Starting phenix.real_space_refine on Mon Jun 16 11:04:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e26_47439/06_2025/9e26_47439.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e26_47439/06_2025/9e26_47439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e26_47439/06_2025/9e26_47439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e26_47439/06_2025/9e26_47439.map" model { file = "/net/cci-nas-00/data/ceres_data/9e26_47439/06_2025/9e26_47439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e26_47439/06_2025/9e26_47439.cif" } resolution = 2.8 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 ------------------------------------------------------------------------------- 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= 0.044 sd= 0.115 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 10 5.49 5 Mg 4 5.21 5 S 102 5.16 5 C 11374 2.51 5 N 3422 2.21 5 O 3532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18444 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "B" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "C" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "D" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "E" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "F" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.91, per 1000 atoms: 0.70 Number of scatterers: 18444 At special positions: 0 Unit cell: (129.78, 145.23, 94.76, 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 102 16.00 P 10 15.00 Mg 4 11.99 O 3532 8.00 N 3422 7.00 C 11374 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: 4.76 Conformation dependent library (CDL) restraints added in 2.5 seconds 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4644 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 12 sheets defined 45.7% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 80 through 97 Processing helix chain 'A' and resid 98 through 105 removed outlier: 3.593A pdb=" N LEU A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 126 Processing helix chain 'A' and resid 130 through 146 Processing helix chain 'A' and resid 150 through 157 removed outlier: 4.246A pdb=" N LEU A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 202 Processing helix chain 'A' and resid 249 through 256 Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 296 through 298 No H-bonds generated for 'chain 'A' and resid 296 through 298' Processing helix chain 'A' and resid 337 through 346 Processing helix chain 'A' and resid 361 through 372 removed outlier: 3.771A pdb=" N ASP A 365 " --> pdb=" O PRO A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 400 Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 480 through 487 Processing helix chain 'A' and resid 489 through 500 removed outlier: 3.554A pdb=" N ALA A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 97 Processing helix chain 'B' and resid 98 through 105 Processing helix chain 'B' and resid 106 through 126 Processing helix chain 'B' and resid 130 through 146 Processing helix chain 'B' and resid 150 through 157 removed outlier: 4.493A pdb=" N LEU B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 203 removed outlier: 4.015A pdb=" N VAL B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 256 Processing helix chain 'B' and resid 260 through 273 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 337 through 346 Processing helix chain 'B' and resid 361 through 372 removed outlier: 3.979A pdb=" N ASP B 365 " --> pdb=" O PRO B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 399 Processing helix chain 'B' and resid 405 through 417 Processing helix chain 'B' and resid 480 through 487 Processing helix chain 'B' and resid 489 through 501 Processing helix chain 'C' and resid 81 through 97 Processing helix chain 'C' and resid 98 through 104 removed outlier: 3.581A pdb=" N LEU C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 126 Processing helix chain 'C' and resid 130 through 146 Processing helix chain 'C' and resid 150 through 157 removed outlier: 4.315A pdb=" N LEU C 154 " --> pdb=" O PRO C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 202 Processing helix chain 'C' and resid 249 through 256 removed outlier: 3.592A pdb=" N LEU C 253 " --> pdb=" O THR C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 286 through 296 Processing helix chain 'C' and resid 337 through 346 Processing helix chain 'C' and resid 361 through 373 removed outlier: 3.617A pdb=" N ASP C 365 " --> pdb=" O PRO C 361 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY C 373 " --> pdb=" O ALA C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 400 Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 480 through 488 Processing helix chain 'C' and resid 489 through 501 Processing helix chain 'D' and resid 81 through 97 Processing helix chain 'D' and resid 98 through 105 removed outlier: 3.625A pdb=" N LEU D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 126 Processing helix chain 'D' and resid 130 through 146 Processing helix chain 'D' and resid 150 through 157 removed outlier: 4.249A pdb=" N LEU D 154 " --> pdb=" O PRO D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 202 Processing helix chain 'D' and resid 249 through 256 Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 337 through 346 Processing helix chain 'D' and resid 361 through 371 removed outlier: 3.799A pdb=" N ASP D 365 " --> pdb=" O PRO D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 400 Processing helix chain 'D' and resid 405 through 417 Processing helix chain 'D' and resid 480 through 487 Processing helix chain 'D' and resid 489 through 500 removed outlier: 3.522A pdb=" N ALA D 500 " --> pdb=" O ALA D 496 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 97 Processing helix chain 'E' and resid 98 through 105 removed outlier: 3.611A pdb=" N LEU E 105 " --> pdb=" O GLN E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 125 Processing helix chain 'E' and resid 130 through 147 Processing helix chain 'E' and resid 150 through 157 removed outlier: 4.162A pdb=" N LEU E 154 " --> pdb=" O PRO E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 202 Processing helix chain 'E' and resid 249 through 256 Processing helix chain 'E' and resid 260 through 273 Processing helix chain 'E' and resid 286 through 295 Processing helix chain 'E' and resid 296 through 298 No H-bonds generated for 'chain 'E' and resid 296 through 298' Processing helix chain 'E' and resid 337 through 346 Processing helix chain 'E' and resid 361 through 372 removed outlier: 3.968A pdb=" N ASP E 365 " --> pdb=" O PRO E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 399 Processing helix chain 'E' and resid 405 through 417 Processing helix chain 'E' and resid 480 through 487 Processing helix chain 'E' and resid 489 through 501 Processing helix chain 'F' and resid 81 through 97 Processing helix chain 'F' and resid 98 through 105 Processing helix chain 'F' and resid 106 through 126 removed outlier: 3.859A pdb=" N GLY F 111 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP F 116 " --> pdb=" O GLU F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 146 Processing helix chain 'F' and resid 150 through 157 removed outlier: 4.351A pdb=" N LEU F 154 " --> pdb=" O PRO F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 202 Processing helix chain 'F' and resid 244 through 248 removed outlier: 3.893A pdb=" N LYS F 247 " --> pdb=" O LYS F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 256 removed outlier: 4.112A pdb=" N LEU F 253 " --> pdb=" O THR F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 286 through 296 Processing helix chain 'F' and resid 337 through 346 Processing helix chain 'F' and resid 361 through 373 removed outlier: 3.615A pdb=" N ASP F 365 " --> pdb=" O PRO F 361 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY F 373 " --> pdb=" O ALA F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 400 Processing helix chain 'F' and resid 405 through 417 Processing helix chain 'F' and resid 480 through 488 Processing helix chain 'F' and resid 489 through 501 Processing sheet with id=AA1, first strand: chain 'A' and resid 178 through 181 removed outlier: 3.879A pdb=" N ASP A 162 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 320 through 324 removed outlier: 6.743A pdb=" N VAL A 304 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LEU A 323 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N THR A 306 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL A 305 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N GLY A 356 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N CYS A 307 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL A 358 " --> pdb=" O CYS A 307 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET A 378 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLY A 356 " --> pdb=" O MET A 378 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N THR A 380 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N HIS A 382 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL A 278 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ALA A 423 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N SER A 280 " --> pdb=" O ALA A 423 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N ARG A 425 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE A 420 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE A 436 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLN A 422 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 11.250A pdb=" N ARG A 432 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 10.467A pdb=" N GLU A 456 " --> pdb=" O ARG A 432 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR A 434 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL A 454 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE A 436 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL A 448 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEU A 442 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL A 467 " --> pdb=" O THR A 458 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 178 through 182 removed outlier: 4.649A pdb=" N VAL B 171 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP B 162 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 320 through 324 removed outlier: 6.371A pdb=" N VAL B 305 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR B 380 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY B 379 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B 278 " --> pdb=" O ILE B 421 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ALA B 423 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER B 280 " --> pdb=" O ALA B 423 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N ARG B 425 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE B 420 " --> pdb=" O ILE B 436 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE B 436 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLN B 422 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 11.157A pdb=" N ARG B 432 " --> pdb=" O GLU B 456 " (cutoff:3.500A) removed outlier: 9.740A pdb=" N GLU B 456 " --> pdb=" O ARG B 432 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR B 434 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL B 454 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE B 436 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL B 448 " --> pdb=" O VAL B 440 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU B 442 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B 467 " --> pdb=" O THR B 458 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 178 through 182 removed outlier: 4.618A pdb=" N VAL C 171 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG C 170 " --> pdb=" O ASN C 166 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP C 162 " --> pdb=" O GLU C 174 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 320 through 324 removed outlier: 6.618A pdb=" N VAL C 305 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR C 380 " --> pdb=" O VAL C 355 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL C 278 " --> pdb=" O ILE C 421 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ALA C 423 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER C 280 " --> pdb=" O ALA C 423 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N ARG C 425 " --> pdb=" O SER C 280 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA C 424 " --> pdb=" O ILE C 433 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ILE C 433 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 11.560A pdb=" N ARG C 432 " --> pdb=" O GLU C 456 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N GLU C 456 " --> pdb=" O ARG C 432 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N THR C 434 " --> pdb=" O VAL C 454 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL C 454 " --> pdb=" O THR C 434 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE C 436 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL C 448 " --> pdb=" O VAL C 440 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU C 442 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N TYR C 455 " --> pdb=" O ARG C 471 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG C 471 " --> pdb=" O TYR C 455 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ILE C 457 " --> pdb=" O LYS C 469 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LYS C 469 " --> pdb=" O ILE C 457 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 178 through 182 removed outlier: 4.641A pdb=" N VAL D 171 " --> pdb=" O THR D 182 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE D 172 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE D 163 " --> pdb=" O PHE D 172 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU D 174 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 320 through 324 removed outlier: 6.733A pdb=" N VAL D 304 " --> pdb=" O VAL D 321 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU D 323 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR D 306 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL D 305 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR D 380 " --> pdb=" O VAL D 355 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS D 435 " --> pdb=" O GLN D 422 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA D 424 " --> pdb=" O ILE D 433 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ILE D 433 " --> pdb=" O ALA D 424 " (cutoff:3.500A) removed outlier: 11.269A pdb=" N ARG D 432 " --> pdb=" O GLU D 456 " (cutoff:3.500A) removed outlier: 10.465A pdb=" N GLU D 456 " --> pdb=" O ARG D 432 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N THR D 434 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL D 454 " --> pdb=" O THR D 434 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE D 436 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL D 448 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU D 442 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL D 446 " --> pdb=" O LEU D 442 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL D 467 " --> pdb=" O THR D 458 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 178 through 182 removed outlier: 4.589A pdb=" N VAL E 171 " --> pdb=" O THR E 182 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ARG E 170 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL E 165 " --> pdb=" O ARG E 170 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N PHE E 172 " --> pdb=" O ILE E 163 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE E 163 " --> pdb=" O PHE E 172 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLU E 174 " --> pdb=" O ALA E 161 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 320 through 324 removed outlier: 6.376A pdb=" N VAL E 305 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR E 380 " --> pdb=" O VAL E 355 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU E 277 " --> pdb=" O GLY E 379 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LEU E 381 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE E 279 " --> pdb=" O LEU E 381 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL E 278 " --> pdb=" O ILE E 421 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ALA E 423 " --> pdb=" O VAL E 278 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER E 280 " --> pdb=" O ALA E 423 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N ARG E 425 " --> pdb=" O SER E 280 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE E 420 " --> pdb=" O ILE E 436 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE E 436 " --> pdb=" O ILE E 420 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN E 422 " --> pdb=" O THR E 434 " (cutoff:3.500A) removed outlier: 17.116A pdb=" N ARG E 431 " --> pdb=" O THR E 458 " (cutoff:3.500A) removed outlier: 13.589A pdb=" N THR E 458 " --> pdb=" O ARG E 431 " (cutoff:3.500A) removed outlier: 10.614A pdb=" N ILE E 433 " --> pdb=" O GLU E 456 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLU E 456 " --> pdb=" O ILE E 433 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N HIS E 435 " --> pdb=" O VAL E 454 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL E 454 " --> pdb=" O HIS E 435 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N THR E 437 " --> pdb=" O LEU E 452 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU E 452 " --> pdb=" O THR E 437 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL E 439 " --> pdb=" O GLN E 450 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN E 450 " --> pdb=" O VAL E 439 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL E 467 " --> pdb=" O THR E 458 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 178 through 182 removed outlier: 4.627A pdb=" N VAL F 171 " --> pdb=" O THR F 182 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG F 170 " --> pdb=" O ASN F 166 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP F 162 " --> pdb=" O GLU F 174 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 320 through 324 removed outlier: 6.659A pdb=" N VAL F 305 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N GLY F 356 " --> pdb=" O VAL F 305 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N CYS F 307 " --> pdb=" O GLY F 356 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR F 380 " --> pdb=" O VAL F 355 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLU F 357 " --> pdb=" O THR F 380 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N HIS F 382 " --> pdb=" O GLU F 357 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL F 278 " --> pdb=" O ILE F 421 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ALA F 423 " --> pdb=" O VAL F 278 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N SER F 280 " --> pdb=" O ALA F 423 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N ARG F 425 " --> pdb=" O SER F 280 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA F 424 " --> pdb=" O ILE F 433 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ILE F 433 " --> pdb=" O ALA F 424 " (cutoff:3.500A) removed outlier: 11.568A pdb=" N ARG F 432 " --> pdb=" O GLU F 456 " (cutoff:3.500A) removed outlier: 10.489A pdb=" N GLU F 456 " --> pdb=" O ARG F 432 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N THR F 434 " --> pdb=" O VAL F 454 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL F 454 " --> pdb=" O THR F 434 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE F 436 " --> pdb=" O LEU F 452 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL F 448 " --> pdb=" O VAL F 440 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LEU F 442 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL F 446 " --> pdb=" O LEU F 442 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N TYR F 455 " --> pdb=" O ARG F 471 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG F 471 " --> pdb=" O TYR F 455 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ILE F 457 " --> pdb=" O LYS F 469 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS F 469 " --> pdb=" O ILE F 457 " (cutoff:3.500A) 1004 hydrogen bonds defined for protein. 2937 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: 6.53 Time building geometry restraints manager: 5.59 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: 6552 1.34 - 1.46: 3189 1.46 - 1.58: 8757 1.58 - 1.70: 10 1.70 - 1.81: 168 Bond restraints: 18676 Sorted by residual: bond pdb=" C VAL E 145 " pdb=" N LEU E 146 " ideal model delta sigma weight residual 1.332 1.357 -0.024 1.40e-02 5.10e+03 3.00e+00 bond pdb=" C VAL F 145 " pdb=" N LEU F 146 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.42e-02 4.96e+03 2.96e+00 bond pdb=" N LEU F 146 " pdb=" CA LEU F 146 " ideal model delta sigma weight residual 1.455 1.473 -0.018 1.29e-02 6.01e+03 2.05e+00 bond pdb=" C4 ADP E 602 " pdb=" C5 ADP E 602 " ideal model delta sigma weight residual 1.490 1.461 0.029 2.00e-02 2.50e+03 2.05e+00 bond pdb=" C4 ADP B 601 " pdb=" C5 ADP B 601 " ideal model delta sigma weight residual 1.490 1.462 0.028 2.00e-02 2.50e+03 1.97e+00 ... (remaining 18671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 24995 1.68 - 3.36: 259 3.36 - 5.04: 92 5.04 - 6.71: 19 6.71 - 8.39: 5 Bond angle restraints: 25370 Sorted by residual: angle pdb=" CG ARG F 491 " pdb=" CD ARG F 491 " pdb=" NE ARG F 491 " ideal model delta sigma weight residual 112.00 118.94 -6.94 2.20e+00 2.07e-01 9.94e+00 angle pdb=" CB MET A 399 " pdb=" CG MET A 399 " pdb=" SD MET A 399 " ideal model delta sigma weight residual 112.70 121.09 -8.39 3.00e+00 1.11e-01 7.83e+00 angle pdb=" C3' ATP A 602 " pdb=" C4' ATP A 602 " pdb=" C5' ATP A 602 " ideal model delta sigma weight residual 115.19 110.40 4.79 1.76e+00 3.23e-01 7.41e+00 angle pdb=" C2' ATP A 602 " pdb=" C3' ATP A 602 " pdb=" O3' ATP A 602 " ideal model delta sigma weight residual 111.83 104.97 6.86 2.67e+00 1.40e-01 6.61e+00 angle pdb=" CB ARG C 491 " pdb=" CG ARG C 491 " pdb=" CD ARG C 491 " ideal model delta sigma weight residual 111.30 117.06 -5.76 2.30e+00 1.89e-01 6.27e+00 ... (remaining 25365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 10387 17.46 - 34.92: 813 34.92 - 52.39: 207 52.39 - 69.85: 54 69.85 - 87.31: 23 Dihedral angle restraints: 11484 sinusoidal: 4284 harmonic: 7200 Sorted by residual: dihedral pdb=" CA HIS D 435 " pdb=" C HIS D 435 " pdb=" N ILE D 436 " pdb=" CA ILE D 436 " ideal model delta harmonic sigma weight residual 180.00 159.24 20.76 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA HIS A 435 " pdb=" C HIS A 435 " pdb=" N ILE A 436 " pdb=" CA ILE A 436 " ideal model delta harmonic sigma weight residual 180.00 159.28 20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA HIS F 435 " pdb=" C HIS F 435 " pdb=" N ILE F 436 " pdb=" CA ILE F 436 " ideal model delta harmonic sigma weight residual 180.00 159.97 20.03 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 11481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2523 0.060 - 0.120: 452 0.120 - 0.179: 29 0.179 - 0.239: 0 0.239 - 0.299: 6 Chirality restraints: 3010 Sorted by residual: chirality pdb=" C3' ATP A 602 " pdb=" C2' ATP A 602 " pdb=" C4' ATP A 602 " pdb=" O3' ATP A 602 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C2' ATP D 602 " pdb=" C1' ATP D 602 " pdb=" C3' ATP D 602 " pdb=" O2' ATP D 602 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C2' ATP A 602 " pdb=" C1' ATP A 602 " pdb=" C3' ATP A 602 " pdb=" O2' ATP A 602 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 3007 not shown) Planarity restraints: 3364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 145 " -0.024 2.00e-02 2.50e+03 4.68e-02 2.19e+01 pdb=" C VAL E 145 " 0.081 2.00e-02 2.50e+03 pdb=" O VAL E 145 " -0.031 2.00e-02 2.50e+03 pdb=" N LEU E 146 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 145 " 0.024 2.00e-02 2.50e+03 4.64e-02 2.15e+01 pdb=" C VAL F 145 " -0.080 2.00e-02 2.50e+03 pdb=" O VAL F 145 " 0.030 2.00e-02 2.50e+03 pdb=" N LEU F 146 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 491 " -0.255 9.50e-02 1.11e+02 1.15e-01 9.01e+00 pdb=" NE ARG C 491 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG C 491 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG C 491 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG C 491 " -0.003 2.00e-02 2.50e+03 ... (remaining 3361 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 146 2.49 - 3.09: 14455 3.09 - 3.69: 28311 3.69 - 4.30: 41231 4.30 - 4.90: 70423 Nonbonded interactions: 154566 Sorted by model distance: nonbonded pdb=" OG1 THR A 288 " pdb="MG MG A 601 " model vdw 1.886 2.170 nonbonded pdb=" OG1 THR D 288 " pdb="MG MG D 601 " model vdw 1.915 2.170 nonbonded pdb="MG MG D 601 " pdb=" O2B ATP D 602 " model vdw 1.924 2.170 nonbonded pdb=" OG1 THR E 288 " pdb="MG MG E 601 " model vdw 1.929 2.170 nonbonded pdb=" OG1 THR B 288 " pdb="MG MG B 602 " model vdw 1.945 2.170 ... (remaining 154561 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and resid 80 through 501) selection = (chain 'B' and resid 80 through 501) selection = chain 'C' selection = (chain 'D' and resid 80 through 501) selection = (chain 'E' and resid 80 through 501) selection = chain 'F' } 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: 0.010 Normalize map: mean=0, sd=1: 0.130 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: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 45.640 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.090 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:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 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 0.040 18676 Z= 0.210 Angle : 0.535 8.393 25370 Z= 0.269 Chirality : 0.046 0.299 3010 Planarity : 0.004 0.115 3364 Dihedral : 14.678 87.311 6840 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.07 % Allowed : 10.14 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.74 (0.18), residues: 2520 helix: 2.62 (0.16), residues: 1140 sheet: -0.61 (0.23), residues: 472 loop : 0.35 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 481 HIS 0.003 0.001 HIS E 382 PHE 0.005 0.001 PHE D 480 TYR 0.006 0.001 TYR D 487 ARG 0.017 0.000 ARG C 491 Details of bonding type rmsd hydrogen bonds : bond 0.11418 ( 1004) hydrogen bonds : angle 5.63490 ( 2937) covalent geometry : bond 0.00470 (18676) covalent geometry : angle 0.53466 (25370) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 748 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 ILE cc_start: 0.7801 (mt) cc_final: 0.7154 (mt) REVERT: A 324 GLU cc_start: 0.6499 (tt0) cc_final: 0.6273 (tp30) REVERT: A 414 VAL cc_start: 0.7811 (t) cc_final: 0.7299 (p) REVERT: A 465 LYS cc_start: 0.5440 (mmmm) cc_final: 0.5061 (mtpp) REVERT: B 225 ASN cc_start: 0.7239 (t0) cc_final: 0.7014 (t0) REVERT: B 250 MET cc_start: 0.7076 (tpp) cc_final: 0.6669 (tpt) REVERT: B 465 LYS cc_start: 0.6633 (mmtp) cc_final: 0.6347 (tmtt) REVERT: C 171 VAL cc_start: 0.7248 (t) cc_final: 0.7015 (t) REVERT: C 298 ILE cc_start: 0.6915 (mt) cc_final: 0.6679 (mt) REVERT: C 299 ASP cc_start: 0.7424 (t0) cc_final: 0.7125 (t70) REVERT: C 325 THR cc_start: 0.6104 (p) cc_final: 0.5729 (p) REVERT: D 247 LYS cc_start: 0.8143 (ttmt) cc_final: 0.7940 (tttt) REVERT: D 279 ILE cc_start: 0.7829 (mm) cc_final: 0.7529 (mm) REVERT: D 324 GLU cc_start: 0.8283 (tt0) cc_final: 0.8045 (tm-30) REVERT: D 351 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7035 (mp0) REVERT: E 173 ILE cc_start: 0.8067 (pt) cc_final: 0.7549 (pp) REVERT: E 178 LYS cc_start: 0.8112 (mmmm) cc_final: 0.7542 (mmmt) REVERT: E 191 GLN cc_start: 0.9157 (tt0) cc_final: 0.8891 (tt0) REVERT: E 193 MET cc_start: 0.8552 (tpt) cc_final: 0.8221 (tpp) REVERT: E 277 LEU cc_start: 0.8110 (tp) cc_final: 0.7554 (mt) REVERT: E 324 GLU cc_start: 0.7317 (tp30) cc_final: 0.7090 (tp30) REVERT: E 345 CYS cc_start: 0.8456 (m) cc_final: 0.7851 (m) REVERT: E 395 SER cc_start: 0.7007 (m) cc_final: 0.6684 (p) REVERT: E 443 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6206 (mp0) REVERT: E 453 PHE cc_start: 0.6852 (t80) cc_final: 0.6560 (m-80) REVERT: F 244 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7246 (mptp) REVERT: F 289 THR cc_start: 0.8131 (m) cc_final: 0.7914 (p) REVERT: F 409 ILE cc_start: 0.5523 (mt) cc_final: 0.5316 (mt) outliers start: 19 outliers final: 6 residues processed: 761 average time/residue: 1.1817 time to fit residues: 1015.3536 Evaluate side-chains 467 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 460 time to evaluate : 2.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 244 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 50.0000 chunk 191 optimal weight: 20.0000 chunk 105 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 128 optimal weight: 50.0000 chunk 102 optimal weight: 0.9990 chunk 197 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 120 optimal weight: 20.0000 chunk 147 optimal weight: 6.9990 chunk 228 optimal weight: 6.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN A 435 HIS B 166 ASN B 180 GLN B 202 GLN B 344 ASN C 166 ASN C 180 GLN C 225 ASN C 344 ASN C 382 HIS D 225 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 ASN D 470 HIS ** E 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN E 225 ASN E 344 ASN E 382 HIS E 450 GLN F 374 HIS F 435 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.111826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.091342 restraints weight = 41500.037| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 3.19 r_work: 0.3151 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 18676 Z= 0.200 Angle : 0.771 13.324 25370 Z= 0.386 Chirality : 0.049 0.203 3010 Planarity : 0.006 0.107 3364 Dihedral : 7.199 83.514 2859 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.62 % Favored : 97.34 % Rotamer: Outliers : 7.83 % Allowed : 21.57 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.52 (0.17), residues: 2520 helix: 2.20 (0.16), residues: 1150 sheet: -0.62 (0.21), residues: 540 loop : 0.65 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 481 HIS 0.005 0.001 HIS F 374 PHE 0.018 0.002 PHE A 297 TYR 0.014 0.002 TYR B 148 ARG 0.013 0.001 ARG E 206 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 1004) hydrogen bonds : angle 4.35892 ( 2937) covalent geometry : bond 0.00456 (18676) covalent geometry : angle 0.77091 (25370) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 543 time to evaluate : 2.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8925 (mm) REVERT: A 178 LYS cc_start: 0.8899 (ptpp) cc_final: 0.8394 (mppt) REVERT: A 218 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8698 (mp) REVERT: A 243 PHE cc_start: 0.8340 (p90) cc_final: 0.7781 (p90) REVERT: A 246 ASP cc_start: 0.8640 (t0) cc_final: 0.8392 (t0) REVERT: A 250 MET cc_start: 0.5529 (pmm) cc_final: 0.4603 (mmm) REVERT: A 270 ILE cc_start: 0.8404 (mt) cc_final: 0.8104 (mt) REVERT: A 314 GLN cc_start: 0.7729 (tm-30) cc_final: 0.7405 (tm-30) REVERT: A 324 GLU cc_start: 0.7486 (tt0) cc_final: 0.6884 (mm-30) REVERT: A 358 VAL cc_start: 0.7716 (OUTLIER) cc_final: 0.7369 (t) REVERT: B 202 GLN cc_start: 0.8646 (tt0) cc_final: 0.8404 (mt0) REVERT: B 225 ASN cc_start: 0.7828 (t0) cc_final: 0.7498 (t0) REVERT: B 316 GLN cc_start: 0.7790 (tp-100) cc_final: 0.7549 (tp-100) REVERT: B 324 GLU cc_start: 0.5954 (mm-30) cc_final: 0.5397 (mm-30) REVERT: B 344 ASN cc_start: 0.8693 (OUTLIER) cc_final: 0.8400 (t0) REVERT: B 384 ASN cc_start: 0.8162 (m-40) cc_final: 0.7205 (m-40) REVERT: C 309 ASP cc_start: 0.8292 (p0) cc_final: 0.7984 (p0) REVERT: C 427 ARG cc_start: 0.7775 (tmm160) cc_final: 0.7531 (tmm160) REVERT: C 475 ILE cc_start: 0.7492 (OUTLIER) cc_final: 0.7274 (pp) REVERT: C 498 ASP cc_start: 0.8788 (p0) cc_final: 0.8527 (p0) REVERT: D 308 GLU cc_start: 0.7594 (tt0) cc_final: 0.7325 (pt0) REVERT: D 324 GLU cc_start: 0.8475 (tt0) cc_final: 0.8152 (tt0) REVERT: D 351 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7693 (mp0) REVERT: D 364 PHE cc_start: 0.6595 (t80) cc_final: 0.6297 (t80) REVERT: D 393 ILE cc_start: 0.8736 (mt) cc_final: 0.8530 (mp) REVERT: D 407 LYS cc_start: 0.8273 (mppt) cc_final: 0.7611 (mmmm) REVERT: E 164 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7633 (mtp) REVERT: E 191 GLN cc_start: 0.9254 (tt0) cc_final: 0.8791 (tt0) REVERT: E 306 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8387 (p) REVERT: E 324 GLU cc_start: 0.8129 (tp30) cc_final: 0.7423 (mm-30) REVERT: E 338 MET cc_start: 0.8163 (tpp) cc_final: 0.7690 (tpp) REVERT: E 341 LEU cc_start: 0.7845 (mt) cc_final: 0.7580 (mm) REVERT: E 344 ASN cc_start: 0.8114 (OUTLIER) cc_final: 0.7354 (t0) REVERT: E 443 GLU cc_start: 0.7526 (mm-30) cc_final: 0.6947 (mp0) REVERT: F 180 GLN cc_start: 0.8824 (pt0) cc_final: 0.8571 (pm20) REVERT: F 213 ILE cc_start: 0.8751 (pp) cc_final: 0.8245 (mp) REVERT: F 245 LYS cc_start: 0.7703 (mtmm) cc_final: 0.7367 (tmmm) REVERT: F 262 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7679 (pm20) REVERT: F 289 THR cc_start: 0.8599 (m) cc_final: 0.8295 (p) REVERT: F 324 GLU cc_start: 0.7591 (tp30) cc_final: 0.7358 (mm-30) REVERT: F 388 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7402 (tm-30) REVERT: F 421 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7716 (mm) REVERT: F 431 ARG cc_start: 0.7708 (ttm-80) cc_final: 0.7216 (ttm170) REVERT: F 480 PHE cc_start: 0.8034 (p90) cc_final: 0.7527 (p90) outliers start: 139 outliers final: 39 residues processed: 612 average time/residue: 1.1360 time to fit residues: 790.6290 Evaluate side-chains 498 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 449 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 275 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 487 TYR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 469 LYS Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain D residue 256 PHE Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 457 ILE Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 180 GLN Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 344 ASN Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 475 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 164 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 39 optimal weight: 30.0000 chunk 94 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 217 optimal weight: 6.9990 chunk 190 optimal weight: 0.9990 chunk 235 optimal weight: 0.0970 chunk 224 optimal weight: 9.9990 chunk 234 optimal weight: 7.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN B 276 ASN B 344 ASN C 276 ASN C 382 HIS C 384 ASN D 191 GLN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 ASN E 166 ASN E 314 GLN E 344 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.110742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.089579 restraints weight = 40972.323| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.27 r_work: 0.3103 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18676 Z= 0.165 Angle : 0.711 11.860 25370 Z= 0.351 Chirality : 0.048 0.241 3010 Planarity : 0.005 0.095 3364 Dihedral : 6.802 86.922 2847 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 5.91 % Allowed : 26.86 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.47 (0.17), residues: 2520 helix: 2.12 (0.16), residues: 1150 sheet: -0.28 (0.22), residues: 532 loop : 0.38 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 481 HIS 0.002 0.001 HIS E 435 PHE 0.016 0.002 PHE D 453 TYR 0.013 0.001 TYR C 486 ARG 0.011 0.001 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.03188 ( 1004) hydrogen bonds : angle 4.13210 ( 2937) covalent geometry : bond 0.00366 (18676) covalent geometry : angle 0.71142 (25370) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 468 time to evaluate : 2.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.9016 (ptpp) cc_final: 0.8428 (mppt) REVERT: A 218 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8750 (mp) REVERT: A 250 MET cc_start: 0.5969 (pmm) cc_final: 0.5211 (mmm) REVERT: A 270 ILE cc_start: 0.8676 (mt) cc_final: 0.8431 (mt) REVERT: A 290 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8128 (tm) REVERT: A 314 GLN cc_start: 0.8374 (tm-30) cc_final: 0.7833 (tm-30) REVERT: A 384 ASN cc_start: 0.8532 (m110) cc_final: 0.8182 (m-40) REVERT: A 434 THR cc_start: 0.7846 (p) cc_final: 0.7638 (p) REVERT: A 482 ASP cc_start: 0.8675 (t0) cc_final: 0.8092 (p0) REVERT: B 180 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7407 (pp30) REVERT: B 324 GLU cc_start: 0.6784 (mm-30) cc_final: 0.6083 (mm-30) REVERT: B 456 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6857 (pm20) REVERT: C 241 ARG cc_start: 0.7876 (mmm-85) cc_final: 0.7631 (mpp80) REVERT: C 301 THR cc_start: 0.8992 (m) cc_final: 0.8752 (p) REVERT: C 309 ASP cc_start: 0.8555 (p0) cc_final: 0.8287 (p0) REVERT: C 368 GLN cc_start: 0.8515 (mm110) cc_final: 0.8311 (mm-40) REVERT: D 308 GLU cc_start: 0.7607 (tt0) cc_final: 0.6370 (pt0) REVERT: D 324 GLU cc_start: 0.8600 (tt0) cc_final: 0.7932 (tp30) REVERT: D 351 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7934 (mp0) REVERT: E 148 TYR cc_start: 0.8466 (m-10) cc_final: 0.8204 (m-10) REVERT: E 173 ILE cc_start: 0.8565 (pp) cc_final: 0.8295 (pp) REVERT: E 186 PHE cc_start: 0.7737 (m-10) cc_final: 0.7424 (m-10) REVERT: E 191 GLN cc_start: 0.9223 (tt0) cc_final: 0.8741 (tt0) REVERT: E 199 ILE cc_start: 0.8523 (pp) cc_final: 0.8281 (pp) REVERT: E 324 GLU cc_start: 0.8272 (tp30) cc_final: 0.7587 (mm-30) REVERT: E 338 MET cc_start: 0.8322 (tpp) cc_final: 0.7879 (tpp) REVERT: E 341 LEU cc_start: 0.8031 (mt) cc_final: 0.7810 (mm) REVERT: E 344 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.7730 (t0) REVERT: E 443 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7275 (mp0) REVERT: F 213 ILE cc_start: 0.8913 (pp) cc_final: 0.8667 (mp) REVERT: F 244 LYS cc_start: 0.8530 (tppt) cc_final: 0.8191 (mmpt) REVERT: F 289 THR cc_start: 0.8773 (m) cc_final: 0.8443 (p) REVERT: F 294 MET cc_start: 0.8804 (tpp) cc_final: 0.8591 (tpp) REVERT: F 307 CYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8426 (m) REVERT: F 324 GLU cc_start: 0.7737 (tp30) cc_final: 0.7513 (mm-30) REVERT: F 388 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7639 (tm-30) REVERT: F 407 LYS cc_start: 0.7800 (tptp) cc_final: 0.7581 (tptp) REVERT: F 421 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7981 (mm) REVERT: F 470 HIS cc_start: 0.8149 (OUTLIER) cc_final: 0.7765 (t-90) outliers start: 105 outliers final: 42 residues processed: 521 average time/residue: 1.0899 time to fit residues: 647.1170 Evaluate side-chains 452 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 401 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 487 TYR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain D residue 256 PHE Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 344 ASN Chi-restraints excluded: chain D residue 457 ILE Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 344 ASN Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 307 CYS Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 470 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 57 optimal weight: 20.0000 chunk 79 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 chunk 219 optimal weight: 3.9990 chunk 42 optimal weight: 120.0000 chunk 142 optimal weight: 6.9990 chunk 187 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 32 optimal weight: 0.0020 chunk 143 optimal weight: 0.5980 overall best weight: 3.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN A 371 ASN A 374 HIS B 225 ASN ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN C 276 ASN C 292 ASN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN ** D 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN E 344 ASN F 225 ASN F 252 ASN F 314 GLN F 344 ASN ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 435 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.096051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.074421 restraints weight = 41831.379| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.14 r_work: 0.3038 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.6783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 18676 Z= 0.183 Angle : 0.726 11.002 25370 Z= 0.362 Chirality : 0.048 0.197 3010 Planarity : 0.005 0.072 3364 Dihedral : 6.475 88.055 2847 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 7.66 % Allowed : 25.73 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.23 (0.17), residues: 2520 helix: 1.96 (0.15), residues: 1150 sheet: -0.44 (0.22), residues: 528 loop : 0.20 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 481 HIS 0.003 0.001 HIS B 374 PHE 0.020 0.002 PHE F 480 TYR 0.011 0.001 TYR F 486 ARG 0.013 0.001 ARG F 347 Details of bonding type rmsd hydrogen bonds : bond 0.03189 ( 1004) hydrogen bonds : angle 4.09820 ( 2937) covalent geometry : bond 0.00424 (18676) covalent geometry : angle 0.72595 (25370) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 436 time to evaluate : 2.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7929 (tm) REVERT: A 227 ILE cc_start: 0.8912 (mm) cc_final: 0.8644 (mm) REVERT: A 250 MET cc_start: 0.6495 (pmm) cc_final: 0.6102 (tpp) REVERT: A 265 ARG cc_start: 0.7849 (mmp80) cc_final: 0.7548 (mtp180) REVERT: A 314 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8148 (tm-30) REVERT: A 324 GLU cc_start: 0.8398 (tt0) cc_final: 0.7257 (tp30) REVERT: A 340 ASP cc_start: 0.8915 (t0) cc_final: 0.8380 (m-30) REVERT: A 391 SER cc_start: 0.8887 (t) cc_final: 0.8668 (p) REVERT: A 434 THR cc_start: 0.8400 (p) cc_final: 0.8153 (p) REVERT: A 482 ASP cc_start: 0.9011 (t0) cc_final: 0.8453 (p0) REVERT: B 185 ARG cc_start: 0.8064 (pmt-80) cc_final: 0.7632 (ptp-110) REVERT: B 250 MET cc_start: 0.8025 (tpp) cc_final: 0.7778 (tpp) REVERT: B 324 GLU cc_start: 0.7502 (mm-30) cc_final: 0.6915 (mm-30) REVERT: B 342 VAL cc_start: 0.8341 (t) cc_final: 0.8135 (t) REVERT: B 357 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8516 (mt-10) REVERT: B 402 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.8284 (m-80) REVERT: B 456 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7219 (pm20) REVERT: B 498 ASP cc_start: 0.7990 (p0) cc_final: 0.7541 (m-30) REVERT: C 193 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8675 (mmt) REVERT: C 253 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8409 (mt) REVERT: C 273 CYS cc_start: 0.8505 (m) cc_final: 0.7751 (p) REVERT: C 337 THR cc_start: 0.8709 (m) cc_final: 0.8309 (p) REVERT: D 206 ARG cc_start: 0.8372 (tmm-80) cc_final: 0.8052 (tmm-80) REVERT: D 211 SER cc_start: 0.8939 (t) cc_final: 0.8723 (t) REVERT: D 344 ASN cc_start: 0.8859 (t0) cc_final: 0.8543 (t0) REVERT: D 351 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8156 (mp0) REVERT: D 411 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8168 (pt0) REVERT: D 469 LYS cc_start: 0.8864 (ptmm) cc_final: 0.8293 (ptmm) REVERT: E 180 GLN cc_start: 0.8272 (pm20) cc_final: 0.7938 (pm20) REVERT: E 186 PHE cc_start: 0.8242 (m-10) cc_final: 0.7936 (m-10) REVERT: E 191 GLN cc_start: 0.9278 (tt0) cc_final: 0.8806 (tt0) REVERT: E 215 ASP cc_start: 0.8733 (p0) cc_final: 0.8438 (t0) REVERT: E 252 ASN cc_start: 0.8521 (m110) cc_final: 0.8280 (m-40) REVERT: E 324 GLU cc_start: 0.8627 (tp30) cc_final: 0.7944 (mm-30) REVERT: E 338 MET cc_start: 0.8618 (tpp) cc_final: 0.8294 (tpp) REVERT: E 443 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7921 (mm-30) REVERT: E 492 GLU cc_start: 0.7853 (tp30) cc_final: 0.6961 (tp30) REVERT: E 495 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8121 (pt0) REVERT: E 498 ASP cc_start: 0.8155 (t0) cc_final: 0.7704 (p0) REVERT: F 180 GLN cc_start: 0.9203 (pt0) cc_final: 0.8641 (pm20) REVERT: F 206 ARG cc_start: 0.8214 (ptm-80) cc_final: 0.7768 (ptm-80) REVERT: F 242 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.9085 (mtpt) REVERT: F 244 LYS cc_start: 0.8562 (tppt) cc_final: 0.8245 (tppt) REVERT: F 245 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7582 (mppt) REVERT: F 246 ASP cc_start: 0.7896 (m-30) cc_final: 0.7316 (m-30) REVERT: F 262 GLU cc_start: 0.7765 (pm20) cc_final: 0.7260 (pm20) REVERT: F 289 THR cc_start: 0.9130 (m) cc_final: 0.8800 (p) REVERT: F 312 GLU cc_start: 0.7885 (pm20) cc_final: 0.7495 (pm20) REVERT: F 324 GLU cc_start: 0.8107 (tp30) cc_final: 0.7650 (mm-30) REVERT: F 340 ASP cc_start: 0.8693 (m-30) cc_final: 0.8403 (m-30) REVERT: F 388 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8340 (tm-30) REVERT: F 410 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8243 (mmtm) REVERT: F 421 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8330 (mp) outliers start: 136 outliers final: 46 residues processed: 522 average time/residue: 1.1843 time to fit residues: 700.2287 Evaluate side-chains 412 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 355 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 402 TYR Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 402 TYR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain D residue 256 PHE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 381 LEU Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 410 LYS Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 454 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 34 optimal weight: 20.0000 chunk 112 optimal weight: 8.9990 chunk 135 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 46 optimal weight: 40.0000 chunk 224 optimal weight: 10.0000 chunk 246 optimal weight: 2.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN B 180 GLN ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 ASN C 191 GLN C 292 ASN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 GLN D 276 ASN D 374 HIS ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN E 344 ASN E 450 GLN F 225 ASN F 314 GLN ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 435 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.100798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.078019 restraints weight = 40934.452| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.18 r_work: 0.2920 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.8816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.189 18676 Z= 0.226 Angle : 0.780 11.643 25370 Z= 0.388 Chirality : 0.052 0.855 3010 Planarity : 0.006 0.072 3364 Dihedral : 6.517 87.610 2847 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 7.04 % Allowed : 27.48 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.05 (0.17), residues: 2520 helix: 1.79 (0.16), residues: 1152 sheet: -0.45 (0.22), residues: 534 loop : 0.09 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 481 HIS 0.006 0.001 HIS A 374 PHE 0.016 0.002 PHE A 297 TYR 0.020 0.002 TYR C 487 ARG 0.029 0.001 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 1004) hydrogen bonds : angle 4.24975 ( 2937) covalent geometry : bond 0.00546 (18676) covalent geometry : angle 0.78017 (25370) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 378 time to evaluate : 2.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.9101 (pptt) cc_final: 0.8693 (pptt) REVERT: A 180 GLN cc_start: 0.9061 (pt0) cc_final: 0.8652 (pm20) REVERT: A 192 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8373 (tm) REVERT: A 247 LYS cc_start: 0.8588 (pmmt) cc_final: 0.7655 (mptp) REVERT: A 324 GLU cc_start: 0.8823 (tt0) cc_final: 0.8181 (tt0) REVERT: A 340 ASP cc_start: 0.9003 (t0) cc_final: 0.8782 (m-30) REVERT: A 348 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7382 (mmm) REVERT: A 365 ASP cc_start: 0.8944 (m-30) cc_final: 0.8715 (m-30) REVERT: A 398 THR cc_start: 0.9254 (m) cc_final: 0.8962 (p) REVERT: A 407 LYS cc_start: 0.9182 (tppp) cc_final: 0.8541 (tppt) REVERT: A 463 HIS cc_start: 0.8413 (m90) cc_final: 0.8079 (m90) REVERT: A 482 ASP cc_start: 0.9229 (t0) cc_final: 0.8862 (p0) REVERT: B 162 ASP cc_start: 0.7631 (m-30) cc_final: 0.7311 (m-30) REVERT: B 245 LYS cc_start: 0.8725 (mppt) cc_final: 0.8483 (mmmm) REVERT: B 339 ARG cc_start: 0.8806 (ttp-170) cc_final: 0.8014 (ttm-80) REVERT: B 343 LYS cc_start: 0.9230 (mtmp) cc_final: 0.8700 (mtmm) REVERT: B 402 TYR cc_start: 0.8718 (OUTLIER) cc_final: 0.8466 (m-80) REVERT: B 456 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7679 (pm20) REVERT: C 174 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7450 (tp30) REVERT: C 178 LYS cc_start: 0.8481 (tmmt) cc_final: 0.8053 (tmmt) REVERT: C 273 CYS cc_start: 0.8836 (m) cc_final: 0.7930 (p) REVERT: C 312 GLU cc_start: 0.8550 (tp30) cc_final: 0.8269 (tp30) REVERT: C 324 GLU cc_start: 0.8918 (tt0) cc_final: 0.7934 (mm-30) REVERT: C 337 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.8928 (p) REVERT: C 407 LYS cc_start: 0.8895 (tppp) cc_final: 0.8219 (tppt) REVERT: C 411 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8633 (mp0) REVERT: D 164 MET cc_start: 0.9212 (OUTLIER) cc_final: 0.8838 (ptp) REVERT: D 174 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8048 (mm-30) REVERT: D 206 ARG cc_start: 0.8307 (tmm-80) cc_final: 0.8015 (tmm-80) REVERT: D 211 SER cc_start: 0.9025 (t) cc_final: 0.8617 (p) REVERT: D 351 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8481 (mp0) REVERT: D 394 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8772 (tt0) REVERT: D 407 LYS cc_start: 0.8839 (mmmm) cc_final: 0.8015 (mmmm) REVERT: D 469 LYS cc_start: 0.9192 (ptmm) cc_final: 0.8716 (ptmm) REVERT: E 180 GLN cc_start: 0.8642 (pm20) cc_final: 0.8405 (pm20) REVERT: E 186 PHE cc_start: 0.8822 (m-80) cc_final: 0.8422 (m-80) REVERT: E 191 GLN cc_start: 0.9293 (tt0) cc_final: 0.8685 (tt0) REVERT: E 215 ASP cc_start: 0.8820 (p0) cc_final: 0.8534 (t0) REVERT: E 251 LYS cc_start: 0.9051 (mmmm) cc_final: 0.8547 (tppp) REVERT: E 324 GLU cc_start: 0.8867 (tp30) cc_final: 0.8347 (mm-30) REVERT: E 344 ASN cc_start: 0.9044 (OUTLIER) cc_final: 0.8464 (t0) REVERT: E 406 SER cc_start: 0.8690 (p) cc_final: 0.8461 (p) REVERT: E 412 MET cc_start: 0.9161 (mtm) cc_final: 0.8773 (mtm) REVERT: E 445 ASP cc_start: 0.9018 (t0) cc_final: 0.8566 (t0) REVERT: E 465 LYS cc_start: 0.8924 (tppt) cc_final: 0.8708 (mmpt) REVERT: E 495 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8416 (pt0) REVERT: E 498 ASP cc_start: 0.8434 (t0) cc_final: 0.8012 (p0) REVERT: F 197 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8769 (mt0) REVERT: F 244 LYS cc_start: 0.8769 (tppt) cc_final: 0.8563 (tppt) REVERT: F 245 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8277 (mppt) REVERT: F 294 MET cc_start: 0.9386 (tpp) cc_final: 0.9137 (mmm) REVERT: F 340 ASP cc_start: 0.8944 (m-30) cc_final: 0.8692 (m-30) REVERT: F 388 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8608 (tt0) outliers start: 125 outliers final: 36 residues processed: 464 average time/residue: 1.4368 time to fit residues: 740.7366 Evaluate side-chains 359 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 311 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 402 TYR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 344 ASN Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 197 GLN Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 388 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 87 optimal weight: 8.9990 chunk 134 optimal weight: 0.5980 chunk 218 optimal weight: 6.9990 chunk 2 optimal weight: 40.0000 chunk 152 optimal weight: 9.9990 chunk 251 optimal weight: 7.9990 chunk 199 optimal weight: 0.8980 chunk 141 optimal weight: 7.9990 chunk 192 optimal weight: 7.9990 chunk 223 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 overall best weight: 4.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 ASN B 317 GLN B 344 ASN ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN E 225 ASN E 314 GLN E 344 ASN F 314 GLN F 368 GLN ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 435 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.101905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.080386 restraints weight = 41915.252| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.20 r_work: 0.2923 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.9307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18676 Z= 0.181 Angle : 0.700 10.146 25370 Z= 0.346 Chirality : 0.048 0.168 3010 Planarity : 0.005 0.062 3364 Dihedral : 6.340 84.601 2847 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 5.35 % Allowed : 29.95 % Favored : 64.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.19 (0.17), residues: 2520 helix: 1.92 (0.16), residues: 1156 sheet: -0.29 (0.22), residues: 512 loop : 0.04 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 481 HIS 0.003 0.001 HIS D 374 PHE 0.034 0.002 PHE D 243 TYR 0.014 0.001 TYR C 487 ARG 0.013 0.001 ARG C 427 Details of bonding type rmsd hydrogen bonds : bond 0.02992 ( 1004) hydrogen bonds : angle 4.04665 ( 2937) covalent geometry : bond 0.00433 (18676) covalent geometry : angle 0.70015 (25370) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 333 time to evaluate : 2.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8370 (tm) REVERT: A 202 GLN cc_start: 0.8817 (tt0) cc_final: 0.8578 (tm-30) REVERT: A 324 GLU cc_start: 0.8816 (tt0) cc_final: 0.8150 (tt0) REVERT: A 365 ASP cc_start: 0.8978 (m-30) cc_final: 0.8712 (m-30) REVERT: A 398 THR cc_start: 0.9264 (m) cc_final: 0.8885 (p) REVERT: A 438 GLU cc_start: 0.7520 (mp0) cc_final: 0.7136 (mp0) REVERT: A 463 HIS cc_start: 0.8584 (m90) cc_final: 0.8270 (m90) REVERT: A 482 ASP cc_start: 0.9247 (t0) cc_final: 0.8963 (p0) REVERT: B 162 ASP cc_start: 0.7894 (m-30) cc_final: 0.7386 (m-30) REVERT: B 174 GLU cc_start: 0.8372 (tt0) cc_final: 0.7919 (tt0) REVERT: B 180 GLN cc_start: 0.8835 (pp30) cc_final: 0.8457 (pp30) REVERT: B 339 ARG cc_start: 0.8922 (ttp-170) cc_final: 0.8166 (ttm-80) REVERT: B 343 LYS cc_start: 0.9160 (mtmp) cc_final: 0.8757 (mtmm) REVERT: B 402 TYR cc_start: 0.8705 (OUTLIER) cc_final: 0.8351 (m-80) REVERT: B 456 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7880 (pm20) REVERT: B 479 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7761 (ttp-170) REVERT: C 174 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7641 (tp30) REVERT: C 178 LYS cc_start: 0.8598 (tmmt) cc_final: 0.8128 (tmmt) REVERT: C 273 CYS cc_start: 0.8902 (m) cc_final: 0.7971 (p) REVERT: C 279 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7770 (mt) REVERT: C 312 GLU cc_start: 0.8523 (tp30) cc_final: 0.8122 (tp30) REVERT: C 339 ARG cc_start: 0.9044 (ttp80) cc_final: 0.8690 (ttm-80) REVERT: C 407 LYS cc_start: 0.8954 (tppp) cc_final: 0.8198 (tppt) REVERT: C 411 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8660 (mp0) REVERT: D 190 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8902 (tm) REVERT: D 211 SER cc_start: 0.9043 (t) cc_final: 0.8678 (p) REVERT: D 277 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8576 (tp) REVERT: D 351 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8457 (mp0) REVERT: D 411 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8308 (pt0) REVERT: D 469 LYS cc_start: 0.9190 (ptmm) cc_final: 0.8761 (ptmm) REVERT: E 180 GLN cc_start: 0.8668 (pm20) cc_final: 0.8361 (pm20) REVERT: E 191 GLN cc_start: 0.9291 (tt0) cc_final: 0.8815 (tt0) REVERT: E 238 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.9032 (mm) REVERT: E 324 GLU cc_start: 0.8905 (tp30) cc_final: 0.8399 (mm-30) REVERT: E 412 MET cc_start: 0.9185 (mtm) cc_final: 0.8787 (mtm) REVERT: E 445 ASP cc_start: 0.9031 (t0) cc_final: 0.8418 (t0) REVERT: E 498 ASP cc_start: 0.8547 (t0) cc_final: 0.8032 (t0) REVERT: F 206 ARG cc_start: 0.8359 (ttp-110) cc_final: 0.7919 (ptm-80) REVERT: F 246 ASP cc_start: 0.8445 (m-30) cc_final: 0.8184 (m-30) REVERT: F 312 GLU cc_start: 0.7966 (pm20) cc_final: 0.7689 (pm20) REVERT: F 341 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8603 (mp) REVERT: F 343 LYS cc_start: 0.9371 (ttmm) cc_final: 0.9152 (tppp) REVERT: F 384 ASN cc_start: 0.9118 (m-40) cc_final: 0.8903 (m110) REVERT: F 388 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8590 (tt0) REVERT: F 469 LYS cc_start: 0.9434 (OUTLIER) cc_final: 0.9091 (tmmm) outliers start: 95 outliers final: 35 residues processed: 400 average time/residue: 1.4241 time to fit residues: 632.1472 Evaluate side-chains 335 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 288 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 402 TYR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 469 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 19 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 81 optimal weight: 0.0980 chunk 37 optimal weight: 20.0000 chunk 84 optimal weight: 120.0000 chunk 95 optimal weight: 6.9990 chunk 58 optimal weight: 30.0000 chunk 41 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 overall best weight: 4.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN E 314 GLN F 314 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.101224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.079590 restraints weight = 41466.653| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.20 r_work: 0.2903 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.9749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18676 Z= 0.182 Angle : 0.721 17.375 25370 Z= 0.355 Chirality : 0.048 0.164 3010 Planarity : 0.006 0.074 3364 Dihedral : 6.272 82.658 2847 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 5.01 % Allowed : 30.86 % Favored : 64.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.22 (0.17), residues: 2520 helix: 2.04 (0.16), residues: 1144 sheet: -0.35 (0.21), residues: 528 loop : 0.01 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 481 HIS 0.004 0.001 HIS B 382 PHE 0.043 0.002 PHE D 243 TYR 0.026 0.002 TYR B 486 ARG 0.021 0.001 ARG B 206 Details of bonding type rmsd hydrogen bonds : bond 0.03020 ( 1004) hydrogen bonds : angle 4.00240 ( 2937) covalent geometry : bond 0.00436 (18676) covalent geometry : angle 0.72096 (25370) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 308 time to evaluate : 3.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8436 (tm) REVERT: A 324 GLU cc_start: 0.8823 (tt0) cc_final: 0.8164 (tt0) REVERT: A 343 LYS cc_start: 0.9282 (ttpp) cc_final: 0.8986 (ttmt) REVERT: A 365 ASP cc_start: 0.9013 (m-30) cc_final: 0.8809 (m-30) REVERT: A 398 THR cc_start: 0.9340 (m) cc_final: 0.9019 (p) REVERT: A 407 LYS cc_start: 0.9173 (tppp) cc_final: 0.8697 (tppt) REVERT: A 463 HIS cc_start: 0.8724 (m90) cc_final: 0.8381 (m90) REVERT: A 482 ASP cc_start: 0.9309 (t0) cc_final: 0.9095 (p0) REVERT: B 162 ASP cc_start: 0.7890 (m-30) cc_final: 0.7418 (m-30) REVERT: B 180 GLN cc_start: 0.8832 (pp30) cc_final: 0.8452 (pp30) REVERT: B 244 LYS cc_start: 0.8741 (tppt) cc_final: 0.8494 (tttp) REVERT: B 245 LYS cc_start: 0.9063 (mmmm) cc_final: 0.8765 (mmmt) REVERT: B 343 LYS cc_start: 0.9226 (mtmp) cc_final: 0.9022 (mtmm) REVERT: B 402 TYR cc_start: 0.8764 (OUTLIER) cc_final: 0.8253 (m-80) REVERT: B 456 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8023 (pm20) REVERT: B 479 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7757 (ttp-170) REVERT: B 498 ASP cc_start: 0.8678 (p0) cc_final: 0.8330 (m-30) REVERT: C 164 MET cc_start: 0.9275 (mtm) cc_final: 0.8935 (mpp) REVERT: C 174 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7620 (tp30) REVERT: C 178 LYS cc_start: 0.8703 (tmmt) cc_final: 0.8242 (ttpp) REVERT: C 273 CYS cc_start: 0.8904 (m) cc_final: 0.8036 (p) REVERT: C 279 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7927 (mt) REVERT: C 309 ASP cc_start: 0.8878 (p0) cc_final: 0.8612 (p0) REVERT: C 312 GLU cc_start: 0.8566 (tp30) cc_final: 0.8137 (tp30) REVERT: C 324 GLU cc_start: 0.8764 (tt0) cc_final: 0.7879 (mm-30) REVERT: C 339 ARG cc_start: 0.8968 (ttp80) cc_final: 0.8370 (tpt-90) REVERT: C 407 LYS cc_start: 0.8997 (tppp) cc_final: 0.8294 (tppt) REVERT: C 411 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8690 (mp0) REVERT: C 427 ARG cc_start: 0.8768 (tmm-80) cc_final: 0.8466 (ttp80) REVERT: C 465 LYS cc_start: 0.8903 (mtmm) cc_final: 0.8684 (mtmm) REVERT: C 469 LYS cc_start: 0.9284 (mtmm) cc_final: 0.9008 (pttm) REVERT: D 174 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8169 (mm-30) REVERT: D 190 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8972 (tm) REVERT: D 211 SER cc_start: 0.9084 (t) cc_final: 0.8754 (p) REVERT: D 351 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8489 (mp0) REVERT: D 411 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8259 (pt0) REVERT: D 469 LYS cc_start: 0.9179 (ptmm) cc_final: 0.8771 (ptmm) REVERT: E 180 GLN cc_start: 0.8715 (pm20) cc_final: 0.8420 (pm20) REVERT: E 186 PHE cc_start: 0.8707 (m-10) cc_final: 0.8318 (m-80) REVERT: E 191 GLN cc_start: 0.9274 (tt0) cc_final: 0.8631 (tt0) REVERT: E 238 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9052 (mm) REVERT: E 324 GLU cc_start: 0.8880 (tp30) cc_final: 0.8418 (mm-30) REVERT: E 445 ASP cc_start: 0.9050 (t0) cc_final: 0.8532 (t0) REVERT: E 498 ASP cc_start: 0.8646 (t0) cc_final: 0.8181 (t0) REVERT: F 164 MET cc_start: 0.9430 (mtm) cc_final: 0.9043 (mtm) REVERT: F 197 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8905 (mt0) REVERT: F 206 ARG cc_start: 0.8432 (ttp-110) cc_final: 0.7933 (ptm-80) REVERT: F 246 ASP cc_start: 0.8449 (m-30) cc_final: 0.8042 (m-30) REVERT: F 312 GLU cc_start: 0.8047 (pm20) cc_final: 0.7692 (pm20) REVERT: F 365 ASP cc_start: 0.9051 (m-30) cc_final: 0.8704 (m-30) REVERT: F 384 ASN cc_start: 0.9090 (m-40) cc_final: 0.8813 (m-40) REVERT: F 407 LYS cc_start: 0.8676 (tptp) cc_final: 0.8452 (tppt) REVERT: F 469 LYS cc_start: 0.9422 (OUTLIER) cc_final: 0.9050 (tmmm) outliers start: 89 outliers final: 43 residues processed: 376 average time/residue: 1.6163 time to fit residues: 676.3424 Evaluate side-chains 338 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 284 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 402 TYR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 197 GLN Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 425 ARG Chi-restraints excluded: chain F residue 469 LYS Chi-restraints excluded: chain F residue 472 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 26 optimal weight: 9.9990 chunk 175 optimal weight: 5.9990 chunk 191 optimal weight: 7.9990 chunk 17 optimal weight: 0.5980 chunk 37 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 211 optimal weight: 50.0000 chunk 222 optimal weight: 0.4980 chunk 157 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 chunk 208 optimal weight: 9.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 314 GLN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 GLN E 202 GLN E 292 ASN F 314 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.100948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.078993 restraints weight = 41373.698| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.20 r_work: 0.2897 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.9977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18676 Z= 0.167 Angle : 0.717 12.950 25370 Z= 0.353 Chirality : 0.047 0.176 3010 Planarity : 0.005 0.054 3364 Dihedral : 6.238 82.327 2847 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.79 % Allowed : 30.63 % Favored : 64.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.18 (0.17), residues: 2520 helix: 2.00 (0.16), residues: 1154 sheet: -0.40 (0.21), residues: 532 loop : -0.00 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 481 HIS 0.002 0.000 HIS C 374 PHE 0.022 0.001 PHE F 256 TYR 0.017 0.001 TYR C 148 ARG 0.012 0.001 ARG C 491 Details of bonding type rmsd hydrogen bonds : bond 0.02960 ( 1004) hydrogen bonds : angle 3.96366 ( 2937) covalent geometry : bond 0.00402 (18676) covalent geometry : angle 0.71730 (25370) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 297 time to evaluate : 2.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8409 (tm) REVERT: A 316 GLN cc_start: 0.8783 (tp-100) cc_final: 0.8503 (pt0) REVERT: A 324 GLU cc_start: 0.8825 (tt0) cc_final: 0.8204 (tt0) REVERT: A 343 LYS cc_start: 0.9276 (ttpp) cc_final: 0.9026 (mtmm) REVERT: A 365 ASP cc_start: 0.9029 (m-30) cc_final: 0.8802 (m-30) REVERT: A 398 THR cc_start: 0.9336 (m) cc_final: 0.8983 (p) REVERT: A 463 HIS cc_start: 0.8746 (m90) cc_final: 0.8373 (m90) REVERT: B 162 ASP cc_start: 0.7915 (m-30) cc_final: 0.7557 (m-30) REVERT: B 206 ARG cc_start: 0.8367 (mmm160) cc_final: 0.7998 (tpp-160) REVERT: B 244 LYS cc_start: 0.8756 (tppt) cc_final: 0.8443 (tttp) REVERT: B 245 LYS cc_start: 0.9116 (mmmm) cc_final: 0.8862 (mmmm) REVERT: B 402 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.8212 (m-80) REVERT: B 479 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7806 (ttp-170) REVERT: B 498 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8289 (m-30) REVERT: C 164 MET cc_start: 0.9267 (mtm) cc_final: 0.8995 (mpp) REVERT: C 174 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7635 (tp30) REVERT: C 178 LYS cc_start: 0.8702 (tmmt) cc_final: 0.8255 (ttpp) REVERT: C 202 GLN cc_start: 0.9124 (tt0) cc_final: 0.8781 (mt0) REVERT: C 206 ARG cc_start: 0.8358 (ttp-110) cc_final: 0.8139 (ttp-110) REVERT: C 273 CYS cc_start: 0.8854 (m) cc_final: 0.7943 (p) REVERT: C 312 GLU cc_start: 0.8529 (tp30) cc_final: 0.8080 (tp30) REVERT: C 324 GLU cc_start: 0.8733 (tt0) cc_final: 0.7839 (mm-30) REVERT: C 339 ARG cc_start: 0.8985 (ttp80) cc_final: 0.8462 (tpt-90) REVERT: C 407 LYS cc_start: 0.9000 (tppp) cc_final: 0.8284 (tppt) REVERT: C 411 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8672 (mp0) REVERT: C 465 LYS cc_start: 0.8895 (mtmm) cc_final: 0.8692 (mtmm) REVERT: C 469 LYS cc_start: 0.9298 (mtmm) cc_final: 0.9088 (pttm) REVERT: C 492 GLU cc_start: 0.9296 (OUTLIER) cc_final: 0.8978 (tp30) REVERT: D 164 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8785 (ptp) REVERT: D 174 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8104 (mm-30) REVERT: D 178 LYS cc_start: 0.8606 (tmmt) cc_final: 0.8221 (pptt) REVERT: D 190 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.9003 (tm) REVERT: D 193 MET cc_start: 0.8957 (tpt) cc_final: 0.8726 (tpt) REVERT: D 202 GLN cc_start: 0.8787 (tt0) cc_final: 0.7998 (tm-30) REVERT: D 351 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8707 (mm-30) REVERT: D 368 GLN cc_start: 0.8982 (mm-40) cc_final: 0.8727 (mm-40) REVERT: D 399 MET cc_start: 0.9018 (pmm) cc_final: 0.8809 (pmm) REVERT: D 411 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8283 (pt0) REVERT: D 469 LYS cc_start: 0.9183 (ptmm) cc_final: 0.8782 (ptmm) REVERT: E 180 GLN cc_start: 0.8733 (pm20) cc_final: 0.8417 (pm20) REVERT: E 186 PHE cc_start: 0.8798 (m-10) cc_final: 0.8572 (m-10) REVERT: E 190 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9171 (tm) REVERT: E 191 GLN cc_start: 0.9259 (tt0) cc_final: 0.8767 (tt0) REVERT: E 238 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9024 (mm) REVERT: E 324 GLU cc_start: 0.8837 (tp30) cc_final: 0.8438 (mm-30) REVERT: E 412 MET cc_start: 0.9302 (mtp) cc_final: 0.8930 (mtp) REVERT: E 445 ASP cc_start: 0.9037 (t0) cc_final: 0.8466 (t0) REVERT: E 498 ASP cc_start: 0.8661 (t0) cc_final: 0.8191 (t0) REVERT: F 246 ASP cc_start: 0.8495 (m-30) cc_final: 0.8109 (m-30) REVERT: F 384 ASN cc_start: 0.9181 (m-40) cc_final: 0.8891 (m-40) REVERT: F 407 LYS cc_start: 0.8758 (tptp) cc_final: 0.8297 (tppt) REVERT: F 411 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8264 (mp0) REVERT: F 427 ARG cc_start: 0.8894 (mtm110) cc_final: 0.8309 (ptp90) REVERT: F 469 LYS cc_start: 0.9395 (OUTLIER) cc_final: 0.9012 (tmmm) outliers start: 85 outliers final: 37 residues processed: 361 average time/residue: 1.5523 time to fit residues: 622.1471 Evaluate side-chains 330 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 280 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 402 TYR Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 247 LYS Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 411 GLU Chi-restraints excluded: chain F residue 425 ARG Chi-restraints excluded: chain F residue 469 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 8.9990 chunk 204 optimal weight: 2.9990 chunk 221 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 208 optimal weight: 4.9990 chunk 2 optimal weight: 40.0000 chunk 43 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN C 314 GLN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN E 292 ASN F 314 GLN ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.100585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.078768 restraints weight = 41585.346| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.19 r_work: 0.2880 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 1.0241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18676 Z= 0.166 Angle : 0.722 12.710 25370 Z= 0.355 Chirality : 0.047 0.182 3010 Planarity : 0.005 0.073 3364 Dihedral : 6.198 82.411 2845 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.83 % Allowed : 31.53 % Favored : 64.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.18 (0.17), residues: 2520 helix: 1.99 (0.16), residues: 1152 sheet: -0.35 (0.21), residues: 532 loop : -0.03 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 481 HIS 0.003 0.001 HIS C 374 PHE 0.038 0.002 PHE D 243 TYR 0.028 0.002 TYR B 486 ARG 0.017 0.001 ARG B 491 Details of bonding type rmsd hydrogen bonds : bond 0.03008 ( 1004) hydrogen bonds : angle 3.95804 ( 2937) covalent geometry : bond 0.00401 (18676) covalent geometry : angle 0.72212 (25370) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 310 time to evaluate : 2.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8451 (tm) REVERT: A 241 ARG cc_start: 0.8746 (mtp85) cc_final: 0.8488 (mtp85) REVERT: A 280 SER cc_start: 0.8916 (m) cc_final: 0.8212 (p) REVERT: A 324 GLU cc_start: 0.8801 (tt0) cc_final: 0.8178 (tt0) REVERT: A 343 LYS cc_start: 0.9267 (ttpp) cc_final: 0.9040 (mtmm) REVERT: A 365 ASP cc_start: 0.9048 (m-30) cc_final: 0.8820 (m-30) REVERT: A 398 THR cc_start: 0.9396 (m) cc_final: 0.9072 (p) REVERT: A 463 HIS cc_start: 0.8753 (m90) cc_final: 0.8367 (m90) REVERT: B 162 ASP cc_start: 0.7959 (m-30) cc_final: 0.7689 (m-30) REVERT: B 197 GLN cc_start: 0.8507 (pt0) cc_final: 0.8191 (pt0) REVERT: B 206 ARG cc_start: 0.8356 (mmm160) cc_final: 0.8036 (tpp-160) REVERT: B 245 LYS cc_start: 0.9165 (mmmm) cc_final: 0.8939 (mmmm) REVERT: B 343 LYS cc_start: 0.9212 (mtmm) cc_final: 0.8858 (mttp) REVERT: B 479 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7732 (ttp-170) REVERT: B 498 ASP cc_start: 0.8692 (p0) cc_final: 0.8397 (m-30) REVERT: C 164 MET cc_start: 0.9296 (mtm) cc_final: 0.8827 (mpp) REVERT: C 174 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7675 (tp30) REVERT: C 178 LYS cc_start: 0.8708 (tmmt) cc_final: 0.8298 (ptpp) REVERT: C 206 ARG cc_start: 0.8400 (ttp-110) cc_final: 0.8185 (ttp-110) REVERT: C 256 PHE cc_start: 0.9111 (m-10) cc_final: 0.8883 (m-10) REVERT: C 273 CYS cc_start: 0.8850 (m) cc_final: 0.7960 (p) REVERT: C 312 GLU cc_start: 0.8558 (tp30) cc_final: 0.8103 (tp30) REVERT: C 324 GLU cc_start: 0.8674 (tt0) cc_final: 0.7777 (mm-30) REVERT: C 339 ARG cc_start: 0.8972 (ttp80) cc_final: 0.8434 (tpt-90) REVERT: C 407 LYS cc_start: 0.9071 (tppp) cc_final: 0.8302 (tppt) REVERT: C 411 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8683 (mp0) REVERT: C 491 ARG cc_start: 0.8792 (ttp80) cc_final: 0.8565 (ttp80) REVERT: C 492 GLU cc_start: 0.9301 (OUTLIER) cc_final: 0.8951 (tp30) REVERT: D 164 MET cc_start: 0.9277 (OUTLIER) cc_final: 0.8861 (ptp) REVERT: D 174 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8059 (mm-30) REVERT: D 178 LYS cc_start: 0.8654 (tmmt) cc_final: 0.8327 (pptt) REVERT: D 202 GLN cc_start: 0.8833 (tt0) cc_final: 0.8015 (tm-30) REVERT: D 351 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8780 (mm-30) REVERT: D 368 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8722 (mm-40) REVERT: D 411 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8253 (pt0) REVERT: D 469 LYS cc_start: 0.9180 (ptmm) cc_final: 0.8927 (ptmm) REVERT: D 479 ARG cc_start: 0.8066 (mtm180) cc_final: 0.7696 (mtp-110) REVERT: E 180 GLN cc_start: 0.8761 (pm20) cc_final: 0.8483 (pm20) REVERT: E 186 PHE cc_start: 0.8676 (m-10) cc_final: 0.8316 (m-80) REVERT: E 191 GLN cc_start: 0.9277 (tt0) cc_final: 0.8650 (tt0) REVERT: E 324 GLU cc_start: 0.8892 (tp30) cc_final: 0.8504 (mm-30) REVERT: E 338 MET cc_start: 0.9080 (tpp) cc_final: 0.8733 (ttp) REVERT: E 359 ARG cc_start: 0.8869 (ttm-80) cc_final: 0.8524 (ttp80) REVERT: E 412 MET cc_start: 0.9305 (mtp) cc_final: 0.8977 (mtp) REVERT: E 445 ASP cc_start: 0.9077 (t0) cc_final: 0.8501 (t0) REVERT: E 498 ASP cc_start: 0.8720 (t0) cc_final: 0.8252 (t0) REVERT: F 246 ASP cc_start: 0.8606 (m-30) cc_final: 0.8400 (m-30) REVERT: F 295 THR cc_start: 0.9316 (t) cc_final: 0.9097 (p) REVERT: F 336 VAL cc_start: 0.9380 (t) cc_final: 0.9159 (p) REVERT: F 384 ASN cc_start: 0.9212 (m-40) cc_final: 0.8959 (m-40) REVERT: F 407 LYS cc_start: 0.8702 (tptp) cc_final: 0.8298 (tppt) REVERT: F 411 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8311 (mp0) REVERT: F 427 ARG cc_start: 0.8926 (mtm110) cc_final: 0.8385 (ptp90) REVERT: F 469 LYS cc_start: 0.9411 (OUTLIER) cc_final: 0.9035 (tmmm) outliers start: 68 outliers final: 34 residues processed: 363 average time/residue: 1.6774 time to fit residues: 672.1523 Evaluate side-chains 338 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 296 time to evaluate : 2.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 463 HIS Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 292 ASN Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 411 GLU Chi-restraints excluded: chain F residue 425 ARG Chi-restraints excluded: chain F residue 469 LYS Chi-restraints excluded: chain F residue 472 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 214 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 205 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 236 optimal weight: 10.0000 chunk 171 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 ASN ** C 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN E 292 ASN F 252 ASN ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.099628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.077581 restraints weight = 41607.479| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.20 r_work: 0.2867 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 1.0450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 18676 Z= 0.195 Angle : 0.765 20.211 25370 Z= 0.373 Chirality : 0.048 0.219 3010 Planarity : 0.005 0.066 3364 Dihedral : 6.249 82.241 2845 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.15 % Allowed : 32.04 % Favored : 64.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.13 (0.17), residues: 2520 helix: 1.95 (0.16), residues: 1154 sheet: -0.32 (0.21), residues: 522 loop : -0.10 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 481 HIS 0.003 0.001 HIS C 374 PHE 0.042 0.002 PHE A 243 TYR 0.034 0.002 TYR E 486 ARG 0.018 0.001 ARG C 427 Details of bonding type rmsd hydrogen bonds : bond 0.03041 ( 1004) hydrogen bonds : angle 4.00151 ( 2937) covalent geometry : bond 0.00469 (18676) covalent geometry : angle 0.76525 (25370) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 296 time to evaluate : 2.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8303 (tm) REVERT: A 280 SER cc_start: 0.8889 (m) cc_final: 0.8191 (p) REVERT: A 324 GLU cc_start: 0.8785 (tt0) cc_final: 0.8208 (tt0) REVERT: A 365 ASP cc_start: 0.9081 (m-30) cc_final: 0.8858 (m-30) REVERT: A 398 THR cc_start: 0.9400 (m) cc_final: 0.9074 (p) REVERT: A 463 HIS cc_start: 0.8811 (m90) cc_final: 0.8447 (m90) REVERT: B 158 ASP cc_start: 0.8852 (p0) cc_final: 0.8428 (t0) REVERT: B 162 ASP cc_start: 0.7972 (m-30) cc_final: 0.7731 (m-30) REVERT: B 197 GLN cc_start: 0.8558 (pt0) cc_final: 0.8298 (pt0) REVERT: B 307 CYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8696 (m) REVERT: B 343 LYS cc_start: 0.9168 (mtmm) cc_final: 0.8921 (mmtp) REVERT: B 411 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8454 (mt-10) REVERT: B 479 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7753 (ttp-170) REVERT: B 487 TYR cc_start: 0.8857 (m-80) cc_final: 0.8655 (m-80) REVERT: B 491 ARG cc_start: 0.8588 (tmm-80) cc_final: 0.8349 (ttp80) REVERT: C 164 MET cc_start: 0.9315 (mtm) cc_final: 0.8821 (mpp) REVERT: C 174 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7459 (tp30) REVERT: C 178 LYS cc_start: 0.8701 (tmmt) cc_final: 0.8398 (ptpp) REVERT: C 206 ARG cc_start: 0.8481 (ttp-110) cc_final: 0.8245 (ttp-110) REVERT: C 256 PHE cc_start: 0.9083 (m-10) cc_final: 0.8876 (m-10) REVERT: C 273 CYS cc_start: 0.8864 (m) cc_final: 0.7968 (p) REVERT: C 324 GLU cc_start: 0.8656 (tt0) cc_final: 0.7733 (mm-30) REVERT: C 339 ARG cc_start: 0.8994 (ttp80) cc_final: 0.8468 (tpt-90) REVERT: C 407 LYS cc_start: 0.9053 (tppp) cc_final: 0.8303 (tppt) REVERT: C 411 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8694 (mp0) REVERT: C 492 GLU cc_start: 0.9301 (OUTLIER) cc_final: 0.8953 (tp30) REVERT: D 164 MET cc_start: 0.9269 (OUTLIER) cc_final: 0.8858 (ptp) REVERT: D 174 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8061 (mm-30) REVERT: D 202 GLN cc_start: 0.8829 (tt0) cc_final: 0.8017 (tm-30) REVERT: D 351 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8806 (mm-30) REVERT: D 368 GLN cc_start: 0.9027 (mm-40) cc_final: 0.8723 (mm-40) REVERT: D 411 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8292 (pt0) REVERT: D 469 LYS cc_start: 0.9187 (ptmm) cc_final: 0.8927 (ptmm) REVERT: D 479 ARG cc_start: 0.8167 (mtm180) cc_final: 0.7767 (mtp-110) REVERT: E 180 GLN cc_start: 0.8735 (pm20) cc_final: 0.8446 (pm20) REVERT: E 186 PHE cc_start: 0.8726 (m-10) cc_final: 0.8325 (m-80) REVERT: E 191 GLN cc_start: 0.9231 (tt0) cc_final: 0.8609 (tt0) REVERT: E 199 ILE cc_start: 0.8811 (pp) cc_final: 0.8596 (mm) REVERT: E 324 GLU cc_start: 0.8866 (tp30) cc_final: 0.8457 (mm-30) REVERT: E 412 MET cc_start: 0.9295 (mtp) cc_final: 0.8922 (mtp) REVERT: E 445 ASP cc_start: 0.9091 (t0) cc_final: 0.8583 (t0) REVERT: E 498 ASP cc_start: 0.8763 (t0) cc_final: 0.8277 (OUTLIER) REVERT: F 246 ASP cc_start: 0.8555 (m-30) cc_final: 0.8290 (m-30) REVERT: F 407 LYS cc_start: 0.8680 (tptp) cc_final: 0.8222 (tppt) REVERT: F 411 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8328 (mp0) REVERT: F 427 ARG cc_start: 0.8946 (mtm110) cc_final: 0.8498 (ptp90) outliers start: 56 outliers final: 33 residues processed: 336 average time/residue: 1.6441 time to fit residues: 608.7359 Evaluate side-chains 321 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 281 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 174 GLU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 411 GLU Chi-restraints excluded: chain F residue 425 ARG Chi-restraints excluded: chain F residue 472 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 26 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 189 optimal weight: 0.0980 chunk 80 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 158 optimal weight: 20.0000 chunk 165 optimal weight: 9.9990 overall best weight: 5.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 GLN C 292 ASN C 314 GLN ** C 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN D 314 GLN E 202 GLN E 292 ASN F 314 GLN ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.096677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.073931 restraints weight = 40943.827| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.11 r_work: 0.2832 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 1.0590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 18676 Z= 0.200 Angle : 0.761 17.423 25370 Z= 0.374 Chirality : 0.048 0.215 3010 Planarity : 0.006 0.082 3364 Dihedral : 6.283 82.914 2845 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.04 % Allowed : 32.21 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.11 (0.17), residues: 2520 helix: 1.93 (0.16), residues: 1154 sheet: -0.32 (0.21), residues: 522 loop : -0.11 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 481 HIS 0.003 0.001 HIS C 374 PHE 0.039 0.002 PHE D 243 TYR 0.029 0.002 TYR B 486 ARG 0.020 0.001 ARG B 206 Details of bonding type rmsd hydrogen bonds : bond 0.03042 ( 1004) hydrogen bonds : angle 4.01900 ( 2937) covalent geometry : bond 0.00484 (18676) covalent geometry : angle 0.76054 (25370) =============================================================================== Job complete usr+sys time: 15502.63 seconds wall clock time: 267 minutes 35.66 seconds (16055.66 seconds total)