Starting phenix.real_space_refine on Fri Feb 6 08:05:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9evb_19997/02_2026/9evb_19997.cif Found real_map, /net/cci-nas-00/data/ceres_data/9evb_19997/02_2026/9evb_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_19997/02_2026/9evb_19997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9evb_19997/02_2026/9evb_19997.map" model { file = "/net/cci-nas-00/data/ceres_data/9evb_19997/02_2026/9evb_19997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9evb_19997/02_2026/9evb_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24090 Number of models: 1 Model: "" Number of chains: 15 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: "B" 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: "C" 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: "D" 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: "E" 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} Time building chain proxies: 5.81, per 1000 atoms: 0.24 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: 2.04 Conformation dependent library (CDL) restraints added in 1.1 seconds 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5530 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 30 sheets defined 28.0% alpha, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 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: 5.01 Time building geometry restraints manager: 2.70 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: 4.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.410 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.060 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:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.100 ------------------------------------------------------------------------------- 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 are 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 : 0.835 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: 0.5690 (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: 0.8641 time to fit residues: 320.8937 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 : 0.945 ------------------------------------------------------------------------------- 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 are 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 : 0.804 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: 0.3216 (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: 0.5937 time to fit residues: 188.8092 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 : 0.862 ------------------------------------------------------------------------------- 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 = 0.257464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.179504 restraints weight = 20352.993| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 6.38 r_work: 0.3636 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 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 are 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 1.37809 ( 10) hydrogen bonds : bond 0.05251 ( 1110) hydrogen bonds : angle 4.71310 ( 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 : 0.871 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: 0.8947 (tttt) cc_final: 0.8646 (tmtm) REVERT: A 374 THR cc_start: 0.7705 (m) cc_final: 0.7287 (p) REVERT: A 376 LYS cc_start: 0.7948 (tttt) cc_final: 0.7342 (tmtt) REVERT: A 389 GLU cc_start: 0.6889 (mt-10) cc_final: 0.6274 (mt-10) REVERT: A 432 GLN cc_start: 0.8507 (mt0) cc_final: 0.7758 (mm110) REVERT: A 480 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7461 (tp30) REVERT: A 569 ARG cc_start: 0.7649 (mtm-85) cc_final: 0.7381 (mmp-170) REVERT: B 68 MET cc_start: 0.3549 (ptm) cc_final: 0.3184 (ptp) REVERT: B 356 LYS cc_start: 0.8923 (tttt) cc_final: 0.8576 (tmtm) REVERT: B 363 LYS cc_start: 0.7523 (mtpt) cc_final: 0.7255 (mttp) REVERT: B 374 THR cc_start: 0.7625 (m) cc_final: 0.7337 (p) REVERT: B 432 GLN cc_start: 0.8451 (mt0) cc_final: 0.7763 (mm110) REVERT: B 465 GLU cc_start: 0.8858 (tt0) cc_final: 0.8559 (tm-30) REVERT: B 480 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7427 (tp30) REVERT: C 162 THR cc_start: 0.5827 (OUTLIER) cc_final: 0.5618 (p) REVERT: C 356 LYS cc_start: 0.8994 (tttt) cc_final: 0.8685 (tmtm) REVERT: C 374 THR cc_start: 0.7677 (m) cc_final: 0.7391 (p) REVERT: C 376 LYS cc_start: 0.7953 (tttt) cc_final: 0.7397 (tmtt) REVERT: C 432 GLN cc_start: 0.8431 (mt0) cc_final: 0.7704 (mm110) REVERT: C 480 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7149 (tm-30) REVERT: C 490 GLU cc_start: 0.8610 (tt0) cc_final: 0.8341 (tm-30) REVERT: D 356 LYS cc_start: 0.8976 (tttt) cc_final: 0.8645 (tmtm) REVERT: D 374 THR cc_start: 0.7596 (m) cc_final: 0.7243 (p) REVERT: D 376 LYS cc_start: 0.7982 (tttt) cc_final: 0.7381 (tmtt) REVERT: D 432 GLN cc_start: 0.8536 (mt0) cc_final: 0.7828 (mm110) REVERT: D 468 ARG cc_start: 0.7687 (mtt180) cc_final: 0.7388 (mpt180) REVERT: D 480 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7378 (tm-30) REVERT: D 498 ARG cc_start: 0.5715 (OUTLIER) cc_final: 0.5422 (mtt180) REVERT: E 356 LYS cc_start: 0.8991 (tttt) cc_final: 0.8646 (tmtm) REVERT: E 374 THR cc_start: 0.7556 (m) cc_final: 0.7098 (p) REVERT: E 379 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8204 (mt-10) REVERT: E 480 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7687 (mp0) outliers start: 52 outliers final: 13 residues processed: 222 average time/residue: 0.6339 time to fit residues: 161.6074 Evaluate side-chains 175 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 480 GLU Chi-restraints excluded: chain E residue 562 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 249 optimal weight: 20.0000 chunk 239 optimal weight: 5.9990 chunk 279 optimal weight: 5.9990 chunk 84 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 257 optimal weight: 20.0000 chunk 102 optimal weight: 0.0670 chunk 38 optimal weight: 3.9990 chunk 162 optimal weight: 0.2980 chunk 290 optimal weight: 4.9990 chunk 230 optimal weight: 0.0770 overall best weight: 1.8880 ------------------------------------------------------------------------------- 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 = 0.4744 r_free = 0.4744 target = 0.259285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.183440 restraints weight = 19708.243| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 4.93 r_work: 0.3572 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24395 Z= 0.171 Angle : 0.629 8.144 33070 Z= 0.341 Chirality : 0.046 0.167 3715 Planarity : 0.005 0.047 4275 Dihedral : 7.058 58.011 3484 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.77 % Allowed : 9.98 % Favored : 87.25 % 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 are not related in a simple way. whole: 0.92 (0.15), residues: 2995 helix: 2.19 (0.20), residues: 695 sheet: 1.22 (0.16), residues: 955 loop : -0.72 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 578 TYR 0.017 0.002 TYR C 542 PHE 0.034 0.002 PHE B 561 TRP 0.009 0.001 TRP D 359 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00342 (24390) covalent geometry : angle 0.62811 (33060) SS BOND : bond 0.00320 ( 5) SS BOND : angle 1.42018 ( 10) hydrogen bonds : bond 0.06952 ( 1110) hydrogen bonds : angle 4.80446 ( 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 : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8979 (tttt) cc_final: 0.8675 (tmtm) REVERT: A 374 THR cc_start: 0.7762 (m) cc_final: 0.7362 (p) REVERT: A 376 LYS cc_start: 0.8044 (tttt) cc_final: 0.7470 (tmtt) REVERT: A 515 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8931 (mp) REVERT: A 569 ARG cc_start: 0.7793 (mtm-85) cc_final: 0.7489 (mmp-170) REVERT: B 68 MET cc_start: 0.3771 (ptm) cc_final: 0.3329 (ptp) REVERT: B 162 THR cc_start: 0.5913 (OUTLIER) cc_final: 0.5700 (p) REVERT: B 356 LYS cc_start: 0.8948 (tttt) cc_final: 0.8670 (tmtm) REVERT: B 363 LYS cc_start: 0.7687 (mtpt) cc_final: 0.7401 (mttp) REVERT: B 374 THR cc_start: 0.7707 (m) cc_final: 0.7426 (p) REVERT: B 384 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7358 (mtt90) REVERT: B 432 GLN cc_start: 0.8511 (mt0) cc_final: 0.7879 (mm110) REVERT: C 356 LYS cc_start: 0.9073 (tttt) cc_final: 0.8784 (tmtm) REVERT: C 374 THR cc_start: 0.7820 (m) cc_final: 0.7528 (p) REVERT: C 384 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7267 (mtt90) REVERT: C 403 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8228 (tt0) REVERT: C 432 GLN cc_start: 0.8579 (mt0) cc_final: 0.7896 (mm110) REVERT: C 480 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7673 (tp30) REVERT: C 490 GLU cc_start: 0.8660 (tt0) cc_final: 0.8398 (tm-30) REVERT: D 221 GLN cc_start: 0.7430 (mm-40) cc_final: 0.6925 (mm110) REVERT: D 356 LYS cc_start: 0.9014 (tttt) cc_final: 0.8743 (tmtm) REVERT: D 374 THR cc_start: 0.7677 (m) cc_final: 0.7302 (p) REVERT: D 376 LYS cc_start: 0.7997 (tttt) cc_final: 0.7394 (tmtt) REVERT: D 432 GLN cc_start: 0.8580 (mt0) cc_final: 0.7901 (mm110) REVERT: D 468 ARG cc_start: 0.7801 (mtt180) cc_final: 0.7458 (mpt180) REVERT: D 480 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7869 (mt-10) REVERT: D 498 ARG cc_start: 0.5895 (OUTLIER) cc_final: 0.5469 (mtt180) REVERT: E 356 LYS cc_start: 0.9022 (tttt) cc_final: 0.8733 (tmtm) REVERT: E 374 THR cc_start: 0.7615 (m) cc_final: 0.7133 (p) REVERT: E 598 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8279 (tptm) outliers start: 71 outliers final: 36 residues processed: 213 average time/residue: 0.6607 time to fit residues: 161.9975 Evaluate side-chains 192 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 147 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 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 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 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 480 GLU 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: 8.9990 chunk 234 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 287 optimal weight: 1.9990 chunk 134 optimal weight: 20.0000 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: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 C 471 GLN D 360 HIS D 471 GLN E 307 ASN E 360 HIS E 471 GLN E 560 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.252183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.172236 restraints weight = 19923.038| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 6.50 r_work: 0.3069 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 24395 Z= 0.179 Angle : 0.637 9.198 33070 Z= 0.345 Chirality : 0.046 0.162 3715 Planarity : 0.005 0.047 4275 Dihedral : 7.245 59.259 3484 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.81 % Allowed : 10.25 % Favored : 86.94 % 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 are not related in a simple way. whole: 0.98 (0.15), residues: 2995 helix: 2.13 (0.19), residues: 695 sheet: 1.38 (0.16), residues: 950 loop : -0.71 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 578 TYR 0.017 0.002 TYR C 542 PHE 0.026 0.003 PHE D 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 0.00362 (24390) covalent geometry : angle 0.63609 (33060) SS BOND : bond 0.00385 ( 5) SS BOND : angle 1.50291 ( 10) hydrogen bonds : bond 0.06902 ( 1110) hydrogen bonds : angle 4.79684 ( 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 225 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 153 time to evaluate : 0.717 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: 0.8976 (tttt) cc_final: 0.8672 (tmtm) REVERT: A 374 THR cc_start: 0.7727 (m) cc_final: 0.7309 (p) REVERT: A 376 LYS cc_start: 0.7870 (tttt) cc_final: 0.7205 (tmtt) REVERT: A 432 GLN cc_start: 0.8587 (mt0) cc_final: 0.7882 (mm110) REVERT: A 515 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8899 (mp) REVERT: A 569 ARG cc_start: 0.7651 (mtm-85) cc_final: 0.7259 (mmp-170) REVERT: B 162 THR cc_start: 0.6072 (OUTLIER) cc_final: 0.5809 (p) REVERT: B 356 LYS cc_start: 0.8970 (tttt) cc_final: 0.8680 (tmtm) REVERT: B 363 LYS cc_start: 0.7622 (mtpt) cc_final: 0.7332 (mttp) REVERT: B 374 THR cc_start: 0.7706 (m) cc_final: 0.7422 (p) REVERT: B 384 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7216 (mtt90) REVERT: B 432 GLN cc_start: 0.8537 (mt0) cc_final: 0.7871 (mm110) REVERT: C 82 MET cc_start: 0.1225 (pmm) cc_final: -0.0821 (mmt) REVERT: C 356 LYS cc_start: 0.9080 (tttt) cc_final: 0.8781 (tmtm) REVERT: C 374 THR cc_start: 0.7682 (m) cc_final: 0.7472 (p) REVERT: C 403 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8017 (tm-30) REVERT: C 432 GLN cc_start: 0.8608 (mt0) cc_final: 0.7905 (mm110) REVERT: C 480 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7575 (tp30) REVERT: D 221 GLN cc_start: 0.7123 (mm-40) cc_final: 0.6517 (mm110) REVERT: D 337 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.8174 (m-30) REVERT: D 356 LYS cc_start: 0.8963 (tttt) cc_final: 0.8680 (tmtm) REVERT: D 374 THR cc_start: 0.7582 (m) cc_final: 0.7278 (p) REVERT: D 376 LYS cc_start: 0.7873 (tttt) cc_final: 0.7189 (tmtt) REVERT: D 432 GLN cc_start: 0.8617 (mt0) cc_final: 0.7924 (mm110) REVERT: D 468 ARG cc_start: 0.7817 (mtt180) cc_final: 0.7458 (mpt180) REVERT: D 480 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7699 (tp30) REVERT: D 498 ARG cc_start: 0.5723 (OUTLIER) cc_final: 0.5389 (mtt180) REVERT: D 515 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8797 (mp) REVERT: E 356 LYS cc_start: 0.9032 (tttt) cc_final: 0.8700 (tmtm) REVERT: E 374 THR cc_start: 0.7568 (m) cc_final: 0.7101 (p) REVERT: E 598 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8231 (tptm) outliers start: 72 outliers final: 36 residues processed: 219 average time/residue: 0.6304 time to fit residues: 159.4491 Evaluate side-chains 192 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 146 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 C residue 562 THR 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 449 SER Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 498 ARG Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 564 SER Chi-restraints excluded: chain D residue 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 328 ASP Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain E residue 480 GLU 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: 0.9990 chunk 64 optimal weight: 5.9990 chunk 230 optimal weight: 0.8980 chunk 25 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 191 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 chunk 245 optimal weight: 0.3980 chunk 260 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 459 ASN D 471 GLN E 221 GLN E 360 HIS E 471 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.254504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.177633 restraints weight = 20160.949| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 5.99 r_work: 0.3491 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.4862 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= 0.124 Angle : 0.534 8.949 33070 Z= 0.286 Chirality : 0.043 0.152 3715 Planarity : 0.004 0.047 4275 Dihedral : 6.589 59.026 3484 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.38 % Allowed : 11.15 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.16), residues: 2995 helix: 2.53 (0.20), residues: 690 sheet: 1.27 (0.17), residues: 980 loop : -0.59 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 578 TYR 0.012 0.001 TYR C 542 PHE 0.026 0.002 PHE E 561 TRP 0.008 0.001 TRP D 359 HIS 0.003 0.001 HIS D 285 Details of bonding type rmsd covalent geometry : bond 0.00240 (24390) covalent geometry : angle 0.53321 (33060) SS BOND : bond 0.00338 ( 5) SS BOND : angle 1.39830 ( 10) hydrogen bonds : bond 0.05418 ( 1110) hydrogen bonds : angle 4.54789 ( 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: 61 poor density : 154 time to evaluate : 0.948 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: 0.8977 (tttt) cc_final: 0.8709 (tmtm) REVERT: A 374 THR cc_start: 0.7633 (m) cc_final: 0.7186 (p) REVERT: A 376 LYS cc_start: 0.7954 (tttt) cc_final: 0.7332 (tmtt) REVERT: A 432 GLN cc_start: 0.8499 (mt0) cc_final: 0.7829 (mm110) REVERT: A 480 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7709 (mt-10) REVERT: A 547 GLU cc_start: 0.8625 (tt0) cc_final: 0.8271 (tm-30) REVERT: A 569 ARG cc_start: 0.7732 (mtm-85) cc_final: 0.7447 (mmp-170) REVERT: B 68 MET cc_start: 0.3136 (ptm) cc_final: 0.2647 (ptp) REVERT: B 162 THR cc_start: 0.6081 (OUTLIER) cc_final: 0.5810 (p) REVERT: B 356 LYS cc_start: 0.8932 (tttt) cc_final: 0.8711 (tmtm) REVERT: B 363 LYS cc_start: 0.7550 (mtpt) cc_final: 0.7314 (mttp) REVERT: B 374 THR cc_start: 0.7517 (m) cc_final: 0.7295 (p) REVERT: B 432 GLN cc_start: 0.8489 (mt0) cc_final: 0.7845 (mm110) REVERT: C 82 MET cc_start: 0.1163 (pmm) cc_final: -0.0743 (mmt) REVERT: C 356 LYS cc_start: 0.9033 (tttt) cc_final: 0.8775 (tmtm) REVERT: C 374 THR cc_start: 0.7526 (m) cc_final: 0.7238 (p) REVERT: C 403 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8177 (tt0) REVERT: C 432 GLN cc_start: 0.8527 (mt0) cc_final: 0.7849 (mm110) REVERT: C 480 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: C 490 GLU cc_start: 0.8659 (tt0) cc_final: 0.8403 (tm-30) REVERT: D 221 GLN cc_start: 0.7402 (mm-40) cc_final: 0.7063 (tp40) REVERT: D 356 LYS cc_start: 0.8963 (tttt) cc_final: 0.8684 (tmtm) REVERT: D 374 THR cc_start: 0.7456 (m) cc_final: 0.7153 (p) REVERT: D 376 LYS cc_start: 0.7957 (tttt) cc_final: 0.7353 (tmtt) REVERT: D 432 GLN cc_start: 0.8587 (mt0) cc_final: 0.7886 (mm110) REVERT: D 468 ARG cc_start: 0.7783 (mtt180) cc_final: 0.7427 (mpt180) REVERT: D 480 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7577 (tm-30) REVERT: D 490 GLU cc_start: 0.8712 (tt0) cc_final: 0.8471 (tm-30) REVERT: D 498 ARG cc_start: 0.5689 (OUTLIER) cc_final: 0.5479 (mtt180) REVERT: E 221 GLN cc_start: 0.7351 (mm-40) cc_final: 0.7053 (tp40) REVERT: E 356 LYS cc_start: 0.9024 (tttt) cc_final: 0.8703 (tmtm) REVERT: E 374 THR cc_start: 0.7293 (m) cc_final: 0.6823 (p) REVERT: E 598 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8172 (tptm) outliers start: 61 outliers final: 31 residues processed: 209 average time/residue: 0.7287 time to fit residues: 174.9607 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 : 0.783 ------------------------------------------------------------------------------- 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 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 C residue 262 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 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 480 GLU Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 598 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 167 optimal weight: 7.9990 chunk 126 optimal weight: 30.0000 chunk 174 optimal weight: 3.9990 chunk 273 optimal weight: 0.0970 chunk 2 optimal weight: 6.9990 chunk 211 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 246 optimal weight: 20.0000 chunk 148 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 283 optimal weight: 0.9980 overall best weight: 2.8184 ------------------------------------------------------------------------------- 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 471 GLN D 471 GLN E 360 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.250708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.169534 restraints weight = 19868.220| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 7.00 r_work: 0.3080 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24395 Z= 0.213 Angle : 0.686 8.929 33070 Z= 0.374 Chirality : 0.048 0.165 3715 Planarity : 0.005 0.050 4275 Dihedral : 7.499 58.775 3484 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.65 % Allowed : 11.19 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.15), residues: 2995 helix: 2.14 (0.19), residues: 695 sheet: 1.27 (0.16), residues: 965 loop : -0.66 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 578 TYR 0.019 0.002 TYR C 542 PHE 0.049 0.003 PHE C 561 TRP 0.010 0.002 TRP D 359 HIS 0.004 0.001 HIS E 285 Details of bonding type rmsd covalent geometry : bond 0.00446 (24390) covalent geometry : angle 0.68574 (33060) SS BOND : bond 0.00394 ( 5) SS BOND : angle 1.57638 ( 10) hydrogen bonds : bond 0.07774 ( 1110) hydrogen bonds : angle 4.84613 ( 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 220 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 152 time to evaluate : 0.959 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: 0.8966 (tttt) cc_final: 0.8668 (tmtm) REVERT: A 374 THR cc_start: 0.7780 (m) cc_final: 0.7374 (p) REVERT: A 376 LYS cc_start: 0.7950 (tttt) cc_final: 0.7317 (tmtt) REVERT: A 569 ARG cc_start: 0.7839 (mtm-85) cc_final: 0.7502 (mtt90) REVERT: B 68 MET cc_start: 0.3062 (ptm) cc_final: 0.2160 (ptp) REVERT: B 162 THR cc_start: 0.6318 (OUTLIER) cc_final: 0.6045 (p) REVERT: B 356 LYS cc_start: 0.8966 (tttt) cc_final: 0.8708 (tmtm) REVERT: B 363 LYS cc_start: 0.7715 (mtpt) cc_final: 0.7394 (mttp) REVERT: B 374 THR cc_start: 0.7677 (m) cc_final: 0.7428 (p) REVERT: B 384 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7234 (mtt90) REVERT: B 432 GLN cc_start: 0.8572 (mt0) cc_final: 0.7910 (mm110) REVERT: B 515 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8804 (mp) REVERT: C 82 MET cc_start: 0.1137 (pmm) cc_final: -0.0685 (mmt) REVERT: C 153 ASN cc_start: 0.7099 (t0) cc_final: 0.6783 (t0) REVERT: C 356 LYS cc_start: 0.9077 (tttt) cc_final: 0.8784 (tmtm) REVERT: C 384 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7237 (mtt90) REVERT: C 403 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8062 (tm-30) REVERT: C 432 GLN cc_start: 0.8668 (mt0) cc_final: 0.7933 (mm110) REVERT: C 480 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7633 (tp30) REVERT: D 82 MET cc_start: 0.1404 (ptp) cc_final: 0.0360 (mmt) REVERT: D 221 GLN cc_start: 0.7259 (mm-40) cc_final: 0.6856 (tp40) REVERT: D 337 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.8203 (m-30) REVERT: D 356 LYS cc_start: 0.8976 (tttt) cc_final: 0.8685 (tmtm) REVERT: D 374 THR cc_start: 0.7575 (m) cc_final: 0.7297 (p) REVERT: D 376 LYS cc_start: 0.7946 (tttt) cc_final: 0.7277 (tmtt) REVERT: D 432 GLN cc_start: 0.8685 (mt0) cc_final: 0.7953 (mm110) REVERT: D 468 ARG cc_start: 0.7905 (mtt180) cc_final: 0.7506 (mpt180) REVERT: D 498 ARG cc_start: 0.5889 (OUTLIER) cc_final: 0.5554 (mtt180) REVERT: E 221 GLN cc_start: 0.7200 (mm-40) cc_final: 0.6874 (tp40) REVERT: E 356 LYS cc_start: 0.9036 (tttt) cc_final: 0.8717 (tmtm) REVERT: E 374 THR cc_start: 0.7597 (m) cc_final: 0.7126 (p) REVERT: E 569 ARG cc_start: 0.7862 (mtm-85) cc_final: 0.7378 (mmp-170) REVERT: E 598 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8317 (tptm) outliers start: 68 outliers final: 34 residues processed: 214 average time/residue: 0.6966 time to fit residues: 170.9860 Evaluate side-chains 190 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 147 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 480 GLU 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: 0.4980 chunk 163 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 135 optimal weight: 7.9990 chunk 281 optimal weight: 0.3980 chunk 58 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 C 471 GLN D 471 GLN E 360 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.252552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.173053 restraints weight = 19929.357| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 6.66 r_work: 0.3529 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24395 Z= 0.149 Angle : 0.578 8.179 33070 Z= 0.312 Chirality : 0.044 0.157 3715 Planarity : 0.004 0.046 4275 Dihedral : 6.915 59.642 3484 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.46 % Allowed : 11.46 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.16), residues: 2995 helix: 2.36 (0.19), residues: 695 sheet: 1.15 (0.17), residues: 990 loop : -0.58 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 578 TYR 0.015 0.002 TYR B 517 PHE 0.026 0.002 PHE B 561 TRP 0.010 0.001 TRP D 359 HIS 0.004 0.001 HIS D 285 Details of bonding type rmsd covalent geometry : bond 0.00296 (24390) covalent geometry : angle 0.57721 (33060) SS BOND : bond 0.00376 ( 5) SS BOND : angle 1.48572 ( 10) hydrogen bonds : bond 0.06162 ( 1110) hydrogen bonds : angle 4.64491 ( 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 214 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 151 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.1565 (ptp) cc_final: 0.0132 (mmm) REVERT: A 356 LYS cc_start: 0.8968 (tttt) cc_final: 0.8691 (tmtm) REVERT: A 374 THR cc_start: 0.7665 (m) cc_final: 0.7238 (p) REVERT: A 376 LYS cc_start: 0.7943 (tttt) cc_final: 0.7334 (tmtt) REVERT: A 432 GLN cc_start: 0.8530 (mt0) cc_final: 0.7823 (mm110) REVERT: A 547 GLU cc_start: 0.8646 (tt0) cc_final: 0.8243 (tm-30) REVERT: A 569 ARG cc_start: 0.7789 (mtm-85) cc_final: 0.7460 (mmp-170) REVERT: B 68 MET cc_start: 0.3157 (ptm) cc_final: 0.2443 (ptp) REVERT: B 82 MET cc_start: 0.1496 (ptp) cc_final: 0.0316 (mmm) REVERT: B 162 THR cc_start: 0.6288 (OUTLIER) cc_final: 0.6021 (p) REVERT: B 356 LYS cc_start: 0.8939 (tttt) cc_final: 0.8693 (tmtm) REVERT: B 363 LYS cc_start: 0.7596 (mtpt) cc_final: 0.7338 (mttp) REVERT: B 374 THR cc_start: 0.7551 (m) cc_final: 0.7346 (p) REVERT: B 432 GLN cc_start: 0.8460 (mt0) cc_final: 0.7812 (mm110) REVERT: C 82 MET cc_start: 0.0980 (pmm) cc_final: -0.0785 (mmm) REVERT: C 356 LYS cc_start: 0.9039 (tttt) cc_final: 0.8756 (tmtm) REVERT: C 384 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7220 (mtt90) REVERT: C 403 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8176 (tt0) REVERT: C 432 GLN cc_start: 0.8542 (mt0) cc_final: 0.7831 (mm110) REVERT: C 480 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7501 (tp30) REVERT: C 567 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7410 (mm) REVERT: D 82 MET cc_start: 0.1470 (ptp) cc_final: 0.0364 (mmt) REVERT: D 221 GLN cc_start: 0.7280 (mm-40) cc_final: 0.6967 (tp40) REVERT: D 356 LYS cc_start: 0.8963 (tttt) cc_final: 0.8675 (tmtm) REVERT: D 374 THR cc_start: 0.7616 (m) cc_final: 0.7326 (p) REVERT: D 376 LYS cc_start: 0.7958 (tttt) cc_final: 0.7324 (tmtt) REVERT: D 432 GLN cc_start: 0.8573 (mt0) cc_final: 0.7873 (mm110) REVERT: D 468 ARG cc_start: 0.7704 (mtt180) cc_final: 0.7467 (mpt180) REVERT: D 480 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7732 (tp30) REVERT: D 498 ARG cc_start: 0.5736 (OUTLIER) cc_final: 0.5430 (mtt180) REVERT: D 515 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8849 (mp) REVERT: E 82 MET cc_start: 0.1482 (ptp) cc_final: 0.0175 (mmm) REVERT: E 221 GLN cc_start: 0.7235 (mm-40) cc_final: 0.6916 (tp40) REVERT: E 356 LYS cc_start: 0.9025 (tttt) cc_final: 0.8709 (tmtm) REVERT: E 374 THR cc_start: 0.7415 (m) cc_final: 0.6935 (p) REVERT: E 598 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8206 (tptm) outliers start: 63 outliers final: 34 residues processed: 207 average time/residue: 0.6883 time to fit residues: 163.6350 Evaluate side-chains 190 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 147 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 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 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 C residue 262 ILE Chi-restraints excluded: chain C residue 286 VAL 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 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 299 VAL Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 498 ARG Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 564 SER Chi-restraints excluded: chain D residue 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 480 GLU 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: 0.8980 chunk 232 optimal weight: 2.9990 chunk 87 optimal weight: 20.0000 chunk 182 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 chunk 140 optimal weight: 8.9990 chunk 245 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 246 optimal weight: 0.8980 chunk 122 optimal weight: 20.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 C 471 GLN D 471 GLN E 360 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.249025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.168232 restraints weight = 19974.498| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 7.06 r_work: 0.3055 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.5448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24395 Z= 0.200 Angle : 0.667 8.222 33070 Z= 0.363 Chirality : 0.047 0.165 3715 Planarity : 0.005 0.047 4275 Dihedral : 7.419 59.703 3484 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.50 % Allowed : 11.62 % Favored : 85.89 % 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 are not related in a simple way. whole: 0.95 (0.16), residues: 2995 helix: 2.18 (0.19), residues: 695 sheet: 1.22 (0.17), residues: 965 loop : -0.68 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 578 TYR 0.019 0.002 TYR C 542 PHE 0.049 0.003 PHE C 561 TRP 0.010 0.002 TRP D 359 HIS 0.004 0.001 HIS E 285 Details of bonding type rmsd covalent geometry : bond 0.00413 (24390) covalent geometry : angle 0.66629 (33060) SS BOND : bond 0.00423 ( 5) SS BOND : angle 1.61607 ( 10) hydrogen bonds : bond 0.07550 ( 1110) hydrogen bonds : angle 4.83773 ( 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 215 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 151 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.1669 (ptp) cc_final: 0.0192 (mmm) REVERT: A 356 LYS cc_start: 0.8956 (tttt) cc_final: 0.8671 (tmtm) REVERT: A 374 THR cc_start: 0.7680 (m) cc_final: 0.7266 (p) REVERT: A 376 LYS cc_start: 0.7862 (tttt) cc_final: 0.7206 (tmtt) REVERT: A 569 ARG cc_start: 0.7746 (mtm-85) cc_final: 0.7392 (mtt90) REVERT: B 68 MET cc_start: 0.2902 (ptm) cc_final: 0.1858 (ptp) REVERT: B 82 MET cc_start: 0.1756 (ptp) cc_final: 0.0475 (mmm) REVERT: B 162 THR cc_start: 0.6459 (OUTLIER) cc_final: 0.6203 (p) REVERT: B 356 LYS cc_start: 0.8926 (tttt) cc_final: 0.8678 (tmtm) REVERT: B 363 LYS cc_start: 0.7731 (mtpt) cc_final: 0.7420 (mttp) REVERT: B 384 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7193 (mtt90) REVERT: B 432 GLN cc_start: 0.8550 (mt0) cc_final: 0.7895 (mm110) REVERT: C 82 MET cc_start: 0.1051 (pmm) cc_final: -0.0734 (mmm) REVERT: C 153 ASN cc_start: 0.7158 (t0) cc_final: 0.6825 (t0) REVERT: C 356 LYS cc_start: 0.9069 (tttt) cc_final: 0.8768 (tmtm) REVERT: C 384 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7206 (mtt90) REVERT: C 403 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.7997 (tm-30) REVERT: C 432 GLN cc_start: 0.8653 (mt0) cc_final: 0.7922 (mm110) REVERT: C 480 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7607 (tp30) REVERT: D 82 MET cc_start: 0.1410 (ptp) cc_final: 0.0396 (mmt) REVERT: D 221 GLN cc_start: 0.7281 (mm-40) cc_final: 0.6879 (tp40) REVERT: D 337 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8158 (m-30) REVERT: D 356 LYS cc_start: 0.8962 (tttt) cc_final: 0.8667 (tmtm) REVERT: D 374 THR cc_start: 0.7598 (m) cc_final: 0.7353 (p) REVERT: D 376 LYS cc_start: 0.7913 (tttt) cc_final: 0.7236 (tmtt) REVERT: D 432 GLN cc_start: 0.8670 (mt0) cc_final: 0.7938 (mm110) REVERT: D 468 ARG cc_start: 0.7910 (mtt180) cc_final: 0.7509 (mpt180) REVERT: D 480 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7758 (tp30) REVERT: D 498 ARG cc_start: 0.5879 (OUTLIER) cc_final: 0.5513 (mtm180) REVERT: D 515 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8837 (mp) REVERT: E 82 MET cc_start: 0.1536 (ptp) cc_final: 0.0334 (mmm) REVERT: E 221 GLN cc_start: 0.7194 (mm-40) cc_final: 0.6883 (tp40) REVERT: E 356 LYS cc_start: 0.9040 (tttt) cc_final: 0.8704 (tmtm) REVERT: E 374 THR cc_start: 0.7554 (m) cc_final: 0.7107 (p) REVERT: E 569 ARG cc_start: 0.7826 (mtm-85) cc_final: 0.7402 (mmp-170) REVERT: E 598 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8294 (tptm) outliers start: 64 outliers final: 36 residues processed: 208 average time/residue: 0.7126 time to fit residues: 169.9331 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 : 0.940 ------------------------------------------------------------------------------- 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 439 LEU Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain 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 449 SER Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 498 ARG Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 564 SER Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain E residue 236 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 480 GLU 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: 6.9990 chunk 47 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 295 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 284 optimal weight: 0.7980 chunk 86 optimal weight: 20.0000 chunk 286 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 255 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 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 A 560 ASN B 360 HIS C 471 GLN D 471 GLN E 360 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.252054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.173292 restraints weight = 19974.331| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 6.50 r_work: 0.3047 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24395 Z= 0.150 Angle : 0.581 7.753 33070 Z= 0.315 Chirality : 0.044 0.157 3715 Planarity : 0.004 0.047 4275 Dihedral : 6.892 59.924 3484 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.95 % Allowed : 12.28 % Favored : 85.77 % 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 are not related in a simple way. whole: 1.01 (0.16), residues: 2995 helix: 2.34 (0.19), residues: 695 sheet: 1.11 (0.17), residues: 990 loop : -0.61 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 578 TYR 0.015 0.002 TYR B 517 PHE 0.026 0.002 PHE D 414 TRP 0.010 0.001 TRP D 359 HIS 0.004 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00299 (24390) covalent geometry : angle 0.58016 (33060) SS BOND : bond 0.00413 ( 5) SS BOND : angle 1.53390 ( 10) hydrogen bonds : bond 0.06184 ( 1110) hydrogen bonds : angle 4.64743 ( 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 201 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 151 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.1586 (ptp) cc_final: 0.0098 (mmm) REVERT: A 356 LYS cc_start: 0.8950 (tttt) cc_final: 0.8667 (tmtm) REVERT: A 374 THR cc_start: 0.7558 (m) cc_final: 0.7106 (p) REVERT: A 376 LYS cc_start: 0.7810 (tttt) cc_final: 0.7097 (tmtt) REVERT: A 432 GLN cc_start: 0.8611 (mt0) cc_final: 0.7877 (mm110) REVERT: A 547 GLU cc_start: 0.8684 (tt0) cc_final: 0.8260 (tm-30) REVERT: A 569 ARG cc_start: 0.7751 (mtm-85) cc_final: 0.7401 (mtt90) REVERT: B 68 MET cc_start: 0.2917 (ptm) cc_final: 0.1873 (ptp) REVERT: B 82 MET cc_start: 0.1711 (ptp) cc_final: 0.0469 (mmm) REVERT: B 162 THR cc_start: 0.6273 (OUTLIER) cc_final: 0.6023 (p) REVERT: B 356 LYS cc_start: 0.8946 (tttt) cc_final: 0.8666 (tmtm) REVERT: B 363 LYS cc_start: 0.7602 (mtpt) cc_final: 0.7286 (mttp) REVERT: B 432 GLN cc_start: 0.8516 (mt0) cc_final: 0.7866 (mm110) REVERT: C 82 MET cc_start: 0.0984 (pmm) cc_final: -0.0620 (mmm) REVERT: C 356 LYS cc_start: 0.9047 (tttt) cc_final: 0.8748 (tmtm) REVERT: C 384 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7159 (mtt90) REVERT: C 403 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8319 (tt0) REVERT: C 432 GLN cc_start: 0.8585 (mt0) cc_final: 0.7873 (mm110) REVERT: C 480 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7473 (tp30) REVERT: C 490 GLU cc_start: 0.8724 (tt0) cc_final: 0.8484 (tm-30) REVERT: C 567 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7210 (mm) REVERT: D 82 MET cc_start: 0.1363 (ptp) cc_final: 0.0302 (mmt) REVERT: D 221 GLN cc_start: 0.7193 (mm-40) cc_final: 0.6890 (tp40) REVERT: D 356 LYS cc_start: 0.8964 (tttt) cc_final: 0.8654 (tmtm) REVERT: D 374 THR cc_start: 0.7497 (m) cc_final: 0.7209 (p) REVERT: D 376 LYS cc_start: 0.7838 (tttt) cc_final: 0.7147 (tmtt) REVERT: D 432 GLN cc_start: 0.8613 (mt0) cc_final: 0.7916 (mm110) REVERT: D 468 ARG cc_start: 0.7831 (mtt180) cc_final: 0.7471 (mpt180) REVERT: D 480 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7702 (tp30) REVERT: D 498 ARG cc_start: 0.5753 (OUTLIER) cc_final: 0.5476 (mtt180) REVERT: D 515 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8795 (mp) REVERT: D 567 LEU cc_start: 0.7479 (mp) cc_final: 0.7118 (mm) REVERT: E 82 MET cc_start: 0.1464 (ptp) cc_final: 0.0250 (mmm) REVERT: E 221 GLN cc_start: 0.7150 (mm-40) cc_final: 0.6874 (tp40) REVERT: E 356 LYS cc_start: 0.9023 (tttt) cc_final: 0.8677 (tmtm) REVERT: E 374 THR cc_start: 0.7346 (m) cc_final: 0.6901 (p) REVERT: E 432 GLN cc_start: 0.8559 (mt0) cc_final: 0.7813 (mm110) REVERT: E 598 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8170 (tptm) outliers start: 50 outliers final: 33 residues processed: 194 average time/residue: 0.7400 time to fit residues: 163.9912 Evaluate side-chains 193 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 151 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 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 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 439 LEU Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 498 ARG Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain E residue 236 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 480 GLU 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: 4.9990 chunk 185 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 256 optimal weight: 20.0000 chunk 262 optimal weight: 8.9990 chunk 181 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 230 optimal weight: 0.7980 chunk 272 optimal weight: 0.8980 overall best weight: 1.4982 ------------------------------------------------------------------------------- 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 471 GLN D 471 GLN E 360 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.255851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.179604 restraints weight = 19718.082| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 4.85 r_work: 0.3456 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24395 Z= 0.149 Angle : 0.577 7.165 33070 Z= 0.312 Chirality : 0.044 0.159 3715 Planarity : 0.004 0.046 4275 Dihedral : 6.610 57.734 3484 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.11 % Allowed : 12.16 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.16), residues: 2995 helix: 2.41 (0.19), residues: 695 sheet: 1.16 (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 0.014 0.002 TYR B 517 PHE 0.038 0.002 PHE C 561 TRP 0.009 0.001 TRP D 359 HIS 0.004 0.001 HIS D 285 Details of bonding type rmsd covalent geometry : bond 0.00296 (24390) covalent geometry : angle 0.57620 (33060) SS BOND : bond 0.00415 ( 5) SS BOND : angle 1.55013 ( 10) hydrogen bonds : bond 0.06249 ( 1110) hydrogen bonds : angle 4.58431 ( 3075) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12345.84 seconds wall clock time: 209 minutes 50.29 seconds (12590.29 seconds total)