Starting phenix.real_space_refine on Fri Jun 27 05:54:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g9b_29863/06_2025/8g9b_29863.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g9b_29863/06_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_29863/06_2025/8g9b_29863.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g9b_29863/06_2025/8g9b_29863.map" model { file = "/net/cci-nas-00/data/ceres_data/8g9b_29863/06_2025/8g9b_29863.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g9b_29863/06_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 19.72, per 1000 atoms: 0.64 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: 9.09 Conformation dependent library (CDL) restraints added in 4.6 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: 4.49 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: 12.36 Time building geometry restraints manager: 10.66 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: 5.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.180 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 77.700 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.150 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:13.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.670 ------------------------------------------------------------------------------- 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 : 3.346 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: 0.7198 (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: 1.2222 time to fit residues: 792.4282 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 : 3.209 ------------------------------------------------------------------------------- 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 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.176058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.128490 restraints weight = 33427.715| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.97 r_work: 0.3204 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 31600 Z= 0.148 Angle : 0.671 11.429 42904 Z= 0.322 Chirality : 0.046 0.190 4872 Planarity : 0.005 0.065 5336 Dihedral : 19.572 179.252 5237 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.74 % Favored : 96.16 % Rotamer: Outliers : 3.41 % Allowed : 14.72 % Favored : 81.86 % 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: 0.04 (0.13), residues: 3880 helix: 1.32 (0.14), residues: 1384 sheet: -0.63 (0.20), residues: 520 loop : -0.68 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 454 PHE 0.008 0.001 PHE D 35 TYR 0.013 0.001 TYR C 509 ARG 0.005 0.000 ARG B 231 Details of bonding type rmsd hydrogen bonds : bond 0.03895 ( 1206) hydrogen bonds : angle 5.43647 ( 3390) covalent geometry : bond 0.00340 (31592) covalent geometry : angle 0.67059 (42904) Misc. bond : bond 0.00085 ( 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 606 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 497 time to evaluate : 4.834 Fit side-chains revert: symmetry clash REVERT: A 195 LYS cc_start: 0.7606 (tptt) cc_final: 0.6847 (tppt) REVERT: A 206 LYS cc_start: 0.7593 (tptp) cc_final: 0.7293 (tptp) REVERT: A 230 ASN cc_start: 0.8012 (t0) cc_final: 0.7784 (t0) REVERT: A 261 ASP cc_start: 0.7824 (m-30) cc_final: 0.7596 (m-30) REVERT: A 412 ARG cc_start: 0.7019 (ptt180) cc_final: 0.6612 (ptt90) REVERT: B 105 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.6778 (ttp-110) REVERT: B 195 LYS cc_start: 0.7750 (tptt) cc_final: 0.7030 (tppt) REVERT: B 288 LYS cc_start: 0.7776 (mttm) cc_final: 0.7494 (mtmp) REVERT: B 410 LYS cc_start: 0.6980 (mtpt) cc_final: 0.6573 (pmtt) REVERT: C 75 GLU cc_start: 0.7091 (tt0) cc_final: 0.6840 (tt0) REVERT: C 230 ASN cc_start: 0.7941 (t0) cc_final: 0.7577 (t160) REVERT: C 335 GLU cc_start: 0.7901 (tt0) cc_final: 0.7572 (tt0) REVERT: C 410 LYS cc_start: 0.6894 (mtmt) cc_final: 0.6500 (pmtt) REVERT: D 195 LYS cc_start: 0.7729 (tptt) cc_final: 0.7102 (tppt) REVERT: D 206 LYS cc_start: 0.7174 (mmtt) cc_final: 0.6848 (mmmt) REVERT: D 265 GLN cc_start: 0.8135 (tt0) cc_final: 0.7601 (tp40) REVERT: D 335 GLU cc_start: 0.7981 (tt0) cc_final: 0.7629 (tt0) REVERT: D 410 LYS cc_start: 0.7204 (mtpt) cc_final: 0.6571 (pmtt) REVERT: E 75 GLU cc_start: 0.6909 (tt0) cc_final: 0.6683 (tt0) REVERT: E 111 GLU cc_start: 0.8396 (tt0) cc_final: 0.7858 (tm-30) REVERT: E 179 MET cc_start: 0.7578 (ptp) cc_final: 0.6955 (ptp) REVERT: E 195 LYS cc_start: 0.7662 (tptt) cc_final: 0.6954 (tppt) REVERT: E 261 ASP cc_start: 0.7929 (m-30) cc_final: 0.7716 (m-30) REVERT: E 265 GLN cc_start: 0.8190 (tt0) cc_final: 0.7620 (tp40) REVERT: E 286 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8239 (ttm) REVERT: E 368 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.7856 (mt0) REVERT: F 195 LYS cc_start: 0.7824 (tptm) cc_final: 0.7207 (tppt) REVERT: F 208 LYS cc_start: 0.7732 (mtpm) cc_final: 0.7192 (mttp) REVERT: F 265 GLN cc_start: 0.8152 (tt0) cc_final: 0.7853 (tt0) REVERT: F 286 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8259 (ttm) REVERT: F 491 GLU cc_start: 0.8582 (tp30) cc_final: 0.8336 (tp30) REVERT: G 48 GLN cc_start: 0.8207 (mt0) cc_final: 0.7932 (mt0) REVERT: G 114 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.8042 (t80) REVERT: G 206 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.6765 (mmmm) REVERT: G 208 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8009 (mtmt) REVERT: G 265 GLN cc_start: 0.8096 (tt0) cc_final: 0.7544 (tp40) REVERT: G 286 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8361 (ttm) REVERT: G 335 GLU cc_start: 0.7961 (tt0) cc_final: 0.7581 (tt0) REVERT: H 75 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6618 (tt0) REVERT: H 105 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.6765 (ttp-110) REVERT: H 111 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8528 (tt0) REVERT: H 114 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7940 (t80) REVERT: H 195 LYS cc_start: 0.7711 (tptm) cc_final: 0.6963 (tppt) REVERT: H 261 ASP cc_start: 0.7765 (m-30) cc_final: 0.7521 (m-30) REVERT: H 286 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8121 (ttm) REVERT: H 325 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.9004 (tpp) REVERT: H 412 ARG cc_start: 0.7142 (ptt180) cc_final: 0.6822 (ptt90) outliers start: 109 outliers final: 36 residues processed: 555 average time/residue: 1.6457 time to fit residues: 1109.9403 Evaluate side-chains 518 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 468 time to evaluate : 3.702 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 147 optimal weight: 2.9990 chunk 334 optimal weight: 0.9990 chunk 101 optimal weight: 0.3980 chunk 81 optimal weight: 2.9990 chunk 320 optimal weight: 0.1980 chunk 283 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 299 optimal weight: 5.9990 chunk 380 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 D 230 ASN D 507 HIS ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN E 230 ASN ** E 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 GLN ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN H 448 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.176117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.130753 restraints weight = 33898.866| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.78 r_work: 0.3242 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 31600 Z= 0.113 Angle : 0.608 12.943 42904 Z= 0.289 Chirality : 0.044 0.169 4872 Planarity : 0.004 0.061 5336 Dihedral : 18.584 177.515 5216 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.30 % Favored : 96.60 % Rotamer: Outliers : 3.60 % Allowed : 15.76 % Favored : 80.64 % 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: 1.41 (0.14), residues: 1400 sheet: -0.31 (0.25), residues: 376 loop : -0.68 (0.13), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 92 PHE 0.008 0.001 PHE E 35 TYR 0.010 0.001 TYR C 509 ARG 0.009 0.000 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.03442 ( 1206) hydrogen bonds : angle 5.13095 ( 3390) covalent geometry : bond 0.00247 (31592) covalent geometry : angle 0.60773 (42904) Misc. bond : bond 0.00026 ( 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 620 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 505 time to evaluate : 3.432 Fit side-chains REVERT: A 195 LYS cc_start: 0.7509 (tptt) cc_final: 0.6765 (tppt) REVERT: A 206 LYS cc_start: 0.7625 (tptp) cc_final: 0.7257 (tptp) REVERT: A 261 ASP cc_start: 0.7778 (m-30) cc_final: 0.7576 (m-30) REVERT: A 274 ASP cc_start: 0.8498 (t0) cc_final: 0.8273 (t0) REVERT: A 385 MET cc_start: 0.8738 (ttm) cc_final: 0.8480 (ttm) REVERT: A 500 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7552 (tt0) REVERT: B 195 LYS cc_start: 0.7802 (tptt) cc_final: 0.7128 (tppt) REVERT: B 286 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8120 (ttm) REVERT: B 288 LYS cc_start: 0.7642 (mttm) cc_final: 0.7353 (mtmp) REVERT: B 410 LYS cc_start: 0.6964 (mtpt) cc_final: 0.6498 (pmtt) REVERT: C 75 GLU cc_start: 0.6947 (tt0) cc_final: 0.6635 (tt0) REVERT: C 111 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7672 (tm-30) REVERT: C 168 GLU cc_start: 0.4558 (OUTLIER) cc_final: 0.4243 (pp20) REVERT: C 206 LYS cc_start: 0.7582 (mmpt) cc_final: 0.7028 (tptt) REVERT: C 230 ASN cc_start: 0.7885 (t0) cc_final: 0.7658 (t160) REVERT: C 335 GLU cc_start: 0.7893 (tt0) cc_final: 0.7511 (tt0) REVERT: C 410 LYS cc_start: 0.6867 (mtmt) cc_final: 0.6404 (pmtt) REVERT: D 195 LYS cc_start: 0.7641 (tptt) cc_final: 0.7013 (tppt) REVERT: D 265 GLN cc_start: 0.8083 (tt0) cc_final: 0.7539 (tp40) REVERT: D 274 ASP cc_start: 0.8356 (t0) cc_final: 0.8143 (t0) REVERT: D 286 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8315 (ttm) REVERT: D 410 LYS cc_start: 0.7166 (mtpt) cc_final: 0.6549 (pmtt) REVERT: E 179 MET cc_start: 0.7556 (ptp) cc_final: 0.6961 (ptp) REVERT: E 195 LYS cc_start: 0.7638 (tptt) cc_final: 0.6921 (tppt) REVERT: E 265 GLN cc_start: 0.8146 (tt0) cc_final: 0.7561 (tp40) REVERT: E 286 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8137 (ttm) REVERT: E 368 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.7836 (mt0) REVERT: F 195 LYS cc_start: 0.7813 (tptm) cc_final: 0.7172 (tppt) REVERT: F 208 LYS cc_start: 0.7593 (mtpm) cc_final: 0.7074 (mttp) REVERT: F 265 GLN cc_start: 0.8137 (tt0) cc_final: 0.7499 (tp40) REVERT: F 491 GLU cc_start: 0.8509 (tp30) cc_final: 0.8231 (tp30) REVERT: G 114 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.8017 (t80) REVERT: G 206 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.6858 (mmmm) REVERT: G 265 GLN cc_start: 0.8048 (tt0) cc_final: 0.7484 (tp40) REVERT: G 286 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8240 (ttm) REVERT: G 288 LYS cc_start: 0.7700 (mttm) cc_final: 0.7347 (mtmp) REVERT: G 335 GLU cc_start: 0.7864 (tt0) cc_final: 0.7467 (tt0) REVERT: H 75 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6592 (tt0) REVERT: H 114 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7875 (t80) REVERT: H 195 LYS cc_start: 0.7680 (tptm) cc_final: 0.6991 (tppt) REVERT: H 206 LYS cc_start: 0.7844 (mmtt) cc_final: 0.7584 (tptp) REVERT: H 261 ASP cc_start: 0.7623 (m-30) cc_final: 0.7383 (m-30) REVERT: H 410 LYS cc_start: 0.6884 (mtmt) cc_final: 0.6453 (pmtt) REVERT: H 412 ARG cc_start: 0.6948 (ptt180) cc_final: 0.6735 (ptt90) REVERT: H 510 GLU cc_start: 0.7580 (mt-10) cc_final: 0.6958 (mt-10) outliers start: 115 outliers final: 52 residues processed: 573 average time/residue: 1.1669 time to fit residues: 815.7782 Evaluate side-chains 535 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 471 time to evaluate : 3.468 ------------------------------------------------------------------------------- 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 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 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 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 270 VAL Chi-restraints excluded: chain D residue 286 MET 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 332 ILE Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 368 GLN Chi-restraints excluded: chain E residue 369 ASN Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 449 ASP Chi-restraints excluded: chain E residue 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 410 LYS Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 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 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: 0.7980 chunk 296 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 210 optimal weight: 9.9990 chunk 321 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 338 optimal weight: 0.8980 chunk 185 optimal weight: 8.9990 chunk 217 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 D 230 ASN ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.172802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.127119 restraints weight = 33835.194| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.76 r_work: 0.3184 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1706 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= 0.179 Angle : 0.647 11.890 42904 Z= 0.310 Chirality : 0.045 0.164 4872 Planarity : 0.004 0.058 5336 Dihedral : 18.041 179.998 5212 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.28 % Favored : 95.62 % Rotamer: Outliers : 4.45 % Allowed : 16.13 % Favored : 79.42 % 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: 0.03 (0.13), residues: 3880 helix: 1.26 (0.14), residues: 1400 sheet: -0.47 (0.22), residues: 512 loop : -0.73 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 93 PHE 0.011 0.001 PHE G 24 TYR 0.013 0.002 TYR H 348 ARG 0.003 0.000 ARG E 412 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 1206) hydrogen bonds : angle 5.14349 ( 3390) covalent geometry : bond 0.00421 (31592) covalent geometry : angle 0.64709 (42904) Misc. bond : bond 0.00047 ( 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 621 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 479 time to evaluate : 3.371 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7050 (tt0) cc_final: 0.6849 (tt0) REVERT: A 195 LYS cc_start: 0.7618 (tptt) cc_final: 0.6923 (tppt) REVERT: A 206 LYS cc_start: 0.7747 (tptp) cc_final: 0.7254 (tptp) REVERT: A 274 ASP cc_start: 0.8493 (t0) cc_final: 0.8217 (t0) REVERT: A 325 MET cc_start: 0.9214 (OUTLIER) cc_final: 0.8991 (tpp) REVERT: A 500 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7491 (tt0) REVERT: B 106 LYS cc_start: 0.8591 (ttmm) cc_final: 0.8358 (ttmt) REVERT: B 111 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.6982 (tm-30) REVERT: B 114 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.7958 (t80) REVERT: B 195 LYS cc_start: 0.7852 (tptt) cc_final: 0.7200 (tppt) REVERT: B 286 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8150 (ttm) REVERT: B 288 LYS cc_start: 0.7740 (mttm) cc_final: 0.7424 (mtmp) REVERT: B 410 LYS cc_start: 0.6942 (mtpt) cc_final: 0.6534 (pmtt) REVERT: C 75 GLU cc_start: 0.7021 (tt0) cc_final: 0.6746 (tt0) REVERT: C 111 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8187 (tm-30) REVERT: C 286 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8249 (ttm) REVERT: C 335 GLU cc_start: 0.7934 (tt0) cc_final: 0.7537 (tt0) REVERT: C 410 LYS cc_start: 0.6954 (mtmt) cc_final: 0.6477 (pmtt) REVERT: D 195 LYS cc_start: 0.7753 (tptt) cc_final: 0.7151 (tppt) REVERT: D 265 GLN cc_start: 0.8056 (tt0) cc_final: 0.7511 (tp40) REVERT: D 274 ASP cc_start: 0.8429 (t0) cc_final: 0.8163 (t0) REVERT: D 286 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8343 (ttm) REVERT: D 335 GLU cc_start: 0.7967 (tt0) cc_final: 0.7534 (tt0) REVERT: D 410 LYS cc_start: 0.7205 (mtpt) cc_final: 0.6681 (pmtt) REVERT: E 111 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8314 (tt0) REVERT: E 179 MET cc_start: 0.7641 (ptp) cc_final: 0.7107 (ptp) REVERT: E 195 LYS cc_start: 0.7760 (tptt) cc_final: 0.7047 (tppt) REVERT: E 265 GLN cc_start: 0.8128 (tt0) cc_final: 0.7578 (tp40) REVERT: E 286 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8166 (ttm) REVERT: F 195 LYS cc_start: 0.7833 (tptm) cc_final: 0.7231 (tppt) REVERT: F 208 LYS cc_start: 0.7794 (mtpm) cc_final: 0.7379 (mttp) REVERT: F 265 GLN cc_start: 0.8148 (tt0) cc_final: 0.7586 (tp40) REVERT: F 286 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8187 (ttm) REVERT: F 491 GLU cc_start: 0.8489 (tp30) cc_final: 0.8256 (tp30) REVERT: G 114 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.8079 (t80) REVERT: G 206 LYS cc_start: 0.7703 (mmtm) cc_final: 0.7064 (mmmm) REVERT: G 208 LYS cc_start: 0.8259 (mtpm) cc_final: 0.7725 (mtmt) REVERT: G 241 LYS cc_start: 0.7639 (ptpt) cc_final: 0.7374 (ptpp) REVERT: G 265 GLN cc_start: 0.8119 (tt0) cc_final: 0.7564 (tp40) REVERT: G 286 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8271 (ttm) REVERT: G 288 LYS cc_start: 0.7827 (mttm) cc_final: 0.7496 (mtmp) REVERT: G 335 GLU cc_start: 0.7924 (tt0) cc_final: 0.7552 (tt0) REVERT: G 410 LYS cc_start: 0.7345 (mtpt) cc_final: 0.6603 (pmtt) REVERT: G 500 GLU cc_start: 0.7980 (tt0) cc_final: 0.7677 (pt0) REVERT: H 75 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6680 (tt0) REVERT: H 111 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8344 (tt0) REVERT: H 114 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.8019 (t80) REVERT: H 195 LYS cc_start: 0.7773 (tptm) cc_final: 0.7083 (tppt) REVERT: H 206 LYS cc_start: 0.7829 (mmtt) cc_final: 0.7499 (tptp) REVERT: H 261 ASP cc_start: 0.7717 (m-30) cc_final: 0.7489 (m-30) REVERT: H 325 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8564 (ttt) REVERT: H 410 LYS cc_start: 0.6963 (mtmt) cc_final: 0.6559 (pmtt) REVERT: H 510 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7164 (mt-10) outliers start: 142 outliers final: 76 residues processed: 575 average time/residue: 1.1184 time to fit residues: 788.3096 Evaluate side-chains 558 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 465 time to evaluate : 3.464 ------------------------------------------------------------------------------- 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 91 ILE 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 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 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 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 270 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 369 ASN Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 474 LYS Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 286 MET Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 369 ASN Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 449 ASP Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 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 H residue 75 GLU Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain H residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 278 optimal weight: 2.9990 chunk 233 optimal weight: 0.0970 chunk 319 optimal weight: 3.9990 chunk 297 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 324 optimal weight: 0.9990 chunk 185 optimal weight: 6.9990 chunk 293 optimal weight: 0.6980 chunk 191 optimal weight: 0.6980 chunk 125 optimal weight: 0.9980 chunk 210 optimal weight: 3.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 ** 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 94 ASN G 100 GLN ** G 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3896 r_free = 0.3896 target = 0.174761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.129496 restraints weight = 33677.628| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.75 r_work: 0.3219 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 31600 Z= 0.116 Angle : 0.604 12.040 42904 Z= 0.285 Chirality : 0.043 0.169 4872 Planarity : 0.004 0.058 5336 Dihedral : 17.299 179.587 5208 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.32 % Favored : 96.57 % Rotamer: Outliers : 4.07 % Allowed : 17.58 % Favored : 78.35 % 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: 0.22 (0.14), residues: 3880 helix: 1.49 (0.14), residues: 1384 sheet: -0.83 (0.22), residues: 512 loop : -0.50 (0.14), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 171 PHE 0.009 0.001 PHE E 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 0.03302 ( 1206) hydrogen bonds : angle 4.98652 ( 3390) covalent geometry : bond 0.00260 (31592) covalent geometry : angle 0.60375 (42904) Misc. bond : bond 0.00027 ( 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 610 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 480 time to evaluate : 3.252 Fit side-chains revert: symmetry clash REVERT: A 195 LYS cc_start: 0.7515 (tptt) cc_final: 0.6802 (tppt) REVERT: A 206 LYS cc_start: 0.7599 (tptp) cc_final: 0.7040 (tptp) REVERT: A 265 GLN cc_start: 0.8116 (tt0) cc_final: 0.7524 (tp40) REVERT: A 274 ASP cc_start: 0.8462 (t0) cc_final: 0.8224 (t0) REVERT: A 500 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7372 (tt0) REVERT: B 106 LYS cc_start: 0.8458 (ttmm) cc_final: 0.8206 (ttmt) REVERT: B 111 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8093 (tm-30) REVERT: B 114 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7834 (t80) REVERT: B 195 LYS cc_start: 0.7676 (tptt) cc_final: 0.7030 (tppt) REVERT: B 286 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8122 (ttm) REVERT: B 288 LYS cc_start: 0.7642 (mttm) cc_final: 0.7364 (mtmp) REVERT: B 410 LYS cc_start: 0.6943 (mtpt) cc_final: 0.6495 (pmtt) REVERT: C 111 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8037 (tm-30) REVERT: C 168 GLU cc_start: 0.4624 (OUTLIER) cc_final: 0.4324 (pp20) REVERT: C 230 ASN cc_start: 0.7941 (t0) cc_final: 0.7681 (t160) REVERT: C 335 GLU cc_start: 0.7921 (tt0) cc_final: 0.7484 (tt0) REVERT: C 410 LYS cc_start: 0.6927 (mtmt) cc_final: 0.6402 (pmtt) REVERT: D 195 LYS cc_start: 0.7640 (tptt) cc_final: 0.7036 (tppt) REVERT: D 265 GLN cc_start: 0.8044 (tt0) cc_final: 0.7459 (tp40) REVERT: D 274 ASP cc_start: 0.8413 (t0) cc_final: 0.8130 (t0) REVERT: D 335 GLU cc_start: 0.7953 (tt0) cc_final: 0.7533 (tt0) REVERT: D 410 LYS cc_start: 0.7158 (mtpt) cc_final: 0.6570 (pmtt) REVERT: E 179 MET cc_start: 0.7613 (ptp) cc_final: 0.7050 (ptp) REVERT: E 195 LYS cc_start: 0.7646 (tptt) cc_final: 0.6926 (tppt) REVERT: E 242 LYS cc_start: 0.7506 (mmtm) cc_final: 0.6994 (mttt) REVERT: E 265 GLN cc_start: 0.8135 (tt0) cc_final: 0.7540 (tp40) REVERT: E 286 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8134 (ttm) REVERT: F 106 LYS cc_start: 0.8495 (ttmm) cc_final: 0.8200 (ttmt) REVERT: F 195 LYS cc_start: 0.7742 (tptm) cc_final: 0.7106 (tppt) REVERT: F 208 LYS cc_start: 0.7632 (mtpm) cc_final: 0.7235 (mttp) REVERT: F 265 GLN cc_start: 0.8106 (tt0) cc_final: 0.7526 (tp40) REVERT: F 491 GLU cc_start: 0.8485 (tp30) cc_final: 0.8250 (tp30) REVERT: G 48 GLN cc_start: 0.8242 (mt0) cc_final: 0.8034 (mt0) REVERT: G 114 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.8042 (t80) REVERT: G 195 LYS cc_start: 0.7647 (tptm) cc_final: 0.7059 (tppt) REVERT: G 206 LYS cc_start: 0.7630 (mmtm) cc_final: 0.7010 (mmmm) REVERT: G 208 LYS cc_start: 0.8132 (mtpm) cc_final: 0.7582 (mtmt) REVERT: G 265 GLN cc_start: 0.8037 (tt0) cc_final: 0.7478 (tp40) REVERT: G 286 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8225 (ttm) REVERT: G 288 LYS cc_start: 0.7720 (mttm) cc_final: 0.7367 (mtmp) REVERT: G 335 GLU cc_start: 0.7874 (tt0) cc_final: 0.7465 (tt0) REVERT: G 410 LYS cc_start: 0.7300 (mtpt) cc_final: 0.6519 (pmtt) REVERT: G 412 ARG cc_start: 0.7017 (ptt180) cc_final: 0.6709 (ptt90) REVERT: G 500 GLU cc_start: 0.7844 (tt0) cc_final: 0.7582 (pt0) REVERT: H 75 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6637 (tt0) REVERT: H 114 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.8001 (t80) REVERT: H 195 LYS cc_start: 0.7680 (tptm) cc_final: 0.7000 (tppt) REVERT: H 206 LYS cc_start: 0.7706 (mmtt) cc_final: 0.7476 (tptp) REVERT: H 261 ASP cc_start: 0.7518 (m-30) cc_final: 0.7297 (m-30) REVERT: H 410 LYS cc_start: 0.6940 (mtmt) cc_final: 0.6482 (pmtt) REVERT: H 420 MET cc_start: 0.5254 (tmm) cc_final: 0.3917 (mpt) REVERT: H 510 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7056 (mt-10) outliers start: 130 outliers final: 64 residues processed: 560 average time/residue: 1.1294 time to fit residues: 769.3833 Evaluate side-chains 541 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 466 time to evaluate : 3.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 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 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 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 329 SER Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 369 ASN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 369 ASN 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 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 318 VAL 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 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 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 270 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: 4.9990 chunk 25 optimal weight: 0.8980 chunk 135 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 chunk 302 optimal weight: 6.9990 chunk 164 optimal weight: 0.7980 chunk 189 optimal weight: 0.4980 chunk 310 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 C 303 ASN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN D 230 ASN ** 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 F 100 GLN ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.172895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.127233 restraints weight = 33867.753| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.76 r_work: 0.3194 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 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 : 0.003 0.032 31600 Z= 0.150 Angle : 0.618 12.063 42904 Z= 0.295 Chirality : 0.044 0.177 4872 Planarity : 0.004 0.057 5336 Dihedral : 16.889 179.460 5208 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.10 % Favored : 95.80 % Rotamer: Outliers : 4.35 % Allowed : 18.14 % Favored : 77.51 % 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: 0.16 (0.13), residues: 3880 helix: 1.37 (0.14), residues: 1400 sheet: -0.60 (0.24), residues: 432 loop : -0.60 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 171 PHE 0.009 0.001 PHE E 24 TYR 0.012 0.001 TYR H 348 ARG 0.004 0.000 ARG H 231 Details of bonding type rmsd hydrogen bonds : bond 0.03635 ( 1206) hydrogen bonds : angle 4.98598 ( 3390) covalent geometry : bond 0.00347 (31592) covalent geometry : angle 0.61824 (42904) Misc. bond : bond 0.00036 ( 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 631 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 492 time to evaluate : 3.409 Fit side-chains REVERT: A 195 LYS cc_start: 0.7626 (tptt) cc_final: 0.6931 (tppt) REVERT: A 206 LYS cc_start: 0.7684 (tptp) cc_final: 0.7145 (tptp) REVERT: A 265 GLN cc_start: 0.8134 (tt0) cc_final: 0.7591 (tp40) REVERT: A 274 ASP cc_start: 0.8463 (t0) cc_final: 0.8245 (t0) REVERT: A 500 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7489 (tt0) REVERT: B 106 LYS cc_start: 0.8522 (ttmm) cc_final: 0.8277 (ttmt) REVERT: B 111 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7949 (tm-30) REVERT: B 114 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.7798 (t80) REVERT: B 195 LYS cc_start: 0.7756 (tptt) cc_final: 0.7118 (tppt) REVERT: B 286 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8152 (ttm) REVERT: B 288 LYS cc_start: 0.7735 (mttm) cc_final: 0.7421 (mtmp) REVERT: B 410 LYS cc_start: 0.7042 (mtpt) cc_final: 0.6546 (pmtt) REVERT: B 420 MET cc_start: 0.5075 (tpp) cc_final: 0.4628 (tpp) REVERT: C 111 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8285 (tm-30) REVERT: C 168 GLU cc_start: 0.4566 (OUTLIER) cc_final: 0.4344 (pp20) REVERT: C 206 LYS cc_start: 0.7941 (mmpt) cc_final: 0.6844 (tptp) REVERT: C 335 GLU cc_start: 0.7957 (tt0) cc_final: 0.7558 (tt0) REVERT: C 410 LYS cc_start: 0.6968 (mtmt) cc_final: 0.6469 (pmtt) REVERT: D 195 LYS cc_start: 0.7717 (tptt) cc_final: 0.7114 (tppt) REVERT: D 265 GLN cc_start: 0.8026 (tt0) cc_final: 0.7486 (tp40) REVERT: D 274 ASP cc_start: 0.8397 (t0) cc_final: 0.8110 (t0) REVERT: D 286 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8326 (ttm) REVERT: D 335 GLU cc_start: 0.7996 (tt0) cc_final: 0.7593 (tt0) REVERT: D 410 LYS cc_start: 0.7168 (mtpt) cc_final: 0.6613 (pmtt) REVERT: E 111 GLU cc_start: 0.8707 (tt0) cc_final: 0.8006 (tm-30) REVERT: E 195 LYS cc_start: 0.7733 (tptt) cc_final: 0.7018 (tppt) REVERT: E 242 LYS cc_start: 0.7724 (mmtm) cc_final: 0.7213 (mttt) REVERT: E 265 GLN cc_start: 0.8103 (tt0) cc_final: 0.7544 (tp40) REVERT: E 286 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8193 (ttm) REVERT: F 106 LYS cc_start: 0.8595 (ttmm) cc_final: 0.8265 (ttmt) REVERT: F 195 LYS cc_start: 0.7838 (tptm) cc_final: 0.7208 (tppt) REVERT: F 208 LYS cc_start: 0.7750 (mtpm) cc_final: 0.7408 (mttp) REVERT: F 265 GLN cc_start: 0.8102 (tt0) cc_final: 0.7551 (tp40) REVERT: F 286 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8215 (ttm) REVERT: F 491 GLU cc_start: 0.8431 (tp30) cc_final: 0.8215 (tp30) REVERT: G 114 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.8088 (t80) REVERT: G 162 ASP cc_start: 0.7157 (m-30) cc_final: 0.6443 (m-30) REVERT: G 195 LYS cc_start: 0.7722 (tptm) cc_final: 0.7129 (tppt) REVERT: G 206 LYS cc_start: 0.7767 (mmtm) cc_final: 0.7137 (mmmm) REVERT: G 208 LYS cc_start: 0.8189 (mtpm) cc_final: 0.7690 (mtmt) REVERT: G 265 GLN cc_start: 0.8037 (tt0) cc_final: 0.7485 (tp40) REVERT: G 286 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8280 (ttm) REVERT: G 288 LYS cc_start: 0.7832 (mttm) cc_final: 0.7509 (mtmp) REVERT: G 335 GLU cc_start: 0.7882 (tt0) cc_final: 0.7492 (tt0) REVERT: G 410 LYS cc_start: 0.7308 (mtpt) cc_final: 0.6582 (pmtt) REVERT: G 412 ARG cc_start: 0.7117 (ptt180) cc_final: 0.6822 (ptt90) REVERT: G 500 GLU cc_start: 0.7973 (tt0) cc_final: 0.7720 (tt0) REVERT: H 75 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6635 (tt0) REVERT: H 114 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.8083 (t80) REVERT: H 195 LYS cc_start: 0.7748 (tptm) cc_final: 0.7071 (tppt) REVERT: H 206 LYS cc_start: 0.7797 (mmtt) cc_final: 0.7541 (tptp) REVERT: H 261 ASP cc_start: 0.7566 (m-30) cc_final: 0.7366 (m-30) REVERT: H 335 GLU cc_start: 0.7937 (tt0) cc_final: 0.7549 (tt0) REVERT: H 410 LYS cc_start: 0.6995 (mtmt) cc_final: 0.6581 (pmtt) outliers start: 139 outliers final: 79 residues processed: 588 average time/residue: 1.1508 time to fit residues: 830.7342 Evaluate side-chains 563 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 471 time to evaluate : 3.272 ------------------------------------------------------------------------------- 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 111 GLU Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 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 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 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 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 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 318 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 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 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 H residue 75 GLU Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 369 ASN Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 474 LYS Rotamers are restrained with sigma=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: 0.7980 chunk 58 optimal weight: 0.5980 chunk 357 optimal weight: 0.8980 chunk 293 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 245 optimal weight: 0.6980 chunk 125 optimal weight: 0.0670 chunk 282 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN E 230 ASN F 100 GLN ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN G 100 GLN ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3910 r_free = 0.3910 target = 0.175915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.130303 restraints weight = 33670.082| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.82 r_work: 0.3219 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 31600 Z= 0.112 Angle : 0.591 11.705 42904 Z= 0.281 Chirality : 0.043 0.151 4872 Planarity : 0.004 0.056 5336 Dihedral : 16.534 179.776 5208 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.07 % Favored : 96.83 % Rotamer: Outliers : 4.07 % Allowed : 19.05 % 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: 0.28 (0.14), residues: 3880 helix: 1.51 (0.14), residues: 1400 sheet: -0.60 (0.24), residues: 432 loop : -0.55 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 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 0.03181 ( 1206) hydrogen bonds : angle 4.87789 ( 3390) covalent geometry : bond 0.00249 (31592) covalent geometry : angle 0.59089 (42904) Misc. bond : bond 0.00022 ( 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 609 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 479 time to evaluate : 3.230 Fit side-chains REVERT: A 195 LYS cc_start: 0.7621 (tptt) cc_final: 0.6920 (tppt) REVERT: A 206 LYS cc_start: 0.7636 (tptp) cc_final: 0.7238 (tptp) REVERT: A 265 GLN cc_start: 0.8134 (tt0) cc_final: 0.7567 (tp40) REVERT: A 274 ASP cc_start: 0.8428 (t0) cc_final: 0.8167 (t0) REVERT: A 500 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7427 (tt0) REVERT: B 106 LYS cc_start: 0.8439 (ttmm) cc_final: 0.8226 (ttmt) REVERT: B 111 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8126 (tm-30) REVERT: B 114 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.7804 (t80) REVERT: B 195 LYS cc_start: 0.7698 (tptt) cc_final: 0.7057 (tppt) REVERT: B 286 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8181 (ttm) REVERT: B 288 LYS cc_start: 0.7723 (mttm) cc_final: 0.7388 (mtmp) REVERT: B 410 LYS cc_start: 0.7054 (mtpt) cc_final: 0.6528 (pmtt) REVERT: B 420 MET cc_start: 0.4915 (tpp) cc_final: 0.4479 (tpp) REVERT: C 106 LYS cc_start: 0.8477 (ttmm) cc_final: 0.8261 (ttmt) REVERT: C 111 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8256 (tm-30) REVERT: C 206 LYS cc_start: 0.7882 (mmpt) cc_final: 0.6779 (tptp) REVERT: C 335 GLU cc_start: 0.7958 (tt0) cc_final: 0.7543 (tt0) REVERT: C 410 LYS cc_start: 0.6976 (mtmt) cc_final: 0.6430 (pmtt) REVERT: D 91 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8171 (mm) REVERT: D 170 GLU cc_start: 0.2796 (OUTLIER) cc_final: 0.2466 (tm-30) REVERT: D 195 LYS cc_start: 0.7641 (tptt) cc_final: 0.7033 (tppt) REVERT: D 265 GLN cc_start: 0.8034 (tt0) cc_final: 0.7472 (tp40) REVERT: D 274 ASP cc_start: 0.8368 (t0) cc_final: 0.8045 (t0) REVERT: D 286 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8288 (ttm) REVERT: D 335 GLU cc_start: 0.7996 (tt0) cc_final: 0.7556 (tt0) REVERT: D 410 LYS cc_start: 0.7249 (mtpt) cc_final: 0.6637 (pmtt) REVERT: E 111 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8037 (tm-30) REVERT: E 195 LYS cc_start: 0.7686 (tptt) cc_final: 0.6968 (tppt) REVERT: E 242 LYS cc_start: 0.7615 (mmtm) cc_final: 0.7100 (mttt) REVERT: E 265 GLN cc_start: 0.8100 (tt0) cc_final: 0.7541 (tp40) REVERT: E 286 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8174 (ttm) REVERT: E 500 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: F 106 LYS cc_start: 0.8518 (ttmm) cc_final: 0.8194 (ttmt) REVERT: F 195 LYS cc_start: 0.7771 (tptm) cc_final: 0.7159 (tppt) REVERT: F 208 LYS cc_start: 0.7668 (mtpm) cc_final: 0.7350 (mttp) REVERT: F 265 GLN cc_start: 0.8109 (tt0) cc_final: 0.7528 (tp40) REVERT: F 491 GLU cc_start: 0.8469 (tp30) cc_final: 0.8268 (tp30) REVERT: G 100 GLN cc_start: 0.8489 (tt0) cc_final: 0.8261 (tt0) REVERT: G 114 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.8058 (t80) REVERT: G 162 ASP cc_start: 0.7108 (m-30) cc_final: 0.6366 (m-30) REVERT: G 195 LYS cc_start: 0.7671 (tptm) cc_final: 0.7086 (tppt) REVERT: G 206 LYS cc_start: 0.7734 (mmtm) cc_final: 0.7080 (tptp) REVERT: G 208 LYS cc_start: 0.8084 (mtpm) cc_final: 0.7569 (mtmt) REVERT: G 265 GLN cc_start: 0.8023 (tt0) cc_final: 0.7453 (tp40) REVERT: G 286 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8250 (ttm) REVERT: G 288 LYS cc_start: 0.7767 (mttm) cc_final: 0.7439 (mtmp) REVERT: G 335 GLU cc_start: 0.7882 (tt0) cc_final: 0.7481 (tt0) REVERT: G 410 LYS cc_start: 0.7276 (mtpt) cc_final: 0.6450 (pmtt) REVERT: G 412 ARG cc_start: 0.7021 (ptt180) cc_final: 0.6750 (ptt90) REVERT: G 500 GLU cc_start: 0.7802 (tt0) cc_final: 0.7498 (pt0) REVERT: H 75 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6641 (tt0) REVERT: H 114 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.8052 (t80) REVERT: H 195 LYS cc_start: 0.7711 (tptm) cc_final: 0.7036 (tppt) REVERT: H 206 LYS cc_start: 0.7740 (mmtt) cc_final: 0.7412 (tptp) REVERT: H 261 ASP cc_start: 0.7520 (m-30) cc_final: 0.7316 (m-30) REVERT: H 335 GLU cc_start: 0.7930 (tt0) cc_final: 0.7515 (tt0) REVERT: H 410 LYS cc_start: 0.7018 (mtmt) cc_final: 0.6565 (pmtt) outliers start: 130 outliers final: 81 residues processed: 569 average time/residue: 1.1139 time to fit residues: 776.1934 Evaluate side-chains 573 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 477 time to evaluate : 3.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 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 325 MET Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 369 ASN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 474 LYS Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 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 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 332 ILE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 386 MET 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 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 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: 0.2980 chunk 25 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 chunk 271 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 186 optimal weight: 0.9980 chunk 308 optimal weight: 1.9990 chunk 285 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 367 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN E 230 ASN F 100 GLN ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** G 243 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 = 0.3888 r_free = 0.3888 target = 0.173840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.128402 restraints weight = 33751.764| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.75 r_work: 0.3223 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2177 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= 0.125 Angle : 0.594 11.444 42904 Z= 0.283 Chirality : 0.043 0.150 4872 Planarity : 0.004 0.056 5336 Dihedral : 16.347 178.381 5208 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.58 % Favored : 96.31 % Rotamer: Outliers : 3.88 % Allowed : 19.67 % Favored : 76.44 % 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: 0.28 (0.14), residues: 3880 helix: 1.51 (0.14), residues: 1400 sheet: -0.60 (0.24), residues: 432 loop : -0.54 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 171 PHE 0.008 0.001 PHE D 35 TYR 0.010 0.001 TYR F 348 ARG 0.003 0.000 ARG D 412 Details of bonding type rmsd hydrogen bonds : bond 0.03296 ( 1206) hydrogen bonds : angle 4.86385 ( 3390) covalent geometry : bond 0.00286 (31592) covalent geometry : angle 0.59395 (42904) Misc. bond : bond 0.00033 ( 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 604 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 480 time to evaluate : 3.373 Fit side-chains REVERT: A 75 GLU cc_start: 0.6944 (tt0) cc_final: 0.6723 (tt0) REVERT: A 195 LYS cc_start: 0.7628 (tptt) cc_final: 0.6916 (tppt) REVERT: A 206 LYS cc_start: 0.7637 (tptp) cc_final: 0.7213 (tptp) REVERT: A 265 GLN cc_start: 0.8124 (tt0) cc_final: 0.7538 (tp40) REVERT: A 274 ASP cc_start: 0.8406 (t0) cc_final: 0.8138 (t0) REVERT: A 500 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7439 (tt0) REVERT: B 106 LYS cc_start: 0.8404 (ttmm) cc_final: 0.8188 (ttmt) REVERT: B 111 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8069 (tm-30) REVERT: B 195 LYS cc_start: 0.7763 (tptt) cc_final: 0.7125 (tppt) REVERT: B 224 ARG cc_start: 0.7997 (ttt90) cc_final: 0.7405 (ttt90) REVERT: B 286 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8146 (ttm) REVERT: B 288 LYS cc_start: 0.7714 (mttm) cc_final: 0.7375 (mtmp) REVERT: B 410 LYS cc_start: 0.7034 (mtpt) cc_final: 0.6501 (pmtt) REVERT: B 420 MET cc_start: 0.4848 (tpp) cc_final: 0.4404 (tpp) REVERT: C 106 LYS cc_start: 0.8457 (ttmm) cc_final: 0.8225 (ttmt) REVERT: C 111 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8301 (tm-30) REVERT: C 195 LYS cc_start: 0.7840 (tptm) cc_final: 0.7351 (tppt) REVERT: C 206 LYS cc_start: 0.7860 (mmpt) cc_final: 0.6709 (tptp) REVERT: C 335 GLU cc_start: 0.7923 (tt0) cc_final: 0.7495 (tt0) REVERT: C 410 LYS cc_start: 0.6952 (mtmt) cc_final: 0.6436 (pmtt) REVERT: D 170 GLU cc_start: 0.2914 (OUTLIER) cc_final: 0.2577 (tm-30) REVERT: D 195 LYS cc_start: 0.7616 (tptt) cc_final: 0.7004 (tppt) REVERT: D 265 GLN cc_start: 0.8054 (tt0) cc_final: 0.7482 (tp40) REVERT: D 274 ASP cc_start: 0.8379 (t0) cc_final: 0.8051 (t0) REVERT: D 335 GLU cc_start: 0.7969 (tt0) cc_final: 0.7510 (tt0) REVERT: D 410 LYS cc_start: 0.7229 (mtpt) cc_final: 0.6615 (pmtt) REVERT: E 100 GLN cc_start: 0.8471 (tt0) cc_final: 0.8232 (tt0) REVERT: E 111 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8029 (tm-30) REVERT: E 195 LYS cc_start: 0.7668 (tptt) cc_final: 0.6951 (tppt) REVERT: E 242 LYS cc_start: 0.7596 (mmtm) cc_final: 0.7065 (mttt) REVERT: E 265 GLN cc_start: 0.8078 (tt0) cc_final: 0.7516 (tp40) REVERT: E 286 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8116 (ttm) REVERT: E 402 PHE cc_start: 0.5961 (m-80) cc_final: 0.5467 (m-80) REVERT: F 106 LYS cc_start: 0.8472 (ttmm) cc_final: 0.8144 (ttmt) REVERT: F 195 LYS cc_start: 0.7754 (tptm) cc_final: 0.7139 (tppt) REVERT: F 208 LYS cc_start: 0.7628 (mtpm) cc_final: 0.7296 (mttp) REVERT: F 265 GLN cc_start: 0.8120 (tt0) cc_final: 0.7551 (tp40) REVERT: F 286 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8149 (ttm) REVERT: F 491 GLU cc_start: 0.8442 (tp30) cc_final: 0.8231 (tp30) REVERT: G 100 GLN cc_start: 0.8480 (tt0) cc_final: 0.8261 (tt0) REVERT: G 162 ASP cc_start: 0.7071 (m-30) cc_final: 0.6367 (m-30) REVERT: G 195 LYS cc_start: 0.7633 (tptm) cc_final: 0.7046 (tppt) REVERT: G 206 LYS cc_start: 0.7723 (mmtm) cc_final: 0.7053 (tptp) REVERT: G 208 LYS cc_start: 0.8083 (mtpm) cc_final: 0.7558 (mtmt) REVERT: G 265 GLN cc_start: 0.8024 (tt0) cc_final: 0.7437 (tp40) REVERT: G 286 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8245 (ttm) REVERT: G 288 LYS cc_start: 0.7748 (mttm) cc_final: 0.7412 (mtmp) REVERT: G 410 LYS cc_start: 0.7268 (mtpt) cc_final: 0.6472 (pmtt) REVERT: G 412 ARG cc_start: 0.7038 (ptt180) cc_final: 0.6771 (ptt90) REVERT: G 500 GLU cc_start: 0.7829 (tt0) cc_final: 0.7473 (pt0) REVERT: H 75 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6673 (tt0) REVERT: H 114 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.8045 (t80) REVERT: H 195 LYS cc_start: 0.7710 (tptm) cc_final: 0.7032 (tppt) REVERT: H 206 LYS cc_start: 0.7706 (mmtt) cc_final: 0.7392 (tptp) REVERT: H 335 GLU cc_start: 0.7911 (tt0) cc_final: 0.7459 (tt0) REVERT: H 410 LYS cc_start: 0.6995 (mtmt) cc_final: 0.6552 (pmtt) outliers start: 124 outliers final: 87 residues processed: 565 average time/residue: 1.6579 time to fit residues: 1161.7227 Evaluate side-chains 567 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 469 time to evaluate : 3.457 ------------------------------------------------------------------------------- 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 325 MET 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 111 GLU Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 325 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 270 VAL Chi-restraints excluded: chain C residue 325 MET 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 114 PHE Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 369 ASN Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 474 LYS Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 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 318 VAL Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 369 ASN Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 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 332 ILE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 386 MET 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 47 ASP Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 369 ASN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 474 LYS Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 273 optimal weight: 0.9990 chunk 158 optimal weight: 9.9990 chunk 179 optimal weight: 1.9990 chunk 254 optimal weight: 10.0000 chunk 306 optimal weight: 2.9990 chunk 361 optimal weight: 2.9990 chunk 318 optimal weight: 0.7980 chunk 146 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 232 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 100 GLN ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.171684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.126029 restraints weight = 33641.960| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.74 r_work: 0.3198 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 31600 Z= 0.153 Angle : 0.617 11.709 42904 Z= 0.295 Chirality : 0.044 0.151 4872 Planarity : 0.004 0.058 5336 Dihedral : 16.221 178.405 5208 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.45 % Favored : 96.44 % Rotamer: Outliers : 3.82 % Allowed : 20.08 % Favored : 76.10 % 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: 0.23 (0.14), residues: 3880 helix: 1.44 (0.14), residues: 1400 sheet: -0.64 (0.24), residues: 432 loop : -0.54 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 171 PHE 0.009 0.001 PHE E 24 TYR 0.012 0.001 TYR H 348 ARG 0.004 0.000 ARG D 412 Details of bonding type rmsd hydrogen bonds : bond 0.03589 ( 1206) hydrogen bonds : angle 4.92181 ( 3390) covalent geometry : bond 0.00359 (31592) covalent geometry : angle 0.61740 (42904) Misc. bond : bond 0.00039 ( 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 603 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 481 time to evaluate : 3.155 Fit side-chains REVERT: A 75 GLU cc_start: 0.7004 (tt0) cc_final: 0.6781 (tt0) REVERT: A 106 LYS cc_start: 0.8538 (ttmm) cc_final: 0.8303 (ttmt) REVERT: A 195 LYS cc_start: 0.7683 (tptt) cc_final: 0.7013 (tppt) REVERT: A 206 LYS cc_start: 0.7567 (tptp) cc_final: 0.7017 (tptp) REVERT: A 265 GLN cc_start: 0.8151 (tt0) cc_final: 0.7597 (tp40) REVERT: A 274 ASP cc_start: 0.8439 (t0) cc_final: 0.8160 (t0) REVERT: A 500 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7459 (tt0) REVERT: B 106 LYS cc_start: 0.8418 (ttmm) cc_final: 0.8180 (ttmt) REVERT: B 111 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7892 (tm-30) REVERT: B 195 LYS cc_start: 0.7751 (tptt) cc_final: 0.7124 (tppt) REVERT: B 224 ARG cc_start: 0.8034 (ttt90) cc_final: 0.7468 (ttt90) REVERT: B 286 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8125 (ttm) REVERT: B 288 LYS cc_start: 0.7712 (mttm) cc_final: 0.7374 (mtmp) REVERT: B 410 LYS cc_start: 0.7065 (mtpt) cc_final: 0.6532 (pmtt) REVERT: B 420 MET cc_start: 0.4790 (tpp) cc_final: 0.4372 (tpp) REVERT: C 106 LYS cc_start: 0.8465 (ttmm) cc_final: 0.8234 (ttmt) REVERT: C 111 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8213 (tm-30) REVERT: C 195 LYS cc_start: 0.7839 (tptm) cc_final: 0.7344 (tppt) REVERT: C 206 LYS cc_start: 0.7862 (mmpt) cc_final: 0.6676 (tptp) REVERT: C 335 GLU cc_start: 0.7935 (tt0) cc_final: 0.7507 (tt0) REVERT: C 420 MET cc_start: 0.4822 (OUTLIER) cc_final: 0.4606 (tpp) REVERT: D 195 LYS cc_start: 0.7647 (tptt) cc_final: 0.7036 (tppt) REVERT: D 265 GLN cc_start: 0.8066 (tt0) cc_final: 0.7493 (tp40) REVERT: D 274 ASP cc_start: 0.8376 (t0) cc_final: 0.8063 (t0) REVERT: D 335 GLU cc_start: 0.7954 (tt0) cc_final: 0.7492 (tt0) REVERT: D 410 LYS cc_start: 0.7211 (mtpt) cc_final: 0.6587 (pmtt) REVERT: E 111 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8017 (tm-30) REVERT: E 195 LYS cc_start: 0.7765 (tptt) cc_final: 0.7050 (tppt) REVERT: E 242 LYS cc_start: 0.7614 (mmtm) cc_final: 0.7069 (mttt) REVERT: E 265 GLN cc_start: 0.8098 (tt0) cc_final: 0.7525 (tp40) REVERT: E 286 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8144 (ttm) REVERT: E 402 PHE cc_start: 0.5983 (m-80) cc_final: 0.5500 (m-80) REVERT: F 106 LYS cc_start: 0.8507 (ttmm) cc_final: 0.8174 (ttmt) REVERT: F 195 LYS cc_start: 0.7758 (tptm) cc_final: 0.7136 (tppt) REVERT: F 208 LYS cc_start: 0.7641 (mtpm) cc_final: 0.7252 (mttp) REVERT: F 265 GLN cc_start: 0.8098 (tt0) cc_final: 0.7516 (tp40) REVERT: F 286 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8174 (ttm) REVERT: F 491 GLU cc_start: 0.8444 (tp30) cc_final: 0.8231 (tp30) REVERT: G 100 GLN cc_start: 0.8536 (tt0) cc_final: 0.8317 (tt0) REVERT: G 162 ASP cc_start: 0.7051 (m-30) cc_final: 0.6337 (m-30) REVERT: G 195 LYS cc_start: 0.7629 (tptm) cc_final: 0.7046 (tppt) REVERT: G 206 LYS cc_start: 0.7745 (mmtm) cc_final: 0.7193 (mmmm) REVERT: G 208 LYS cc_start: 0.8107 (mtpm) cc_final: 0.7593 (mtmt) REVERT: G 265 GLN cc_start: 0.8018 (tt0) cc_final: 0.7430 (tp40) REVERT: G 286 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8241 (ttm) REVERT: G 410 LYS cc_start: 0.7281 (mtpt) cc_final: 0.6498 (pmtt) REVERT: G 412 ARG cc_start: 0.7116 (ptt180) cc_final: 0.6830 (ptt90) REVERT: G 500 GLU cc_start: 0.7878 (tt0) cc_final: 0.7479 (pt0) REVERT: H 75 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6661 (tt0) REVERT: H 114 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.8034 (t80) REVERT: H 195 LYS cc_start: 0.7650 (tptm) cc_final: 0.6989 (tppt) REVERT: H 224 ARG cc_start: 0.8083 (ttt90) cc_final: 0.7441 (ttt90) REVERT: H 335 GLU cc_start: 0.7921 (tt0) cc_final: 0.7474 (tt0) REVERT: H 410 LYS cc_start: 0.7069 (mtmt) cc_final: 0.6581 (pmtt) outliers start: 122 outliers final: 86 residues processed: 563 average time/residue: 1.1375 time to fit residues: 781.0567 Evaluate side-chains 565 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 468 time to evaluate : 3.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 325 MET 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 49 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 325 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 270 VAL Chi-restraints excluded: chain C residue 325 MET 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 420 MET 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 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 318 VAL Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 369 ASN Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 474 LYS Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 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 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 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: 20.0000 chunk 371 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 326 optimal weight: 0.9980 chunk 65 optimal weight: 0.0060 chunk 172 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 232 optimal weight: 0.3980 chunk 305 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 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 230 ASN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN E 230 ASN ** E 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN F 243 GLN ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN H 243 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.174540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.128983 restraints weight = 33758.377| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.76 r_work: 0.3233 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 31600 Z= 0.114 Angle : 0.593 11.156 42904 Z= 0.281 Chirality : 0.043 0.146 4872 Planarity : 0.004 0.057 5336 Dihedral : 15.902 178.365 5208 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.20 % Favored : 96.70 % Rotamer: Outliers : 3.41 % Allowed : 20.65 % Favored : 75.94 % 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: 0.32 (0.14), residues: 3880 helix: 1.54 (0.14), residues: 1400 sheet: -0.62 (0.24), residues: 432 loop : -0.50 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS F 171 PHE 0.009 0.001 PHE D 35 TYR 0.009 0.001 TYR G 509 ARG 0.003 0.000 ARG H 412 Details of bonding type rmsd hydrogen bonds : bond 0.03156 ( 1206) hydrogen bonds : angle 4.83113 ( 3390) covalent geometry : bond 0.00256 (31592) covalent geometry : angle 0.59257 (42904) Misc. bond : bond 0.00023 ( 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 579 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 470 time to evaluate : 3.501 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.6930 (tt0) cc_final: 0.6702 (tt0) REVERT: A 106 LYS cc_start: 0.8535 (ttmm) cc_final: 0.8301 (ttmt) REVERT: A 195 LYS cc_start: 0.7647 (tptt) cc_final: 0.6976 (tppt) REVERT: A 206 LYS cc_start: 0.7532 (tptp) cc_final: 0.7088 (tptp) REVERT: A 265 GLN cc_start: 0.8122 (tt0) cc_final: 0.7557 (tp40) REVERT: A 274 ASP cc_start: 0.8399 (t0) cc_final: 0.8115 (t0) REVERT: A 500 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7470 (tt0) REVERT: B 106 LYS cc_start: 0.8377 (ttmm) cc_final: 0.8146 (ttmt) REVERT: B 111 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7776 (tm-30) REVERT: B 195 LYS cc_start: 0.7731 (tptt) cc_final: 0.7067 (tppt) REVERT: B 224 ARG cc_start: 0.8033 (ttt90) cc_final: 0.7459 (ttt90) REVERT: B 286 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8077 (ttm) REVERT: B 288 LYS cc_start: 0.7715 (mttm) cc_final: 0.7372 (mtmp) REVERT: B 410 LYS cc_start: 0.7043 (mtpt) cc_final: 0.6490 (pmtt) REVERT: B 420 MET cc_start: 0.4660 (tpp) cc_final: 0.4283 (tpp) REVERT: C 106 LYS cc_start: 0.8454 (ttmm) cc_final: 0.8224 (ttmt) REVERT: C 111 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8223 (tm-30) REVERT: C 195 LYS cc_start: 0.7773 (tptm) cc_final: 0.7292 (tppt) REVERT: C 335 GLU cc_start: 0.7930 (tt0) cc_final: 0.7496 (tt0) REVERT: C 410 LYS cc_start: 0.6956 (mtmt) cc_final: 0.6427 (pmtt) REVERT: D 195 LYS cc_start: 0.7594 (tptt) cc_final: 0.6955 (tppt) REVERT: D 265 GLN cc_start: 0.8060 (tt0) cc_final: 0.7481 (tp40) REVERT: D 274 ASP cc_start: 0.8391 (t0) cc_final: 0.8072 (t0) REVERT: D 410 LYS cc_start: 0.7204 (mtpt) cc_final: 0.6594 (pmtt) REVERT: E 100 GLN cc_start: 0.8436 (tt0) cc_final: 0.8197 (tt0) REVERT: E 111 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8057 (tm-30) REVERT: E 195 LYS cc_start: 0.7701 (tptt) cc_final: 0.6982 (tppt) REVERT: E 242 LYS cc_start: 0.7577 (mmtm) cc_final: 0.7046 (mttt) REVERT: E 265 GLN cc_start: 0.8050 (tt0) cc_final: 0.7492 (tp40) REVERT: E 286 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8102 (ttm) REVERT: E 402 PHE cc_start: 0.5997 (m-80) cc_final: 0.5518 (m-80) REVERT: F 106 LYS cc_start: 0.8445 (ttmm) cc_final: 0.8164 (ttmt) REVERT: F 195 LYS cc_start: 0.7727 (tptm) cc_final: 0.7113 (tppt) REVERT: F 208 LYS cc_start: 0.7569 (mtpm) cc_final: 0.7231 (mttp) REVERT: F 265 GLN cc_start: 0.8078 (tt0) cc_final: 0.7504 (tp40) REVERT: F 286 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8151 (ttm) REVERT: F 491 GLU cc_start: 0.8467 (tp30) cc_final: 0.8259 (tp30) REVERT: G 100 GLN cc_start: 0.8479 (tt0) cc_final: 0.8247 (tt0) REVERT: G 162 ASP cc_start: 0.7051 (m-30) cc_final: 0.6354 (m-30) REVERT: G 195 LYS cc_start: 0.7572 (tptm) cc_final: 0.6980 (tppt) REVERT: G 206 LYS cc_start: 0.7716 (mmtm) cc_final: 0.7261 (mmmm) REVERT: G 208 LYS cc_start: 0.8034 (mtpm) cc_final: 0.7534 (mtmt) REVERT: G 265 GLN cc_start: 0.8030 (tt0) cc_final: 0.7456 (tp40) REVERT: G 286 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8245 (ttm) REVERT: G 410 LYS cc_start: 0.7234 (mtpt) cc_final: 0.6515 (pmtt) REVERT: G 412 ARG cc_start: 0.6960 (ptt180) cc_final: 0.6699 (ptt90) REVERT: G 500 GLU cc_start: 0.7818 (tt0) cc_final: 0.7464 (pt0) REVERT: H 75 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6567 (tt0) REVERT: H 114 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.8043 (t80) REVERT: H 195 LYS cc_start: 0.7694 (tptm) cc_final: 0.7049 (tppt) REVERT: H 206 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7158 (tptp) REVERT: H 224 ARG cc_start: 0.8035 (ttt90) cc_final: 0.7405 (ttt90) REVERT: H 335 GLU cc_start: 0.7896 (tt0) cc_final: 0.7466 (tt0) REVERT: H 410 LYS cc_start: 0.7115 (mtmt) cc_final: 0.6600 (pmtt) outliers start: 109 outliers final: 84 residues processed: 544 average time/residue: 1.1886 time to fit residues: 795.8279 Evaluate side-chains 559 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 464 time to evaluate : 3.497 ------------------------------------------------------------------------------- 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 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 49 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 325 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 437 ILE 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 270 VAL Chi-restraints excluded: chain D residue 369 ASN Chi-restraints excluded: chain D residue 417 LEU 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 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 286 MET Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 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 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 206 LYS 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 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 287 optimal weight: 4.9990 chunk 354 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 271 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 318 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN E 92 HIS E 230 ASN ** E 448 GLN ** 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 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.171252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.125326 restraints weight = 33461.568| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.74 r_work: 0.3184 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 31600 Z= 0.197 Angle : 0.650 11.357 42904 Z= 0.314 Chirality : 0.045 0.150 4872 Planarity : 0.004 0.059 5336 Dihedral : 16.032 177.903 5208 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.36 % Favored : 95.52 % Rotamer: Outliers : 3.54 % Allowed : 20.65 % Favored : 75.81 % 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: 0.11 (0.13), residues: 3880 helix: 1.31 (0.14), residues: 1400 sheet: -0.57 (0.22), residues: 512 loop : -0.62 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 93 PHE 0.012 0.001 PHE G 24 TYR 0.013 0.002 TYR G 348 ARG 0.005 0.000 ARG H 412 Details of bonding type rmsd hydrogen bonds : bond 0.03998 ( 1206) hydrogen bonds : angle 5.01783 ( 3390) covalent geometry : bond 0.00465 (31592) covalent geometry : angle 0.65008 (42904) Misc. bond : bond 0.00057 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23234.10 seconds wall clock time: 404 minutes 51.40 seconds (24291.40 seconds total)