Starting phenix.real_space_refine on Fri May 23 12:03:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fuz_29482/05_2025/8fuz_29482.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fuz_29482/05_2025/8fuz_29482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fuz_29482/05_2025/8fuz_29482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fuz_29482/05_2025/8fuz_29482.map" model { file = "/net/cci-nas-00/data/ceres_data/8fuz_29482/05_2025/8fuz_29482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fuz_29482/05_2025/8fuz_29482.cif" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.237 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 144 5.16 5 C 15072 2.51 5 N 4096 2.21 5 O 4672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24008 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2934 Classifications: {'peptide': 390} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 376} Chain breaks: 2 Chain: "B" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2934 Classifications: {'peptide': 390} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 376} Chain breaks: 2 Chain: "C" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2934 Classifications: {'peptide': 390} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 376} Chain breaks: 2 Chain: "D" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2934 Classifications: {'peptide': 390} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 376} Chain breaks: 2 Chain: "E" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2934 Classifications: {'peptide': 390} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 376} Chain breaks: 2 Chain: "F" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2934 Classifications: {'peptide': 390} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 376} Chain breaks: 2 Chain: "G" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2934 Classifications: {'peptide': 390} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 376} Chain breaks: 2 Chain: "H" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2934 Classifications: {'peptide': 390} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 376} Chain breaks: 2 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "G" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "H" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Time building chain proxies: 14.02, per 1000 atoms: 0.58 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: 5.85 Conformation dependent library (CDL) restraints added in 2.8 seconds 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5600 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 32 sheets defined 43.8% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.44 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 Processing helix chain 'A' and resid 19 through 24 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 75 through 85 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 255 through 267 Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 342 through 355 Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.872A pdb=" N LYS A 422 " --> pdb=" O ASP A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 472 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 75 through 85 Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 255 through 267 Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 306 through 317 Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 342 through 355 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 369 through 379 Processing helix chain 'B' and resid 387 through 391 Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.921A pdb=" N LYS B 422 " --> pdb=" O ASP B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 472 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 494 through 502 Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 255 through 267 Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 306 through 317 Processing helix chain 'C' and resid 332 through 338 Processing helix chain 'C' and resid 342 through 355 Processing helix chain 'C' and resid 356 through 358 No H-bonds generated for 'chain 'C' and resid 356 through 358' Processing helix chain 'C' and resid 369 through 379 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.653A pdb=" N LYS C 422 " --> pdb=" O ASP C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 472 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 494 through 502 Processing helix chain 'D' and resid 2 through 6 Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 75 through 85 Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 255 through 267 Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'D' and resid 306 through 317 Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 342 through 355 Processing helix chain 'D' and resid 356 through 358 No H-bonds generated for 'chain 'D' and resid 356 through 358' Processing helix chain 'D' and resid 369 through 379 Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 416 through 422 removed outlier: 3.872A pdb=" N LYS D 422 " --> pdb=" O ASP D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 472 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 494 through 502 Processing helix chain 'E' and resid 2 through 6 Processing helix chain 'E' and resid 19 through 24 Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 45 through 49 Processing helix chain 'E' and resid 75 through 85 Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 255 through 267 Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 306 through 317 Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 342 through 355 Processing helix chain 'E' and resid 356 through 358 No H-bonds generated for 'chain 'E' and resid 356 through 358' Processing helix chain 'E' and resid 369 through 379 Processing helix chain 'E' and resid 416 through 422 removed outlier: 3.847A pdb=" N LYS E 422 " --> pdb=" O ASP E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 472 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 494 through 502 Processing helix chain 'F' and resid 2 through 6 Processing helix chain 'F' and resid 19 through 24 Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 45 through 49 Processing helix chain 'F' and resid 75 through 85 Processing helix chain 'F' and resid 96 through 109 Processing helix chain 'F' and resid 255 through 267 Processing helix chain 'F' and resid 280 through 294 Processing helix chain 'F' and resid 306 through 317 Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 342 through 355 Processing helix chain 'F' and resid 356 through 358 No H-bonds generated for 'chain 'F' and resid 356 through 358' Processing helix chain 'F' and resid 369 through 379 Processing helix chain 'F' and resid 387 through 391 Processing helix chain 'F' and resid 416 through 422 removed outlier: 3.955A pdb=" N LYS F 422 " --> pdb=" O ASP F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 472 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 494 through 502 Processing helix chain 'G' and resid 2 through 6 Processing helix chain 'G' and resid 19 through 24 Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 45 through 49 Processing helix chain 'G' and resid 75 through 85 Processing helix chain 'G' and resid 96 through 109 Processing helix chain 'G' and resid 255 through 267 Processing helix chain 'G' and resid 280 through 294 Processing helix chain 'G' and resid 306 through 317 Processing helix chain 'G' and resid 332 through 338 Processing helix chain 'G' and resid 342 through 355 Processing helix chain 'G' and resid 356 through 358 No H-bonds generated for 'chain 'G' and resid 356 through 358' Processing helix chain 'G' and resid 369 through 379 Processing helix chain 'G' and resid 416 through 422 removed outlier: 3.694A pdb=" N LYS G 422 " --> pdb=" O ASP G 418 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 472 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 475 through 485 Processing helix chain 'G' and resid 494 through 502 Processing helix chain 'H' and resid 2 through 6 Processing helix chain 'H' and resid 19 through 24 Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 45 through 49 Processing helix chain 'H' and resid 75 through 85 Processing helix chain 'H' and resid 96 through 109 Processing helix chain 'H' and resid 255 through 267 Processing helix chain 'H' and resid 280 through 294 Processing helix chain 'H' and resid 306 through 317 Processing helix chain 'H' and resid 332 through 338 Processing helix chain 'H' and resid 342 through 355 Processing helix chain 'H' and resid 356 through 358 No H-bonds generated for 'chain 'H' and resid 356 through 358' Processing helix chain 'H' and resid 369 through 379 Processing helix chain 'H' and resid 387 through 391 Processing helix chain 'H' and resid 416 through 422 removed outlier: 3.963A pdb=" N LYS H 422 " --> pdb=" O ASP H 418 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 472 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 475 through 485 Processing helix chain 'H' and resid 494 through 502 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.417A pdb=" N ALA A 248 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL A 299 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ARG A 322 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY A 301 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ASP A 364 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N VAL A 323 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N MET A 385 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL A 66 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 401 through 402 removed outlier: 3.548A pdb=" N SER A 444 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER D 508 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.611A pdb=" N SER A 508 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 444 " --> pdb=" O GLU A 510 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.416A pdb=" N ALA B 248 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B 299 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ARG B 322 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLY B 301 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N MET B 385 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 66 " --> pdb=" O MET B 386 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 508 through 510 removed outlier: 3.611A pdb=" N SER B 508 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER C 444 " --> pdb=" O GLU B 510 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.423A pdb=" N ALA C 248 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL C 299 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ARG C 322 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY C 301 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU C 321 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ASP C 364 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N VAL C 323 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N MET C 385 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL C 66 " --> pdb=" O MET C 386 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 508 through 510 removed outlier: 3.611A pdb=" N SER C 508 " --> pdb=" O ALA D 446 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER D 444 " --> pdb=" O GLU C 510 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.421A pdb=" N ALA D 248 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL D 299 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ARG D 322 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLY D 301 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N MET D 385 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL D 66 " --> pdb=" O MET D 386 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AB9, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC1, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.421A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL E 299 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ARG E 322 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY E 301 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU E 321 " --> pdb=" O ILE E 362 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASP E 364 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N VAL E 323 " --> pdb=" O ASP E 364 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N MET E 385 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL E 66 " --> pdb=" O MET E 386 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 401 through 403 removed outlier: 3.565A pdb=" N SER E 444 " --> pdb=" O GLU H 510 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER H 508 " --> pdb=" O ALA E 446 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 508 through 510 removed outlier: 3.605A pdb=" N SER E 508 " --> pdb=" O ALA F 446 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER F 444 " --> pdb=" O GLU E 510 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AC5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AC6, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.418A pdb=" N ALA F 248 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL F 299 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ARG F 322 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLY F 301 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ASP F 364 " --> pdb=" O LEU F 321 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N VAL F 323 " --> pdb=" O ASP F 364 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N MET F 385 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL F 66 " --> pdb=" O MET F 386 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 508 through 510 removed outlier: 3.610A pdb=" N SER F 508 " --> pdb=" O ALA G 446 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER G 444 " --> pdb=" O GLU F 510 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AC9, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AD1, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.420A pdb=" N ALA G 248 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL G 299 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ARG G 322 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY G 301 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N MET G 385 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL G 66 " --> pdb=" O MET G 386 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 508 through 510 removed outlier: 3.614A pdb=" N SER G 508 " --> pdb=" O ALA H 446 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER H 444 " --> pdb=" O GLU G 510 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AD4, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AD5, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.420A pdb=" N ALA H 248 " --> pdb=" O VAL H 272 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL H 299 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ARG H 322 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY H 301 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ASP H 364 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N VAL H 323 " --> pdb=" O ASP H 364 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N MET H 385 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL H 66 " --> pdb=" O MET H 386 " (cutoff:3.500A) 973 hydrogen bonds defined for protein. 2727 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.10 Time building geometry restraints manager: 6.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 4009 1.30 - 1.43: 6117 1.43 - 1.56: 14025 1.56 - 1.69: 33 1.69 - 1.82: 240 Bond restraints: 24424 Sorted by residual: bond pdb=" C5 IMP B 601 " pdb=" C6 IMP B 601 " ideal model delta sigma weight residual 1.390 1.529 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C5 IMP G 601 " pdb=" C6 IMP G 601 " ideal model delta sigma weight residual 1.390 1.528 -0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" C5 IMP D 601 " pdb=" C6 IMP D 601 " ideal model delta sigma weight residual 1.390 1.528 -0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" C5 IMP A 601 " pdb=" C6 IMP A 601 " ideal model delta sigma weight residual 1.390 1.528 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" C5 IMP E 601 " pdb=" C6 IMP E 601 " ideal model delta sigma weight residual 1.390 1.528 -0.138 2.00e-02 2.50e+03 4.75e+01 ... (remaining 24419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 31914 1.95 - 3.89: 871 3.89 - 5.84: 154 5.84 - 7.79: 55 7.79 - 9.73: 46 Bond angle restraints: 33040 Sorted by residual: angle pdb=" N ASP A 274 " pdb=" CA ASP A 274 " pdb=" C ASP A 274 " ideal model delta sigma weight residual 108.23 116.70 -8.47 1.72e+00 3.38e-01 2.43e+01 angle pdb=" N ASP D 274 " pdb=" CA ASP D 274 " pdb=" C ASP D 274 " ideal model delta sigma weight residual 108.23 116.70 -8.47 1.72e+00 3.38e-01 2.43e+01 angle pdb=" N ASP F 274 " pdb=" CA ASP F 274 " pdb=" C ASP F 274 " ideal model delta sigma weight residual 107.99 116.65 -8.66 1.76e+00 3.23e-01 2.42e+01 angle pdb=" N ASP C 274 " pdb=" CA ASP C 274 " pdb=" C ASP C 274 " ideal model delta sigma weight residual 107.99 116.61 -8.62 1.76e+00 3.23e-01 2.40e+01 angle pdb=" N ASP E 274 " pdb=" CA ASP E 274 " pdb=" C ASP E 274 " ideal model delta sigma weight residual 107.99 116.59 -8.60 1.76e+00 3.23e-01 2.38e+01 ... (remaining 33035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.64: 13651 25.64 - 51.27: 985 51.27 - 76.91: 166 76.91 - 102.54: 46 102.54 - 128.18: 8 Dihedral angle restraints: 14856 sinusoidal: 6032 harmonic: 8824 Sorted by residual: dihedral pdb=" C5' IMP B 601 " pdb=" O5' IMP B 601 " pdb=" P IMP B 601 " pdb=" O2P IMP B 601 " ideal model delta sinusoidal sigma weight residual -168.07 -39.89 -128.18 1 2.00e+01 2.50e-03 3.88e+01 dihedral pdb=" C5' IMP E 601 " pdb=" O5' IMP E 601 " pdb=" P IMP E 601 " pdb=" O2P IMP E 601 " ideal model delta sinusoidal sigma weight residual 191.93 71.57 120.36 1 2.00e+01 2.50e-03 3.61e+01 dihedral pdb=" C5' IMP G 601 " pdb=" O5' IMP G 601 " pdb=" P IMP G 601 " pdb=" O2P IMP G 601 " ideal model delta sinusoidal sigma weight residual 191.93 73.06 118.87 1 2.00e+01 2.50e-03 3.56e+01 ... (remaining 14853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2801 0.057 - 0.114: 854 0.114 - 0.170: 93 0.170 - 0.227: 16 0.227 - 0.284: 4 Chirality restraints: 3768 Sorted by residual: chirality pdb=" C3D NAD B 602 " pdb=" C2D NAD B 602 " pdb=" C4D NAD B 602 " pdb=" O3D NAD B 602 " both_signs ideal model delta sigma weight residual False -2.73 -2.44 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA ASP G 28 " pdb=" N ASP G 28 " pdb=" C ASP G 28 " pdb=" CB ASP G 28 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA ASP D 28 " pdb=" N ASP D 28 " pdb=" C ASP D 28 " pdb=" CB ASP D 28 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 3765 not shown) Planarity restraints: 4176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 230 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.49e+00 pdb=" C ASN A 230 " 0.032 2.00e-02 2.50e+03 pdb=" O ASN A 230 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG A 231 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS F 26 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.44e+00 pdb=" C CYS F 26 " -0.032 2.00e-02 2.50e+03 pdb=" O CYS F 26 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY F 27 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 26 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.42e+00 pdb=" C CYS C 26 " 0.032 2.00e-02 2.50e+03 pdb=" O CYS C 26 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY C 27 " -0.011 2.00e-02 2.50e+03 ... (remaining 4173 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4142 2.77 - 3.30: 22715 3.30 - 3.83: 42281 3.83 - 4.37: 52059 4.37 - 4.90: 84515 Nonbonded interactions: 205712 Sorted by model distance: nonbonded pdb=" NH1 ARG B 512 " pdb=" OD1 ASP C 418 " model vdw 2.232 3.120 nonbonded pdb=" NH1 ARG F 512 " pdb=" OD1 ASP G 418 " model vdw 2.275 3.120 nonbonded pdb=" OD1 ASP E 418 " pdb=" NH1 ARG H 512 " model vdw 2.282 3.120 nonbonded pdb=" NH1 ARG E 512 " pdb=" OD1 ASP F 418 " model vdw 2.284 3.120 nonbonded pdb=" OG1 THR A 31 " pdb=" OE2 GLU D 500 " model vdw 2.319 3.040 ... (remaining 205707 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.950 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 53.490 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.130 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:14.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.139 24432 Z= 0.368 Angle : 0.858 9.734 33040 Z= 0.424 Chirality : 0.053 0.284 3768 Planarity : 0.005 0.054 4176 Dihedral : 18.075 128.180 9256 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.17 % Allowed : 19.57 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.16), residues: 3072 helix: 1.72 (0.15), residues: 1200 sheet: 0.03 (0.23), residues: 432 loop : -0.08 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 454 PHE 0.018 0.003 PHE E 401 TYR 0.016 0.002 TYR A 353 ARG 0.007 0.001 ARG A 105 Details of bonding type rmsd hydrogen bonds : bond 0.12972 ( 973) hydrogen bonds : angle 5.91576 ( 2727) covalent geometry : bond 0.00743 (24424) covalent geometry : angle 0.85753 (33040) Misc. bond : bond 0.00073 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 445 time to evaluate : 2.592 Fit side-chains REVERT: A 1 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.5982 (mpt) REVERT: C 78 MET cc_start: 0.9259 (tpp) cc_final: 0.8937 (tpp) REVERT: D 1 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6017 (mpt) REVERT: E 78 MET cc_start: 0.9266 (tpp) cc_final: 0.8962 (tpp) REVERT: E 230 ASN cc_start: 0.7574 (OUTLIER) cc_final: 0.7371 (p0) REVERT: F 1 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6180 (mpt) REVERT: G 1 MET cc_start: 0.7006 (OUTLIER) cc_final: 0.6066 (mpt) REVERT: G 78 MET cc_start: 0.9265 (tpp) cc_final: 0.8974 (tpp) REVERT: H 1 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6089 (mpt) REVERT: H 78 MET cc_start: 0.9259 (tpp) cc_final: 0.8946 (tpp) outliers start: 29 outliers final: 16 residues processed: 463 average time/residue: 1.6964 time to fit residues: 875.1593 Evaluate side-chains 414 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 392 time to evaluate : 2.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain E residue 230 ASN Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 291 LYS Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 230 ASN Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 291 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 0.6980 chunk 236 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 244 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 chunk 182 optimal weight: 3.9990 chunk 283 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 33 ASN A 48 GLN A 283 GLN A 368 GLN B 33 ASN B 48 GLN B 283 GLN C 21 GLN C 33 ASN C 48 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN D 33 ASN D 48 GLN D 283 GLN E 21 GLN E 33 ASN E 48 GLN E 283 GLN E 368 GLN F 33 ASN F 48 GLN F 283 GLN G 21 GLN G 33 ASN G 48 GLN G 283 GLN G 368 GLN H 21 GLN H 33 ASN H 48 GLN H 94 ASN H 283 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.102124 restraints weight = 22133.363| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.24 r_work: 0.3015 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 24432 Z= 0.119 Angle : 0.534 7.086 33040 Z= 0.286 Chirality : 0.043 0.153 3768 Planarity : 0.004 0.036 4176 Dihedral : 10.837 98.877 3888 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.85 % Allowed : 17.81 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.16), residues: 3072 helix: 2.01 (0.16), residues: 1200 sheet: 0.10 (0.23), residues: 432 loop : -0.05 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 93 PHE 0.011 0.001 PHE A 24 TYR 0.013 0.001 TYR F 353 ARG 0.003 0.000 ARG G 105 Details of bonding type rmsd hydrogen bonds : bond 0.04697 ( 973) hydrogen bonds : angle 5.16004 ( 2727) covalent geometry : bond 0.00255 (24424) covalent geometry : angle 0.53429 (33040) Misc. bond : bond 0.00028 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 418 time to evaluate : 2.622 Fit side-chains REVERT: A 1 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6928 (mmt) REVERT: A 450 LYS cc_start: 0.8542 (mttp) cc_final: 0.8311 (mttm) REVERT: C 78 MET cc_start: 0.9294 (tpp) cc_final: 0.8964 (tpp) REVERT: C 450 LYS cc_start: 0.8555 (mttp) cc_final: 0.8328 (mttm) REVERT: E 78 MET cc_start: 0.9283 (tpp) cc_final: 0.8961 (tpp) REVERT: G 78 MET cc_start: 0.9290 (tpp) cc_final: 0.8966 (tpp) REVERT: G 112 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7102 (mm-40) REVERT: H 1 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.6886 (mmt) REVERT: H 78 MET cc_start: 0.9296 (tpp) cc_final: 0.8964 (tpp) outliers start: 71 outliers final: 21 residues processed: 468 average time/residue: 1.7121 time to fit residues: 894.2950 Evaluate side-chains 405 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 381 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 230 ASN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 474 LYS Chi-restraints excluded: chain H residue 510 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 293 optimal weight: 0.2980 chunk 223 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 299 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 282 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 291 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 283 GLN A 368 GLN B 48 GLN B 283 GLN 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 D 368 GLN E 48 GLN E 283 GLN E 368 GLN F 48 GLN F 283 GLN F 368 GLN G 48 GLN G 283 GLN G 368 GLN H 21 GLN H 48 GLN H 283 GLN H 368 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.124603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.101137 restraints weight = 22033.740| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.24 r_work: 0.2998 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.0910 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= 0.137 Angle : 0.551 7.561 33040 Z= 0.295 Chirality : 0.043 0.146 3768 Planarity : 0.004 0.036 4176 Dihedral : 10.455 99.920 3857 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.34 % Allowed : 17.00 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.16), residues: 3072 helix: 2.03 (0.15), residues: 1200 sheet: -0.05 (0.23), residues: 424 loop : 0.03 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 93 PHE 0.012 0.002 PHE E 24 TYR 0.014 0.002 TYR A 353 ARG 0.004 0.000 ARG G 105 Details of bonding type rmsd hydrogen bonds : bond 0.05070 ( 973) hydrogen bonds : angle 5.12147 ( 2727) covalent geometry : bond 0.00298 (24424) covalent geometry : angle 0.55055 (33040) Misc. bond : bond 0.00033 ( 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 484 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 401 time to evaluate : 2.637 Fit side-chains REVERT: A 1 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6934 (mmt) REVERT: A 291 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8353 (mptt) REVERT: A 450 LYS cc_start: 0.8547 (mttp) cc_final: 0.8311 (mttm) REVERT: C 78 MET cc_start: 0.9325 (tpp) cc_final: 0.8996 (tpp) REVERT: C 291 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8336 (mptt) REVERT: C 450 LYS cc_start: 0.8554 (mttp) cc_final: 0.8289 (mttm) REVERT: D 112 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7153 (mm-40) REVERT: E 78 MET cc_start: 0.9319 (tpp) cc_final: 0.8997 (tpp) REVERT: F 291 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8349 (mptt) REVERT: G 78 MET cc_start: 0.9326 (tpp) cc_final: 0.9000 (tpp) REVERT: H 1 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6884 (mmt) REVERT: H 78 MET cc_start: 0.9325 (tpp) cc_final: 0.8991 (tpp) outliers start: 83 outliers final: 22 residues processed: 468 average time/residue: 1.6460 time to fit residues: 864.2997 Evaluate side-chains 440 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 412 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 474 LYS 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 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 61 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 289 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 194 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 260 optimal weight: 4.9990 chunk 150 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN B 48 GLN B 243 GLN B 283 GLN B 368 GLN C 48 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 48 GLN ** D 283 GLN ** 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.123078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.099410 restraints weight = 22179.240| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.25 r_work: 0.2974 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 24432 Z= 0.173 Angle : 0.597 8.235 33040 Z= 0.319 Chirality : 0.045 0.149 3768 Planarity : 0.004 0.038 4176 Dihedral : 10.597 102.857 3857 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.85 % Allowed : 17.24 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.16), residues: 3072 helix: 1.93 (0.15), residues: 1200 sheet: -0.11 (0.23), residues: 424 loop : 0.01 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 93 PHE 0.015 0.002 PHE A 24 TYR 0.015 0.002 TYR F 353 ARG 0.004 0.000 ARG H 407 Details of bonding type rmsd hydrogen bonds : bond 0.05709 ( 973) hydrogen bonds : angle 5.26339 ( 2727) covalent geometry : bond 0.00386 (24424) covalent geometry : angle 0.59682 (33040) Misc. bond : bond 0.00044 ( 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 493 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 422 time to evaluate : 2.762 Fit side-chains REVERT: A 1 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.6929 (mmt) REVERT: A 291 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8332 (mptt) REVERT: A 450 LYS cc_start: 0.8549 (mttp) cc_final: 0.8296 (mttm) REVERT: B 241 LYS cc_start: 0.7833 (mtpt) cc_final: 0.7609 (mtpt) REVERT: B 335 GLU cc_start: 0.8161 (pt0) cc_final: 0.7746 (mp0) REVERT: C 291 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8307 (mptt) REVERT: C 450 LYS cc_start: 0.8542 (mttp) cc_final: 0.8280 (mttm) REVERT: D 112 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7120 (mm-40) REVERT: D 447 VAL cc_start: 0.8953 (m) cc_final: 0.8742 (t) REVERT: E 335 GLU cc_start: 0.8166 (pt0) cc_final: 0.7754 (mp0) REVERT: E 438 LYS cc_start: 0.8601 (mttm) cc_final: 0.8376 (mmtm) REVERT: F 291 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8347 (mptt) REVERT: F 335 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: F 447 VAL cc_start: 0.8956 (m) cc_final: 0.8720 (t) REVERT: G 112 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7137 (mm-40) REVERT: H 1 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6857 (mmt) REVERT: H 291 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8371 (mptt) REVERT: H 447 VAL cc_start: 0.8954 (m) cc_final: 0.8708 (t) outliers start: 71 outliers final: 32 residues processed: 478 average time/residue: 1.6208 time to fit residues: 868.4386 Evaluate side-chains 437 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 396 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain D residue 112 GLN 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 F residue 237 SER Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 474 LYS Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 230 ASN Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain H residue 444 SER 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 163 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 283 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 213 optimal weight: 0.0570 chunk 266 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 230 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN B 48 GLN B 283 GLN B 368 GLN C 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.126101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.102586 restraints weight = 22233.754| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.25 r_work: 0.3021 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 24432 Z= 0.105 Angle : 0.499 7.684 33040 Z= 0.267 Chirality : 0.041 0.140 3768 Planarity : 0.004 0.037 4176 Dihedral : 10.043 93.578 3857 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.26 % Allowed : 17.36 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.16), residues: 3072 helix: 2.06 (0.16), residues: 1232 sheet: -0.04 (0.23), residues: 424 loop : -0.02 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 92 PHE 0.009 0.001 PHE E 24 TYR 0.012 0.001 TYR G 353 ARG 0.002 0.000 ARG B 407 Details of bonding type rmsd hydrogen bonds : bond 0.04223 ( 973) hydrogen bonds : angle 4.92196 ( 2727) covalent geometry : bond 0.00221 (24424) covalent geometry : angle 0.49909 (33040) Misc. bond : bond 0.00016 ( 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 491 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 410 time to evaluate : 2.684 Fit side-chains REVERT: A 1 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6865 (mmt) REVERT: A 291 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8344 (mptt) REVERT: B 241 LYS cc_start: 0.7805 (mtpt) cc_final: 0.7569 (mtpt) REVERT: D 335 GLU cc_start: 0.8128 (pt0) cc_final: 0.7697 (mp0) REVERT: E 438 LYS cc_start: 0.8561 (mttm) cc_final: 0.8333 (mmtm) REVERT: F 291 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8324 (mptt) REVERT: F 335 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: H 1 MET cc_start: 0.7038 (OUTLIER) cc_final: 0.6825 (mmt) REVERT: H 291 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8391 (mptt) outliers start: 81 outliers final: 29 residues processed: 466 average time/residue: 1.5778 time to fit residues: 827.2983 Evaluate side-chains 425 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 390 time to evaluate : 2.807 ------------------------------------------------------------------------------- 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 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 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 F residue 237 SER Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 116 optimal weight: 6.9990 chunk 157 optimal weight: 0.3980 chunk 215 optimal weight: 4.9990 chunk 277 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 169 optimal weight: 0.7980 chunk 105 optimal weight: 7.9990 chunk 263 optimal weight: 0.9980 chunk 280 optimal weight: 0.3980 chunk 117 optimal weight: 6.9990 chunk 240 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN C 48 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 48 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN E 48 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.125754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.102224 restraints weight = 22072.992| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.24 r_work: 0.3013 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 24432 Z= 0.112 Angle : 0.509 7.672 33040 Z= 0.272 Chirality : 0.042 0.134 3768 Planarity : 0.004 0.036 4176 Dihedral : 9.912 92.880 3853 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.69 % Allowed : 18.21 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.15), residues: 3072 helix: 2.08 (0.15), residues: 1232 sheet: -0.01 (0.22), residues: 424 loop : -0.02 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 93 PHE 0.019 0.001 PHE G 401 TYR 0.013 0.001 TYR B 353 ARG 0.002 0.000 ARG E 407 Details of bonding type rmsd hydrogen bonds : bond 0.04409 ( 973) hydrogen bonds : angle 4.90189 ( 2727) covalent geometry : bond 0.00239 (24424) covalent geometry : angle 0.50862 (33040) Misc. bond : bond 0.00015 ( 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 466 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 399 time to evaluate : 2.683 Fit side-chains REVERT: A 1 MET cc_start: 0.7059 (OUTLIER) cc_final: 0.6858 (mmt) REVERT: A 291 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8349 (mptt) REVERT: A 450 LYS cc_start: 0.8501 (mttp) cc_final: 0.8172 (mttm) REVERT: B 241 LYS cc_start: 0.7812 (mtpt) cc_final: 0.7574 (mtpt) REVERT: B 335 GLU cc_start: 0.8084 (pt0) cc_final: 0.7686 (mp0) REVERT: E 335 GLU cc_start: 0.8085 (pt0) cc_final: 0.7683 (mp0) REVERT: E 438 LYS cc_start: 0.8569 (mttm) cc_final: 0.8352 (mmtm) REVERT: F 291 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8330 (mptt) REVERT: F 335 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: G 112 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7127 (mm-40) REVERT: H 1 MET cc_start: 0.7009 (OUTLIER) cc_final: 0.6803 (mmt) REVERT: H 291 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8372 (mptt) outliers start: 67 outliers final: 31 residues processed: 445 average time/residue: 1.6604 time to fit residues: 826.3080 Evaluate side-chains 411 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 373 time to evaluate : 2.803 ------------------------------------------------------------------------------- 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 237 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 474 LYS Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain H residue 444 SER Chi-restraints excluded: chain H residue 474 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 240 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 250 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 278 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN C 48 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 48 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN ** E 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.122246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.098598 restraints weight = 22165.305| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.24 r_work: 0.2962 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 24432 Z= 0.212 Angle : 0.644 8.555 33040 Z= 0.344 Chirality : 0.048 0.151 3768 Planarity : 0.005 0.044 4176 Dihedral : 10.601 106.885 3853 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.69 % Allowed : 18.21 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.15), residues: 3072 helix: 1.89 (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 HIS 0.005 0.001 HIS A 93 PHE 0.017 0.002 PHE F 401 TYR 0.016 0.002 TYR A 353 ARG 0.004 0.001 ARG G 407 Details of bonding type rmsd hydrogen bonds : bond 0.06286 ( 973) hydrogen bonds : angle 5.32067 ( 2727) covalent geometry : bond 0.00479 (24424) covalent geometry : angle 0.64374 (33040) Misc. bond : bond 0.00038 ( 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 458 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 391 time to evaluate : 2.505 Fit side-chains REVERT: A 1 MET cc_start: 0.7042 (OUTLIER) cc_final: 0.6823 (mmt) REVERT: A 330 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.8981 (pp) REVERT: B 241 LYS cc_start: 0.7847 (mtpt) cc_final: 0.7624 (mtpt) REVERT: E 438 LYS cc_start: 0.8618 (mttm) cc_final: 0.8413 (mmtm) REVERT: F 335 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: G 112 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7130 (mm-40) REVERT: H 291 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8356 (mptt) REVERT: H 330 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.8905 (pp) outliers start: 67 outliers final: 33 residues processed: 447 average time/residue: 1.5804 time to fit residues: 793.2478 Evaluate side-chains 423 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 384 time to evaluate : 2.774 ------------------------------------------------------------------------------- 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 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 237 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 277 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 277 GLN Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 277 GLN 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 230 ASN Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 444 SER Chi-restraints excluded: chain H residue 474 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 190 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 300 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 236 optimal weight: 0.0870 chunk 48 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** C 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 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.124265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.100782 restraints weight = 22056.055| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.24 r_work: 0.2994 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24432 Z= 0.135 Angle : 0.553 8.155 33040 Z= 0.296 Chirality : 0.043 0.144 3768 Planarity : 0.004 0.037 4176 Dihedral : 10.153 98.773 3850 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.25 % Allowed : 18.65 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.16), residues: 3072 helix: 2.09 (0.16), residues: 1200 sheet: -0.08 (0.23), residues: 424 loop : 0.02 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 93 PHE 0.016 0.002 PHE F 401 TYR 0.013 0.002 TYR E 353 ARG 0.002 0.000 ARG F 407 Details of bonding type rmsd hydrogen bonds : bond 0.04969 ( 973) hydrogen bonds : angle 5.08370 ( 2727) covalent geometry : bond 0.00294 (24424) covalent geometry : angle 0.55320 (33040) Misc. bond : bond 0.00020 ( 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 445 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 389 time to evaluate : 2.618 Fit side-chains REVERT: B 241 LYS cc_start: 0.7824 (mtpt) cc_final: 0.7610 (mtpt) REVERT: B 330 ILE cc_start: 0.9364 (OUTLIER) cc_final: 0.8968 (pp) REVERT: D 330 ILE cc_start: 0.9365 (OUTLIER) cc_final: 0.8966 (pp) REVERT: E 330 ILE cc_start: 0.9351 (OUTLIER) cc_final: 0.8957 (pp) REVERT: E 438 LYS cc_start: 0.8581 (mttm) cc_final: 0.8365 (mmtm) REVERT: F 330 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.8959 (pp) REVERT: F 335 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: G 112 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7140 (mm-40) REVERT: G 330 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.8961 (pp) REVERT: H 291 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8358 (mptt) REVERT: H 330 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.8908 (pp) outliers start: 56 outliers final: 31 residues processed: 436 average time/residue: 1.6167 time to fit residues: 792.5240 Evaluate side-chains 436 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 396 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 474 LYS Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain H residue 230 ASN Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 444 SER Chi-restraints excluded: chain H residue 474 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 190 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 288 optimal weight: 5.9990 chunk 259 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 chunk 268 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** C 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 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 = 0.3400 r_free = 0.3400 target = 0.122545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.098961 restraints weight = 22094.414| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.24 r_work: 0.2967 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.1081 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= 0.191 Angle : 0.628 8.511 33040 Z= 0.336 Chirality : 0.046 0.154 3768 Planarity : 0.005 0.042 4176 Dihedral : 10.424 104.567 3847 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.21 % Allowed : 18.81 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.15), residues: 3072 helix: 1.89 (0.15), residues: 1200 sheet: -0.13 (0.23), residues: 424 loop : -0.04 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 93 PHE 0.015 0.002 PHE H 24 TYR 0.015 0.002 TYR G 353 ARG 0.003 0.000 ARG D 407 Details of bonding type rmsd hydrogen bonds : bond 0.06010 ( 973) hydrogen bonds : angle 5.27221 ( 2727) covalent geometry : bond 0.00429 (24424) covalent geometry : angle 0.62838 (33040) Misc. bond : bond 0.00033 ( 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 452 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 397 time to evaluate : 2.751 Fit side-chains REVERT: A 330 ILE cc_start: 0.9370 (OUTLIER) cc_final: 0.8993 (pp) REVERT: B 241 LYS cc_start: 0.7841 (mtpt) cc_final: 0.7627 (mtpt) REVERT: C 330 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.8993 (pp) REVERT: F 335 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: G 112 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7155 (mm-40) REVERT: G 330 ILE cc_start: 0.9363 (OUTLIER) cc_final: 0.8962 (pp) REVERT: H 291 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8358 (mptt) REVERT: H 330 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.8912 (pp) outliers start: 55 outliers final: 30 residues processed: 447 average time/residue: 1.6338 time to fit residues: 818.3817 Evaluate side-chains 415 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 378 time to evaluate : 2.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 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 237 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 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 E residue 237 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 474 LYS Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain H residue 230 ASN Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 444 SER Chi-restraints excluded: chain H residue 474 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 61 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 176 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 224 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** C 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.122262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.098658 restraints weight = 22146.141| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.24 r_work: 0.2959 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 24432 Z= 0.205 Angle : 0.650 8.838 33040 Z= 0.347 Chirality : 0.047 0.159 3768 Planarity : 0.005 0.047 4176 Dihedral : 10.481 104.960 3847 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.97 % Allowed : 19.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.15), residues: 3072 helix: 1.80 (0.15), residues: 1200 sheet: -0.22 (0.23), residues: 424 loop : -0.07 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 93 PHE 0.016 0.002 PHE H 24 TYR 0.015 0.002 TYR D 353 ARG 0.004 0.001 ARG B 407 Details of bonding type rmsd hydrogen bonds : bond 0.06167 ( 973) hydrogen bonds : angle 5.32320 ( 2727) covalent geometry : bond 0.00462 (24424) covalent geometry : angle 0.64988 (33040) Misc. bond : bond 0.00039 ( 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 431 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 382 time to evaluate : 2.589 Fit side-chains REVERT: A 330 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.9007 (pp) REVERT: B 241 LYS cc_start: 0.7846 (mtpt) cc_final: 0.7630 (mtpt) REVERT: B 330 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.9033 (pp) REVERT: C 330 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.9007 (pp) REVERT: D 330 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.9033 (pp) REVERT: E 330 ILE cc_start: 0.9361 (OUTLIER) cc_final: 0.9021 (pp) REVERT: F 330 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.9025 (pp) REVERT: F 335 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: G 112 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7161 (mm-40) REVERT: G 330 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.8964 (pp) REVERT: H 330 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.8921 (pp) outliers start: 49 outliers final: 32 residues processed: 424 average time/residue: 1.6033 time to fit residues: 763.9567 Evaluate side-chains 429 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 387 time to evaluate : 2.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 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 237 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 330 ILE 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 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 330 ILE Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 474 LYS Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain G residue 512 ARG Chi-restraints excluded: chain H residue 230 ASN Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 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 195 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 265 optimal weight: 0.9990 chunk 231 optimal weight: 0.0970 chunk 117 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 272 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN B 94 ASN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.126025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.102656 restraints weight = 22068.261| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.24 r_work: 0.3023 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24432 Z= 0.107 Angle : 0.517 7.814 33040 Z= 0.277 Chirality : 0.042 0.145 3768 Planarity : 0.004 0.038 4176 Dihedral : 9.748 92.623 3847 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.89 % Allowed : 19.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.15), residues: 3072 helix: 2.05 (0.16), residues: 1232 sheet: -0.08 (0.22), residues: 424 loop : -0.04 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 93 PHE 0.016 0.001 PHE F 401 TYR 0.013 0.001 TYR G 353 ARG 0.002 0.000 ARG H 407 Details of bonding type rmsd hydrogen bonds : bond 0.04158 ( 973) hydrogen bonds : angle 4.89911 ( 2727) covalent geometry : bond 0.00226 (24424) covalent geometry : angle 0.51650 (33040) Misc. bond : bond 0.00015 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23161.84 seconds wall clock time: 401 minutes 14.24 seconds (24074.24 seconds total)