Starting phenix.real_space_refine on Mon Aug 25 00:43:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9evb_19997/08_2025/9evb_19997.cif Found real_map, /net/cci-nas-00/data/ceres_data/9evb_19997/08_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_19997/08_2025/9evb_19997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9evb_19997/08_2025/9evb_19997.map" model { file = "/net/cci-nas-00/data/ceres_data/9evb_19997/08_2025/9evb_19997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9evb_19997/08_2025/9evb_19997.cif" } resolution = 2.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.10, per 1000 atoms: 0.17 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: 1.35 Conformation dependent library (CDL) restraints added in 852.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.78 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: 3.65 Time building geometry restraints manager: 1.79 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: 0.07 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 37 through 902 or resid 904)) selection = (chain 'B' and (resid 37 through 902 or resid 904)) selection = (chain 'C' and (resid 37 through 902 or resid 904)) selection = (chain 'D' and (resid 37 through 902 or resid 904)) selection = (chain 'E' and (resid 37 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: 4.720 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: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.240 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.020 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:7.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.060 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (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 ARG 0.029 0.003 ARG D 312 TYR 0.060 0.007 TYR B 65 PHE 0.031 0.007 PHE D 399 TRP 0.042 0.008 TRP B 482 HIS 0.019 0.006 HIS D 144 Details of bonding type rmsd covalent geometry : bond 0.00643 (24390) covalent geometry : angle 1.04469 (33060) SS BOND : bond 0.00511 ( 5) SS BOND : angle 2.50943 ( 10) hydrogen bonds : bond 0.17533 ( 1110) hydrogen bonds : angle 6.67105 ( 3075) *********************** 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 : 0.651 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: 0.6911 time to fit residues: 257.0754 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 : 0.695 ------------------------------------------------------------------------------- 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 197 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 3.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 HIS A 344 GLN A 360 HIS A 459 ASN B 233 HIS B 344 GLN B 360 HIS B 560 ASN C 233 HIS C 344 GLN C 360 HIS D 233 HIS D 344 GLN D 360 HIS D 432 GLN E 233 HIS E 344 GLN E 360 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.250850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.167704 restraints weight = 19845.652| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 6.97 r_work: 0.3449 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.084 24395 Z= 0.401 Angle : 1.040 10.735 33070 Z= 0.567 Chirality : 0.062 0.264 3715 Planarity : 0.008 0.089 4275 Dihedral : 9.162 59.319 3507 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 5.15 % Allowed : 7.68 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.15), residues: 2995 helix: 1.34 (0.19), residues: 695 sheet: 0.89 (0.15), residues: 935 loop : -1.00 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 578 TYR 0.026 0.005 TYR A 218 PHE 0.044 0.006 PHE E 561 TRP 0.017 0.004 TRP A 482 HIS 0.006 0.002 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00895 (24390) covalent geometry : angle 1.03976 (33060) SS BOND : bond 0.00367 ( 5) SS BOND : angle 1.71304 ( 10) hydrogen bonds : bond 0.10269 ( 1110) hydrogen bonds : angle 5.50851 ( 3075) *********************** 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 287 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 155 time to evaluate : 0.860 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 356 LYS cc_start: 0.9012 (tttt) cc_final: 0.8709 (tmtm) REVERT: A 374 THR cc_start: 0.7942 (m) cc_final: 0.7584 (p) REVERT: A 376 LYS cc_start: 0.7906 (tttt) cc_final: 0.7321 (tmtt) REVERT: A 468 ARG cc_start: 0.7763 (mtt180) cc_final: 0.7547 (mpt180) REVERT: B 68 MET cc_start: 0.3740 (ptm) cc_final: 0.3217 (ptp) REVERT: B 356 LYS cc_start: 0.9046 (tttt) cc_final: 0.8732 (tmtm) REVERT: B 363 LYS cc_start: 0.7782 (mtpt) cc_final: 0.7536 (mttp) REVERT: B 374 THR cc_start: 0.7945 (m) cc_final: 0.7554 (p) REVERT: B 376 LYS cc_start: 0.7978 (tttt) cc_final: 0.7381 (tmtt) REVERT: B 384 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7366 (mtt90) REVERT: B 468 ARG cc_start: 0.7806 (mtt180) cc_final: 0.7582 (mpt180) REVERT: C 290 ASP cc_start: 0.1355 (OUTLIER) cc_final: 0.0459 (t70) REVERT: C 356 LYS cc_start: 0.9130 (tttt) cc_final: 0.8807 (tmtm) REVERT: C 374 THR cc_start: 0.8010 (m) cc_final: 0.7734 (p) REVERT: C 376 LYS cc_start: 0.7967 (tttt) cc_final: 0.7699 (ttmt) REVERT: C 480 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7745 (tp30) REVERT: C 490 GLU cc_start: 0.8669 (tt0) cc_final: 0.8447 (tm-30) REVERT: C 498 ARG cc_start: 0.6035 (OUTLIER) cc_final: 0.5618 (mtt180) REVERT: D 356 LYS cc_start: 0.9059 (tttt) cc_final: 0.8738 (tmtm) REVERT: D 374 THR cc_start: 0.7857 (m) cc_final: 0.7506 (p) REVERT: D 376 LYS cc_start: 0.8023 (tttt) cc_final: 0.7393 (tmtt) REVERT: D 468 ARG cc_start: 0.7716 (mtt180) cc_final: 0.7426 (mpt180) REVERT: D 498 ARG cc_start: 0.6070 (OUTLIER) cc_final: 0.5589 (mtt180) REVERT: D 515 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8757 (mp) REVERT: E 356 LYS cc_start: 0.9112 (tttt) cc_final: 0.8752 (tmtm) REVERT: E 515 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8745 (mp) outliers start: 132 outliers final: 51 residues processed: 275 average time/residue: 0.5366 time to fit residues: 170.9220 Evaluate side-chains 199 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 141 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 379 GLU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 473 VAL 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 A residue 637 THR Chi-restraints excluded: chain B residue 162 THR 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 281 GLU Chi-restraints excluded: chain B residue 379 GLU 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 82 MET 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 439 LEU Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 473 VAL 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 290 ASP Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 458 THR Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 498 ARG Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 564 SER Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 501 THR Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 637 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 292 optimal weight: 0.8980 chunk 278 optimal weight: 0.9990 chunk 152 optimal weight: 0.9980 chunk 246 optimal weight: 20.0000 chunk 228 optimal weight: 0.7980 chunk 229 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 76 optimal weight: 30.0000 chunk 132 optimal weight: 0.0670 chunk 191 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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 344 GLN C 360 HIS C 489 GLN D 344 GLN D 360 HIS E 344 GLN E 360 HIS E 489 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.257450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.180925 restraints weight = 20353.124| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 5.83 r_work: 0.3642 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24395 Z= 0.117 Angle : 0.545 6.157 33070 Z= 0.293 Chirality : 0.043 0.160 3715 Planarity : 0.004 0.048 4275 Dihedral : 7.080 58.799 3493 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.03 % Allowed : 10.25 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.15), residues: 2995 helix: 2.25 (0.20), residues: 695 sheet: 0.99 (0.16), residues: 985 loop : -0.66 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 498 TYR 0.012 0.001 TYR B 517 PHE 0.018 0.002 PHE B 496 TRP 0.009 0.001 TRP D 359 HIS 0.003 0.001 HIS E 360 Details of bonding type rmsd covalent geometry : bond 0.00219 (24390) covalent geometry : angle 0.54477 (33060) SS BOND : bond 0.00277 ( 5) SS BOND : angle 1.37810 ( 10) hydrogen bonds : bond 0.05251 ( 1110) hydrogen bonds : angle 4.71311 ( 3075) *********************** 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 224 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 172 time to evaluate : 0.889 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 356 LYS cc_start: 0.8950 (tttt) cc_final: 0.8667 (tmtm) REVERT: A 374 THR cc_start: 0.7719 (m) cc_final: 0.7307 (p) REVERT: A 376 LYS cc_start: 0.7973 (tttt) cc_final: 0.7385 (tmtt) REVERT: A 389 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6290 (mt-10) REVERT: A 432 GLN cc_start: 0.8506 (mt0) cc_final: 0.7784 (mm110) REVERT: A 480 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7491 (tp30) REVERT: A 569 ARG cc_start: 0.7656 (mtm-85) cc_final: 0.7436 (mmp-170) REVERT: B 68 MET cc_start: 0.3519 (ptm) cc_final: 0.3156 (ptp) REVERT: B 356 LYS cc_start: 0.8932 (tttt) cc_final: 0.8603 (tmtm) REVERT: B 363 LYS cc_start: 0.7558 (mtpt) cc_final: 0.7298 (mttp) REVERT: B 374 THR cc_start: 0.7639 (m) cc_final: 0.7352 (p) REVERT: B 432 GLN cc_start: 0.8449 (mt0) cc_final: 0.7787 (mm110) REVERT: B 465 GLU cc_start: 0.8849 (tt0) cc_final: 0.8557 (tm-30) REVERT: B 480 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7466 (tp30) REVERT: C 162 THR cc_start: 0.5800 (OUTLIER) cc_final: 0.5592 (p) REVERT: C 356 LYS cc_start: 0.8999 (tttt) cc_final: 0.8707 (tmtm) REVERT: C 374 THR cc_start: 0.7690 (m) cc_final: 0.7402 (p) REVERT: C 376 LYS cc_start: 0.7969 (tttt) cc_final: 0.7437 (tmtt) REVERT: C 432 GLN cc_start: 0.8430 (mt0) cc_final: 0.7728 (mm110) REVERT: C 480 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7209 (tm-30) REVERT: C 490 GLU cc_start: 0.8612 (tt0) cc_final: 0.8346 (tm-30) REVERT: D 356 LYS cc_start: 0.8984 (tttt) cc_final: 0.8669 (tmtm) REVERT: D 374 THR cc_start: 0.7613 (m) cc_final: 0.7263 (p) REVERT: D 376 LYS cc_start: 0.8003 (tttt) cc_final: 0.7425 (tmtt) REVERT: D 432 GLN cc_start: 0.8537 (mt0) cc_final: 0.7853 (mm110) REVERT: D 468 ARG cc_start: 0.7673 (mtt180) cc_final: 0.7417 (mpt180) REVERT: D 480 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7438 (tm-30) REVERT: D 498 ARG cc_start: 0.5725 (OUTLIER) cc_final: 0.5453 (mtt180) REVERT: E 356 LYS cc_start: 0.8993 (tttt) cc_final: 0.8668 (tmtm) REVERT: E 374 THR cc_start: 0.7569 (m) cc_final: 0.7116 (p) REVERT: E 379 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8211 (mt-10) outliers start: 52 outliers final: 13 residues processed: 222 average time/residue: 0.5688 time to fit residues: 145.6440 Evaluate side-chains 174 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 480 GLU Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 262 ILE 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 498 ARG Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 439 LEU 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 249 optimal weight: 20.0000 chunk 239 optimal weight: 5.9990 chunk 279 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 257 optimal weight: 20.0000 chunk 102 optimal weight: 0.0270 chunk 38 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 chunk 290 optimal weight: 4.9990 chunk 230 optimal weight: 0.0970 overall best weight: 2.0242 ------------------------------------------------------------------------------- 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 489 GLN B 307 ASN B 489 GLN C 344 GLN C 471 GLN D 221 GLN D 307 ASN D 344 GLN D 360 HIS D 471 GLN E 344 GLN E 360 HIS E 471 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.259021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.183121 restraints weight = 19703.266| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 4.93 r_work: 0.3458 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24395 Z= 0.178 Angle : 0.640 8.230 33070 Z= 0.348 Chirality : 0.046 0.168 3715 Planarity : 0.005 0.047 4275 Dihedral : 7.146 57.702 3484 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.77 % Allowed : 10.02 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.15), residues: 2995 helix: 2.16 (0.20), residues: 695 sheet: 1.22 (0.16), residues: 955 loop : -0.73 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 578 TYR 0.018 0.002 TYR C 542 PHE 0.035 0.003 PHE B 561 TRP 0.009 0.002 TRP D 359 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00360 (24390) covalent geometry : angle 0.63968 (33060) SS BOND : bond 0.00325 ( 5) SS BOND : angle 1.42201 ( 10) hydrogen bonds : bond 0.07103 ( 1110) hydrogen bonds : angle 4.82663 ( 3075) *********************** 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 220 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 149 time to evaluate : 0.712 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 356 LYS cc_start: 0.9011 (tttt) cc_final: 0.8713 (tmtm) REVERT: A 374 THR cc_start: 0.7774 (m) cc_final: 0.7377 (p) REVERT: A 376 LYS cc_start: 0.8052 (tttt) cc_final: 0.7474 (tmtt) REVERT: A 515 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8948 (mp) REVERT: A 569 ARG cc_start: 0.7755 (mtm-85) cc_final: 0.7493 (mmp-170) REVERT: B 68 MET cc_start: 0.3808 (ptm) cc_final: 0.3366 (ptp) REVERT: B 162 THR cc_start: 0.5982 (OUTLIER) cc_final: 0.5760 (p) REVERT: B 356 LYS cc_start: 0.8969 (tttt) cc_final: 0.8703 (tmtm) REVERT: B 363 LYS cc_start: 0.7738 (mtpt) cc_final: 0.7462 (mttp) REVERT: B 374 THR cc_start: 0.7746 (m) cc_final: 0.7459 (p) REVERT: B 384 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7350 (mtt90) REVERT: B 432 GLN cc_start: 0.8507 (mt0) cc_final: 0.7899 (mm110) REVERT: C 356 LYS cc_start: 0.9093 (tttt) cc_final: 0.8812 (tmtm) REVERT: C 374 THR cc_start: 0.7841 (m) cc_final: 0.7548 (p) REVERT: C 376 LYS cc_start: 0.8009 (tttt) cc_final: 0.7466 (tmtt) REVERT: C 403 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7925 (tm-30) REVERT: C 432 GLN cc_start: 0.8610 (mt0) cc_final: 0.7921 (mm110) REVERT: C 480 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7674 (tp30) REVERT: C 490 GLU cc_start: 0.8689 (tt0) cc_final: 0.8473 (tm-30) REVERT: D 221 GLN cc_start: 0.7325 (mm-40) cc_final: 0.6804 (mm110) REVERT: D 356 LYS cc_start: 0.9012 (tttt) cc_final: 0.8755 (tmtm) REVERT: D 374 THR cc_start: 0.7722 (m) cc_final: 0.7348 (p) REVERT: D 376 LYS cc_start: 0.7990 (tttt) cc_final: 0.7407 (tmtt) REVERT: D 432 GLN cc_start: 0.8585 (mt0) cc_final: 0.7933 (mm110) REVERT: D 468 ARG cc_start: 0.7734 (mtt180) cc_final: 0.7463 (mpt180) REVERT: D 480 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7918 (mt-10) REVERT: D 498 ARG cc_start: 0.5914 (OUTLIER) cc_final: 0.5499 (mtt180) REVERT: E 356 LYS cc_start: 0.9036 (tttt) cc_final: 0.8753 (tmtm) REVERT: E 374 THR cc_start: 0.7638 (m) cc_final: 0.7165 (p) REVERT: E 598 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8289 (tptm) outliers start: 71 outliers final: 37 residues processed: 214 average time/residue: 0.6162 time to fit residues: 151.8932 Evaluate side-chains 193 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain B residue 162 THR 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 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 480 GLU 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 279 ILE Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 403 GLN Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 279 ILE 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 562 THR Chi-restraints excluded: chain D residue 564 SER Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 598 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 231 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 234 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 287 optimal weight: 0.9980 chunk 134 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 235 optimal weight: 1.9990 chunk 214 optimal weight: 6.9990 chunk 298 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 307 ASN D 360 HIS D 471 GLN E 307 ASN E 360 HIS E 471 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.253858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.174809 restraints weight = 20039.810| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 6.34 r_work: 0.3473 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24395 Z= 0.147 Angle : 0.577 8.731 33070 Z= 0.311 Chirality : 0.044 0.157 3715 Planarity : 0.004 0.046 4275 Dihedral : 6.629 59.711 3484 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.50 % Allowed : 10.45 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.16), residues: 2995 helix: 2.35 (0.20), residues: 690 sheet: 1.20 (0.16), residues: 990 loop : -0.66 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 578 TYR 0.014 0.002 TYR E 517 PHE 0.028 0.002 PHE B 561 TRP 0.009 0.001 TRP D 359 HIS 0.003 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00291 (24390) covalent geometry : angle 0.57668 (33060) SS BOND : bond 0.00364 ( 5) SS BOND : angle 1.42680 ( 10) hydrogen bonds : bond 0.06017 ( 1110) hydrogen bonds : angle 4.63059 ( 3075) *********************** 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 218 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 154 time to evaluate : 1.000 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: A 356 LYS cc_start: 0.9001 (tttt) cc_final: 0.8718 (tmtm) REVERT: A 374 THR cc_start: 0.7699 (m) cc_final: 0.7244 (p) REVERT: A 376 LYS cc_start: 0.7958 (tttt) cc_final: 0.7346 (tmtt) REVERT: A 432 GLN cc_start: 0.8510 (mt0) cc_final: 0.7829 (mm110) REVERT: A 480 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7729 (mt-10) REVERT: A 547 GLU cc_start: 0.8661 (tt0) cc_final: 0.8264 (tm-30) REVERT: A 569 ARG cc_start: 0.7618 (mtm-85) cc_final: 0.7376 (mmp-170) REVERT: B 162 THR cc_start: 0.6083 (OUTLIER) cc_final: 0.5843 (p) REVERT: B 356 LYS cc_start: 0.8956 (tttt) cc_final: 0.8693 (tmtm) REVERT: B 363 LYS cc_start: 0.7599 (mtpt) cc_final: 0.7355 (mttp) REVERT: B 374 THR cc_start: 0.7632 (m) cc_final: 0.7351 (p) REVERT: B 432 GLN cc_start: 0.8404 (mt0) cc_final: 0.7808 (mm110) REVERT: C 356 LYS cc_start: 0.9030 (tttt) cc_final: 0.8746 (tmtm) REVERT: C 374 THR cc_start: 0.7538 (m) cc_final: 0.7263 (p) REVERT: C 376 LYS cc_start: 0.7924 (tttt) cc_final: 0.7347 (tmtt) REVERT: C 384 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7213 (mtt90) REVERT: C 403 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8150 (tt0) REVERT: C 432 GLN cc_start: 0.8521 (mt0) cc_final: 0.7832 (mm110) REVERT: C 480 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7503 (tp30) REVERT: C 490 GLU cc_start: 0.8661 (tt0) cc_final: 0.8401 (tm-30) REVERT: D 82 MET cc_start: 0.1916 (ptp) cc_final: 0.0633 (mmt) REVERT: D 356 LYS cc_start: 0.8971 (tttt) cc_final: 0.8691 (tmtm) REVERT: D 374 THR cc_start: 0.7540 (m) cc_final: 0.7177 (p) REVERT: D 376 LYS cc_start: 0.7969 (tttt) cc_final: 0.7340 (tmtt) REVERT: D 432 GLN cc_start: 0.8589 (mt0) cc_final: 0.7895 (mm110) REVERT: D 468 ARG cc_start: 0.7721 (mtt180) cc_final: 0.7462 (mpt180) REVERT: D 480 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7741 (tp30) REVERT: D 498 ARG cc_start: 0.5642 (OUTLIER) cc_final: 0.5435 (mtt180) REVERT: E 356 LYS cc_start: 0.9030 (tttt) cc_final: 0.8728 (tmtm) REVERT: E 374 THR cc_start: 0.7411 (m) cc_final: 0.6933 (p) REVERT: E 598 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8187 (tptm) outliers start: 64 outliers final: 38 residues processed: 212 average time/residue: 0.6972 time to fit residues: 170.7111 Evaluate side-chains 197 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 151 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 328 ASP 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 562 THR Chi-restraints excluded: chain B residue 162 THR 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 328 ASP Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 480 GLU 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 279 ILE Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain C residue 403 GLN Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 279 ILE 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 562 THR Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 598 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 75 optimal weight: 30.0000 chunk 64 optimal weight: 10.0000 chunk 230 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 191 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 245 optimal weight: 0.8980 chunk 260 optimal weight: 0.0770 chunk 5 optimal weight: 0.9980 overall best weight: 1.3740 ------------------------------------------------------------------------------- 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 D 221 GLN D 360 HIS D 471 GLN E 221 GLN E 360 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.252270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.173277 restraints weight = 20070.239| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 6.85 r_work: 0.3059 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24395 Z= 0.141 Angle : 0.566 9.199 33070 Z= 0.305 Chirality : 0.044 0.158 3715 Planarity : 0.004 0.045 4275 Dihedral : 6.459 58.753 3484 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.46 % Allowed : 10.84 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.16), residues: 2995 helix: 2.45 (0.20), residues: 690 sheet: 1.34 (0.17), residues: 975 loop : -0.58 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 578 TYR 0.015 0.002 TYR B 517 PHE 0.033 0.002 PHE C 561 TRP 0.008 0.001 TRP D 359 HIS 0.003 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00276 (24390) covalent geometry : angle 0.56508 (33060) SS BOND : bond 0.00349 ( 5) SS BOND : angle 1.41028 ( 10) hydrogen bonds : bond 0.06089 ( 1110) hydrogen bonds : angle 4.61227 ( 3075) *********************** 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 215 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 152 time to evaluate : 0.800 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: A 356 LYS cc_start: 0.8998 (tttt) cc_final: 0.8690 (tmtm) REVERT: A 374 THR cc_start: 0.7481 (m) cc_final: 0.6968 (p) REVERT: A 376 LYS cc_start: 0.7895 (tttt) cc_final: 0.7195 (tmtt) REVERT: A 432 GLN cc_start: 0.8619 (mt0) cc_final: 0.7900 (mm110) REVERT: A 547 GLU cc_start: 0.8668 (tt0) cc_final: 0.8271 (tm-30) REVERT: A 569 ARG cc_start: 0.7647 (mtm-85) cc_final: 0.7287 (mmp-170) REVERT: B 68 MET cc_start: 0.3150 (ptm) cc_final: 0.2878 (ptp) REVERT: B 162 THR cc_start: 0.5986 (OUTLIER) cc_final: 0.5738 (p) REVERT: B 356 LYS cc_start: 0.8939 (tttt) cc_final: 0.8687 (tmtm) REVERT: B 363 LYS cc_start: 0.7563 (mtpt) cc_final: 0.7304 (mttp) REVERT: B 374 THR cc_start: 0.7449 (m) cc_final: 0.7215 (p) REVERT: B 384 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7265 (mtt90) REVERT: B 432 GLN cc_start: 0.8520 (mt0) cc_final: 0.7877 (mm110) REVERT: C 82 MET cc_start: 0.1167 (pmm) cc_final: -0.0740 (mmt) REVERT: C 356 LYS cc_start: 0.9058 (tttt) cc_final: 0.8779 (tmtm) REVERT: C 374 THR cc_start: 0.7456 (m) cc_final: 0.7139 (p) REVERT: C 376 LYS cc_start: 0.7863 (tttt) cc_final: 0.7243 (tmtt) REVERT: C 384 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7171 (mtt90) REVERT: C 403 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8332 (tt0) REVERT: C 432 GLN cc_start: 0.8587 (mt0) cc_final: 0.7895 (mm110) REVERT: C 480 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7537 (tp30) REVERT: C 490 GLU cc_start: 0.8762 (tt0) cc_final: 0.8544 (tm-30) REVERT: D 221 GLN cc_start: 0.7227 (mm-40) cc_final: 0.6921 (tp40) REVERT: D 356 LYS cc_start: 0.8979 (tttt) cc_final: 0.8675 (tmtm) REVERT: D 374 THR cc_start: 0.7364 (m) cc_final: 0.6993 (p) REVERT: D 376 LYS cc_start: 0.7870 (tttt) cc_final: 0.7219 (tmtt) REVERT: D 432 GLN cc_start: 0.8637 (mt0) cc_final: 0.7935 (mm110) REVERT: D 468 ARG cc_start: 0.7777 (mtt180) cc_final: 0.7392 (mpt180) REVERT: D 498 ARG cc_start: 0.5661 (OUTLIER) cc_final: 0.5383 (mtt180) REVERT: D 515 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8840 (mp) REVERT: E 221 GLN cc_start: 0.7038 (mm-40) cc_final: 0.6707 (tp-100) REVERT: E 356 LYS cc_start: 0.8996 (tttt) cc_final: 0.8690 (tmtm) REVERT: E 374 THR cc_start: 0.7260 (m) cc_final: 0.6776 (p) REVERT: E 598 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8188 (tptm) outliers start: 63 outliers final: 36 residues processed: 209 average time/residue: 0.5831 time to fit residues: 140.3801 Evaluate side-chains 194 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 150 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain B residue 162 THR 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 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 480 GLU 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 279 ILE Chi-restraints excluded: chain C residue 328 ASP Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain C residue 403 GLN Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 562 THR 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 567 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 598 LYS Chi-restraints excluded: chain E residue 633 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 167 optimal weight: 4.9990 chunk 126 optimal weight: 30.0000 chunk 174 optimal weight: 5.9990 chunk 273 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 211 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 246 optimal weight: 30.0000 chunk 148 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 283 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 D 360 HIS D 459 ASN D 471 GLN E 360 HIS E 560 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.250035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.169714 restraints weight = 19805.581| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 6.63 r_work: 0.2985 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 24395 Z= 0.244 Angle : 0.737 9.508 33070 Z= 0.403 Chirality : 0.050 0.201 3715 Planarity : 0.005 0.054 4275 Dihedral : 7.833 59.580 3484 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.88 % Allowed : 10.84 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.15), residues: 2995 helix: 2.05 (0.19), residues: 695 sheet: 1.18 (0.17), residues: 955 loop : -0.71 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 578 TYR 0.021 0.003 TYR C 542 PHE 0.060 0.004 PHE E 561 TRP 0.011 0.002 TRP D 359 HIS 0.004 0.001 HIS E 285 Details of bonding type rmsd covalent geometry : bond 0.00519 (24390) covalent geometry : angle 0.73636 (33060) SS BOND : bond 0.00413 ( 5) SS BOND : angle 1.57753 ( 10) hydrogen bonds : bond 0.08308 ( 1110) hydrogen bonds : angle 4.94368 ( 3075) *********************** 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 226 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 152 time to evaluate : 1.137 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 356 LYS cc_start: 0.8969 (tttt) cc_final: 0.8661 (tmtm) REVERT: A 374 THR cc_start: 0.7766 (m) cc_final: 0.7413 (p) REVERT: A 376 LYS cc_start: 0.7919 (tttt) cc_final: 0.7289 (tmtt) REVERT: A 569 ARG cc_start: 0.7783 (mtm-85) cc_final: 0.7295 (mmp-170) REVERT: B 162 THR cc_start: 0.6276 (OUTLIER) cc_final: 0.6014 (p) REVERT: B 356 LYS cc_start: 0.8994 (tttt) cc_final: 0.8700 (tmtm) REVERT: B 363 LYS cc_start: 0.7735 (mtpt) cc_final: 0.7437 (mttp) REVERT: B 374 THR cc_start: 0.7784 (m) cc_final: 0.7518 (p) REVERT: B 384 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7256 (mtt90) REVERT: B 432 GLN cc_start: 0.8586 (mt0) cc_final: 0.7916 (mm-40) REVERT: B 515 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8785 (mp) REVERT: C 82 MET cc_start: 0.1231 (pmm) cc_final: -0.0653 (mmt) REVERT: C 153 ASN cc_start: 0.6998 (t0) cc_final: 0.6667 (t0) REVERT: C 356 LYS cc_start: 0.9095 (tttt) cc_final: 0.8791 (tmtm) REVERT: C 376 LYS cc_start: 0.7900 (tttt) cc_final: 0.7578 (ttmt) REVERT: C 384 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7209 (mtt90) REVERT: C 403 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8065 (tm-30) REVERT: C 480 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7614 (tp30) REVERT: D 82 MET cc_start: 0.1423 (ptp) cc_final: 0.0403 (mmt) REVERT: D 221 GLN cc_start: 0.7111 (mm-40) cc_final: 0.6666 (mm110) REVERT: D 337 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.8282 (m-30) REVERT: D 356 LYS cc_start: 0.9005 (tttt) cc_final: 0.8698 (tmtm) REVERT: D 374 THR cc_start: 0.7593 (m) cc_final: 0.7314 (p) REVERT: D 376 LYS cc_start: 0.7938 (tttt) cc_final: 0.7256 (tmtt) REVERT: D 432 GLN cc_start: 0.8671 (mt0) cc_final: 0.7947 (mm110) REVERT: D 468 ARG cc_start: 0.7762 (mtt180) cc_final: 0.7471 (mpt180) REVERT: D 480 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7737 (tp30) REVERT: D 498 ARG cc_start: 0.5935 (OUTLIER) cc_final: 0.5614 (mtt180) REVERT: D 515 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8807 (mp) REVERT: E 221 GLN cc_start: 0.6926 (mm-40) cc_final: 0.6614 (tp40) REVERT: E 356 LYS cc_start: 0.9053 (tttt) cc_final: 0.8694 (tmtm) REVERT: E 374 THR cc_start: 0.7730 (m) cc_final: 0.7308 (p) REVERT: E 569 ARG cc_start: 0.7782 (mtm-85) cc_final: 0.7257 (mmp-170) REVERT: E 598 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8338 (tptm) outliers start: 74 outliers final: 35 residues processed: 218 average time/residue: 0.6645 time to fit residues: 166.6162 Evaluate side-chains 191 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 145 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 562 THR Chi-restraints excluded: chain B residue 162 THR 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 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 480 GLU Chi-restraints excluded: chain B residue 515 LEU 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 262 ILE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain C residue 403 GLN Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 498 ARG Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 564 SER Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 279 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 562 THR Chi-restraints excluded: chain E residue 598 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 225 optimal weight: 0.6980 chunk 163 optimal weight: 1.9990 chunk 146 optimal weight: 30.0000 chunk 179 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 248 optimal weight: 8.9990 chunk 166 optimal weight: 0.6980 chunk 135 optimal weight: 0.0370 chunk 281 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.8460 ------------------------------------------------------------------------------- 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 B 560 ASN C 432 GLN D 360 HIS E 360 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.254543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.179681 restraints weight = 20117.897| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 5.56 r_work: 0.3128 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 24395 Z= 0.119 Angle : 0.524 8.492 33070 Z= 0.281 Chirality : 0.042 0.149 3715 Planarity : 0.004 0.048 4275 Dihedral : 6.641 58.112 3484 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.11 % Allowed : 11.70 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.16), residues: 2995 helix: 2.56 (0.19), residues: 690 sheet: 1.17 (0.17), residues: 995 loop : -0.60 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 578 TYR 0.012 0.001 TYR E 517 PHE 0.055 0.002 PHE E 561 TRP 0.008 0.001 TRP D 359 HIS 0.003 0.001 HIS E 360 Details of bonding type rmsd covalent geometry : bond 0.00227 (24390) covalent geometry : angle 0.52381 (33060) SS BOND : bond 0.00337 ( 5) SS BOND : angle 1.39331 ( 10) hydrogen bonds : bond 0.05083 ( 1110) hydrogen bonds : angle 4.50327 ( 3075) *********************** 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 208 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 154 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.1665 (ptp) cc_final: 0.0167 (mmm) REVERT: A 356 LYS cc_start: 0.8978 (tttt) cc_final: 0.8650 (tmtm) REVERT: A 374 THR cc_start: 0.7497 (m) cc_final: 0.7028 (p) REVERT: A 376 LYS cc_start: 0.7864 (tttt) cc_final: 0.7167 (tmtt) REVERT: A 432 GLN cc_start: 0.8553 (mt0) cc_final: 0.7846 (mm110) REVERT: A 547 GLU cc_start: 0.8596 (tt0) cc_final: 0.8207 (tm-30) REVERT: A 569 ARG cc_start: 0.7704 (mtm-85) cc_final: 0.7281 (mmp-170) REVERT: B 68 MET cc_start: 0.3042 (ptm) cc_final: 0.2403 (ptp) REVERT: B 162 THR cc_start: 0.6280 (OUTLIER) cc_final: 0.5997 (p) REVERT: B 356 LYS cc_start: 0.8958 (tttt) cc_final: 0.8661 (tmtm) REVERT: B 363 LYS cc_start: 0.7569 (mtpt) cc_final: 0.7313 (mttp) REVERT: B 374 THR cc_start: 0.7419 (m) cc_final: 0.7218 (p) REVERT: B 432 GLN cc_start: 0.8513 (mt0) cc_final: 0.7866 (mm110) REVERT: B 560 ASN cc_start: 0.8626 (t0) cc_final: 0.8350 (t0) REVERT: C 82 MET cc_start: 0.1002 (pmm) cc_final: -0.0772 (mmm) REVERT: C 356 LYS cc_start: 0.9003 (tttt) cc_final: 0.8708 (tmtm) REVERT: C 376 LYS cc_start: 0.7853 (tttt) cc_final: 0.7218 (tmtt) REVERT: C 403 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8267 (tt0) REVERT: C 432 GLN cc_start: 0.8479 (mt0) cc_final: 0.7791 (mm110) REVERT: C 480 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7168 (tm-30) REVERT: C 490 GLU cc_start: 0.8705 (tt0) cc_final: 0.8469 (tm-30) REVERT: C 567 LEU cc_start: 0.7620 (mp) cc_final: 0.7234 (mm) REVERT: D 82 MET cc_start: 0.1504 (ptp) cc_final: 0.0365 (mmt) REVERT: D 356 LYS cc_start: 0.8953 (tttt) cc_final: 0.8649 (tmtm) REVERT: D 374 THR cc_start: 0.7325 (m) cc_final: 0.7038 (p) REVERT: D 376 LYS cc_start: 0.7834 (tttt) cc_final: 0.7153 (tmtt) REVERT: D 432 GLN cc_start: 0.8569 (mt0) cc_final: 0.7873 (mm110) REVERT: D 468 ARG cc_start: 0.7793 (mtt180) cc_final: 0.7411 (mpt180) REVERT: D 480 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7650 (tp30) REVERT: D 490 GLU cc_start: 0.8756 (tt0) cc_final: 0.8522 (tm-30) REVERT: D 498 ARG cc_start: 0.5609 (OUTLIER) cc_final: 0.5315 (mtt180) REVERT: E 82 MET cc_start: 0.1645 (ptp) cc_final: 0.0238 (mmm) REVERT: E 221 GLN cc_start: 0.7091 (mm-40) cc_final: 0.6801 (tp40) REVERT: E 356 LYS cc_start: 0.9008 (tttt) cc_final: 0.8647 (tmtm) REVERT: E 374 THR cc_start: 0.7224 (m) cc_final: 0.6768 (p) REVERT: E 432 GLN cc_start: 0.8522 (mt0) cc_final: 0.7780 (mm110) REVERT: E 598 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8090 (tptm) outliers start: 54 outliers final: 28 residues processed: 203 average time/residue: 0.7166 time to fit residues: 166.9804 Evaluate side-chains 187 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 562 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 236 VAL 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 449 SER Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 286 VAL 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 562 THR 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 562 THR Chi-restraints excluded: chain D residue 564 SER Chi-restraints excluded: chain D residue 603 VAL 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 562 THR Chi-restraints excluded: chain E residue 598 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 236 optimal weight: 6.9990 chunk 232 optimal weight: 0.6980 chunk 87 optimal weight: 8.9990 chunk 182 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 140 optimal weight: 0.0870 chunk 245 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 246 optimal weight: 7.9990 chunk 122 optimal weight: 20.0000 overall best weight: 1.9564 ------------------------------------------------------------------------------- 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 471 GLN D 360 HIS D 471 GLN E 360 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.251770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.171695 restraints weight = 20063.727| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 6.87 r_work: 0.3029 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24395 Z= 0.169 Angle : 0.611 7.805 33070 Z= 0.331 Chirality : 0.045 0.160 3715 Planarity : 0.005 0.046 4275 Dihedral : 6.972 59.903 3484 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.18 % Allowed : 11.81 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.16), residues: 2995 helix: 2.34 (0.19), residues: 695 sheet: 1.18 (0.17), residues: 990 loop : -0.60 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 578 TYR 0.017 0.002 TYR C 542 PHE 0.034 0.003 PHE D 561 TRP 0.009 0.002 TRP D 359 HIS 0.003 0.001 HIS E 360 Details of bonding type rmsd covalent geometry : bond 0.00342 (24390) covalent geometry : angle 0.61023 (33060) SS BOND : bond 0.00407 ( 5) SS BOND : angle 1.53899 ( 10) hydrogen bonds : bond 0.06778 ( 1110) hydrogen bonds : angle 4.67039 ( 3075) *********************** 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 209 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 153 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.1572 (ptp) cc_final: 0.0216 (mmm) REVERT: A 356 LYS cc_start: 0.8941 (tttt) cc_final: 0.8657 (tmtm) REVERT: A 374 THR cc_start: 0.7596 (m) cc_final: 0.7141 (p) REVERT: A 376 LYS cc_start: 0.7811 (tttt) cc_final: 0.7116 (tmtt) REVERT: A 432 GLN cc_start: 0.8600 (mt0) cc_final: 0.7891 (mm110) REVERT: A 480 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7745 (tp30) REVERT: A 547 GLU cc_start: 0.8719 (tt0) cc_final: 0.8310 (tm-30) REVERT: A 569 ARG cc_start: 0.7748 (mtm-85) cc_final: 0.7277 (mmp-170) REVERT: B 82 MET cc_start: 0.1584 (ptp) cc_final: 0.0409 (mmm) REVERT: B 162 THR cc_start: 0.6200 (OUTLIER) cc_final: 0.5938 (p) REVERT: B 356 LYS cc_start: 0.8945 (tttt) cc_final: 0.8673 (tmtm) REVERT: B 363 LYS cc_start: 0.7607 (mtpt) cc_final: 0.7289 (mttp) REVERT: B 384 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7216 (mtt90) REVERT: B 432 GLN cc_start: 0.8540 (mt0) cc_final: 0.7878 (mm110) REVERT: C 68 MET cc_start: 0.3084 (pmm) cc_final: 0.2869 (ptp) REVERT: C 82 MET cc_start: 0.0949 (pmm) cc_final: -0.0813 (mmm) REVERT: C 356 LYS cc_start: 0.9070 (tttt) cc_final: 0.8780 (tmtm) REVERT: C 376 LYS cc_start: 0.7826 (tttt) cc_final: 0.7248 (tmtt) REVERT: C 384 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7111 (mtt90) REVERT: C 403 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8009 (tm-30) REVERT: C 432 GLN cc_start: 0.8590 (mt0) cc_final: 0.7882 (mm110) REVERT: C 480 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7570 (tp30) REVERT: C 490 GLU cc_start: 0.8728 (tt0) cc_final: 0.8494 (tm-30) REVERT: D 82 MET cc_start: 0.1317 (ptp) cc_final: 0.0281 (mmt) REVERT: D 221 GLN cc_start: 0.7167 (mm-40) cc_final: 0.6865 (tp40) REVERT: D 356 LYS cc_start: 0.8947 (tttt) cc_final: 0.8653 (tmtm) REVERT: D 374 THR cc_start: 0.7486 (m) cc_final: 0.7161 (p) REVERT: D 376 LYS cc_start: 0.7825 (tttt) cc_final: 0.7140 (tmtt) REVERT: D 432 GLN cc_start: 0.8636 (mt0) cc_final: 0.7938 (mm110) REVERT: D 468 ARG cc_start: 0.7819 (mtt180) cc_final: 0.7458 (mpt180) REVERT: D 480 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7723 (tp30) REVERT: D 498 ARG cc_start: 0.5751 (OUTLIER) cc_final: 0.5463 (mtt180) REVERT: E 82 MET cc_start: 0.1435 (ptp) cc_final: 0.0198 (mmm) REVERT: E 221 GLN cc_start: 0.6991 (mm-40) cc_final: 0.6721 (tp40) REVERT: E 356 LYS cc_start: 0.9029 (tttt) cc_final: 0.8690 (tmtm) REVERT: E 374 THR cc_start: 0.7397 (m) cc_final: 0.6937 (p) REVERT: E 569 ARG cc_start: 0.7827 (mtm-85) cc_final: 0.7342 (mmp-170) REVERT: E 598 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8226 (tptm) outliers start: 56 outliers final: 29 residues processed: 200 average time/residue: 0.7449 time to fit residues: 170.1197 Evaluate side-chains 185 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 562 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 236 VAL 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 449 SER 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 C residue 262 ILE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain C residue 403 GLN Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 562 THR 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 562 THR Chi-restraints excluded: chain D residue 564 SER Chi-restraints excluded: chain D residue 603 VAL 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 562 THR Chi-restraints excluded: chain E residue 598 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 274 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 295 optimal weight: 5.9990 chunk 35 optimal weight: 0.4980 chunk 284 optimal weight: 0.1980 chunk 86 optimal weight: 20.0000 chunk 286 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 255 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN A 360 HIS B 360 HIS B 560 ASN C 471 GLN D 360 HIS D 471 GLN E 360 HIS E 459 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.255168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.181094 restraints weight = 20282.127| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 5.49 r_work: 0.3551 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 24395 Z= 0.107 Angle : 0.502 6.822 33070 Z= 0.269 Chirality : 0.042 0.153 3715 Planarity : 0.004 0.048 4275 Dihedral : 6.199 58.903 3484 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.40 % Allowed : 12.63 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.16), residues: 2995 helix: 2.69 (0.20), residues: 690 sheet: 1.22 (0.17), residues: 1000 loop : -0.54 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 498 TYR 0.011 0.001 TYR A 542 PHE 0.031 0.002 PHE E 561 TRP 0.008 0.001 TRP D 359 HIS 0.004 0.001 HIS E 360 Details of bonding type rmsd covalent geometry : bond 0.00204 (24390) covalent geometry : angle 0.50125 (33060) SS BOND : bond 0.00336 ( 5) SS BOND : angle 1.39626 ( 10) hydrogen bonds : bond 0.04753 ( 1110) hydrogen bonds : angle 4.39576 ( 3075) ********************** 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 184 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.1698 (ptp) cc_final: 0.0222 (mmm) REVERT: A 356 LYS cc_start: 0.8877 (tttt) cc_final: 0.8650 (tmtm) REVERT: A 374 THR cc_start: 0.7458 (m) cc_final: 0.6928 (p) REVERT: A 376 LYS cc_start: 0.7929 (tttt) cc_final: 0.7299 (tmtt) REVERT: A 432 GLN cc_start: 0.8469 (mt0) cc_final: 0.7783 (mm110) REVERT: A 480 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7692 (tp30) REVERT: A 547 GLU cc_start: 0.8584 (tt0) cc_final: 0.8231 (tm-30) REVERT: A 562 THR cc_start: 0.7525 (OUTLIER) cc_final: 0.7258 (t) REVERT: A 569 ARG cc_start: 0.7763 (mtm-85) cc_final: 0.7444 (mmp-170) REVERT: B 68 MET cc_start: 0.3118 (ptm) cc_final: 0.2410 (ptp) REVERT: B 82 MET cc_start: 0.1668 (ptp) cc_final: 0.0394 (mmm) REVERT: B 162 THR cc_start: 0.6344 (OUTLIER) cc_final: 0.6050 (p) REVERT: B 356 LYS cc_start: 0.8899 (tttt) cc_final: 0.8632 (tmtm) REVERT: B 363 LYS cc_start: 0.7554 (mtpt) cc_final: 0.7304 (mttp) REVERT: B 432 GLN cc_start: 0.8473 (mt0) cc_final: 0.7819 (mm110) REVERT: B 465 GLU cc_start: 0.8857 (tt0) cc_final: 0.8558 (tm-30) REVERT: C 82 MET cc_start: 0.1073 (pmm) cc_final: -0.0742 (mmm) REVERT: C 356 LYS cc_start: 0.8980 (tttt) cc_final: 0.8713 (tmtm) REVERT: C 376 LYS cc_start: 0.7893 (tttt) cc_final: 0.7335 (tmtt) REVERT: C 432 GLN cc_start: 0.8451 (mt0) cc_final: 0.7791 (mm110) REVERT: C 480 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7224 (tm-30) REVERT: C 490 GLU cc_start: 0.8633 (tt0) cc_final: 0.8377 (tm-30) REVERT: C 561 PHE cc_start: 0.7418 (t80) cc_final: 0.7165 (p90) REVERT: C 567 LEU cc_start: 0.7707 (mp) cc_final: 0.7347 (mm) REVERT: D 82 MET cc_start: 0.1438 (ptp) cc_final: 0.0398 (mmt) REVERT: D 356 LYS cc_start: 0.8921 (tttt) cc_final: 0.8649 (tmtm) REVERT: D 374 THR cc_start: 0.7348 (m) cc_final: 0.6989 (p) REVERT: D 376 LYS cc_start: 0.7921 (tttt) cc_final: 0.7306 (tmtt) REVERT: D 432 GLN cc_start: 0.8580 (mt0) cc_final: 0.7901 (mm110) REVERT: D 468 ARG cc_start: 0.7776 (mtt180) cc_final: 0.7430 (mpt180) REVERT: D 480 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7735 (tp30) REVERT: D 490 GLU cc_start: 0.8731 (tt0) cc_final: 0.8520 (tm-30) REVERT: D 498 ARG cc_start: 0.5591 (OUTLIER) cc_final: 0.5383 (mtt180) REVERT: D 567 LEU cc_start: 0.7345 (mp) cc_final: 0.7028 (mm) REVERT: E 82 MET cc_start: 0.1520 (ptp) cc_final: 0.0180 (mmm) REVERT: E 221 GLN cc_start: 0.7390 (mm-40) cc_final: 0.7106 (tp40) REVERT: E 356 LYS cc_start: 0.8943 (tttt) cc_final: 0.8663 (tmtm) REVERT: E 374 THR cc_start: 0.7207 (m) cc_final: 0.6649 (p) REVERT: E 432 GLN cc_start: 0.8441 (mt0) cc_final: 0.7728 (mm110) REVERT: E 598 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8150 (tptm) outliers start: 36 outliers final: 19 residues processed: 178 average time/residue: 0.7680 time to fit residues: 155.4419 Evaluate side-chains 174 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 480 GLU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 480 GLU 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 562 THR Chi-restraints excluded: chain D residue 564 SER Chi-restraints excluded: chain D residue 603 VAL 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 562 THR Chi-restraints excluded: chain E residue 598 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 236 optimal weight: 7.9990 chunk 185 optimal weight: 0.0870 chunk 164 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 256 optimal weight: 20.0000 chunk 262 optimal weight: 5.9990 chunk 181 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 230 optimal weight: 0.4980 chunk 272 optimal weight: 2.9990 overall best weight: 2.3164 ------------------------------------------------------------------------------- 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 471 GLN D 360 HIS D 471 GLN E 360 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.255003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.177755 restraints weight = 19623.794| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 4.88 r_work: 0.3428 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24395 Z= 0.187 Angle : 0.639 7.557 33070 Z= 0.347 Chirality : 0.046 0.162 3715 Planarity : 0.005 0.045 4275 Dihedral : 6.983 58.782 3484 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.79 % Allowed : 12.20 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.16), residues: 2995 helix: 2.33 (0.19), residues: 695 sheet: 1.32 (0.17), residues: 965 loop : -0.59 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 578 TYR 0.018 0.002 TYR C 542 PHE 0.038 0.003 PHE D 561 TRP 0.009 0.002 TRP D 359 HIS 0.004 0.001 HIS C 285 Details of bonding type rmsd covalent geometry : bond 0.00386 (24390) covalent geometry : angle 0.63820 (33060) SS BOND : bond 0.00445 ( 5) SS BOND : angle 1.59842 ( 10) hydrogen bonds : bond 0.07163 ( 1110) hydrogen bonds : angle 4.68868 ( 3075) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11569.64 seconds wall clock time: 196 minutes 43.57 seconds (11803.57 seconds total)