Starting phenix.real_space_refine on Thu Sep 18 17:14:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e27_47442/09_2025/9e27_47442.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e27_47442/09_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_47442/09_2025/9e27_47442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e27_47442/09_2025/9e27_47442.map" model { file = "/net/cci-nas-00/data/ceres_data/9e27_47442/09_2025/9e27_47442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e27_47442/09_2025/9e27_47442.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 1} 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: {'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 1} 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: {'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 1} 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: {'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 1} 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: {'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 1} 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: {'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 1} 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: 5.11, per 1000 atoms: 0.28 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: 1.89 Conformation dependent library (CDL) restraints added in 869.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.89 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: 3.71 Time building geometry restraints manager: 2.39 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: 0.01 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: 0.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.790 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.880 ------------------------------------------------------------------------------- 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 : 8.47 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG A 359 TYR 0.007 0.001 TYR C 402 PHE 0.006 0.001 PHE A 480 TRP 0.006 0.001 TRP C 481 HIS 0.002 0.001 HIS D 435 Details of bonding type rmsd covalent geometry : bond 0.00322 (18730) covalent geometry : angle 0.52512 (25456) hydrogen bonds : bond 0.11720 ( 958) hydrogen bonds : angle 5.66192 ( 2802) *********************** 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 : 0.745 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: 0.2301 time to fit residues: 110.8735 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 : 0.803 ------------------------------------------------------------------------------- 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 216 optimal weight: 9.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 247 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.096456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.074853 restraints weight = 42354.672| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 3.28 r_work: 0.3061 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18730 Z= 0.166 Angle : 0.592 7.195 25456 Z= 0.296 Chirality : 0.045 0.152 3018 Planarity : 0.005 0.051 3366 Dihedral : 7.079 157.898 2869 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.69 % Allowed : 13.54 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.18), residues: 2520 helix: 2.27 (0.16), residues: 1080 sheet: -0.94 (0.22), residues: 524 loop : 0.37 (0.22), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 387 TYR 0.017 0.002 TYR D 148 PHE 0.013 0.001 PHE E 480 TRP 0.012 0.002 TRP C 481 HIS 0.003 0.001 HIS B 319 Details of bonding type rmsd covalent geometry : bond 0.00382 (18730) covalent geometry : angle 0.59219 (25456) hydrogen bonds : bond 0.03336 ( 958) hydrogen bonds : angle 4.36914 ( 2802) *********************** 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 343 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 313 time to evaluate : 0.765 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 306 THR cc_start: 0.9054 (m) cc_final: 0.8801 (p) REVERT: A 324 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7604 (tm-30) REVERT: A 339 ARG cc_start: 0.9201 (tmm-80) cc_final: 0.8873 (tmm-80) REVERT: A 368 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8306 (mp10) REVERT: A 398 THR cc_start: 0.9699 (m) cc_final: 0.9373 (p) REVERT: A 410 LYS cc_start: 0.9264 (mttm) cc_final: 0.8927 (mptp) REVERT: B 174 GLU cc_start: 0.8381 (tt0) cc_final: 0.8172 (tt0) REVERT: B 180 GLN cc_start: 0.8866 (mt0) cc_final: 0.8577 (mm110) REVERT: B 185 ARG cc_start: 0.8489 (ttm110) cc_final: 0.7900 (ttm-80) REVERT: B 187 ARG cc_start: 0.8682 (mtm110) cc_final: 0.8406 (mtm110) REVERT: B 191 GLN cc_start: 0.8465 (tt0) cc_final: 0.8187 (tt0) REVERT: B 326 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8672 (ttp-170) REVERT: B 347 ARG cc_start: 0.8878 (mtm-85) cc_final: 0.8536 (mtt-85) REVERT: B 438 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7447 (mt-10) REVERT: B 450 GLN cc_start: 0.8439 (tt0) cc_final: 0.7919 (tt0) REVERT: B 475 ILE cc_start: 0.6676 (mm) cc_final: 0.6036 (mm) REVERT: C 148 TYR cc_start: 0.8367 (m-80) cc_final: 0.8167 (m-80) REVERT: C 162 ASP cc_start: 0.8210 (t0) cc_final: 0.7995 (t0) REVERT: C 174 GLU cc_start: 0.8459 (tt0) cc_final: 0.7803 (tm-30) REVERT: D 306 THR cc_start: 0.9056 (m) cc_final: 0.8841 (p) REVERT: D 324 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7704 (tm-30) REVERT: D 339 ARG cc_start: 0.9182 (tmm-80) cc_final: 0.8831 (tmm-80) REVERT: D 378 MET cc_start: 0.8588 (mtm) cc_final: 0.8380 (mtt) REVERT: E 180 GLN cc_start: 0.8870 (mt0) cc_final: 0.8594 (mm110) REVERT: E 245 LYS cc_start: 0.8857 (mptt) cc_final: 0.8632 (mmtm) REVERT: E 326 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8692 (ttp-170) REVERT: E 347 ARG cc_start: 0.8893 (mtm-85) cc_final: 0.8605 (mtt-85) REVERT: F 174 GLU cc_start: 0.8310 (tt0) cc_final: 0.7899 (tm-30) REVERT: F 351 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8462 (mm-30) REVERT: F 489 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8640 (pp) REVERT: F 497 LEU cc_start: 0.9122 (tp) cc_final: 0.8848 (tt) outliers start: 30 outliers final: 14 residues processed: 337 average time/residue: 0.2151 time to fit residues: 98.9475 Evaluate side-chains 276 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 258 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 404 LEU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 309 ASP 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 337 THR Chi-restraints excluded: chain F residue 367 LEU 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 215 optimal weight: 40.0000 chunk 76 optimal weight: 20.0000 chunk 141 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 214 optimal weight: 50.0000 chunk 244 optimal weight: 0.2980 chunk 20 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 165 optimal weight: 50.0000 chunk 250 optimal weight: 6.9990 overall best weight: 5.6588 ------------------------------------------------------------------------------- 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** ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.096173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.074694 restraints weight = 42722.779| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.29 r_work: 0.3054 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18730 Z= 0.169 Angle : 0.585 10.208 25456 Z= 0.286 Chirality : 0.045 0.151 3018 Planarity : 0.004 0.048 3366 Dihedral : 6.927 159.626 2869 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.26 % Allowed : 14.45 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.18), residues: 2520 helix: 2.23 (0.16), residues: 1082 sheet: -0.92 (0.22), residues: 528 loop : 0.29 (0.22), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 349 TYR 0.017 0.002 TYR C 148 PHE 0.028 0.001 PHE A 243 TRP 0.008 0.001 TRP C 481 HIS 0.003 0.001 HIS E 319 Details of bonding type rmsd covalent geometry : bond 0.00390 (18730) covalent geometry : angle 0.58535 (25456) hydrogen bonds : bond 0.03091 ( 958) hydrogen bonds : angle 4.10797 ( 2802) *********************** 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 325 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 285 time to evaluate : 0.756 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 148 TYR cc_start: 0.9096 (m-80) cc_final: 0.8844 (m-10) REVERT: A 243 PHE cc_start: 0.8774 (t80) cc_final: 0.7705 (t80) REVERT: A 251 LYS cc_start: 0.9223 (mmmm) cc_final: 0.8958 (tppt) REVERT: A 306 THR cc_start: 0.9055 (m) cc_final: 0.8825 (p) REVERT: A 324 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7612 (tm-30) REVERT: A 368 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8072 (mp10) REVERT: A 398 THR cc_start: 0.9688 (m) cc_final: 0.9361 (p) REVERT: B 180 GLN cc_start: 0.8806 (mt0) cc_final: 0.8528 (mm110) REVERT: B 185 ARG cc_start: 0.8449 (ttm110) cc_final: 0.7870 (ttm-80) REVERT: B 187 ARG cc_start: 0.8723 (mtm110) cc_final: 0.8248 (mtm110) REVERT: B 191 GLN cc_start: 0.8497 (tt0) cc_final: 0.8105 (tt0) REVERT: B 197 GLN cc_start: 0.9360 (mt0) cc_final: 0.8978 (mp10) REVERT: B 326 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8641 (ttp-170) REVERT: B 347 ARG cc_start: 0.8918 (mtm-85) cc_final: 0.8592 (mtt-85) REVERT: B 450 GLN cc_start: 0.8521 (tt0) cc_final: 0.8290 (tt0) REVERT: C 339 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8512 (ttt90) REVERT: C 340 ASP cc_start: 0.8785 (m-30) cc_final: 0.8459 (m-30) REVERT: C 489 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8729 (pp) REVERT: D 314 GLN cc_start: 0.8947 (mt0) cc_final: 0.8736 (mt0) REVERT: D 324 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7673 (tm-30) REVERT: D 398 THR cc_start: 0.9691 (m) cc_final: 0.9367 (p) REVERT: E 174 GLU cc_start: 0.8327 (tt0) cc_final: 0.8119 (tt0) REVERT: E 180 GLN cc_start: 0.8836 (mt0) cc_final: 0.8563 (mm110) REVERT: E 245 LYS cc_start: 0.8946 (mptt) cc_final: 0.8703 (mmtm) REVERT: E 326 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8658 (ttp-170) REVERT: E 347 ARG cc_start: 0.8909 (mtm-85) cc_final: 0.8635 (mtt-85) REVERT: E 418 ASP cc_start: 0.7976 (m-30) cc_final: 0.7667 (m-30) REVERT: F 351 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8469 (mm-30) REVERT: F 489 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8655 (pp) REVERT: F 491 ARG cc_start: 0.8872 (mmm160) cc_final: 0.8530 (mmm160) REVERT: F 497 LEU cc_start: 0.9141 (tp) cc_final: 0.8857 (tt) outliers start: 40 outliers final: 21 residues processed: 314 average time/residue: 0.1989 time to fit residues: 87.1198 Evaluate side-chains 275 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 248 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 200 VAL 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 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 489 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 19 optimal weight: 8.9990 chunk 158 optimal weight: 30.0000 chunk 64 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 246 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 139 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 46 optimal weight: 30.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 314 GLN ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.095632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.074248 restraints weight = 43032.629| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.29 r_work: 0.3041 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18730 Z= 0.181 Angle : 0.584 9.498 25456 Z= 0.286 Chirality : 0.045 0.147 3018 Planarity : 0.004 0.049 3366 Dihedral : 6.818 160.252 2869 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.54 % Allowed : 15.01 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.17), residues: 2520 helix: 2.10 (0.16), residues: 1090 sheet: -0.87 (0.22), residues: 498 loop : 0.07 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 206 TYR 0.015 0.002 TYR B 148 PHE 0.026 0.001 PHE D 243 TRP 0.007 0.001 TRP C 481 HIS 0.003 0.001 HIS E 435 Details of bonding type rmsd covalent geometry : bond 0.00419 (18730) covalent geometry : angle 0.58435 (25456) hydrogen bonds : bond 0.02950 ( 958) hydrogen bonds : angle 3.99773 ( 2802) *********************** 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 316 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 271 time to evaluate : 0.928 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: 0.9145 (m-80) cc_final: 0.8939 (m-10) REVERT: A 251 LYS cc_start: 0.9237 (mmmm) cc_final: 0.9036 (tppt) REVERT: A 306 THR cc_start: 0.9072 (m) cc_final: 0.8809 (p) REVERT: A 324 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7632 (tm-30) REVERT: A 368 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8107 (mp10) REVERT: B 180 GLN cc_start: 0.8812 (mt0) cc_final: 0.8518 (mm110) REVERT: B 187 ARG cc_start: 0.8716 (mtm110) cc_final: 0.8155 (mtm110) REVERT: B 191 GLN cc_start: 0.8536 (tt0) cc_final: 0.8091 (tt0) REVERT: B 197 GLN cc_start: 0.9388 (mt0) cc_final: 0.8953 (mp10) REVERT: B 326 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8566 (ttp-170) REVERT: B 347 ARG cc_start: 0.8934 (mtm-85) cc_final: 0.8605 (mtt-85) REVERT: B 438 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7922 (mt-10) REVERT: B 450 GLN cc_start: 0.8554 (tt0) cc_final: 0.8057 (tt0) REVERT: C 339 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8520 (ttt90) REVERT: C 340 ASP cc_start: 0.8793 (m-30) cc_final: 0.8492 (m-30) REVERT: C 489 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8779 (pp) REVERT: C 491 ARG cc_start: 0.9042 (mmm160) cc_final: 0.8779 (mmm160) REVERT: D 324 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7709 (tm-30) REVERT: E 180 GLN cc_start: 0.8808 (mt0) cc_final: 0.8501 (mm110) REVERT: E 197 GLN cc_start: 0.9384 (mt0) cc_final: 0.9016 (mt0) REVERT: E 326 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8598 (ttp-170) REVERT: E 347 ARG cc_start: 0.8896 (mtm-85) cc_final: 0.8635 (mtt-85) REVERT: E 418 ASP cc_start: 0.8034 (m-30) cc_final: 0.7671 (m-30) REVERT: F 339 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8510 (ttm-80) REVERT: F 351 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8426 (mm-30) REVERT: F 489 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8735 (pp) REVERT: F 497 LEU cc_start: 0.9170 (tp) cc_final: 0.8876 (tt) outliers start: 45 outliers final: 30 residues processed: 304 average time/residue: 0.2110 time to fit residues: 88.2934 Evaluate side-chains 268 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 231 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 292 ASN 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 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 337 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 336 VAL Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain E residue 192 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 253 LEU Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 294 MET 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 208 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 203 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 244 optimal weight: 6.9990 chunk 220 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 90 optimal weight: 0.0770 chunk 95 optimal weight: 5.9990 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 314 GLN ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN D 314 GLN ** E 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.096279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.074998 restraints weight = 42529.487| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.28 r_work: 0.3057 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18730 Z= 0.148 Angle : 0.565 9.307 25456 Z= 0.277 Chirality : 0.044 0.150 3018 Planarity : 0.004 0.049 3366 Dihedral : 6.606 160.668 2869 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.71 % Allowed : 15.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.17), residues: 2520 helix: 2.13 (0.16), residues: 1088 sheet: -0.96 (0.22), residues: 508 loop : 0.09 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 392 TYR 0.015 0.002 TYR E 402 PHE 0.018 0.001 PHE E 364 TRP 0.006 0.001 TRP C 481 HIS 0.002 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00339 (18730) covalent geometry : angle 0.56535 (25456) hydrogen bonds : bond 0.02810 ( 958) hydrogen bonds : angle 3.89877 ( 2802) *********************** 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 340 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 292 time to evaluate : 0.765 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 148 TYR cc_start: 0.9128 (m-80) cc_final: 0.8924 (m-10) REVERT: A 306 THR cc_start: 0.9066 (m) cc_final: 0.8825 (p) REVERT: A 324 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7598 (tm-30) REVERT: A 368 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8087 (mp10) REVERT: B 180 GLN cc_start: 0.8804 (mt0) cc_final: 0.8509 (mm110) REVERT: B 187 ARG cc_start: 0.8725 (mtm110) cc_final: 0.8153 (mtm110) REVERT: B 191 GLN cc_start: 0.8521 (tt0) cc_final: 0.8225 (tt0) REVERT: B 197 GLN cc_start: 0.9381 (mt0) cc_final: 0.9108 (mp10) REVERT: B 326 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8604 (ttp-170) REVERT: B 347 ARG cc_start: 0.8925 (mtm-85) cc_final: 0.8600 (mtt-85) REVERT: B 410 LYS cc_start: 0.9391 (mttt) cc_final: 0.9105 (mtpt) REVERT: C 306 THR cc_start: 0.9230 (OUTLIER) cc_final: 0.8975 (p) REVERT: C 339 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8563 (ttm-80) REVERT: C 340 ASP cc_start: 0.8769 (m-30) cc_final: 0.8503 (m-30) REVERT: C 489 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8737 (pp) REVERT: C 491 ARG cc_start: 0.9036 (mmm160) cc_final: 0.8728 (mmm160) REVERT: D 243 PHE cc_start: 0.8878 (t80) cc_final: 0.8647 (t80) REVERT: D 324 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7672 (tm-30) REVERT: D 410 LYS cc_start: 0.9297 (mptt) cc_final: 0.9010 (mmtm) REVERT: E 180 GLN cc_start: 0.8804 (mt0) cc_final: 0.8503 (mm110) REVERT: E 326 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8613 (ttp-170) REVERT: E 347 ARG cc_start: 0.8868 (mtm-85) cc_final: 0.8620 (mtt-85) REVERT: F 339 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8529 (ttm-80) REVERT: F 340 ASP cc_start: 0.8866 (m-30) cc_final: 0.8642 (m-30) REVERT: F 351 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8421 (mm-30) REVERT: F 489 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8731 (pp) REVERT: F 497 LEU cc_start: 0.9165 (tp) cc_final: 0.8869 (tt) outliers start: 48 outliers final: 28 residues processed: 330 average time/residue: 0.2112 time to fit residues: 96.0870 Evaluate side-chains 292 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 256 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 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 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 489 LEU 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 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 214 CYS Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain F residue 339 ARG 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 186 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 36 optimal weight: 0.4980 chunk 139 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 67 optimal weight: 0.3980 chunk 32 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 233 optimal weight: 8.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- 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** B 450 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.097241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.075949 restraints weight = 42081.489| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 3.26 r_work: 0.3079 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18730 Z= 0.124 Angle : 0.564 8.730 25456 Z= 0.275 Chirality : 0.044 0.149 3018 Planarity : 0.005 0.061 3366 Dihedral : 6.488 159.848 2869 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.43 % Allowed : 16.20 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.17), residues: 2520 helix: 2.21 (0.16), residues: 1086 sheet: -0.84 (0.22), residues: 518 loop : 0.13 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 206 TYR 0.017 0.001 TYR E 402 PHE 0.028 0.001 PHE E 364 TRP 0.014 0.002 TRP F 481 HIS 0.002 0.001 HIS E 319 Details of bonding type rmsd covalent geometry : bond 0.00284 (18730) covalent geometry : angle 0.56363 (25456) hydrogen bonds : bond 0.02660 ( 958) hydrogen bonds : angle 3.75452 ( 2802) *********************** 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 338 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 295 time to evaluate : 0.810 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 251 LYS cc_start: 0.9216 (mmmm) cc_final: 0.9004 (tppt) REVERT: A 368 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8088 (mp10) REVERT: A 398 THR cc_start: 0.9613 (m) cc_final: 0.9251 (p) REVERT: A 422 GLN cc_start: 0.8056 (tp40) cc_final: 0.7503 (tp40) REVERT: B 180 GLN cc_start: 0.8816 (mt0) cc_final: 0.8526 (mm110) REVERT: B 187 ARG cc_start: 0.8665 (mtm110) cc_final: 0.8156 (mtm110) REVERT: B 191 GLN cc_start: 0.8488 (tt0) cc_final: 0.8166 (tt0) REVERT: B 326 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8542 (ttp-170) REVERT: B 347 ARG cc_start: 0.8910 (mtm-85) cc_final: 0.8590 (mtt-85) REVERT: B 410 LYS cc_start: 0.9398 (mttt) cc_final: 0.9115 (mtmt) REVERT: C 162 ASP cc_start: 0.8127 (t0) cc_final: 0.7911 (m-30) REVERT: C 278 VAL cc_start: 0.8705 (t) cc_final: 0.8455 (p) REVERT: C 306 THR cc_start: 0.9212 (OUTLIER) cc_final: 0.8982 (p) REVERT: C 338 MET cc_start: 0.9105 (tpp) cc_final: 0.8795 (tpp) REVERT: C 339 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8570 (ttm-80) REVERT: C 340 ASP cc_start: 0.8722 (m-30) cc_final: 0.8519 (m-30) REVERT: C 359 ARG cc_start: 0.9220 (ptp90) cc_final: 0.9014 (ptm160) REVERT: D 251 LYS cc_start: 0.9247 (mmmm) cc_final: 0.8998 (tppt) REVERT: D 324 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7761 (tm-30) REVERT: E 180 GLN cc_start: 0.8788 (mt0) cc_final: 0.8495 (mm110) REVERT: E 193 MET cc_start: 0.8925 (tpp) cc_final: 0.8635 (tmm) REVERT: E 197 GLN cc_start: 0.9337 (mt0) cc_final: 0.9062 (mp10) REVERT: E 326 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8559 (ttp-170) REVERT: E 347 ARG cc_start: 0.8831 (mtm-85) cc_final: 0.8607 (mtt-85) REVERT: F 337 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8339 (p) REVERT: F 339 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8551 (ttm-80) REVERT: F 351 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8411 (mm-30) REVERT: F 489 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8828 (pp) REVERT: F 491 ARG cc_start: 0.9100 (mmm160) cc_final: 0.8764 (mmm160) REVERT: F 497 LEU cc_start: 0.9196 (tp) cc_final: 0.8891 (tt) outliers start: 43 outliers final: 26 residues processed: 329 average time/residue: 0.2017 time to fit residues: 91.4995 Evaluate side-chains 284 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 250 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 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 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 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 338 MET 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 326 ARG Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain F residue 251 LYS Chi-restraints excluded: chain F residue 253 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 193 optimal weight: 10.0000 chunk 248 optimal weight: 50.0000 chunk 160 optimal weight: 7.9990 chunk 174 optimal weight: 10.0000 chunk 224 optimal weight: 6.9990 chunk 148 optimal weight: 8.9990 chunk 71 optimal weight: 30.0000 chunk 79 optimal weight: 6.9990 chunk 204 optimal weight: 10.0000 chunk 234 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.094644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.073387 restraints weight = 42871.260| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.28 r_work: 0.3025 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18730 Z= 0.223 Angle : 0.618 10.021 25456 Z= 0.303 Chirality : 0.046 0.166 3018 Planarity : 0.005 0.062 3366 Dihedral : 6.522 163.550 2869 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.77 % Allowed : 16.65 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.17), residues: 2520 helix: 2.06 (0.16), residues: 1088 sheet: -0.97 (0.22), residues: 518 loop : 0.06 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 206 TYR 0.018 0.002 TYR E 402 PHE 0.031 0.001 PHE E 364 TRP 0.009 0.001 TRP C 481 HIS 0.003 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00517 (18730) covalent geometry : angle 0.61759 (25456) hydrogen bonds : bond 0.02992 ( 958) hydrogen bonds : angle 3.90781 ( 2802) *********************** 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 315 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 266 time to evaluate : 0.801 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: 0.8759 (OUTLIER) cc_final: 0.8127 (mp10) REVERT: B 187 ARG cc_start: 0.8701 (mtm110) cc_final: 0.8468 (mtm180) REVERT: B 193 MET cc_start: 0.9339 (mmm) cc_final: 0.9094 (tmm) REVERT: B 326 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8546 (ttp-170) REVERT: B 347 ARG cc_start: 0.8968 (mtm-85) cc_final: 0.8646 (mtt-85) REVERT: B 410 LYS cc_start: 0.9417 (mttt) cc_final: 0.9134 (mtmt) REVERT: C 162 ASP cc_start: 0.8185 (t0) cc_final: 0.7915 (m-30) REVERT: C 306 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.8914 (p) REVERT: C 339 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8581 (ttm-80) REVERT: C 340 ASP cc_start: 0.8799 (m-30) cc_final: 0.8591 (m-30) REVERT: C 491 ARG cc_start: 0.9023 (mmm160) cc_final: 0.8738 (mmm160) REVERT: D 251 LYS cc_start: 0.9278 (mmmm) cc_final: 0.9077 (tppt) REVERT: D 324 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7761 (tm-30) REVERT: D 368 GLN cc_start: 0.8922 (mm-40) cc_final: 0.8655 (mp10) REVERT: D 410 LYS cc_start: 0.9300 (mptt) cc_final: 0.9031 (mmtm) REVERT: E 180 GLN cc_start: 0.8817 (mt0) cc_final: 0.8501 (mm110) REVERT: E 187 ARG cc_start: 0.8671 (mtm180) cc_final: 0.8182 (mtm180) REVERT: E 326 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8591 (ttp-170) REVERT: E 347 ARG cc_start: 0.8886 (mtm-85) cc_final: 0.8641 (mtt-85) REVERT: F 339 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8530 (ttm-80) REVERT: F 489 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8835 (pp) REVERT: F 497 LEU cc_start: 0.9204 (tp) cc_final: 0.8888 (tt) outliers start: 49 outliers final: 36 residues processed: 303 average time/residue: 0.2008 time to fit residues: 84.2657 Evaluate side-chains 295 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 252 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 269 VAL 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 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 337 THR Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 269 VAL 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 338 MET Chi-restraints excluded: chain D residue 402 TYR 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 34 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 230 optimal weight: 40.0000 chunk 214 optimal weight: 8.9990 chunk 164 optimal weight: 40.0000 chunk 110 optimal weight: 7.9990 chunk 225 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 186 optimal weight: 7.9990 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 314 GLN ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN B 450 GLN ** 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 = 0.3596 r_free = 0.3596 target = 0.095345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.074034 restraints weight = 42307.969| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.26 r_work: 0.3035 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18730 Z= 0.180 Angle : 0.600 9.407 25456 Z= 0.294 Chirality : 0.045 0.163 3018 Planarity : 0.005 0.047 3366 Dihedral : 6.534 163.028 2869 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.48 % Allowed : 17.33 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.17), residues: 2520 helix: 2.04 (0.16), residues: 1088 sheet: -0.99 (0.22), residues: 518 loop : 0.03 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 206 TYR 0.016 0.002 TYR E 148 PHE 0.030 0.001 PHE A 243 TRP 0.009 0.001 TRP C 481 HIS 0.003 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00418 (18730) covalent geometry : angle 0.60035 (25456) hydrogen bonds : bond 0.02821 ( 958) hydrogen bonds : angle 3.85540 ( 2802) *********************** 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 312 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 268 time to evaluate : 0.668 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 206 ARG cc_start: 0.8232 (ttp80) cc_final: 0.7978 (ttp80) REVERT: A 368 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8097 (mp10) REVERT: A 410 LYS cc_start: 0.9164 (mmtm) cc_final: 0.8912 (mmtm) REVERT: B 187 ARG cc_start: 0.8705 (mtm110) cc_final: 0.8460 (mtm180) REVERT: B 193 MET cc_start: 0.9343 (mmm) cc_final: 0.9051 (tmm) REVERT: B 326 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8518 (ttp-170) REVERT: B 347 ARG cc_start: 0.8960 (mtm-85) cc_final: 0.8630 (mtt-85) REVERT: B 498 ASP cc_start: 0.8999 (t0) cc_final: 0.8765 (t0) REVERT: C 162 ASP cc_start: 0.8157 (t0) cc_final: 0.7892 (m-30) REVERT: C 278 VAL cc_start: 0.8745 (t) cc_final: 0.8455 (p) REVERT: C 306 THR cc_start: 0.9238 (OUTLIER) cc_final: 0.8917 (p) REVERT: C 339 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8507 (ttm-80) REVERT: C 340 ASP cc_start: 0.8776 (m-30) cc_final: 0.8560 (m-30) REVERT: C 491 ARG cc_start: 0.9025 (mmm160) cc_final: 0.8738 (mmm160) REVERT: D 324 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7745 (tm-30) REVERT: E 180 GLN cc_start: 0.8801 (mt0) cc_final: 0.8490 (mm110) REVERT: E 187 ARG cc_start: 0.8666 (mtm180) cc_final: 0.8039 (mtm110) REVERT: E 193 MET cc_start: 0.9315 (tmm) cc_final: 0.8805 (tpp) REVERT: E 197 GLN cc_start: 0.9322 (mt0) cc_final: 0.9077 (mp10) REVERT: E 326 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8556 (ttp-170) REVERT: E 347 ARG cc_start: 0.8876 (mtm-85) cc_final: 0.8666 (mtt-85) REVERT: F 339 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8496 (ttm-80) REVERT: F 489 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8838 (pp) REVERT: F 491 ARG cc_start: 0.9106 (mmm160) cc_final: 0.8745 (mmm160) REVERT: F 497 LEU cc_start: 0.9183 (tp) cc_final: 0.8864 (tt) outliers start: 44 outliers final: 32 residues processed: 301 average time/residue: 0.1966 time to fit residues: 82.6682 Evaluate side-chains 303 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 264 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 402 TYR 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 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 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 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 214 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 112 optimal weight: 5.9990 chunk 174 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 86 optimal weight: 0.4980 chunk 95 optimal weight: 5.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- 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 368 GLN ** E 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.096493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.075293 restraints weight = 42269.357| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 3.27 r_work: 0.3067 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18730 Z= 0.136 Angle : 0.600 8.859 25456 Z= 0.291 Chirality : 0.045 0.151 3018 Planarity : 0.004 0.047 3366 Dihedral : 6.421 160.642 2869 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.43 % Allowed : 17.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.17), residues: 2520 helix: 2.08 (0.16), residues: 1088 sheet: -0.95 (0.22), residues: 518 loop : 0.03 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 206 TYR 0.012 0.001 TYR B 148 PHE 0.020 0.001 PHE E 364 TRP 0.005 0.001 TRP C 481 HIS 0.002 0.001 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00318 (18730) covalent geometry : angle 0.59969 (25456) hydrogen bonds : bond 0.02680 ( 958) hydrogen bonds : angle 3.74807 ( 2802) *********************** 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 329 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 286 time to evaluate : 0.792 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 206 ARG cc_start: 0.8305 (ttp80) cc_final: 0.8050 (ttp80) REVERT: A 364 PHE cc_start: 0.9358 (t80) cc_final: 0.8601 (t80) REVERT: A 368 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.7865 (mp10) REVERT: B 174 GLU cc_start: 0.8533 (tt0) cc_final: 0.8288 (tt0) REVERT: B 326 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8527 (ttp-170) REVERT: B 347 ARG cc_start: 0.8926 (mtm-85) cc_final: 0.8593 (mtt-85) REVERT: B 498 ASP cc_start: 0.9008 (t0) cc_final: 0.8769 (t0) REVERT: C 162 ASP cc_start: 0.8118 (t0) cc_final: 0.7876 (m-30) REVERT: C 278 VAL cc_start: 0.8713 (t) cc_final: 0.8480 (p) REVERT: C 306 THR cc_start: 0.9213 (OUTLIER) cc_final: 0.8915 (p) REVERT: C 339 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8493 (ttm-80) REVERT: C 340 ASP cc_start: 0.8730 (m-30) cc_final: 0.8513 (m-30) REVERT: C 491 ARG cc_start: 0.9025 (mmm160) cc_final: 0.8741 (mmm160) REVERT: D 250 MET cc_start: 0.8422 (tpt) cc_final: 0.7977 (tpt) REVERT: D 324 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7739 (tm-30) REVERT: E 180 GLN cc_start: 0.8786 (mt0) cc_final: 0.8485 (mm110) REVERT: E 187 ARG cc_start: 0.8652 (mtm180) cc_final: 0.8005 (mtm110) REVERT: E 193 MET cc_start: 0.9304 (tmm) cc_final: 0.8800 (tpp) REVERT: E 197 GLN cc_start: 0.9285 (mt0) cc_final: 0.9056 (mp10) REVERT: E 326 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8557 (ttp-170) REVERT: E 347 ARG cc_start: 0.8847 (mtm-85) cc_final: 0.8561 (mtt-85) REVERT: F 338 MET cc_start: 0.9113 (tpp) cc_final: 0.8875 (tpp) REVERT: F 339 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8575 (ttm-80) REVERT: F 489 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8840 (pp) REVERT: F 491 ARG cc_start: 0.9098 (mmm160) cc_final: 0.8731 (mmm160) REVERT: F 497 LEU cc_start: 0.9165 (tp) cc_final: 0.8847 (tt) outliers start: 43 outliers final: 28 residues processed: 316 average time/residue: 0.1939 time to fit residues: 85.6429 Evaluate side-chains 307 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 272 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 402 TYR 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 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 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 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 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 111 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 246 optimal weight: 0.5980 chunk 32 optimal weight: 0.0980 chunk 11 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 205 optimal weight: 20.0000 chunk 34 optimal weight: 0.9990 chunk 190 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.097576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.076363 restraints weight = 42097.148| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.27 r_work: 0.3080 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 18730 Z= 0.120 Angle : 0.595 8.191 25456 Z= 0.291 Chirality : 0.045 0.150 3018 Planarity : 0.004 0.048 3366 Dihedral : 6.287 158.358 2869 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.20 % Allowed : 18.06 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.17), residues: 2520 helix: 2.14 (0.16), residues: 1084 sheet: -0.92 (0.22), residues: 518 loop : 0.04 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 491 TYR 0.014 0.001 TYR C 148 PHE 0.031 0.001 PHE A 243 TRP 0.005 0.001 TRP C 481 HIS 0.002 0.000 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00282 (18730) covalent geometry : angle 0.59495 (25456) hydrogen bonds : bond 0.02617 ( 958) hydrogen bonds : angle 3.67369 ( 2802) ********************** 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 332 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 293 time to evaluate : 0.831 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: A 206 ARG cc_start: 0.8304 (ttp80) cc_final: 0.8050 (ttp80) REVERT: A 324 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7739 (pp20) REVERT: A 364 PHE cc_start: 0.9367 (t80) cc_final: 0.8652 (t80) REVERT: A 368 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.7849 (mp10) REVERT: B 174 GLU cc_start: 0.8419 (tt0) cc_final: 0.8206 (tt0) REVERT: B 326 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8532 (ttp-170) REVERT: B 347 ARG cc_start: 0.8890 (mtm-85) cc_final: 0.8542 (mtt-85) REVERT: B 498 ASP cc_start: 0.8990 (t0) cc_final: 0.8712 (t0) REVERT: C 162 ASP cc_start: 0.8093 (t0) cc_final: 0.7865 (m-30) REVERT: C 306 THR cc_start: 0.9199 (OUTLIER) cc_final: 0.8882 (p) REVERT: C 338 MET cc_start: 0.9132 (tpp) cc_final: 0.8865 (tpp) REVERT: C 339 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8410 (ttm-80) REVERT: C 491 ARG cc_start: 0.9049 (mmm160) cc_final: 0.8761 (mmm160) REVERT: D 250 MET cc_start: 0.8429 (tpt) cc_final: 0.8083 (tpt) REVERT: D 294 MET cc_start: 0.9137 (tpt) cc_final: 0.8910 (tpt) REVERT: D 324 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7780 (pp20) REVERT: D 362 GLU cc_start: 0.8639 (pm20) cc_final: 0.8384 (pm20) REVERT: D 398 THR cc_start: 0.9564 (m) cc_final: 0.9214 (p) REVERT: E 180 GLN cc_start: 0.8791 (mt0) cc_final: 0.8497 (mm110) REVERT: E 187 ARG cc_start: 0.8616 (mtm180) cc_final: 0.7924 (mtm110) REVERT: E 193 MET cc_start: 0.9297 (tmm) cc_final: 0.8821 (tpp) REVERT: E 197 GLN cc_start: 0.9279 (mt0) cc_final: 0.9046 (mp10) REVERT: E 326 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8564 (ttp-170) REVERT: E 347 ARG cc_start: 0.8838 (mtm-85) cc_final: 0.8545 (mtt-85) REVERT: F 339 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8459 (ttm-80) REVERT: F 491 ARG cc_start: 0.9101 (mmm160) cc_final: 0.8743 (mmm160) outliers start: 39 outliers final: 27 residues processed: 320 average time/residue: 0.1932 time to fit residues: 86.5483 Evaluate side-chains 304 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 271 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 402 TYR 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 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 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 164 optimal weight: 50.0000 chunk 69 optimal weight: 7.9990 chunk 231 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 167 optimal weight: 8.9990 chunk 230 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 118 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- 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 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3632 r_free = 0.3632 target = 0.098267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.077019 restraints weight = 42586.920| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.33 r_work: 0.3081 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18730 Z= 0.130 Angle : 0.616 8.364 25456 Z= 0.299 Chirality : 0.045 0.179 3018 Planarity : 0.005 0.073 3366 Dihedral : 6.222 157.781 2869 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.14 % Allowed : 18.57 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.17), residues: 2520 helix: 2.14 (0.16), residues: 1088 sheet: -0.90 (0.22), residues: 518 loop : 0.01 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 477 TYR 0.010 0.001 TYR B 148 PHE 0.032 0.001 PHE A 243 TRP 0.011 0.001 TRP C 481 HIS 0.002 0.001 HIS B 319 Details of bonding type rmsd covalent geometry : bond 0.00307 (18730) covalent geometry : angle 0.61620 (25456) hydrogen bonds : bond 0.02615 ( 958) hydrogen bonds : angle 3.64739 ( 2802) =============================================================================== Job complete usr+sys time: 4794.73 seconds wall clock time: 82 minutes 56.19 seconds (4976.19 seconds total)