Starting phenix.real_space_refine on Thu May 29 01:37:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g9b_29863/05_2025/8g9b_29863.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g9b_29863/05_2025/8g9b_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8g9b_29863/05_2025/8g9b_29863.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g9b_29863/05_2025/8g9b_29863.map" model { file = "/net/cci-nas-00/data/ceres_data/8g9b_29863/05_2025/8g9b_29863.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g9b_29863/05_2025/8g9b_29863.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.242 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 18.93, per 1000 atoms: 0.61 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: 8.60 Conformation dependent library (CDL) restraints added in 4.2 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: 4.34 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: 12.08 Time building geometry restraints manager: 9.89 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: 18532 35.67 - 71.34: 735 71.34 - 107.01: 72 107.01 - 142.67: 37 142.67 - 178.34: 24 Dihedral angle restraints: 19400 sinusoidal: 8280 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 19397 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: 0.04 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: 4.780 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: 0.030 Extract box with map and model: 1.390 Check model and map are aligned: 0.260 Set scattering table: 0.310 Process input model: 72.000 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.160 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:11.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 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 : 20.265 178.344 12296 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 10.81 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (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 HIS 0.007 0.001 HIS B 171 PHE 0.016 0.001 PHE D 401 TYR 0.016 0.001 TYR H 233 ARG 0.014 0.001 ARG H 105 Details of bonding type rmsd hydrogen bonds : bond 0.13772 ( 1206) hydrogen bonds : angle 6.36927 ( 3390) covalent geometry : bond 0.00746 (31592) covalent geometry : angle 1.09275 (42904) Misc. bond : bond 0.09038 ( 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 : 3.414 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: A 420 MET cc_start: 0.4224 (tpp) cc_final: 0.4016 (tpp) 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: 0.7189 (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: 0.7499 (mtmp) REVERT: B 410 LYS cc_start: 0.6832 (mtpt) cc_final: 0.6560 (pmtt) REVERT: C 75 GLU cc_start: 0.6974 (tt0) cc_final: 0.6760 (tt0) REVERT: C 206 LYS cc_start: 0.7286 (mmmt) cc_final: 0.6657 (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: 0.7609 (tt0) REVERT: D 195 LYS cc_start: 0.7783 (tptt) cc_final: 0.7187 (tppt) REVERT: D 265 GLN cc_start: 0.7963 (tt0) cc_final: 0.7669 (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: 0.6596 (pmtt) REVERT: D 483 MET cc_start: 0.9582 (tmm) cc_final: 0.9332 (tmm) REVERT: D 500 GLU cc_start: 0.8138 (tt0) cc_final: 0.7709 (tt0) REVERT: E 195 LYS cc_start: 0.7896 (tptt) cc_final: 0.7190 (tppt) REVERT: E 265 GLN cc_start: 0.7984 (tt0) cc_final: 0.7615 (mp10) REVERT: F 18 LEU cc_start: 0.9264 (mt) cc_final: 0.8982 (mp) REVERT: F 195 LYS cc_start: 0.7930 (tptm) cc_final: 0.7405 (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: 0.8074 (mt0) REVERT: G 208 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8198 (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: 0.7171 (tppt) REVERT: H 261 ASP cc_start: 0.7717 (m-30) cc_final: 0.7484 (m-30) REVERT: H 412 ARG cc_start: 0.7115 (ptt180) cc_final: 0.6878 (ptt90) REVERT: H 420 MET cc_start: 0.4589 (tpp) cc_final: 0.4002 (ptp) outliers start: 19 outliers final: 8 residues processed: 537 average time/residue: 1.2134 time to fit residues: 787.3481 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 : 3.613 ------------------------------------------------------------------------------- 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 324 optimal weight: 0.9990 chunk 291 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 300 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 183 optimal weight: 0.6980 chunk 224 optimal weight: 0.9990 chunk 348 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 GLN ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS 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** 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 = 0.3909 r_free = 0.3909 target = 0.176031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.129220 restraints weight = 33429.276| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.85 r_work: 0.3219 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 31600 Z= 0.146 Angle : 0.666 11.441 42904 Z= 0.321 Chirality : 0.045 0.182 4872 Planarity : 0.005 0.066 5336 Dihedral : 19.595 179.867 5237 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.71 % Favored : 96.19 % Rotamer: Outliers : 3.32 % Allowed : 14.72 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.13), residues: 3880 helix: 1.33 (0.14), residues: 1384 sheet: -0.62 (0.20), residues: 520 loop : -0.68 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 454 PHE 0.008 0.001 PHE B 35 TYR 0.013 0.001 TYR C 509 ARG 0.007 0.000 ARG B 231 Details of bonding type rmsd hydrogen bonds : bond 0.04012 ( 1206) hydrogen bonds : angle 5.44222 ( 3390) covalent geometry : bond 0.00331 (31592) covalent geometry : angle 0.66613 (42904) Misc. bond : bond 0.00067 ( 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 605 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 499 time to evaluate : 3.503 Fit side-chains REVERT: A 195 LYS cc_start: 0.7495 (tptt) cc_final: 0.6723 (tppt) REVERT: A 206 LYS cc_start: 0.7335 (tptp) cc_final: 0.6963 (tptp) REVERT: A 230 ASN cc_start: 0.7878 (t0) cc_final: 0.7648 (t0) REVERT: A 261 ASP cc_start: 0.7760 (m-30) cc_final: 0.7524 (m-30) REVERT: A 412 ARG cc_start: 0.6947 (ptt180) cc_final: 0.6527 (ptt90) REVERT: B 105 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6621 (ttp-110) REVERT: B 111 GLU cc_start: 0.8425 (tt0) cc_final: 0.8151 (tm-30) REVERT: B 112 GLN cc_start: 0.7703 (pt0) cc_final: 0.7494 (pt0) REVERT: B 195 LYS cc_start: 0.7641 (tptt) cc_final: 0.6919 (tppt) REVERT: B 288 LYS cc_start: 0.7633 (mttm) cc_final: 0.7320 (mtmp) REVERT: B 410 LYS cc_start: 0.6927 (mtpt) cc_final: 0.6440 (pmtt) REVERT: C 75 GLU cc_start: 0.7034 (tt0) cc_final: 0.6762 (tt0) REVERT: C 230 ASN cc_start: 0.7788 (t0) cc_final: 0.7432 (t160) REVERT: C 335 GLU cc_start: 0.7851 (tt0) cc_final: 0.7485 (tt0) REVERT: C 410 LYS cc_start: 0.6825 (mtmt) cc_final: 0.6359 (pmtt) REVERT: D 195 LYS cc_start: 0.7638 (tptt) cc_final: 0.7002 (tppt) REVERT: D 206 LYS cc_start: 0.7029 (mmtt) cc_final: 0.6660 (mmmt) REVERT: D 265 GLN cc_start: 0.8152 (tt0) cc_final: 0.7544 (tp40) REVERT: D 335 GLU cc_start: 0.7936 (tt0) cc_final: 0.7543 (tt0) REVERT: D 410 LYS cc_start: 0.7129 (mtpt) cc_final: 0.6436 (pmtt) REVERT: E 75 GLU cc_start: 0.6866 (tt0) cc_final: 0.6665 (tt0) REVERT: E 111 GLU cc_start: 0.8381 (tt0) cc_final: 0.7739 (tm-30) REVERT: E 179 MET cc_start: 0.7571 (ptp) cc_final: 0.6935 (ptp) REVERT: E 195 LYS cc_start: 0.7562 (tptt) cc_final: 0.6843 (tppt) REVERT: E 261 ASP cc_start: 0.7858 (m-30) cc_final: 0.7637 (m-30) REVERT: E 265 GLN cc_start: 0.8198 (tt0) cc_final: 0.7550 (tp40) REVERT: E 286 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8128 (ttm) REVERT: E 368 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.7780 (mt0) REVERT: F 195 LYS cc_start: 0.7715 (tptm) cc_final: 0.7095 (tppt) REVERT: F 208 LYS cc_start: 0.7591 (mtpm) cc_final: 0.7023 (mttp) REVERT: F 265 GLN cc_start: 0.8166 (tt0) cc_final: 0.7859 (tt0) REVERT: F 286 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8135 (ttm) REVERT: F 491 GLU cc_start: 0.8569 (tp30) cc_final: 0.8308 (tp30) REVERT: G 48 GLN cc_start: 0.8143 (mt0) cc_final: 0.7859 (mt0) REVERT: G 75 GLU cc_start: 0.7011 (tt0) cc_final: 0.6807 (tt0) REVERT: G 114 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7957 (t80) REVERT: G 206 LYS cc_start: 0.7280 (OUTLIER) cc_final: 0.6607 (mmtt) REVERT: G 208 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7838 (mttp) REVERT: G 254 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7760 (tp30) REVERT: G 265 GLN cc_start: 0.8056 (tt0) cc_final: 0.7463 (tp40) REVERT: G 286 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8239 (ttm) REVERT: G 335 GLU cc_start: 0.7897 (tt0) cc_final: 0.7477 (tt0) REVERT: H 75 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6534 (tt0) REVERT: H 105 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.6598 (ttp-110) REVERT: H 111 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8497 (tt0) REVERT: H 114 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7840 (t80) REVERT: H 195 LYS cc_start: 0.7627 (tptm) cc_final: 0.6882 (tppt) REVERT: H 206 LYS cc_start: 0.7706 (mmtt) cc_final: 0.7411 (tptm) REVERT: H 261 ASP cc_start: 0.7682 (m-30) cc_final: 0.7433 (m-30) REVERT: H 286 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8002 (ttm) REVERT: H 325 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8968 (tpp) REVERT: H 352 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8687 (tm-30) REVERT: H 412 ARG cc_start: 0.7078 (ptt180) cc_final: 0.6730 (ptt90) REVERT: H 420 MET cc_start: 0.4997 (tpp) cc_final: 0.4772 (tmm) outliers start: 106 outliers final: 37 residues processed: 556 average time/residue: 1.1945 time to fit residues: 806.4484 Evaluate side-chains 523 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 472 time to evaluate : 3.190 ------------------------------------------------------------------------------- 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 369 ASN Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 474 LYS 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 437 ILE 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 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 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 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 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 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 286 MET Chi-restraints excluded: chain H residue 325 MET 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 24 optimal weight: 0.0770 chunk 147 optimal weight: 1.9990 chunk 334 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 320 optimal weight: 1.9990 chunk 283 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 299 optimal weight: 5.9990 chunk 380 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** 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 Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.175136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.131107 restraints weight = 33897.005| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.88 r_work: 0.3253 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31600 Z= 0.123 Angle : 0.616 13.701 42904 Z= 0.294 Chirality : 0.044 0.167 4872 Planarity : 0.004 0.061 5336 Dihedral : 18.651 178.023 5216 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.43 % Favored : 96.47 % Rotamer: Outliers : 3.70 % Allowed : 15.57 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.13), residues: 3880 helix: 1.44 (0.14), residues: 1384 sheet: -0.68 (0.23), residues: 424 loop : -0.59 (0.14), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 454 PHE 0.008 0.001 PHE D 35 TYR 0.011 0.001 TYR C 509 ARG 0.007 0.000 ARG C 161 Details of bonding type rmsd hydrogen bonds : bond 0.03551 ( 1206) hydrogen bonds : angle 5.17241 ( 3390) covalent geometry : bond 0.00276 (31592) covalent geometry : angle 0.61621 (42904) Misc. bond : bond 0.00027 ( 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 611 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 493 time to evaluate : 3.159 Fit side-chains revert: symmetry clash REVERT: A 195 LYS cc_start: 0.7569 (tptt) cc_final: 0.6830 (tppt) REVERT: A 206 LYS cc_start: 0.7615 (tptp) cc_final: 0.7209 (tptp) REVERT: A 274 ASP cc_start: 0.8488 (t0) cc_final: 0.8259 (t0) REVERT: A 385 MET cc_start: 0.8762 (ttm) cc_final: 0.8507 (ttm) REVERT: A 412 ARG cc_start: 0.6970 (ptt180) cc_final: 0.6762 (ptt90) REVERT: A 500 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7557 (tt0) REVERT: B 112 GLN cc_start: 0.7662 (pt0) cc_final: 0.7425 (pt0) REVERT: B 195 LYS cc_start: 0.7853 (tptt) cc_final: 0.7146 (tppt) REVERT: B 286 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8155 (ttm) REVERT: B 288 LYS cc_start: 0.7704 (mttm) cc_final: 0.7438 (mtmp) REVERT: B 410 LYS cc_start: 0.6987 (mtpt) cc_final: 0.6548 (pmtt) REVERT: C 75 GLU cc_start: 0.6963 (tt0) cc_final: 0.6730 (tt0) REVERT: C 111 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7812 (tm-30) REVERT: C 168 GLU cc_start: 0.4563 (OUTLIER) cc_final: 0.4271 (pp20) REVERT: C 206 LYS cc_start: 0.7653 (mmpt) cc_final: 0.7079 (tptt) REVERT: C 230 ASN cc_start: 0.7964 (t0) cc_final: 0.7635 (t160) REVERT: C 335 GLU cc_start: 0.7907 (tt0) cc_final: 0.7553 (tt0) REVERT: C 410 LYS cc_start: 0.6879 (mtmt) cc_final: 0.6434 (pmtt) REVERT: D 195 LYS cc_start: 0.7712 (tptt) cc_final: 0.7090 (tppt) REVERT: D 265 GLN cc_start: 0.8082 (tt0) cc_final: 0.7578 (tp40) REVERT: D 274 ASP cc_start: 0.8378 (t0) cc_final: 0.8175 (t0) REVERT: D 286 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8346 (ttm) REVERT: D 410 LYS cc_start: 0.7187 (mtpt) cc_final: 0.6660 (pmtt) REVERT: E 179 MET cc_start: 0.7564 (ptp) cc_final: 0.6958 (ptp) REVERT: E 195 LYS cc_start: 0.7696 (tptt) cc_final: 0.6991 (tppt) REVERT: E 265 GLN cc_start: 0.8106 (tt0) cc_final: 0.7552 (tp40) REVERT: E 286 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8191 (ttm) REVERT: F 195 LYS cc_start: 0.7872 (tptm) cc_final: 0.7246 (tppt) REVERT: F 208 LYS cc_start: 0.7690 (mtpm) cc_final: 0.7197 (mttp) REVERT: F 265 GLN cc_start: 0.8133 (tt0) cc_final: 0.7533 (tp40) REVERT: F 491 GLU cc_start: 0.8477 (tp30) cc_final: 0.8231 (tp30) REVERT: G 75 GLU cc_start: 0.7073 (tt0) cc_final: 0.6784 (tt0) REVERT: G 114 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.8053 (t80) REVERT: G 206 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.6925 (mmmm) REVERT: G 241 LYS cc_start: 0.7684 (ptmt) cc_final: 0.7447 (ptpp) REVERT: G 265 GLN cc_start: 0.8054 (tt0) cc_final: 0.7536 (tp40) REVERT: G 286 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8297 (ttm) REVERT: G 288 LYS cc_start: 0.7760 (mttm) cc_final: 0.7433 (mtmp) REVERT: G 335 GLU cc_start: 0.7885 (tt0) cc_final: 0.7507 (tt0) REVERT: H 75 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6603 (tt0) REVERT: H 114 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.7927 (t80) REVERT: H 195 LYS cc_start: 0.7751 (tptm) cc_final: 0.7096 (tppt) REVERT: H 261 ASP cc_start: 0.7662 (m-30) cc_final: 0.7426 (m-30) REVERT: H 325 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8977 (tpp) REVERT: H 335 GLU cc_start: 0.7939 (tt0) cc_final: 0.7485 (tt0) REVERT: H 352 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8626 (tm-30) REVERT: H 410 LYS cc_start: 0.6924 (mtmt) cc_final: 0.6533 (pmtt) REVERT: H 412 ARG cc_start: 0.7014 (ptt180) cc_final: 0.6799 (ptt90) REVERT: H 510 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7042 (mt-10) outliers start: 118 outliers final: 58 residues processed: 567 average time/residue: 1.1129 time to fit residues: 771.4964 Evaluate side-chains 537 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 467 time to evaluate : 3.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 318 VAL 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 270 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 474 LYS 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 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 270 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 369 ASN 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 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 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 114 PHE 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 443 VAL Chi-restraints excluded: chain G residue 47 ASP 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 379 optimal weight: 0.8980 chunk 296 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 chunk 210 optimal weight: 9.9990 chunk 321 optimal weight: 1.9990 chunk 248 optimal weight: 0.0270 chunk 338 optimal weight: 0.9980 chunk 185 optimal weight: 9.9990 chunk 217 optimal weight: 1.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 202 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN E 230 ASN E 303 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 Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.174059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.128332 restraints weight = 33893.996| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.77 r_work: 0.3208 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31600 Z= 0.140 Angle : 0.618 11.540 42904 Z= 0.293 Chirality : 0.044 0.163 4872 Planarity : 0.004 0.058 5336 Dihedral : 17.945 179.931 5212 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.79 % Favored : 96.11 % Rotamer: Outliers : 4.17 % Allowed : 16.17 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.13), residues: 3880 helix: 1.40 (0.14), residues: 1400 sheet: -0.46 (0.23), residues: 472 loop : -0.63 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 454 PHE 0.009 0.001 PHE G 24 TYR 0.012 0.001 TYR C 509 ARG 0.003 0.000 ARG E 412 Details of bonding type rmsd hydrogen bonds : bond 0.03558 ( 1206) hydrogen bonds : angle 5.05048 ( 3390) covalent geometry : bond 0.00322 (31592) covalent geometry : angle 0.61770 (42904) Misc. bond : bond 0.00031 ( 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 612 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 479 time to evaluate : 3.448 Fit side-chains revert: symmetry clash REVERT: A 195 LYS cc_start: 0.7533 (tptt) cc_final: 0.6784 (tppt) REVERT: A 206 LYS cc_start: 0.7517 (tptp) cc_final: 0.7030 (tptp) REVERT: A 274 ASP cc_start: 0.8488 (t0) cc_final: 0.8191 (t0) REVERT: A 325 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8974 (tpp) REVERT: A 412 ARG cc_start: 0.6992 (ptt180) cc_final: 0.6740 (ptt90) REVERT: A 500 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7377 (tt0) REVERT: B 106 LYS cc_start: 0.8502 (ttmm) cc_final: 0.8240 (ttmt) REVERT: B 112 GLN cc_start: 0.7652 (pt0) cc_final: 0.7432 (pt0) REVERT: B 195 LYS cc_start: 0.7744 (tptt) cc_final: 0.7085 (tppt) REVERT: B 286 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8128 (ttm) REVERT: B 288 LYS cc_start: 0.7634 (mttm) cc_final: 0.7292 (mtmp) REVERT: B 410 LYS cc_start: 0.6935 (mtpt) cc_final: 0.6504 (pmtt) REVERT: C 75 GLU cc_start: 0.6965 (tt0) cc_final: 0.6666 (tt0) REVERT: C 111 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8002 (tm-30) REVERT: C 206 LYS cc_start: 0.7691 (mmpt) cc_final: 0.7055 (tptt) REVERT: C 230 ASN cc_start: 0.7959 (t0) cc_final: 0.7724 (t160) REVERT: C 335 GLU cc_start: 0.7900 (tt0) cc_final: 0.7461 (tt0) REVERT: C 410 LYS cc_start: 0.6892 (mtmt) cc_final: 0.6400 (pmtt) REVERT: D 195 LYS cc_start: 0.7670 (tptt) cc_final: 0.7061 (tppt) REVERT: D 231 ARG cc_start: 0.7023 (OUTLIER) cc_final: 0.6807 (ppt90) REVERT: D 265 GLN cc_start: 0.8056 (tt0) cc_final: 0.7482 (tp40) REVERT: D 274 ASP cc_start: 0.8419 (t0) cc_final: 0.8154 (t0) REVERT: D 286 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8299 (ttm) REVERT: D 335 GLU cc_start: 0.7961 (tt0) cc_final: 0.7494 (tt0) REVERT: D 410 LYS cc_start: 0.7165 (mtpt) cc_final: 0.6614 (pmtt) REVERT: E 179 MET cc_start: 0.7622 (ptp) cc_final: 0.7082 (ptp) REVERT: E 195 LYS cc_start: 0.7677 (tptt) cc_final: 0.6959 (tppt) REVERT: E 265 GLN cc_start: 0.8140 (tt0) cc_final: 0.7547 (tp40) REVERT: E 286 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8150 (ttm) REVERT: F 195 LYS cc_start: 0.7769 (tptm) cc_final: 0.7129 (tppt) REVERT: F 208 LYS cc_start: 0.7678 (mtpm) cc_final: 0.7238 (mttp) REVERT: F 265 GLN cc_start: 0.8122 (tt0) cc_final: 0.7500 (tp40) REVERT: F 491 GLU cc_start: 0.8496 (tp30) cc_final: 0.8235 (tp30) REVERT: G 75 GLU cc_start: 0.7028 (tt0) cc_final: 0.6816 (tt0) REVERT: G 114 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.8023 (t80) REVERT: G 195 LYS cc_start: 0.7653 (tptm) cc_final: 0.7070 (tppt) REVERT: G 206 LYS cc_start: 0.7582 (mmtm) cc_final: 0.6954 (mmmm) REVERT: G 208 LYS cc_start: 0.8177 (mtpm) cc_final: 0.7627 (mtmt) REVERT: G 265 GLN cc_start: 0.8066 (tt0) cc_final: 0.7503 (tp40) REVERT: G 286 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8226 (ttm) REVERT: G 288 LYS cc_start: 0.7715 (mttm) cc_final: 0.7362 (mtmp) REVERT: G 335 GLU cc_start: 0.7891 (tt0) cc_final: 0.7549 (tt0) REVERT: G 410 LYS cc_start: 0.7315 (mtpt) cc_final: 0.6530 (pmtt) REVERT: G 412 ARG cc_start: 0.7015 (ptt180) cc_final: 0.6801 (ptt90) REVERT: G 500 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7589 (pt0) REVERT: H 75 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6570 (tt0) REVERT: H 114 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7990 (t80) REVERT: H 195 LYS cc_start: 0.7702 (tptm) cc_final: 0.7016 (tppt) REVERT: H 261 ASP cc_start: 0.7519 (m-30) cc_final: 0.7285 (m-30) REVERT: H 325 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8981 (tpp) REVERT: H 335 GLU cc_start: 0.7923 (tt0) cc_final: 0.7446 (tt0) REVERT: H 410 LYS cc_start: 0.6908 (mtmt) cc_final: 0.6476 (pmtt) REVERT: H 510 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7020 (mt-10) outliers start: 133 outliers final: 72 residues processed: 563 average time/residue: 1.1281 time to fit residues: 782.1806 Evaluate side-chains 548 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 463 time to evaluate : 3.361 ------------------------------------------------------------------------------- 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 325 MET Chi-restraints excluded: chain A residue 327 SER 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 60 THR 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 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 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 C residue 474 LYS Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 231 ARG 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 15 ASP 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 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 449 ASP Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 159 SER 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 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 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 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 187 VAL Chi-restraints excluded: chain H residue 241 LYS 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 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 278 optimal weight: 3.9990 chunk 233 optimal weight: 5.9990 chunk 319 optimal weight: 4.9990 chunk 297 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 324 optimal weight: 1.9990 chunk 185 optimal weight: 6.9990 chunk 293 optimal weight: 0.7980 chunk 191 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 202 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 Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.173711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.128197 restraints weight = 33651.276| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.75 r_work: 0.3203 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 31600 Z= 0.153 Angle : 0.624 12.220 42904 Z= 0.297 Chirality : 0.044 0.171 4872 Planarity : 0.004 0.056 5336 Dihedral : 17.412 179.733 5208 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.61 % Favored : 96.29 % Rotamer: Outliers : 4.45 % Allowed : 17.01 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.13), residues: 3880 helix: 1.37 (0.14), residues: 1400 sheet: -0.55 (0.24), residues: 432 loop : -0.63 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 454 PHE 0.009 0.001 PHE G 24 TYR 0.011 0.001 TYR H 348 ARG 0.003 0.000 ARG D 412 Details of bonding type rmsd hydrogen bonds : bond 0.03663 ( 1206) hydrogen bonds : angle 5.03640 ( 3390) covalent geometry : bond 0.00357 (31592) covalent geometry : angle 0.62368 (42904) Misc. bond : bond 0.00044 ( 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 617 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 475 time to evaluate : 3.178 Fit side-chains revert: symmetry clash REVERT: A 195 LYS cc_start: 0.7558 (tptt) cc_final: 0.6846 (tppt) REVERT: A 206 LYS cc_start: 0.7493 (tptp) cc_final: 0.6909 (tptp) REVERT: A 265 GLN cc_start: 0.8122 (tt0) cc_final: 0.7537 (tp40) REVERT: A 274 ASP cc_start: 0.8478 (t0) cc_final: 0.8257 (t0) REVERT: A 412 ARG cc_start: 0.7010 (ptt180) cc_final: 0.6729 (ptt90) REVERT: A 500 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7417 (tt0) REVERT: B 106 LYS cc_start: 0.8477 (ttmm) cc_final: 0.8224 (ttmt) REVERT: B 111 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.7928 (tm-30) REVERT: B 112 GLN cc_start: 0.7731 (pt0) cc_final: 0.7467 (pt0) REVERT: B 195 LYS cc_start: 0.7708 (tptt) cc_final: 0.7058 (tppt) REVERT: B 286 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8153 (ttm) REVERT: B 288 LYS cc_start: 0.7674 (mttm) cc_final: 0.7336 (mtmp) REVERT: B 410 LYS cc_start: 0.6976 (mtpt) cc_final: 0.6516 (pmtt) REVERT: B 420 MET cc_start: 0.5059 (tpp) cc_final: 0.4578 (tpp) REVERT: C 111 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.7965 (tm-30) REVERT: C 206 LYS cc_start: 0.7738 (mmpt) cc_final: 0.6721 (tptp) REVERT: C 335 GLU cc_start: 0.7913 (tt0) cc_final: 0.7490 (tt0) REVERT: C 410 LYS cc_start: 0.6921 (mtmt) cc_final: 0.6412 (pmtt) REVERT: C 510 GLU cc_start: 0.7635 (tt0) cc_final: 0.7152 (mt-10) REVERT: D 195 LYS cc_start: 0.7667 (tptt) cc_final: 0.7063 (tppt) REVERT: D 231 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.6827 (ppt90) REVERT: D 265 GLN cc_start: 0.8040 (tt0) cc_final: 0.7465 (tp40) REVERT: D 274 ASP cc_start: 0.8428 (t0) cc_final: 0.8144 (t0) REVERT: D 335 GLU cc_start: 0.7975 (tt0) cc_final: 0.7517 (tt0) REVERT: D 410 LYS cc_start: 0.7174 (mtpt) cc_final: 0.6603 (pmtt) REVERT: D 412 ARG cc_start: 0.6861 (ptt90) cc_final: 0.6639 (ptt90) REVERT: E 195 LYS cc_start: 0.7677 (tptt) cc_final: 0.6954 (tppt) REVERT: E 242 LYS cc_start: 0.7588 (mmtm) cc_final: 0.7068 (mttt) REVERT: E 265 GLN cc_start: 0.8107 (tt0) cc_final: 0.7520 (tp40) REVERT: E 286 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8144 (ttm) REVERT: F 195 LYS cc_start: 0.7768 (tptm) cc_final: 0.7166 (tppt) REVERT: F 208 LYS cc_start: 0.7696 (mtpm) cc_final: 0.7224 (mttp) REVERT: F 265 GLN cc_start: 0.8133 (tt0) cc_final: 0.7545 (tp40) REVERT: F 286 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8114 (ttm) REVERT: F 325 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.9018 (tpp) REVERT: F 491 GLU cc_start: 0.8466 (tp30) cc_final: 0.8263 (tp30) REVERT: G 48 GLN cc_start: 0.8258 (mt0) cc_final: 0.8044 (mt0) REVERT: G 114 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.8028 (t80) REVERT: G 195 LYS cc_start: 0.7677 (tptm) cc_final: 0.7083 (tppt) REVERT: G 206 LYS cc_start: 0.7655 (mmtm) cc_final: 0.6995 (mmmm) REVERT: G 208 LYS cc_start: 0.8167 (mtpm) cc_final: 0.7621 (mtmt) REVERT: G 265 GLN cc_start: 0.8059 (tt0) cc_final: 0.7498 (tp40) REVERT: G 286 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8254 (ttm) REVERT: G 288 LYS cc_start: 0.7746 (mttm) cc_final: 0.7395 (mtmp) REVERT: G 335 GLU cc_start: 0.7887 (tt0) cc_final: 0.7494 (tt0) REVERT: G 410 LYS cc_start: 0.7323 (mtpt) cc_final: 0.6546 (pmtt) REVERT: G 412 ARG cc_start: 0.6986 (ptt180) cc_final: 0.6769 (ptt90) REVERT: G 500 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7419 (pt0) REVERT: H 75 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6654 (tt0) REVERT: H 114 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.8017 (t80) REVERT: H 195 LYS cc_start: 0.7723 (tptm) cc_final: 0.7028 (tppt) REVERT: H 261 ASP cc_start: 0.7559 (m-30) cc_final: 0.7344 (m-30) REVERT: H 325 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8976 (tpp) REVERT: H 335 GLU cc_start: 0.7900 (tt0) cc_final: 0.7451 (tt0) REVERT: H 410 LYS cc_start: 0.6943 (mtmt) cc_final: 0.6488 (pmtt) REVERT: H 510 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7038 (mt-10) outliers start: 142 outliers final: 78 residues processed: 571 average time/residue: 1.1421 time to fit residues: 794.5513 Evaluate side-chains 553 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 461 time to evaluate : 3.336 ------------------------------------------------------------------------------- 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 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 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 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 270 VAL 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 D residue 159 SER Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 369 ASN Chi-restraints excluded: chain D residue 383 THR 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 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 449 ASP 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 185 LEU 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 325 MET Chi-restraints excluded: chain F residue 331 CYS 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 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 185 LEU Chi-restraints excluded: chain H residue 187 VAL 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 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 64 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 302 optimal weight: 8.9990 chunk 164 optimal weight: 0.9990 chunk 189 optimal weight: 0.7980 chunk 310 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** 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 171 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.172183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.126591 restraints weight = 33855.956| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.76 r_work: 0.3178 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31600 Z= 0.180 Angle : 0.638 12.145 42904 Z= 0.307 Chirality : 0.045 0.159 4872 Planarity : 0.004 0.058 5336 Dihedral : 17.055 179.435 5208 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.07 % Favored : 95.82 % Rotamer: Outliers : 4.64 % Allowed : 17.76 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.13), residues: 3880 helix: 1.28 (0.14), residues: 1400 sheet: -0.50 (0.22), residues: 512 loop : -0.70 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 171 PHE 0.009 0.001 PHE G 24 TYR 0.012 0.001 TYR G 348 ARG 0.003 0.000 ARG H 412 Details of bonding type rmsd hydrogen bonds : bond 0.03898 ( 1206) hydrogen bonds : angle 5.06332 ( 3390) covalent geometry : bond 0.00426 (31592) covalent geometry : angle 0.63815 (42904) Misc. bond : bond 0.00055 ( 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 637 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 489 time to evaluate : 3.210 Fit side-chains REVERT: A 195 LYS cc_start: 0.7591 (tptt) cc_final: 0.6888 (tppt) REVERT: A 206 LYS cc_start: 0.7490 (tptp) cc_final: 0.6915 (tptp) REVERT: A 265 GLN cc_start: 0.8096 (tt0) cc_final: 0.7489 (tp40) REVERT: A 274 ASP cc_start: 0.8491 (t0) cc_final: 0.8265 (t0) REVERT: A 412 ARG cc_start: 0.7088 (ptt180) cc_final: 0.6772 (ptt90) REVERT: A 500 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7450 (tt0) REVERT: B 106 LYS cc_start: 0.8468 (ttmm) cc_final: 0.8241 (ttmt) REVERT: B 150 MET cc_start: 0.7698 (mmm) cc_final: 0.7473 (tpt) REVERT: B 195 LYS cc_start: 0.7710 (tptt) cc_final: 0.7069 (tppt) REVERT: B 224 ARG cc_start: 0.8052 (ttt90) cc_final: 0.7456 (ttt90) REVERT: B 286 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8060 (ttm) REVERT: B 288 LYS cc_start: 0.7699 (mttm) cc_final: 0.7360 (mtmp) REVERT: B 410 LYS cc_start: 0.7067 (mtpt) cc_final: 0.6530 (pmtt) REVERT: B 420 MET cc_start: 0.5029 (tpp) cc_final: 0.4565 (tpp) REVERT: C 111 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8243 (tm-30) REVERT: C 168 GLU cc_start: 0.4642 (OUTLIER) cc_final: 0.4403 (pp20) REVERT: C 206 LYS cc_start: 0.7868 (mmpt) cc_final: 0.6725 (tptp) REVERT: C 286 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8276 (ttm) REVERT: C 335 GLU cc_start: 0.7942 (tt0) cc_final: 0.7521 (tt0) REVERT: C 410 LYS cc_start: 0.6943 (mtmt) cc_final: 0.6408 (pmtt) REVERT: C 412 ARG cc_start: 0.6427 (OUTLIER) cc_final: 0.6157 (ptt180) REVERT: D 195 LYS cc_start: 0.7696 (tptt) cc_final: 0.7081 (tppt) REVERT: D 231 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.6871 (ppt90) REVERT: D 265 GLN cc_start: 0.8082 (tt0) cc_final: 0.7487 (tp40) REVERT: D 274 ASP cc_start: 0.8412 (t0) cc_final: 0.8100 (t0) REVERT: D 286 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8284 (ttm) REVERT: D 335 GLU cc_start: 0.7938 (tt0) cc_final: 0.7469 (tt0) REVERT: D 410 LYS cc_start: 0.7188 (mtpt) cc_final: 0.6610 (pmtt) REVERT: E 195 LYS cc_start: 0.7703 (tptt) cc_final: 0.6981 (tppt) REVERT: E 242 LYS cc_start: 0.7628 (mmtm) cc_final: 0.7104 (mttt) REVERT: E 265 GLN cc_start: 0.8078 (tt0) cc_final: 0.7467 (tp40) REVERT: E 286 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8125 (ttm) REVERT: E 402 PHE cc_start: 0.6040 (m-80) cc_final: 0.5479 (m-80) REVERT: E 500 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7705 (tt0) REVERT: F 58 LYS cc_start: 0.8385 (mttt) cc_final: 0.8015 (mtmp) REVERT: F 195 LYS cc_start: 0.7790 (tptm) cc_final: 0.7192 (tppt) REVERT: F 208 LYS cc_start: 0.7728 (mtpm) cc_final: 0.7265 (mttp) REVERT: F 265 GLN cc_start: 0.8090 (tt0) cc_final: 0.7492 (tp40) REVERT: F 286 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8136 (ttm) REVERT: F 325 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.9011 (tpp) REVERT: F 412 ARG cc_start: 0.6644 (ptt90) cc_final: 0.6430 (ptt90) REVERT: G 48 GLN cc_start: 0.8272 (mt0) cc_final: 0.8060 (mt0) REVERT: G 114 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.8025 (t80) REVERT: G 162 ASP cc_start: 0.7103 (m-30) cc_final: 0.6430 (m-30) REVERT: G 195 LYS cc_start: 0.7688 (tptm) cc_final: 0.7090 (tppt) REVERT: G 206 LYS cc_start: 0.7721 (mmtm) cc_final: 0.7073 (mmmm) REVERT: G 208 LYS cc_start: 0.8196 (mtpm) cc_final: 0.7739 (mttp) REVERT: G 265 GLN cc_start: 0.8069 (tt0) cc_final: 0.7472 (tp40) REVERT: G 286 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8254 (ttm) REVERT: G 288 LYS cc_start: 0.7760 (mttm) cc_final: 0.7401 (mtmp) REVERT: G 410 LYS cc_start: 0.7296 (mtpt) cc_final: 0.6527 (pmtt) REVERT: G 500 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7422 (pt0) REVERT: H 75 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6669 (tt0) REVERT: H 114 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.8019 (t80) REVERT: H 195 LYS cc_start: 0.7742 (tptm) cc_final: 0.7056 (tppt) REVERT: H 206 LYS cc_start: 0.7701 (mmtt) cc_final: 0.7437 (tptp) REVERT: H 261 ASP cc_start: 0.7554 (m-30) cc_final: 0.7347 (m-30) REVERT: H 325 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8983 (tpp) REVERT: H 410 LYS cc_start: 0.6976 (mtmt) cc_final: 0.6519 (pmtt) outliers start: 148 outliers final: 85 residues processed: 588 average time/residue: 1.1301 time to fit residues: 818.2977 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 : 3.116 ------------------------------------------------------------------------------- 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 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 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 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 168 GLU 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 364 ASP Chi-restraints excluded: chain C residue 369 ASN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 412 ARG Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 231 ARG 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 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 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 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 185 LEU 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 325 MET Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 386 MET 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 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 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 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 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 104 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 357 optimal weight: 1.9990 chunk 293 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 245 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 chunk 282 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN 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 Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.174545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.128675 restraints weight = 33568.127| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.82 r_work: 0.3175 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 31600 Z= 0.153 Angle : 0.622 11.676 42904 Z= 0.298 Chirality : 0.044 0.155 4872 Planarity : 0.004 0.057 5336 Dihedral : 16.817 178.968 5208 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.58 % Favored : 96.31 % Rotamer: Outliers : 4.14 % Allowed : 18.98 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.13), residues: 3880 helix: 1.33 (0.14), residues: 1400 sheet: -0.51 (0.22), residues: 512 loop : -0.68 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 171 PHE 0.009 0.001 PHE D 35 TYR 0.011 0.001 TYR B 348 ARG 0.003 0.000 ARG H 412 Details of bonding type rmsd hydrogen bonds : bond 0.03654 ( 1206) hydrogen bonds : angle 5.01805 ( 3390) covalent geometry : bond 0.00357 (31592) covalent geometry : angle 0.62175 (42904) Misc. bond : bond 0.00042 ( 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 613 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 481 time to evaluate : 3.468 Fit side-chains REVERT: A 195 LYS cc_start: 0.7668 (tptt) cc_final: 0.6972 (tppt) REVERT: A 206 LYS cc_start: 0.7468 (tptp) cc_final: 0.7052 (tptp) REVERT: A 265 GLN cc_start: 0.8116 (tt0) cc_final: 0.7508 (tp40) REVERT: A 274 ASP cc_start: 0.8476 (t0) cc_final: 0.8224 (t0) REVERT: A 412 ARG cc_start: 0.7086 (ptt180) cc_final: 0.6777 (ptt90) REVERT: A 500 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7463 (tt0) REVERT: B 106 LYS cc_start: 0.8496 (ttmm) cc_final: 0.8277 (ttmt) REVERT: B 195 LYS cc_start: 0.7698 (tptt) cc_final: 0.7074 (tppt) REVERT: B 224 ARG cc_start: 0.8034 (ttt90) cc_final: 0.7440 (ttt90) REVERT: B 286 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8163 (ttm) REVERT: B 288 LYS cc_start: 0.7734 (mttm) cc_final: 0.7403 (mtmp) REVERT: B 410 LYS cc_start: 0.7097 (mtpt) cc_final: 0.6555 (pmtt) REVERT: C 111 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8291 (tm-30) REVERT: C 206 LYS cc_start: 0.7900 (mmpt) cc_final: 0.6760 (tptp) REVERT: C 335 GLU cc_start: 0.7969 (tt0) cc_final: 0.7560 (tt0) REVERT: C 410 LYS cc_start: 0.6987 (mtmt) cc_final: 0.6445 (pmtt) REVERT: C 412 ARG cc_start: 0.6211 (OUTLIER) cc_final: 0.5937 (ptt180) REVERT: D 91 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8143 (mm) REVERT: D 195 LYS cc_start: 0.7685 (tptt) cc_final: 0.7080 (tppt) REVERT: D 231 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6934 (ppt90) REVERT: D 265 GLN cc_start: 0.8084 (tt0) cc_final: 0.7498 (tp40) REVERT: D 274 ASP cc_start: 0.8400 (t0) cc_final: 0.8077 (t0) REVERT: D 286 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8305 (ttm) REVERT: D 410 LYS cc_start: 0.7269 (mtpt) cc_final: 0.6645 (pmtt) REVERT: E 111 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8059 (tm-30) REVERT: E 195 LYS cc_start: 0.7703 (tptt) cc_final: 0.6984 (tppt) REVERT: E 242 LYS cc_start: 0.7647 (mmtm) cc_final: 0.7102 (mttt) REVERT: E 265 GLN cc_start: 0.8093 (tt0) cc_final: 0.7524 (tp40) REVERT: E 286 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8138 (ttm) REVERT: E 402 PHE cc_start: 0.6051 (m-80) cc_final: 0.5492 (m-80) REVERT: E 500 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7662 (tt0) REVERT: F 58 LYS cc_start: 0.8401 (mttt) cc_final: 0.8044 (mtmp) REVERT: F 195 LYS cc_start: 0.7795 (tptm) cc_final: 0.7204 (tppt) REVERT: F 208 LYS cc_start: 0.7705 (mtpm) cc_final: 0.7274 (mttp) REVERT: F 265 GLN cc_start: 0.8088 (tt0) cc_final: 0.7498 (tp40) REVERT: F 286 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8156 (ttm) REVERT: F 412 ARG cc_start: 0.6590 (ptt90) cc_final: 0.6312 (ptt90) REVERT: G 48 GLN cc_start: 0.8282 (mt0) cc_final: 0.8072 (mt0) REVERT: G 114 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.8053 (t80) REVERT: G 162 ASP cc_start: 0.7132 (m-30) cc_final: 0.6423 (m-30) REVERT: G 195 LYS cc_start: 0.7687 (tptm) cc_final: 0.7093 (tppt) REVERT: G 206 LYS cc_start: 0.7736 (mmtm) cc_final: 0.7059 (tptp) REVERT: G 208 LYS cc_start: 0.8168 (mtpm) cc_final: 0.7671 (mtmt) REVERT: G 265 GLN cc_start: 0.8059 (tt0) cc_final: 0.7465 (tp40) REVERT: G 286 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8276 (ttm) REVERT: G 288 LYS cc_start: 0.7782 (mttm) cc_final: 0.7435 (mtmp) REVERT: G 410 LYS cc_start: 0.7301 (mtpt) cc_final: 0.6538 (pmtt) REVERT: G 500 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7447 (pt0) REVERT: H 75 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6654 (tt0) REVERT: H 114 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.8044 (t80) REVERT: H 195 LYS cc_start: 0.7670 (tptm) cc_final: 0.7005 (tppt) REVERT: H 206 LYS cc_start: 0.7710 (mmtt) cc_final: 0.7411 (tptp) REVERT: H 410 LYS cc_start: 0.7024 (mtmt) cc_final: 0.6569 (pmtt) outliers start: 132 outliers final: 84 residues processed: 573 average time/residue: 1.1253 time to fit residues: 789.6959 Evaluate side-chains 568 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 468 time to evaluate : 3.391 ------------------------------------------------------------------------------- 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 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 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 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 364 ASP Chi-restraints excluded: chain C residue 369 ASN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 412 ARG Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 231 ARG 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 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 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 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 185 LEU 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 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 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 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 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 318 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 383 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 271 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 308 optimal weight: 0.5980 chunk 285 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 367 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 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** ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.176342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.130892 restraints weight = 33605.564| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.78 r_work: 0.3213 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 31600 Z= 0.120 Angle : 0.598 11.400 42904 Z= 0.285 Chirality : 0.043 0.151 4872 Planarity : 0.004 0.056 5336 Dihedral : 16.498 179.483 5208 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.63 % Favored : 96.26 % Rotamer: Outliers : 3.88 % Allowed : 19.74 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.14), residues: 3880 helix: 1.45 (0.14), residues: 1400 sheet: -0.58 (0.24), residues: 432 loop : -0.55 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS F 171 PHE 0.009 0.001 PHE D 35 TYR 0.010 0.001 TYR G 509 ARG 0.003 0.000 ARG F 341 Details of bonding type rmsd hydrogen bonds : bond 0.03308 ( 1206) hydrogen bonds : angle 4.91101 ( 3390) covalent geometry : bond 0.00273 (31592) covalent geometry : angle 0.59843 (42904) Misc. bond : bond 0.00026 ( 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 605 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 481 time to evaluate : 3.350 Fit side-chains REVERT: A 195 LYS cc_start: 0.7699 (tptt) cc_final: 0.7040 (tppt) REVERT: A 206 LYS cc_start: 0.7470 (tptp) cc_final: 0.7033 (tptp) REVERT: A 265 GLN cc_start: 0.8112 (tt0) cc_final: 0.7538 (tp40) REVERT: A 274 ASP cc_start: 0.8420 (t0) cc_final: 0.8142 (t0) REVERT: A 500 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7448 (tt0) REVERT: B 106 LYS cc_start: 0.8460 (ttmm) cc_final: 0.8240 (ttmt) REVERT: B 195 LYS cc_start: 0.7694 (tptt) cc_final: 0.7069 (tppt) REVERT: B 224 ARG cc_start: 0.8060 (ttt90) cc_final: 0.7439 (ttt90) REVERT: B 286 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8110 (ttm) REVERT: B 288 LYS cc_start: 0.7735 (mttm) cc_final: 0.7409 (mtmp) REVERT: B 410 LYS cc_start: 0.7086 (mtpt) cc_final: 0.6559 (pmtt) REVERT: B 420 MET cc_start: 0.4934 (tpp) cc_final: 0.4527 (tpp) REVERT: C 111 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8162 (tm-30) REVERT: C 195 LYS cc_start: 0.7842 (tptm) cc_final: 0.7367 (tppt) REVERT: C 206 LYS cc_start: 0.7876 (mmpt) cc_final: 0.6772 (tptp) REVERT: C 335 GLU cc_start: 0.7947 (tt0) cc_final: 0.7536 (tt0) REVERT: C 412 ARG cc_start: 0.6042 (OUTLIER) cc_final: 0.5795 (ptt180) REVERT: D 91 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8101 (mm) REVERT: D 195 LYS cc_start: 0.7637 (tptt) cc_final: 0.7026 (tppt) REVERT: D 265 GLN cc_start: 0.8058 (tt0) cc_final: 0.7496 (tp40) REVERT: D 274 ASP cc_start: 0.8376 (t0) cc_final: 0.8037 (t0) REVERT: D 286 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8281 (ttm) REVERT: D 410 LYS cc_start: 0.7248 (mtpt) cc_final: 0.6630 (pmtt) REVERT: E 111 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8074 (tm-30) REVERT: E 195 LYS cc_start: 0.7690 (tptt) cc_final: 0.6970 (tppt) REVERT: E 242 LYS cc_start: 0.7672 (mmtm) cc_final: 0.7138 (mttt) REVERT: E 265 GLN cc_start: 0.8096 (tt0) cc_final: 0.7546 (tp40) REVERT: E 286 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8133 (ttm) REVERT: E 402 PHE cc_start: 0.5969 (m-80) cc_final: 0.5473 (m-80) REVERT: E 500 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7617 (tt0) REVERT: F 195 LYS cc_start: 0.7765 (tptm) cc_final: 0.7150 (tppt) REVERT: F 208 LYS cc_start: 0.7671 (mtpm) cc_final: 0.7258 (mttp) REVERT: F 265 GLN cc_start: 0.8096 (tt0) cc_final: 0.7521 (tp40) REVERT: G 48 GLN cc_start: 0.8268 (mt0) cc_final: 0.8060 (mt0) REVERT: G 100 GLN cc_start: 0.8506 (tt0) cc_final: 0.8281 (tt0) REVERT: G 114 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.8067 (t80) REVERT: G 162 ASP cc_start: 0.7104 (m-30) cc_final: 0.6395 (m-30) REVERT: G 195 LYS cc_start: 0.7665 (tptm) cc_final: 0.7073 (tppt) REVERT: G 206 LYS cc_start: 0.7749 (mmtm) cc_final: 0.7271 (mmmm) REVERT: G 208 LYS cc_start: 0.8094 (mtpm) cc_final: 0.7602 (mtmt) REVERT: G 265 GLN cc_start: 0.8037 (tt0) cc_final: 0.7452 (tp40) REVERT: G 286 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8257 (ttm) REVERT: G 288 LYS cc_start: 0.7800 (mttm) cc_final: 0.7457 (mtmp) REVERT: G 410 LYS cc_start: 0.7287 (mtpt) cc_final: 0.6578 (pmtt) REVERT: G 500 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7466 (tt0) REVERT: H 75 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6652 (tt0) REVERT: H 114 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.8069 (t80) REVERT: H 195 LYS cc_start: 0.7641 (tptm) cc_final: 0.7009 (tppt) REVERT: H 206 LYS cc_start: 0.7719 (mmtt) cc_final: 0.7393 (tptp) outliers start: 124 outliers final: 79 residues processed: 565 average time/residue: 1.2331 time to fit residues: 857.6255 Evaluate side-chains 564 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 471 time to evaluate : 3.247 ------------------------------------------------------------------------------- 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 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 60 THR 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 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 318 VAL 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 412 ARG 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 91 ILE Chi-restraints excluded: chain D residue 159 SER 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 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 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 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 185 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 331 CYS 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 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 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 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 185 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 318 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 273 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 179 optimal weight: 2.9990 chunk 254 optimal weight: 0.9980 chunk 306 optimal weight: 3.9990 chunk 361 optimal weight: 1.9990 chunk 318 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 155 optimal weight: 0.0670 chunk 170 optimal weight: 0.5980 chunk 232 optimal weight: 0.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 C 303 ASN ** 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 92 HIS ** 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** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.173718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.128310 restraints weight = 33631.570| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.75 r_work: 0.3218 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2244 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 : 0.598 11.120 42904 Z= 0.285 Chirality : 0.043 0.148 4872 Planarity : 0.004 0.056 5336 Dihedral : 16.220 179.754 5208 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.43 % Favored : 96.47 % Rotamer: Outliers : 3.38 % Allowed : 20.61 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.14), residues: 3880 helix: 1.49 (0.14), residues: 1400 sheet: -0.57 (0.24), residues: 432 loop : -0.52 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS F 171 PHE 0.009 0.001 PHE D 35 TYR 0.010 0.001 TYR F 348 ARG 0.004 0.000 ARG D 412 Details of bonding type rmsd hydrogen bonds : bond 0.03274 ( 1206) hydrogen bonds : angle 4.87284 ( 3390) covalent geometry : bond 0.00273 (31592) covalent geometry : angle 0.59754 (42904) Misc. bond : bond 0.00026 ( 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 580 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 472 time to evaluate : 3.594 Fit side-chains REVERT: A 195 LYS cc_start: 0.7692 (tptt) cc_final: 0.7066 (tppt) REVERT: A 206 LYS cc_start: 0.7539 (tptp) cc_final: 0.7103 (tptp) REVERT: A 265 GLN cc_start: 0.8120 (tt0) cc_final: 0.7567 (tp40) REVERT: A 274 ASP cc_start: 0.8393 (t0) cc_final: 0.8123 (t0) REVERT: A 500 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7489 (tt0) REVERT: B 106 LYS cc_start: 0.8463 (ttmm) cc_final: 0.8245 (ttmt) REVERT: B 195 LYS cc_start: 0.7787 (tptt) cc_final: 0.7164 (tppt) REVERT: B 224 ARG cc_start: 0.8095 (ttt90) cc_final: 0.7472 (ttt90) REVERT: B 286 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8122 (ttm) REVERT: B 288 LYS cc_start: 0.7756 (mttm) cc_final: 0.7434 (mtmp) REVERT: B 410 LYS cc_start: 0.7086 (mtpt) cc_final: 0.6585 (pmtt) REVERT: B 420 MET cc_start: 0.4852 (tpp) cc_final: 0.4429 (tpp) REVERT: C 111 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8108 (tm-30) REVERT: C 195 LYS cc_start: 0.7883 (tptm) cc_final: 0.7413 (tppt) REVERT: C 206 LYS cc_start: 0.7917 (mmpt) cc_final: 0.6827 (tptp) REVERT: C 335 GLU cc_start: 0.7944 (tt0) cc_final: 0.7523 (tt0) REVERT: C 412 ARG cc_start: 0.6064 (OUTLIER) cc_final: 0.4604 (ppt170) REVERT: D 91 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8131 (mm) REVERT: D 195 LYS cc_start: 0.7667 (tptt) cc_final: 0.7055 (tppt) REVERT: D 265 GLN cc_start: 0.8079 (tt0) cc_final: 0.7524 (tp40) REVERT: D 274 ASP cc_start: 0.8378 (t0) cc_final: 0.8056 (t0) REVERT: D 410 LYS cc_start: 0.7223 (mtpt) cc_final: 0.6619 (pmtt) REVERT: E 100 GLN cc_start: 0.8477 (tt0) cc_final: 0.8199 (tt0) REVERT: E 111 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8074 (tm-30) REVERT: E 195 LYS cc_start: 0.7801 (tptt) cc_final: 0.7105 (tppt) REVERT: E 242 LYS cc_start: 0.7713 (mmtm) cc_final: 0.7189 (mttt) REVERT: E 265 GLN cc_start: 0.8076 (tt0) cc_final: 0.7538 (tp40) REVERT: E 286 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8145 (ttm) REVERT: E 402 PHE cc_start: 0.6035 (m-80) cc_final: 0.5524 (m-80) REVERT: E 500 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7645 (tt0) REVERT: F 195 LYS cc_start: 0.7796 (tptm) cc_final: 0.7183 (tppt) REVERT: F 208 LYS cc_start: 0.7667 (mtpm) cc_final: 0.7284 (mttp) REVERT: F 265 GLN cc_start: 0.8090 (tt0) cc_final: 0.7537 (tp40) REVERT: G 48 GLN cc_start: 0.8280 (mt0) cc_final: 0.8070 (mt0) REVERT: G 100 GLN cc_start: 0.8519 (tt0) cc_final: 0.8287 (tt0) REVERT: G 162 ASP cc_start: 0.7124 (m-30) cc_final: 0.6416 (m-30) REVERT: G 195 LYS cc_start: 0.7659 (tptm) cc_final: 0.7079 (tppt) REVERT: G 206 LYS cc_start: 0.7770 (mmtm) cc_final: 0.7312 (mmmm) REVERT: G 208 LYS cc_start: 0.8108 (mtpm) cc_final: 0.7633 (mtmt) REVERT: G 265 GLN cc_start: 0.8019 (tt0) cc_final: 0.7475 (tp40) REVERT: G 286 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8281 (ttm) REVERT: G 288 LYS cc_start: 0.7783 (mttm) cc_final: 0.7480 (mtmp) REVERT: G 410 LYS cc_start: 0.7302 (mtpt) cc_final: 0.6534 (pmtt) REVERT: G 500 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7587 (tt0) REVERT: H 75 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6702 (tt0) REVERT: H 114 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.8089 (t80) REVERT: H 195 LYS cc_start: 0.7677 (tptm) cc_final: 0.7053 (tppt) REVERT: H 206 LYS cc_start: 0.7794 (mmtt) cc_final: 0.7467 (tptp) REVERT: H 274 ASP cc_start: 0.8470 (t0) cc_final: 0.8176 (t0) outliers start: 108 outliers final: 83 residues processed: 543 average time/residue: 1.1468 time to fit residues: 762.8144 Evaluate side-chains 563 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 468 time to evaluate : 3.387 ------------------------------------------------------------------------------- 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 325 MET 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 60 THR 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 332 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 437 ILE 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 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 412 ARG 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 91 ILE Chi-restraints excluded: chain D residue 159 SER 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 111 GLU Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 269 ASP 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 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 185 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 331 CYS 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 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 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 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 185 LEU 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 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 352 optimal weight: 0.0050 chunk 371 optimal weight: 0.0980 chunk 119 optimal weight: 0.0670 chunk 326 optimal weight: 0.3980 chunk 65 optimal weight: 0.0010 chunk 172 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 232 optimal weight: 0.0670 chunk 305 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 70 optimal weight: 0.0020 overall best weight: 0.0284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 GLN A 202 GLN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** D 230 ASN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 243 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.179679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.135141 restraints weight = 33745.983| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.76 r_work: 0.3298 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 31600 Z= 0.091 Angle : 0.575 10.605 42904 Z= 0.271 Chirality : 0.042 0.141 4872 Planarity : 0.004 0.057 5336 Dihedral : 15.654 179.661 5208 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.17 % Favored : 96.73 % Rotamer: Outliers : 2.54 % Allowed : 21.68 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.14), residues: 3880 helix: 1.65 (0.14), residues: 1416 sheet: -0.38 (0.23), residues: 456 loop : -0.60 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS F 171 PHE 0.008 0.001 PHE D 35 TYR 0.009 0.001 TYR F 12 ARG 0.005 0.000 ARG D 412 Details of bonding type rmsd hydrogen bonds : bond 0.02628 ( 1206) hydrogen bonds : angle 4.68305 ( 3390) covalent geometry : bond 0.00189 (31592) covalent geometry : angle 0.57499 (42904) Misc. bond : bond 0.00015 ( 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 597 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 516 time to evaluate : 3.577 Fit side-chains revert: symmetry clash REVERT: A 195 LYS cc_start: 0.7688 (tptt) cc_final: 0.7033 (tppt) REVERT: A 206 LYS cc_start: 0.7499 (tptp) cc_final: 0.7139 (tptp) REVERT: A 265 GLN cc_start: 0.8053 (tt0) cc_final: 0.7498 (tp40) REVERT: A 274 ASP cc_start: 0.8348 (t0) cc_final: 0.8072 (t0) REVERT: B 106 LYS cc_start: 0.8455 (ttmm) cc_final: 0.8247 (ttmt) REVERT: B 112 GLN cc_start: 0.7547 (pm20) cc_final: 0.7096 (pm20) REVERT: B 179 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7264 (ptp) REVERT: B 195 LYS cc_start: 0.7707 (tptt) cc_final: 0.7078 (tppt) REVERT: B 265 GLN cc_start: 0.8158 (tt0) cc_final: 0.7595 (tp40) REVERT: B 274 ASP cc_start: 0.8381 (t0) cc_final: 0.8108 (t0) REVERT: B 286 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8128 (ttm) REVERT: B 288 LYS cc_start: 0.7726 (mttm) cc_final: 0.7398 (mtmp) REVERT: B 410 LYS cc_start: 0.7025 (mtpt) cc_final: 0.6511 (pmtt) REVERT: B 420 MET cc_start: 0.4534 (tpp) cc_final: 0.4154 (tpp) REVERT: C 111 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8201 (tm-30) REVERT: C 195 LYS cc_start: 0.7787 (tptm) cc_final: 0.7289 (tppt) REVERT: C 335 GLU cc_start: 0.7949 (tt0) cc_final: 0.7528 (tt0) REVERT: C 412 ARG cc_start: 0.6131 (OUTLIER) cc_final: 0.5848 (ptt180) REVERT: C 500 GLU cc_start: 0.7800 (tt0) cc_final: 0.7535 (tt0) REVERT: D 91 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8068 (mm) REVERT: D 195 LYS cc_start: 0.7552 (tptt) cc_final: 0.6917 (tppt) REVERT: D 265 GLN cc_start: 0.8004 (tt0) cc_final: 0.7495 (tp40) REVERT: D 274 ASP cc_start: 0.8371 (t0) cc_final: 0.8083 (t0) REVERT: D 410 LYS cc_start: 0.7187 (mtpt) cc_final: 0.6587 (pmtt) REVERT: D 500 GLU cc_start: 0.7828 (tt0) cc_final: 0.7570 (tt0) REVERT: E 100 GLN cc_start: 0.8400 (tt0) cc_final: 0.8154 (tt0) REVERT: E 195 LYS cc_start: 0.7664 (tptt) cc_final: 0.7030 (tppt) REVERT: E 242 LYS cc_start: 0.7629 (mmtm) cc_final: 0.6999 (mmtt) REVERT: E 286 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8085 (ttm) REVERT: F 195 LYS cc_start: 0.7736 (tptm) cc_final: 0.7140 (tppt) REVERT: F 206 LYS cc_start: 0.7648 (mmtt) cc_final: 0.7407 (mmtt) REVERT: F 208 LYS cc_start: 0.7465 (mtpm) cc_final: 0.7113 (mttp) REVERT: F 265 GLN cc_start: 0.8057 (tt0) cc_final: 0.7570 (tp40) REVERT: F 377 LEU cc_start: 0.9408 (mt) cc_final: 0.9151 (mt) REVERT: F 411 TYR cc_start: 0.7432 (t80) cc_final: 0.7170 (t80) REVERT: G 48 GLN cc_start: 0.8161 (mt0) cc_final: 0.7960 (mt0) REVERT: G 100 GLN cc_start: 0.8442 (tt0) cc_final: 0.8221 (tt0) REVERT: G 195 LYS cc_start: 0.7489 (tptm) cc_final: 0.6883 (tppt) REVERT: G 206 LYS cc_start: 0.7717 (mmtm) cc_final: 0.7285 (mmmm) REVERT: G 208 LYS cc_start: 0.7947 (mtpm) cc_final: 0.7437 (mtmt) REVERT: G 265 GLN cc_start: 0.7935 (tt0) cc_final: 0.7445 (tp40) REVERT: G 286 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8261 (ttm) REVERT: G 288 LYS cc_start: 0.7737 (mttm) cc_final: 0.7430 (mtmp) REVERT: G 335 GLU cc_start: 0.7891 (tt0) cc_final: 0.7505 (tt0) REVERT: G 410 LYS cc_start: 0.7293 (mtpt) cc_final: 0.6609 (pmtt) REVERT: G 500 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7484 (tt0) REVERT: H 75 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6490 (tt0) REVERT: H 195 LYS cc_start: 0.7713 (tptm) cc_final: 0.7050 (tppt) REVERT: H 206 LYS cc_start: 0.7815 (mmtt) cc_final: 0.7558 (tptp) REVERT: H 274 ASP cc_start: 0.8494 (t0) cc_final: 0.8263 (t0) REVERT: H 410 LYS cc_start: 0.7080 (mtmt) cc_final: 0.6649 (pmtt) REVERT: H 411 TYR cc_start: 0.7619 (t80) cc_final: 0.7248 (t80) outliers start: 81 outliers final: 60 residues processed: 572 average time/residue: 1.1115 time to fit residues: 788.8871 Evaluate side-chains 550 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 481 time to evaluate : 3.274 ------------------------------------------------------------------------------- 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 152 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 318 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 B residue 60 THR 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 286 MET Chi-restraints excluded: chain B residue 329 SER 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 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 329 SER Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 412 ARG Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 270 VAL 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 286 MET 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 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 185 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL 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 F residue 453 ILE 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 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 185 LEU Chi-restraints excluded: chain H residue 270 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 287 optimal weight: 5.9990 chunk 354 optimal weight: 0.0980 chunk 128 optimal weight: 0.0570 chunk 120 optimal weight: 0.7980 chunk 271 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 192 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 318 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 chunk 166 optimal weight: 0.6980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 GLN A 202 GLN A 303 ASN A 312 ASN ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN B 230 ASN C 100 GLN C 312 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 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 94 ASN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 230 ASN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.183763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.137157 restraints weight = 33228.180| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.92 r_work: 0.3258 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 31600 Z= 0.101 Angle : 0.581 12.857 42904 Z= 0.273 Chirality : 0.042 0.178 4872 Planarity : 0.004 0.057 5336 Dihedral : 15.533 179.485 5208 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.22 % Favored : 96.68 % Rotamer: Outliers : 2.57 % Allowed : 22.02 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.14), residues: 3880 helix: 1.74 (0.14), residues: 1400 sheet: -0.46 (0.24), residues: 416 loop : -0.45 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS F 171 PHE 0.008 0.001 PHE C 35 TYR 0.009 0.001 TYR D 353 ARG 0.003 0.000 ARG D 412 Details of bonding type rmsd hydrogen bonds : bond 0.02861 ( 1206) hydrogen bonds : angle 4.69329 ( 3390) covalent geometry : bond 0.00221 (31592) covalent geometry : angle 0.58099 (42904) Misc. bond : bond 0.00024 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21140.57 seconds wall clock time: 364 minutes 58.37 seconds (21898.37 seconds total)