Starting phenix.real_space_refine on Mon Jul 6 00:21:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g9b_29863/07_2026/8g9b_29863.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g9b_29863/07_2026/8g9b_29863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g9b_29863/07_2026/8g9b_29863.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g9b_29863/07_2026/8g9b_29863.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g9b_29863/07_2026/8g9b_29863.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g9b_29863/07_2026/8g9b_29863.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8g9b_29863/07_2026/8g9b_29863.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g9b_29863/07_2026/8g9b_29863.cif" } resolution = 3.0 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= 0.242 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 96 5.49 5 S 168 5.16 5 C 19248 2.51 5 N 5344 2.21 5 O 6184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 122 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31040 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3718 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 470} Chain breaks: 1 Chain: "B" Number of atoms: 3718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3718 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 470} Chain breaks: 1 Chain: "C" Number of atoms: 3718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3718 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 470} Chain breaks: 1 Chain: "D" Number of atoms: 3718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3718 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 470} Chain breaks: 1 Chain: "E" Number of atoms: 3718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3718 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 470} Chain breaks: 1 Chain: "F" Number of atoms: 3718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3718 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 470} Chain breaks: 1 Chain: "G" Number of atoms: 3718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3718 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 470} Chain breaks: 1 Chain: "H" Number of atoms: 3718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3718 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 470} Chain breaks: 1 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "F" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "H" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Time building chain proxies: 6.95, per 1000 atoms: 0.22 Number of scatterers: 31040 At special positions: 0 Unit cell: (151.74, 151.74, 110.433, 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 168 16.00 P 96 15.00 O 6184 8.00 N 5344 7.00 C 19248 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: 2.59 Conformation dependent library (CDL) restraints added in 1.3 seconds 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7104 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 48 sheets defined 39.7% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 19 through 25 Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.631A pdb=" N VAL A 49 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 85 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.749A pdb=" N VAL A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 254 through 267 removed outlier: 4.102A pdb=" N TYR A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 316 removed outlier: 3.540A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 356 removed outlier: 3.904A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 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 removed outlier: 3.578A pdb=" N ARG A 480 " --> pdb=" O LEU A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.547A pdb=" N GLN B 48 " --> pdb=" O THR B 45 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B 49 " --> pdb=" O ALA B 46 " (cutoff:3.500A) No H-bonds generated for '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 126 through 138 removed outlier: 3.721A pdb=" N VAL B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 224 through 233 Processing helix chain 'B' and resid 255 through 267 removed outlier: 4.082A pdb=" N ARG B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 306 through 316 Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 342 through 356 removed outlier: 3.957A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 Processing helix chain 'B' and resid 452 through 472 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 475 through 486 removed outlier: 3.552A pdb=" N ARG B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 502 Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 45 through 49 removed outlier: 3.560A pdb=" N GLN C 48 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL C 49 " --> pdb=" O ALA C 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 49' Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 127 through 138 removed outlier: 3.527A pdb=" N PHE C 131 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 163 Processing helix chain 'C' and resid 174 through 178 removed outlier: 4.432A pdb=" N GLU C 177 " --> pdb=" O PHE C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 224 through 233 Processing helix chain 'C' and resid 255 through 267 removed outlier: 4.256A pdb=" N ARG C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 306 through 316 removed outlier: 3.544A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 342 through 357 removed outlier: 3.938A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE C 357 " --> pdb=" O TYR C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 Processing helix chain 'C' and resid 416 through 420 removed outlier: 3.976A pdb=" N ALA C 419 " --> pdb=" O SER C 416 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET C 420 " --> pdb=" O LEU C 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 420' Processing helix chain 'C' and resid 452 through 472 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 475 through 486 removed outlier: 3.508A pdb=" N ARG C 480 " --> pdb=" O LEU C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 502 Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 45 through 49 removed outlier: 3.594A pdb=" N GLN D 48 " --> pdb=" O THR D 45 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL D 49 " --> pdb=" O ALA D 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 49' Processing helix chain 'D' and resid 76 through 85 Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 126 through 138 removed outlier: 4.054A pdb=" N VAL D 130 " --> pdb=" O ARG D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 224 through 233 Processing helix chain 'D' and resid 254 through 267 removed outlier: 4.096A pdb=" N TYR D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.590A pdb=" N MET D 286 " --> pdb=" O PHE D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 317 Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 342 through 356 removed outlier: 3.970A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 Processing helix chain 'D' and resid 452 through 472 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 475 through 486 removed outlier: 3.567A pdb=" N ARG D 480 " --> pdb=" O LEU D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 502 Processing helix chain 'E' and resid 19 through 25 Processing helix chain 'E' and resid 45 through 49 removed outlier: 3.778A pdb=" N VAL E 49 " --> pdb=" O ALA E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 85 Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 126 through 138 Processing helix chain 'E' and resid 159 through 164 removed outlier: 3.553A pdb=" N ILE E 163 " --> pdb=" O SER E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 203 Processing helix chain 'E' and resid 224 through 233 removed outlier: 3.521A pdb=" N ARG E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 267 removed outlier: 4.093A pdb=" N TYR E 258 " --> pdb=" O GLU E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 306 through 317 removed outlier: 3.815A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 342 through 357 removed outlier: 3.969A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE E 357 " --> pdb=" O TYR E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 379 Processing helix chain 'E' and resid 416 through 420 removed outlier: 4.207A pdb=" N MET E 420 " --> pdb=" O LEU E 417 " (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 486 Processing helix chain 'E' and resid 494 through 502 Processing helix chain 'F' and resid 19 through 24 Processing helix chain 'F' and resid 45 through 49 removed outlier: 3.738A pdb=" N VAL F 49 " --> pdb=" O ALA F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 85 Processing helix chain 'F' and resid 96 through 109 Processing helix chain 'F' and resid 126 through 138 removed outlier: 3.867A pdb=" N VAL F 130 " --> pdb=" O ARG F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 163 Processing helix chain 'F' and resid 174 through 178 removed outlier: 4.366A pdb=" N GLU F 177 " --> pdb=" O PHE F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 224 through 233 Processing helix chain 'F' and resid 255 through 267 removed outlier: 4.033A pdb=" N ARG F 259 " --> pdb=" O ASP F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 Processing helix chain 'F' and resid 306 through 316 Processing helix chain 'F' and resid 332 through 337 Processing helix chain 'F' and resid 342 through 357 removed outlier: 3.970A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE F 357 " --> pdb=" O TYR F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 379 Processing helix chain 'F' and resid 387 through 391 Processing helix chain 'F' and resid 452 through 472 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 475 through 486 Processing helix chain 'F' and resid 494 through 502 Processing helix chain 'G' and resid 19 through 25 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 removed outlier: 3.645A pdb=" N VAL G 49 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 85 Processing helix chain 'G' and resid 96 through 109 Processing helix chain 'G' and resid 127 through 138 Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 193 through 205 Processing helix chain 'G' and resid 224 through 233 Processing helix chain 'G' and resid 254 through 267 removed outlier: 4.152A pdb=" N TYR G 258 " --> pdb=" O GLU G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 Processing helix chain 'G' and resid 306 through 316 Processing helix chain 'G' and resid 332 through 337 Processing helix chain 'G' and resid 342 through 356 removed outlier: 3.955A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 379 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 removed outlier: 3.544A pdb=" N ARG G 480 " --> pdb=" O LEU G 476 " (cutoff:3.500A) Processing helix chain 'G' and resid 494 through 502 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 removed outlier: 3.681A pdb=" N VAL H 49 " --> pdb=" O ALA H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 85 Processing helix chain 'H' and resid 96 through 109 Processing helix chain 'H' and resid 126 through 138 removed outlier: 3.796A pdb=" N VAL H 130 " --> pdb=" O ARG H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 163 Processing helix chain 'H' and resid 193 through 205 Processing helix chain 'H' and resid 224 through 233 Processing helix chain 'H' and resid 255 through 267 removed outlier: 4.177A pdb=" N ARG H 259 " --> pdb=" O ASP H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 Processing helix chain 'H' and resid 306 through 316 Processing helix chain 'H' and resid 332 through 337 Processing helix chain 'H' and resid 342 through 356 removed outlier: 3.997A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 379 Processing helix chain 'H' and resid 452 through 472 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 475 through 486 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 56 removed outlier: 6.603A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 3.934A pdb=" N ILE A 88 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER A 67 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A 90 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLY A 89 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ALA A 249 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE A 91 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 320 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASP A 364 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL A 323 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N MET A 385 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 145 Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 189 removed outlier: 6.725A pdb=" N LEU A 209 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE A 221 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE A 211 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 403 removed outlier: 3.894A pdb=" N SER D 508 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.791A pdb=" N SER A 508 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER B 444 " --> pdb=" O GLU A 510 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 37 removed outlier: 8.642A pdb=" N GLY C 29 " --> pdb=" O PHE B 490 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LYS B 492 " --> pdb=" O GLY C 29 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.977A pdb=" N ILE B 88 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B 67 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE B 90 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B 320 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 383 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 66 " --> pdb=" O MET B 386 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 115 through 116 removed outlier: 6.650A pdb=" N ILE B 211 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE B 221 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU B 209 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ALA B 188 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 142 through 145 Processing sheet with id=AB4, first strand: chain 'B' and resid 508 through 510 removed outlier: 4.001A pdb=" N SER B 508 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER C 444 " --> pdb=" O GLU B 510 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 35 through 37 removed outlier: 8.284A pdb=" N GLY D 29 " --> pdb=" O PHE C 490 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LYS C 492 " --> pdb=" O GLY D 29 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.564A pdb=" N THR C 383 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA C 320 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASN C 303 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA C 248 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE C 91 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 115 through 116 removed outlier: 6.450A pdb=" N ILE C 211 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE C 221 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU C 209 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA C 188 " --> pdb=" O VAL C 212 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 142 through 145 Processing sheet with id=AC1, first strand: chain 'C' and resid 508 through 510 removed outlier: 3.742A pdb=" N SER C 508 " --> pdb=" O ALA D 446 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER D 444 " --> pdb=" O GLU C 510 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AC3, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC4, first strand: chain 'D' and resid 65 through 67 removed outlier: 4.007A pdb=" N ILE D 88 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER D 67 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE D 90 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLY D 89 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ALA D 249 " --> pdb=" O GLY D 89 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE D 91 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA D 320 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN D 303 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N MET D 385 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 142 through 145 Processing sheet with id=AC6, first strand: chain 'D' and resid 188 through 189 Processing sheet with id=AC7, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.885A pdb=" N LEU E 65 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N PHE E 90 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER E 67 " --> pdb=" O PHE E 90 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLY E 89 " --> pdb=" O GLY E 247 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ALA E 249 " --> pdb=" O GLY E 89 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE E 91 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA E 320 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ASN E 303 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N MET E 385 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 115 through 116 removed outlier: 6.436A pdb=" N ILE E 211 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE E 221 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU E 209 " --> pdb=" O ILE E 221 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 142 through 145 Processing sheet with id=AD3, first strand: chain 'E' and resid 400 through 403 removed outlier: 3.625A pdb=" N SER E 444 " --> pdb=" O GLU H 510 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER H 508 " --> pdb=" O ALA E 446 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 508 through 510 removed outlier: 3.862A pdb=" N SER E 508 " --> pdb=" O ALA F 446 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AD6, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD7, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.930A pdb=" N ILE F 88 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER F 67 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE F 90 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA F 248 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA F 320 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ASP F 364 " --> pdb=" O LEU F 321 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N VAL F 323 " --> pdb=" O ASP F 364 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N MET F 385 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 142 through 145 Processing sheet with id=AD9, first strand: chain 'F' and resid 188 through 189 removed outlier: 6.705A pdb=" N LEU F 209 " --> pdb=" O ILE F 221 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE F 221 " --> pdb=" O LEU F 209 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE F 211 " --> pdb=" O VAL F 219 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 508 through 510 removed outlier: 3.682A pdb=" N SER F 508 " --> pdb=" O ALA G 446 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER G 444 " --> pdb=" O GLU F 510 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AE3, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AE4, first strand: chain 'G' and resid 65 through 67 removed outlier: 4.027A pdb=" N ILE G 88 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER G 67 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE G 90 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLY G 89 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ALA G 249 " --> pdb=" O GLY G 89 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE G 91 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA G 320 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASN G 303 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR G 383 " --> pdb=" O VAL G 361 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 142 through 145 Processing sheet with id=AE6, first strand: chain 'G' and resid 188 through 189 removed outlier: 6.067A pdb=" N ALA G 188 " --> pdb=" O VAL G 212 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 508 through 510 removed outlier: 3.775A pdb=" N SER G 508 " --> pdb=" O ALA H 446 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AE9, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AF1, first strand: chain 'H' and resid 65 through 67 removed outlier: 3.947A pdb=" N ILE H 88 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER H 67 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE H 90 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLY H 89 " --> pdb=" O GLY H 247 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ALA H 249 " --> pdb=" O GLY H 89 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE H 91 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA H 320 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASN H 303 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ASP H 364 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL H 323 " --> pdb=" O ASP H 364 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N MET H 385 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 115 through 116 removed outlier: 6.607A pdb=" N ILE H 211 " --> pdb=" O VAL H 219 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ILE H 221 " --> pdb=" O LEU H 209 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU H 209 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA H 188 " --> pdb=" O VAL H 212 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 142 through 145 1206 hydrogen bonds defined for protein. 3390 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: 6.55 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5156 1.31 - 1.43: 7776 1.43 - 1.56: 18228 1.56 - 1.69: 160 1.69 - 1.82: 272 Bond restraints: 31592 Sorted by residual: bond pdb=" C4 ATP H 603 " pdb=" C5 ATP H 603 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.03e+01 bond pdb=" C4 ATP G 603 " pdb=" C5 ATP G 603 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.00e+01 bond pdb=" C4 ATP A 603 " pdb=" C5 ATP A 603 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.95e+01 bond pdb=" C4 ATP D 603 " pdb=" C5 ATP D 603 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.95e+01 bond pdb=" C4 ATP F 603 " pdb=" C5 ATP F 603 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.83e+01 ... (remaining 31587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.98: 42695 5.98 - 11.96: 189 11.96 - 17.94: 11 17.94 - 23.93: 6 23.93 - 29.91: 3 Bond angle restraints: 42904 Sorted by residual: angle pdb=" PB ATP C 603 " pdb=" O3B ATP C 603 " pdb=" PG ATP C 603 " ideal model delta sigma weight residual 139.87 109.96 29.91 1.00e+00 1.00e+00 8.94e+02 angle pdb=" PB ATP B 603 " pdb=" O3B ATP B 603 " pdb=" PG ATP B 603 " ideal model delta sigma weight residual 139.87 112.44 27.43 1.00e+00 1.00e+00 7.52e+02 angle pdb=" PA ATP C 603 " pdb=" O3A ATP C 603 " pdb=" PB ATP C 603 " ideal model delta sigma weight residual 136.83 112.04 24.79 1.00e+00 1.00e+00 6.14e+02 angle pdb=" PB ATP E 603 " pdb=" O3B ATP E 603 " pdb=" PG ATP E 603 " ideal model delta sigma weight residual 139.87 120.46 19.41 1.00e+00 1.00e+00 3.77e+02 angle pdb=" PB ATP A 603 " pdb=" O3B ATP A 603 " pdb=" PG ATP A 603 " ideal model delta sigma weight residual 139.87 120.48 19.39 1.00e+00 1.00e+00 3.76e+02 ... (remaining 42899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.67: 18130 35.67 - 71.34: 501 71.34 - 107.01: 60 107.01 - 142.67: 37 142.67 - 178.34: 24 Dihedral angle restraints: 18752 sinusoidal: 7632 harmonic: 11120 Sorted by residual: dihedral pdb=" O3A GTP D 601 " pdb=" O3B GTP D 601 " pdb=" PB GTP D 601 " pdb=" PG GTP D 601 " ideal model delta sinusoidal sigma weight residual -56.21 122.14 -178.34 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O3B GTP E 602 " pdb=" O3A GTP E 602 " pdb=" PB GTP E 602 " pdb=" PA GTP E 602 " ideal model delta sinusoidal sigma weight residual 291.08 113.13 177.95 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' IMP F 604 " pdb=" O5' IMP F 604 " pdb=" P IMP F 604 " pdb=" O2P IMP F 604 " ideal model delta sinusoidal sigma weight residual 191.93 16.12 175.81 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 18749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4095 0.069 - 0.138: 693 0.138 - 0.207: 70 0.207 - 0.276: 12 0.276 - 0.346: 2 Chirality restraints: 4872 Sorted by residual: chirality pdb=" CA PHE A 114 " pdb=" N PHE A 114 " pdb=" C PHE A 114 " pdb=" CB PHE A 114 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA LYS H 206 " pdb=" N LYS H 206 " pdb=" C LYS H 206 " pdb=" CB LYS H 206 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA LYS B 208 " pdb=" N LYS B 208 " pdb=" C LYS B 208 " pdb=" CB LYS B 208 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 4869 not shown) Planarity restraints: 5336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 233 " 0.062 5.00e-02 4.00e+02 9.22e-02 1.36e+01 pdb=" N PRO D 234 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO D 234 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO D 234 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 231 " -0.306 9.50e-02 1.11e+02 1.37e-01 1.20e+01 pdb=" NE ARG B 231 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG B 231 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 231 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 231 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 209 " -0.055 5.00e-02 4.00e+02 8.33e-02 1.11e+01 pdb=" N PRO B 210 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 210 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 210 " -0.045 5.00e-02 4.00e+02 ... (remaining 5333 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 149 2.49 - 3.09: 21415 3.09 - 3.69: 47866 3.69 - 4.30: 71763 4.30 - 4.90: 119217 Nonbonded interactions: 260410 Sorted by model distance: nonbonded pdb=" OG SER C 159 " pdb=" O2A ATP C 603 " model vdw 1.886 3.040 nonbonded pdb=" CB SER C 159 " pdb=" O2A ATP C 603 " model vdw 1.960 3.440 nonbonded pdb=" SG CYS C 331 " pdb=" N3 IMP C 604 " model vdw 2.023 2.784 nonbonded pdb=" O3' GTP D 602 " pdb=" O3G GTP D 602 " model vdw 2.053 3.040 nonbonded pdb=" OG SER F 204 " pdb=" CG LYS F 206 " model vdw 2.158 3.440 ... (remaining 260405 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: 0.02 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: 4.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.920 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 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 : 0.008 0.256 31600 Z= 0.452 Angle : 1.093 29.907 42904 Z= 0.648 Chirality : 0.051 0.346 4872 Planarity : 0.006 0.137 5336 Dihedral : 19.216 178.344 11648 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.99 % Favored : 95.85 % Rotamer: Outliers : 0.60 % Allowed : 14.82 % Favored : 84.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.13), residues: 3880 helix: 1.15 (0.14), residues: 1400 sheet: -0.26 (0.22), residues: 432 loop : -0.78 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 105 TYR 0.016 0.001 TYR H 233 PHE 0.016 0.001 PHE D 401 HIS 0.007 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00746 / 0.43 (31592) covalent geometry : angle 1.09275 / 0.65 (42904) hydrogen bonds : bond 0.13772 / 9.20 ( 1206) hydrogen bonds : angle 6.36927 / 4.51 ( 3390) Misc. bond : bond 0.09038 / 4.52 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 521 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 LYS cc_start: 0.7725 (tptt) cc_final: 0.7002 (tppt) REVERT: A 261 ASP cc_start: 0.7784 (m-30) cc_final: 0.7541 (m-30) REVERT: B 112 GLN cc_start: 0.7568 (pt0) cc_final: 0.7341 (pm20) REVERT: B 195 LYS cc_start: 0.7869 (tptt) cc_final: 0.7190 (tppt) REVERT: B 233 TYR cc_start: 0.8432 (m-80) cc_final: 0.7782 (m-80) REVERT: B 288 LYS cc_start: 0.7734 (mttm) cc_final: 0.7500 (mtmp) REVERT: B 410 LYS cc_start: 0.6832 (mtpt) cc_final: 0.6559 (pmtt) REVERT: C 75 GLU cc_start: 0.6974 (tt0) cc_final: 0.6758 (tt0) REVERT: C 206 LYS cc_start: 0.7286 (mmmt) cc_final: 0.6658 (mmmt) REVERT: C 335 GLU cc_start: 0.7625 (tt0) cc_final: 0.7337 (tt0) REVERT: C 410 LYS cc_start: 0.6753 (mtmt) cc_final: 0.6513 (pmtt) REVERT: C 500 GLU cc_start: 0.7991 (tt0) cc_final: 0.7608 (tt0) REVERT: D 195 LYS cc_start: 0.7783 (tptt) cc_final: 0.7189 (tppt) REVERT: D 265 GLN cc_start: 0.7963 (tt0) cc_final: 0.7670 (tt0) REVERT: D 335 GLU cc_start: 0.7569 (tt0) cc_final: 0.7316 (tt0) REVERT: D 410 LYS cc_start: 0.7007 (mtpt) cc_final: 0.6595 (pmtt) REVERT: D 483 MET cc_start: 0.9582 (tmm) cc_final: 0.9331 (tmm) REVERT: D 500 GLU cc_start: 0.8138 (tt0) cc_final: 0.7708 (tt0) REVERT: E 195 LYS cc_start: 0.7896 (tptt) cc_final: 0.7190 (tppt) REVERT: E 265 GLN cc_start: 0.7985 (tt0) cc_final: 0.7614 (mp10) REVERT: F 18 LEU cc_start: 0.9264 (mt) cc_final: 0.8983 (mp) REVERT: F 195 LYS cc_start: 0.7930 (tptm) cc_final: 0.7406 (tppt) REVERT: F 491 GLU cc_start: 0.8389 (tp30) cc_final: 0.8100 (tp30) REVERT: G 48 GLN cc_start: 0.8338 (mt0) cc_final: 0.8046 (mt0) REVERT: G 208 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8195 (mttp) REVERT: G 265 GLN cc_start: 0.7988 (tt0) cc_final: 0.7627 (tp40) REVERT: G 335 GLU cc_start: 0.7645 (tt0) cc_final: 0.7321 (tt0) REVERT: H 195 LYS cc_start: 0.7904 (tptm) cc_final: 0.7199 (tppt) REVERT: H 261 ASP cc_start: 0.7716 (m-30) cc_final: 0.7484 (m-30) REVERT: H 412 ARG cc_start: 0.7115 (ptt180) cc_final: 0.6882 (ptt90) REVERT: H 420 MET cc_start: 0.4589 (tpp) cc_final: 0.4024 (ptp) outliers start: 19 outliers final: 8 residues processed: 537 average time/residue: 0.5676 time to fit residues: 367.8766 Evaluate side-chains 496 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 487 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain G residue 161 ARG Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 208 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 GLN ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 HIS B 92 HIS B 100 GLN B 112 GLN ** B 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN E 230 ASN E 465 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN F 171 HIS ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 507 HIS G 48 GLN G 92 HIS ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 469 GLN H 100 GLN H 265 GLN H 448 GLN H 507 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.172294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.127236 restraints weight = 34003.029| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.93 r_work: 0.3197 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 31600 Z= 0.170 Angle : 0.693 11.344 42904 Z= 0.333 Chirality : 0.046 0.203 4872 Planarity : 0.005 0.067 5336 Dihedral : 18.593 179.631 4589 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.79 % Favored : 96.11 % Rotamer: Outliers : 3.85 % Allowed : 14.66 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.13), residues: 3880 helix: 1.24 (0.14), residues: 1384 sheet: -0.61 (0.20), residues: 520 loop : -0.71 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 231 TYR 0.014 0.001 TYR C 509 PHE 0.009 0.001 PHE F 24 HIS 0.005 0.001 HIS D 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (31592) covalent geometry : angle 0.69275 / 0.33 (42904) hydrogen bonds : bond 0.04138 / 2.78 ( 1206) hydrogen bonds : angle 5.44833 / 3.85 ( 3390) Misc. bond : bond 0.00034 / 0.02 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 490 time to evaluate : 1.185 Fit side-chains REVERT: A 75 GLU cc_start: 0.7011 (tt0) cc_final: 0.6795 (tt0) REVERT: A 195 LYS cc_start: 0.7631 (tptt) cc_final: 0.6869 (tppt) REVERT: A 206 LYS cc_start: 0.7599 (tptp) cc_final: 0.7246 (tptp) REVERT: A 261 ASP cc_start: 0.7833 (m-30) cc_final: 0.7612 (m-30) REVERT: A 385 MET cc_start: 0.8732 (ttm) cc_final: 0.8480 (ttm) REVERT: A 412 ARG cc_start: 0.7044 (ptt180) cc_final: 0.6624 (ptt90) REVERT: A 500 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7454 (tt0) REVERT: B 105 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.6765 (ttp-110) REVERT: B 195 LYS cc_start: 0.7809 (tptt) cc_final: 0.7086 (tppt) REVERT: B 288 LYS cc_start: 0.7727 (mttm) cc_final: 0.7427 (mtmp) REVERT: B 410 LYS cc_start: 0.6980 (mtpt) cc_final: 0.6545 (pmtt) REVERT: B 450 LYS cc_start: 0.7697 (mtpp) cc_final: 0.7291 (mtmm) REVERT: C 75 GLU cc_start: 0.7081 (tt0) cc_final: 0.6831 (tt0) REVERT: C 230 ASN cc_start: 0.7943 (t0) cc_final: 0.7599 (t160) REVERT: C 335 GLU cc_start: 0.7871 (tt0) cc_final: 0.7524 (tt0) REVERT: C 410 LYS cc_start: 0.6862 (mtmt) cc_final: 0.6430 (pmtt) REVERT: D 75 GLU cc_start: 0.6858 (mt-10) cc_final: 0.6657 (tt0) REVERT: D 195 LYS cc_start: 0.7729 (tptt) cc_final: 0.7093 (tppt) REVERT: D 206 LYS cc_start: 0.7146 (mmtt) cc_final: 0.6833 (mmmt) REVERT: D 265 GLN cc_start: 0.8153 (tt0) cc_final: 0.7589 (tp40) REVERT: D 335 GLU cc_start: 0.7934 (tt0) cc_final: 0.7572 (tt0) REVERT: D 410 LYS cc_start: 0.7184 (mtpt) cc_final: 0.6525 (pmtt) REVERT: E 75 GLU cc_start: 0.6989 (tt0) cc_final: 0.6744 (tt0) REVERT: E 111 GLU cc_start: 0.8408 (tt0) cc_final: 0.7748 (tm-30) REVERT: E 179 MET cc_start: 0.7582 (ptp) cc_final: 0.6937 (ptp) REVERT: E 195 LYS cc_start: 0.7667 (tptt) cc_final: 0.7016 (tppt) REVERT: E 261 ASP cc_start: 0.7882 (m-30) cc_final: 0.7670 (m-30) REVERT: E 265 GLN cc_start: 0.8209 (tt0) cc_final: 0.7642 (tp40) REVERT: E 286 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8130 (ttm) REVERT: E 368 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.7789 (mt0) REVERT: F 195 LYS cc_start: 0.7812 (tptm) cc_final: 0.7184 (tppt) REVERT: F 208 LYS cc_start: 0.7665 (mtpm) cc_final: 0.7108 (mttp) REVERT: F 265 GLN cc_start: 0.8151 (tt0) cc_final: 0.7856 (tt0) REVERT: F 286 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8195 (ttm) REVERT: F 491 GLU cc_start: 0.8553 (tp30) cc_final: 0.8316 (tp30) REVERT: G 48 GLN cc_start: 0.8220 (mt0) cc_final: 0.7908 (mt0) REVERT: G 75 GLU cc_start: 0.6984 (tt0) cc_final: 0.6777 (tt0) REVERT: G 114 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.8004 (t80) REVERT: G 206 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.6779 (mmtt) REVERT: G 208 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7930 (mttp) REVERT: G 254 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7801 (tp30) REVERT: G 265 GLN cc_start: 0.8071 (tt0) cc_final: 0.7477 (tp40) REVERT: G 286 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8290 (ttm) REVERT: G 335 GLU cc_start: 0.7874 (tt0) cc_final: 0.7549 (tt0) REVERT: H 75 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6645 (tt0) REVERT: H 105 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.6710 (ttp-110) REVERT: H 111 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8460 (tt0) REVERT: H 114 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7919 (t80) REVERT: H 195 LYS cc_start: 0.7729 (tptm) cc_final: 0.7051 (tppt) REVERT: H 261 ASP cc_start: 0.7703 (m-30) cc_final: 0.7459 (m-30) REVERT: H 325 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.8992 (tpp) REVERT: H 352 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8683 (tm-30) REVERT: H 412 ARG cc_start: 0.7115 (ptt180) cc_final: 0.6768 (ptt90) outliers start: 123 outliers final: 45 residues processed: 560 average time/residue: 0.5994 time to fit residues: 406.2005 Evaluate side-chains 518 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 459 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 369 ASN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 369 ASN Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 368 GLN Chi-restraints excluded: chain E residue 369 ASN Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 449 ASP Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 369 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain H residue 369 ASN Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 474 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 299 optimal weight: 2.9990 chunk 325 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 214 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 277 optimal weight: 0.8980 chunk 238 optimal weight: 0.3980 chunk 330 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 GLN ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN ** B 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN D 230 ASN D 507 HIS ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN E 230 ASN ** E 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.170588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.124883 restraints weight = 33964.383| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.75 r_work: 0.3171 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 31600 Z= 0.190 Angle : 0.671 13.156 42904 Z= 0.323 Chirality : 0.046 0.174 4872 Planarity : 0.005 0.062 5336 Dihedral : 17.834 178.198 4568 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.12 % Favored : 95.77 % Rotamer: Outliers : 4.54 % Allowed : 15.63 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.13), residues: 3880 helix: 1.08 (0.14), residues: 1408 sheet: -0.43 (0.23), residues: 432 loop : -0.78 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 161 TYR 0.013 0.002 TYR G 348 PHE 0.011 0.001 PHE G 24 HIS 0.004 0.001 HIS G 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (31592) covalent geometry : angle 0.67147 / 0.32 (42904) hydrogen bonds : bond 0.04297 / 2.91 ( 1206) hydrogen bonds : angle 5.30129 / 3.75 ( 3390) Misc. bond : bond 0.00048 / 0.03 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 499 time to evaluate : 1.186 Fit side-chains REVERT: A 75 GLU cc_start: 0.7062 (tt0) cc_final: 0.6860 (tt0) REVERT: A 195 LYS cc_start: 0.7658 (tptt) cc_final: 0.6965 (tppt) REVERT: A 206 LYS cc_start: 0.7708 (tptp) cc_final: 0.7290 (tptp) REVERT: A 412 ARG cc_start: 0.7094 (ptt180) cc_final: 0.6830 (ptt90) REVERT: B 111 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8331 (tm-30) REVERT: B 112 GLN cc_start: 0.7510 (pt0) cc_final: 0.7196 (pt0) REVERT: B 114 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.7962 (t80) REVERT: B 195 LYS cc_start: 0.7888 (tptt) cc_final: 0.7234 (tppt) REVERT: B 286 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8143 (ttm) REVERT: B 288 LYS cc_start: 0.7754 (mttm) cc_final: 0.7466 (mtmp) REVERT: B 410 LYS cc_start: 0.6984 (mtpt) cc_final: 0.6558 (pmtt) REVERT: B 412 ARG cc_start: 0.7105 (ptt180) cc_final: 0.6865 (ptt90) REVERT: B 450 LYS cc_start: 0.7765 (mtpp) cc_final: 0.7345 (mtmm) REVERT: C 75 GLU cc_start: 0.7072 (tt0) cc_final: 0.6811 (tt0) REVERT: C 111 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8152 (tm-30) REVERT: C 168 GLU cc_start: 0.4674 (OUTLIER) cc_final: 0.4384 (pp20) REVERT: C 206 LYS cc_start: 0.7892 (mmmt) cc_final: 0.6903 (tptp) REVERT: C 335 GLU cc_start: 0.7906 (tt0) cc_final: 0.7554 (tt0) REVERT: C 410 LYS cc_start: 0.6925 (mtmt) cc_final: 0.6477 (pmtt) REVERT: D 75 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6585 (tt0) REVERT: D 195 LYS cc_start: 0.7760 (tptt) cc_final: 0.7152 (tppt) REVERT: D 265 GLN cc_start: 0.8139 (tt0) cc_final: 0.7573 (tp40) REVERT: D 286 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8413 (ttm) REVERT: D 335 GLU cc_start: 0.7945 (tt0) cc_final: 0.7562 (tt0) REVERT: D 410 LYS cc_start: 0.7188 (mtpt) cc_final: 0.6685 (pmtt) REVERT: E 195 LYS cc_start: 0.7765 (tptt) cc_final: 0.7091 (tppt) REVERT: E 206 LYS cc_start: 0.7873 (tptp) cc_final: 0.7450 (tptp) REVERT: E 286 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8140 (ttm) REVERT: F 195 LYS cc_start: 0.7858 (tptm) cc_final: 0.7215 (tppt) REVERT: F 208 LYS cc_start: 0.7807 (mtpm) cc_final: 0.7362 (mttp) REVERT: F 491 GLU cc_start: 0.8500 (tp30) cc_final: 0.8260 (tp30) REVERT: G 75 GLU cc_start: 0.7103 (tt0) cc_final: 0.6857 (tt0) REVERT: G 114 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.8036 (t80) REVERT: G 206 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.6997 (mmtt) REVERT: G 208 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7928 (mtmt) REVERT: G 265 GLN cc_start: 0.8056 (tt0) cc_final: 0.7485 (tp40) REVERT: G 286 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8298 (ttm) REVERT: G 288 LYS cc_start: 0.7809 (mttm) cc_final: 0.7502 (mtmp) REVERT: G 335 GLU cc_start: 0.7904 (tt0) cc_final: 0.7557 (tt0) REVERT: G 410 LYS cc_start: 0.7362 (mtpt) cc_final: 0.6583 (pmtt) REVERT: H 75 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6691 (tt0) REVERT: H 114 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.8005 (t80) REVERT: H 195 LYS cc_start: 0.7794 (tptm) cc_final: 0.7109 (tppt) REVERT: H 206 LYS cc_start: 0.7791 (tppt) cc_final: 0.7428 (tptp) REVERT: H 261 ASP cc_start: 0.7731 (m-30) cc_final: 0.7499 (m-30) REVERT: H 325 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8980 (tpp) REVERT: H 410 LYS cc_start: 0.6974 (mtmt) cc_final: 0.6562 (pmtt) REVERT: H 510 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7424 (mt-10) outliers start: 145 outliers final: 71 residues processed: 584 average time/residue: 0.5754 time to fit residues: 408.7681 Evaluate side-chains 552 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 467 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 369 ASN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 369 ASN Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 474 LYS Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 369 ASN Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 449 ASP Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 369 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 369 ASN Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 474 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 75 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 273 optimal weight: 0.0020 chunk 364 optimal weight: 2.9990 chunk 375 optimal weight: 0.6980 chunk 139 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 232 optimal weight: 0.0980 chunk 255 optimal weight: 5.9990 chunk 226 optimal weight: 1.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 GLN ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN E 230 ASN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 GLN G 100 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN H 448 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.178315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.132452 restraints weight = 33550.960| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.84 r_work: 0.3217 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 31600 Z= 0.107 Angle : 0.605 11.139 42904 Z= 0.286 Chirality : 0.043 0.161 4872 Planarity : 0.004 0.058 5336 Dihedral : 17.074 178.385 4568 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.17 % Favored : 96.73 % Rotamer: Outliers : 3.76 % Allowed : 17.36 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.13), residues: 3880 helix: 1.39 (0.14), residues: 1400 sheet: -0.40 (0.23), residues: 456 loop : -0.73 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 341 TYR 0.011 0.001 TYR C 509 PHE 0.008 0.001 PHE D 35 HIS 0.002 0.000 HIS D 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (31592) covalent geometry : angle 0.60542 / 0.29 (42904) hydrogen bonds : bond 0.03256 / 2.22 ( 1206) hydrogen bonds : angle 5.04288 / 3.55 ( 3390) Misc. bond : bond 0.00022 / 0.01 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 493 time to evaluate : 1.543 Fit side-chains REVERT: A 195 LYS cc_start: 0.7555 (tptt) cc_final: 0.6856 (tppt) REVERT: A 206 LYS cc_start: 0.7713 (tptp) cc_final: 0.7182 (tptp) REVERT: A 265 GLN cc_start: 0.8117 (tt0) cc_final: 0.7542 (tp40) REVERT: A 412 ARG cc_start: 0.6908 (ptt180) cc_final: 0.6676 (ptt90) REVERT: A 500 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7374 (tt0) REVERT: B 114 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.7985 (t80) REVERT: B 195 LYS cc_start: 0.7746 (tptt) cc_final: 0.7107 (tppt) REVERT: B 286 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8116 (ttm) REVERT: B 288 LYS cc_start: 0.7690 (mttm) cc_final: 0.7416 (mtmp) REVERT: B 410 LYS cc_start: 0.6972 (mtpt) cc_final: 0.6510 (pmtt) REVERT: C 111 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8032 (tm-30) REVERT: C 206 LYS cc_start: 0.7885 (mmmt) cc_final: 0.6856 (tptp) REVERT: C 230 ASN cc_start: 0.7974 (t0) cc_final: 0.7722 (t160) REVERT: C 335 GLU cc_start: 0.7934 (tt0) cc_final: 0.7511 (tt0) REVERT: C 410 LYS cc_start: 0.6925 (mtmt) cc_final: 0.6409 (pmtt) REVERT: D 195 LYS cc_start: 0.7668 (tptt) cc_final: 0.7070 (tppt) REVERT: D 265 GLN cc_start: 0.8095 (tt0) cc_final: 0.7521 (tp40) REVERT: D 274 ASP cc_start: 0.8318 (t0) cc_final: 0.8098 (t0) REVERT: D 335 GLU cc_start: 0.8004 (tt0) cc_final: 0.7551 (tt0) REVERT: D 410 LYS cc_start: 0.7195 (mtpt) cc_final: 0.6645 (pmtt) REVERT: D 412 ARG cc_start: 0.7001 (ptt180) cc_final: 0.6607 (ptt90) REVERT: E 195 LYS cc_start: 0.7670 (tptt) cc_final: 0.6955 (tppt) REVERT: E 206 LYS cc_start: 0.7812 (tptp) cc_final: 0.7227 (tptp) REVERT: E 242 LYS cc_start: 0.7609 (mmtm) cc_final: 0.7076 (mttt) REVERT: E 265 GLN cc_start: 0.8099 (tt0) cc_final: 0.7535 (tp40) REVERT: E 286 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8145 (ttm) REVERT: E 500 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7607 (tt0) REVERT: F 195 LYS cc_start: 0.7757 (tptm) cc_final: 0.7164 (tppt) REVERT: F 208 LYS cc_start: 0.7689 (mtpm) cc_final: 0.7279 (mttp) REVERT: F 265 GLN cc_start: 0.8087 (tt0) cc_final: 0.7528 (tp40) REVERT: F 274 ASP cc_start: 0.8401 (t0) cc_final: 0.8197 (t0) REVERT: F 286 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8148 (ttm) REVERT: F 491 GLU cc_start: 0.8480 (tp30) cc_final: 0.8257 (tp30) REVERT: G 48 GLN cc_start: 0.8245 (mt0) cc_final: 0.7983 (mt0) REVERT: G 75 GLU cc_start: 0.7125 (tt0) cc_final: 0.6912 (tt0) REVERT: G 114 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.8043 (t80) REVERT: G 195 LYS cc_start: 0.7682 (tptm) cc_final: 0.7104 (tppt) REVERT: G 206 LYS cc_start: 0.7506 (mmtm) cc_final: 0.6890 (mmmm) REVERT: G 241 LYS cc_start: 0.7635 (ptmt) cc_final: 0.7425 (ptpp) REVERT: G 265 GLN cc_start: 0.8035 (tt0) cc_final: 0.7504 (tp40) REVERT: G 286 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8253 (ttm) REVERT: G 288 LYS cc_start: 0.7732 (mttm) cc_final: 0.7395 (mtmp) REVERT: G 410 LYS cc_start: 0.7391 (mtpt) cc_final: 0.6593 (pmtt) REVERT: G 500 GLU cc_start: 0.7863 (tt0) cc_final: 0.7602 (pt0) REVERT: H 75 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6644 (tt0) REVERT: H 114 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.7934 (t80) REVERT: H 195 LYS cc_start: 0.7687 (tptm) cc_final: 0.6999 (tppt) REVERT: H 206 LYS cc_start: 0.7804 (tppt) cc_final: 0.7458 (tptp) REVERT: H 261 ASP cc_start: 0.7548 (m-30) cc_final: 0.7323 (m-30) REVERT: H 410 LYS cc_start: 0.6939 (mtmt) cc_final: 0.6524 (pmtt) REVERT: H 412 ARG cc_start: 0.6906 (ptt180) cc_final: 0.6620 (ptt90) REVERT: H 510 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7334 (mt-10) outliers start: 120 outliers final: 57 residues processed: 563 average time/residue: 0.5432 time to fit residues: 373.5110 Evaluate side-chains 539 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 471 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 474 LYS Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 369 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 474 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 183 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 209 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 238 optimal weight: 0.6980 chunk 235 optimal weight: 0.7980 chunk 214 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 273 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 GLN ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN E 230 ASN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 GLN ** G 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN H 171 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.174992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.129567 restraints weight = 33739.470| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.76 r_work: 0.3206 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 31600 Z= 0.132 Angle : 0.614 11.429 42904 Z= 0.289 Chirality : 0.044 0.171 4872 Planarity : 0.004 0.059 5336 Dihedral : 16.510 179.531 4560 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.02 % Favored : 95.88 % Rotamer: Outliers : 4.26 % Allowed : 17.86 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.13), residues: 3880 helix: 1.40 (0.14), residues: 1400 sheet: -0.49 (0.25), residues: 416 loop : -0.65 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 412 TYR 0.011 0.001 TYR F 348 PHE 0.009 0.001 PHE G 24 HIS 0.003 0.001 HIS G 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (31592) covalent geometry : angle 0.61437 / 0.29 (42904) hydrogen bonds : bond 0.03513 / 2.38 ( 1206) hydrogen bonds : angle 4.98412 / 3.51 ( 3390) Misc. bond : bond 0.00035 / 0.02 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 487 time to evaluate : 1.128 Fit side-chains REVERT: A 75 GLU cc_start: 0.7017 (tt0) cc_final: 0.6798 (tt0) REVERT: A 195 LYS cc_start: 0.7601 (tptt) cc_final: 0.6903 (tppt) REVERT: A 206 LYS cc_start: 0.7754 (tptp) cc_final: 0.7223 (tptp) REVERT: A 265 GLN cc_start: 0.8145 (tt0) cc_final: 0.7586 (tp40) REVERT: A 412 ARG cc_start: 0.7006 (ptt180) cc_final: 0.6736 (ptt90) REVERT: A 500 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7503 (tt0) REVERT: B 111 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8008 (tm-30) REVERT: B 114 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7932 (t80) REVERT: B 195 LYS cc_start: 0.7776 (tptt) cc_final: 0.7131 (tppt) REVERT: B 286 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8133 (ttm) REVERT: B 288 LYS cc_start: 0.7714 (mttm) cc_final: 0.7401 (mtmp) REVERT: B 410 LYS cc_start: 0.6977 (mtpt) cc_final: 0.6513 (pmtt) REVERT: C 111 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8238 (tm-30) REVERT: C 206 LYS cc_start: 0.7975 (mmmt) cc_final: 0.6982 (tptp) REVERT: C 230 ASN cc_start: 0.8012 (t0) cc_final: 0.7758 (t160) REVERT: C 335 GLU cc_start: 0.7957 (tt0) cc_final: 0.7564 (tt0) REVERT: C 410 LYS cc_start: 0.6958 (mtmt) cc_final: 0.6472 (pmtt) REVERT: D 106 LYS cc_start: 0.8626 (ttmm) cc_final: 0.8397 (ttmt) REVERT: D 195 LYS cc_start: 0.7716 (tptt) cc_final: 0.7113 (tppt) REVERT: D 265 GLN cc_start: 0.8054 (tt0) cc_final: 0.7527 (tp40) REVERT: D 274 ASP cc_start: 0.8300 (t0) cc_final: 0.8068 (t0) REVERT: D 286 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8294 (ttm) REVERT: D 335 GLU cc_start: 0.7982 (tt0) cc_final: 0.7534 (tt0) REVERT: D 410 LYS cc_start: 0.7177 (mtpt) cc_final: 0.6650 (pmtt) REVERT: D 412 ARG cc_start: 0.7032 (ptt180) cc_final: 0.6627 (ptt90) REVERT: E 195 LYS cc_start: 0.7723 (tptt) cc_final: 0.7011 (tppt) REVERT: E 206 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7399 (tptp) REVERT: E 242 LYS cc_start: 0.7776 (mmtm) cc_final: 0.7181 (mttt) REVERT: E 265 GLN cc_start: 0.8086 (tt0) cc_final: 0.7544 (tp40) REVERT: E 286 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8153 (ttm) REVERT: F 195 LYS cc_start: 0.7817 (tptm) cc_final: 0.7228 (tppt) REVERT: F 208 LYS cc_start: 0.7762 (mtpm) cc_final: 0.7352 (mttp) REVERT: F 265 GLN cc_start: 0.8098 (tt0) cc_final: 0.7576 (tp40) REVERT: F 274 ASP cc_start: 0.8359 (t0) cc_final: 0.8146 (t0) REVERT: F 286 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8181 (ttm) REVERT: F 491 GLU cc_start: 0.8437 (tp30) cc_final: 0.8228 (tp30) REVERT: G 48 GLN cc_start: 0.8267 (mt0) cc_final: 0.8042 (mt0) REVERT: G 114 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.8096 (t80) REVERT: G 195 LYS cc_start: 0.7707 (tptm) cc_final: 0.7125 (tppt) REVERT: G 206 LYS cc_start: 0.7692 (mmtm) cc_final: 0.7079 (mmmm) REVERT: G 208 LYS cc_start: 0.8209 (mtpp) cc_final: 0.7649 (mttp) REVERT: G 265 GLN cc_start: 0.8039 (tt0) cc_final: 0.7490 (tp40) REVERT: G 286 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8303 (ttm) REVERT: G 288 LYS cc_start: 0.7771 (mttm) cc_final: 0.7442 (mtmp) REVERT: G 410 LYS cc_start: 0.7375 (mtpt) cc_final: 0.6591 (pmtt) REVERT: G 412 ARG cc_start: 0.7030 (ptt180) cc_final: 0.6791 (ptt90) REVERT: G 500 GLU cc_start: 0.7915 (tt0) cc_final: 0.7585 (pt0) REVERT: H 75 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6658 (tt0) REVERT: H 114 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7998 (t80) REVERT: H 195 LYS cc_start: 0.7747 (tptm) cc_final: 0.7070 (tppt) REVERT: H 206 LYS cc_start: 0.7815 (tppt) cc_final: 0.7428 (tptp) REVERT: H 261 ASP cc_start: 0.7566 (m-30) cc_final: 0.7361 (m-30) REVERT: H 410 LYS cc_start: 0.6976 (mtmt) cc_final: 0.6569 (pmtt) REVERT: H 510 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7313 (mt-10) outliers start: 136 outliers final: 72 residues processed: 582 average time/residue: 0.5348 time to fit residues: 379.7546 Evaluate side-chains 552 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 467 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 369 ASN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 474 LYS Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 410 LYS Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 369 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 369 ASN Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 474 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 257 optimal weight: 8.9990 chunk 349 optimal weight: 0.6980 chunk 280 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 34 optimal weight: 0.0050 chunk 8 optimal weight: 0.5980 chunk 248 optimal weight: 0.0070 chunk 100 optimal weight: 2.9990 overall best weight: 0.4614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 GLN A 202 GLN ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN C 100 GLN C 303 ASN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN E 230 ASN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 GLN ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN H 243 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.178159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.132587 restraints weight = 33591.077| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.83 r_work: 0.3239 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 31600 Z= 0.101 Angle : 0.587 11.195 42904 Z= 0.275 Chirality : 0.043 0.151 4872 Planarity : 0.004 0.057 5336 Dihedral : 16.020 179.355 4560 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.17 % Favored : 96.73 % Rotamer: Outliers : 3.70 % Allowed : 19.11 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.14), residues: 3880 helix: 1.53 (0.14), residues: 1400 sheet: -0.52 (0.24), residues: 416 loop : -0.58 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 341 TYR 0.008 0.001 TYR D 353 PHE 0.009 0.001 PHE D 35 HIS 0.003 0.000 HIS F 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (31592) covalent geometry : angle 0.58722 / 0.28 (42904) hydrogen bonds : bond 0.03085 / 2.10 ( 1206) hydrogen bonds : angle 4.85298 / 3.41 ( 3390) Misc. bond : bond 0.00025 / 0.01 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 489 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8593 (ttmm) cc_final: 0.8354 (ttmt) REVERT: A 195 LYS cc_start: 0.7620 (tptt) cc_final: 0.6910 (tppt) REVERT: A 206 LYS cc_start: 0.7756 (tptp) cc_final: 0.7347 (tptp) REVERT: A 265 GLN cc_start: 0.8099 (tt0) cc_final: 0.7547 (tp40) REVERT: A 412 ARG cc_start: 0.6883 (ptt180) cc_final: 0.6495 (ptt90) REVERT: B 111 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.7988 (tm-30) REVERT: B 114 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.7950 (t80) REVERT: B 195 LYS cc_start: 0.7683 (tptt) cc_final: 0.7029 (tppt) REVERT: B 286 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8160 (ttm) REVERT: B 288 LYS cc_start: 0.7706 (mttm) cc_final: 0.7439 (mtmp) REVERT: B 410 LYS cc_start: 0.7009 (mtpt) cc_final: 0.6480 (pmtt) REVERT: C 106 LYS cc_start: 0.8464 (ttmm) cc_final: 0.8258 (ttmt) REVERT: C 111 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8263 (tm-30) REVERT: C 168 GLU cc_start: 0.4586 (OUTLIER) cc_final: 0.4374 (pp20) REVERT: C 206 LYS cc_start: 0.7965 (mmmt) cc_final: 0.6954 (tptp) REVERT: C 230 ASN cc_start: 0.7965 (t0) cc_final: 0.7717 (t160) REVERT: C 335 GLU cc_start: 0.7982 (tt0) cc_final: 0.7581 (tt0) REVERT: C 410 LYS cc_start: 0.6936 (mtmt) cc_final: 0.6415 (pmtt) REVERT: C 500 GLU cc_start: 0.7808 (tt0) cc_final: 0.7573 (tt0) REVERT: D 106 LYS cc_start: 0.8566 (ttmm) cc_final: 0.8323 (ttmt) REVERT: D 195 LYS cc_start: 0.7636 (tptt) cc_final: 0.7029 (tppt) REVERT: D 265 GLN cc_start: 0.8064 (tt0) cc_final: 0.7510 (tp40) REVERT: D 274 ASP cc_start: 0.8302 (t0) cc_final: 0.8062 (t0) REVERT: D 286 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8277 (ttm) REVERT: D 335 GLU cc_start: 0.7980 (tt0) cc_final: 0.7569 (tt0) REVERT: D 410 LYS cc_start: 0.7193 (mtpt) cc_final: 0.6638 (pmtt) REVERT: E 195 LYS cc_start: 0.7665 (tptt) cc_final: 0.6958 (tppt) REVERT: E 206 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7615 (tptp) REVERT: E 242 LYS cc_start: 0.7762 (mmtm) cc_final: 0.7217 (mmtt) REVERT: E 265 GLN cc_start: 0.8087 (tt0) cc_final: 0.7539 (tp40) REVERT: E 286 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8149 (ttm) REVERT: F 195 LYS cc_start: 0.7765 (tptm) cc_final: 0.7146 (tppt) REVERT: F 208 LYS cc_start: 0.7675 (mtpm) cc_final: 0.7288 (mttp) REVERT: F 265 GLN cc_start: 0.8092 (tt0) cc_final: 0.7563 (tp40) REVERT: F 274 ASP cc_start: 0.8332 (t0) cc_final: 0.8103 (t0) REVERT: F 286 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8119 (ttm) REVERT: F 491 GLU cc_start: 0.8460 (tp30) cc_final: 0.8258 (tp30) REVERT: G 48 GLN cc_start: 0.8242 (mt0) cc_final: 0.8019 (mt0) REVERT: G 100 GLN cc_start: 0.8500 (tt0) cc_final: 0.8258 (tt0) REVERT: G 195 LYS cc_start: 0.7668 (tptm) cc_final: 0.7086 (tppt) REVERT: G 206 LYS cc_start: 0.7657 (mmtm) cc_final: 0.7042 (mmmm) REVERT: G 208 LYS cc_start: 0.8160 (mtpp) cc_final: 0.7563 (mttp) REVERT: G 265 GLN cc_start: 0.7985 (tt0) cc_final: 0.7440 (tp40) REVERT: G 286 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8265 (ttm) REVERT: G 335 GLU cc_start: 0.7898 (tt0) cc_final: 0.7506 (tt0) REVERT: G 410 LYS cc_start: 0.7327 (mtpt) cc_final: 0.6519 (pmtt) REVERT: G 412 ARG cc_start: 0.6908 (ptt180) cc_final: 0.6675 (ptt90) REVERT: G 491 GLU cc_start: 0.8635 (tp30) cc_final: 0.8433 (tp30) REVERT: G 500 GLU cc_start: 0.7839 (tt0) cc_final: 0.7542 (pt0) REVERT: H 75 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6652 (tt0) REVERT: H 114 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.8035 (t80) REVERT: H 195 LYS cc_start: 0.7700 (tptm) cc_final: 0.7021 (tppt) REVERT: H 261 ASP cc_start: 0.7525 (m-30) cc_final: 0.7320 (m-30) REVERT: H 410 LYS cc_start: 0.6981 (mtmt) cc_final: 0.6575 (pmtt) REVERT: H 510 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7154 (mt-10) outliers start: 118 outliers final: 72 residues processed: 568 average time/residue: 0.5256 time to fit residues: 365.4559 Evaluate side-chains 559 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 475 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 369 ASN Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 474 LYS Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 369 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 474 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 330 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 370 optimal weight: 0.0170 chunk 184 optimal weight: 1.9990 chunk 309 optimal weight: 6.9990 chunk 299 optimal weight: 5.9990 chunk 306 optimal weight: 3.9990 chunk 262 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 243 optimal weight: 3.9990 chunk 335 optimal weight: 4.9990 overall best weight: 1.7224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 GLN A 202 GLN ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN C 303 ASN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN E 230 ASN F 92 HIS F 100 GLN ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN H 243 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.171942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.126248 restraints weight = 33600.437| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.74 r_work: 0.3157 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 31600 Z= 0.220 Angle : 0.669 11.586 42904 Z= 0.321 Chirality : 0.046 0.192 4872 Planarity : 0.004 0.058 5336 Dihedral : 16.089 179.076 4560 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.54 % Favored : 95.36 % Rotamer: Outliers : 4.45 % Allowed : 18.98 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.13), residues: 3880 helix: 1.25 (0.14), residues: 1400 sheet: -0.59 (0.22), residues: 512 loop : -0.69 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 412 TYR 0.013 0.002 TYR B 348 PHE 0.011 0.002 PHE G 24 HIS 0.005 0.001 HIS C 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.22 (31592) covalent geometry : angle 0.66851 / 0.32 (42904) hydrogen bonds : bond 0.04192 / 2.83 ( 1206) hydrogen bonds : angle 5.07414 / 3.57 ( 3390) Misc. bond : bond 0.00065 / 0.04 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 497 time to evaluate : 1.467 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7086 (tt0) cc_final: 0.6841 (tt0) REVERT: A 106 LYS cc_start: 0.8591 (ttmm) cc_final: 0.8342 (ttmt) REVERT: A 195 LYS cc_start: 0.7750 (tptt) cc_final: 0.7083 (tppt) REVERT: A 206 LYS cc_start: 0.7707 (tptp) cc_final: 0.7381 (tptp) REVERT: A 265 GLN cc_start: 0.8172 (tt0) cc_final: 0.7573 (tp40) REVERT: A 412 ARG cc_start: 0.7089 (ptt180) cc_final: 0.6759 (ptt90) REVERT: A 500 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7488 (tt0) REVERT: B 106 LYS cc_start: 0.8440 (ttmm) cc_final: 0.8220 (ttmt) REVERT: B 112 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7067 (pm20) REVERT: B 195 LYS cc_start: 0.7725 (tptt) cc_final: 0.7064 (tppt) REVERT: B 286 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8072 (ttm) REVERT: B 288 LYS cc_start: 0.7692 (mttm) cc_final: 0.7343 (mtmp) REVERT: B 410 LYS cc_start: 0.7038 (mtpt) cc_final: 0.6485 (pmtt) REVERT: B 420 MET cc_start: 0.5038 (tpp) cc_final: 0.4643 (tpp) REVERT: C 58 LYS cc_start: 0.8199 (mtmm) cc_final: 0.7987 (mtmp) REVERT: C 75 GLU cc_start: 0.7028 (tt0) cc_final: 0.6766 (tt0) REVERT: C 106 LYS cc_start: 0.8481 (ttmm) cc_final: 0.8260 (ttmt) REVERT: C 111 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8271 (tm-30) REVERT: C 206 LYS cc_start: 0.7846 (mmmt) cc_final: 0.6798 (tptp) REVERT: C 286 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8277 (ttm) REVERT: C 335 GLU cc_start: 0.7937 (tt0) cc_final: 0.7518 (tt0) REVERT: C 410 LYS cc_start: 0.6957 (mtmt) cc_final: 0.6431 (pmtt) REVERT: D 75 GLU cc_start: 0.6817 (mt-10) cc_final: 0.6602 (tt0) REVERT: D 106 LYS cc_start: 0.8569 (ttmm) cc_final: 0.8322 (ttmt) REVERT: D 170 GLU cc_start: 0.2995 (OUTLIER) cc_final: 0.2675 (tm-30) REVERT: D 195 LYS cc_start: 0.7718 (tptt) cc_final: 0.7103 (tppt) REVERT: D 265 GLN cc_start: 0.8104 (tt0) cc_final: 0.7502 (tp40) REVERT: D 274 ASP cc_start: 0.8411 (t0) cc_final: 0.8178 (t0) REVERT: D 335 GLU cc_start: 0.7941 (tt0) cc_final: 0.7462 (tt0) REVERT: D 410 LYS cc_start: 0.7207 (mtpt) cc_final: 0.6621 (pmtt) REVERT: E 195 LYS cc_start: 0.7728 (tptt) cc_final: 0.7009 (tppt) REVERT: E 206 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7313 (tptp) REVERT: E 265 GLN cc_start: 0.8087 (tt0) cc_final: 0.7515 (tp40) REVERT: E 286 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8091 (ttm) REVERT: E 402 PHE cc_start: 0.6026 (m-80) cc_final: 0.5440 (m-80) REVERT: F 58 LYS cc_start: 0.8401 (mttt) cc_final: 0.8046 (mtmp) REVERT: F 195 LYS cc_start: 0.7784 (tptm) cc_final: 0.7153 (tppt) REVERT: F 208 LYS cc_start: 0.7790 (mtpm) cc_final: 0.7314 (mttp) REVERT: F 265 GLN cc_start: 0.8085 (tt0) cc_final: 0.7496 (tp40) REVERT: F 274 ASP cc_start: 0.8356 (t0) cc_final: 0.8083 (t0) REVERT: F 286 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8154 (ttm) REVERT: F 410 LYS cc_start: 0.7288 (OUTLIER) cc_final: 0.6727 (pmtt) REVERT: F 491 GLU cc_start: 0.8429 (tp30) cc_final: 0.8219 (tp30) REVERT: G 48 GLN cc_start: 0.8302 (mt0) cc_final: 0.8082 (mt0) REVERT: G 162 ASP cc_start: 0.7031 (m-30) cc_final: 0.6260 (m-30) REVERT: G 195 LYS cc_start: 0.7706 (tptm) cc_final: 0.7113 (tppt) REVERT: G 206 LYS cc_start: 0.7703 (mmtm) cc_final: 0.7029 (mmmm) REVERT: G 208 LYS cc_start: 0.8293 (mtpp) cc_final: 0.7709 (mttp) REVERT: G 265 GLN cc_start: 0.8032 (tt0) cc_final: 0.7434 (tp40) REVERT: G 286 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8199 (ttm) REVERT: G 288 LYS cc_start: 0.7777 (mttm) cc_final: 0.7425 (mtmp) REVERT: G 335 GLU cc_start: 0.7876 (tt0) cc_final: 0.7460 (tt0) REVERT: G 410 LYS cc_start: 0.7308 (mtpt) cc_final: 0.6547 (pmtt) REVERT: G 412 ARG cc_start: 0.7111 (ptt180) cc_final: 0.6859 (ptt180) REVERT: G 500 GLU cc_start: 0.7843 (tt0) cc_final: 0.7378 (pt0) REVERT: H 75 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6687 (tt0) REVERT: H 114 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.8038 (t80) REVERT: H 195 LYS cc_start: 0.7697 (tptm) cc_final: 0.7027 (tppt) REVERT: H 224 ARG cc_start: 0.8086 (ttt90) cc_final: 0.7461 (ttt90) REVERT: H 410 LYS cc_start: 0.7016 (mtmt) cc_final: 0.6556 (pmtt) REVERT: H 510 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7172 (mt-10) outliers start: 142 outliers final: 90 residues processed: 599 average time/residue: 0.5151 time to fit residues: 376.4872 Evaluate side-chains 581 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 478 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 412 ARG Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 369 ASN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 369 ASN Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 474 LYS Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 369 ASN Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 410 LYS Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 369 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain H residue 369 ASN Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 453 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 276 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 chunk 334 optimal weight: 0.8980 chunk 196 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 269 optimal weight: 1.9990 chunk 373 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 337 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 GLN ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN E 230 ASN F 100 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 GLN ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN G 100 GLN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 243 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.171192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.125475 restraints weight = 33762.840| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.75 r_work: 0.3187 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31600 Z= 0.147 Angle : 0.623 11.164 42904 Z= 0.297 Chirality : 0.044 0.154 4872 Planarity : 0.004 0.057 5336 Dihedral : 15.909 178.674 4560 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.04 % Favored : 96.86 % Rotamer: Outliers : 4.17 % Allowed : 19.86 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.13), residues: 3880 helix: 1.33 (0.14), residues: 1400 sheet: -0.60 (0.22), residues: 512 loop : -0.67 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 224 TYR 0.011 0.001 TYR F 348 PHE 0.008 0.001 PHE E 35 HIS 0.003 0.001 HIS F 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (31592) covalent geometry : angle 0.62260 / 0.30 (42904) hydrogen bonds : bond 0.03590 / 2.43 ( 1206) hydrogen bonds : angle 5.00061 / 3.52 ( 3390) Misc. bond : bond 0.00032 / 0.02 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 476 time to evaluate : 1.212 Fit side-chains REVERT: A 106 LYS cc_start: 0.8588 (ttmm) cc_final: 0.8336 (ttmt) REVERT: A 195 LYS cc_start: 0.7693 (tptt) cc_final: 0.7029 (tppt) REVERT: A 206 LYS cc_start: 0.7638 (tptp) cc_final: 0.7324 (tptp) REVERT: A 265 GLN cc_start: 0.8167 (tt0) cc_final: 0.7572 (tp40) REVERT: A 412 ARG cc_start: 0.7034 (ptt180) cc_final: 0.6776 (ptt90) REVERT: A 500 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7494 (tt0) REVERT: B 106 LYS cc_start: 0.8430 (ttmm) cc_final: 0.8211 (ttmt) REVERT: B 114 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.7902 (t80) REVERT: B 195 LYS cc_start: 0.7667 (tptt) cc_final: 0.7025 (tppt) REVERT: B 288 LYS cc_start: 0.7663 (mttm) cc_final: 0.7351 (mtmp) REVERT: B 410 LYS cc_start: 0.7043 (mtpt) cc_final: 0.6484 (pmtt) REVERT: B 420 MET cc_start: 0.4857 (tpp) cc_final: 0.4445 (tpp) REVERT: C 106 LYS cc_start: 0.8479 (ttmm) cc_final: 0.8253 (ttmt) REVERT: C 111 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8303 (tm-30) REVERT: C 206 LYS cc_start: 0.7805 (mmmt) cc_final: 0.6787 (tptp) REVERT: C 241 LYS cc_start: 0.7570 (ttmt) cc_final: 0.7370 (ttmm) REVERT: C 335 GLU cc_start: 0.7932 (tt0) cc_final: 0.7508 (tt0) REVERT: C 410 LYS cc_start: 0.6961 (mtmt) cc_final: 0.6425 (pmtt) REVERT: D 106 LYS cc_start: 0.8555 (ttmm) cc_final: 0.8300 (ttmt) REVERT: D 170 GLU cc_start: 0.2952 (OUTLIER) cc_final: 0.2619 (tm-30) REVERT: D 195 LYS cc_start: 0.7668 (tptt) cc_final: 0.7053 (tppt) REVERT: D 265 GLN cc_start: 0.8106 (tt0) cc_final: 0.7503 (tp40) REVERT: D 274 ASP cc_start: 0.8394 (t0) cc_final: 0.8169 (t0) REVERT: D 286 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8312 (ttm) REVERT: D 410 LYS cc_start: 0.7233 (mtpt) cc_final: 0.6633 (pmtt) REVERT: E 111 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8001 (tm-30) REVERT: E 195 LYS cc_start: 0.7692 (tptt) cc_final: 0.6979 (tppt) REVERT: E 206 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7317 (tptp) REVERT: E 242 LYS cc_start: 0.7583 (mmtm) cc_final: 0.6888 (mttt) REVERT: E 265 GLN cc_start: 0.8091 (tt0) cc_final: 0.7523 (tp40) REVERT: E 286 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8048 (ttm) REVERT: E 402 PHE cc_start: 0.5992 (m-80) cc_final: 0.5435 (m-80) REVERT: F 58 LYS cc_start: 0.8382 (mttt) cc_final: 0.8019 (mtmp) REVERT: F 195 LYS cc_start: 0.7755 (tptm) cc_final: 0.7139 (tppt) REVERT: F 208 LYS cc_start: 0.7699 (mtpm) cc_final: 0.7268 (mttp) REVERT: F 265 GLN cc_start: 0.8079 (tt0) cc_final: 0.7476 (tp40) REVERT: F 274 ASP cc_start: 0.8336 (t0) cc_final: 0.8073 (t0) REVERT: F 286 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8101 (ttm) REVERT: F 491 GLU cc_start: 0.8450 (tp30) cc_final: 0.8250 (tp30) REVERT: G 48 GLN cc_start: 0.8259 (mt0) cc_final: 0.8038 (mt0) REVERT: G 100 GLN cc_start: 0.8500 (tt0) cc_final: 0.8262 (tt0) REVERT: G 195 LYS cc_start: 0.7637 (tptm) cc_final: 0.7051 (tppt) REVERT: G 206 LYS cc_start: 0.7661 (mmtm) cc_final: 0.7112 (mmmm) REVERT: G 208 LYS cc_start: 0.8223 (mtpp) cc_final: 0.7654 (mttp) REVERT: G 265 GLN cc_start: 0.8052 (tt0) cc_final: 0.7433 (tp40) REVERT: G 286 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8245 (ttm) REVERT: G 288 LYS cc_start: 0.7768 (mttm) cc_final: 0.7408 (mtmp) REVERT: G 410 LYS cc_start: 0.7319 (mtpt) cc_final: 0.6610 (pmtt) REVERT: G 412 ARG cc_start: 0.7001 (ptt180) cc_final: 0.6636 (ptt90) REVERT: G 500 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7393 (pt0) REVERT: H 75 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6621 (tt0) REVERT: H 114 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.8051 (t80) REVERT: H 195 LYS cc_start: 0.7635 (tptm) cc_final: 0.6974 (tppt) REVERT: H 206 LYS cc_start: 0.7610 (tppt) cc_final: 0.6332 (tptp) REVERT: H 224 ARG cc_start: 0.8053 (ttt90) cc_final: 0.7433 (ttt90) REVERT: H 410 LYS cc_start: 0.7008 (mtmt) cc_final: 0.6530 (pmtt) REVERT: H 510 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7121 (mt-10) outliers start: 133 outliers final: 90 residues processed: 563 average time/residue: 0.5414 time to fit residues: 372.5959 Evaluate side-chains 576 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 473 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 412 ARG Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 369 ASN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 369 ASN Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 412 ARG Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 474 LYS Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 369 ASN Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 369 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 453 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 169 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 155 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 264 optimal weight: 0.7980 chunk 292 optimal weight: 3.9990 chunk 270 optimal weight: 0.8980 chunk 356 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 279 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 GLN ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN C 100 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN E 230 ASN ** E 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.171147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.125578 restraints weight = 33605.035| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.74 r_work: 0.3174 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 31600 Z= 0.176 Angle : 0.640 11.078 42904 Z= 0.306 Chirality : 0.045 0.152 4872 Planarity : 0.004 0.057 5336 Dihedral : 15.775 178.735 4560 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.41 % Favored : 95.49 % Rotamer: Outliers : 3.88 % Allowed : 20.49 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.13), residues: 3880 helix: 1.25 (0.14), residues: 1400 sheet: -0.63 (0.21), residues: 512 loop : -0.69 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 224 TYR 0.013 0.002 TYR H 348 PHE 0.010 0.001 PHE G 24 HIS 0.003 0.001 HIS F 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (31592) covalent geometry : angle 0.63984 / 0.31 (42904) hydrogen bonds : bond 0.03881 / 2.62 ( 1206) hydrogen bonds : angle 5.04895 / 3.55 ( 3390) Misc. bond : bond 0.00039 / 0.02 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 477 time to evaluate : 0.935 Fit side-chains REVERT: A 106 LYS cc_start: 0.8585 (ttmm) cc_final: 0.8331 (ttmt) REVERT: A 111 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7854 (tm-30) REVERT: A 195 LYS cc_start: 0.7734 (tptt) cc_final: 0.7089 (tppt) REVERT: A 206 LYS cc_start: 0.7693 (tptp) cc_final: 0.7371 (tptp) REVERT: A 265 GLN cc_start: 0.8168 (tt0) cc_final: 0.7570 (tp40) REVERT: A 412 ARG cc_start: 0.7029 (ptt180) cc_final: 0.6706 (ptt90) REVERT: A 500 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7475 (tt0) REVERT: B 106 LYS cc_start: 0.8458 (ttmm) cc_final: 0.8223 (ttmt) REVERT: B 112 GLN cc_start: 0.7608 (pm20) cc_final: 0.7123 (pm20) REVERT: B 195 LYS cc_start: 0.7673 (tptt) cc_final: 0.7023 (tppt) REVERT: B 288 LYS cc_start: 0.7695 (mttm) cc_final: 0.7385 (mtmp) REVERT: B 410 LYS cc_start: 0.7073 (mtpt) cc_final: 0.6516 (pmtt) REVERT: B 420 MET cc_start: 0.4681 (tpp) cc_final: 0.4325 (tpp) REVERT: C 106 LYS cc_start: 0.8500 (ttmm) cc_final: 0.8251 (ttmt) REVERT: C 111 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8236 (tm-30) REVERT: C 195 LYS cc_start: 0.7811 (tptm) cc_final: 0.7316 (tppt) REVERT: C 206 LYS cc_start: 0.7778 (mmmt) cc_final: 0.6809 (tptp) REVERT: C 335 GLU cc_start: 0.7927 (tt0) cc_final: 0.7503 (tt0) REVERT: C 410 LYS cc_start: 0.6958 (mtmt) cc_final: 0.6437 (pmtt) REVERT: D 75 GLU cc_start: 0.6785 (mt-10) cc_final: 0.6528 (tt0) REVERT: D 106 LYS cc_start: 0.8562 (ttmm) cc_final: 0.8321 (ttmt) REVERT: D 170 GLU cc_start: 0.3044 (OUTLIER) cc_final: 0.2715 (tm-30) REVERT: D 195 LYS cc_start: 0.7700 (tptt) cc_final: 0.7083 (tppt) REVERT: D 265 GLN cc_start: 0.8127 (tt0) cc_final: 0.7533 (tp40) REVERT: D 274 ASP cc_start: 0.8399 (t0) cc_final: 0.8156 (t0) REVERT: D 410 LYS cc_start: 0.7239 (mtpt) cc_final: 0.6629 (pmtt) REVERT: E 100 GLN cc_start: 0.8512 (tt0) cc_final: 0.8227 (tt0) REVERT: E 111 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.7977 (tm-30) REVERT: E 195 LYS cc_start: 0.7804 (tptt) cc_final: 0.7097 (tppt) REVERT: E 206 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7466 (tptp) REVERT: E 265 GLN cc_start: 0.8080 (tt0) cc_final: 0.7496 (tp40) REVERT: E 286 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8082 (ttm) REVERT: E 402 PHE cc_start: 0.6075 (m-80) cc_final: 0.5465 (m-80) REVERT: F 58 LYS cc_start: 0.8398 (mttt) cc_final: 0.8032 (mtmp) REVERT: F 195 LYS cc_start: 0.7772 (tptm) cc_final: 0.7142 (tppt) REVERT: F 208 LYS cc_start: 0.7765 (mtpm) cc_final: 0.7318 (mttp) REVERT: F 265 GLN cc_start: 0.8139 (tt0) cc_final: 0.7534 (tp40) REVERT: F 274 ASP cc_start: 0.8319 (t0) cc_final: 0.8044 (t0) REVERT: F 286 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8105 (ttm) REVERT: F 491 GLU cc_start: 0.8446 (tp30) cc_final: 0.8242 (tp30) REVERT: G 48 GLN cc_start: 0.8293 (mt0) cc_final: 0.8072 (mt0) REVERT: G 162 ASP cc_start: 0.7030 (m-30) cc_final: 0.6267 (m-30) REVERT: G 195 LYS cc_start: 0.7637 (tptm) cc_final: 0.7039 (tppt) REVERT: G 206 LYS cc_start: 0.7700 (mmtm) cc_final: 0.7131 (mmmm) REVERT: G 208 LYS cc_start: 0.8271 (mtpp) cc_final: 0.7713 (mttp) REVERT: G 265 GLN cc_start: 0.8048 (tt0) cc_final: 0.7452 (tp40) REVERT: G 286 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8204 (ttm) REVERT: G 288 LYS cc_start: 0.7764 (mttm) cc_final: 0.7414 (mtmp) REVERT: G 335 GLU cc_start: 0.7871 (tt0) cc_final: 0.7437 (tt0) REVERT: G 410 LYS cc_start: 0.7265 (mtpt) cc_final: 0.6591 (pmtt) REVERT: G 412 ARG cc_start: 0.7060 (ptt180) cc_final: 0.6811 (ptt180) REVERT: G 500 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7540 (tt0) REVERT: H 75 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6683 (tt0) REVERT: H 98 GLU cc_start: 0.7788 (mp0) cc_final: 0.7419 (mp0) REVERT: H 114 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.8065 (t80) REVERT: H 195 LYS cc_start: 0.7675 (tptm) cc_final: 0.7015 (tppt) REVERT: H 206 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.6232 (tptp) REVERT: H 265 GLN cc_start: 0.8160 (tt0) cc_final: 0.7844 (tt0) REVERT: H 410 LYS cc_start: 0.7041 (mtmt) cc_final: 0.6589 (pmtt) REVERT: H 510 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7180 (mt-10) outliers start: 124 outliers final: 90 residues processed: 563 average time/residue: 0.5054 time to fit residues: 347.8072 Evaluate side-chains 571 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 468 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 412 ARG Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 369 ASN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 369 ASN Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 474 LYS Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 369 ASN Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 369 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 453 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 323 optimal weight: 0.1980 chunk 128 optimal weight: 0.9980 chunk 282 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 239 optimal weight: 4.9990 chunk 343 optimal weight: 2.9990 chunk 355 optimal weight: 1.9990 chunk 301 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 350 optimal weight: 0.5980 chunk 373 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 GLN ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN B 243 GLN ** B 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 ASN ** E 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN G 100 GLN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.179076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.132614 restraints weight = 33328.514| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.89 r_work: 0.3195 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31600 Z= 0.120 Angle : 0.605 10.997 42904 Z= 0.287 Chirality : 0.043 0.148 4872 Planarity : 0.004 0.056 5336 Dihedral : 15.500 178.464 4560 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.14 % Favored : 96.75 % Rotamer: Outliers : 3.45 % Allowed : 21.05 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.14), residues: 3880 helix: 1.43 (0.14), residues: 1400 sheet: -0.63 (0.21), residues: 512 loop : -0.64 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 224 TYR 0.010 0.001 TYR F 348 PHE 0.009 0.001 PHE D 35 HIS 0.003 0.001 HIS F 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (31592) covalent geometry : angle 0.60526 / 0.29 (42904) hydrogen bonds : bond 0.03301 / 2.24 ( 1206) hydrogen bonds : angle 4.91799 / 3.45 ( 3390) Misc. bond : bond 0.00024 / 0.01 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 477 time to evaluate : 1.168 Fit side-chains REVERT: A 106 LYS cc_start: 0.8620 (ttmm) cc_final: 0.8377 (ttmt) REVERT: A 195 LYS cc_start: 0.7714 (tptt) cc_final: 0.7056 (tppt) REVERT: A 206 LYS cc_start: 0.7696 (tptp) cc_final: 0.7377 (tptp) REVERT: A 265 GLN cc_start: 0.8161 (tt0) cc_final: 0.7604 (tp40) REVERT: A 412 ARG cc_start: 0.6908 (ptt180) cc_final: 0.6679 (ptt90) REVERT: A 500 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7472 (tt0) REVERT: B 106 LYS cc_start: 0.8499 (ttmm) cc_final: 0.8289 (ttmt) REVERT: B 112 GLN cc_start: 0.7507 (pm20) cc_final: 0.7006 (pm20) REVERT: B 179 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7293 (ptp) REVERT: B 195 LYS cc_start: 0.7664 (tptt) cc_final: 0.6999 (tppt) REVERT: B 288 LYS cc_start: 0.7678 (mttm) cc_final: 0.7403 (mtmp) REVERT: B 410 LYS cc_start: 0.7049 (mtpt) cc_final: 0.6475 (pmtt) REVERT: B 420 MET cc_start: 0.4559 (tpp) cc_final: 0.4218 (tpp) REVERT: C 106 LYS cc_start: 0.8519 (ttmm) cc_final: 0.8299 (ttmt) REVERT: C 111 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8427 (tm-30) REVERT: C 195 LYS cc_start: 0.7842 (tptm) cc_final: 0.7367 (tppt) REVERT: C 206 LYS cc_start: 0.7838 (mmmt) cc_final: 0.7321 (tptp) REVERT: C 335 GLU cc_start: 0.7952 (tt0) cc_final: 0.7515 (tt0) REVERT: C 410 LYS cc_start: 0.6994 (mtmt) cc_final: 0.6469 (pmtt) REVERT: D 15 ASP cc_start: 0.7669 (t0) cc_final: 0.7453 (t0) REVERT: D 106 LYS cc_start: 0.8567 (ttmm) cc_final: 0.8322 (ttmt) REVERT: D 170 GLU cc_start: 0.2925 (OUTLIER) cc_final: 0.2587 (tm-30) REVERT: D 195 LYS cc_start: 0.7616 (tptt) cc_final: 0.6973 (tppt) REVERT: D 265 GLN cc_start: 0.8121 (tt0) cc_final: 0.7531 (tp40) REVERT: D 274 ASP cc_start: 0.8382 (t0) cc_final: 0.8160 (t0) REVERT: D 410 LYS cc_start: 0.7259 (mtpt) cc_final: 0.6656 (pmtt) REVERT: E 91 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.8097 (mm) REVERT: E 111 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8082 (tm-30) REVERT: E 195 LYS cc_start: 0.7797 (tptt) cc_final: 0.7092 (tppt) REVERT: E 206 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7535 (tptp) REVERT: E 242 LYS cc_start: 0.7608 (mmtm) cc_final: 0.7020 (mttt) REVERT: E 265 GLN cc_start: 0.8042 (tt0) cc_final: 0.7530 (tp40) REVERT: E 286 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8116 (ttm) REVERT: E 402 PHE cc_start: 0.6081 (m-80) cc_final: 0.5459 (m-80) REVERT: F 195 LYS cc_start: 0.7733 (tptm) cc_final: 0.7124 (tppt) REVERT: F 208 LYS cc_start: 0.7720 (mtpm) cc_final: 0.7334 (mttp) REVERT: F 265 GLN cc_start: 0.8122 (tt0) cc_final: 0.7558 (tp40) REVERT: F 274 ASP cc_start: 0.8345 (t0) cc_final: 0.8112 (t0) REVERT: F 286 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8179 (ttm) REVERT: F 410 LYS cc_start: 0.7299 (mtmt) cc_final: 0.6739 (pmtt) REVERT: F 411 TYR cc_start: 0.7953 (t80) cc_final: 0.7714 (t80) REVERT: G 48 GLN cc_start: 0.8245 (mt0) cc_final: 0.8023 (mt0) REVERT: G 100 GLN cc_start: 0.8528 (tt0) cc_final: 0.8287 (tt0) REVERT: G 195 LYS cc_start: 0.7592 (tptm) cc_final: 0.7009 (tppt) REVERT: G 206 LYS cc_start: 0.7678 (mmtm) cc_final: 0.7152 (mmmm) REVERT: G 208 LYS cc_start: 0.8177 (mtpp) cc_final: 0.7644 (mttp) REVERT: G 265 GLN cc_start: 0.8054 (tt0) cc_final: 0.7440 (tp40) REVERT: G 286 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8299 (ttm) REVERT: G 288 LYS cc_start: 0.7742 (mttm) cc_final: 0.7409 (mtmp) REVERT: G 410 LYS cc_start: 0.7284 (mtpt) cc_final: 0.6565 (pmtt) REVERT: G 412 ARG cc_start: 0.6945 (ptt180) cc_final: 0.6693 (ptt90) REVERT: G 500 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7524 (tt0) REVERT: H 75 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6683 (tt0) REVERT: H 114 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.8038 (t80) REVERT: H 195 LYS cc_start: 0.7664 (tptm) cc_final: 0.7015 (tppt) REVERT: H 206 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.6453 (tptp) REVERT: H 410 LYS cc_start: 0.7072 (mtmt) cc_final: 0.6606 (pmtt) REVERT: H 510 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7186 (mt-10) outliers start: 110 outliers final: 79 residues processed: 550 average time/residue: 0.5354 time to fit residues: 359.4938 Evaluate side-chains 567 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 474 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 369 ASN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 369 ASN Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 474 LYS Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 369 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 474 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 375 optimal weight: 0.5980 chunk 209 optimal weight: 0.2980 chunk 121 optimal weight: 3.9990 chunk 370 optimal weight: 0.8980 chunk 364 optimal weight: 0.0670 chunk 68 optimal weight: 0.0870 chunk 179 optimal weight: 2.9990 chunk 144 optimal weight: 0.0670 chunk 136 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 293 optimal weight: 0.7980 overall best weight: 0.2234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 GLN A 202 GLN ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN ** B 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN E 230 ASN ** E 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.181883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.135949 restraints weight = 33578.953| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.90 r_work: 0.3260 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 31600 Z= 0.094 Angle : 0.576 10.526 42904 Z= 0.270 Chirality : 0.042 0.142 4872 Planarity : 0.004 0.058 5336 Dihedral : 15.033 177.682 4560 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.61 % Favored : 96.26 % Rotamer: Outliers : 2.94 % Allowed : 21.68 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.14), residues: 3880 helix: 1.66 (0.14), residues: 1400 sheet: -0.47 (0.23), residues: 456 loop : -0.53 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 224 TYR 0.009 0.001 TYR H 509 PHE 0.009 0.001 PHE D 35 HIS 0.003 0.001 HIS F 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 (31592) covalent geometry : angle 0.57632 / 0.27 (42904) hydrogen bonds : bond 0.02745 / 1.87 ( 1206) hydrogen bonds : angle 4.72008 / 3.30 ( 3390) Misc. bond : bond 0.00007 / 0.00 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10050.48 seconds wall clock time: 172 minutes 12.04 seconds (10332.04 seconds total)