F 177 ASN cc_start: 0.8275 (t0) cc_final: 0.7513 (t0) REVERT: A 95 GLN cc_start: 0.6834 (OUTLIER) cc_final: 0.6319 (mt0) REVERT: A 100 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8273 (m) REVERT: A 165 LYS cc_start: 0.8206 (tttt) cc_final: 0.7899 (tttm) REVERT: A 201 LEU cc_start: 0.9212 (tp) cc_final: 0.8917 (pp) REVERT: B 54 GLN cc_start: 0.9182 (mt0) cc_final: 0.8843 (mm110) REVERT: B 58 ARG cc_start: 0.8048 (ttm110) cc_final: 0.7581 (tpp-160) REVERT: B 136 LEU cc_start: 0.8099 (pp) cc_final: 0.7739 (mp) REVERT: B 190 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.6718 (t0) REVERT: C 56 ASN cc_start: 0.7908 (m-40) cc_final: 0.7381 (m-40) REVERT: C 205 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8738 (pp) REVERT: D 98 LEU cc_start: 0.8801 (tp) cc_final: 0.8321 (tp) REVERT: D 196 ARG cc_start: 0.8197 (ptm-80) cc_final: 0.7833 (ttp80) REVERT: E 133 MET cc_start: 0.8484 (ppp) cc_final: 0.8084 (ppp) outliers start: 38 outliers final: 28 residues processed: 217 average time/residue: 0.1243 time to fit residues: 39.0979 Evaluate side-chains 216 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 169 HIS 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 240 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 255 ARG 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 190 ASP 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 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 212 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 178 LEU 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 52 optimal weight: 0.5980 chunk 135 optimal weight: 10.0000 chunk 32 optimal weight: 30.0000 chunk 35 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 59 optimal weight: 0.4980 chunk 4 optimal weight: 0.0070 chunk 106 optimal weight: 0.8980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 169 HIS ** 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 263 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 = 0.125642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.096742 restraints weight = 36559.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.096965 restraints weight = 24395.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.097757 restraints weight = 19155.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.098172 restraints weight = 17514.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.098305 restraints weight = 16282.225| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.5009 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= 0.144 Angle : 0.873 17.611 18018 Z= 0.410 Chirality : 0.047 0.243 2042 Planarity : 0.006 0.092 2325 Dihedral : 8.213 118.553 1871 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Rotamer: Outliers : 2.67 % Allowed : 19.88 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.21), residues: 1618 helix: -0.68 (0.19), residues: 751 sheet: -1.77 (0.45), residues: 132 loop : -2.35 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 59 TYR 0.016 0.001 TYR B 129 PHE 0.011 0.001 PHE E 307 TRP 0.015 0.001 TRP D 241 HIS 0.019 0.001 HIS F 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (13314) covalent geometry : angle 0.87337 / 0.41 (18018) hydrogen bonds : bond 0.03605 / 2.41 ( 436) hydrogen bonds : angle 4.84280 / 3.41 ( 1221) ********************** 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 231 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 194 time to evaluate : 0.533 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: 0.8178 (t0) cc_final: 0.7395 (t0) REVERT: A 95 GLN cc_start: 0.6799 (OUTLIER) cc_final: 0.6289 (mt0) REVERT: A 100 VAL cc_start: 0.8527 (OUTLIER) cc_final: 0.8268 (m) REVERT: A 165 LYS cc_start: 0.8128 (tttt) cc_final: 0.7440 (tttm) REVERT: A 201 LEU cc_start: 0.9136 (tp) cc_final: 0.8869 (pp) REVERT: B 54 GLN cc_start: 0.9115 (mt0) cc_final: 0.8831 (mm110) REVERT: B 58 ARG cc_start: 0.7993 (ttm110) cc_final: 0.7599 (tpp-160) REVERT: B 136 LEU cc_start: 0.7972 (pp) cc_final: 0.7671 (mp) REVERT: B 276 MET cc_start: 0.7271 (mtp) cc_final: 0.7045 (mtm) REVERT: C 205 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8862 (pp) REVERT: C 227 HIS cc_start: 0.6618 (t-90) cc_final: 0.6409 (t-90) REVERT: D 98 LEU cc_start: 0.8799 (tp) cc_final: 0.8336 (tp) REVERT: D 196 ARG cc_start: 0.8162 (ptm-80) cc_final: 0.7835 (ttp80) REVERT: E 133 MET cc_start: 0.8393 (ppp) cc_final: 0.8039 (ppp) outliers start: 37 outliers final: 28 residues processed: 223 average time/residue: 0.1252 time to fit residues: 40.4478 Evaluate side-chains 213 residues out of total 1389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 169 HIS 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 95 GLN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 255 ARG 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 215 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 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 212 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 152 LEU 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 137 optimal weight: 6.9990 chunk 106 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 chunk 23 optimal weight: 20.0000 chunk 25 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 98 optimal weight: 0.5980 chunk 144 optimal weight: 0.0270 chunk 124 optimal weight: 0.0050 chunk 16 optimal weight: 4.9990 overall best weight: 0.4052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 169 HIS ** F 206 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.125971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.095682 restraints weight = 36697.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.096980 restraints weight = 26439.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.097773 restraints weight = 19343.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.098181 restraints weight = 18382.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.098317 restraints weight = 16606.091| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13314 Z= 0.143 Angle : 0.871 17.408 18018 Z= 0.414 Chirality : 0.047 0.238 2042 Planarity : 0.006 0.091 2325 Dihedral : 8.127 117.007 1871 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.06 % Favored : 88.94 % Rotamer: Outliers : 2.38 % Allowed : 20.46 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 4.21 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.21), residues: 1618 helix: -0.65 (0.19), residues: 749 sheet: -1.76 (0.45), residues: 137 loop : -2.38 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 48 TYR 0.021 0.001 TYR C 188 PHE 0.012 0.001 PHE E 307 TRP 0.018 0.001 TRP F 241 HIS 0.032 0.002 HIS F 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (13314) covalent geometry : angle 0.87054 / 0.41 (18018) hydrogen bonds : bond 0.03628 / 2.43 ( 436) hydrogen bonds : angle 4.88260 / 3.44 ( 1221) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2295.54 seconds wall clock time: 40 minutes 32.98 seconds (2432.98 seconds total)