Starting phenix.real_space_refine on Fri Aug 7 21:38:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fuz_29482/08_2026/8fuz_29482.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fuz_29482/08_2026/8fuz_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8fuz_29482/08_2026/8fuz_29482.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fuz_29482/08_2026/8fuz_29482.cif" model { file = "/net/cci-nas-00/data/ceres_data/8fuz_29482/08_2026/8fuz_29482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fuz_29482/08_2026/8fuz_29482.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fuz_29482/08_2026/8fuz_29482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fuz_29482/08_2026/8fuz_29482.map" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Time building chain proxies: 5.86, per 1000 atoms: 0.24 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: 1.73 Conformation dependent library (CDL) restraints added in 1.4 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: 0.92 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: 5.02 Time building geometry restraints manager: 2.44 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: 31850 1.95 - 3.89: 895 3.89 - 5.84: 170 5.84 - 7.79: 63 7.79 - 9.73: 62 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: 13338 25.64 - 51.27: 915 51.27 - 76.91: 155 76.91 - 102.54: 40 102.54 - 128.18: 8 Dihedral angle restraints: 14456 sinusoidal: 5632 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 14453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2793 0.057 - 0.114: 854 0.114 - 0.170: 93 0.170 - 0.227: 16 0.227 - 0.284: 12 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=" C2' IMP F 601 " pdb=" C1' IMP F 601 " pdb=" C3' IMP F 601 " pdb=" O2' IMP F 601 " both_signs ideal model delta sigma weight residual False -2.47 -2.75 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C2' IMP G 601 " pdb=" C1' IMP G 601 " pdb=" C3' IMP G 601 " pdb=" O2' IMP G 601 " both_signs ideal model delta sigma weight residual False -2.47 -2.75 0.28 2.00e-01 2.50e+01 1.95e+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: 0.01 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: 6.690 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: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 23.980 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9095 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= 0.370 Angle : 0.895 9.734 33040 Z= 0.432 Chirality : 0.054 0.284 3768 Planarity : 0.005 0.054 4176 Dihedral : 17.811 128.180 8856 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.16), 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 ARG 0.007 0.001 ARG A 105 TYR 0.016 0.002 TYR A 353 PHE 0.018 0.003 PHE E 401 HIS 0.004 0.001 HIS F 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00747 / 0.37 (24424) covalent geometry : angle 0.89471 / 0.43 (33040) hydrogen bonds : bond 0.12972 / 8.73 ( 973) hydrogen bonds : angle 5.91576 / 4.16 ( 2727) Misc. bond : bond 0.00073 / 0.03 ( 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 : 0.893 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: 0.8572 time to fit residues: 442.1757 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 : 0.931 ------------------------------------------------------------------------------- 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 197 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN A 33 ASN A 48 GLN A 283 GLN A 368 GLN B 33 ASN B 48 GLN B 283 GLN B 368 GLN C 21 GLN C 33 ASN C 48 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 21 GLN D 33 ASN D 48 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 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 F 368 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 H 368 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.099018 restraints weight = 22131.266| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.24 r_work: 0.2966 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9093 moved from start: 0.0733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24432 Z= 0.195 Angle : 0.672 8.056 33040 Z= 0.348 Chirality : 0.048 0.170 3768 Planarity : 0.005 0.045 4176 Dihedral : 9.619 108.422 3488 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.66 % Allowed : 16.00 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.15), residues: 3072 helix: 1.73 (0.15), residues: 1200 sheet: -0.12 (0.24), residues: 424 loop : -0.06 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 407 TYR 0.015 0.002 TYR F 353 PHE 0.016 0.002 PHE E 24 HIS 0.004 0.001 HIS E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.20 (24424) covalent geometry : angle 0.67163 / 0.35 (33040) hydrogen bonds : bond 0.06162 / 4.02 ( 973) hydrogen bonds : angle 5.43223 / 3.80 ( 2727) Misc. bond : bond 0.00056 / 0.02 ( 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 506 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 415 time to evaluate : 0.922 Fit side-chains REVERT: A 1 MET cc_start: 0.7131 (OUTLIER) cc_final: 0.6842 (mmt) REVERT: A 291 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8373 (mptt) REVERT: A 450 LYS cc_start: 0.8584 (mttp) cc_final: 0.8363 (mttm) REVERT: B 241 LYS cc_start: 0.7850 (mtpt) cc_final: 0.7639 (mtpt) REVERT: B 335 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: C 78 MET cc_start: 0.9335 (tpp) cc_final: 0.9012 (tpp) REVERT: C 450 LYS cc_start: 0.8588 (mttp) cc_final: 0.8369 (mttm) REVERT: D 1 MET cc_start: 0.7165 (OUTLIER) cc_final: 0.6945 (mmt) REVERT: E 78 MET cc_start: 0.9332 (tpp) cc_final: 0.9010 (tpp) REVERT: E 335 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7460 (mp0) REVERT: F 1 MET cc_start: 0.7076 (OUTLIER) cc_final: 0.6871 (mmt) REVERT: G 1 MET cc_start: 0.6968 (OUTLIER) cc_final: 0.6745 (mmt) REVERT: G 78 MET cc_start: 0.9336 (tpp) cc_final: 0.9015 (tpp) REVERT: G 112 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7129 (mm-40) REVERT: H 1 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6902 (mmt) REVERT: H 78 MET cc_start: 0.9334 (tpp) cc_final: 0.9012 (tpp) outliers start: 91 outliers final: 36 residues processed: 484 average time/residue: 0.7856 time to fit residues: 426.3762 Evaluate side-chains 416 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 371 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 283 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 335 GLU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 510 GLU 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 1 MET Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 474 LYS Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 237 SER 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 230 ASN Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 283 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 126 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 167 optimal weight: 0.0040 chunk 66 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN A 283 GLN A 368 GLN B 48 GLN B 243 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 E 368 GLN F 48 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.099044 restraints weight = 22228.588| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.24 r_work: 0.2967 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24432 Z= 0.180 Angle : 0.646 8.435 33040 Z= 0.335 Chirality : 0.046 0.170 3768 Planarity : 0.005 0.041 4176 Dihedral : 9.296 106.740 3474 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.90 % Allowed : 16.12 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.15), residues: 3072 helix: 1.79 (0.15), residues: 1200 sheet: -0.17 (0.23), residues: 424 loop : -0.07 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 407 TYR 0.014 0.002 TYR A 353 PHE 0.016 0.002 PHE E 24 HIS 0.004 0.001 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (24424) covalent geometry : angle 0.64592 / 0.33 (33040) hydrogen bonds : bond 0.05907 / 3.85 ( 973) hydrogen bonds : angle 5.34466 / 3.75 ( 2727) Misc. bond : bond 0.00041 / 0.02 ( 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 482 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 385 time to evaluate : 0.957 Fit side-chains REVERT: A 1 MET cc_start: 0.7027 (OUTLIER) cc_final: 0.6818 (mmt) REVERT: A 450 LYS cc_start: 0.8580 (mttp) cc_final: 0.8353 (mttm) REVERT: B 241 LYS cc_start: 0.7847 (mtpt) cc_final: 0.7637 (mtpt) REVERT: B 335 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7442 (mp0) REVERT: C 450 LYS cc_start: 0.8593 (mttp) cc_final: 0.8361 (mttm) REVERT: D 1 MET cc_start: 0.7124 (OUTLIER) cc_final: 0.6909 (mmt) REVERT: E 335 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7438 (mp0) REVERT: E 438 LYS cc_start: 0.8616 (mttm) cc_final: 0.8409 (mmtm) REVERT: F 1 MET cc_start: 0.7026 (OUTLIER) cc_final: 0.6806 (mmt) REVERT: F 335 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7455 (mp0) REVERT: G 1 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6877 (mmt) REVERT: H 1 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6836 (mmt) outliers start: 97 outliers final: 31 residues processed: 460 average time/residue: 0.7533 time to fit residues: 389.2344 Evaluate side-chains 449 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 410 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 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 335 GLU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 474 LYS Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 1 MET 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 1 MET Chi-restraints excluded: chain G residue 237 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 1 MET Chi-restraints excluded: chain H residue 230 ASN Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 444 SER Chi-restraints excluded: chain H residue 474 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 265 optimal weight: 0.3980 chunk 134 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 214 optimal weight: 0.0570 chunk 161 optimal weight: 2.9990 chunk 293 optimal weight: 1.9990 chunk 267 optimal weight: 2.9990 chunk 191 optimal weight: 0.4980 chunk 122 optimal weight: 1.9990 chunk 230 optimal weight: 4.9990 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.125063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.101588 restraints weight = 22038.068| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.24 r_work: 0.3005 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9064 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 24432 Z= 0.117 Angle : 0.554 8.087 33040 Z= 0.285 Chirality : 0.043 0.143 3768 Planarity : 0.004 0.038 4176 Dihedral : 8.827 100.137 3474 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.45 % Allowed : 17.32 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.15), residues: 3072 helix: 1.95 (0.15), residues: 1232 sheet: -0.13 (0.23), residues: 424 loop : -0.04 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 105 TYR 0.013 0.001 TYR G 353 PHE 0.011 0.001 PHE E 24 HIS 0.002 0.001 HIS H 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (24424) covalent geometry : angle 0.55397 / 0.29 (33040) hydrogen bonds : bond 0.04594 / 3.01 ( 973) hydrogen bonds : angle 5.05034 / 3.54 ( 2727) Misc. bond : bond 0.00014 / 0.01 ( 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 490 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 429 time to evaluate : 0.960 Fit side-chains REVERT: A 1 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6868 (mmt) REVERT: A 291 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8375 (mptt) REVERT: A 450 LYS cc_start: 0.8531 (mttp) cc_final: 0.8300 (mttm) REVERT: B 241 LYS cc_start: 0.7832 (mtpt) cc_final: 0.7629 (mtpt) REVERT: B 447 VAL cc_start: 0.8914 (m) cc_final: 0.8711 (t) REVERT: C 447 VAL cc_start: 0.8874 (m) cc_final: 0.8673 (t) REVERT: C 450 LYS cc_start: 0.8525 (mttp) cc_final: 0.8283 (mttm) REVERT: D 1 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.6838 (mmt) REVERT: D 335 GLU cc_start: 0.8125 (pt0) cc_final: 0.7718 (mp0) REVERT: D 447 VAL cc_start: 0.8917 (m) cc_final: 0.8716 (t) REVERT: E 438 LYS cc_start: 0.8570 (mttm) cc_final: 0.8355 (mmtm) REVERT: F 335 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7423 (mp0) REVERT: G 1 MET cc_start: 0.7083 (OUTLIER) cc_final: 0.6864 (mmt) REVERT: G 112 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7126 (mm-40) REVERT: H 1 MET cc_start: 0.7055 (OUTLIER) cc_final: 0.6822 (mmt) REVERT: H 291 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8359 (mptt) outliers start: 61 outliers final: 19 residues processed: 469 average time/residue: 0.7985 time to fit residues: 417.7974 Evaluate side-chains 404 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 377 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 291 LYS 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 438 LYS Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 474 LYS Chi-restraints excluded: chain G residue 1 MET 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 1 MET Chi-restraints excluded: chain H residue 230 ASN Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain H residue 474 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 141 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 256 optimal weight: 0.5980 chunk 138 optimal weight: 3.9990 chunk 287 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 289 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.123422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.099807 restraints weight = 22046.853| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.24 r_work: 0.2975 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9085 moved from start: 0.1011 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= 0.157 Angle : 0.612 8.407 33040 Z= 0.315 Chirality : 0.045 0.155 3768 Planarity : 0.004 0.038 4176 Dihedral : 8.868 103.767 3461 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.73 % Allowed : 17.56 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.15), residues: 3072 helix: 1.85 (0.15), residues: 1232 sheet: -0.12 (0.23), residues: 424 loop : -0.09 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 105 TYR 0.014 0.002 TYR G 353 PHE 0.014 0.002 PHE E 24 HIS 0.003 0.001 HIS E 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (24424) covalent geometry : angle 0.61236 / 0.32 (33040) hydrogen bonds : bond 0.05469 / 3.56 ( 973) hydrogen bonds : angle 5.17827 / 3.63 ( 2727) Misc. bond : bond 0.00019 / 0.01 ( 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 457 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 389 time to evaluate : 0.943 Fit side-chains REVERT: A 1 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6881 (mmt) REVERT: A 291 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8333 (mptt) REVERT: A 447 VAL cc_start: 0.8924 (m) cc_final: 0.8715 (t) REVERT: A 450 LYS cc_start: 0.8540 (mttp) cc_final: 0.8241 (mttm) REVERT: B 241 LYS cc_start: 0.7837 (mtpt) cc_final: 0.7637 (mtpt) REVERT: C 450 LYS cc_start: 0.8546 (mttp) cc_final: 0.8242 (mttm) REVERT: D 1 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6828 (mmt) REVERT: F 335 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7405 (mp0) REVERT: G 1 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6867 (mmt) REVERT: H 1 MET cc_start: 0.7043 (OUTLIER) cc_final: 0.6815 (mmt) REVERT: H 291 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8366 (mptt) REVERT: H 330 ILE cc_start: 0.9351 (OUTLIER) cc_final: 0.8911 (pp) REVERT: H 335 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7359 (mp0) outliers start: 68 outliers final: 27 residues processed: 435 average time/residue: 0.8060 time to fit residues: 393.3701 Evaluate side-chains 415 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 379 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 277 GLN Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 444 SER 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 1 MET Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 510 GLU 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 E residue 510 GLU 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 1 MET 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 1 MET Chi-restraints excluded: chain H residue 230 ASN 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 335 GLU Chi-restraints excluded: chain H residue 444 SER Chi-restraints excluded: chain H residue 474 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 149 optimal weight: 0.0870 chunk 162 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 168 optimal weight: 0.0980 chunk 135 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 255 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 172 optimal weight: 7.9990 chunk 280 optimal weight: 2.9990 overall best weight: 1.2364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3414 r_free = 0.3414 target = 0.123624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.100012 restraints weight = 22108.567| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.24 r_work: 0.2979 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9083 moved from start: 0.1053 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= 0.150 Angle : 0.603 8.469 33040 Z= 0.311 Chirality : 0.045 0.148 3768 Planarity : 0.004 0.038 4176 Dihedral : 8.828 102.984 3461 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.93 % Allowed : 17.04 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.15), residues: 3072 helix: 1.86 (0.15), residues: 1232 sheet: -0.11 (0.23), residues: 424 loop : -0.10 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 407 TYR 0.014 0.002 TYR B 353 PHE 0.013 0.002 PHE E 24 HIS 0.003 0.001 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (24424) covalent geometry : angle 0.60256 / 0.31 (33040) hydrogen bonds : bond 0.05282 / 3.45 ( 973) hydrogen bonds : angle 5.14263 / 3.61 ( 2727) Misc. bond : bond 0.00020 / 0.01 ( 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 462 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 389 time to evaluate : 0.867 Fit side-chains REVERT: A 1 MET cc_start: 0.7088 (OUTLIER) cc_final: 0.6870 (mmt) REVERT: A 291 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8371 (mptt) REVERT: A 450 LYS cc_start: 0.8524 (mttp) cc_final: 0.8260 (mttm) REVERT: C 450 LYS cc_start: 0.8524 (mttp) cc_final: 0.8261 (mttm) REVERT: D 1 MET cc_start: 0.7022 (OUTLIER) cc_final: 0.6804 (mmt) REVERT: E 335 GLU cc_start: 0.8108 (pt0) cc_final: 0.7688 (mp0) REVERT: F 335 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7428 (mp0) REVERT: G 1 MET cc_start: 0.7043 (OUTLIER) cc_final: 0.6834 (mmt) REVERT: G 112 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7124 (mm-40) REVERT: H 1 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6811 (mmt) REVERT: H 291 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8366 (mptt) outliers start: 73 outliers final: 34 residues processed: 443 average time/residue: 0.7801 time to fit residues: 387.1098 Evaluate side-chains 413 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 371 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 438 LYS 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 C residue 510 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 510 GLU 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 E residue 510 GLU 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 1 MET 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 1 MET Chi-restraints excluded: chain H residue 230 ASN 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 211 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 227 optimal weight: 5.9990 chunk 220 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 264 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 270 optimal weight: 0.1980 chunk 143 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.123803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.100232 restraints weight = 22009.988| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.24 r_work: 0.2986 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9079 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24432 Z= 0.143 Angle : 0.594 8.422 33040 Z= 0.306 Chirality : 0.044 0.146 3768 Planarity : 0.004 0.038 4176 Dihedral : 8.782 102.105 3461 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.89 % Allowed : 17.36 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.15), residues: 3072 helix: 1.88 (0.15), residues: 1232 sheet: -0.09 (0.23), residues: 424 loop : -0.08 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 407 TYR 0.014 0.002 TYR G 353 PHE 0.012 0.002 PHE E 24 HIS 0.003 0.001 HIS F 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (24424) covalent geometry : angle 0.59422 / 0.31 (33040) hydrogen bonds : bond 0.05150 / 3.37 ( 973) hydrogen bonds : angle 5.10287 / 3.58 ( 2727) Misc. bond : bond 0.00016 / 0.01 ( 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 452 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 380 time to evaluate : 1.121 Fit side-chains REVERT: A 1 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6854 (mmt) REVERT: A 291 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8373 (mptt) REVERT: A 450 LYS cc_start: 0.8508 (mttp) cc_final: 0.8242 (mttm) REVERT: C 450 LYS cc_start: 0.8511 (mttp) cc_final: 0.8230 (mttm) REVERT: D 1 MET cc_start: 0.7006 (OUTLIER) cc_final: 0.6799 (mmt) REVERT: F 335 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7437 (mp0) REVERT: H 1 MET cc_start: 0.7026 (OUTLIER) cc_final: 0.6813 (mmt) REVERT: H 291 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8367 (mptt) outliers start: 72 outliers final: 35 residues processed: 435 average time/residue: 0.8314 time to fit residues: 405.1545 Evaluate side-chains 426 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 385 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 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 438 LYS 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 C residue 510 GLU Chi-restraints excluded: chain D residue 1 MET 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 E residue 510 GLU Chi-restraints excluded: chain F residue 255 ASP 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 1 MET 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 231 optimal weight: 0.0870 chunk 35 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 139 optimal weight: 0.7980 chunk 170 optimal weight: 0.6980 chunk 203 optimal weight: 0.7980 chunk 253 optimal weight: 2.9990 chunk 214 optimal weight: 0.4980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.126145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.102739 restraints weight = 22001.067| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.24 r_work: 0.3024 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9050 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24432 Z= 0.102 Angle : 0.532 8.046 33040 Z= 0.274 Chirality : 0.042 0.135 3768 Planarity : 0.004 0.038 4176 Dihedral : 8.413 95.150 3456 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.01 % Allowed : 18.53 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.16), residues: 3072 helix: 2.10 (0.16), residues: 1232 sheet: 0.04 (0.24), residues: 384 loop : 0.06 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 105 TYR 0.012 0.001 TYR G 353 PHE 0.009 0.001 PHE H 24 HIS 0.002 0.001 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (24424) covalent geometry : angle 0.53205 / 0.27 (33040) hydrogen bonds : bond 0.04116 / 2.71 ( 973) hydrogen bonds : angle 4.84787 / 3.41 ( 2727) Misc. bond : bond 0.00007 / 0.00 ( 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 450 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 400 time to evaluate : 0.968 Fit side-chains REVERT: A 1 MET cc_start: 0.7017 (OUTLIER) cc_final: 0.6816 (mmt) REVERT: A 291 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8335 (mptt) REVERT: A 450 LYS cc_start: 0.8441 (mttp) cc_final: 0.8186 (mttm) REVERT: B 335 GLU cc_start: 0.8058 (pt0) cc_final: 0.7682 (mp0) REVERT: C 450 LYS cc_start: 0.8380 (mttp) cc_final: 0.8140 (mttm) REVERT: E 335 GLU cc_start: 0.8056 (pt0) cc_final: 0.7652 (mp0) REVERT: F 335 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: H 291 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8378 (mptt) REVERT: H 330 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.8937 (pp) outliers start: 50 outliers final: 27 residues processed: 437 average time/residue: 0.8425 time to fit residues: 411.8908 Evaluate side-chains 438 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 406 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 277 GLN Chi-restraints excluded: chain B residue 438 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 237 SER 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 E residue 510 GLU 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 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 474 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 270 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 278 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 266 optimal weight: 3.9990 chunk 279 optimal weight: 0.1980 chunk 205 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.123296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.099665 restraints weight = 22062.438| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.24 r_work: 0.2974 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9087 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 24432 Z= 0.165 Angle : 0.624 8.456 33040 Z= 0.322 Chirality : 0.045 0.159 3768 Planarity : 0.004 0.037 4176 Dihedral : 8.706 103.764 3450 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.29 % Allowed : 18.53 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.16), residues: 3072 helix: 2.04 (0.15), residues: 1200 sheet: -0.11 (0.23), residues: 424 loop : 0.02 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 407 TYR 0.015 0.002 TYR G 353 PHE 0.016 0.002 PHE D 401 HIS 0.003 0.001 HIS G 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (24424) covalent geometry : angle 0.62398 / 0.32 (33040) hydrogen bonds : bond 0.05530 / 3.60 ( 973) hydrogen bonds : angle 5.15904 / 3.62 ( 2727) Misc. bond : bond 0.00018 / 0.01 ( 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 455 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 398 time to evaluate : 1.143 Fit side-chains REVERT: A 291 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8360 (mptt) REVERT: A 330 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.9004 (pp) REVERT: C 330 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.9006 (pp) REVERT: F 335 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: G 112 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7157 (mm-40) REVERT: H 291 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8368 (mptt) REVERT: H 330 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.8943 (pp) outliers start: 57 outliers final: 30 residues processed: 445 average time/residue: 0.8298 time to fit residues: 413.4254 Evaluate side-chains 416 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 379 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 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 444 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 237 SER 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 E residue 510 GLU Chi-restraints excluded: chain F residue 26 CYS 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 239 optimal weight: 0.8980 chunk 217 optimal weight: 0.7980 chunk 276 optimal weight: 3.9990 chunk 309 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 chunk 228 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 57 optimal weight: 0.0570 chunk 234 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN B 48 GLN B 283 GLN B 368 GLN C 48 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 48 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.126094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.102600 restraints weight = 22127.222| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.24 r_work: 0.3018 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9050 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24432 Z= 0.107 Angle : 0.550 8.118 33040 Z= 0.283 Chirality : 0.042 0.137 3768 Planarity : 0.004 0.038 4176 Dihedral : 8.315 95.399 3447 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.57 % Allowed : 19.57 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.15), residues: 3072 helix: 1.97 (0.15), residues: 1272 sheet: -0.09 (0.23), residues: 424 loop : -0.00 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 407 TYR 0.013 0.001 TYR G 353 PHE 0.016 0.001 PHE D 401 HIS 0.002 0.001 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (24424) covalent geometry : angle 0.55003 / 0.28 (33040) hydrogen bonds : bond 0.04155 / 2.73 ( 973) hydrogen bonds : angle 4.87313 / 3.43 ( 2727) Misc. bond : bond 0.00006 / 0.00 ( 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 426 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 387 time to evaluate : 1.000 Fit side-chains REVERT: A 291 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8330 (mptt) REVERT: D 335 GLU cc_start: 0.8170 (pt0) cc_final: 0.7698 (mp0) REVERT: F 335 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: G 112 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7144 (mm-40) REVERT: H 291 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8345 (mptt) outliers start: 39 outliers final: 29 residues processed: 419 average time/residue: 0.8149 time to fit residues: 382.0944 Evaluate side-chains 412 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 379 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 237 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain D residue 237 SER 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 E residue 510 GLU 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 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 474 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 6 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 297 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 212 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 48 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 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 = 0.3426 r_free = 0.3426 target = 0.124560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.100984 restraints weight = 22033.810| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.24 r_work: 0.2993 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24432 Z= 0.135 Angle : 0.593 8.308 33040 Z= 0.305 Chirality : 0.044 0.139 3768 Planarity : 0.004 0.037 4176 Dihedral : 8.454 98.707 3447 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.69 % Allowed : 19.61 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.15), residues: 3072 helix: 2.00 (0.15), residues: 1232 sheet: -0.15 (0.22), residues: 424 loop : -0.03 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 407 TYR 0.013 0.002 TYR D 353 PHE 0.021 0.002 PHE G 401 HIS 0.003 0.001 HIS B 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (24424) covalent geometry : angle 0.59267 / 0.30 (33040) hydrogen bonds : bond 0.04917 / 3.21 ( 973) hydrogen bonds : angle 4.98884 / 3.50 ( 2727) Misc. bond : bond 0.00011 / 0.00 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11528.84 seconds wall clock time: 196 minutes 33.57 seconds (11793.57 seconds total)