Starting phenix.real_space_refine on Mon Aug 25 00:51:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fuz_29482/08_2025/8fuz_29482.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fuz_29482/08_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_29482/08_2025/8fuz_29482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fuz_29482/08_2025/8fuz_29482.map" model { file = "/net/cci-nas-00/data/ceres_data/8fuz_29482/08_2025/8fuz_29482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fuz_29482/08_2025/8fuz_29482.cif" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.237 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 144 5.16 5 C 15072 2.51 5 N 4096 2.21 5 O 4672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.72, per 1000 atoms: 0.20 Number of scatterers: 24008 At special positions: 0 Unit cell: (134.88, 135.723, 120.549, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 144 16.00 P 24 15.00 O 4672 8.00 N 4096 7.00 C 15072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5600 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 32 sheets defined 43.8% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 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: 3.95 Time building geometry restraints manager: 2.46 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.470 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: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.860 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.250 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.16), residues: 3072 helix: 1.72 (0.15), residues: 1200 sheet: 0.03 (0.23), residues: 432 loop : -0.08 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 105 TYR 0.016 0.002 TYR A 353 PHE 0.018 0.003 PHE E 401 HIS 0.004 0.001 HIS F 454 Details of bonding type rmsd covalent geometry : bond 0.00743 (24424) covalent geometry : angle 0.85753 (33040) hydrogen bonds : bond 0.12972 ( 973) hydrogen bonds : angle 5.91576 ( 2727) 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 : 0.580 Fit side-chains REVERT: A 1 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.5982 (mpt) REVERT: C 78 MET cc_start: 0.9259 (tpp) cc_final: 0.8937 (tpp) REVERT: D 1 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6017 (mpt) REVERT: E 78 MET cc_start: 0.9266 (tpp) cc_final: 0.8962 (tpp) REVERT: E 230 ASN cc_start: 0.7574 (OUTLIER) cc_final: 0.7371 (p0) REVERT: F 1 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6180 (mpt) REVERT: G 1 MET cc_start: 0.7006 (OUTLIER) cc_final: 0.6066 (mpt) REVERT: G 78 MET cc_start: 0.9265 (tpp) cc_final: 0.8974 (tpp) REVERT: H 1 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6089 (mpt) REVERT: H 78 MET cc_start: 0.9259 (tpp) cc_final: 0.8946 (tpp) outliers start: 29 outliers final: 16 residues processed: 463 average time/residue: 0.7631 time to fit residues: 393.3868 Evaluate side-chains 414 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 392 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain E residue 230 ASN Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 291 LYS Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 230 ASN Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 291 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 B 368 GLN C 21 GLN C 33 ASN C 48 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 21 GLN D 33 ASN D 48 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN E 21 GLN E 33 ASN E 48 GLN E 283 GLN E 368 GLN F 33 ASN F 283 GLN F 368 GLN G 21 GLN G 33 ASN G 48 GLN G 283 GLN G 368 GLN H 21 GLN H 33 ASN H 48 GLN H 94 ASN H 283 GLN H 368 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.099081 restraints weight = 22135.171| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.24 r_work: 0.2964 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.0727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24432 Z= 0.195 Angle : 0.641 7.983 33040 Z= 0.343 Chirality : 0.048 0.168 3768 Planarity : 0.005 0.046 4176 Dihedral : 11.288 106.198 3888 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.62 % Allowed : 16.16 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.15), residues: 3072 helix: 1.73 (0.15), residues: 1200 sheet: -0.13 (0.24), residues: 424 loop : -0.06 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 407 TYR 0.015 0.002 TYR B 353 PHE 0.016 0.002 PHE E 24 HIS 0.004 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00439 (24424) covalent geometry : angle 0.64055 (33040) hydrogen bonds : bond 0.06179 ( 973) hydrogen bonds : angle 5.43818 ( 2727) Misc. bond : bond 0.00069 ( 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 505 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 415 time to evaluate : 0.679 Fit side-chains REVERT: A 1 MET cc_start: 0.7133 (OUTLIER) cc_final: 0.6845 (mmt) REVERT: A 291 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8369 (mptt) REVERT: A 450 LYS cc_start: 0.8579 (mttp) cc_final: 0.8356 (mttm) REVERT: B 241 LYS cc_start: 0.7851 (mtpt) cc_final: 0.7640 (mtpt) REVERT: B 335 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: C 78 MET cc_start: 0.9333 (tpp) cc_final: 0.9008 (tpp) REVERT: C 450 LYS cc_start: 0.8587 (mttp) cc_final: 0.8368 (mttm) REVERT: D 1 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6941 (mmt) REVERT: E 78 MET cc_start: 0.9328 (tpp) cc_final: 0.9006 (tpp) REVERT: E 335 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: F 1 MET cc_start: 0.7089 (OUTLIER) cc_final: 0.6882 (mmt) REVERT: G 1 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.6864 (mmt) REVERT: G 78 MET cc_start: 0.9337 (tpp) cc_final: 0.9014 (tpp) REVERT: G 112 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7142 (mm-40) REVERT: H 1 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6900 (mmt) REVERT: H 78 MET cc_start: 0.9335 (tpp) cc_final: 0.9012 (tpp) outliers start: 90 outliers final: 35 residues processed: 484 average time/residue: 0.7060 time to fit residues: 382.4062 Evaluate side-chains 416 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 372 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 474 LYS Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 444 SER Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 230 ASN Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 444 SER Chi-restraints excluded: chain H residue 474 LYS Chi-restraints excluded: chain H residue 510 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 126 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 0.0870 chunk 177 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 167 optimal weight: 0.0870 chunk 66 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- 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 243 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN C 48 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 48 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN E 48 GLN E 283 GLN E 368 GLN F 48 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN G 48 GLN G 283 GLN G 368 GLN H 48 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.124898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.101444 restraints weight = 22276.527| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.24 r_work: 0.3003 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 24432 Z= 0.120 Angle : 0.531 7.796 33040 Z= 0.284 Chirality : 0.042 0.145 3768 Planarity : 0.004 0.037 4176 Dihedral : 10.556 98.187 3874 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.97 % Allowed : 17.48 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.16), residues: 3072 helix: 2.04 (0.15), residues: 1200 sheet: -0.09 (0.23), residues: 424 loop : 0.01 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 407 TYR 0.013 0.001 TYR B 353 PHE 0.011 0.001 PHE E 24 HIS 0.002 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00258 (24424) covalent geometry : angle 0.53130 (33040) hydrogen bonds : bond 0.04727 ( 973) hydrogen bonds : angle 5.10769 ( 2727) Misc. bond : bond 0.00026 ( 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 463 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 389 time to evaluate : 0.826 Fit side-chains REVERT: A 1 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6932 (mmt) REVERT: A 450 LYS cc_start: 0.8538 (mttp) cc_final: 0.8307 (mttm) REVERT: C 78 MET cc_start: 0.9326 (tpp) cc_final: 0.9010 (tpp) REVERT: C 450 LYS cc_start: 0.8551 (mttp) cc_final: 0.8323 (mttm) REVERT: D 1 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6889 (mmt) REVERT: E 78 MET cc_start: 0.9319 (tpp) cc_final: 0.9012 (tpp) REVERT: E 438 LYS cc_start: 0.8594 (mttm) cc_final: 0.8374 (mmtm) REVERT: F 1 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.6833 (mmt) REVERT: G 1 MET cc_start: 0.7120 (OUTLIER) cc_final: 0.6912 (mmt) REVERT: G 78 MET cc_start: 0.9324 (tpp) cc_final: 0.9011 (tpp) REVERT: H 1 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.6857 (mmt) REVERT: H 78 MET cc_start: 0.9325 (tpp) cc_final: 0.9007 (tpp) outliers start: 74 outliers final: 18 residues processed: 446 average time/residue: 0.7661 time to fit residues: 381.5241 Evaluate side-chains 430 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 407 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 474 LYS Chi-restraints excluded: chain G residue 1 MET 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 474 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 265 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 214 optimal weight: 0.5980 chunk 161 optimal weight: 2.9990 chunk 293 optimal weight: 3.9990 chunk 267 optimal weight: 2.9990 chunk 191 optimal weight: 0.2980 chunk 122 optimal weight: 1.9990 chunk 230 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 368 GLN B 48 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN C 48 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 48 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN E 48 GLN E 368 GLN F 48 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN G 48 GLN G 368 GLN H 48 GLN H 283 GLN H 368 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.123798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.100238 restraints weight = 22032.976| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.24 r_work: 0.2982 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.0970 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= 0.146 Angle : 0.563 8.146 33040 Z= 0.300 Chirality : 0.044 0.144 3768 Planarity : 0.004 0.037 4176 Dihedral : 10.547 100.570 3866 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.14 % Allowed : 17.08 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.15), residues: 3072 helix: 2.01 (0.15), residues: 1200 sheet: -0.11 (0.23), residues: 424 loop : -0.00 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 105 TYR 0.014 0.002 TYR G 353 PHE 0.013 0.002 PHE E 24 HIS 0.003 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00321 (24424) covalent geometry : angle 0.56263 (33040) hydrogen bonds : bond 0.05278 ( 973) hydrogen bonds : angle 5.17138 ( 2727) Misc. bond : bond 0.00030 ( 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 503 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 425 time to evaluate : 0.768 Fit side-chains REVERT: A 1 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6850 (mmt) REVERT: A 291 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8343 (mptt) REVERT: A 450 LYS cc_start: 0.8539 (mttp) cc_final: 0.8289 (mttm) REVERT: B 241 LYS cc_start: 0.7827 (mtpt) cc_final: 0.7602 (mtpt) REVERT: B 447 VAL cc_start: 0.8921 (m) cc_final: 0.8708 (t) REVERT: C 447 VAL cc_start: 0.8924 (m) cc_final: 0.8685 (t) REVERT: C 450 LYS cc_start: 0.8551 (mttp) cc_final: 0.8301 (mttm) REVERT: E 438 LYS cc_start: 0.8596 (mttm) cc_final: 0.8374 (mmtm) REVERT: F 447 VAL cc_start: 0.8915 (m) cc_final: 0.8703 (t) REVERT: G 112 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7130 (mm-40) REVERT: H 291 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8326 (mptt) REVERT: H 447 VAL cc_start: 0.8915 (m) cc_final: 0.8692 (t) outliers start: 78 outliers final: 34 residues processed: 480 average time/residue: 0.7267 time to fit residues: 390.0483 Evaluate side-chains 423 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 385 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 D residue 237 SER Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 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 255 ASP Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 283 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 141 optimal weight: 1.9990 chunk 276 optimal weight: 4.9990 chunk 256 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 287 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 289 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN B 48 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN C 48 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 48 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN E 48 GLN E 368 GLN F 48 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN G 48 GLN G 368 GLN H 48 GLN H 283 GLN H 368 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.123543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.099898 restraints weight = 22067.057| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.24 r_work: 0.2977 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24432 Z= 0.156 Angle : 0.576 8.269 33040 Z= 0.307 Chirality : 0.044 0.145 3768 Planarity : 0.004 0.038 4176 Dihedral : 10.412 101.140 3852 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.93 % Allowed : 17.32 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.15), residues: 3072 helix: 1.83 (0.15), residues: 1232 sheet: -0.10 (0.23), residues: 424 loop : -0.10 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 407 TYR 0.014 0.002 TYR G 353 PHE 0.013 0.002 PHE E 24 HIS 0.003 0.001 HIS D 93 Details of bonding type rmsd covalent geometry : bond 0.00346 (24424) covalent geometry : angle 0.57575 (33040) hydrogen bonds : bond 0.05430 ( 973) hydrogen bonds : angle 5.18499 ( 2727) Misc. bond : bond 0.00031 ( 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 463 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 390 time to evaluate : 0.951 Fit side-chains REVERT: A 1 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6880 (mmt) REVERT: A 291 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8375 (mptt) REVERT: A 447 VAL cc_start: 0.8918 (m) cc_final: 0.8705 (t) REVERT: A 450 LYS cc_start: 0.8547 (mttp) cc_final: 0.8246 (mttm) REVERT: B 241 LYS cc_start: 0.7832 (mtpt) cc_final: 0.7607 (mtpt) REVERT: C 450 LYS cc_start: 0.8552 (mttp) cc_final: 0.8287 (mttm) REVERT: E 438 LYS cc_start: 0.8597 (mttm) cc_final: 0.8380 (mmtm) REVERT: F 335 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: H 291 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8365 (mptt) REVERT: H 330 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.8899 (pp) outliers start: 73 outliers final: 35 residues processed: 446 average time/residue: 0.6997 time to fit residues: 350.2299 Evaluate side-chains 417 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 377 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 474 LYS Chi-restraints excluded: chain G residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 149 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 168 optimal weight: 0.0470 chunk 135 optimal weight: 1.9990 chunk 238 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 255 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 172 optimal weight: 6.9990 chunk 280 optimal weight: 2.9990 overall best weight: 1.7284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN B 48 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** C 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 48 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN H 48 GLN H 283 GLN H 368 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.122460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.098863 restraints weight = 22033.267| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.24 r_work: 0.2961 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1017 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= 0.189 Angle : 0.622 8.608 33040 Z= 0.332 Chirality : 0.047 0.153 3768 Planarity : 0.005 0.040 4176 Dihedral : 10.567 104.368 3852 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.93 % Allowed : 16.96 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.15), residues: 3072 helix: 1.88 (0.15), residues: 1200 sheet: -0.13 (0.23), residues: 424 loop : -0.05 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 407 TYR 0.015 0.002 TYR F 353 PHE 0.015 0.002 PHE H 24 HIS 0.004 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00425 (24424) covalent geometry : angle 0.62163 (33040) hydrogen bonds : bond 0.06013 ( 973) hydrogen bonds : angle 5.28563 ( 2727) Misc. bond : bond 0.00039 ( 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 452 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 379 time to evaluate : 0.903 Fit side-chains REVERT: A 1 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6770 (mmt) REVERT: A 450 LYS cc_start: 0.8543 (mttp) cc_final: 0.8271 (mttm) REVERT: B 241 LYS cc_start: 0.7845 (mtpt) cc_final: 0.7626 (mtpt) REVERT: D 112 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7059 (mm-40) REVERT: F 335 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: G 112 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7135 (mm-40) REVERT: H 291 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8359 (mptt) REVERT: H 330 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.8950 (pp) outliers start: 73 outliers final: 35 residues processed: 440 average time/residue: 0.6972 time to fit residues: 344.5128 Evaluate side-chains 422 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 381 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 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 277 GLN 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 E residue 510 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 211 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 220 optimal weight: 4.9990 chunk 97 optimal weight: 0.0370 chunk 264 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 270 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.7864 ------------------------------------------------------------------------------- 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 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN F 48 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN H 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 = 0.3397 r_free = 0.3397 target = 0.122314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.098760 restraints weight = 21978.269| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.24 r_work: 0.2963 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24432 Z= 0.193 Angle : 0.627 8.759 33040 Z= 0.335 Chirality : 0.047 0.158 3768 Planarity : 0.005 0.041 4176 Dihedral : 10.559 104.215 3852 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.93 % Allowed : 17.04 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.15), residues: 3072 helix: 1.81 (0.15), residues: 1200 sheet: -0.19 (0.23), residues: 424 loop : -0.07 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 407 TYR 0.015 0.002 TYR B 353 PHE 0.015 0.002 PHE A 24 HIS 0.004 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00434 (24424) covalent geometry : angle 0.62726 (33040) hydrogen bonds : bond 0.06032 ( 973) hydrogen bonds : angle 5.29644 ( 2727) Misc. bond : bond 0.00037 ( 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 461 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 388 time to evaluate : 0.940 Fit side-chains REVERT: A 1 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.6705 (mmt) REVERT: A 330 ILE cc_start: 0.9371 (OUTLIER) cc_final: 0.9004 (pp) REVERT: A 450 LYS cc_start: 0.8546 (mttp) cc_final: 0.8260 (mttm) REVERT: B 241 LYS cc_start: 0.7848 (mtpt) cc_final: 0.7629 (mtpt) REVERT: B 330 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.9005 (pp) REVERT: C 112 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7200 (mm-40) REVERT: C 291 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8331 (mptt) REVERT: C 450 LYS cc_start: 0.8538 (mttp) cc_final: 0.8291 (mttm) REVERT: D 330 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9001 (pp) REVERT: E 112 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7212 (mm-40) REVERT: E 330 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.8997 (pp) REVERT: F 330 ILE cc_start: 0.9365 (OUTLIER) cc_final: 0.8996 (pp) REVERT: F 335 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: G 112 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7127 (mm-40) REVERT: G 330 ILE cc_start: 0.9361 (OUTLIER) cc_final: 0.8996 (pp) REVERT: H 112 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7179 (mm-40) REVERT: H 330 ILE cc_start: 0.9358 (OUTLIER) cc_final: 0.8956 (pp) outliers start: 73 outliers final: 37 residues processed: 445 average time/residue: 0.6989 time to fit residues: 348.4034 Evaluate side-chains 425 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 374 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 230 ASN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 112 GLN 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 E residue 510 GLU Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 277 GLN 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 112 GLN Chi-restraints excluded: chain H residue 230 ASN Chi-restraints excluded: chain H residue 237 SER Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 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 231 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 170 optimal weight: 0.7980 chunk 203 optimal weight: 3.9990 chunk 253 optimal weight: 3.9990 chunk 214 optimal weight: 0.2980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 94 ASN ** 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 94 ASN ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.124674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.101253 restraints weight = 21963.510| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.23 r_work: 0.2997 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24432 Z= 0.118 Angle : 0.533 8.167 33040 Z= 0.285 Chirality : 0.042 0.143 3768 Planarity : 0.004 0.040 4176 Dihedral : 10.086 96.803 3852 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.01 % Allowed : 18.05 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.15), residues: 3072 helix: 1.95 (0.15), residues: 1232 sheet: -0.09 (0.23), residues: 424 loop : -0.09 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 105 TYR 0.012 0.001 TYR G 353 PHE 0.011 0.001 PHE E 24 HIS 0.002 0.001 HIS F 93 Details of bonding type rmsd covalent geometry : bond 0.00250 (24424) covalent geometry : angle 0.53331 (33040) hydrogen bonds : bond 0.04669 ( 973) hydrogen bonds : angle 5.01186 ( 2727) Misc. bond : bond 0.00016 ( 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 427 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 377 time to evaluate : 1.057 Fit side-chains REVERT: A 450 LYS cc_start: 0.8510 (mttp) cc_final: 0.8235 (mttm) REVERT: B 241 LYS cc_start: 0.7832 (mtpt) cc_final: 0.7617 (mtpt) REVERT: C 450 LYS cc_start: 0.8493 (mttp) cc_final: 0.8261 (mttm) REVERT: D 112 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7044 (mm-40) REVERT: F 335 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7351 (mp0) outliers start: 50 outliers final: 28 residues processed: 417 average time/residue: 0.7336 time to fit residues: 342.1228 Evaluate side-chains 435 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 405 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 277 GLN Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 474 LYS Chi-restraints excluded: chain G residue 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 277 GLN 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 270 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 278 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 266 optimal weight: 4.9990 chunk 279 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN F 48 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN H 48 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.122100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.098541 restraints weight = 22052.542| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.24 r_work: 0.2953 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 24432 Z= 0.206 Angle : 0.643 8.711 33040 Z= 0.344 Chirality : 0.047 0.156 3768 Planarity : 0.005 0.044 4176 Dihedral : 10.500 106.126 3847 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.41 % Allowed : 17.77 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.15), residues: 3072 helix: 1.86 (0.15), residues: 1200 sheet: -0.17 (0.23), residues: 424 loop : -0.08 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 105 TYR 0.016 0.002 TYR G 353 PHE 0.016 0.002 PHE H 24 HIS 0.005 0.001 HIS D 93 Details of bonding type rmsd covalent geometry : bond 0.00461 (24424) covalent geometry : angle 0.64307 (33040) hydrogen bonds : bond 0.06247 ( 973) hydrogen bonds : angle 5.31261 ( 2727) Misc. bond : bond 0.00035 ( 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 465 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 405 time to evaluate : 0.723 Fit side-chains REVERT: A 112 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7255 (mm-40) REVERT: A 330 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.8996 (pp) REVERT: A 450 LYS cc_start: 0.8533 (mttp) cc_final: 0.8287 (mttp) REVERT: B 241 LYS cc_start: 0.7864 (mtpt) cc_final: 0.7648 (mtpt) REVERT: B 330 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.8995 (pp) REVERT: C 112 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7184 (mm-40) REVERT: C 330 ILE cc_start: 0.9373 (OUTLIER) cc_final: 0.8999 (pp) REVERT: D 112 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7063 (mm-40) REVERT: D 330 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.8993 (pp) REVERT: E 112 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7218 (mm-40) REVERT: E 330 ILE cc_start: 0.9361 (OUTLIER) cc_final: 0.8987 (pp) REVERT: F 330 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.8987 (pp) REVERT: F 335 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: G 112 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7179 (mm-40) REVERT: G 330 ILE cc_start: 0.9363 (OUTLIER) cc_final: 0.8986 (pp) REVERT: H 330 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.8965 (pp) REVERT: H 335 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7394 (mp0) outliers start: 60 outliers final: 33 residues processed: 456 average time/residue: 0.7553 time to fit residues: 384.4063 Evaluate side-chains 421 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 373 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 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 444 SER Chi-restraints excluded: chain C residue 26 CYS Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain D residue 112 GLN Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 112 GLN 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 E residue 510 GLU Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 237 SER Chi-restraints excluded: chain F residue 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 237 SER Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain H residue 444 SER Chi-restraints excluded: chain H residue 474 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 239 optimal weight: 0.7980 chunk 217 optimal weight: 1.9990 chunk 276 optimal weight: 3.9990 chunk 309 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 228 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 57 optimal weight: 0.0980 chunk 234 optimal weight: 0.0570 chunk 127 optimal weight: 0.9980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN B 283 GLN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.126134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.102825 restraints weight = 22169.476| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.23 r_work: 0.3025 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24432 Z= 0.103 Angle : 0.514 8.016 33040 Z= 0.275 Chirality : 0.042 0.142 3768 Planarity : 0.004 0.041 4176 Dihedral : 9.714 91.974 3847 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.61 % Allowed : 18.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.16), residues: 3072 helix: 1.95 (0.15), residues: 1272 sheet: 0.01 (0.24), residues: 384 loop : 0.02 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 105 TYR 0.013 0.001 TYR G 353 PHE 0.008 0.001 PHE A 24 HIS 0.002 0.001 HIS H 92 Details of bonding type rmsd covalent geometry : bond 0.00213 (24424) covalent geometry : angle 0.51408 (33040) hydrogen bonds : bond 0.04075 ( 973) hydrogen bonds : angle 4.88444 ( 2727) Misc. bond : bond 0.00012 ( 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 417 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 377 time to evaluate : 1.037 Fit side-chains REVERT: A 450 LYS cc_start: 0.8413 (mttp) cc_final: 0.8165 (mttm) REVERT: B 241 LYS cc_start: 0.7812 (mtpt) cc_final: 0.7600 (mtpt) REVERT: C 450 LYS cc_start: 0.8393 (mttp) cc_final: 0.8173 (mttm) REVERT: F 335 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: H 330 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.8970 (pp) outliers start: 40 outliers final: 26 residues processed: 410 average time/residue: 0.8378 time to fit residues: 383.4072 Evaluate side-chains 420 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 392 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 283 GLN Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain F residue 474 LYS Chi-restraints excluded: chain G residue 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 277 GLN Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 474 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 6 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 211 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 297 optimal weight: 0.0670 chunk 127 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 212 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN B 48 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 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 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 = 0.3440 r_free = 0.3440 target = 0.125688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.102230 restraints weight = 22057.469| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.24 r_work: 0.3015 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24432 Z= 0.112 Angle : 0.522 7.940 33040 Z= 0.279 Chirality : 0.042 0.138 3768 Planarity : 0.004 0.039 4176 Dihedral : 9.649 91.840 3847 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.85 % Allowed : 18.41 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.15), residues: 3072 helix: 1.97 (0.15), residues: 1272 sheet: -0.06 (0.22), residues: 424 loop : -0.02 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 105 TYR 0.012 0.001 TYR A 353 PHE 0.010 0.001 PHE E 24 HIS 0.002 0.001 HIS G 454 Details of bonding type rmsd covalent geometry : bond 0.00237 (24424) covalent geometry : angle 0.52202 (33040) hydrogen bonds : bond 0.04369 ( 973) hydrogen bonds : angle 4.87259 ( 2727) Misc. bond : bond 0.00014 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10447.71 seconds wall clock time: 178 minutes 10.76 seconds (10690.76 seconds total)