Starting phenix.real_space_refine on Fri Jun 20 21:30:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9evb_19997/06_2025/9evb_19997.cif Found real_map, /net/cci-nas-00/data/ceres_data/9evb_19997/06_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_19997/06_2025/9evb_19997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9evb_19997/06_2025/9evb_19997.map" model { file = "/net/cci-nas-00/data/ceres_data/9evb_19997/06_2025/9evb_19997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9evb_19997/06_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 13.07, per 1000 atoms: 0.54 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: 6.27 Conformation dependent library (CDL) restraints added in 2.7 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: 2.91 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: 8.27 Time building geometry restraints manager: 7.58 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: 0.13 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: 3.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.900 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 51.610 Find NCS groups from input model: 1.410 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: 0.000 Load rotamer database and sin/cos tables:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.030 ------------------------------------------------------------------------------- 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 : 2.362 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: 1.6873 time to fit residues: 631.3364 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 : 2.351 ------------------------------------------------------------------------------- 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 = 0.4552 r_free = 0.4552 target = 0.246945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.230226 restraints weight = 19363.652| |-----------------------------------------------------------------------------| r_work (start): 0.4407 rms_B_bonded: 0.43 r_work: 0.4299 rms_B_bonded: 0.95 restraints_weight: 0.5000 r_work: 0.4254 rms_B_bonded: 1.48 restraints_weight: 0.2500 r_work (final): 0.4254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 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 : 2.307 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: 0.7727 (OUTLIER) cc_final: 0.7511 (mt-10) REVERT: A 480 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6969 (mt-10) REVERT: C 577 ASP cc_start: 0.8170 (m-30) cc_final: 0.7954 (m-30) REVERT: D 480 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7304 (mt-10) outliers start: 80 outliers final: 18 residues processed: 243 average time/residue: 1.2596 time to fit residues: 354.0660 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 : 2.309 ------------------------------------------------------------------------------- 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: 4.9990 chunk 251 optimal weight: 9.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- 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 = 0.4651 r_free = 0.4651 target = 0.251444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.169709 restraints weight = 19800.758| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 6.90 r_work: 0.3462 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 24395 Z= 0.259 Angle : 0.791 8.058 33070 Z= 0.429 Chirality : 0.052 0.189 3715 Planarity : 0.006 0.057 4275 Dihedral : 7.648 59.496 3481 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.24 % Allowed : 9.01 % 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: 0.74 (0.15), residues: 2995 helix: 1.91 (0.19), residues: 695 sheet: 1.10 (0.16), residues: 955 loop : -0.74 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP E 121 HIS 0.004 0.001 HIS B 233 PHE 0.048 0.004 PHE B 561 TYR 0.018 0.003 TYR C 542 ARG 0.008 0.001 ARG D 513 Details of bonding type rmsd hydrogen bonds : bond 0.08418 ( 1110) hydrogen bonds : angle 5.06612 ( 3075) SS BOND : bond 0.00523 ( 5) SS BOND : angle 1.82941 ( 10) covalent geometry : bond 0.00551 (24390) covalent geometry : angle 0.79026 (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 230 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 147 time to evaluate : 2.526 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: 0.8681 (OUTLIER) cc_final: 0.8376 (mm110) REVERT: A 468 ARG cc_start: 0.7772 (mtt180) cc_final: 0.7510 (mpt180) REVERT: B 384 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7355 (mtt90) REVERT: B 403 GLN cc_start: 0.8522 (tm-30) cc_final: 0.8057 (mm-40) REVERT: C 290 ASP cc_start: 0.0909 (OUTLIER) cc_final: 0.0240 (t70) REVERT: C 403 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.7969 (tm-30) REVERT: C 480 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7232 (tm-30) REVERT: C 498 ARG cc_start: 0.6045 (OUTLIER) cc_final: 0.5777 (ptt90) REVERT: D 403 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8074 (mm110) REVERT: D 490 GLU cc_start: 0.8708 (tt0) cc_final: 0.8478 (tm-30) REVERT: D 515 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8835 (mp) REVERT: E 376 LYS cc_start: 0.8276 (tmtt) cc_final: 0.7705 (ttmt) outliers start: 83 outliers final: 36 residues processed: 218 average time/residue: 1.4673 time to fit residues: 366.4079 Evaluate side-chains 180 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 137 time to evaluate : 2.768 ------------------------------------------------------------------------------- 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 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 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 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 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: 0.9980 chunk 179 optimal weight: 2.9990 chunk 73 optimal weight: 30.0000 chunk 163 optimal weight: 0.6980 chunk 9 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 250 optimal weight: 20.0000 chunk 219 optimal weight: 0.7980 chunk 129 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 307 ASN B 360 HIS B 489 GLN C 307 ASN C 360 HIS C 471 GLN C 489 GLN D 307 ASN D 360 HIS D 489 GLN E 360 HIS E 471 GLN E 489 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.260172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.187144 restraints weight = 19945.947| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 4.50 r_work: 0.3587 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.4101 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= 0.157 Angle : 0.604 9.821 33070 Z= 0.326 Chirality : 0.045 0.162 3715 Planarity : 0.005 0.047 4275 Dihedral : 6.717 56.012 3481 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.26 % Allowed : 10.10 % Favored : 87.64 % 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: 0.93 (0.15), residues: 2995 helix: 2.23 (0.20), residues: 695 sheet: 1.15 (0.16), residues: 990 loop : -0.72 (0.17), residues: 1310 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 0.044 0.002 PHE E 561 TYR 0.015 0.002 TYR B 517 ARG 0.004 0.000 ARG E 578 Details of bonding type rmsd hydrogen bonds : bond 0.06378 ( 1110) hydrogen bonds : angle 4.70753 ( 3075) SS BOND : bond 0.00450 ( 5) SS BOND : angle 1.59717 ( 10) covalent geometry : bond 0.00314 (24390) covalent geometry : angle 0.60352 (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 201 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 143 time to evaluate : 2.519 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: 0.8693 (OUTLIER) cc_final: 0.8401 (mm110) REVERT: A 468 ARG cc_start: 0.7806 (mtt180) cc_final: 0.7484 (mpt180) REVERT: A 480 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7708 (tp30) REVERT: A 569 ARG cc_start: 0.7731 (mtm-85) cc_final: 0.7447 (mmp-170) REVERT: B 384 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7362 (mtt90) REVERT: B 403 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8056 (mm-40) REVERT: C 403 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8213 (mm110) REVERT: C 480 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6497 (mm-30) REVERT: D 403 GLN cc_start: 0.8458 (tm-30) cc_final: 0.7994 (mm-40) REVERT: D 480 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7748 (tp30) REVERT: E 68 MET cc_start: 0.2524 (ptp) cc_final: 0.2167 (ptt) outliers start: 58 outliers final: 27 residues processed: 188 average time/residue: 1.4304 time to fit residues: 308.3901 Evaluate side-chains 171 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 2.425 ------------------------------------------------------------------------------- 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 637 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 480 GLU 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 439 LEU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 480 GLU 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: 0.4980 chunk 6 optimal weight: 10.0000 chunk 145 optimal weight: 20.0000 chunk 213 optimal weight: 0.4980 chunk 151 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 130 optimal weight: 30.0000 chunk 106 optimal weight: 7.9990 chunk 240 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 overall best weight: 1.9582 ------------------------------------------------------------------------------- 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 360 HIS C 360 HIS C 471 GLN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.258223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.184189 restraints weight = 19868.317| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 4.63 r_work: 0.3198 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24395 Z= 0.173 Angle : 0.630 10.458 33070 Z= 0.340 Chirality : 0.046 0.163 3715 Planarity : 0.005 0.046 4275 Dihedral : 6.887 59.925 3480 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.88 % Allowed : 10.10 % Favored : 87.02 % 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: 0.99 (0.15), residues: 2995 helix: 2.19 (0.19), residues: 695 sheet: 1.28 (0.16), residues: 955 loop : -0.66 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 359 HIS 0.004 0.001 HIS A 285 PHE 0.049 0.003 PHE E 561 TYR 0.016 0.002 TYR C 542 ARG 0.005 0.000 ARG E 578 Details of bonding type rmsd hydrogen bonds : bond 0.06966 ( 1110) hydrogen bonds : angle 4.70617 ( 3075) SS BOND : bond 0.00451 ( 5) SS BOND : angle 1.54137 ( 10) covalent geometry : bond 0.00350 (24390) covalent geometry : angle 0.62981 (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 227 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 153 time to evaluate : 2.885 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: 0.8586 (OUTLIER) cc_final: 0.8335 (mm110) REVERT: A 515 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8825 (mp) REVERT: A 569 ARG cc_start: 0.7641 (mtm-85) cc_final: 0.7396 (mmp-170) REVERT: B 384 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7102 (mtt90) REVERT: B 403 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8097 (mm110) REVERT: C 376 LYS cc_start: 0.8048 (tmtt) cc_final: 0.7489 (ttpp) REVERT: C 490 GLU cc_start: 0.8573 (tt0) cc_final: 0.8352 (tm-30) REVERT: D 337 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7853 (m-30) REVERT: D 403 GLN cc_start: 0.8395 (tm-30) cc_final: 0.7916 (mm-40) REVERT: D 480 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7739 (mt-10) REVERT: E 68 MET cc_start: 0.2736 (ptp) cc_final: 0.2222 (ptt) REVERT: E 498 ARG cc_start: 0.6187 (OUTLIER) cc_final: 0.5476 (ptt-90) outliers start: 74 outliers final: 31 residues processed: 215 average time/residue: 1.7378 time to fit residues: 433.7381 Evaluate side-chains 183 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 3.913 ------------------------------------------------------------------------------- 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 A residue 637 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 480 GLU 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 439 LEU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 337 ASP 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 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 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: 9.9990 chunk 77 optimal weight: 8.9990 chunk 155 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 291 optimal weight: 6.9990 chunk 94 optimal weight: 0.5980 chunk 279 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 13 optimal weight: 30.0000 chunk 68 optimal weight: 20.0000 chunk 269 optimal weight: 10.0000 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 HIS A 489 GLN B 360 HIS C 360 HIS C 471 GLN D 221 GLN D 360 HIS D 471 GLN E 360 HIS E 471 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.247955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.168368 restraints weight = 19705.745| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 6.53 r_work: 0.2962 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 24395 Z= 0.265 Angle : 0.788 11.461 33070 Z= 0.429 Chirality : 0.052 0.197 3715 Planarity : 0.006 0.061 4275 Dihedral : 8.392 59.673 3480 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.12 % Allowed : 10.72 % Favored : 86.16 % 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: 1.87 (0.19), residues: 695 sheet: 1.12 (0.16), residues: 950 loop : -0.84 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP C 482 HIS 0.004 0.001 HIS E 285 PHE 0.058 0.004 PHE E 561 TYR 0.020 0.003 TYR C 542 ARG 0.008 0.001 ARG B 578 Details of bonding type rmsd hydrogen bonds : bond 0.08752 ( 1110) hydrogen bonds : angle 5.04218 ( 3075) SS BOND : bond 0.00618 ( 5) SS BOND : angle 1.83321 ( 10) covalent geometry : bond 0.00570 (24390) covalent geometry : angle 0.78729 (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 227 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 147 time to evaluate : 2.487 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 403 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8302 (mm-40) REVERT: A 515 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8843 (mp) REVERT: A 569 ARG cc_start: 0.7673 (mtm-85) cc_final: 0.7232 (mmp-170) REVERT: B 384 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7258 (mtt90) REVERT: B 403 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8167 (mm110) REVERT: C 82 MET cc_start: 0.1325 (OUTLIER) cc_final: -0.0740 (mmt) REVERT: C 376 LYS cc_start: 0.8151 (tmtt) cc_final: 0.7543 (ttpp) REVERT: C 403 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8038 (tm-30) REVERT: C 480 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7145 (tm-30) REVERT: D 82 MET cc_start: 0.1479 (OUTLIER) cc_final: -0.0324 (mmt) REVERT: D 221 GLN cc_start: 0.7176 (mm-40) cc_final: 0.6592 (mm110) REVERT: D 337 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8317 (m-30) REVERT: D 384 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7247 (mtm110) REVERT: D 403 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8084 (mm110) REVERT: D 515 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8797 (mp) REVERT: E 82 MET cc_start: 0.1531 (ptp) cc_final: 0.0281 (mmm) REVERT: E 376 LYS cc_start: 0.8143 (tmtt) cc_final: 0.7529 (ttmt) REVERT: E 498 ARG cc_start: 0.6506 (OUTLIER) cc_final: 0.6086 (ptt-90) REVERT: E 598 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8215 (tptm) outliers start: 80 outliers final: 38 residues processed: 213 average time/residue: 1.3684 time to fit residues: 336.8064 Evaluate side-chains 194 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 143 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 637 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 480 GLU 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 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 515 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 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 515 LEU Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 564 SER Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 637 THR 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 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: 1.9990 chunk 38 optimal weight: 0.9980 chunk 265 optimal weight: 30.0000 chunk 272 optimal weight: 0.9990 chunk 182 optimal weight: 30.0000 chunk 244 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 216 optimal weight: 3.9990 chunk 193 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 432 GLN E 471 GLN E 560 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.251913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.173554 restraints weight = 19965.129| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 6.31 r_work: 0.3017 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.5216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24395 Z= 0.160 Angle : 0.607 10.406 33070 Z= 0.327 Chirality : 0.045 0.158 3715 Planarity : 0.005 0.048 4275 Dihedral : 7.392 59.344 3480 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.53 % Allowed : 11.38 % Favored : 86.08 % 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: 0.88 (0.16), residues: 2995 helix: 2.23 (0.19), residues: 695 sheet: 1.07 (0.17), residues: 985 loop : -0.73 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 359 HIS 0.004 0.001 HIS D 285 PHE 0.050 0.002 PHE E 561 TYR 0.015 0.002 TYR B 517 ARG 0.004 0.000 ARG C 498 Details of bonding type rmsd hydrogen bonds : bond 0.06490 ( 1110) hydrogen bonds : angle 4.73875 ( 3075) SS BOND : bond 0.00495 ( 5) SS BOND : angle 1.66181 ( 10) covalent geometry : bond 0.00321 (24390) covalent geometry : angle 0.60611 (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 214 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 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: A 403 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8302 (mm-40) REVERT: A 480 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7616 (tp30) REVERT: A 515 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8907 (mp) REVERT: A 569 ARG cc_start: 0.7690 (mtm-85) cc_final: 0.7266 (mmp-170) REVERT: B 82 MET cc_start: 0.1355 (pmm) cc_final: -0.0369 (mmt) REVERT: B 384 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7211 (mtt90) REVERT: B 403 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8085 (mm-40) REVERT: C 82 MET cc_start: 0.0965 (OUTLIER) cc_final: -0.0909 (mmt) REVERT: C 480 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6570 (mm-30) REVERT: D 82 MET cc_start: 0.1321 (OUTLIER) cc_final: -0.0451 (mmm) REVERT: D 221 GLN cc_start: 0.7122 (mm-40) cc_final: 0.6824 (tp40) REVERT: D 403 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8069 (mm110) REVERT: D 480 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7719 (tp30) REVERT: D 498 ARG cc_start: 0.5860 (OUTLIER) cc_final: 0.5585 (ptt90) REVERT: D 515 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8793 (mp) REVERT: E 82 MET cc_start: 0.1442 (ptp) cc_final: 0.0164 (mmm) REVERT: E 221 GLN cc_start: 0.6987 (mm-40) cc_final: 0.6708 (tp40) REVERT: E 376 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7753 (tmtt) REVERT: E 498 ARG cc_start: 0.6337 (OUTLIER) cc_final: 0.5631 (ptt-90) REVERT: E 547 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8255 (tm-30) REVERT: E 598 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8111 (tptm) outliers start: 65 outliers final: 33 residues processed: 201 average time/residue: 1.4355 time to fit residues: 331.5793 Evaluate side-chains 192 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 144 time to evaluate : 2.451 ------------------------------------------------------------------------------- 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 A residue 637 THR Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 279 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 480 GLU 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 439 LEU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 328 ASP 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 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 D residue 567 LEU Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 328 ASP 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 547 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 226 optimal weight: 10.0000 chunk 235 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 4 optimal weight: 0.3980 chunk 121 optimal weight: 20.0000 chunk 225 optimal weight: 0.9990 chunk 201 optimal weight: 10.0000 chunk 286 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 265 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 360 HIS C 471 GLN D 360 HIS D 471 GLN E 360 HIS E 471 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.237581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.211911 restraints weight = 18974.818| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 0.65 r_work: 0.4059 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.4004 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.5369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24395 Z= 0.158 Angle : 0.599 9.968 33070 Z= 0.323 Chirality : 0.045 0.161 3715 Planarity : 0.005 0.049 4275 Dihedral : 6.975 59.798 3480 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.14 % Allowed : 12.12 % Favored : 85.73 % 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: 2.31 (0.19), residues: 695 sheet: 1.13 (0.17), residues: 985 loop : -0.67 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 359 HIS 0.004 0.001 HIS D 285 PHE 0.049 0.002 PHE E 561 TYR 0.015 0.002 TYR C 542 ARG 0.005 0.000 ARG E 578 Details of bonding type rmsd hydrogen bonds : bond 0.06534 ( 1110) hydrogen bonds : angle 4.67238 ( 3075) SS BOND : bond 0.00483 ( 5) SS BOND : angle 1.68355 ( 10) covalent geometry : bond 0.00314 (24390) covalent geometry : angle 0.59823 (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 205 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 150 time to evaluate : 2.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.3086 (ptp) cc_final: 0.1455 (mmm) REVERT: A 465 GLU cc_start: 0.8080 (tt0) cc_final: 0.7841 (tm-30) REVERT: A 515 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8817 (mp) REVERT: B 82 MET cc_start: 0.2719 (OUTLIER) cc_final: 0.0912 (mmm) REVERT: B 384 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7335 (mtt90) REVERT: C 82 MET cc_start: 0.2210 (OUTLIER) cc_final: 0.0255 (mmt) REVERT: C 480 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6641 (mm-30) REVERT: C 490 GLU cc_start: 0.8049 (tt0) cc_final: 0.7828 (tm-30) REVERT: C 567 LEU cc_start: 0.7938 (mp) cc_final: 0.7737 (mm) REVERT: D 82 MET cc_start: 0.2464 (OUTLIER) cc_final: 0.0714 (mmm) REVERT: D 221 GLN cc_start: 0.7476 (mm-40) cc_final: 0.7214 (tp40) REVERT: D 498 ARG cc_start: 0.5431 (OUTLIER) cc_final: 0.5223 (ptt90) REVERT: D 515 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8760 (mp) REVERT: E 82 MET cc_start: 0.2892 (ptp) cc_final: 0.1404 (mmm) REVERT: E 498 ARG cc_start: 0.5809 (OUTLIER) cc_final: 0.4925 (ptt-90) outliers start: 55 outliers final: 33 residues processed: 194 average time/residue: 1.3838 time to fit residues: 310.4609 Evaluate side-chains 189 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 2.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 VAL 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 637 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 328 ASP Chi-restraints excluded: chain B residue 384 ARG 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 480 GLU 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 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 82 MET Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 449 SER 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 262 ILE Chi-restraints excluded: chain E residue 328 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 11 optimal weight: 5.9990 chunk 190 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 253 optimal weight: 30.0000 chunk 115 optimal weight: 4.9990 chunk 180 optimal weight: 30.0000 chunk 64 optimal weight: 6.9990 chunk 288 optimal weight: 0.8980 chunk 204 optimal weight: 0.8980 chunk 80 optimal weight: 0.1980 chunk 171 optimal weight: 5.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- 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 360 HIS C 338 GLN C 360 HIS C 471 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 HIS D 471 GLN E 360 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.235923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.210140 restraints weight = 18911.419| |-----------------------------------------------------------------------------| r_work (start): 0.4209 rms_B_bonded: 0.64 r_work: 0.4038 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3992 rms_B_bonded: 1.77 restraints_weight: 0.2500 r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.5606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 24395 Z= 0.204 Angle : 0.674 9.382 33070 Z= 0.367 Chirality : 0.047 0.164 3715 Planarity : 0.005 0.047 4275 Dihedral : 7.576 58.822 3480 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.46 % Allowed : 11.89 % Favored : 85.65 % 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: 0.88 (0.15), residues: 2995 helix: 2.15 (0.19), residues: 695 sheet: 1.16 (0.17), residues: 965 loop : -0.71 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 359 HIS 0.003 0.001 HIS E 285 PHE 0.065 0.003 PHE E 561 TYR 0.019 0.002 TYR C 542 ARG 0.005 0.001 ARG D 513 Details of bonding type rmsd hydrogen bonds : bond 0.07531 ( 1110) hydrogen bonds : angle 4.83500 ( 3075) SS BOND : bond 0.00560 ( 5) SS BOND : angle 1.79257 ( 10) covalent geometry : bond 0.00426 (24390) covalent geometry : angle 0.67382 (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 211 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 148 time to evaluate : 2.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.3088 (ptp) cc_final: 0.1463 (mmm) REVERT: A 515 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8816 (mp) REVERT: B 82 MET cc_start: 0.2747 (OUTLIER) cc_final: 0.0996 (mmm) REVERT: B 384 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7352 (mtt90) REVERT: B 420 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6927 (mtp-110) REVERT: B 560 ASN cc_start: 0.8189 (t0) cc_final: 0.7925 (t0) REVERT: C 82 MET cc_start: 0.2219 (OUTLIER) cc_final: 0.0308 (mmm) REVERT: D 82 MET cc_start: 0.2387 (OUTLIER) cc_final: 0.0675 (mmm) REVERT: D 221 GLN cc_start: 0.7409 (mm-40) cc_final: 0.7146 (tp40) REVERT: D 498 ARG cc_start: 0.5554 (OUTLIER) cc_final: 0.5296 (ptt90) REVERT: D 515 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8782 (mp) REVERT: E 82 MET cc_start: 0.2931 (ptp) cc_final: 0.1446 (mmm) REVERT: E 498 ARG cc_start: 0.5929 (OUTLIER) cc_final: 0.5261 (ptt-90) REVERT: E 598 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8103 (tptm) outliers start: 63 outliers final: 33 residues processed: 197 average time/residue: 1.3806 time to fit residues: 313.5886 Evaluate side-chains 184 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 141 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 340 VAL 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 490 GLU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 384 ARG Chi-restraints excluded: chain B residue 420 ARG 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 480 GLU 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 439 LEU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 439 LEU 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 D residue 637 THR Chi-restraints excluded: chain E residue 262 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 25 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 271 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 146 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 153 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 360 HIS A 560 ASN B 360 HIS C 338 GLN C 403 GLN C 471 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 HIS D 471 GLN D 560 ASN E 360 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.237598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.212419 restraints weight = 19061.537| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 0.65 r_work: 0.4053 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.4007 rms_B_bonded: 1.83 restraints_weight: 0.2500 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.5618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24395 Z= 0.152 Angle : 0.586 8.549 33070 Z= 0.316 Chirality : 0.044 0.158 3715 Planarity : 0.005 0.048 4275 Dihedral : 7.025 59.350 3480 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.14 % Allowed : 12.32 % Favored : 85.54 % 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: 1.03 (0.16), residues: 2995 helix: 2.34 (0.19), residues: 695 sheet: 1.14 (0.17), residues: 1015 loop : -0.64 (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 A 360 PHE 0.089 0.002 PHE E 561 TYR 0.014 0.002 TYR B 517 ARG 0.004 0.000 ARG E 578 Details of bonding type rmsd hydrogen bonds : bond 0.06187 ( 1110) hydrogen bonds : angle 4.64768 ( 3075) SS BOND : bond 0.00495 ( 5) SS BOND : angle 1.68241 ( 10) covalent geometry : bond 0.00306 (24390) covalent geometry : angle 0.58517 (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 204 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 149 time to evaluate : 2.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.3001 (ptp) cc_final: 0.1383 (mmm) REVERT: A 465 GLU cc_start: 0.8084 (tt0) cc_final: 0.7857 (tm-30) REVERT: A 515 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8800 (mp) REVERT: B 82 MET cc_start: 0.2791 (OUTLIER) cc_final: 0.1071 (mmm) REVERT: B 384 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7321 (mtt90) REVERT: C 82 MET cc_start: 0.2178 (OUTLIER) cc_final: 0.0447 (mmm) REVERT: C 480 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6589 (mm-30) REVERT: C 490 GLU cc_start: 0.8021 (tt0) cc_final: 0.7792 (tm-30) REVERT: D 82 MET cc_start: 0.2419 (OUTLIER) cc_final: 0.0709 (mmm) REVERT: D 221 GLN cc_start: 0.7444 (mm-40) cc_final: 0.7203 (tp40) REVERT: D 498 ARG cc_start: 0.5408 (OUTLIER) cc_final: 0.5142 (ptt90) REVERT: D 515 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8791 (mp) REVERT: E 82 MET cc_start: 0.2812 (ptp) cc_final: 0.1333 (mmm) REVERT: E 221 GLN cc_start: 0.7309 (mm-40) cc_final: 0.7081 (tp40) REVERT: E 498 ARG cc_start: 0.5717 (OUTLIER) cc_final: 0.4730 (ptt-90) REVERT: E 598 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.8032 (tptm) outliers start: 55 outliers final: 32 residues processed: 190 average time/residue: 1.4341 time to fit residues: 313.4962 Evaluate side-chains 189 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 340 VAL 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 560 ASN Chi-restraints excluded: chain A residue 637 THR 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 439 LEU Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 567 LEU 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 439 LEU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 498 ARG Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 560 ASN 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 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=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: 0.7980 chunk 18 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 212 optimal weight: 0.6980 chunk 211 optimal weight: 0.7980 chunk 82 optimal weight: 20.0000 chunk 109 optimal weight: 6.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 360 HIS C 403 GLN C 471 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 HIS D 471 GLN D 560 ASN E 360 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.237802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.212596 restraints weight = 19007.459| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 0.66 r_work: 0.4061 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.4018 rms_B_bonded: 1.75 restraints_weight: 0.2500 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.5618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 24395 Z= 0.160 Angle : 0.828 59.200 33070 Z= 0.486 Chirality : 0.045 0.375 3715 Planarity : 0.005 0.047 4275 Dihedral : 7.020 59.346 3480 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.03 % Allowed : 12.55 % Favored : 85.42 % Cbeta Deviations : 0.07 % 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: 2.30 (0.19), residues: 695 sheet: 1.15 (0.17), residues: 1015 loop : -0.64 (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 A 40 PHE 0.083 0.002 PHE E 561 TYR 0.015 0.001 TYR B 517 ARG 0.004 0.000 ARG C 498 Details of bonding type rmsd hydrogen bonds : bond 0.06130 ( 1110) hydrogen bonds : angle 4.66764 ( 3075) SS BOND : bond 0.00431 ( 5) SS BOND : angle 1.64838 ( 10) covalent geometry : bond 0.00307 (24390) covalent geometry : angle 0.82724 (33060) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20578.56 seconds wall clock time: 355 minutes 24.55 seconds (21324.55 seconds total)