Starting phenix.real_space_refine on Thu Jun 12 08:12:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bp6_44762/06_2025/9bp6_44762.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bp6_44762/06_2025/9bp6_44762.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bp6_44762/06_2025/9bp6_44762.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bp6_44762/06_2025/9bp6_44762.map" model { file = "/net/cci-nas-00/data/ceres_data/9bp6_44762/06_2025/9bp6_44762.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bp6_44762/06_2025/9bp6_44762.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 93 5.16 5 C 8562 2.51 5 N 2320 2.21 5 O 2640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13631 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3405 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 3348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3348 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 3389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3389 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "Q" Number of atoms: 3357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3357 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.17, per 1000 atoms: 0.82 Number of scatterers: 13631 At special positions: 0 Unit cell: (74.2, 75.26, 196.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 93 16.00 P 12 15.00 Mg 4 11.99 O 2640 8.00 N 2320 7.00 C 8562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 1.7 seconds 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3196 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 10 sheets defined 55.7% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 removed outlier: 3.778A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 51 removed outlier: 3.714A pdb=" N ASP A 47 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER A 48 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N PHE A 49 " --> pdb=" O ASP A 46 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.758A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 85 removed outlier: 4.406A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 82 through 85' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 129 removed outlier: 4.225A pdb=" N ILE A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.450A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 4.304A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.563A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.785A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.848A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.782A pdb=" N GLN A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.638A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 401 removed outlier: 4.178A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 3.885A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 411 " --> pdb=" O TRP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 436 removed outlier: 3.979A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY A 436 " --> pdb=" O TYR A 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 40 through 46 removed outlier: 4.039A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 106 through 127 removed outlier: 4.190A pdb=" N GLU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 Processing helix chain 'B' and resid 180 through 195 removed outlier: 4.235A pdb=" N HIS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.553A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 removed outlier: 3.623A pdb=" N ARG B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 277 through 282 removed outlier: 4.140A pdb=" N GLN B 280 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG B 282 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 296 through 299 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.705A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 390 removed outlier: 4.045A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 394 removed outlier: 4.408A pdb=" N PHE B 394 " --> pdb=" O ARG B 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 391 through 394' Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 404 through 428 removed outlier: 3.943A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 29 Processing helix chain 'I' and resid 44 through 52 removed outlier: 4.226A pdb=" N PHE I 49 " --> pdb=" O GLY I 45 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASN I 50 " --> pdb=" O ASP I 46 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR I 51 " --> pdb=" O ASP I 47 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE I 52 " --> pdb=" O SER I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 81 Processing helix chain 'I' and resid 88 through 90 No H-bonds generated for 'chain 'I' and resid 88 through 90' Processing helix chain 'I' and resid 102 through 108 Processing helix chain 'I' and resid 110 through 129 removed outlier: 4.238A pdb=" N ILE I 114 " --> pdb=" O ILE I 110 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASP I 116 " --> pdb=" O LYS I 112 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU I 117 " --> pdb=" O GLU I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 161 Processing helix chain 'I' and resid 182 through 198 removed outlier: 3.525A pdb=" N ASN I 186 " --> pdb=" O VAL I 182 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N HIS I 192 " --> pdb=" O ILE I 188 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR I 193 " --> pdb=" O LEU I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 218 Processing helix chain 'I' and resid 223 through 244 removed outlier: 3.642A pdb=" N LEU I 227 " --> pdb=" O THR I 223 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N SER I 241 " --> pdb=" O SER I 237 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LEU I 242 " --> pdb=" O ILE I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 260 Processing helix chain 'I' and resid 277 through 282 removed outlier: 4.427A pdb=" N TYR I 282 " --> pdb=" O ALA I 278 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 296 Processing helix chain 'I' and resid 297 through 301 removed outlier: 3.654A pdb=" N ASN I 300 " --> pdb=" O GLU I 297 " (cutoff:3.500A) Processing helix chain 'I' and resid 324 through 338 removed outlier: 3.535A pdb=" N VAL I 328 " --> pdb=" O VAL I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 383 through 400 removed outlier: 4.050A pdb=" N ALA I 387 " --> pdb=" O ALA I 383 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET I 398 " --> pdb=" O LYS I 394 " (cutoff:3.500A) Processing helix chain 'I' and resid 404 through 411 removed outlier: 3.982A pdb=" N TYR I 408 " --> pdb=" O PHE I 404 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU I 411 " --> pdb=" O TRP I 407 " (cutoff:3.500A) Processing helix chain 'I' and resid 415 through 436 removed outlier: 4.017A pdb=" N SER I 419 " --> pdb=" O GLU I 415 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY I 436 " --> pdb=" O TYR I 432 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 29 Processing helix chain 'Q' and resid 40 through 46 removed outlier: 4.173A pdb=" N LEU Q 44 " --> pdb=" O SER Q 40 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG Q 46 " --> pdb=" O LEU Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 49 No H-bonds generated for 'chain 'Q' and resid 47 through 49' Processing helix chain 'Q' and resid 69 through 78 removed outlier: 4.445A pdb=" N MET Q 73 " --> pdb=" O GLU Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 85 removed outlier: 3.806A pdb=" N PHE Q 85 " --> pdb=" O GLY Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 86 through 88 No H-bonds generated for 'chain 'Q' and resid 86 through 88' Processing helix chain 'Q' and resid 100 through 106 Processing helix chain 'Q' and resid 108 through 126 removed outlier: 4.017A pdb=" N LEU Q 112 " --> pdb=" O GLU Q 108 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASP Q 114 " --> pdb=" O ALA Q 110 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER Q 115 " --> pdb=" O GLU Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 142 through 159 Processing helix chain 'Q' and resid 180 through 195 removed outlier: 3.529A pdb=" N ASN Q 184 " --> pdb=" O VAL Q 180 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS Q 190 " --> pdb=" O THR Q 186 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN Q 191 " --> pdb=" O LEU Q 187 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU Q 194 " --> pdb=" O HIS Q 190 " (cutoff:3.500A) Processing helix chain 'Q' and resid 203 through 214 Processing helix chain 'Q' and resid 221 through 237 removed outlier: 3.630A pdb=" N LEU Q 225 " --> pdb=" O THR Q 221 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR Q 237 " --> pdb=" O MET Q 233 " (cutoff:3.500A) Processing helix chain 'Q' and resid 237 through 242 removed outlier: 3.982A pdb=" N ARG Q 241 " --> pdb=" O THR Q 237 " (cutoff:3.500A) Processing helix chain 'Q' and resid 249 through 258 Processing helix chain 'Q' and resid 275 through 282 removed outlier: 4.097A pdb=" N GLN Q 280 " --> pdb=" O ARG Q 276 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TYR Q 281 " --> pdb=" O GLY Q 277 " (cutoff:3.500A) Processing helix chain 'Q' and resid 285 through 295 Processing helix chain 'Q' and resid 296 through 299 Processing helix chain 'Q' and resid 322 through 337 removed outlier: 3.562A pdb=" N VAL Q 326 " --> pdb=" O SER Q 322 " (cutoff:3.500A) Processing helix chain 'Q' and resid 338 through 341 Processing helix chain 'Q' and resid 374 through 391 removed outlier: 4.058A pdb=" N PHE Q 378 " --> pdb=" O ILE Q 374 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ARG Q 391 " --> pdb=" O ALA Q 387 " (cutoff:3.500A) Processing helix chain 'Q' and resid 394 through 402 removed outlier: 4.157A pdb=" N TYR Q 398 " --> pdb=" O PHE Q 394 " (cutoff:3.500A) Processing helix chain 'Q' and resid 404 through 428 removed outlier: 3.643A pdb=" N PHE Q 408 " --> pdb=" O ASP Q 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.011A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE A 5 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N PHE A 138 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE A 7 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N SER A 140 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N VAL A 9 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273 Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.289A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ALA B 9 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N MET B 164 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 10.529A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 13.736A pdb=" N ASP B 203 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AA6, first strand: chain 'I' and resid 92 through 94 removed outlier: 8.127A pdb=" N ILE I 93 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE I 67 " --> pdb=" O ILE I 93 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N VAL I 66 " --> pdb=" O CYS I 4 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N SER I 6 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N VAL I 68 " --> pdb=" O SER I 6 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N HIS I 8 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N GLU I 3 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE I 135 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE I 5 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N VAL I 137 " --> pdb=" O ILE I 5 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE I 7 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N HIS I 139 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL I 9 " --> pdb=" O HIS I 139 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU I 167 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N PHE I 135 " --> pdb=" O LEU I 167 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N PHE I 169 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL I 137 " --> pdb=" O PHE I 169 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE I 171 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N HIS I 139 " --> pdb=" O ILE I 171 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AA8, first strand: chain 'I' and resid 269 through 273 removed outlier: 6.840A pdb=" N ALA I 374 " --> pdb=" O TYR I 319 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR I 319 " --> pdb=" O ALA I 374 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N CYS I 376 " --> pdb=" O LEU I 317 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU I 317 " --> pdb=" O CYS I 376 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU I 378 " --> pdb=" O CYS I 315 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N CYS I 315 " --> pdb=" O LEU I 378 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN I 380 " --> pdb=" O MET I 313 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Q' and resid 90 through 92 removed outlier: 8.423A pdb=" N VAL Q 91 " --> pdb=" O ALA Q 63 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU Q 65 " --> pdb=" O VAL Q 91 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N ILE Q 64 " --> pdb=" O ILE Q 4 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N HIS Q 6 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N VAL Q 66 " --> pdb=" O HIS Q 6 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N GLN Q 8 " --> pdb=" O VAL Q 66 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLU Q 3 " --> pdb=" O GLN Q 131 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N PHE Q 133 " --> pdb=" O GLU Q 3 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N VAL Q 5 " --> pdb=" O PHE Q 133 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N LEU Q 135 " --> pdb=" O VAL Q 5 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE Q 7 " --> pdb=" O LEU Q 135 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N HIS Q 137 " --> pdb=" O ILE Q 7 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ALA Q 9 " --> pdb=" O HIS Q 137 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLN Q 131 " --> pdb=" O ILE Q 163 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ASN Q 165 " --> pdb=" O GLN Q 131 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N PHE Q 133 " --> pdb=" O ASN Q 165 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE Q 167 " --> pdb=" O PHE Q 133 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU Q 135 " --> pdb=" O PHE Q 167 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL Q 169 " --> pdb=" O LEU Q 135 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N HIS Q 137 " --> pdb=" O VAL Q 169 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N MET Q 164 " --> pdb=" O GLU Q 198 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N TYR Q 200 " --> pdb=" O MET Q 164 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR Q 166 " --> pdb=" O TYR Q 200 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ILE Q 202 " --> pdb=" O THR Q 166 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER Q 168 " --> pdb=" O ILE Q 202 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR Q 199 " --> pdb=" O PHE Q 266 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N CYS Q 201 " --> pdb=" O PRO Q 268 " (cutoff:3.500A) removed outlier: 10.364A pdb=" N PHE Q 270 " --> pdb=" O CYS Q 201 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N PHE Q 265 " --> pdb=" O SER Q 371 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N SER Q 371 " --> pdb=" O PHE Q 265 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Q' and resid 51 through 53 660 hydrogen bonds defined for protein. 1935 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.05 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4494 1.34 - 1.47: 3358 1.47 - 1.59: 5921 1.59 - 1.72: 16 1.72 - 1.85: 150 Bond restraints: 13939 Sorted by residual: bond pdb=" N MET B 257 " pdb=" CA MET B 257 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.32e-02 5.74e+03 8.73e+00 bond pdb=" N ILE A 219 " pdb=" CA ILE A 219 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.11e+00 bond pdb=" N GLU A 220 " pdb=" CA GLU A 220 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.19e-02 7.06e+03 7.89e+00 bond pdb=" N LEU I 132 " pdb=" CA LEU I 132 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.23e-02 6.61e+03 7.75e+00 bond pdb=" N CYS A 129 " pdb=" CA CYS A 129 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.30e-02 5.92e+03 7.53e+00 ... (remaining 13934 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 18596 2.78 - 5.56: 302 5.56 - 8.34: 44 8.34 - 11.11: 4 11.11 - 13.89: 2 Bond angle restraints: 18948 Sorted by residual: angle pdb=" CB MET I 425 " pdb=" CG MET I 425 " pdb=" SD MET I 425 " ideal model delta sigma weight residual 112.70 126.59 -13.89 3.00e+00 1.11e-01 2.14e+01 angle pdb=" N GLY I 134 " pdb=" CA GLY I 134 " pdb=" C GLY I 134 " ideal model delta sigma weight residual 111.27 118.44 -7.17 1.67e+00 3.59e-01 1.84e+01 angle pdb=" CB MET A 154 " pdb=" CG MET A 154 " pdb=" SD MET A 154 " ideal model delta sigma weight residual 112.70 124.23 -11.53 3.00e+00 1.11e-01 1.48e+01 angle pdb=" CB ARG Q 359 " pdb=" CG ARG Q 359 " pdb=" CD ARG Q 359 " ideal model delta sigma weight residual 111.30 119.77 -8.47 2.30e+00 1.89e-01 1.36e+01 angle pdb=" N LYS A 326 " pdb=" CA LYS A 326 " pdb=" CB LYS A 326 " ideal model delta sigma weight residual 110.01 104.95 5.06 1.45e+00 4.76e-01 1.22e+01 ... (remaining 18943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 8098 35.74 - 71.48: 180 71.48 - 107.22: 18 107.22 - 142.96: 4 142.96 - 178.69: 2 Dihedral angle restraints: 8302 sinusoidal: 3312 harmonic: 4990 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -109.43 178.69 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP I 501 " pdb=" O5' GTP I 501 " pdb=" PA GTP I 501 " pdb=" O3A GTP I 501 " ideal model delta sinusoidal sigma weight residual 69.27 -125.51 -165.22 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -34.91 139.50 1 2.00e+01 2.50e-03 4.23e+01 ... (remaining 8299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1763 0.066 - 0.133: 265 0.133 - 0.199: 46 0.199 - 0.265: 1 0.265 - 0.332: 3 Chirality restraints: 2078 Sorted by residual: chirality pdb=" CB THR I 191 " pdb=" CA THR I 191 " pdb=" OG1 THR I 191 " pdb=" CG2 THR I 191 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CB THR A 191 " pdb=" CA THR A 191 " pdb=" OG1 THR A 191 " pdb=" CG2 THR A 191 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA ILE A 219 " pdb=" N ILE A 219 " pdb=" C ILE A 219 " pdb=" CB ILE A 219 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 2075 not shown) Planarity restraints: 2467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 218 " 0.017 2.00e-02 2.50e+03 3.50e-02 1.23e+01 pdb=" C ASP A 218 " -0.061 2.00e-02 2.50e+03 pdb=" O ASP A 218 " 0.023 2.00e-02 2.50e+03 pdb=" N ILE A 219 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 214 " -0.256 9.50e-02 1.11e+02 1.15e-01 9.65e+00 pdb=" NE ARG I 214 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG I 214 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG I 214 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG I 214 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS I 88 " -0.049 5.00e-02 4.00e+02 7.36e-02 8.68e+00 pdb=" N PRO I 89 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO I 89 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO I 89 " -0.041 5.00e-02 4.00e+02 ... (remaining 2464 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 67 2.55 - 3.14: 10600 3.14 - 3.73: 21427 3.73 - 4.31: 29913 4.31 - 4.90: 51349 Nonbonded interactions: 113356 Sorted by model distance: nonbonded pdb=" O3G G2P Q 501 " pdb="MG MG Q 502 " model vdw 1.963 2.170 nonbonded pdb=" O1G GTP I 501 " pdb="MG MG I 502 " model vdw 1.963 2.170 nonbonded pdb=" O2B G2P Q 501 " pdb="MG MG Q 502 " model vdw 1.964 2.170 nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 1.971 2.170 nonbonded pdb=" OE2 GLU Q 69 " pdb="MG MG Q 502 " model vdw 1.979 2.170 ... (remaining 113351 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 1 through 120 or (resid 121 and (name N or name CA or name \ C or name O or name CB )) or resid 122 through 162 or (resid 163 and (name N or \ name CA or name C or name O or name CB )) or resid 164 through 220 or (resid 22 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 222 through \ 441 or resid 501 through 502)) selection = chain 'I' } ncs_group { reference = chain 'B' selection = (chain 'Q' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 281 or (resid 282 through 283 and (name N or name CA or nam \ e C or name O or name CB )) or resid 284 through 429 or resid 501 through 502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.270 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: 0.500 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 34.650 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 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 : 0.005 0.056 13939 Z= 0.251 Angle : 0.882 13.893 18948 Z= 0.464 Chirality : 0.051 0.332 2078 Planarity : 0.006 0.115 2467 Dihedral : 16.030 178.695 5106 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.14 % Allowed : 12.78 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.19), residues: 1720 helix: 1.18 (0.18), residues: 792 sheet: 0.51 (0.33), residues: 232 loop : -1.06 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 21 HIS 0.008 0.001 HIS B 307 PHE 0.028 0.002 PHE B 20 TYR 0.020 0.002 TYR A 210 ARG 0.021 0.001 ARG I 214 Details of bonding type rmsd hydrogen bonds : bond 0.08677 ( 660) hydrogen bonds : angle 5.13863 ( 1935) covalent geometry : bond 0.00532 (13939) covalent geometry : angle 0.88226 (18948) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 308 time to evaluate : 1.642 Fit side-chains REVERT: A 77 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7796 (mt-10) REVERT: A 120 ASP cc_start: 0.6782 (m-30) cc_final: 0.6245 (m-30) REVERT: A 290 GLU cc_start: 0.7645 (mp0) cc_final: 0.7362 (mp0) REVERT: A 313 MET cc_start: 0.8068 (mtm) cc_final: 0.7798 (ttm) REVERT: B 69 GLU cc_start: 0.7769 (pt0) cc_final: 0.6271 (pm20) REVERT: B 163 ILE cc_start: 0.8458 (mt) cc_final: 0.8162 (tp) REVERT: B 164 MET cc_start: 0.7680 (ttm) cc_final: 0.7426 (mtp) REVERT: B 262 ARG cc_start: 0.7878 (mtm180) cc_final: 0.7626 (mtm-85) REVERT: B 281 TYR cc_start: 0.6253 (m-80) cc_final: 0.5573 (m-80) REVERT: B 307 HIS cc_start: 0.7700 (m-70) cc_final: 0.7368 (m90) REVERT: B 320 ARG cc_start: 0.8175 (mtp85) cc_final: 0.7941 (mtp85) REVERT: B 407 GLU cc_start: 0.7541 (mp0) cc_final: 0.7163 (tt0) REVERT: I 75 ILE cc_start: 0.7320 (mm) cc_final: 0.6923 (mm) REVERT: I 280 LYS cc_start: 0.7681 (mttt) cc_final: 0.6083 (mmtt) REVERT: I 287 SER cc_start: 0.7048 (t) cc_final: 0.6767 (p) REVERT: I 414 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7303 (mt-10) REVERT: Q 22 GLU cc_start: 0.7893 (tt0) cc_final: 0.7479 (mt-10) REVERT: Q 83 GLN cc_start: 0.7638 (tp40) cc_final: 0.7225 (tt0) REVERT: Q 108 GLU cc_start: 0.6695 (mm-30) cc_final: 0.6419 (mm-30) REVERT: Q 125 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6532 (mp0) REVERT: Q 176 SER cc_start: 0.8404 (p) cc_final: 0.8029 (t) REVERT: Q 274 THR cc_start: 0.8795 (p) cc_final: 0.8528 (p) REVERT: Q 275 SER cc_start: 0.6504 (t) cc_final: 0.6060 (t) REVERT: Q 284 LEU cc_start: 0.6915 (tp) cc_final: 0.6570 (pt) REVERT: Q 288 GLU cc_start: 0.7478 (mp0) cc_final: 0.7054 (mp0) REVERT: Q 425 TYR cc_start: 0.7297 (m-80) cc_final: 0.6985 (m-80) outliers start: 2 outliers final: 0 residues processed: 309 average time/residue: 0.2868 time to fit residues: 124.1110 Evaluate side-chains 167 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 125 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 44 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 133 optimal weight: 0.0020 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS A 101 ASN A 133 GLN A 226 ASN A 329 ASN A 372 GLN B 307 HIS B 414 ASN I 50 ASN I 88 HIS I 128 GLN I 300 ASN Q 6 HIS Q 8 GLN Q 99 ASN Q 190 HIS Q 247 ASN Q 279 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.101220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.088816 restraints weight = 20465.386| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.42 r_work: 0.3206 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13939 Z= 0.163 Angle : 0.572 6.161 18948 Z= 0.299 Chirality : 0.045 0.212 2078 Planarity : 0.004 0.061 2467 Dihedral : 11.013 173.484 1972 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.20 % Allowed : 13.54 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.20), residues: 1720 helix: 1.56 (0.18), residues: 800 sheet: 0.57 (0.32), residues: 252 loop : -1.00 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 21 HIS 0.009 0.002 HIS Q 190 PHE 0.023 0.001 PHE B 20 TYR 0.014 0.001 TYR I 224 ARG 0.005 0.001 ARG Q 262 Details of bonding type rmsd hydrogen bonds : bond 0.04855 ( 660) hydrogen bonds : angle 4.57646 ( 1935) covalent geometry : bond 0.00385 (13939) covalent geometry : angle 0.57219 (18948) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 1.704 Fit side-chains revert: symmetry clash REVERT: A 120 ASP cc_start: 0.7593 (m-30) cc_final: 0.7240 (m-30) REVERT: A 123 ARG cc_start: 0.8413 (tpp-160) cc_final: 0.8211 (ttm-80) REVERT: A 214 ARG cc_start: 0.7619 (ttp80) cc_final: 0.7319 (ttp80) REVERT: A 432 TYR cc_start: 0.8390 (OUTLIER) cc_final: 0.6992 (t80) REVERT: B 164 MET cc_start: 0.8377 (ttm) cc_final: 0.8061 (mtp) REVERT: B 202 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8096 (mp) REVERT: I 120 ASP cc_start: 0.7532 (m-30) cc_final: 0.7294 (m-30) REVERT: I 280 LYS cc_start: 0.8544 (mttt) cc_final: 0.7054 (mmtt) REVERT: I 295 CYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7930 (t) REVERT: I 377 MET cc_start: 0.8178 (ttp) cc_final: 0.7952 (ttp) REVERT: I 432 TYR cc_start: 0.8203 (OUTLIER) cc_final: 0.6452 (t80) REVERT: Q 163 ILE cc_start: 0.8477 (mt) cc_final: 0.8018 (pt) REVERT: Q 164 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8429 (ttt) REVERT: Q 257 MET cc_start: 0.7796 (tpp) cc_final: 0.7575 (mmm) REVERT: Q 267 MET cc_start: 0.8668 (ttm) cc_final: 0.8367 (ttm) outliers start: 32 outliers final: 19 residues processed: 193 average time/residue: 0.2879 time to fit residues: 79.1102 Evaluate side-chains 157 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 217 LEU Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain I residue 295 CYS Chi-restraints excluded: chain I residue 432 TYR Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 138 SER Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 164 MET Chi-restraints excluded: chain Q residue 190 HIS Chi-restraints excluded: chain Q residue 237 THR Chi-restraints excluded: chain Q residue 304 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 76 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 chunk 154 optimal weight: 0.9980 chunk 113 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 125 optimal weight: 0.3980 chunk 123 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS B 8 GLN B 245 GLN B 247 ASN I 128 GLN Q 190 HIS Q 347 ASN Q 348 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.097632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.084963 restraints weight = 20732.522| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.46 r_work: 0.3099 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13939 Z= 0.197 Angle : 0.585 5.986 18948 Z= 0.309 Chirality : 0.046 0.193 2078 Planarity : 0.004 0.054 2467 Dihedral : 11.183 170.584 1969 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.96 % Allowed : 13.13 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.20), residues: 1720 helix: 1.46 (0.18), residues: 796 sheet: 0.14 (0.30), residues: 278 loop : -1.06 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 21 HIS 0.020 0.002 HIS Q 190 PHE 0.027 0.002 PHE B 20 TYR 0.014 0.001 TYR Q 425 ARG 0.005 0.001 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.05403 ( 660) hydrogen bonds : angle 4.66429 ( 1935) covalent geometry : bond 0.00466 (13939) covalent geometry : angle 0.58473 (18948) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 143 time to evaluate : 1.458 Fit side-chains revert: symmetry clash REVERT: A 120 ASP cc_start: 0.7658 (m-30) cc_final: 0.7302 (m-30) REVERT: A 214 ARG cc_start: 0.7870 (ttp80) cc_final: 0.7615 (ttp80) REVERT: A 432 TYR cc_start: 0.8391 (OUTLIER) cc_final: 0.7039 (t80) REVERT: B 73 MET cc_start: 0.8928 (mmm) cc_final: 0.8717 (mmm) REVERT: B 164 MET cc_start: 0.8590 (ttm) cc_final: 0.8279 (mtp) REVERT: B 202 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8002 (mp) REVERT: B 307 HIS cc_start: 0.7822 (m90) cc_final: 0.7533 (m90) REVERT: I 1 MET cc_start: 0.8067 (tpp) cc_final: 0.7673 (tpp) REVERT: I 295 CYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8297 (t) REVERT: I 309 HIS cc_start: 0.7851 (m-70) cc_final: 0.7640 (m-70) REVERT: I 432 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.6702 (t80) REVERT: Q 163 ILE cc_start: 0.8690 (mt) cc_final: 0.8298 (pt) REVERT: Q 164 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8450 (ttm) REVERT: Q 257 MET cc_start: 0.7838 (tpp) cc_final: 0.7633 (mmm) REVERT: Q 267 MET cc_start: 0.8717 (ttm) cc_final: 0.8503 (ttm) outliers start: 43 outliers final: 19 residues processed: 176 average time/residue: 0.2877 time to fit residues: 72.1601 Evaluate side-chains 156 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 295 CYS Chi-restraints excluded: chain I residue 378 LEU Chi-restraints excluded: chain I residue 432 TYR Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 138 SER Chi-restraints excluded: chain Q residue 164 MET Chi-restraints excluded: chain Q residue 304 ASP Chi-restraints excluded: chain Q residue 365 VAL Chi-restraints excluded: chain Q residue 377 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 147 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 156 optimal weight: 0.0050 chunk 95 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 129 optimal weight: 0.5980 chunk 145 optimal weight: 0.0970 chunk 34 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS B 8 GLN B 37 HIS I 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.099214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.086748 restraints weight = 20458.132| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.43 r_work: 0.3145 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13939 Z= 0.125 Angle : 0.505 6.102 18948 Z= 0.264 Chirality : 0.043 0.191 2078 Planarity : 0.004 0.053 2467 Dihedral : 10.972 172.809 1969 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.27 % Allowed : 14.43 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.20), residues: 1720 helix: 1.64 (0.19), residues: 798 sheet: 0.14 (0.30), residues: 278 loop : -1.00 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 21 HIS 0.004 0.001 HIS B 105 PHE 0.023 0.001 PHE B 20 TYR 0.010 0.001 TYR I 24 ARG 0.006 0.000 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.04333 ( 660) hydrogen bonds : angle 4.42831 ( 1935) covalent geometry : bond 0.00283 (13939) covalent geometry : angle 0.50492 (18948) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.7604 (m-30) cc_final: 0.7238 (m-30) REVERT: A 432 TYR cc_start: 0.8328 (OUTLIER) cc_final: 0.7014 (t80) REVERT: B 164 MET cc_start: 0.8511 (ttm) cc_final: 0.8220 (mtp) REVERT: B 202 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7848 (mp) REVERT: B 307 HIS cc_start: 0.7888 (m90) cc_final: 0.7601 (m90) REVERT: I 1 MET cc_start: 0.7965 (tpp) cc_final: 0.7648 (tpp) REVERT: I 295 CYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8167 (t) REVERT: I 338 LYS cc_start: 0.8346 (ttmm) cc_final: 0.8052 (tttt) REVERT: I 432 TYR cc_start: 0.8370 (OUTLIER) cc_final: 0.6626 (t80) REVERT: Q 163 ILE cc_start: 0.8693 (mt) cc_final: 0.8370 (pt) REVERT: Q 164 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8407 (ttm) REVERT: Q 257 MET cc_start: 0.7691 (tpp) cc_final: 0.7419 (mmm) REVERT: Q 300 MET cc_start: 0.7999 (mmt) cc_final: 0.7459 (mmt) outliers start: 33 outliers final: 20 residues processed: 177 average time/residue: 0.2864 time to fit residues: 71.5621 Evaluate side-chains 160 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain I residue 31 GLN Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain I residue 295 CYS Chi-restraints excluded: chain I residue 378 LEU Chi-restraints excluded: chain I residue 432 TYR Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain Q residue 138 SER Chi-restraints excluded: chain Q residue 164 MET Chi-restraints excluded: chain Q residue 274 THR Chi-restraints excluded: chain Q residue 275 SER Chi-restraints excluded: chain Q residue 288 GLU Chi-restraints excluded: chain Q residue 365 VAL Chi-restraints excluded: chain Q residue 377 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 94 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS B 8 GLN B 37 HIS I 128 GLN I 258 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.094586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.081986 restraints weight = 20922.672| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.44 r_work: 0.3049 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 13939 Z= 0.256 Angle : 0.619 6.215 18948 Z= 0.327 Chirality : 0.048 0.191 2078 Planarity : 0.005 0.052 2467 Dihedral : 11.452 174.963 1969 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.09 % Allowed : 14.50 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.20), residues: 1720 helix: 1.39 (0.19), residues: 788 sheet: -0.16 (0.30), residues: 278 loop : -1.16 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 21 HIS 0.007 0.002 HIS I 192 PHE 0.021 0.002 PHE B 20 TYR 0.013 0.002 TYR Q 425 ARG 0.006 0.001 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.06025 ( 660) hydrogen bonds : angle 4.79470 ( 1935) covalent geometry : bond 0.00615 (13939) covalent geometry : angle 0.61923 (18948) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 138 time to evaluate : 1.266 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8321 (tpp) cc_final: 0.8058 (tpp) REVERT: A 120 ASP cc_start: 0.7727 (m-30) cc_final: 0.7354 (m-30) REVERT: A 358 GLN cc_start: 0.8753 (tp40) cc_final: 0.8395 (mm-40) REVERT: A 425 MET cc_start: 0.8621 (mmm) cc_final: 0.8142 (tpt) REVERT: A 432 TYR cc_start: 0.8356 (OUTLIER) cc_final: 0.6981 (t80) REVERT: B 164 MET cc_start: 0.8709 (ttm) cc_final: 0.8264 (mtp) REVERT: B 202 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8097 (mp) REVERT: B 307 HIS cc_start: 0.7873 (m90) cc_final: 0.7589 (m90) REVERT: B 394 PHE cc_start: 0.5181 (OUTLIER) cc_final: 0.4703 (t80) REVERT: I 1 MET cc_start: 0.8036 (tpp) cc_final: 0.7790 (tpp) REVERT: I 295 CYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8391 (t) REVERT: I 432 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.6552 (t80) REVERT: Q 163 ILE cc_start: 0.8825 (mt) cc_final: 0.8527 (pt) REVERT: Q 164 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8594 (ttm) REVERT: Q 257 MET cc_start: 0.7932 (tpp) cc_final: 0.7698 (mmm) REVERT: Q 300 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7790 (mtt) outliers start: 45 outliers final: 28 residues processed: 172 average time/residue: 0.3015 time to fit residues: 72.9376 Evaluate side-chains 162 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 234 ILE Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain I residue 295 CYS Chi-restraints excluded: chain I residue 328 VAL Chi-restraints excluded: chain I residue 378 LEU Chi-restraints excluded: chain I residue 432 TYR Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 138 SER Chi-restraints excluded: chain Q residue 164 MET Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain Q residue 275 SER Chi-restraints excluded: chain Q residue 288 GLU Chi-restraints excluded: chain Q residue 300 MET Chi-restraints excluded: chain Q residue 365 VAL Chi-restraints excluded: chain Q residue 377 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 77 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 152 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 70 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN A 309 HIS B 6 HIS B 8 GLN B 37 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.096664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.084025 restraints weight = 20815.430| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.44 r_work: 0.3090 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13939 Z= 0.154 Angle : 0.533 6.947 18948 Z= 0.280 Chirality : 0.044 0.189 2078 Planarity : 0.004 0.052 2467 Dihedral : 11.213 176.440 1969 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.37 % Allowed : 14.43 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.20), residues: 1720 helix: 1.48 (0.19), residues: 798 sheet: -0.18 (0.30), residues: 278 loop : -1.09 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 21 HIS 0.005 0.001 HIS Q 396 PHE 0.019 0.001 PHE B 20 TYR 0.009 0.001 TYR I 24 ARG 0.007 0.000 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.04807 ( 660) hydrogen bonds : angle 4.57090 ( 1935) covalent geometry : bond 0.00359 (13939) covalent geometry : angle 0.53324 (18948) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 138 time to evaluate : 1.538 Fit side-chains revert: symmetry clash REVERT: A 120 ASP cc_start: 0.7670 (m-30) cc_final: 0.7332 (m-30) REVERT: A 358 GLN cc_start: 0.8657 (tp40) cc_final: 0.8282 (mm-40) REVERT: A 425 MET cc_start: 0.8704 (mmm) cc_final: 0.8406 (tpt) REVERT: A 432 TYR cc_start: 0.8311 (OUTLIER) cc_final: 0.6975 (t80) REVERT: B 164 MET cc_start: 0.8612 (ttm) cc_final: 0.8226 (mtp) REVERT: B 202 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.7992 (mp) REVERT: B 307 HIS cc_start: 0.7898 (m90) cc_final: 0.7562 (m90) REVERT: B 394 PHE cc_start: 0.4912 (OUTLIER) cc_final: 0.4499 (t80) REVERT: I 1 MET cc_start: 0.7907 (tpp) cc_final: 0.7642 (tpp) REVERT: I 227 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7847 (mt) REVERT: I 295 CYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8271 (t) REVERT: I 338 LYS cc_start: 0.8422 (ttmm) cc_final: 0.8084 (tttt) REVERT: I 432 TYR cc_start: 0.8402 (OUTLIER) cc_final: 0.6612 (t80) REVERT: Q 163 ILE cc_start: 0.8778 (mt) cc_final: 0.8523 (pt) REVERT: Q 164 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8487 (ttm) REVERT: Q 282 ARG cc_start: 0.7694 (ttm170) cc_final: 0.7406 (ttm170) REVERT: Q 300 MET cc_start: 0.8045 (mmt) cc_final: 0.7186 (mtt) outliers start: 49 outliers final: 29 residues processed: 175 average time/residue: 0.3072 time to fit residues: 75.5210 Evaluate side-chains 167 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 234 ILE Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 285 GLN Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain I residue 295 CYS Chi-restraints excluded: chain I residue 328 VAL Chi-restraints excluded: chain I residue 378 LEU Chi-restraints excluded: chain I residue 432 TYR Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 138 SER Chi-restraints excluded: chain Q residue 164 MET Chi-restraints excluded: chain Q residue 275 SER Chi-restraints excluded: chain Q residue 288 GLU Chi-restraints excluded: chain Q residue 365 VAL Chi-restraints excluded: chain Q residue 377 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 7 optimal weight: 0.8980 chunk 163 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 HIS A 309 HIS B 37 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.095851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.083233 restraints weight = 20721.019| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.42 r_work: 0.3071 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13939 Z= 0.191 Angle : 0.565 6.603 18948 Z= 0.297 Chirality : 0.045 0.192 2078 Planarity : 0.004 0.052 2467 Dihedral : 11.267 175.721 1969 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.16 % Allowed : 14.64 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.20), residues: 1720 helix: 1.43 (0.19), residues: 798 sheet: -0.22 (0.30), residues: 280 loop : -1.07 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 21 HIS 0.005 0.001 HIS I 192 PHE 0.018 0.002 PHE B 20 TYR 0.011 0.001 TYR Q 425 ARG 0.007 0.000 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.05242 ( 660) hydrogen bonds : angle 4.64394 ( 1935) covalent geometry : bond 0.00454 (13939) covalent geometry : angle 0.56479 (18948) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 137 time to evaluate : 1.651 Fit side-chains revert: symmetry clash REVERT: A 120 ASP cc_start: 0.7647 (m-30) cc_final: 0.7321 (m-30) REVERT: A 358 GLN cc_start: 0.8603 (tp40) cc_final: 0.8203 (mm-40) REVERT: A 432 TYR cc_start: 0.8316 (OUTLIER) cc_final: 0.6947 (t80) REVERT: B 164 MET cc_start: 0.8632 (ttm) cc_final: 0.8214 (mtp) REVERT: B 202 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7935 (mp) REVERT: B 307 HIS cc_start: 0.7872 (m90) cc_final: 0.7607 (m90) REVERT: B 394 PHE cc_start: 0.4937 (OUTLIER) cc_final: 0.4511 (t80) REVERT: I 1 MET cc_start: 0.7941 (tpp) cc_final: 0.7681 (tpp) REVERT: I 18 ASN cc_start: 0.7708 (m110) cc_final: 0.7496 (m-40) REVERT: I 227 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7844 (mt) REVERT: I 295 CYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8333 (t) REVERT: I 341 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7595 (mp) REVERT: I 432 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.6559 (t80) REVERT: Q 163 ILE cc_start: 0.8800 (mt) cc_final: 0.8554 (pt) REVERT: Q 164 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8513 (ttm) REVERT: Q 282 ARG cc_start: 0.7785 (ttm170) cc_final: 0.7469 (ttm170) REVERT: Q 300 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7297 (mtt) outliers start: 46 outliers final: 33 residues processed: 173 average time/residue: 0.2942 time to fit residues: 72.3967 Evaluate side-chains 175 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 133 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 234 ILE Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 285 GLN Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain I residue 295 CYS Chi-restraints excluded: chain I residue 328 VAL Chi-restraints excluded: chain I residue 341 ILE Chi-restraints excluded: chain I residue 378 LEU Chi-restraints excluded: chain I residue 432 TYR Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain Q residue 138 SER Chi-restraints excluded: chain Q residue 164 MET Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 275 SER Chi-restraints excluded: chain Q residue 288 GLU Chi-restraints excluded: chain Q residue 300 MET Chi-restraints excluded: chain Q residue 365 VAL Chi-restraints excluded: chain Q residue 377 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 152 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 129 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 167 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS B 37 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.095436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.082762 restraints weight = 20733.702| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.42 r_work: 0.3063 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13939 Z= 0.197 Angle : 0.567 6.815 18948 Z= 0.298 Chirality : 0.045 0.191 2078 Planarity : 0.004 0.052 2467 Dihedral : 11.286 175.632 1969 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.64 % Allowed : 14.23 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.20), residues: 1720 helix: 1.46 (0.19), residues: 790 sheet: -0.32 (0.30), residues: 280 loop : -1.15 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 21 HIS 0.005 0.001 HIS Q 396 PHE 0.018 0.002 PHE B 20 TYR 0.011 0.001 TYR Q 425 ARG 0.007 0.000 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.05253 ( 660) hydrogen bonds : angle 4.66333 ( 1935) covalent geometry : bond 0.00471 (13939) covalent geometry : angle 0.56721 (18948) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 139 time to evaluate : 1.451 Fit side-chains revert: symmetry clash REVERT: A 120 ASP cc_start: 0.7689 (m-30) cc_final: 0.7348 (m-30) REVERT: A 358 GLN cc_start: 0.8597 (tp40) cc_final: 0.8205 (mm-40) REVERT: A 425 MET cc_start: 0.8797 (mmm) cc_final: 0.8239 (tpt) REVERT: A 432 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.6944 (t80) REVERT: B 202 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.7990 (mp) REVERT: B 307 HIS cc_start: 0.7803 (m90) cc_final: 0.7503 (m90) REVERT: B 394 PHE cc_start: 0.4946 (OUTLIER) cc_final: 0.4515 (t80) REVERT: I 18 ASN cc_start: 0.7738 (m110) cc_final: 0.7526 (m-40) REVERT: I 227 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7825 (mt) REVERT: I 295 CYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8366 (t) REVERT: I 338 LYS cc_start: 0.8471 (ttmm) cc_final: 0.8059 (tttt) REVERT: I 341 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7592 (mp) REVERT: I 432 TYR cc_start: 0.8430 (OUTLIER) cc_final: 0.6655 (t80) REVERT: Q 163 ILE cc_start: 0.8831 (mt) cc_final: 0.8587 (pt) REVERT: Q 164 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8593 (ttm) REVERT: Q 282 ARG cc_start: 0.7782 (ttm170) cc_final: 0.7439 (ttm170) REVERT: Q 300 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7292 (mtt) outliers start: 53 outliers final: 38 residues processed: 182 average time/residue: 0.3039 time to fit residues: 77.2247 Evaluate side-chains 182 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 135 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 234 ILE Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 285 GLN Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain I residue 295 CYS Chi-restraints excluded: chain I residue 304 LYS Chi-restraints excluded: chain I residue 328 VAL Chi-restraints excluded: chain I residue 341 ILE Chi-restraints excluded: chain I residue 378 LEU Chi-restraints excluded: chain I residue 432 TYR Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 138 SER Chi-restraints excluded: chain Q residue 164 MET Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 219 THR Chi-restraints excluded: chain Q residue 275 SER Chi-restraints excluded: chain Q residue 288 GLU Chi-restraints excluded: chain Q residue 300 MET Chi-restraints excluded: chain Q residue 365 VAL Chi-restraints excluded: chain Q residue 377 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 169 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 165 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS B 37 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.095782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.083053 restraints weight = 20647.139| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.42 r_work: 0.3074 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13939 Z= 0.185 Angle : 0.564 8.589 18948 Z= 0.296 Chirality : 0.045 0.191 2078 Planarity : 0.004 0.053 2467 Dihedral : 11.237 175.520 1969 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.57 % Allowed : 13.95 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.20), residues: 1720 helix: 1.46 (0.19), residues: 790 sheet: -0.35 (0.30), residues: 280 loop : -1.17 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 21 HIS 0.005 0.001 HIS I 192 PHE 0.013 0.001 PHE A 149 TYR 0.010 0.001 TYR Q 425 ARG 0.008 0.000 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.05132 ( 660) hydrogen bonds : angle 4.64468 ( 1935) covalent geometry : bond 0.00441 (13939) covalent geometry : angle 0.56356 (18948) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 137 time to evaluate : 1.537 Fit side-chains revert: symmetry clash REVERT: A 120 ASP cc_start: 0.7661 (m-30) cc_final: 0.7334 (m-30) REVERT: A 358 GLN cc_start: 0.8583 (tp40) cc_final: 0.8180 (mm-40) REVERT: A 425 MET cc_start: 0.8803 (mmm) cc_final: 0.8150 (tpt) REVERT: A 432 TYR cc_start: 0.8288 (OUTLIER) cc_final: 0.6924 (t80) REVERT: B 202 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.7955 (mp) REVERT: B 307 HIS cc_start: 0.7731 (m90) cc_final: 0.7443 (m90) REVERT: B 394 PHE cc_start: 0.5004 (OUTLIER) cc_final: 0.4530 (t80) REVERT: I 18 ASN cc_start: 0.7705 (m110) cc_final: 0.7490 (m-40) REVERT: I 227 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7873 (mt) REVERT: I 295 CYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8362 (t) REVERT: I 341 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7589 (mp) REVERT: I 432 TYR cc_start: 0.8435 (OUTLIER) cc_final: 0.6646 (t80) REVERT: Q 163 ILE cc_start: 0.8783 (mt) cc_final: 0.8533 (pt) REVERT: Q 164 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8698 (ttm) REVERT: Q 282 ARG cc_start: 0.7820 (ttm170) cc_final: 0.7433 (ttm170) REVERT: Q 300 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7295 (mtt) outliers start: 52 outliers final: 38 residues processed: 176 average time/residue: 0.2985 time to fit residues: 74.0475 Evaluate side-chains 181 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 134 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 234 ILE Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 285 GLN Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain I residue 295 CYS Chi-restraints excluded: chain I residue 304 LYS Chi-restraints excluded: chain I residue 328 VAL Chi-restraints excluded: chain I residue 341 ILE Chi-restraints excluded: chain I residue 378 LEU Chi-restraints excluded: chain I residue 432 TYR Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 138 SER Chi-restraints excluded: chain Q residue 164 MET Chi-restraints excluded: chain Q residue 219 THR Chi-restraints excluded: chain Q residue 275 SER Chi-restraints excluded: chain Q residue 288 GLU Chi-restraints excluded: chain Q residue 300 MET Chi-restraints excluded: chain Q residue 365 VAL Chi-restraints excluded: chain Q residue 377 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.2980 chunk 148 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 35 optimal weight: 0.1980 chunk 68 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 132 optimal weight: 0.0170 chunk 71 optimal weight: 0.4980 chunk 33 optimal weight: 0.6980 overall best weight: 0.3418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS B 37 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.098410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.085716 restraints weight = 20598.901| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.44 r_work: 0.3121 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13939 Z= 0.121 Angle : 0.510 9.472 18948 Z= 0.265 Chirality : 0.043 0.187 2078 Planarity : 0.004 0.054 2467 Dihedral : 10.945 176.516 1969 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.54 % Allowed : 15.19 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.20), residues: 1720 helix: 1.66 (0.19), residues: 798 sheet: -0.22 (0.30), residues: 280 loop : -1.03 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 21 HIS 0.004 0.001 HIS Q 396 PHE 0.012 0.001 PHE A 149 TYR 0.008 0.001 TYR A 172 ARG 0.008 0.000 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.04172 ( 660) hydrogen bonds : angle 4.42769 ( 1935) covalent geometry : bond 0.00277 (13939) covalent geometry : angle 0.50961 (18948) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 1.449 Fit side-chains revert: symmetry clash REVERT: A 120 ASP cc_start: 0.7648 (m-30) cc_final: 0.7321 (m-30) REVERT: A 425 MET cc_start: 0.8782 (mmm) cc_final: 0.8549 (tpt) REVERT: A 432 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.6954 (t80) REVERT: B 307 HIS cc_start: 0.7626 (m90) cc_final: 0.7368 (m90) REVERT: B 394 PHE cc_start: 0.4650 (OUTLIER) cc_final: 0.4286 (t80) REVERT: I 128 GLN cc_start: 0.6975 (mp10) cc_final: 0.6701 (mp10) REVERT: I 254 GLU cc_start: 0.5504 (mm-30) cc_final: 0.5167 (mm-30) REVERT: I 295 CYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8274 (t) REVERT: I 338 LYS cc_start: 0.8406 (ttmm) cc_final: 0.8049 (tttt) REVERT: I 432 TYR cc_start: 0.8413 (OUTLIER) cc_final: 0.6687 (t80) REVERT: Q 163 ILE cc_start: 0.8743 (mt) cc_final: 0.8542 (pt) REVERT: Q 164 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8649 (ttm) REVERT: Q 282 ARG cc_start: 0.7832 (ttm170) cc_final: 0.7508 (ttm170) REVERT: Q 297 LYS cc_start: 0.8782 (mmtm) cc_final: 0.8546 (mmtm) REVERT: Q 300 MET cc_start: 0.7982 (mmt) cc_final: 0.7366 (mtt) outliers start: 37 outliers final: 28 residues processed: 175 average time/residue: 0.3053 time to fit residues: 74.7785 Evaluate side-chains 172 residues out of total 1472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 234 ILE Chi-restraints excluded: chain I residue 285 GLN Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain I residue 295 CYS Chi-restraints excluded: chain I residue 328 VAL Chi-restraints excluded: chain I residue 378 LEU Chi-restraints excluded: chain I residue 432 TYR Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain Q residue 138 SER Chi-restraints excluded: chain Q residue 164 MET Chi-restraints excluded: chain Q residue 219 THR Chi-restraints excluded: chain Q residue 275 SER Chi-restraints excluded: chain Q residue 288 GLU Chi-restraints excluded: chain Q residue 365 VAL Chi-restraints excluded: chain Q residue 377 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 153 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 155 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 84 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS B 37 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.096883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.084226 restraints weight = 20728.262| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.43 r_work: 0.3077 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13939 Z= 0.178 Angle : 0.563 10.199 18948 Z= 0.293 Chirality : 0.045 0.194 2078 Planarity : 0.004 0.053 2467 Dihedral : 11.128 175.416 1969 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.68 % Allowed : 15.26 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.20), residues: 1720 helix: 1.58 (0.19), residues: 790 sheet: -0.18 (0.30), residues: 276 loop : -1.12 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 21 HIS 0.005 0.001 HIS Q 396 PHE 0.012 0.001 PHE A 149 TYR 0.010 0.001 TYR Q 425 ARG 0.009 0.000 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.04981 ( 660) hydrogen bonds : angle 4.55899 ( 1935) covalent geometry : bond 0.00423 (13939) covalent geometry : angle 0.56276 (18948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6624.79 seconds wall clock time: 114 minutes 33.08 seconds (6873.08 seconds total)