Starting phenix.real_space_refine on Fri Jun 20 21:54:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fuz_29482/06_2025/8fuz_29482.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fuz_29482/06_2025/8fuz_29482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fuz_29482/06_2025/8fuz_29482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fuz_29482/06_2025/8fuz_29482.map" model { file = "/net/cci-nas-00/data/ceres_data/8fuz_29482/06_2025/8fuz_29482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fuz_29482/06_2025/8fuz_29482.cif" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.237 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: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 144 5.16 5 C 15072 2.51 5 N 4096 2.21 5 O 4672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24008 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2934 Classifications: {'peptide': 390} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 376} Chain breaks: 2 Chain: "B" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2934 Classifications: {'peptide': 390} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 376} Chain breaks: 2 Chain: "C" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2934 Classifications: {'peptide': 390} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 376} Chain breaks: 2 Chain: "D" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2934 Classifications: {'peptide': 390} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 376} Chain breaks: 2 Chain: "E" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2934 Classifications: {'peptide': 390} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 376} Chain breaks: 2 Chain: "F" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2934 Classifications: {'peptide': 390} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 376} Chain breaks: 2 Chain: "G" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2934 Classifications: {'peptide': 390} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 376} Chain breaks: 2 Chain: "H" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2934 Classifications: {'peptide': 390} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 376} Chain breaks: 2 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "G" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "H" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Time building chain proxies: 16.47, per 1000 atoms: 0.69 Number of scatterers: 24008 At special positions: 0 Unit cell: (134.88, 135.723, 120.549, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 144 16.00 P 24 15.00 O 4672 8.00 N 4096 7.00 C 15072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.80 Conformation dependent library (CDL) restraints added in 3.3 seconds 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5600 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 32 sheets defined 43.8% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.62 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 Processing helix chain 'A' and resid 19 through 24 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 75 through 85 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 255 through 267 Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 342 through 355 Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.872A pdb=" N LYS A 422 " --> pdb=" O ASP A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 472 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 75 through 85 Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 255 through 267 Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 306 through 317 Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 342 through 355 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 369 through 379 Processing helix chain 'B' and resid 387 through 391 Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.921A pdb=" N LYS B 422 " --> pdb=" O ASP B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 472 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 494 through 502 Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 255 through 267 Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 306 through 317 Processing helix chain 'C' and resid 332 through 338 Processing helix chain 'C' and resid 342 through 355 Processing helix chain 'C' and resid 356 through 358 No H-bonds generated for 'chain 'C' and resid 356 through 358' Processing helix chain 'C' and resid 369 through 379 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.653A pdb=" N LYS C 422 " --> pdb=" O ASP C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 472 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 494 through 502 Processing helix chain 'D' and resid 2 through 6 Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 75 through 85 Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 255 through 267 Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'D' and resid 306 through 317 Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 342 through 355 Processing helix chain 'D' and resid 356 through 358 No H-bonds generated for 'chain 'D' and resid 356 through 358' Processing helix chain 'D' and resid 369 through 379 Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 416 through 422 removed outlier: 3.872A pdb=" N LYS D 422 " --> pdb=" O ASP D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 472 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 494 through 502 Processing helix chain 'E' and resid 2 through 6 Processing helix chain 'E' and resid 19 through 24 Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 45 through 49 Processing helix chain 'E' and resid 75 through 85 Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 255 through 267 Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 306 through 317 Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 342 through 355 Processing helix chain 'E' and resid 356 through 358 No H-bonds generated for 'chain 'E' and resid 356 through 358' Processing helix chain 'E' and resid 369 through 379 Processing helix chain 'E' and resid 416 through 422 removed outlier: 3.847A pdb=" N LYS E 422 " --> pdb=" O ASP E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 472 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 494 through 502 Processing helix chain 'F' and resid 2 through 6 Processing helix chain 'F' and resid 19 through 24 Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 45 through 49 Processing helix chain 'F' and resid 75 through 85 Processing helix chain 'F' and resid 96 through 109 Processing helix chain 'F' and resid 255 through 267 Processing helix chain 'F' and resid 280 through 294 Processing helix chain 'F' and resid 306 through 317 Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 342 through 355 Processing helix chain 'F' and resid 356 through 358 No H-bonds generated for 'chain 'F' and resid 356 through 358' Processing helix chain 'F' and resid 369 through 379 Processing helix chain 'F' and resid 387 through 391 Processing helix chain 'F' and resid 416 through 422 removed outlier: 3.955A pdb=" N LYS F 422 " --> pdb=" O ASP F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 472 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 494 through 502 Processing helix chain 'G' and resid 2 through 6 Processing helix chain 'G' and resid 19 through 24 Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 45 through 49 Processing helix chain 'G' and resid 75 through 85 Processing helix chain 'G' and resid 96 through 109 Processing helix chain 'G' and resid 255 through 267 Processing helix chain 'G' and resid 280 through 294 Processing helix chain 'G' and resid 306 through 317 Processing helix chain 'G' and resid 332 through 338 Processing helix chain 'G' and resid 342 through 355 Processing helix chain 'G' and resid 356 through 358 No H-bonds generated for 'chain 'G' and resid 356 through 358' Processing helix chain 'G' and resid 369 through 379 Processing helix chain 'G' and resid 416 through 422 removed outlier: 3.694A pdb=" N LYS G 422 " --> pdb=" O ASP G 418 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 472 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 475 through 485 Processing helix chain 'G' and resid 494 through 502 Processing helix chain 'H' and resid 2 through 6 Processing helix chain 'H' and resid 19 through 24 Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 45 through 49 Processing helix chain 'H' and resid 75 through 85 Processing helix chain 'H' and resid 96 through 109 Processing helix chain 'H' and resid 255 through 267 Processing helix chain 'H' and resid 280 through 294 Processing helix chain 'H' and resid 306 through 317 Processing helix chain 'H' and resid 332 through 338 Processing helix chain 'H' and resid 342 through 355 Processing helix chain 'H' and resid 356 through 358 No H-bonds generated for 'chain 'H' and resid 356 through 358' Processing helix chain 'H' and resid 369 through 379 Processing helix chain 'H' and resid 387 through 391 Processing helix chain 'H' and resid 416 through 422 removed outlier: 3.963A pdb=" N LYS H 422 " --> pdb=" O ASP H 418 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 472 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 475 through 485 Processing helix chain 'H' and resid 494 through 502 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.417A pdb=" N ALA A 248 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL A 299 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ARG A 322 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY A 301 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ASP A 364 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N VAL A 323 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N MET A 385 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL A 66 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 401 through 402 removed outlier: 3.548A pdb=" N SER A 444 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER D 508 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.611A pdb=" N SER A 508 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 444 " --> pdb=" O GLU A 510 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.416A pdb=" N ALA B 248 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B 299 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ARG B 322 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLY B 301 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N MET B 385 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 66 " --> pdb=" O MET B 386 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 508 through 510 removed outlier: 3.611A pdb=" N SER B 508 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER C 444 " --> pdb=" O GLU B 510 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.423A pdb=" N ALA C 248 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL C 299 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ARG C 322 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY C 301 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU C 321 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ASP C 364 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N VAL C 323 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N MET C 385 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL C 66 " --> pdb=" O MET C 386 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 508 through 510 removed outlier: 3.611A pdb=" N SER C 508 " --> pdb=" O ALA D 446 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER D 444 " --> pdb=" O GLU C 510 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.421A pdb=" N ALA D 248 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL D 299 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ARG D 322 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLY D 301 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N MET D 385 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL D 66 " --> pdb=" O MET D 386 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AB9, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC1, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.421A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL E 299 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ARG E 322 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY E 301 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU E 321 " --> pdb=" O ILE E 362 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASP E 364 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N VAL E 323 " --> pdb=" O ASP E 364 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N MET E 385 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL E 66 " --> pdb=" O MET E 386 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 401 through 403 removed outlier: 3.565A pdb=" N SER E 444 " --> pdb=" O GLU H 510 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER H 508 " --> pdb=" O ALA E 446 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 508 through 510 removed outlier: 3.605A pdb=" N SER E 508 " --> pdb=" O ALA F 446 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER F 444 " --> pdb=" O GLU E 510 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AC5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AC6, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.418A pdb=" N ALA F 248 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL F 299 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ARG F 322 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLY F 301 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ASP F 364 " --> pdb=" O LEU F 321 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N VAL F 323 " --> pdb=" O ASP F 364 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N MET F 385 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL F 66 " --> pdb=" O MET F 386 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 508 through 510 removed outlier: 3.610A pdb=" N SER F 508 " --> pdb=" O ALA G 446 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER G 444 " --> pdb=" O GLU F 510 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AC9, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AD1, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.420A pdb=" N ALA G 248 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL G 299 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ARG G 322 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY G 301 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N MET G 385 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL G 66 " --> pdb=" O MET G 386 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 508 through 510 removed outlier: 3.614A pdb=" N SER G 508 " --> pdb=" O ALA H 446 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER H 444 " --> pdb=" O GLU G 510 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AD4, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AD5, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.420A pdb=" N ALA H 248 " --> pdb=" O VAL H 272 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL H 299 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ARG H 322 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY H 301 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ASP H 364 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N VAL H 323 " --> pdb=" O ASP H 364 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N MET H 385 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL H 66 " --> pdb=" O MET H 386 " (cutoff:3.500A) 973 hydrogen bonds defined for protein. 2727 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.24 Time building geometry restraints manager: 7.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 4009 1.30 - 1.43: 6117 1.43 - 1.56: 14025 1.56 - 1.69: 33 1.69 - 1.82: 240 Bond restraints: 24424 Sorted by residual: bond pdb=" C5 IMP B 601 " pdb=" C6 IMP B 601 " ideal model delta sigma weight residual 1.390 1.529 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C5 IMP G 601 " pdb=" C6 IMP G 601 " ideal model delta sigma weight residual 1.390 1.528 -0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" C5 IMP D 601 " pdb=" C6 IMP D 601 " ideal model delta sigma weight residual 1.390 1.528 -0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" C5 IMP A 601 " pdb=" C6 IMP A 601 " ideal model delta sigma weight residual 1.390 1.528 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" C5 IMP E 601 " pdb=" C6 IMP E 601 " ideal model delta sigma weight residual 1.390 1.528 -0.138 2.00e-02 2.50e+03 4.75e+01 ... (remaining 24419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 31914 1.95 - 3.89: 871 3.89 - 5.84: 154 5.84 - 7.79: 55 7.79 - 9.73: 46 Bond angle restraints: 33040 Sorted by residual: angle pdb=" N ASP A 274 " pdb=" CA ASP A 274 " pdb=" C ASP A 274 " ideal model delta sigma weight residual 108.23 116.70 -8.47 1.72e+00 3.38e-01 2.43e+01 angle pdb=" N ASP D 274 " pdb=" CA ASP D 274 " pdb=" C ASP D 274 " ideal model delta sigma weight residual 108.23 116.70 -8.47 1.72e+00 3.38e-01 2.43e+01 angle pdb=" N ASP F 274 " pdb=" CA ASP F 274 " pdb=" C ASP F 274 " ideal model delta sigma weight residual 107.99 116.65 -8.66 1.76e+00 3.23e-01 2.42e+01 angle pdb=" N ASP C 274 " pdb=" CA ASP C 274 " pdb=" C ASP C 274 " ideal model delta sigma weight residual 107.99 116.61 -8.62 1.76e+00 3.23e-01 2.40e+01 angle pdb=" N ASP E 274 " pdb=" CA ASP E 274 " pdb=" C ASP E 274 " ideal model delta sigma weight residual 107.99 116.59 -8.60 1.76e+00 3.23e-01 2.38e+01 ... (remaining 33035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.64: 13651 25.64 - 51.27: 985 51.27 - 76.91: 166 76.91 - 102.54: 46 102.54 - 128.18: 8 Dihedral angle restraints: 14856 sinusoidal: 6032 harmonic: 8824 Sorted by residual: dihedral pdb=" C5' IMP B 601 " pdb=" O5' IMP B 601 " pdb=" P IMP B 601 " pdb=" O2P IMP B 601 " ideal model delta sinusoidal sigma weight residual -168.07 -39.89 -128.18 1 2.00e+01 2.50e-03 3.88e+01 dihedral pdb=" C5' IMP E 601 " pdb=" O5' IMP E 601 " pdb=" P IMP E 601 " pdb=" O2P IMP E 601 " ideal model delta sinusoidal sigma weight residual 191.93 71.57 120.36 1 2.00e+01 2.50e-03 3.61e+01 dihedral pdb=" C5' IMP G 601 " pdb=" O5' IMP G 601 " pdb=" P IMP G 601 " pdb=" O2P IMP G 601 " ideal model delta sinusoidal sigma weight residual 191.93 73.06 118.87 1 2.00e+01 2.50e-03 3.56e+01 ... (remaining 14853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2801 0.057 - 0.114: 854 0.114 - 0.170: 93 0.170 - 0.227: 16 0.227 - 0.284: 4 Chirality restraints: 3768 Sorted by residual: chirality pdb=" C3D NAD B 602 " pdb=" C2D NAD B 602 " pdb=" C4D NAD B 602 " pdb=" O3D NAD B 602 " both_signs ideal model delta sigma weight residual False -2.73 -2.44 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA ASP G 28 " pdb=" N ASP G 28 " pdb=" C ASP G 28 " pdb=" CB ASP G 28 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA ASP D 28 " pdb=" N ASP D 28 " pdb=" C ASP D 28 " pdb=" CB ASP D 28 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 3765 not shown) Planarity restraints: 4176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 230 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.49e+00 pdb=" C ASN A 230 " 0.032 2.00e-02 2.50e+03 pdb=" O ASN A 230 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG A 231 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS F 26 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.44e+00 pdb=" C CYS F 26 " -0.032 2.00e-02 2.50e+03 pdb=" O CYS F 26 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY F 27 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 26 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.42e+00 pdb=" C CYS C 26 " 0.032 2.00e-02 2.50e+03 pdb=" O CYS C 26 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY C 27 " -0.011 2.00e-02 2.50e+03 ... (remaining 4173 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4142 2.77 - 3.30: 22715 3.30 - 3.83: 42281 3.83 - 4.37: 52059 4.37 - 4.90: 84515 Nonbonded interactions: 205712 Sorted by model distance: nonbonded pdb=" NH1 ARG B 512 " pdb=" OD1 ASP C 418 " model vdw 2.232 3.120 nonbonded pdb=" NH1 ARG F 512 " pdb=" OD1 ASP G 418 " model vdw 2.275 3.120 nonbonded pdb=" OD1 ASP E 418 " pdb=" NH1 ARG H 512 " model vdw 2.282 3.120 nonbonded pdb=" NH1 ARG E 512 " pdb=" OD1 ASP F 418 " model vdw 2.284 3.120 nonbonded pdb=" OG1 THR A 31 " pdb=" OE2 GLU D 500 " model vdw 2.319 3.040 ... (remaining 205707 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.940 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 60.620 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 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 : 0.007 0.139 24432 Z= 0.368 Angle : 0.858 9.734 33040 Z= 0.424 Chirality : 0.053 0.284 3768 Planarity : 0.005 0.054 4176 Dihedral : 18.075 128.180 9256 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.17 % Allowed : 19.57 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.16), residues: 3072 helix: 1.72 (0.15), residues: 1200 sheet: 0.03 (0.23), residues: 432 loop : -0.08 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 454 PHE 0.018 0.003 PHE E 401 TYR 0.016 0.002 TYR A 353 ARG 0.007 0.001 ARG A 105 Details of bonding type rmsd hydrogen bonds : bond 0.12972 ( 973) hydrogen bonds : angle 5.91576 ( 2727) covalent geometry : bond 0.00743 (24424) covalent geometry : angle 0.85753 (33040) Misc. bond : bond 0.00073 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 445 time to evaluate : 2.859 Fit side-chains REVERT: A 1 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.5982 (mpt) REVERT: C 78 MET cc_start: 0.9259 (tpp) cc_final: 0.8937 (tpp) REVERT: D 1 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6017 (mpt) REVERT: E 78 MET cc_start: 0.9266 (tpp) cc_final: 0.8962 (tpp) REVERT: E 230 ASN cc_start: 0.7574 (OUTLIER) cc_final: 0.7371 (p0) REVERT: F 1 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6180 (mpt) REVERT: G 1 MET cc_start: 0.7006 (OUTLIER) cc_final: 0.6066 (mpt) REVERT: G 78 MET cc_start: 0.9265 (tpp) cc_final: 0.8974 (tpp) REVERT: H 1 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6089 (mpt) REVERT: H 78 MET cc_start: 0.9259 (tpp) cc_final: 0.8946 (tpp) outliers start: 29 outliers final: 16 residues processed: 463 average time/residue: 1.7775 time to fit residues: 916.1191 Evaluate side-chains 414 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 392 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain E residue 230 ASN Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 291 LYS Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 230 ASN Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 291 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 0.6980 chunk 236 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 244 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 chunk 182 optimal weight: 3.9990 chunk 283 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 33 ASN A 48 GLN A 283 GLN A 368 GLN B 33 ASN B 48 GLN B 283 GLN C 21 GLN C 33 ASN C 48 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN D 33 ASN D 48 GLN D 283 GLN E 21 GLN E 33 ASN E 48 GLN E 283 GLN E 368 GLN F 33 ASN F 48 GLN F 283 GLN G 21 GLN G 33 ASN G 48 GLN G 283 GLN G 368 GLN H 21 GLN H 33 ASN H 48 GLN H 94 ASN H 283 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.102121 restraints weight = 22133.892| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.24 r_work: 0.3014 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 24432 Z= 0.119 Angle : 0.534 7.075 33040 Z= 0.286 Chirality : 0.043 0.153 3768 Planarity : 0.004 0.036 4176 Dihedral : 10.839 98.907 3888 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.85 % Allowed : 17.81 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.16), residues: 3072 helix: 2.01 (0.16), residues: 1200 sheet: 0.10 (0.23), residues: 432 loop : -0.05 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 93 PHE 0.011 0.001 PHE A 24 TYR 0.013 0.001 TYR F 353 ARG 0.003 0.000 ARG G 105 Details of bonding type rmsd hydrogen bonds : bond 0.04700 ( 973) hydrogen bonds : angle 5.16071 ( 2727) covalent geometry : bond 0.00255 (24424) covalent geometry : angle 0.53443 (33040) Misc. bond : bond 0.00028 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 418 time to evaluate : 2.568 Fit side-chains REVERT: A 1 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6929 (mmt) REVERT: A 450 LYS cc_start: 0.8542 (mttp) cc_final: 0.8311 (mttm) REVERT: C 78 MET cc_start: 0.9293 (tpp) cc_final: 0.8964 (tpp) REVERT: C 450 LYS cc_start: 0.8555 (mttp) cc_final: 0.8327 (mttm) REVERT: E 78 MET cc_start: 0.9282 (tpp) cc_final: 0.8961 (tpp) REVERT: G 78 MET cc_start: 0.9289 (tpp) cc_final: 0.8965 (tpp) REVERT: G 112 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7109 (mm-40) REVERT: H 1 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6888 (mmt) REVERT: H 78 MET cc_start: 0.9296 (tpp) cc_final: 0.8965 (tpp) outliers start: 71 outliers final: 21 residues processed: 468 average time/residue: 1.7298 time to fit residues: 902.4427 Evaluate side-chains 405 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 381 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 230 ASN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 474 LYS Chi-restraints excluded: chain H residue 510 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 293 optimal weight: 0.9980 chunk 223 optimal weight: 0.0470 chunk 25 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 chunk 299 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 282 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 291 optimal weight: 0.8980 chunk 251 optimal weight: 2.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN B 48 GLN B 283 GLN B 368 GLN C 21 GLN C 48 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 48 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN E 48 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN F 48 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN G 48 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN H 21 GLN H 48 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.102182 restraints weight = 22079.673| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.24 r_work: 0.3014 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 24432 Z= 0.119 Angle : 0.525 7.339 33040 Z= 0.281 Chirality : 0.042 0.143 3768 Planarity : 0.004 0.035 4176 Dihedral : 10.307 97.079 3857 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.09 % Allowed : 17.68 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.16), residues: 3072 helix: 2.10 (0.15), residues: 1200 sheet: -0.01 (0.23), residues: 424 loop : 0.03 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 93 PHE 0.011 0.001 PHE E 24 TYR 0.013 0.001 TYR A 353 ARG 0.003 0.000 ARG G 105 Details of bonding type rmsd hydrogen bonds : bond 0.04658 ( 973) hydrogen bonds : angle 5.02567 ( 2727) covalent geometry : bond 0.00255 (24424) covalent geometry : angle 0.52455 (33040) Misc. bond : bond 0.00027 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 403 time to evaluate : 2.538 Fit side-chains REVERT: A 1 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6922 (mmt) REVERT: A 291 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8374 (mptt) REVERT: A 450 LYS cc_start: 0.8516 (mttp) cc_final: 0.8279 (mttm) REVERT: B 283 GLN cc_start: 0.9320 (OUTLIER) cc_final: 0.8782 (tt0) REVERT: C 78 MET cc_start: 0.9323 (tpp) cc_final: 0.9016 (tpp) REVERT: C 291 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8338 (mptt) REVERT: C 450 LYS cc_start: 0.8530 (mttp) cc_final: 0.8266 (mttm) REVERT: D 112 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7135 (mm-40) REVERT: E 78 MET cc_start: 0.9319 (tpp) cc_final: 0.9019 (tpp) REVERT: F 291 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8325 (mptt) REVERT: G 78 MET cc_start: 0.9318 (tpp) cc_final: 0.9009 (tpp) REVERT: H 78 MET cc_start: 0.9326 (tpp) cc_final: 0.9016 (tpp) outliers start: 77 outliers final: 21 residues processed: 464 average time/residue: 1.6396 time to fit residues: 853.3260 Evaluate side-chains 432 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 405 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 230 ASN Chi-restraints excluded: chain H residue 444 SER Chi-restraints excluded: chain H residue 474 LYS Chi-restraints excluded: chain H residue 510 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 61 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 chunk 289 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 194 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 260 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN B 48 GLN B 243 GLN B 368 GLN C 48 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 48 GLN D 283 GLN D 368 GLN E 48 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN F 48 GLN F 283 GLN F 368 GLN G 48 GLN G 283 GLN G 368 GLN H 48 GLN H 283 GLN H 368 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.124620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.101005 restraints weight = 22213.147| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.25 r_work: 0.2994 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24432 Z= 0.134 Angle : 0.542 7.726 33040 Z= 0.289 Chirality : 0.043 0.140 3768 Planarity : 0.004 0.036 4176 Dihedral : 10.271 98.890 3852 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.93 % Allowed : 17.73 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.16), residues: 3072 helix: 2.09 (0.15), residues: 1200 sheet: -0.08 (0.23), residues: 424 loop : 0.04 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 93 PHE 0.016 0.002 PHE B 401 TYR 0.014 0.002 TYR A 353 ARG 0.003 0.000 ARG E 407 Details of bonding type rmsd hydrogen bonds : bond 0.04979 ( 973) hydrogen bonds : angle 5.07771 ( 2727) covalent geometry : bond 0.00292 (24424) covalent geometry : angle 0.54231 (33040) Misc. bond : bond 0.00029 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 426 time to evaluate : 2.621 Fit side-chains REVERT: A 1 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6930 (mmt) REVERT: A 291 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8338 (mptt) REVERT: A 450 LYS cc_start: 0.8511 (mttp) cc_final: 0.8264 (mttm) REVERT: B 241 LYS cc_start: 0.7819 (mtpt) cc_final: 0.7594 (mtpt) REVERT: B 335 GLU cc_start: 0.8105 (pt0) cc_final: 0.7723 (mp0) REVERT: B 447 VAL cc_start: 0.8897 (m) cc_final: 0.8697 (t) REVERT: C 291 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8319 (mptt) REVERT: C 447 VAL cc_start: 0.8890 (m) cc_final: 0.8671 (t) REVERT: C 450 LYS cc_start: 0.8501 (mttp) cc_final: 0.8245 (mttm) REVERT: D 112 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7129 (mm-40) REVERT: E 335 GLU cc_start: 0.8114 (pt0) cc_final: 0.7725 (mp0) REVERT: F 291 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8308 (mptt) REVERT: F 335 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7422 (mp0) REVERT: G 112 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7118 (mm-40) REVERT: H 291 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8326 (mptt) outliers start: 73 outliers final: 35 residues processed: 484 average time/residue: 1.6698 time to fit residues: 904.3434 Evaluate side-chains 426 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 383 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 474 LYS Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain H residue 230 ASN Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain H residue 444 SER Chi-restraints excluded: chain H residue 474 LYS Chi-restraints excluded: chain H residue 510 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 163 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 202 optimal weight: 0.9990 chunk 107 optimal weight: 0.3980 chunk 82 optimal weight: 2.9990 chunk 283 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 213 optimal weight: 0.0770 chunk 266 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 230 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 283 GLN A 368 GLN B 48 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN C 48 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 48 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN E 48 GLN E 283 GLN E 368 GLN F 48 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN G 48 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN H 48 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.126655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.103173 restraints weight = 22250.167| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.25 r_work: 0.3030 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 24432 Z= 0.101 Angle : 0.490 7.421 33040 Z= 0.262 Chirality : 0.041 0.135 3768 Planarity : 0.004 0.035 4176 Dihedral : 9.892 91.551 3852 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.97 % Allowed : 17.68 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.16), residues: 3072 helix: 2.11 (0.16), residues: 1232 sheet: -0.03 (0.22), residues: 424 loop : 0.02 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 92 PHE 0.016 0.001 PHE G 401 TYR 0.013 0.001 TYR G 353 ARG 0.003 0.000 ARG E 407 Details of bonding type rmsd hydrogen bonds : bond 0.04074 ( 973) hydrogen bonds : angle 4.84940 ( 2727) covalent geometry : bond 0.00212 (24424) covalent geometry : angle 0.48990 (33040) Misc. bond : bond 0.00014 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 399 time to evaluate : 2.597 Fit side-chains REVERT: A 291 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8300 (mptt) REVERT: B 241 LYS cc_start: 0.7821 (mtpt) cc_final: 0.7589 (mtpt) REVERT: C 291 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8338 (mptt) REVERT: F 291 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8325 (mptt) REVERT: F 335 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: H 291 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8393 (mptt) outliers start: 74 outliers final: 27 residues processed: 452 average time/residue: 1.6349 time to fit residues: 829.1121 Evaluate side-chains 419 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 387 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 474 LYS Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain H residue 444 SER Chi-restraints excluded: chain H residue 474 LYS Chi-restraints excluded: chain H residue 510 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 116 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 277 optimal weight: 4.9990 chunk 124 optimal weight: 0.2980 chunk 169 optimal weight: 8.9990 chunk 105 optimal weight: 0.7980 chunk 263 optimal weight: 0.8980 chunk 280 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 chunk 240 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN B 48 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN C 48 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 48 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN E 48 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN F 48 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN G 48 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN H 48 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.124312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.100711 restraints weight = 22026.641| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.24 r_work: 0.2993 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24432 Z= 0.142 Angle : 0.552 7.817 33040 Z= 0.294 Chirality : 0.043 0.139 3768 Planarity : 0.004 0.035 4176 Dihedral : 10.106 99.211 3847 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.77 % Allowed : 17.93 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.15), residues: 3072 helix: 2.13 (0.16), residues: 1200 sheet: -0.08 (0.22), residues: 424 loop : 0.03 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 93 PHE 0.016 0.002 PHE H 401 TYR 0.014 0.002 TYR H 353 ARG 0.003 0.000 ARG G 407 Details of bonding type rmsd hydrogen bonds : bond 0.05106 ( 973) hydrogen bonds : angle 5.04982 ( 2727) covalent geometry : bond 0.00312 (24424) covalent geometry : angle 0.55192 (33040) Misc. bond : bond 0.00025 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 395 time to evaluate : 2.774 Fit side-chains REVERT: A 291 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8329 (mptt) REVERT: B 241 LYS cc_start: 0.7830 (mtpt) cc_final: 0.7594 (mtpt) REVERT: C 291 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8334 (mptt) REVERT: E 335 GLU cc_start: 0.8136 (pt0) cc_final: 0.7721 (mp0) REVERT: E 438 LYS cc_start: 0.8587 (mttm) cc_final: 0.8365 (mmtm) REVERT: F 291 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8313 (mptt) REVERT: F 335 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: G 112 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7124 (mm-40) REVERT: H 291 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8335 (mptt) REVERT: H 330 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.8855 (pp) outliers start: 69 outliers final: 35 residues processed: 445 average time/residue: 1.6585 time to fit residues: 826.8861 Evaluate side-chains 415 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 373 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 474 LYS Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 444 SER Chi-restraints excluded: chain H residue 474 LYS Chi-restraints excluded: chain H residue 510 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 240 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 107 optimal weight: 0.2980 chunk 43 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 261 optimal weight: 0.8980 chunk 250 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 278 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN B 48 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN C 48 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 48 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN E 48 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN F 48 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN G 48 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN H 48 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.123332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.099641 restraints weight = 22161.194| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.25 r_work: 0.2978 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 24432 Z= 0.166 Angle : 0.590 8.254 33040 Z= 0.314 Chirality : 0.045 0.145 3768 Planarity : 0.004 0.038 4176 Dihedral : 10.291 102.229 3847 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.73 % Allowed : 17.93 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.16), residues: 3072 helix: 2.00 (0.15), residues: 1200 sheet: -0.11 (0.23), residues: 424 loop : 0.01 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 93 PHE 0.017 0.002 PHE F 401 TYR 0.015 0.002 TYR E 353 ARG 0.003 0.000 ARG D 407 Details of bonding type rmsd hydrogen bonds : bond 0.05578 ( 973) hydrogen bonds : angle 5.17799 ( 2727) covalent geometry : bond 0.00369 (24424) covalent geometry : angle 0.58976 (33040) Misc. bond : bond 0.00030 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 389 time to evaluate : 2.603 Fit side-chains REVERT: A 112 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7172 (mm-40) REVERT: A 291 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8322 (mptt) REVERT: B 241 LYS cc_start: 0.7829 (mtpt) cc_final: 0.7602 (mtpt) REVERT: C 291 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8335 (mptt) REVERT: D 112 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7132 (mm-40) REVERT: F 291 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8327 (mptt) REVERT: F 335 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: H 291 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8347 (mptt) REVERT: H 330 ILE cc_start: 0.9349 (OUTLIER) cc_final: 0.8869 (pp) outliers start: 68 outliers final: 33 residues processed: 441 average time/residue: 1.6264 time to fit residues: 805.1052 Evaluate side-chains 427 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 386 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 474 LYS Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 444 SER Chi-restraints excluded: chain H residue 474 LYS Chi-restraints excluded: chain H residue 510 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 190 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 300 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 236 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 105 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN B 48 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN C 48 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 48 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN E 283 GLN E 368 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN H 48 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.121866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.098312 restraints weight = 21980.598| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.24 r_work: 0.2953 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24432 Z= 0.222 Angle : 0.663 8.781 33040 Z= 0.354 Chirality : 0.048 0.157 3768 Planarity : 0.005 0.047 4176 Dihedral : 10.614 107.955 3847 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.93 % Allowed : 17.68 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.15), residues: 3072 helix: 1.77 (0.15), residues: 1200 sheet: -0.16 (0.23), residues: 424 loop : -0.08 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 93 PHE 0.017 0.002 PHE H 24 TYR 0.016 0.002 TYR H 353 ARG 0.004 0.001 ARG D 407 Details of bonding type rmsd hydrogen bonds : bond 0.06507 ( 973) hydrogen bonds : angle 5.36582 ( 2727) covalent geometry : bond 0.00503 (24424) covalent geometry : angle 0.66336 (33040) Misc. bond : bond 0.00043 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 390 time to evaluate : 2.827 Fit side-chains REVERT: A 112 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7189 (mm-40) REVERT: A 291 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8340 (mptt) REVERT: A 330 ILE cc_start: 0.9371 (OUTLIER) cc_final: 0.8962 (pp) REVERT: B 241 LYS cc_start: 0.7849 (mtpt) cc_final: 0.7635 (mtpt) REVERT: B 330 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.8960 (pp) REVERT: D 112 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7133 (mm-40) REVERT: D 330 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.8957 (pp) REVERT: E 330 ILE cc_start: 0.9364 (OUTLIER) cc_final: 0.8952 (pp) REVERT: F 330 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.8997 (pp) REVERT: F 335 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: G 112 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7154 (mm-40) REVERT: G 330 ILE cc_start: 0.9364 (OUTLIER) cc_final: 0.8947 (pp) REVERT: H 112 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7161 (mm-40) REVERT: H 291 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8361 (mptt) REVERT: H 330 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.8928 (pp) outliers start: 73 outliers final: 36 residues processed: 450 average time/residue: 1.6699 time to fit residues: 848.6735 Evaluate side-chains 423 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 373 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 474 LYS Chi-restraints excluded: chain G residue 26 CYS Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 230 ASN Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 444 SER Chi-restraints excluded: chain H residue 474 LYS Chi-restraints excluded: chain H residue 510 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 190 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 288 optimal weight: 4.9990 chunk 259 optimal weight: 3.9990 chunk 249 optimal weight: 0.7980 chunk 268 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN C 48 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 48 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN E 368 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN H 48 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.121891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.098357 restraints weight = 22078.461| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.24 r_work: 0.2950 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24432 Z= 0.218 Angle : 0.657 8.776 33040 Z= 0.351 Chirality : 0.048 0.160 3768 Planarity : 0.005 0.045 4176 Dihedral : 10.608 106.901 3847 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.57 % Allowed : 18.37 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.15), residues: 3072 helix: 1.73 (0.15), residues: 1200 sheet: -0.23 (0.23), residues: 424 loop : -0.09 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 93 PHE 0.017 0.002 PHE A 24 TYR 0.016 0.002 TYR H 353 ARG 0.003 0.001 ARG G 407 Details of bonding type rmsd hydrogen bonds : bond 0.06380 ( 973) hydrogen bonds : angle 5.37541 ( 2727) covalent geometry : bond 0.00493 (24424) covalent geometry : angle 0.65725 (33040) Misc. bond : bond 0.00046 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 373 time to evaluate : 2.746 Fit side-chains REVERT: A 112 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7196 (mm-40) REVERT: A 291 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8347 (mptt) REVERT: A 330 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.8977 (pp) REVERT: B 241 LYS cc_start: 0.7854 (mtpt) cc_final: 0.7638 (mtpt) REVERT: B 330 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.8976 (pp) REVERT: C 330 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.9009 (pp) REVERT: D 112 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7148 (mm-40) REVERT: D 330 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.8975 (pp) REVERT: E 330 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.8970 (pp) REVERT: F 330 ILE cc_start: 0.9371 (OUTLIER) cc_final: 0.8970 (pp) REVERT: F 335 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: G 112 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7175 (mm-40) REVERT: G 330 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.8967 (pp) REVERT: H 112 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7228 (mm-40) REVERT: H 291 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8374 (mptt) REVERT: H 330 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.8940 (pp) outliers start: 64 outliers final: 35 residues processed: 427 average time/residue: 1.7632 time to fit residues: 842.2189 Evaluate side-chains 424 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 374 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 474 LYS Chi-restraints excluded: chain G residue 26 CYS Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 230 ASN Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 444 SER Chi-restraints excluded: chain H residue 474 LYS Chi-restraints excluded: chain H residue 510 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 61 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 227 optimal weight: 3.9990 chunk 63 optimal weight: 0.1980 chunk 224 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN H 48 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.124056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.100544 restraints weight = 22166.929| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.24 r_work: 0.2987 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24432 Z= 0.135 Angle : 0.556 8.197 33040 Z= 0.298 Chirality : 0.043 0.149 3768 Planarity : 0.004 0.039 4176 Dihedral : 10.153 98.817 3847 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.29 % Allowed : 18.61 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.16), residues: 3072 helix: 2.05 (0.15), residues: 1200 sheet: -0.14 (0.23), residues: 424 loop : 0.03 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 93 PHE 0.014 0.002 PHE H 401 TYR 0.013 0.002 TYR G 353 ARG 0.003 0.000 ARG E 407 Details of bonding type rmsd hydrogen bonds : bond 0.04972 ( 973) hydrogen bonds : angle 5.10356 ( 2727) covalent geometry : bond 0.00293 (24424) covalent geometry : angle 0.55628 (33040) Misc. bond : bond 0.00024 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 378 time to evaluate : 2.772 Fit side-chains REVERT: A 112 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7186 (mm-40) REVERT: B 241 LYS cc_start: 0.7840 (mtpt) cc_final: 0.7624 (mtpt) REVERT: D 112 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7167 (mm-40) REVERT: F 335 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7390 (mp0) outliers start: 57 outliers final: 35 residues processed: 426 average time/residue: 1.6400 time to fit residues: 784.8539 Evaluate side-chains 426 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 388 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 474 LYS Chi-restraints excluded: chain G residue 26 CYS Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 444 SER Chi-restraints excluded: chain H residue 474 LYS Chi-restraints excluded: chain H residue 510 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 195 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 265 optimal weight: 0.3980 chunk 231 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 272 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 192 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN E 283 GLN E 368 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.123934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.100386 restraints weight = 21962.909| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.24 r_work: 0.2988 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24432 Z= 0.139 Angle : 0.565 8.083 33040 Z= 0.301 Chirality : 0.044 0.147 3768 Planarity : 0.004 0.038 4176 Dihedral : 10.126 99.534 3847 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.13 % Allowed : 18.85 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.16), residues: 3072 helix: 2.05 (0.15), residues: 1200 sheet: -0.15 (0.23), residues: 424 loop : 0.02 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 454 PHE 0.015 0.002 PHE A 401 TYR 0.013 0.002 TYR C 353 ARG 0.003 0.000 ARG F 407 Details of bonding type rmsd hydrogen bonds : bond 0.05091 ( 973) hydrogen bonds : angle 5.09245 ( 2727) covalent geometry : bond 0.00303 (24424) covalent geometry : angle 0.56468 (33040) Misc. bond : bond 0.00019 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25799.35 seconds wall clock time: 444 minutes 38.10 seconds (26678.10 seconds total)