Starting phenix.real_space_refine on Fri May 23 11:12:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9evb_19997/05_2025/9evb_19997.cif Found real_map, /net/cci-nas-00/data/ceres_data/9evb_19997/05_2025/9evb_19997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9evb_19997/05_2025/9evb_19997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9evb_19997/05_2025/9evb_19997.map" model { file = "/net/cci-nas-00/data/ceres_data/9evb_19997/05_2025/9evb_19997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9evb_19997/05_2025/9evb_19997.cif" } resolution = 2.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.085 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: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 15475 2.51 5 N 3870 2.21 5 O 4690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24090 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4709 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 572} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 68 Unusual residues: {'C14': 1, 'D10': 3, 'OCT': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 68 Unusual residues: {'C14': 1, 'D10': 3, 'OCT': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 68 Unusual residues: {'C14': 1, 'D10': 3, 'OCT': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 68 Unusual residues: {'C14': 1, 'D10': 3, 'OCT': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "E" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 68 Unusual residues: {'C14': 1, 'D10': 3, 'OCT': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "C" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "D" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Restraints were copied for chains: B, C, D, E Time building chain proxies: 13.78, per 1000 atoms: 0.57 Number of scatterers: 24090 At special positions: 0 Unit cell: (146.427, 143.042, 154.045, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 4690 8.00 N 3870 7.00 C 15475 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 371 " - pdb=" SG CYS A 373 " distance=2.04 Simple disulfide: pdb=" SG CYS B 371 " - pdb=" SG CYS B 373 " distance=2.04 Simple disulfide: pdb=" SG CYS C 371 " - pdb=" SG CYS C 373 " distance=2.04 Simple disulfide: pdb=" SG CYS D 371 " - pdb=" SG CYS D 373 " distance=2.04 Simple disulfide: pdb=" SG CYS E 371 " - pdb=" SG CYS E 373 " distance=2.04 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: 6.42 Conformation dependent library (CDL) restraints added in 2.9 seconds 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5530 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 30 sheets defined 28.0% alpha, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.81 Creating SS restraints... Processing helix chain 'A' and resid 88 through 98 Processing helix chain 'A' and resid 106 through 118 Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 196 through 199 Processing helix chain 'A' and resid 362 through 365 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 382 through 391 Processing helix chain 'A' and resid 514 through 536 removed outlier: 3.970A pdb=" N TYR A 518 " --> pdb=" O ASN A 514 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N VAL A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Proline residue: A 525 - end of helix removed outlier: 3.780A pdb=" N ILE A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 539 No H-bonds generated for 'chain 'A' and resid 537 through 539' Processing helix chain 'A' and resid 541 through 564 removed outlier: 3.603A pdb=" N LEU A 554 " --> pdb=" O SER A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 567 No H-bonds generated for 'chain 'A' and resid 565 through 567' Processing helix chain 'A' and resid 574 through 604 removed outlier: 3.518A pdb=" N VAL A 591 " --> pdb=" O THR A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 636 removed outlier: 3.503A pdb=" N ALA A 609 " --> pdb=" O LYS A 605 " (cutoff:3.500A) Proline residue: A 621 - end of helix Processing helix chain 'B' and resid 88 through 98 Processing helix chain 'B' and resid 106 through 118 Processing helix chain 'B' and resid 178 through 182 Processing helix chain 'B' and resid 196 through 199 Processing helix chain 'B' and resid 362 through 365 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 382 through 391 Processing helix chain 'B' and resid 514 through 536 removed outlier: 3.970A pdb=" N TYR B 518 " --> pdb=" O ASN B 514 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N VAL B 524 " --> pdb=" O LEU B 520 " (cutoff:3.500A) Proline residue: B 525 - end of helix removed outlier: 3.780A pdb=" N ILE B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 539 No H-bonds generated for 'chain 'B' and resid 537 through 539' Processing helix chain 'B' and resid 541 through 564 removed outlier: 3.603A pdb=" N LEU B 554 " --> pdb=" O SER B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 567 No H-bonds generated for 'chain 'B' and resid 565 through 567' Processing helix chain 'B' and resid 574 through 604 removed outlier: 3.517A pdb=" N VAL B 591 " --> pdb=" O THR B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 636 removed outlier: 3.503A pdb=" N ALA B 609 " --> pdb=" O LYS B 605 " (cutoff:3.500A) Proline residue: B 621 - end of helix Processing helix chain 'C' and resid 88 through 98 Processing helix chain 'C' and resid 106 through 118 Processing helix chain 'C' and resid 178 through 182 Processing helix chain 'C' and resid 196 through 199 Processing helix chain 'C' and resid 362 through 365 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 382 through 391 Processing helix chain 'C' and resid 514 through 536 removed outlier: 3.970A pdb=" N TYR C 518 " --> pdb=" O ASN C 514 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N VAL C 524 " --> pdb=" O LEU C 520 " (cutoff:3.500A) Proline residue: C 525 - end of helix removed outlier: 3.780A pdb=" N ILE C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 539 No H-bonds generated for 'chain 'C' and resid 537 through 539' Processing helix chain 'C' and resid 541 through 564 removed outlier: 3.602A pdb=" N LEU C 554 " --> pdb=" O SER C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 567 No H-bonds generated for 'chain 'C' and resid 565 through 567' Processing helix chain 'C' and resid 574 through 604 removed outlier: 3.518A pdb=" N VAL C 591 " --> pdb=" O THR C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 636 removed outlier: 3.503A pdb=" N ALA C 609 " --> pdb=" O LYS C 605 " (cutoff:3.500A) Proline residue: C 621 - end of helix Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 106 through 118 Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 362 through 365 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'D' and resid 382 through 391 Processing helix chain 'D' and resid 514 through 536 removed outlier: 3.971A pdb=" N TYR D 518 " --> pdb=" O ASN D 514 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N VAL D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Proline residue: D 525 - end of helix removed outlier: 3.780A pdb=" N ILE D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 539 No H-bonds generated for 'chain 'D' and resid 537 through 539' Processing helix chain 'D' and resid 541 through 564 removed outlier: 3.602A pdb=" N LEU D 554 " --> pdb=" O SER D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 567 No H-bonds generated for 'chain 'D' and resid 565 through 567' Processing helix chain 'D' and resid 574 through 604 removed outlier: 3.517A pdb=" N VAL D 591 " --> pdb=" O THR D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 636 removed outlier: 3.503A pdb=" N ALA D 609 " --> pdb=" O LYS D 605 " (cutoff:3.500A) Proline residue: D 621 - end of helix Processing helix chain 'E' and resid 88 through 98 Processing helix chain 'E' and resid 106 through 118 Processing helix chain 'E' and resid 178 through 182 Processing helix chain 'E' and resid 196 through 199 Processing helix chain 'E' and resid 362 through 365 Processing helix chain 'E' and resid 367 through 371 Processing helix chain 'E' and resid 382 through 391 Processing helix chain 'E' and resid 514 through 536 removed outlier: 3.970A pdb=" N TYR E 518 " --> pdb=" O ASN E 514 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N VAL E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) Proline residue: E 525 - end of helix removed outlier: 3.780A pdb=" N ILE E 536 " --> pdb=" O VAL E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 539 No H-bonds generated for 'chain 'E' and resid 537 through 539' Processing helix chain 'E' and resid 541 through 564 removed outlier: 3.602A pdb=" N LEU E 554 " --> pdb=" O SER E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 567 No H-bonds generated for 'chain 'E' and resid 565 through 567' Processing helix chain 'E' and resid 574 through 604 removed outlier: 3.518A pdb=" N VAL E 591 " --> pdb=" O THR E 587 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 636 removed outlier: 3.503A pdb=" N ALA E 609 " --> pdb=" O LYS E 605 " (cutoff:3.500A) Proline residue: E 621 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 45 removed outlier: 3.618A pdb=" N GLY A 43 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A 168 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N SER A 167 " --> pdb=" O THR A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 122 removed outlier: 4.120A pdb=" N GLY A 120 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 79 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLY A 141 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP A 57 " --> pdb=" O GLY A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 204 through 212 removed outlier: 4.180A pdb=" N ALA A 298 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 218 through 222 removed outlier: 7.325A pdb=" N LEU A 247 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N PHE A 259 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU A 249 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 376 through 379 removed outlier: 4.324A pdb=" N GLN A 411 " --> pdb=" O PHE A 424 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE A 424 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE A 413 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER A 422 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL A 415 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG A 420 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 341 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL A 352 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE A 339 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N THR A 354 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ASP A 337 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N LYS A 356 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ALA A 335 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N SER A 358 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N GLY A 333 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N HIS A 360 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 9.428A pdb=" N THR A 331 " --> pdb=" O HIS A 360 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASP A 328 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASN A 464 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A 330 " --> pdb=" O ASN A 464 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE A 466 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL A 332 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 397 through 399 removed outlier: 5.041A pdb=" N SER A 503 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER A 486 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LYS A 512 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N VAL A 484 " --> pdb=" O LYS A 512 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 38 through 45 removed outlier: 3.618A pdb=" N GLY B 43 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE B 168 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N SER B 167 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 120 through 122 removed outlier: 4.121A pdb=" N GLY B 120 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 79 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLY B 141 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP B 57 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 204 through 212 removed outlier: 4.180A pdb=" N ALA B 298 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 218 through 222 removed outlier: 7.326A pdb=" N LEU B 247 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N PHE B 259 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU B 249 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 376 through 379 removed outlier: 4.323A pdb=" N GLN B 411 " --> pdb=" O PHE B 424 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE B 424 " --> pdb=" O GLN B 411 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE B 413 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER B 422 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL B 415 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG B 420 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY B 341 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL B 352 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE B 339 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N THR B 354 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ASP B 337 " --> pdb=" O THR B 354 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N LYS B 356 " --> pdb=" O ALA B 335 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ALA B 335 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N SER B 358 " --> pdb=" O GLY B 333 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N GLY B 333 " --> pdb=" O SER B 358 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N HIS B 360 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 9.428A pdb=" N THR B 331 " --> pdb=" O HIS B 360 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASP B 328 " --> pdb=" O ILE B 462 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASN B 464 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL B 330 " --> pdb=" O ASN B 464 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE B 466 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL B 332 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 397 through 399 removed outlier: 5.041A pdb=" N SER B 503 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER B 486 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LYS B 512 " --> pdb=" O VAL B 484 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N VAL B 484 " --> pdb=" O LYS B 512 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 38 through 45 removed outlier: 3.618A pdb=" N GLY C 43 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE C 168 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N SER C 167 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 120 through 122 removed outlier: 4.120A pdb=" N GLY C 120 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 79 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLY C 141 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP C 57 " --> pdb=" O GLY C 141 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 204 through 212 removed outlier: 4.180A pdb=" N ALA C 298 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 218 through 222 removed outlier: 7.325A pdb=" N LEU C 247 " --> pdb=" O PHE C 259 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N PHE C 259 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU C 249 " --> pdb=" O LEU C 257 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 376 through 379 removed outlier: 4.323A pdb=" N GLN C 411 " --> pdb=" O PHE C 424 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE C 424 " --> pdb=" O GLN C 411 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE C 413 " --> pdb=" O SER C 422 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N SER C 422 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL C 415 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG C 420 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY C 341 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL C 352 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE C 339 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N THR C 354 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ASP C 337 " --> pdb=" O THR C 354 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N LYS C 356 " --> pdb=" O ALA C 335 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ALA C 335 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N SER C 358 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N GLY C 333 " --> pdb=" O SER C 358 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N HIS C 360 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 9.428A pdb=" N THR C 331 " --> pdb=" O HIS C 360 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASP C 328 " --> pdb=" O ILE C 462 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASN C 464 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL C 330 " --> pdb=" O ASN C 464 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE C 466 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL C 332 " --> pdb=" O ILE C 466 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 397 through 399 removed outlier: 5.041A pdb=" N SER C 503 " --> pdb=" O LEU C 454 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER C 486 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LYS C 512 " --> pdb=" O VAL C 484 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N VAL C 484 " --> pdb=" O LYS C 512 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 38 through 45 removed outlier: 3.618A pdb=" N GLY D 43 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE D 168 " --> pdb=" O GLY D 43 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N SER D 167 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 120 through 122 removed outlier: 4.121A pdb=" N GLY D 120 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D 79 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLY D 141 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP D 57 " --> pdb=" O GLY D 141 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 204 through 212 removed outlier: 4.180A pdb=" N ALA D 298 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 218 through 222 removed outlier: 7.326A pdb=" N LEU D 247 " --> pdb=" O PHE D 259 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N PHE D 259 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU D 249 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 376 through 379 removed outlier: 4.323A pdb=" N GLN D 411 " --> pdb=" O PHE D 424 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N PHE D 424 " --> pdb=" O GLN D 411 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE D 413 " --> pdb=" O SER D 422 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER D 422 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL D 415 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG D 420 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY D 341 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL D 352 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE D 339 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N THR D 354 " --> pdb=" O ASP D 337 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ASP D 337 " --> pdb=" O THR D 354 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N LYS D 356 " --> pdb=" O ALA D 335 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ALA D 335 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N SER D 358 " --> pdb=" O GLY D 333 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N GLY D 333 " --> pdb=" O SER D 358 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N HIS D 360 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 9.427A pdb=" N THR D 331 " --> pdb=" O HIS D 360 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASP D 328 " --> pdb=" O ILE D 462 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASN D 464 " --> pdb=" O ASP D 328 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL D 330 " --> pdb=" O ASN D 464 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE D 466 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL D 332 " --> pdb=" O ILE D 466 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 397 through 399 removed outlier: 5.041A pdb=" N SER D 503 " --> pdb=" O LEU D 454 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER D 486 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LYS D 512 " --> pdb=" O VAL D 484 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N VAL D 484 " --> pdb=" O LYS D 512 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 38 through 45 removed outlier: 3.617A pdb=" N GLY E 43 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE E 168 " --> pdb=" O GLY E 43 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N SER E 167 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 120 through 122 removed outlier: 4.121A pdb=" N GLY E 120 " --> pdb=" O ILE E 81 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL E 79 " --> pdb=" O ASP E 122 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLY E 141 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP E 57 " --> pdb=" O GLY E 141 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 204 through 212 removed outlier: 4.180A pdb=" N ALA E 298 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 218 through 222 removed outlier: 7.326A pdb=" N LEU E 247 " --> pdb=" O PHE E 259 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N PHE E 259 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU E 249 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 376 through 379 removed outlier: 4.324A pdb=" N GLN E 411 " --> pdb=" O PHE E 424 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE E 424 " --> pdb=" O GLN E 411 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE E 413 " --> pdb=" O SER E 422 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N SER E 422 " --> pdb=" O ILE E 413 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL E 415 " --> pdb=" O ARG E 420 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG E 420 " --> pdb=" O VAL E 415 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY E 341 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL E 352 " --> pdb=" O ILE E 339 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE E 339 " --> pdb=" O VAL E 352 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N THR E 354 " --> pdb=" O ASP E 337 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ASP E 337 " --> pdb=" O THR E 354 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N LYS E 356 " --> pdb=" O ALA E 335 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ALA E 335 " --> pdb=" O LYS E 356 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N SER E 358 " --> pdb=" O GLY E 333 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N GLY E 333 " --> pdb=" O SER E 358 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N HIS E 360 " --> pdb=" O THR E 331 " (cutoff:3.500A) removed outlier: 9.427A pdb=" N THR E 331 " --> pdb=" O HIS E 360 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASP E 328 " --> pdb=" O ILE E 462 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASN E 464 " --> pdb=" O ASP E 328 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL E 330 " --> pdb=" O ASN E 464 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE E 466 " --> pdb=" O VAL E 330 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL E 332 " --> pdb=" O ILE E 466 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 397 through 399 removed outlier: 5.041A pdb=" N SER E 503 " --> pdb=" O LEU E 454 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER E 486 " --> pdb=" O LEU E 510 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LYS E 512 " --> pdb=" O VAL E 484 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N VAL E 484 " --> pdb=" O LYS E 512 " (cutoff:3.500A) 1110 hydrogen bonds defined for protein. 3075 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: 9.40 Time building geometry restraints manager: 7.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6947 1.34 - 1.46: 5454 1.46 - 1.58: 11909 1.58 - 1.71: 0 1.71 - 1.83: 80 Bond restraints: 24390 Sorted by residual: bond pdb=" C GLU D 490 " pdb=" N ILE D 491 " ideal model delta sigma weight residual 1.330 1.356 -0.026 1.26e-02 6.30e+03 4.25e+00 bond pdb=" C GLU E 490 " pdb=" N ILE E 491 " ideal model delta sigma weight residual 1.330 1.356 -0.026 1.26e-02 6.30e+03 4.19e+00 bond pdb=" C GLU A 490 " pdb=" N ILE A 491 " ideal model delta sigma weight residual 1.330 1.356 -0.026 1.26e-02 6.30e+03 4.14e+00 bond pdb=" C GLU C 490 " pdb=" N ILE C 491 " ideal model delta sigma weight residual 1.330 1.356 -0.025 1.26e-02 6.30e+03 4.02e+00 bond pdb=" C GLU B 490 " pdb=" N ILE B 491 " ideal model delta sigma weight residual 1.330 1.356 -0.025 1.26e-02 6.30e+03 3.98e+00 ... (remaining 24385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 30653 1.88 - 3.77: 1993 3.77 - 5.65: 352 5.65 - 7.53: 52 7.53 - 9.41: 10 Bond angle restraints: 33060 Sorted by residual: angle pdb=" N ALA B 433 " pdb=" CA ALA B 433 " pdb=" C ALA B 433 " ideal model delta sigma weight residual 108.76 113.82 -5.06 1.44e+00 4.82e-01 1.23e+01 angle pdb=" N ALA A 433 " pdb=" CA ALA A 433 " pdb=" C ALA A 433 " ideal model delta sigma weight residual 108.76 113.77 -5.01 1.44e+00 4.82e-01 1.21e+01 angle pdb=" N ALA D 433 " pdb=" CA ALA D 433 " pdb=" C ALA D 433 " ideal model delta sigma weight residual 108.76 113.77 -5.01 1.44e+00 4.82e-01 1.21e+01 angle pdb=" N ALA C 433 " pdb=" CA ALA C 433 " pdb=" C ALA C 433 " ideal model delta sigma weight residual 108.76 113.76 -5.00 1.44e+00 4.82e-01 1.20e+01 angle pdb=" N ALA E 433 " pdb=" CA ALA E 433 " pdb=" C ALA E 433 " ideal model delta sigma weight residual 108.76 113.75 -4.99 1.44e+00 4.82e-01 1.20e+01 ... (remaining 33055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 13518 17.94 - 35.87: 731 35.87 - 53.81: 141 53.81 - 71.74: 15 71.74 - 89.68: 10 Dihedral angle restraints: 14415 sinusoidal: 5780 harmonic: 8635 Sorted by residual: dihedral pdb=" CA GLU C 497 " pdb=" C GLU C 497 " pdb=" N ARG C 498 " pdb=" CA ARG C 498 " ideal model delta harmonic sigma weight residual -180.00 -157.19 -22.81 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA GLU B 497 " pdb=" C GLU B 497 " pdb=" N ARG B 498 " pdb=" CA ARG B 498 " ideal model delta harmonic sigma weight residual -180.00 -157.20 -22.80 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA GLU A 497 " pdb=" C GLU A 497 " pdb=" N ARG A 498 " pdb=" CA ARG A 498 " ideal model delta harmonic sigma weight residual 180.00 -157.21 -22.79 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 14412 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2870 0.068 - 0.136: 706 0.136 - 0.204: 109 0.204 - 0.272: 10 0.272 - 0.340: 20 Chirality restraints: 3715 Sorted by residual: chirality pdb=" CG LEU B 325 " pdb=" CB LEU B 325 " pdb=" CD1 LEU B 325 " pdb=" CD2 LEU B 325 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CG LEU D 325 " pdb=" CB LEU D 325 " pdb=" CD1 LEU D 325 " pdb=" CD2 LEU D 325 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CG LEU E 325 " pdb=" CB LEU E 325 " pdb=" CD1 LEU E 325 " pdb=" CD2 LEU E 325 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.87e+00 ... (remaining 3712 not shown) Planarity restraints: 4275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 65 " -0.006 2.00e-02 2.50e+03 3.17e-02 2.01e+01 pdb=" CG TYR E 65 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR E 65 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR E 65 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR E 65 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR E 65 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR E 65 " -0.060 2.00e-02 2.50e+03 pdb=" OH TYR E 65 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 65 " -0.006 2.00e-02 2.50e+03 3.16e-02 2.00e+01 pdb=" CG TYR B 65 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR B 65 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 65 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 65 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR B 65 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR B 65 " -0.060 2.00e-02 2.50e+03 pdb=" OH TYR B 65 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 65 " 0.006 2.00e-02 2.50e+03 3.16e-02 2.00e+01 pdb=" CG TYR C 65 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR C 65 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR C 65 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 65 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR C 65 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR C 65 " 0.059 2.00e-02 2.50e+03 pdb=" OH TYR C 65 " -0.051 2.00e-02 2.50e+03 ... (remaining 4272 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1726 2.74 - 3.28: 21948 3.28 - 3.82: 37587 3.82 - 4.36: 45933 4.36 - 4.90: 79108 Nonbonded interactions: 186302 Sorted by model distance: nonbonded pdb=" O LEU D 539 " pdb=" O HOH D1001 " model vdw 2.200 3.040 nonbonded pdb=" O LEU B 539 " pdb=" O HOH B1001 " model vdw 2.200 3.040 nonbonded pdb=" O LEU E 539 " pdb=" O HOH E 801 " model vdw 2.200 3.040 nonbonded pdb=" O LEU A 539 " pdb=" O HOH A1001 " model vdw 2.200 3.040 nonbonded pdb=" O LEU C 539 " pdb=" O HOH C1001 " model vdw 2.200 3.040 ... (remaining 186297 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: 0.15 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 37 through 637 or resid 901 through 902 or resid 904)) selection = (chain 'B' and (resid 37 through 637 or resid 901 through 902 or resid 904)) selection = (chain 'C' and (resid 37 through 637 or resid 901 through 902 or resid 904)) selection = (chain 'D' and (resid 37 through 637 or resid 901 through 902 or resid 904)) selection = (chain 'E' and (resid 37 through 637 or resid 701 through 702 or resid 704)) } 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: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.090 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 53.420 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 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 : 0.006 0.046 24395 Z= 0.315 Angle : 1.045 9.414 33070 Z= 0.564 Chirality : 0.063 0.340 3715 Planarity : 0.011 0.091 4275 Dihedral : 11.684 89.678 8870 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.67 % Favored : 95.99 % Rotamer: Outliers : 1.36 % Allowed : 4.48 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 2995 helix: 0.72 (0.18), residues: 715 sheet: 0.77 (0.16), residues: 950 loop : -1.02 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.008 TRP B 482 HIS 0.019 0.006 HIS D 144 PHE 0.031 0.007 PHE D 399 TYR 0.060 0.007 TYR B 65 ARG 0.029 0.003 ARG D 312 Details of bonding type rmsd hydrogen bonds : bond 0.17533 ( 1110) hydrogen bonds : angle 6.67105 ( 3075) SS BOND : bond 0.00511 ( 5) SS BOND : angle 2.50943 ( 10) covalent geometry : bond 0.00643 (24390) covalent geometry : angle 1.04469 (33060) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 303 time to evaluate : 2.580 Fit side-chains revert: symmetry clash REVERT: A 223 THR cc_start: 0.6752 (m) cc_final: 0.6429 (p) REVERT: A 356 LYS cc_start: 0.8979 (tttt) cc_final: 0.8689 (tmtm) REVERT: A 374 THR cc_start: 0.7471 (m) cc_final: 0.6934 (p) REVERT: A 376 LYS cc_start: 0.7596 (tttt) cc_final: 0.6917 (tptt) REVERT: A 432 GLN cc_start: 0.8451 (mt0) cc_final: 0.8096 (mm110) REVERT: A 435 ASP cc_start: 0.7673 (m-30) cc_final: 0.6892 (p0) REVERT: A 498 ARG cc_start: 0.5907 (OUTLIER) cc_final: 0.5401 (ptt-90) REVERT: A 547 GLU cc_start: 0.8340 (tt0) cc_final: 0.8133 (tm-30) REVERT: A 577 ASP cc_start: 0.8394 (m-30) cc_final: 0.8034 (m-30) REVERT: A 615 TRP cc_start: 0.8191 (m-10) cc_final: 0.7664 (m100) REVERT: B 82 MET cc_start: 0.1996 (ptp) cc_final: 0.0622 (mmp) REVERT: B 206 GLN cc_start: 0.5790 (tt0) cc_final: 0.5558 (tt0) REVERT: B 347 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7772 (mt-10) REVERT: B 356 LYS cc_start: 0.8945 (tttt) cc_final: 0.8680 (tmtm) REVERT: B 374 THR cc_start: 0.7359 (m) cc_final: 0.6796 (p) REVERT: B 376 LYS cc_start: 0.7548 (tttt) cc_final: 0.6793 (tptt) REVERT: B 432 GLN cc_start: 0.8262 (mt0) cc_final: 0.7956 (mm-40) REVERT: B 435 ASP cc_start: 0.7928 (m-30) cc_final: 0.7007 (p0) REVERT: B 498 ARG cc_start: 0.5691 (OUTLIER) cc_final: 0.5204 (ptt90) REVERT: B 577 ASP cc_start: 0.8333 (m-30) cc_final: 0.8016 (m-30) REVERT: C 347 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7762 (mt-10) REVERT: C 356 LYS cc_start: 0.8994 (tttt) cc_final: 0.8708 (tmtm) REVERT: C 374 THR cc_start: 0.7452 (m) cc_final: 0.6970 (p) REVERT: C 376 LYS cc_start: 0.7600 (tttt) cc_final: 0.6901 (tptt) REVERT: C 435 ASP cc_start: 0.7851 (m-30) cc_final: 0.6956 (p0) REVERT: C 498 ARG cc_start: 0.5813 (OUTLIER) cc_final: 0.5337 (ptt90) REVERT: C 577 ASP cc_start: 0.8378 (m-30) cc_final: 0.8053 (m-30) REVERT: C 615 TRP cc_start: 0.7996 (m-10) cc_final: 0.7524 (m100) REVERT: D 82 MET cc_start: 0.1853 (ptp) cc_final: 0.0677 (mmp) REVERT: D 206 GLN cc_start: 0.6073 (tt0) cc_final: 0.5767 (tt0) REVERT: D 347 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7534 (mt-10) REVERT: D 356 LYS cc_start: 0.8962 (tttt) cc_final: 0.8683 (tmtm) REVERT: D 374 THR cc_start: 0.7526 (m) cc_final: 0.7002 (p) REVERT: D 376 LYS cc_start: 0.7602 (tttt) cc_final: 0.6904 (tptt) REVERT: D 435 ASP cc_start: 0.7887 (m-30) cc_final: 0.6930 (p0) REVERT: D 498 ARG cc_start: 0.5617 (OUTLIER) cc_final: 0.5252 (ptt90) REVERT: D 577 ASP cc_start: 0.8433 (m-30) cc_final: 0.8118 (m-30) REVERT: E 82 MET cc_start: 0.1652 (ptp) cc_final: 0.0520 (mmp) REVERT: E 347 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7679 (mt-10) REVERT: E 356 LYS cc_start: 0.8937 (tttt) cc_final: 0.8657 (tmtm) REVERT: E 376 LYS cc_start: 0.7542 (tttt) cc_final: 0.6833 (tptt) REVERT: E 435 ASP cc_start: 0.7838 (m-30) cc_final: 0.6957 (p0) REVERT: E 498 ARG cc_start: 0.5700 (OUTLIER) cc_final: 0.5309 (ptt90) REVERT: E 577 ASP cc_start: 0.8320 (m-30) cc_final: 0.8009 (m-30) outliers start: 35 outliers final: 7 residues processed: 333 average time/residue: 1.6445 time to fit residues: 614.5359 Evaluate side-chains 181 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 498 ARG Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 498 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 20.0000 chunk 227 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 153 optimal weight: 0.9990 chunk 121 optimal weight: 9.9990 chunk 235 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 175 optimal weight: 0.7980 chunk 272 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 HIS A 459 ASN B 233 HIS B 360 HIS B 560 ASN C 233 HIS C 360 HIS D 233 HIS D 360 HIS E 233 HIS E 360 HIS E 432 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.246817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.229626 restraints weight = 19365.640| |-----------------------------------------------------------------------------| r_work (start): 0.4403 rms_B_bonded: 0.46 r_work: 0.4293 rms_B_bonded: 0.98 restraints_weight: 0.5000 r_work: 0.4250 rms_B_bonded: 1.45 restraints_weight: 0.2500 r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24395 Z= 0.136 Angle : 0.579 6.565 33070 Z= 0.310 Chirality : 0.044 0.168 3715 Planarity : 0.005 0.044 4275 Dihedral : 6.824 58.212 3507 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.12 % Allowed : 8.34 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.16), residues: 2995 helix: 2.20 (0.20), residues: 695 sheet: 0.87 (0.16), residues: 980 loop : -0.35 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 359 HIS 0.005 0.001 HIS E 360 PHE 0.019 0.002 PHE A 366 TYR 0.014 0.002 TYR E 517 ARG 0.004 0.000 ARG D 521 Details of bonding type rmsd hydrogen bonds : bond 0.05702 ( 1110) hydrogen bonds : angle 4.84908 ( 3075) SS BOND : bond 0.00117 ( 5) SS BOND : angle 1.52348 ( 10) covalent geometry : bond 0.00262 (24390) covalent geometry : angle 0.57894 (33060) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 167 time to evaluate : 2.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7511 (mt-10) REVERT: A 480 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6969 (mt-10) REVERT: C 577 ASP cc_start: 0.8168 (m-30) cc_final: 0.7952 (m-30) REVERT: D 480 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7302 (mt-10) outliers start: 80 outliers final: 18 residues processed: 243 average time/residue: 1.3474 time to fit residues: 377.7250 Evaluate side-chains 159 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 564 SER Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 564 SER Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 564 SER Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 564 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 161 optimal weight: 0.9980 chunk 124 optimal weight: 20.0000 chunk 173 optimal weight: 5.9990 chunk 85 optimal weight: 20.0000 chunk 240 optimal weight: 20.0000 chunk 238 optimal weight: 4.9990 chunk 146 optimal weight: 20.0000 chunk 92 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 251 optimal weight: 9.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 HIS A 344 GLN A 360 HIS A 432 GLN B 338 GLN B 344 GLN B 432 GLN C 344 GLN C 360 HIS C 432 GLN C 471 GLN D 338 GLN D 344 GLN D 360 HIS D 432 GLN E 338 GLN E 344 GLN E 360 HIS E 471 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.258180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.180835 restraints weight = 19609.467| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 5.12 r_work: 0.3155 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 24395 Z= 0.265 Angle : 0.800 8.464 33070 Z= 0.434 Chirality : 0.052 0.185 3715 Planarity : 0.006 0.060 4275 Dihedral : 7.713 59.193 3481 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.55 % Allowed : 8.46 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.15), residues: 2995 helix: 1.89 (0.19), residues: 695 sheet: 1.08 (0.16), residues: 955 loop : -0.74 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP C 407 HIS 0.004 0.001 HIS B 233 PHE 0.051 0.004 PHE B 561 TYR 0.019 0.003 TYR C 542 ARG 0.008 0.001 ARG D 513 Details of bonding type rmsd hydrogen bonds : bond 0.08580 ( 1110) hydrogen bonds : angle 5.08583 ( 3075) SS BOND : bond 0.00492 ( 5) SS BOND : angle 1.76269 ( 10) covalent geometry : bond 0.00569 (24390) covalent geometry : angle 0.79955 (33060) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 147 time to evaluate : 2.554 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 403 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8387 (mm110) REVERT: A 468 ARG cc_start: 0.7918 (mtt180) cc_final: 0.7534 (mpt180) REVERT: A 569 ARG cc_start: 0.7811 (mtm-85) cc_final: 0.7522 (mmp-170) REVERT: B 384 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7322 (mtt90) REVERT: B 403 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8129 (mm-40) REVERT: B 468 ARG cc_start: 0.7919 (mtt180) cc_final: 0.7623 (mpt180) REVERT: C 290 ASP cc_start: 0.0962 (OUTLIER) cc_final: 0.0282 (t70) REVERT: C 403 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8096 (tm-30) REVERT: C 468 ARG cc_start: 0.7775 (mtt180) cc_final: 0.7531 (mpt180) REVERT: C 480 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7288 (tm-30) REVERT: C 498 ARG cc_start: 0.6052 (OUTLIER) cc_final: 0.5790 (ptt90) REVERT: D 356 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8580 (tmtm) REVERT: D 403 GLN cc_start: 0.8645 (tm-30) cc_final: 0.8143 (mm110) REVERT: D 468 ARG cc_start: 0.7838 (mtt180) cc_final: 0.7495 (mpt180) REVERT: D 515 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8816 (mp) REVERT: E 376 LYS cc_start: 0.8217 (tmtt) cc_final: 0.7619 (ttmt) REVERT: E 468 ARG cc_start: 0.7792 (mtt180) cc_final: 0.7487 (mpt180) REVERT: E 498 ARG cc_start: 0.6089 (OUTLIER) cc_final: 0.5871 (ptt-90) outliers start: 91 outliers final: 38 residues processed: 226 average time/residue: 1.4438 time to fit residues: 374.7079 Evaluate side-chains 187 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 140 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 384 ARG Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 403 GLN Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 356 LYS Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 498 ARG Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 564 SER Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 356 LYS Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 498 ARG Chi-restraints excluded: chain E residue 562 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 182 optimal weight: 20.0000 chunk 281 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 163 optimal weight: 0.6980 chunk 9 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 250 optimal weight: 20.0000 chunk 219 optimal weight: 0.9990 chunk 129 optimal weight: 20.0000 chunk 37 optimal weight: 0.9980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN A 360 HIS A 560 ASN B 338 GLN B 360 HIS C 344 GLN C 360 HIS C 471 GLN D 360 HIS E 360 HIS E 471 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.261777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.189000 restraints weight = 20150.442| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 4.60 r_work: 0.3534 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 24395 Z= 0.126 Angle : 0.553 9.250 33070 Z= 0.297 Chirality : 0.043 0.159 3715 Planarity : 0.004 0.046 4275 Dihedral : 6.495 55.119 3481 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.87 % Allowed : 10.37 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.16), residues: 2995 helix: 2.39 (0.20), residues: 695 sheet: 1.18 (0.16), residues: 990 loop : -0.69 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 359 HIS 0.003 0.001 HIS E 360 PHE 0.037 0.002 PHE E 561 TYR 0.013 0.001 TYR B 517 ARG 0.003 0.000 ARG A 498 Details of bonding type rmsd hydrogen bonds : bond 0.05572 ( 1110) hydrogen bonds : angle 4.61746 ( 3075) SS BOND : bond 0.00376 ( 5) SS BOND : angle 1.48886 ( 10) covalent geometry : bond 0.00239 (24390) covalent geometry : angle 0.55279 (33060) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 146 time to evaluate : 2.692 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 366 PHE cc_start: 0.5159 (t80) cc_final: 0.4731 (t80) REVERT: A 403 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8339 (mm-40) REVERT: A 468 ARG cc_start: 0.7741 (mtt180) cc_final: 0.7480 (mpt180) REVERT: A 480 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7749 (tp30) REVERT: B 403 GLN cc_start: 0.8494 (tm-30) cc_final: 0.8153 (mm110) REVERT: C 403 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8221 (mm110) REVERT: C 490 GLU cc_start: 0.8678 (tt0) cc_final: 0.8426 (tm-30) REVERT: D 403 GLN cc_start: 0.8433 (tm-30) cc_final: 0.7980 (mm-40) REVERT: D 468 ARG cc_start: 0.7676 (mtt180) cc_final: 0.7406 (mpt180) REVERT: D 480 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7587 (tm-30) REVERT: E 468 ARG cc_start: 0.7684 (mtt180) cc_final: 0.7444 (mpt180) outliers start: 48 outliers final: 24 residues processed: 187 average time/residue: 1.4923 time to fit residues: 318.4227 Evaluate side-chains 170 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 564 SER Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 637 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 64 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 213 optimal weight: 0.6980 chunk 151 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 36 optimal weight: 0.3980 chunk 130 optimal weight: 30.0000 chunk 106 optimal weight: 9.9990 chunk 240 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 overall best weight: 3.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 HIS B 307 ASN B 338 GLN B 360 HIS B 489 GLN C 307 ASN C 344 GLN C 360 HIS C 471 GLN D 307 ASN D 360 HIS D 471 GLN E 307 ASN E 360 HIS E 432 GLN E 471 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.255778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.179781 restraints weight = 19659.203| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 4.85 r_work: 0.3021 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 24395 Z= 0.274 Angle : 0.805 11.362 33070 Z= 0.438 Chirality : 0.053 0.201 3715 Planarity : 0.006 0.059 4275 Dihedral : 8.250 59.786 3480 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.27 % Allowed : 9.86 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.15), residues: 2995 helix: 1.83 (0.19), residues: 695 sheet: 1.11 (0.16), residues: 955 loop : -0.87 (0.16), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP B 482 HIS 0.003 0.001 HIS A 233 PHE 0.055 0.004 PHE C 561 TYR 0.021 0.003 TYR C 542 ARG 0.009 0.001 ARG C 578 Details of bonding type rmsd hydrogen bonds : bond 0.08896 ( 1110) hydrogen bonds : angle 5.03663 ( 3075) SS BOND : bond 0.00597 ( 5) SS BOND : angle 1.75087 ( 10) covalent geometry : bond 0.00589 (24390) covalent geometry : angle 0.80449 (33060) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 153 time to evaluate : 2.739 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 389 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6509 (mt-10) REVERT: A 403 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8358 (mm-40) REVERT: A 468 ARG cc_start: 0.7927 (mtt180) cc_final: 0.7512 (mpt180) REVERT: A 515 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8900 (mp) REVERT: A 569 ARG cc_start: 0.7799 (mtm-85) cc_final: 0.7395 (mmp-170) REVERT: B 384 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7338 (mtt90) REVERT: B 403 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8247 (mm110) REVERT: C 403 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8150 (tm-30) REVERT: C 468 ARG cc_start: 0.7809 (mtt180) cc_final: 0.7537 (mpt180) REVERT: D 221 GLN cc_start: 0.7125 (mm-40) cc_final: 0.6894 (mm110) REVERT: D 337 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8312 (m-30) REVERT: D 384 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7344 (mtm110) REVERT: D 403 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8179 (mm110) REVERT: D 468 ARG cc_start: 0.7883 (mtt180) cc_final: 0.7504 (mpt180) REVERT: E 376 LYS cc_start: 0.8233 (tmtt) cc_final: 0.8008 (tmtt) REVERT: E 468 ARG cc_start: 0.7894 (mtt180) cc_final: 0.7509 (mpt180) REVERT: E 498 ARG cc_start: 0.6328 (OUTLIER) cc_final: 0.5811 (ptt-90) outliers start: 84 outliers final: 38 residues processed: 223 average time/residue: 1.3664 time to fit residues: 352.0330 Evaluate side-chains 194 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 147 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 384 ARG Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 403 GLN Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 384 ARG Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 564 SER Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 356 LYS Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 498 ARG Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 637 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 166 optimal weight: 5.9990 chunk 77 optimal weight: 20.0000 chunk 155 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 291 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 279 optimal weight: 5.9990 chunk 139 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 68 optimal weight: 0.8980 chunk 269 optimal weight: 5.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 HIS B 360 HIS C 360 HIS C 471 GLN D 360 HIS E 221 GLN E 360 HIS E 471 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.256722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.182402 restraints weight = 19631.088| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 4.71 r_work: 0.3041 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24395 Z= 0.212 Angle : 0.685 11.032 33070 Z= 0.373 Chirality : 0.048 0.166 3715 Planarity : 0.005 0.049 4275 Dihedral : 7.761 57.364 3480 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.92 % Allowed : 10.60 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.15), residues: 2995 helix: 2.01 (0.19), residues: 695 sheet: 1.04 (0.16), residues: 985 loop : -0.83 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 359 HIS 0.003 0.001 HIS D 285 PHE 0.050 0.003 PHE C 561 TYR 0.016 0.003 TYR C 542 ARG 0.006 0.001 ARG E 578 Details of bonding type rmsd hydrogen bonds : bond 0.07426 ( 1110) hydrogen bonds : angle 4.85090 ( 3075) SS BOND : bond 0.00574 ( 5) SS BOND : angle 1.72351 ( 10) covalent geometry : bond 0.00445 (24390) covalent geometry : angle 0.68468 (33060) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 149 time to evaluate : 2.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 LYS cc_start: 0.8165 (tmtt) cc_final: 0.7953 (tmtt) REVERT: A 403 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8413 (mm110) REVERT: A 468 ARG cc_start: 0.7890 (mtt180) cc_final: 0.7492 (mpt180) REVERT: A 515 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8921 (mp) REVERT: A 569 ARG cc_start: 0.7760 (mtm-85) cc_final: 0.7377 (mmp-170) REVERT: B 82 MET cc_start: 0.1436 (OUTLIER) cc_final: -0.0347 (mmt) REVERT: B 384 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7286 (mtt90) REVERT: B 403 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8225 (mm110) REVERT: C 82 MET cc_start: 0.1468 (pmm) cc_final: -0.0720 (mmt) REVERT: C 468 ARG cc_start: 0.7804 (mtt180) cc_final: 0.7508 (mpt180) REVERT: C 480 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6717 (mm-30) REVERT: D 82 MET cc_start: 0.1409 (pmm) cc_final: -0.0401 (mmt) REVERT: D 337 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.8257 (m-30) REVERT: D 384 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7302 (mtm110) REVERT: D 403 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8160 (mm110) REVERT: D 468 ARG cc_start: 0.7858 (mtt180) cc_final: 0.7485 (mpt180) REVERT: D 480 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7797 (tp30) REVERT: D 515 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8852 (mp) REVERT: E 376 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7936 (tmtt) REVERT: E 468 ARG cc_start: 0.7861 (mtt180) cc_final: 0.7463 (mpt180) REVERT: E 498 ARG cc_start: 0.6234 (OUTLIER) cc_final: 0.5650 (ptt-90) REVERT: E 598 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8208 (tptm) outliers start: 75 outliers final: 33 residues processed: 209 average time/residue: 1.3493 time to fit residues: 324.6529 Evaluate side-chains 192 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 145 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 384 ARG Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 384 ARG Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 564 SER Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 376 LYS Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 498 ARG Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 598 LYS Chi-restraints excluded: chain E residue 637 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 289 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 265 optimal weight: 9.9990 chunk 272 optimal weight: 0.8980 chunk 182 optimal weight: 30.0000 chunk 244 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 216 optimal weight: 0.5980 chunk 193 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 HIS A 560 ASN B 338 GLN B 360 HIS C 471 GLN D 360 HIS E 221 GLN E 360 HIS E 560 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.259484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.185848 restraints weight = 20017.857| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 4.90 r_work: 0.3203 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24395 Z= 0.127 Angle : 0.546 10.029 33070 Z= 0.292 Chirality : 0.043 0.155 3715 Planarity : 0.004 0.047 4275 Dihedral : 6.948 59.955 3480 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.03 % Allowed : 11.93 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.16), residues: 2995 helix: 2.47 (0.19), residues: 690 sheet: 1.23 (0.16), residues: 1010 loop : -0.71 (0.17), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 359 HIS 0.003 0.001 HIS D 285 PHE 0.036 0.002 PHE C 561 TYR 0.013 0.001 TYR B 517 ARG 0.003 0.000 ARG E 578 Details of bonding type rmsd hydrogen bonds : bond 0.05511 ( 1110) hydrogen bonds : angle 4.56266 ( 3075) SS BOND : bond 0.00414 ( 5) SS BOND : angle 1.58656 ( 10) covalent geometry : bond 0.00246 (24390) covalent geometry : angle 0.54521 (33060) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 149 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8397 (mm-40) REVERT: A 468 ARG cc_start: 0.7847 (mtt180) cc_final: 0.7476 (mpt180) REVERT: A 480 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7641 (tp30) REVERT: A 515 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8919 (mp) REVERT: A 569 ARG cc_start: 0.7727 (mtm-85) cc_final: 0.7383 (mmp-170) REVERT: B 82 MET cc_start: 0.1435 (OUTLIER) cc_final: -0.0361 (mmt) REVERT: B 403 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8182 (mm110) REVERT: C 82 MET cc_start: 0.1085 (pmm) cc_final: -0.0866 (mmt) REVERT: C 468 ARG cc_start: 0.7777 (mtt180) cc_final: 0.7508 (mpt180) REVERT: C 490 GLU cc_start: 0.8762 (tt0) cc_final: 0.8541 (tm-30) REVERT: D 82 MET cc_start: 0.1377 (pmm) cc_final: -0.0457 (mmm) REVERT: D 403 GLN cc_start: 0.8571 (tm-30) cc_final: 0.8027 (mm-40) REVERT: D 468 ARG cc_start: 0.7795 (mtt180) cc_final: 0.7449 (mpt180) REVERT: D 480 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7704 (tp30) REVERT: D 515 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8843 (mp) REVERT: E 82 MET cc_start: 0.1635 (ptp) cc_final: 0.0290 (mmm) REVERT: E 221 GLN cc_start: 0.7248 (mm-40) cc_final: 0.6935 (tp40) REVERT: E 376 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7918 (tmtt) REVERT: E 432 GLN cc_start: 0.8542 (mt0) cc_final: 0.7839 (mm110) REVERT: E 468 ARG cc_start: 0.7820 (mtt180) cc_final: 0.7492 (mpt180) outliers start: 52 outliers final: 23 residues processed: 191 average time/residue: 1.4080 time to fit residues: 308.0477 Evaluate side-chains 178 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 564 SER Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 376 LYS Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 637 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 226 optimal weight: 10.0000 chunk 235 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 225 optimal weight: 0.9980 chunk 201 optimal weight: 5.9990 chunk 286 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 265 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS B 338 GLN B 360 HIS C 360 HIS C 471 GLN D 360 HIS D 471 GLN E 360 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.254186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.180398 restraints weight = 19527.444| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 4.57 r_work: 0.2977 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.5453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 24395 Z= 0.280 Angle : 0.799 10.913 33070 Z= 0.436 Chirality : 0.053 0.223 3715 Planarity : 0.006 0.060 4275 Dihedral : 8.403 59.880 3480 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.77 % Allowed : 11.62 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.15), residues: 2995 helix: 1.93 (0.19), residues: 695 sheet: 1.16 (0.17), residues: 930 loop : -0.87 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP C 407 HIS 0.003 0.001 HIS E 285 PHE 0.036 0.004 PHE D 561 TYR 0.021 0.003 TYR C 542 ARG 0.007 0.001 ARG E 578 Details of bonding type rmsd hydrogen bonds : bond 0.08866 ( 1110) hydrogen bonds : angle 5.02970 ( 3075) SS BOND : bond 0.00656 ( 5) SS BOND : angle 1.90945 ( 10) covalent geometry : bond 0.00606 (24390) covalent geometry : angle 0.79842 (33060) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 147 time to evaluate : 2.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.1624 (ptp) cc_final: 0.0174 (mmm) REVERT: A 403 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8387 (mm-40) REVERT: A 468 ARG cc_start: 0.7893 (mtt180) cc_final: 0.7464 (mpt180) REVERT: A 515 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8911 (mp) REVERT: A 569 ARG cc_start: 0.7856 (mtm-85) cc_final: 0.7506 (mtt90) REVERT: B 82 MET cc_start: 0.1441 (OUTLIER) cc_final: -0.0279 (mmt) REVERT: B 384 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7289 (mtt90) REVERT: B 403 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8235 (mm110) REVERT: B 515 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8809 (mp) REVERT: C 82 MET cc_start: 0.1131 (OUTLIER) cc_final: -0.0802 (mmt) REVERT: C 153 ASN cc_start: 0.7327 (t0) cc_final: 0.7025 (t0) REVERT: C 403 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8105 (tm-30) REVERT: C 468 ARG cc_start: 0.7803 (mtt180) cc_final: 0.7549 (mpt180) REVERT: D 82 MET cc_start: 0.1439 (OUTLIER) cc_final: -0.0355 (mmm) REVERT: D 337 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8249 (m-30) REVERT: D 403 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8158 (mm110) REVERT: D 468 ARG cc_start: 0.7876 (mtt180) cc_final: 0.7495 (mpt180) REVERT: D 515 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8874 (mp) REVERT: E 82 MET cc_start: 0.1480 (ptp) cc_final: 0.0229 (mmm) REVERT: E 221 GLN cc_start: 0.7174 (mm-40) cc_final: 0.6858 (tp40) REVERT: E 376 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7627 (ttpt) REVERT: E 468 ARG cc_start: 0.7860 (mtt180) cc_final: 0.7481 (mpt180) REVERT: E 569 ARG cc_start: 0.7877 (mtm-85) cc_final: 0.7378 (mmp-170) outliers start: 71 outliers final: 35 residues processed: 205 average time/residue: 1.3791 time to fit residues: 326.9363 Evaluate side-chains 190 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 142 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 384 ARG Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 403 GLN Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 564 SER Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 376 LYS Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 637 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 11 optimal weight: 7.9990 chunk 190 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 253 optimal weight: 20.0000 chunk 115 optimal weight: 3.9990 chunk 180 optimal weight: 30.0000 chunk 64 optimal weight: 9.9990 chunk 288 optimal weight: 1.9990 chunk 204 optimal weight: 10.0000 chunk 80 optimal weight: 0.0000 chunk 171 optimal weight: 4.9990 overall best weight: 3.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS B 360 HIS C 471 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 HIS D 560 ASN E 360 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.254142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.183321 restraints weight = 19585.241| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 4.18 r_work: 0.3120 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.5728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 24395 Z= 0.257 Angle : 0.757 10.888 33070 Z= 0.414 Chirality : 0.051 0.212 3715 Planarity : 0.006 0.052 4275 Dihedral : 8.217 59.513 3480 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.65 % Allowed : 11.73 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.15), residues: 2995 helix: 1.84 (0.19), residues: 695 sheet: 0.94 (0.17), residues: 955 loop : -0.92 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 482 HIS 0.003 0.001 HIS A 285 PHE 0.045 0.004 PHE C 561 TYR 0.020 0.003 TYR C 542 ARG 0.008 0.001 ARG E 578 Details of bonding type rmsd hydrogen bonds : bond 0.08214 ( 1110) hydrogen bonds : angle 5.04634 ( 3075) SS BOND : bond 0.00697 ( 5) SS BOND : angle 1.94588 ( 10) covalent geometry : bond 0.00553 (24390) covalent geometry : angle 0.75676 (33060) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 153 time to evaluate : 2.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.1635 (ptp) cc_final: 0.0219 (mmm) REVERT: A 384 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7301 (mtt90) REVERT: A 403 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8390 (mm110) REVERT: A 468 ARG cc_start: 0.7802 (mtt180) cc_final: 0.7497 (mpt180) REVERT: A 515 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8903 (mp) REVERT: A 569 ARG cc_start: 0.7889 (mtm-85) cc_final: 0.7556 (mtp85) REVERT: B 82 MET cc_start: 0.1918 (OUTLIER) cc_final: 0.0039 (mmt) REVERT: B 384 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7313 (mtt90) REVERT: B 403 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8226 (mm110) REVERT: B 515 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8839 (mp) REVERT: C 82 MET cc_start: 0.1084 (OUTLIER) cc_final: -0.0779 (mmm) REVERT: C 153 ASN cc_start: 0.7267 (t0) cc_final: 0.6942 (t0) REVERT: C 384 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7270 (mtt90) REVERT: C 403 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8299 (mm110) REVERT: D 82 MET cc_start: 0.1572 (OUTLIER) cc_final: -0.0164 (mmm) REVERT: D 384 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7255 (mtm110) REVERT: D 403 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8165 (mm110) REVERT: D 468 ARG cc_start: 0.7805 (mtt180) cc_final: 0.7504 (mpt180) REVERT: D 480 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7809 (tp30) REVERT: D 515 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8840 (mp) REVERT: E 82 MET cc_start: 0.1578 (ptp) cc_final: 0.0359 (mmm) REVERT: E 221 GLN cc_start: 0.7095 (mm-40) cc_final: 0.6784 (tp40) REVERT: E 376 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7918 (tmtt) REVERT: E 468 ARG cc_start: 0.7755 (mtt180) cc_final: 0.7507 (mpt180) REVERT: E 598 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8277 (tptm) outliers start: 68 outliers final: 31 residues processed: 206 average time/residue: 1.3496 time to fit residues: 320.1961 Evaluate side-chains 197 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 150 time to evaluate : 2.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 384 ARG Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 384 ARG Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain C residue 403 GLN Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 384 ARG Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 356 LYS Chi-restraints excluded: chain E residue 376 LYS Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 598 LYS Chi-restraints excluded: chain E residue 637 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 25 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 271 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 122 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 153 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 ASN A 360 HIS B 40 HIS B 338 GLN B 360 HIS C 40 HIS C 471 GLN C 489 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 HIS E 360 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.257824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.185781 restraints weight = 19909.016| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 4.70 r_work: 0.3231 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.5668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24395 Z= 0.132 Angle : 0.559 9.401 33070 Z= 0.300 Chirality : 0.044 0.155 3715 Planarity : 0.004 0.050 4275 Dihedral : 7.266 59.171 3480 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.72 % Allowed : 12.87 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.16), residues: 2995 helix: 2.41 (0.19), residues: 690 sheet: 0.91 (0.17), residues: 990 loop : -0.77 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 359 HIS 0.003 0.001 HIS E 360 PHE 0.033 0.002 PHE C 561 TYR 0.013 0.001 TYR B 517 ARG 0.004 0.000 ARG E 498 Details of bonding type rmsd hydrogen bonds : bond 0.05627 ( 1110) hydrogen bonds : angle 4.64402 ( 3075) SS BOND : bond 0.00462 ( 5) SS BOND : angle 1.68505 ( 10) covalent geometry : bond 0.00255 (24390) covalent geometry : angle 0.55810 (33060) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 155 time to evaluate : 2.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.1655 (ptp) cc_final: 0.0111 (mmm) REVERT: A 403 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8407 (mm-40) REVERT: A 468 ARG cc_start: 0.7795 (mtt180) cc_final: 0.7523 (mpt180) REVERT: A 480 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7618 (tp30) REVERT: A 515 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8911 (mp) REVERT: A 569 ARG cc_start: 0.7781 (mtm-85) cc_final: 0.7395 (mmp-170) REVERT: B 82 MET cc_start: 0.1775 (OUTLIER) cc_final: 0.0043 (mmm) REVERT: B 403 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8147 (mm-40) REVERT: C 82 MET cc_start: 0.0930 (OUTLIER) cc_final: -0.0708 (mmm) REVERT: C 490 GLU cc_start: 0.8778 (tt0) cc_final: 0.8553 (tm-30) REVERT: C 567 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7373 (mm) REVERT: D 82 MET cc_start: 0.1510 (OUTLIER) cc_final: -0.0083 (mmm) REVERT: D 403 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8041 (mm-40) REVERT: D 418 ASP cc_start: 0.7303 (m-30) cc_final: 0.6888 (p0) REVERT: D 468 ARG cc_start: 0.7743 (mtt180) cc_final: 0.7512 (mpt180) REVERT: D 480 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7690 (tp30) REVERT: D 515 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8849 (mp) REVERT: D 567 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7202 (mm) REVERT: E 82 MET cc_start: 0.1614 (ptp) cc_final: 0.0237 (mmm) REVERT: E 221 GLN cc_start: 0.7178 (mm-40) cc_final: 0.6881 (tp40) REVERT: E 432 GLN cc_start: 0.8566 (mt0) cc_final: 0.7873 (mm110) REVERT: E 468 ARG cc_start: 0.7707 (mtt180) cc_final: 0.7494 (mpt180) REVERT: E 598 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8121 (tptm) outliers start: 44 outliers final: 21 residues processed: 187 average time/residue: 1.4350 time to fit residues: 308.2464 Evaluate side-chains 185 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 598 LYS Chi-restraints excluded: chain E residue 637 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 145 optimal weight: 20.0000 chunk 119 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 18 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 235 optimal weight: 5.9990 chunk 212 optimal weight: 0.6980 chunk 211 optimal weight: 0.6980 chunk 82 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS A 560 ASN B 360 HIS C 471 GLN D 360 HIS D 459 ASN D 471 GLN E 360 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.244271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.164985 restraints weight = 19276.460| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 5.09 r_work: 0.3121 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.5679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 24395 Z= 0.112 Angle : 0.512 8.061 33070 Z= 0.274 Chirality : 0.042 0.152 3715 Planarity : 0.004 0.049 4275 Dihedral : 6.291 57.820 3480 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.72 % Allowed : 12.94 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.16), residues: 2995 helix: 2.72 (0.19), residues: 690 sheet: 1.16 (0.16), residues: 1020 loop : -0.66 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 359 HIS 0.004 0.001 HIS E 360 PHE 0.032 0.002 PHE D 561 TYR 0.011 0.001 TYR C 542 ARG 0.004 0.000 ARG E 498 Details of bonding type rmsd hydrogen bonds : bond 0.04785 ( 1110) hydrogen bonds : angle 4.40051 ( 3075) SS BOND : bond 0.00397 ( 5) SS BOND : angle 1.60242 ( 10) covalent geometry : bond 0.00217 (24390) covalent geometry : angle 0.51158 (33060) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21976.17 seconds wall clock time: 378 minutes 36.67 seconds (22716.67 seconds total)