Starting phenix.real_space_refine on Mon Jun 16 12:26:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e27_47442/06_2025/9e27_47442.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e27_47442/06_2025/9e27_47442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e27_47442/06_2025/9e27_47442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e27_47442/06_2025/9e27_47442.map" model { file = "/net/cci-nas-00/data/ceres_data/9e27_47442/06_2025/9e27_47442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e27_47442/06_2025/9e27_47442.cif" } resolution = 3.2 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= 0.047 sd= 0.118 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 14 5.49 5 Mg 6 5.21 5 S 98 5.16 5 C 11394 2.51 5 N 3432 2.21 5 O 3552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18496 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3053 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 151 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: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3053 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 151 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: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3053 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 151 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: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3053 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 151 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: "C" 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} Chain: "F" 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: 11.46, per 1000 atoms: 0.62 Number of scatterers: 18496 At special positions: 0 Unit cell: (133.9, 143.17, 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 98 16.00 P 14 15.00 Mg 6 11.99 O 3552 8.00 N 3432 7.00 C 11394 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: 4.69 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: 97 helices and 15 sheets defined 45.1% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 80 through 95 removed outlier: 3.577A pdb=" N ALA A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASN A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 105 removed outlier: 4.021A pdb=" N LEU A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN A 104 " --> pdb=" O SER A 100 " (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: 4.488A 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: 4.175A 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: 3.783A pdb=" N ASP A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 3.713A 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 removed outlier: 3.643A pdb=" N LEU B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLN B 104 " --> pdb=" O SER B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 125 Processing helix chain 'B' and resid 130 through 146 Processing helix chain 'B' and resid 151 through 157 Processing helix chain 'B' and resid 188 through 202 removed outlier: 3.746A pdb=" N GLN B 202 " --> pdb=" O ARG B 198 " (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: 4.159A 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 500 removed outlier: 3.528A pdb=" N ASP B 498 " --> pdb=" O ALA B 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 97 Processing helix chain 'C' and resid 99 through 104 removed outlier: 4.192A pdb=" N GLN C 104 " --> pdb=" O SER C 100 " (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 151 through 157 Processing helix chain 'C' and resid 188 through 202 Processing helix chain 'C' and resid 249 through 256 Processing helix chain 'C' and resid 260 through 272 Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 296 through 298 No H-bonds generated for 'chain 'C' and resid 296 through 298' Processing helix chain 'C' and resid 337 through 347 removed outlier: 3.755A pdb=" N ARG C 347 " --> pdb=" O LYS C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 372 removed outlier: 4.039A pdb=" N ASP C 365 " --> pdb=" O PRO C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 400 removed outlier: 3.526A pdb=" N SER C 391 " --> pdb=" O ARG C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 480 through 487 Processing helix chain 'C' and resid 489 through 500 removed outlier: 3.553A pdb=" N LEU C 493 " --> pdb=" O LEU C 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 95 removed outlier: 4.226A pdb=" N ASN D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 105 removed outlier: 3.954A pdb=" N LEU D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN D 104 " --> pdb=" O SER D 100 " (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: 4.554A 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 295 Processing helix chain 'D' and resid 296 through 298 No H-bonds generated for 'chain 'D' and resid 296 through 298' Processing helix chain 'D' and resid 337 through 346 Processing helix chain 'D' and resid 361 through 372 removed outlier: 4.197A 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: 3.817A pdb=" N ASP D 498 " --> pdb=" O ALA D 494 " (cutoff:3.500A) removed outlier: 3.721A 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: 3.544A pdb=" N LEU E 102 " --> pdb=" O ASP E 98 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN E 104 " --> pdb=" O SER E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 125 Processing helix chain 'E' and resid 130 through 146 Processing helix chain 'E' and resid 148 through 150 No H-bonds generated for 'chain 'E' and resid 148 through 150' Processing helix chain 'E' and resid 151 through 157 Processing helix chain 'E' and resid 188 through 202 removed outlier: 3.738A pdb=" N GLN E 202 " --> pdb=" O ARG E 198 " (cutoff:3.500A) 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: 4.178A 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 499 Processing helix chain 'F' and resid 81 through 97 Processing helix chain 'F' and resid 98 through 104 removed outlier: 4.075A pdb=" N LEU F 102 " --> pdb=" O ASP F 98 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLN F 104 " --> pdb=" O SER F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 126 Processing helix chain 'F' and resid 130 through 146 Processing helix chain 'F' and resid 151 through 157 Processing helix chain 'F' and resid 188 through 202 Processing helix chain 'F' and resid 249 through 256 Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 286 through 295 Processing helix chain 'F' and resid 296 through 298 No H-bonds generated for 'chain 'F' and resid 296 through 298' Processing helix chain 'F' and resid 337 through 348 removed outlier: 3.551A pdb=" N ARG F 347 " --> pdb=" O LYS F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 372 removed outlier: 4.009A pdb=" N ASP F 365 " --> pdb=" O PRO F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 400 removed outlier: 3.747A pdb=" N SER F 391 " --> pdb=" O ARG F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 417 Processing helix chain 'F' and resid 480 through 487 Processing helix chain 'F' and resid 489 through 500 removed outlier: 3.740A pdb=" N LEU F 493 " --> pdb=" O LEU F 489 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP F 498 " --> pdb=" O ALA F 494 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 178 through 181 removed outlier: 3.905A pdb=" N ASP A 162 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 277 through 281 removed outlier: 7.010A pdb=" N VAL A 419 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N SER A 280 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE A 421 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE A 420 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE A 436 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLN A 422 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 11.343A pdb=" N ARG A 432 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N GLU A 456 " --> pdb=" O ARG A 432 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N THR A 434 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL A 454 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE A 436 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL A 448 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU A 442 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL A 467 " --> pdb=" O THR A 458 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 320 through 324 removed outlier: 6.305A pdb=" N VAL A 305 " --> pdb=" O ILE A 354 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 178 through 182 removed outlier: 4.371A pdb=" N VAL B 171 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP B 162 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 320 through 323 removed outlier: 6.376A pdb=" N VAL B 304 " --> pdb=" O VAL B 321 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU B 323 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N THR B 306 " --> pdb=" O LEU B 323 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE B 353 " --> pdb=" O MET B 378 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N THR B 380 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N VAL B 355 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 9.847A pdb=" N HIS B 382 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY B 379 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL B 278 " --> pdb=" O ILE B 421 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ALA B 423 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N SER B 280 " --> pdb=" O ALA B 423 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N ARG B 425 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA B 424 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ILE B 433 " --> pdb=" O ALA B 424 " (cutoff:3.500A) removed outlier: 16.556A pdb=" N ARG B 431 " --> pdb=" O THR B 458 " (cutoff:3.500A) removed outlier: 13.259A pdb=" N THR B 458 " --> pdb=" O ARG B 431 " (cutoff:3.500A) removed outlier: 10.897A pdb=" N ILE B 433 " --> pdb=" O GLU B 456 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N GLU B 456 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N HIS B 435 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL B 454 " --> pdb=" O HIS B 435 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR B 437 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU B 452 " --> pdb=" O THR B 437 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N VAL B 439 " --> pdb=" O GLN B 450 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLN B 450 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY B 441 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL B 467 " --> pdb=" O THR B 458 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 178 through 181 removed outlier: 3.876A pdb=" N ASP C 162 " --> pdb=" O GLU C 174 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 277 through 281 removed outlier: 7.056A pdb=" N VAL C 278 " --> pdb=" O ILE C 421 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ALA C 423 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N SER C 280 " --> pdb=" O ALA C 423 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ARG C 425 " --> pdb=" O SER C 280 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA C 424 " --> pdb=" O ILE C 433 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ILE C 433 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 10.713A pdb=" N ARG C 432 " --> pdb=" O GLU C 456 " (cutoff:3.500A) removed outlier: 9.421A pdb=" N GLU C 456 " --> pdb=" O ARG C 432 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N THR C 434 " --> pdb=" O VAL C 454 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL C 454 " --> pdb=" O THR C 434 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE C 436 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL C 448 " --> pdb=" O VAL C 440 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU C 442 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL C 467 " --> pdb=" O THR C 458 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 320 through 324 removed outlier: 6.703A pdb=" N VAL C 304 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEU C 323 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N THR C 306 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL C 305 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 178 through 181 removed outlier: 6.756A pdb=" N PHE D 172 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE D 163 " --> pdb=" O PHE D 172 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLU D 174 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 277 through 281 removed outlier: 3.537A pdb=" N ALA D 423 " --> pdb=" O SER D 280 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE D 420 " --> pdb=" O ILE D 436 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE D 436 " --> pdb=" O ILE D 420 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN D 422 " --> pdb=" O THR D 434 " (cutoff:3.500A) removed outlier: 11.427A pdb=" N ARG D 432 " --> pdb=" O GLU D 456 " (cutoff:3.500A) removed outlier: 9.603A pdb=" N GLU D 456 " --> pdb=" O ARG D 432 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N THR D 434 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL D 454 " --> pdb=" O THR D 434 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE D 436 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL D 448 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU D 442 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL D 446 " --> pdb=" O LEU D 442 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL D 467 " --> pdb=" O THR D 458 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 320 through 324 removed outlier: 6.436A pdb=" N VAL D 305 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 178 through 182 removed outlier: 4.506A pdb=" N VAL E 171 " --> pdb=" O THR E 182 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASP E 162 " --> pdb=" O GLU E 174 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 320 through 323 removed outlier: 6.413A pdb=" N VAL E 304 " --> pdb=" O VAL E 321 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU E 323 " --> pdb=" O VAL E 304 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N THR E 306 " --> pdb=" O LEU E 323 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE E 353 " --> pdb=" O MET E 378 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N THR E 380 " --> pdb=" O ILE E 353 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL E 355 " --> pdb=" O THR E 380 " (cutoff:3.500A) removed outlier: 9.851A pdb=" N HIS E 382 " --> pdb=" O VAL E 355 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL E 278 " --> pdb=" O ILE E 421 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ALA E 423 " --> pdb=" O VAL E 278 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N SER E 280 " --> pdb=" O ALA E 423 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N ARG E 425 " --> pdb=" O SER E 280 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA E 424 " --> pdb=" O ILE E 433 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ILE E 433 " --> pdb=" O ALA E 424 " (cutoff:3.500A) removed outlier: 11.492A pdb=" N ARG E 432 " --> pdb=" O GLU E 456 " (cutoff:3.500A) removed outlier: 9.857A pdb=" N GLU E 456 " --> pdb=" O ARG E 432 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N THR E 434 " --> pdb=" O VAL E 454 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL E 454 " --> pdb=" O THR E 434 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE E 436 " --> pdb=" O LEU E 452 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL E 448 " --> pdb=" O VAL E 440 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LEU E 442 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL E 446 " --> pdb=" O LEU E 442 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VAL E 467 " --> pdb=" O THR E 458 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 178 through 182 removed outlier: 4.807A pdb=" N VAL F 171 " --> pdb=" O THR F 182 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP F 162 " --> pdb=" O GLU F 174 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 320 through 324 removed outlier: 6.634A pdb=" N VAL F 304 " --> pdb=" O VAL F 321 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LEU F 323 " --> pdb=" O VAL F 304 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N THR F 306 " --> pdb=" O LEU F 323 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL F 305 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR F 380 " --> pdb=" O VAL F 355 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL F 278 " --> pdb=" O ILE F 421 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ALA F 423 " --> pdb=" O VAL F 278 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N SER F 280 " --> pdb=" O ALA F 423 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ARG F 425 " --> pdb=" O SER F 280 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA F 424 " --> pdb=" O ILE F 433 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ILE F 433 " --> pdb=" O ALA F 424 " (cutoff:3.500A) removed outlier: 10.889A pdb=" N ARG F 432 " --> pdb=" O GLU F 456 " (cutoff:3.500A) removed outlier: 9.410A pdb=" N GLU F 456 " --> pdb=" O ARG F 432 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR F 434 " --> pdb=" O VAL F 454 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL F 454 " --> pdb=" O THR F 434 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE F 436 " --> pdb=" O LEU F 452 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL F 448 " --> pdb=" O VAL F 440 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU F 442 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL F 446 " --> pdb=" O LEU F 442 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL F 467 " --> pdb=" O THR F 458 " (cutoff:3.500A) 958 hydrogen bonds defined for protein. 2802 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: 6.30 Time building geometry restraints manager: 5.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6557 1.34 - 1.46: 3482 1.46 - 1.58: 8509 1.58 - 1.69: 18 1.69 - 1.81: 164 Bond restraints: 18730 Sorted by residual: bond pdb=" C4 ADP B 601 " pdb=" C5 ADP B 601 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.56e+00 bond pdb=" C4 ADP E 601 " pdb=" C5 ADP E 601 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.51e+00 bond pdb=" C4 ADP C 601 " pdb=" C5 ADP C 601 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.42e+00 bond pdb=" C4 ADP F 601 " pdb=" C5 ADP F 601 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.40e+00 bond pdb=" CA VAL A 336 " pdb=" CB VAL A 336 " ideal model delta sigma weight residual 1.540 1.527 0.013 1.36e-02 5.41e+03 9.37e-01 ... (remaining 18725 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 24878 1.34 - 2.68: 407 2.68 - 4.02: 114 4.02 - 5.35: 32 5.35 - 6.69: 25 Bond angle restraints: 25456 Sorted by residual: angle pdb=" N VAL B 203 " pdb=" CA VAL B 203 " pdb=" C VAL B 203 " ideal model delta sigma weight residual 111.91 109.46 2.45 8.90e-01 1.26e+00 7.60e+00 angle pdb=" C3' ATP D 602 " pdb=" C4' ATP D 602 " pdb=" C5' ATP D 602 " ideal model delta sigma weight residual 115.19 110.84 4.35 1.76e+00 3.23e-01 6.10e+00 angle pdb=" C1' ATP A 602 " pdb=" C2' ATP A 602 " pdb=" O2' ATP A 602 " ideal model delta sigma weight residual 110.58 103.89 6.69 2.79e+00 1.28e-01 5.74e+00 angle pdb=" C1' ATP D 602 " pdb=" C2' ATP D 602 " pdb=" O2' ATP D 602 " ideal model delta sigma weight residual 110.58 103.93 6.65 2.79e+00 1.28e-01 5.67e+00 angle pdb=" C3' ATP A 602 " pdb=" C4' ATP A 602 " pdb=" C5' ATP A 602 " ideal model delta sigma weight residual 115.19 111.01 4.18 1.76e+00 3.23e-01 5.64e+00 ... (remaining 25451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.19: 11162 31.19 - 62.37: 314 62.37 - 93.55: 24 93.55 - 124.74: 1 124.74 - 155.92: 1 Dihedral angle restraints: 11502 sinusoidal: 4302 harmonic: 7200 Sorted by residual: dihedral pdb=" O2A ADP F 601 " pdb=" O3A ADP F 601 " pdb=" PA ADP F 601 " pdb=" PB ADP F 601 " ideal model delta sinusoidal sigma weight residual -60.00 95.93 -155.92 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" C5' ADP C 601 " pdb=" O5' ADP C 601 " pdb=" PA ADP C 601 " pdb=" O2A ADP C 601 " ideal model delta sinusoidal sigma weight residual -60.00 44.33 -104.32 1 2.00e+01 2.50e-03 2.99e+01 dihedral pdb=" O2A ADP C 601 " pdb=" O3A ADP C 601 " pdb=" PA ADP C 601 " pdb=" PB ADP C 601 " ideal model delta sinusoidal sigma weight residual -60.00 7.83 -67.83 1 2.00e+01 2.50e-03 1.49e+01 ... (remaining 11499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2532 0.059 - 0.118: 437 0.118 - 0.177: 43 0.177 - 0.237: 2 0.237 - 0.296: 4 Chirality restraints: 3018 Sorted by residual: 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 -2.98 0.30 2.00e-01 2.50e+01 2.19e+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 2.18e+00 chirality pdb=" C3' ATP D 602 " pdb=" C2' ATP D 602 " pdb=" C4' ATP D 602 " pdb=" O3' ATP D 602 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 3015 not shown) Planarity restraints: 3366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 299 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.00e+00 pdb=" N PRO E 300 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO E 300 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 300 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 299 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO B 300 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 300 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 300 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 228 " 0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO D 229 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO D 229 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 229 " 0.016 5.00e-02 4.00e+02 ... (remaining 3363 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 237 2.52 - 3.11: 15246 3.11 - 3.71: 29045 3.71 - 4.30: 38986 4.30 - 4.90: 67613 Nonbonded interactions: 151127 Sorted by model distance: nonbonded pdb=" O1B ADP E 601 " pdb="MG MG E 602 " model vdw 1.923 2.170 nonbonded pdb=" O1B ADP B 601 " pdb="MG MG B 602 " model vdw 1.931 2.170 nonbonded pdb="MG MG A 601 " pdb=" O1G ATP A 602 " model vdw 1.968 2.170 nonbonded pdb=" OG SER E 280 " pdb=" OE1 GLN E 422 " model vdw 1.968 3.040 nonbonded pdb=" OG1 THR B 288 " pdb="MG MG B 602 " model vdw 1.976 2.170 ... (remaining 151122 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 272 or (resid 273 and (name N or name CA or nam \ e C or name O or name CB )) or resid 274 through 501)) selection = (chain 'B' and (resid 80 through 272 or (resid 273 and (name N or name CA or nam \ e C or name O or name CB )) or resid 274 or (resid 275 and (name N or name CA or \ name C or name O or name CB )) or resid 276 through 501)) selection = (chain 'C' and (resid 80 through 274 or (resid 275 and (name N or name CA or nam \ e C or name O or name CB )) or resid 276 through 501)) selection = (chain 'D' and (resid 80 through 272 or (resid 273 and (name N or name CA or nam \ e C or name O or name CB )) or resid 274 through 501)) selection = (chain 'E' and (resid 80 through 272 or (resid 273 and (name N or name CA or nam \ e C or name O or name CB )) or resid 274 or (resid 275 and (name N or name CA or \ name C or name O or name CB )) or resid 276 through 501)) selection = (chain 'F' and (resid 80 through 274 or (resid 275 and (name N or name CA or nam \ e C or name O or name CB )) or resid 276 through 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.080 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: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 44.530 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 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 : 0.003 0.030 18730 Z= 0.150 Angle : 0.525 6.693 25456 Z= 0.264 Chirality : 0.045 0.296 3018 Planarity : 0.003 0.035 3366 Dihedral : 14.218 155.924 6858 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.11 % Allowed : 12.98 % Favored : 86.91 % 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: 1.35 (0.18), residues: 2520 helix: 2.41 (0.17), residues: 1062 sheet: -0.98 (0.22), residues: 490 loop : 0.33 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 481 HIS 0.002 0.001 HIS D 435 PHE 0.006 0.001 PHE A 480 TYR 0.007 0.001 TYR C 402 ARG 0.004 0.000 ARG A 359 Details of bonding type rmsd hydrogen bonds : bond 0.11720 ( 958) hydrogen bonds : angle 5.66192 ( 2802) covalent geometry : bond 0.00322 (18730) covalent geometry : angle 0.52512 (25456) *********************** 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 360 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 358 time to evaluate : 2.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.8985 (mmmm) cc_final: 0.8785 (mmtm) REVERT: A 314 GLN cc_start: 0.9001 (mt0) cc_final: 0.8646 (mt0) REVERT: A 368 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7760 (mp10) REVERT: A 469 LYS cc_start: 0.8783 (ptmm) cc_final: 0.8299 (ptmm) REVERT: A 475 ILE cc_start: 0.8054 (mm) cc_final: 0.7718 (mm) REVERT: B 174 GLU cc_start: 0.8373 (tt0) cc_final: 0.8051 (tt0) REVERT: B 180 GLN cc_start: 0.8558 (mt0) cc_final: 0.8186 (mm110) REVERT: B 185 ARG cc_start: 0.8523 (ttm110) cc_final: 0.7834 (ttm-80) REVERT: B 197 GLN cc_start: 0.9247 (mt0) cc_final: 0.8813 (mp10) REVERT: B 312 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8043 (pm20) REVERT: B 347 ARG cc_start: 0.8972 (mtm-85) cc_final: 0.8766 (mtm-85) REVERT: B 407 LYS cc_start: 0.9143 (tppp) cc_final: 0.8943 (tppt) REVERT: B 438 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6910 (mt-10) REVERT: B 450 GLN cc_start: 0.7703 (tt0) cc_final: 0.7092 (tt0) REVERT: B 475 ILE cc_start: 0.5729 (mm) cc_final: 0.5118 (mm) REVERT: C 162 ASP cc_start: 0.8190 (t0) cc_final: 0.7971 (t0) REVERT: C 410 LYS cc_start: 0.9035 (mttm) cc_final: 0.8619 (mttm) REVERT: C 450 GLN cc_start: 0.8040 (pt0) cc_final: 0.6903 (pt0) REVERT: C 497 LEU cc_start: 0.8921 (tp) cc_final: 0.8688 (tt) REVERT: D 314 GLN cc_start: 0.8974 (mt0) cc_final: 0.8768 (mt0) REVERT: D 324 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7590 (tm-30) REVERT: D 362 GLU cc_start: 0.8623 (pm20) cc_final: 0.8394 (pm20) REVERT: D 411 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8545 (mt-10) REVERT: D 469 LYS cc_start: 0.8725 (ptmm) cc_final: 0.8304 (ptmm) REVERT: D 475 ILE cc_start: 0.7934 (mm) cc_final: 0.7654 (mm) REVERT: E 174 GLU cc_start: 0.8488 (tt0) cc_final: 0.8114 (tt0) REVERT: E 180 GLN cc_start: 0.8567 (mt0) cc_final: 0.8198 (mm110) REVERT: E 197 GLN cc_start: 0.9241 (mt0) cc_final: 0.8810 (mp10) REVERT: E 242 LYS cc_start: 0.8505 (mtpt) cc_final: 0.8281 (mtmt) REVERT: E 312 GLU cc_start: 0.8427 (mt-10) cc_final: 0.7969 (pm20) REVERT: E 347 ARG cc_start: 0.9043 (mtm-85) cc_final: 0.8699 (mtt-85) REVERT: E 351 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8157 (mp0) REVERT: E 422 GLN cc_start: 0.6794 (tp40) cc_final: 0.6389 (tp40) REVERT: F 174 GLU cc_start: 0.7888 (tt0) cc_final: 0.7263 (tm-30) REVERT: F 314 GLN cc_start: 0.8729 (tt0) cc_final: 0.8399 (tp40) REVERT: F 351 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8309 (mm-30) REVERT: F 450 GLN cc_start: 0.7979 (pt0) cc_final: 0.6832 (pt0) REVERT: F 497 LEU cc_start: 0.8940 (tp) cc_final: 0.8653 (tt) outliers start: 2 outliers final: 0 residues processed: 359 average time/residue: 0.4715 time to fit residues: 229.0240 Evaluate side-chains 292 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 291 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 128 optimal weight: 0.6980 chunk 102 optimal weight: 20.0000 chunk 197 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 120 optimal weight: 40.0000 chunk 147 optimal weight: 7.9990 chunk 228 optimal weight: 30.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN F 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.096961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.075360 restraints weight = 42269.516| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 3.28 r_work: 0.3071 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18730 Z= 0.152 Angle : 0.586 7.163 25456 Z= 0.293 Chirality : 0.045 0.152 3018 Planarity : 0.005 0.045 3366 Dihedral : 7.077 157.324 2869 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.47 % Allowed : 13.43 % Favored : 85.10 % 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: 1.34 (0.18), residues: 2520 helix: 2.32 (0.16), residues: 1080 sheet: -0.90 (0.22), residues: 524 loop : 0.40 (0.22), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 481 HIS 0.003 0.001 HIS B 319 PHE 0.011 0.001 PHE D 243 TYR 0.015 0.002 TYR D 148 ARG 0.009 0.001 ARG F 387 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 958) hydrogen bonds : angle 4.37212 ( 2802) covalent geometry : bond 0.00347 (18730) covalent geometry : angle 0.58640 (25456) *********************** 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 341 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 315 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 THR cc_start: 0.9044 (m) cc_final: 0.8776 (p) REVERT: A 324 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7617 (tm-30) REVERT: A 339 ARG cc_start: 0.9193 (tmm-80) cc_final: 0.8870 (tmm-80) REVERT: A 368 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8339 (mp10) REVERT: A 398 THR cc_start: 0.9701 (m) cc_final: 0.9375 (p) REVERT: B 180 GLN cc_start: 0.8864 (mt0) cc_final: 0.8570 (mm110) REVERT: B 185 ARG cc_start: 0.8485 (ttm110) cc_final: 0.7874 (ttm-80) REVERT: B 187 ARG cc_start: 0.8645 (mtm110) cc_final: 0.8335 (mtm110) REVERT: B 191 GLN cc_start: 0.8432 (tt0) cc_final: 0.8169 (tt0) REVERT: B 326 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8661 (ttp-170) REVERT: B 347 ARG cc_start: 0.8889 (mtm-85) cc_final: 0.8548 (mtt-85) REVERT: B 438 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7624 (mt-10) REVERT: B 475 ILE cc_start: 0.6659 (mm) cc_final: 0.6083 (mm) REVERT: C 148 TYR cc_start: 0.8357 (m-80) cc_final: 0.8150 (m-80) REVERT: C 174 GLU cc_start: 0.8466 (tt0) cc_final: 0.7777 (tm-30) REVERT: D 306 THR cc_start: 0.9057 (m) cc_final: 0.8826 (p) REVERT: D 324 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7701 (tm-30) REVERT: D 339 ARG cc_start: 0.9162 (tmm-80) cc_final: 0.8820 (tmm-80) REVERT: D 368 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8577 (mm-40) REVERT: E 180 GLN cc_start: 0.8851 (mt0) cc_final: 0.8576 (mm110) REVERT: E 245 LYS cc_start: 0.8808 (mptt) cc_final: 0.8589 (mmtm) REVERT: E 326 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8663 (ttp-170) REVERT: E 347 ARG cc_start: 0.8913 (mtm-85) cc_final: 0.8627 (mtt-85) REVERT: F 351 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8475 (mm-30) REVERT: F 489 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8632 (pp) REVERT: F 497 LEU cc_start: 0.9120 (tp) cc_final: 0.8848 (tt) outliers start: 26 outliers final: 11 residues processed: 333 average time/residue: 0.4303 time to fit residues: 195.7051 Evaluate side-chains 275 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 260 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain E residue 326 ARG Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 489 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 6 optimal weight: 40.0000 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 85 optimal weight: 50.0000 chunk 84 optimal weight: 50.0000 chunk 12 optimal weight: 9.9990 chunk 164 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 228 optimal weight: 30.0000 chunk 61 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN D 314 GLN ** E 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.096120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.074631 restraints weight = 42295.630| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.28 r_work: 0.3046 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18730 Z= 0.179 Angle : 0.588 10.314 25456 Z= 0.288 Chirality : 0.045 0.164 3018 Planarity : 0.004 0.047 3366 Dihedral : 6.942 160.189 2869 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.43 % Allowed : 14.16 % Favored : 83.41 % 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: 2.24 (0.16), residues: 1080 sheet: -0.92 (0.22), residues: 528 loop : 0.28 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 481 HIS 0.004 0.001 HIS E 319 PHE 0.028 0.001 PHE A 243 TYR 0.017 0.002 TYR C 148 ARG 0.010 0.001 ARG F 477 Details of bonding type rmsd hydrogen bonds : bond 0.03115 ( 958) hydrogen bonds : angle 4.09219 ( 2802) covalent geometry : bond 0.00413 (18730) covalent geometry : angle 0.58784 (25456) *********************** 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 334 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 291 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 TYR cc_start: 0.9111 (m-80) cc_final: 0.8857 (m-10) REVERT: A 243 PHE cc_start: 0.8785 (t80) cc_final: 0.7733 (t80) REVERT: A 251 LYS cc_start: 0.9217 (mmmm) cc_final: 0.8946 (tppt) REVERT: A 306 THR cc_start: 0.9069 (m) cc_final: 0.8825 (p) REVERT: A 324 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7572 (tm-30) REVERT: A 339 ARG cc_start: 0.9158 (tmm-80) cc_final: 0.8855 (tmm-80) REVERT: A 368 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8093 (mp10) REVERT: A 398 THR cc_start: 0.9693 (m) cc_final: 0.9366 (p) REVERT: B 180 GLN cc_start: 0.8804 (mt0) cc_final: 0.8512 (mm110) REVERT: B 185 ARG cc_start: 0.8447 (ttm110) cc_final: 0.7869 (ttm-80) REVERT: B 187 ARG cc_start: 0.8755 (mtm110) cc_final: 0.8260 (mtm110) REVERT: B 191 GLN cc_start: 0.8549 (tt0) cc_final: 0.8184 (tt0) REVERT: B 197 GLN cc_start: 0.9364 (mt0) cc_final: 0.8973 (mp10) REVERT: B 326 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8642 (ttp-170) REVERT: B 347 ARG cc_start: 0.8919 (mtm-85) cc_final: 0.8600 (mtt-85) REVERT: B 438 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7750 (mt-10) REVERT: C 174 GLU cc_start: 0.8471 (tt0) cc_final: 0.7788 (tm-30) REVERT: C 339 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.8508 (ttt90) REVERT: C 340 ASP cc_start: 0.8829 (m-30) cc_final: 0.8509 (m-30) REVERT: C 489 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8732 (pp) REVERT: D 245 LYS cc_start: 0.8442 (mmtt) cc_final: 0.8239 (mmtm) REVERT: D 306 THR cc_start: 0.9056 (m) cc_final: 0.8834 (p) REVERT: D 324 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7672 (tm-30) REVERT: D 396 MET cc_start: 0.8549 (mtt) cc_final: 0.8309 (mtp) REVERT: D 407 LYS cc_start: 0.9240 (tptm) cc_final: 0.9021 (tptm) REVERT: E 180 GLN cc_start: 0.8806 (mt0) cc_final: 0.8527 (mm110) REVERT: E 245 LYS cc_start: 0.8970 (mptt) cc_final: 0.8735 (mmtm) REVERT: E 326 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8663 (ttp-170) REVERT: E 347 ARG cc_start: 0.8910 (mtm-85) cc_final: 0.8634 (mtt-85) REVERT: E 418 ASP cc_start: 0.8001 (m-30) cc_final: 0.7669 (m-30) REVERT: F 351 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8491 (mm-30) REVERT: F 407 LYS cc_start: 0.9254 (tppt) cc_final: 0.9049 (tppt) REVERT: F 489 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8647 (pp) REVERT: F 491 ARG cc_start: 0.8904 (mmm160) cc_final: 0.8575 (mmm160) REVERT: F 497 LEU cc_start: 0.9136 (tp) cc_final: 0.8848 (tt) outliers start: 43 outliers final: 22 residues processed: 322 average time/residue: 0.4254 time to fit residues: 188.2751 Evaluate side-chains 266 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 238 time to evaluate : 2.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 326 ARG Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 294 MET Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 489 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 17 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 46 optimal weight: 50.0000 chunk 151 optimal weight: 8.9990 chunk 161 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 188 optimal weight: 30.0000 chunk 5 optimal weight: 80.0000 chunk 217 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 137 optimal weight: 6.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN ** E 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.095116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.073740 restraints weight = 42694.149| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 3.24 r_work: 0.3037 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18730 Z= 0.216 Angle : 0.598 9.872 25456 Z= 0.295 Chirality : 0.045 0.143 3018 Planarity : 0.004 0.049 3366 Dihedral : 6.842 161.559 2869 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.48 % Allowed : 14.84 % Favored : 82.67 % 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: 1.08 (0.17), residues: 2520 helix: 2.11 (0.16), residues: 1090 sheet: -0.99 (0.22), residues: 522 loop : 0.21 (0.22), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 481 HIS 0.003 0.001 HIS B 435 PHE 0.025 0.001 PHE D 243 TYR 0.017 0.002 TYR B 148 ARG 0.006 0.000 ARG C 206 Details of bonding type rmsd hydrogen bonds : bond 0.03061 ( 958) hydrogen bonds : angle 4.05968 ( 2802) covalent geometry : bond 0.00502 (18730) covalent geometry : angle 0.59805 (25456) *********************** 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 315 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 271 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 TYR cc_start: 0.9130 (m-80) cc_final: 0.8929 (m-10) REVERT: A 324 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7608 (tm-30) REVERT: A 339 ARG cc_start: 0.9145 (tmm-80) cc_final: 0.8848 (tmm-80) REVERT: A 368 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8087 (mp10) REVERT: B 180 GLN cc_start: 0.8791 (mt0) cc_final: 0.8514 (mm110) REVERT: B 187 ARG cc_start: 0.8698 (mtm110) cc_final: 0.8113 (mtm110) REVERT: B 191 GLN cc_start: 0.8561 (tt0) cc_final: 0.8104 (tt0) REVERT: B 193 MET cc_start: 0.9062 (tpp) cc_final: 0.8811 (tmm) REVERT: B 197 GLN cc_start: 0.9387 (mt0) cc_final: 0.8892 (mt0) REVERT: B 326 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8583 (ttp-170) REVERT: B 347 ARG cc_start: 0.8934 (mtm-85) cc_final: 0.8629 (mtt-85) REVERT: B 410 LYS cc_start: 0.9395 (mttp) cc_final: 0.9094 (mtpt) REVERT: C 339 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8494 (ttt90) REVERT: C 340 ASP cc_start: 0.8852 (m-30) cc_final: 0.8538 (m-30) REVERT: C 489 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8790 (pp) REVERT: C 491 ARG cc_start: 0.9033 (mmm160) cc_final: 0.8783 (mmm160) REVERT: D 306 THR cc_start: 0.9110 (m) cc_final: 0.8846 (p) REVERT: D 324 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7687 (tm-30) REVERT: D 404 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8996 (mp) REVERT: D 407 LYS cc_start: 0.9230 (tptm) cc_final: 0.9021 (tptm) REVERT: E 180 GLN cc_start: 0.8805 (mt0) cc_final: 0.8522 (mm110) REVERT: E 193 MET cc_start: 0.9006 (tpp) cc_final: 0.8797 (tmm) REVERT: E 197 GLN cc_start: 0.9369 (mt0) cc_final: 0.9021 (mt0) REVERT: E 326 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8631 (ttp-170) REVERT: E 347 ARG cc_start: 0.8874 (mtm-85) cc_final: 0.8625 (mtt-85) REVERT: E 418 ASP cc_start: 0.7996 (m-30) cc_final: 0.7638 (m-30) REVERT: F 339 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8560 (ttm-80) REVERT: F 351 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8407 (mm-30) REVERT: F 489 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8749 (pp) REVERT: F 497 LEU cc_start: 0.9179 (tp) cc_final: 0.8877 (tt) outliers start: 44 outliers final: 30 residues processed: 302 average time/residue: 0.4158 time to fit residues: 172.7578 Evaluate side-chains 271 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 233 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 326 ARG Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain F residue 214 CYS Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 294 MET Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 489 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 231 optimal weight: 3.9990 chunk 237 optimal weight: 0.0010 chunk 173 optimal weight: 100.0000 chunk 176 optimal weight: 6.9990 chunk 150 optimal weight: 0.3980 chunk 82 optimal weight: 6.9990 chunk 215 optimal weight: 0.4980 chunk 143 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 overall best weight: 2.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN ** E 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.097642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.076263 restraints weight = 42534.663| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.29 r_work: 0.3086 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18730 Z= 0.112 Angle : 0.548 8.565 25456 Z= 0.267 Chirality : 0.044 0.154 3018 Planarity : 0.004 0.048 3366 Dihedral : 6.658 158.947 2869 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.03 % Allowed : 15.74 % Favored : 82.22 % 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: 1.21 (0.17), residues: 2520 helix: 2.22 (0.16), residues: 1088 sheet: -0.85 (0.22), residues: 520 loop : 0.23 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 481 HIS 0.003 0.001 HIS E 319 PHE 0.013 0.001 PHE D 243 TYR 0.011 0.001 TYR B 148 ARG 0.007 0.000 ARG A 392 Details of bonding type rmsd hydrogen bonds : bond 0.02664 ( 958) hydrogen bonds : angle 3.79685 ( 2802) covalent geometry : bond 0.00254 (18730) covalent geometry : angle 0.54764 (25456) *********************** 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 343 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 307 time to evaluate : 2.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 TYR cc_start: 0.9089 (m-80) cc_final: 0.8880 (m-10) REVERT: A 251 LYS cc_start: 0.9192 (mmmm) cc_final: 0.8978 (tppt) REVERT: A 324 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7647 (tm-30) REVERT: A 368 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8099 (mp10) REVERT: A 410 LYS cc_start: 0.9272 (mptt) cc_final: 0.8917 (mmtm) REVERT: B 180 GLN cc_start: 0.8799 (mt0) cc_final: 0.8520 (mm110) REVERT: B 197 GLN cc_start: 0.9372 (mt0) cc_final: 0.9067 (mt0) REVERT: B 326 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8550 (ttp-170) REVERT: B 347 ARG cc_start: 0.8889 (mtm-85) cc_final: 0.8601 (mtt-85) REVERT: B 410 LYS cc_start: 0.9408 (mttp) cc_final: 0.9117 (mtpt) REVERT: C 306 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.9019 (p) REVERT: C 338 MET cc_start: 0.9142 (tpp) cc_final: 0.8849 (tpp) REVERT: C 339 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8485 (ttm-80) REVERT: C 340 ASP cc_start: 0.8786 (m-30) cc_final: 0.8488 (m-30) REVERT: C 491 ARG cc_start: 0.9023 (mmm160) cc_final: 0.8765 (mmm160) REVERT: D 324 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7656 (tm-30) REVERT: E 174 GLU cc_start: 0.8254 (tt0) cc_final: 0.7915 (tt0) REVERT: E 180 GLN cc_start: 0.8795 (mt0) cc_final: 0.8512 (mm110) REVERT: E 197 GLN cc_start: 0.9365 (mt0) cc_final: 0.9149 (mt0) REVERT: E 250 MET cc_start: 0.8957 (tpp) cc_final: 0.8218 (tpt) REVERT: E 326 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8568 (ttp-170) REVERT: E 347 ARG cc_start: 0.8823 (mtm-85) cc_final: 0.8589 (mtt-85) REVERT: E 418 ASP cc_start: 0.7935 (m-30) cc_final: 0.7564 (m-30) REVERT: E 438 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7864 (pm20) REVERT: F 339 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8592 (ttm-80) REVERT: F 340 ASP cc_start: 0.8825 (m-30) cc_final: 0.8617 (m-30) REVERT: F 351 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8392 (mm-30) REVERT: F 489 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8769 (pp) REVERT: F 497 LEU cc_start: 0.9159 (tp) cc_final: 0.8865 (tt) outliers start: 36 outliers final: 17 residues processed: 335 average time/residue: 0.4457 time to fit residues: 205.3128 Evaluate side-chains 275 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 251 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain E residue 326 ARG Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 489 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 163 optimal weight: 7.9990 chunk 86 optimal weight: 0.3980 chunk 153 optimal weight: 4.9990 chunk 100 optimal weight: 30.0000 chunk 95 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 224 optimal weight: 5.9990 chunk 213 optimal weight: 20.0000 chunk 172 optimal weight: 20.0000 chunk 211 optimal weight: 30.0000 chunk 216 optimal weight: 9.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.098114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.076479 restraints weight = 42712.657| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.35 r_work: 0.3072 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18730 Z= 0.134 Angle : 0.567 9.049 25456 Z= 0.276 Chirality : 0.044 0.150 3018 Planarity : 0.005 0.063 3366 Dihedral : 6.365 159.470 2869 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.65 % Allowed : 15.63 % Favored : 81.72 % 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: 1.20 (0.17), residues: 2520 helix: 2.20 (0.16), residues: 1088 sheet: -0.75 (0.22), residues: 510 loop : 0.14 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 481 HIS 0.002 0.001 HIS D 319 PHE 0.031 0.001 PHE E 364 TYR 0.018 0.001 TYR E 402 ARG 0.012 0.000 ARG B 206 Details of bonding type rmsd hydrogen bonds : bond 0.02687 ( 958) hydrogen bonds : angle 3.74003 ( 2802) covalent geometry : bond 0.00309 (18730) covalent geometry : angle 0.56740 (25456) *********************** 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 327 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 280 time to evaluate : 2.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 TYR cc_start: 0.9097 (m-80) cc_final: 0.8896 (m-10) REVERT: A 251 LYS cc_start: 0.9208 (mmmm) cc_final: 0.8989 (tppt) REVERT: A 368 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8106 (mp10) REVERT: A 422 GLN cc_start: 0.8034 (tp40) cc_final: 0.7474 (tp40) REVERT: B 180 GLN cc_start: 0.8816 (mt0) cc_final: 0.8515 (mm110) REVERT: B 326 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8571 (ttp-170) REVERT: B 347 ARG cc_start: 0.8898 (mtm-85) cc_final: 0.8581 (mtt-85) REVERT: B 498 ASP cc_start: 0.8981 (t0) cc_final: 0.8754 (t0) REVERT: C 278 VAL cc_start: 0.8704 (t) cc_final: 0.8456 (p) REVERT: C 306 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.8905 (p) REVERT: C 339 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8626 (ttm-80) REVERT: C 340 ASP cc_start: 0.8817 (m-30) cc_final: 0.8612 (m-30) REVERT: C 491 ARG cc_start: 0.9078 (mmm160) cc_final: 0.8757 (mmm160) REVERT: D 324 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7780 (pp20) REVERT: D 477 ARG cc_start: 0.8743 (ttm170) cc_final: 0.8337 (mmt90) REVERT: E 180 GLN cc_start: 0.8789 (mt0) cc_final: 0.8490 (mm110) REVERT: E 193 MET cc_start: 0.9329 (mmm) cc_final: 0.8941 (tpp) REVERT: E 197 GLN cc_start: 0.9382 (mt0) cc_final: 0.9095 (mp10) REVERT: E 250 MET cc_start: 0.8949 (tpp) cc_final: 0.8116 (tpt) REVERT: E 326 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8569 (ttp-170) REVERT: E 347 ARG cc_start: 0.8823 (mtm-85) cc_final: 0.8598 (mtt-85) REVERT: E 438 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7914 (pm20) REVERT: F 339 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8472 (ttm-80) REVERT: F 340 ASP cc_start: 0.8834 (m-30) cc_final: 0.8613 (m-30) REVERT: F 489 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8800 (pp) REVERT: F 497 LEU cc_start: 0.9173 (tp) cc_final: 0.8873 (tt) outliers start: 47 outliers final: 29 residues processed: 318 average time/residue: 0.4432 time to fit residues: 196.7698 Evaluate side-chains 296 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 259 time to evaluate : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 251 LYS Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain E residue 326 ARG Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 489 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 8 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 202 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 155 optimal weight: 20.0000 chunk 190 optimal weight: 1.9990 chunk 243 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 65 optimal weight: 30.0000 chunk 145 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN C 292 ASN ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN ** E 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.095817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.074531 restraints weight = 42567.682| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.29 r_work: 0.3044 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18730 Z= 0.187 Angle : 0.589 9.470 25456 Z= 0.289 Chirality : 0.045 0.167 3018 Planarity : 0.005 0.047 3366 Dihedral : 6.376 161.470 2869 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.48 % Allowed : 16.25 % Favored : 81.26 % 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: 1.10 (0.17), residues: 2520 helix: 2.11 (0.16), residues: 1088 sheet: -0.82 (0.22), residues: 510 loop : 0.10 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 481 HIS 0.002 0.001 HIS D 435 PHE 0.026 0.001 PHE E 364 TYR 0.017 0.002 TYR B 148 ARG 0.008 0.000 ARG B 206 Details of bonding type rmsd hydrogen bonds : bond 0.02832 ( 958) hydrogen bonds : angle 3.80902 ( 2802) covalent geometry : bond 0.00435 (18730) covalent geometry : angle 0.58923 (25456) *********************** 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 317 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 273 time to evaluate : 2.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8107 (mp10) REVERT: A 410 LYS cc_start: 0.9263 (mptt) cc_final: 0.8969 (mmtm) REVERT: B 180 GLN cc_start: 0.8825 (mt0) cc_final: 0.8514 (mm110) REVERT: B 187 ARG cc_start: 0.8562 (mtm180) cc_final: 0.7938 (mtm110) REVERT: B 326 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8526 (ttp-170) REVERT: B 347 ARG cc_start: 0.8932 (mtm-85) cc_final: 0.8627 (mtt-85) REVERT: B 498 ASP cc_start: 0.8997 (t0) cc_final: 0.8773 (t0) REVERT: C 278 VAL cc_start: 0.8723 (t) cc_final: 0.8440 (p) REVERT: C 306 THR cc_start: 0.9236 (OUTLIER) cc_final: 0.8930 (p) REVERT: C 339 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8560 (ttm-80) REVERT: C 340 ASP cc_start: 0.8810 (m-30) cc_final: 0.8569 (m-30) REVERT: C 491 ARG cc_start: 0.9050 (mmm160) cc_final: 0.8772 (mmm160) REVERT: D 324 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7766 (tm-30) REVERT: D 368 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8666 (mp10) REVERT: D 407 LYS cc_start: 0.9280 (tptm) cc_final: 0.9033 (tptm) REVERT: D 410 LYS cc_start: 0.9370 (mptt) cc_final: 0.9087 (mmtm) REVERT: D 477 ARG cc_start: 0.8747 (ttm170) cc_final: 0.8328 (mmt90) REVERT: E 180 GLN cc_start: 0.8785 (mt0) cc_final: 0.8479 (mm110) REVERT: E 245 LYS cc_start: 0.9012 (mptt) cc_final: 0.8783 (mmtm) REVERT: E 326 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8564 (ttp-170) REVERT: E 347 ARG cc_start: 0.8867 (mtm-85) cc_final: 0.8634 (mtt-85) REVERT: E 438 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7957 (pm20) REVERT: F 337 THR cc_start: 0.9168 (OUTLIER) cc_final: 0.8364 (p) REVERT: F 339 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8557 (ttm-80) REVERT: F 340 ASP cc_start: 0.8866 (m-30) cc_final: 0.8665 (m-30) REVERT: F 489 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8827 (pp) REVERT: F 491 ARG cc_start: 0.9116 (mmm160) cc_final: 0.8775 (mmm160) REVERT: F 497 LEU cc_start: 0.9187 (tp) cc_final: 0.8858 (tt) outliers start: 44 outliers final: 32 residues processed: 305 average time/residue: 0.4151 time to fit residues: 177.3593 Evaluate side-chains 286 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 245 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain E residue 326 ARG Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 489 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 118 optimal weight: 0.6980 chunk 107 optimal weight: 20.0000 chunk 76 optimal weight: 7.9990 chunk 206 optimal weight: 20.0000 chunk 185 optimal weight: 8.9990 chunk 222 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 239 optimal weight: 6.9990 chunk 125 optimal weight: 20.0000 chunk 146 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN ** E 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.096238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.074784 restraints weight = 42559.286| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.31 r_work: 0.3050 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18730 Z= 0.162 Angle : 0.595 9.427 25456 Z= 0.290 Chirality : 0.045 0.153 3018 Planarity : 0.005 0.058 3366 Dihedral : 6.437 161.405 2869 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.77 % Allowed : 16.25 % Favored : 80.98 % 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: 1.10 (0.17), residues: 2520 helix: 2.11 (0.16), residues: 1088 sheet: -0.83 (0.22), residues: 510 loop : 0.11 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 481 HIS 0.002 0.001 HIS B 435 PHE 0.030 0.001 PHE D 243 TYR 0.015 0.001 TYR B 148 ARG 0.008 0.000 ARG F 206 Details of bonding type rmsd hydrogen bonds : bond 0.02763 ( 958) hydrogen bonds : angle 3.77341 ( 2802) covalent geometry : bond 0.00378 (18730) covalent geometry : angle 0.59545 (25456) *********************** 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 326 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 277 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.8891 (mmtm) cc_final: 0.8683 (mmtm) REVERT: A 368 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8077 (mp10) REVERT: B 180 GLN cc_start: 0.8825 (mt0) cc_final: 0.8518 (mm110) REVERT: B 187 ARG cc_start: 0.8458 (mtm180) cc_final: 0.7869 (ptt90) REVERT: B 326 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8571 (ttp-170) REVERT: B 347 ARG cc_start: 0.8927 (mtm-85) cc_final: 0.8613 (mtt-85) REVERT: B 498 ASP cc_start: 0.8993 (t0) cc_final: 0.8763 (t0) REVERT: C 278 VAL cc_start: 0.8754 (t) cc_final: 0.8493 (p) REVERT: C 306 THR cc_start: 0.9233 (OUTLIER) cc_final: 0.8927 (p) REVERT: C 339 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8514 (ttm-80) REVERT: C 340 ASP cc_start: 0.8798 (m-30) cc_final: 0.8558 (m-30) REVERT: C 491 ARG cc_start: 0.9063 (mmm160) cc_final: 0.8776 (mmm160) REVERT: D 324 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7752 (tm-30) REVERT: D 410 LYS cc_start: 0.9367 (mptt) cc_final: 0.9088 (mmtm) REVERT: D 477 ARG cc_start: 0.8768 (ttm170) cc_final: 0.8348 (mmt90) REVERT: E 180 GLN cc_start: 0.8808 (mt0) cc_final: 0.8498 (mm110) REVERT: E 187 ARG cc_start: 0.8711 (mtm180) cc_final: 0.8237 (mtm180) REVERT: E 245 LYS cc_start: 0.9016 (mptt) cc_final: 0.8774 (mmtm) REVERT: E 326 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8560 (ttp-170) REVERT: E 347 ARG cc_start: 0.8862 (mtm-85) cc_final: 0.8631 (mtt-85) REVERT: F 337 THR cc_start: 0.9146 (OUTLIER) cc_final: 0.8341 (p) REVERT: F 339 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8546 (ttm-80) REVERT: F 340 ASP cc_start: 0.8854 (m-30) cc_final: 0.8649 (m-30) REVERT: F 489 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8822 (pp) REVERT: F 491 ARG cc_start: 0.9107 (mmm160) cc_final: 0.8763 (mmm160) REVERT: F 497 LEU cc_start: 0.9193 (tp) cc_final: 0.8865 (tt) outliers start: 49 outliers final: 34 residues processed: 313 average time/residue: 0.4301 time to fit residues: 190.9574 Evaluate side-chains 304 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 262 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 402 TYR Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain E residue 166 ASN Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain E residue 326 ARG Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 489 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 54 optimal weight: 1.9990 chunk 168 optimal weight: 120.0000 chunk 214 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 127 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 chunk 173 optimal weight: 110.0000 chunk 220 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN ** E 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.098156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.076878 restraints weight = 42398.460| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 3.31 r_work: 0.3095 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 18730 Z= 0.112 Angle : 0.573 7.984 25456 Z= 0.279 Chirality : 0.044 0.150 3018 Planarity : 0.004 0.047 3366 Dihedral : 6.149 158.271 2869 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.60 % Allowed : 16.42 % Favored : 80.98 % 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: 1.15 (0.17), residues: 2520 helix: 2.17 (0.16), residues: 1088 sheet: -0.77 (0.22), residues: 510 loop : 0.11 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 481 HIS 0.002 0.000 HIS A 319 PHE 0.031 0.001 PHE D 243 TYR 0.010 0.001 TYR B 148 ARG 0.009 0.000 ARG F 206 Details of bonding type rmsd hydrogen bonds : bond 0.02562 ( 958) hydrogen bonds : angle 3.62418 ( 2802) covalent geometry : bond 0.00260 (18730) covalent geometry : angle 0.57297 (25456) *********************** 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 345 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 299 time to evaluate : 2.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.8869 (mmtm) cc_final: 0.8659 (mmtm) REVERT: A 364 PHE cc_start: 0.9336 (t80) cc_final: 0.8575 (t80) REVERT: A 368 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.7829 (mp10) REVERT: A 398 THR cc_start: 0.9580 (m) cc_final: 0.9240 (p) REVERT: B 180 GLN cc_start: 0.8822 (mt0) cc_final: 0.8520 (mm110) REVERT: B 187 ARG cc_start: 0.8303 (mtm180) cc_final: 0.7854 (ptt90) REVERT: B 324 GLU cc_start: 0.8641 (pt0) cc_final: 0.8360 (pt0) REVERT: B 326 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8517 (ttp-170) REVERT: B 347 ARG cc_start: 0.8882 (mtm-85) cc_final: 0.8557 (mtt-85) REVERT: B 498 ASP cc_start: 0.8969 (t0) cc_final: 0.8705 (t0) REVERT: C 306 THR cc_start: 0.9206 (OUTLIER) cc_final: 0.8897 (p) REVERT: C 338 MET cc_start: 0.9124 (tpp) cc_final: 0.8834 (tpp) REVERT: C 339 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8483 (ttm-80) REVERT: C 359 ARG cc_start: 0.9169 (ptp90) cc_final: 0.8946 (ptm160) REVERT: C 477 ARG cc_start: 0.9138 (tpp80) cc_final: 0.8887 (tpp80) REVERT: C 491 ARG cc_start: 0.9050 (mmm160) cc_final: 0.8764 (mmm160) REVERT: D 250 MET cc_start: 0.8781 (tpp) cc_final: 0.8568 (tpt) REVERT: D 324 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7749 (tm-30) REVERT: D 362 GLU cc_start: 0.8644 (pm20) cc_final: 0.8405 (pm20) REVERT: D 368 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8656 (mp10) REVERT: D 398 THR cc_start: 0.9581 (m) cc_final: 0.9236 (p) REVERT: D 410 LYS cc_start: 0.9313 (mptt) cc_final: 0.9062 (mmtm) REVERT: D 477 ARG cc_start: 0.8722 (ttm170) cc_final: 0.8283 (mmt90) REVERT: E 180 GLN cc_start: 0.8809 (mt0) cc_final: 0.8515 (mm110) REVERT: E 187 ARG cc_start: 0.8699 (mtm180) cc_final: 0.8196 (mtm180) REVERT: E 245 LYS cc_start: 0.8997 (mptt) cc_final: 0.8758 (mmtm) REVERT: E 250 MET cc_start: 0.8945 (tpp) cc_final: 0.8116 (tpt) REVERT: E 326 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8565 (ttp-170) REVERT: E 347 ARG cc_start: 0.8790 (mtm-85) cc_final: 0.8586 (mtt-85) REVERT: E 396 MET cc_start: 0.9108 (ttm) cc_final: 0.8882 (mtp) REVERT: F 339 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8407 (ttm-80) REVERT: F 340 ASP cc_start: 0.8738 (m-30) cc_final: 0.8535 (m-30) REVERT: F 489 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8807 (pp) REVERT: F 491 ARG cc_start: 0.9100 (mmm160) cc_final: 0.8751 (mmm160) outliers start: 46 outliers final: 31 residues processed: 334 average time/residue: 0.4043 time to fit residues: 189.3874 Evaluate side-chains 316 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 278 time to evaluate : 2.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 402 TYR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 402 TYR Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain E residue 326 ARG Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain F residue 166 ASN Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 489 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 138 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 194 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 47 optimal weight: 120.0000 chunk 129 optimal weight: 30.0000 chunk 163 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 110 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN ** E 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.097126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.075760 restraints weight = 42326.898| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 3.30 r_work: 0.3073 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18730 Z= 0.145 Angle : 0.600 8.189 25456 Z= 0.292 Chirality : 0.045 0.151 3018 Planarity : 0.005 0.048 3366 Dihedral : 6.117 159.387 2869 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.31 % Allowed : 17.38 % Favored : 80.30 % 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: 2.11 (0.16), residues: 1090 sheet: -0.78 (0.22), residues: 510 loop : 0.10 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 481 HIS 0.002 0.001 HIS B 319 PHE 0.030 0.001 PHE D 243 TYR 0.015 0.001 TYR C 402 ARG 0.013 0.000 ARG A 491 Details of bonding type rmsd hydrogen bonds : bond 0.02669 ( 958) hydrogen bonds : angle 3.66348 ( 2802) covalent geometry : bond 0.00339 (18730) covalent geometry : angle 0.59981 (25456) ********************** 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 323 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 282 time to evaluate : 2.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LYS cc_start: 0.8904 (mmtm) cc_final: 0.8586 (mmtm) REVERT: A 206 ARG cc_start: 0.8325 (ttp80) cc_final: 0.8113 (ttp80) REVERT: A 368 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8135 (mp10) REVERT: A 398 THR cc_start: 0.9567 (m) cc_final: 0.9228 (p) REVERT: B 180 GLN cc_start: 0.8839 (mt0) cc_final: 0.8570 (mm110) REVERT: B 187 ARG cc_start: 0.8343 (mtm180) cc_final: 0.7879 (ptt90) REVERT: B 324 GLU cc_start: 0.8693 (pt0) cc_final: 0.8403 (pt0) REVERT: B 326 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8600 (ttp-170) REVERT: B 347 ARG cc_start: 0.8923 (mtm-85) cc_final: 0.8708 (mtt-85) REVERT: B 498 ASP cc_start: 0.8968 (t0) cc_final: 0.8687 (t0) REVERT: C 306 THR cc_start: 0.9204 (OUTLIER) cc_final: 0.8931 (p) REVERT: C 339 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8633 (ttm-80) REVERT: C 359 ARG cc_start: 0.9226 (ptp90) cc_final: 0.9010 (ptm160) REVERT: C 477 ARG cc_start: 0.9111 (tpp80) cc_final: 0.8845 (tpp80) REVERT: C 491 ARG cc_start: 0.9087 (mmm160) cc_final: 0.8793 (mmm160) REVERT: D 250 MET cc_start: 0.8794 (tpp) cc_final: 0.7957 (tpt) REVERT: D 324 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7770 (tm-30) REVERT: D 338 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8303 (tpp) REVERT: D 398 THR cc_start: 0.9592 (m) cc_final: 0.9242 (p) REVERT: D 477 ARG cc_start: 0.8702 (ttm170) cc_final: 0.8263 (mmt90) REVERT: E 180 GLN cc_start: 0.8809 (mt0) cc_final: 0.8511 (mm110) REVERT: E 187 ARG cc_start: 0.8678 (mtm180) cc_final: 0.8166 (mtm180) REVERT: E 193 MET cc_start: 0.9253 (mmm) cc_final: 0.8723 (tmm) REVERT: E 197 GLN cc_start: 0.9446 (mt0) cc_final: 0.8861 (mt0) REVERT: E 245 LYS cc_start: 0.9007 (mptt) cc_final: 0.8764 (mmtm) REVERT: E 326 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8584 (ttp-170) REVERT: E 347 ARG cc_start: 0.8804 (mtm-85) cc_final: 0.8593 (mtt-85) REVERT: F 339 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8475 (ttm-80) REVERT: F 489 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8814 (pp) REVERT: F 491 ARG cc_start: 0.9076 (mmm160) cc_final: 0.8743 (mmm160) outliers start: 41 outliers final: 33 residues processed: 313 average time/residue: 0.4211 time to fit residues: 187.4240 Evaluate side-chains 306 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 265 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 307 CYS Chi-restraints excluded: chain A residue 368 GLN Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 307 CYS Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain D residue 402 TYR Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain E residue 166 ASN Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain E residue 326 ARG Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain E residue 378 MET Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain F residue 166 ASN Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 489 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 181 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 243 optimal weight: 9.9990 chunk 81 optimal weight: 30.0000 chunk 129 optimal weight: 50.0000 chunk 219 optimal weight: 8.9990 chunk 56 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 HIS ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN ** E 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.095604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.074268 restraints weight = 42764.167| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.30 r_work: 0.3043 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18730 Z= 0.202 Angle : 0.625 9.008 25456 Z= 0.308 Chirality : 0.046 0.177 3018 Planarity : 0.005 0.047 3366 Dihedral : 6.296 163.406 2869 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.43 % Allowed : 17.55 % Favored : 80.02 % 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: 1.01 (0.17), residues: 2520 helix: 2.06 (0.16), residues: 1086 sheet: -0.89 (0.22), residues: 510 loop : 0.05 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 481 HIS 0.002 0.001 HIS B 435 PHE 0.030 0.001 PHE D 243 TYR 0.018 0.002 TYR F 402 ARG 0.008 0.001 ARG F 206 Details of bonding type rmsd hydrogen bonds : bond 0.02876 ( 958) hydrogen bonds : angle 3.77960 ( 2802) covalent geometry : bond 0.00469 (18730) covalent geometry : angle 0.62493 (25456) =============================================================================== Job complete usr+sys time: 9570.18 seconds wall clock time: 167 minutes 28.87 seconds (10048.87 seconds total)