Starting phenix.real_space_refine on Sun Feb 18 04:12:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwq_35062/02_2024/8hwq_35062.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwq_35062/02_2024/8hwq_35062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwq_35062/02_2024/8hwq_35062.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwq_35062/02_2024/8hwq_35062.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwq_35062/02_2024/8hwq_35062.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwq_35062/02_2024/8hwq_35062.pdb" } resolution = 3.58 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= 0.006 sd= 0.063 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: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 13587 2.51 5 N 3430 2.21 5 O 3654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 9": "OE1" <-> "OE2" Residue "F TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 31": "OE1" <-> "OE2" Residue "F TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 139": "OD1" <-> "OD2" Residue "F PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 188": "OE1" <-> "OE2" Residue "F TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 31": "OE1" <-> "OE2" Residue "A ASP 139": "OD1" <-> "OD2" Residue "A PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B ASP 35": "OD1" <-> "OD2" Residue "B PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B GLU 238": "OE1" <-> "OE2" Residue "B TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C ASP 35": "OD1" <-> "OD2" Residue "C PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 139": "OD1" <-> "OD2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C GLU 238": "OE1" <-> "OE2" Residue "C TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 9": "OE1" <-> "OE2" Residue "D TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 31": "OE1" <-> "OE2" Residue "D PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 139": "OD1" <-> "OD2" Residue "D PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 188": "OE1" <-> "OE2" Residue "D TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 238": "OE1" <-> "OE2" Residue "E TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 31": "OE1" <-> "OE2" Residue "E ASP 35": "OD1" <-> "OD2" Residue "E TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 139": "OD1" <-> "OD2" Residue "E PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 188": "OE1" <-> "OE2" Residue "E GLU 238": "OE1" <-> "OE2" Residue "E TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G ASP 35": "OD1" <-> "OD2" Residue "G PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 188": "OE1" <-> "OE2" Residue "G TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 238": "OE1" <-> "OE2" Residue "G TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20783 Number of models: 1 Model: "" Number of chains: 7 Chain: "F" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2969 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain breaks: 2 Chain: "A" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2969 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain breaks: 2 Chain: "B" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2969 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain breaks: 2 Chain: "C" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2969 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain breaks: 2 Chain: "D" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2969 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain breaks: 2 Chain: "E" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2969 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain breaks: 2 Chain: "G" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2969 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain breaks: 2 Time building chain proxies: 10.65, per 1000 atoms: 0.51 Number of scatterers: 20783 At special positions: 0 Unit cell: (125.33, 124.5, 126.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 3654 8.00 N 3430 7.00 C 13587 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 - 3.50 Amino acid : False - 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=0, symmetry=0 Time building additional restraints: 7.63 Conformation dependent library (CDL) restraints added in 3.6 seconds 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5040 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 14 sheets defined 63.4% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'F' and resid 2 through 11 removed outlier: 4.049A pdb=" N GLU F 9 " --> pdb=" O HIS F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 54 Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 73 through 83 Processing helix chain 'F' and resid 104 through 122 removed outlier: 4.181A pdb=" N LYS F 108 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Proline residue: F 111 - end of helix Processing helix chain 'F' and resid 122 through 132 Processing helix chain 'F' and resid 132 through 148 Processing helix chain 'F' and resid 159 through 168 removed outlier: 3.634A pdb=" N LYS F 167 " --> pdb=" O LYS F 163 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER F 168 " --> pdb=" O ILE F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 174 Processing helix chain 'F' and resid 177 through 183 removed outlier: 3.734A pdb=" N ALA F 181 " --> pdb=" O GLU F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 201 removed outlier: 3.515A pdb=" N ALA F 197 " --> pdb=" O GLU F 193 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG F 201 " --> pdb=" O ALA F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 230 removed outlier: 3.635A pdb=" N THR F 208 " --> pdb=" O SER F 204 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU F 216 " --> pdb=" O ARG F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 282 removed outlier: 4.073A pdb=" N VAL F 277 " --> pdb=" O SER F 273 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR F 280 " --> pdb=" O SER F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 296 removed outlier: 4.256A pdb=" N VAL F 286 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU F 294 " --> pdb=" O ASN F 290 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS F 295 " --> pdb=" O LEU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 308 removed outlier: 3.701A pdb=" N MET F 307 " --> pdb=" O SER F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 317 removed outlier: 4.124A pdb=" N LEU F 313 " --> pdb=" O PRO F 309 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU F 314 " --> pdb=" O ALA F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 335 removed outlier: 3.673A pdb=" N VAL F 328 " --> pdb=" O ASN F 324 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 349 removed outlier: 3.537A pdb=" N LEU F 349 " --> pdb=" O LEU F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 367 removed outlier: 4.025A pdb=" N VAL F 365 " --> pdb=" O ASN F 361 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP F 367 " --> pdb=" O ASP F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 374 Processing helix chain 'A' and resid 3 through 11 removed outlier: 4.077A pdb=" N GLU A 9 " --> pdb=" O HIS A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 54 Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 104 through 122 removed outlier: 4.173A pdb=" N LYS A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 132 through 148 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 159 through 168 removed outlier: 3.503A pdb=" N LYS A 163 " --> pdb=" O GLN A 159 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A 167 " --> pdb=" O LYS A 163 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 168 " --> pdb=" O ILE A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 177 through 183 removed outlier: 3.785A pdb=" N ALA A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 201 removed outlier: 3.538A pdb=" N ALA A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 230 removed outlier: 3.749A pdb=" N THR A 208 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 282 removed outlier: 4.078A pdb=" N VAL A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 296 removed outlier: 4.267A pdb=" N VAL A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 308 removed outlier: 3.711A pdb=" N MET A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 317 removed outlier: 4.136A pdb=" N LEU A 313 " --> pdb=" O PRO A 309 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 removed outlier: 3.755A pdb=" N VAL A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 removed outlier: 3.543A pdb=" N LEU A 349 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 removed outlier: 4.049A pdb=" N VAL A 365 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASP A 367 " --> pdb=" O ASP A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 3 through 11 removed outlier: 4.067A pdb=" N GLU B 9 " --> pdb=" O HIS B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 54 Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 73 through 83 Processing helix chain 'B' and resid 104 through 122 removed outlier: 4.202A pdb=" N LYS B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 122 through 132 Processing helix chain 'B' and resid 132 through 148 Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 159 through 168 removed outlier: 3.521A pdb=" N LYS B 163 " --> pdb=" O GLN B 159 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B 167 " --> pdb=" O LYS B 163 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER B 168 " --> pdb=" O ILE B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 177 through 183 removed outlier: 3.739A pdb=" N ALA B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 201 removed outlier: 3.566A pdb=" N ALA B 197 " --> pdb=" O GLU B 193 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG B 201 " --> pdb=" O ALA B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 230 removed outlier: 3.617A pdb=" N THR B 208 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 282 removed outlier: 4.010A pdb=" N VAL B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TYR B 280 " --> pdb=" O SER B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 296 removed outlier: 4.287A pdb=" N VAL B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 288 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 308 removed outlier: 3.700A pdb=" N MET B 307 " --> pdb=" O SER B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 317 removed outlier: 4.138A pdb=" N LEU B 313 " --> pdb=" O PRO B 309 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 335 removed outlier: 3.848A pdb=" N VAL B 328 " --> pdb=" O ASN B 324 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 349 removed outlier: 3.537A pdb=" N LEU B 349 " --> pdb=" O LEU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 367 removed outlier: 4.049A pdb=" N VAL B 365 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASP B 367 " --> pdb=" O ASP B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 3 through 11 removed outlier: 4.090A pdb=" N GLU C 9 " --> pdb=" O HIS C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 54 Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 73 through 83 Processing helix chain 'C' and resid 104 through 122 removed outlier: 4.158A pdb=" N LYS C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Proline residue: C 111 - end of helix Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 132 through 148 Processing helix chain 'C' and resid 159 through 168 removed outlier: 3.500A pdb=" N LYS C 163 " --> pdb=" O GLN C 159 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS C 167 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C 168 " --> pdb=" O ILE C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 174 Processing helix chain 'C' and resid 177 through 183 removed outlier: 3.745A pdb=" N ALA C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 201 removed outlier: 3.588A pdb=" N ALA C 197 " --> pdb=" O GLU C 193 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG C 201 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 230 removed outlier: 3.622A pdb=" N THR C 208 " --> pdb=" O SER C 204 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU C 216 " --> pdb=" O ARG C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 282 removed outlier: 4.080A pdb=" N VAL C 277 " --> pdb=" O SER C 273 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR C 280 " --> pdb=" O SER C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 296 removed outlier: 4.263A pdb=" N VAL C 286 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 308 removed outlier: 3.700A pdb=" N MET C 307 " --> pdb=" O SER C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 317 removed outlier: 4.138A pdb=" N LEU C 313 " --> pdb=" O PRO C 309 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 335 removed outlier: 3.659A pdb=" N VAL C 328 " --> pdb=" O ASN C 324 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 349 removed outlier: 3.547A pdb=" N LEU C 349 " --> pdb=" O LEU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 367 removed outlier: 4.024A pdb=" N VAL C 365 " --> pdb=" O ASN C 361 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ASP C 367 " --> pdb=" O ASP C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 3 through 11 removed outlier: 4.059A pdb=" N GLU D 9 " --> pdb=" O HIS D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 54 Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 73 through 83 Processing helix chain 'D' and resid 104 through 122 removed outlier: 4.178A pdb=" N LYS D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) Proline residue: D 111 - end of helix Processing helix chain 'D' and resid 122 through 132 Processing helix chain 'D' and resid 132 through 148 Processing helix chain 'D' and resid 159 through 168 removed outlier: 3.514A pdb=" N LYS D 163 " --> pdb=" O GLN D 159 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS D 167 " --> pdb=" O LYS D 163 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER D 168 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 174 Processing helix chain 'D' and resid 177 through 183 removed outlier: 3.739A pdb=" N ALA D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 201 removed outlier: 3.508A pdb=" N ALA D 197 " --> pdb=" O GLU D 193 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG D 201 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 230 removed outlier: 3.625A pdb=" N THR D 208 " --> pdb=" O SER D 204 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 216 " --> pdb=" O ARG D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 282 removed outlier: 4.064A pdb=" N VAL D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYR D 280 " --> pdb=" O SER D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 296 removed outlier: 4.260A pdb=" N VAL D 286 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU D 294 " --> pdb=" O ASN D 290 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 308 removed outlier: 3.713A pdb=" N MET D 307 " --> pdb=" O SER D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 317 removed outlier: 4.077A pdb=" N LEU D 313 " --> pdb=" O PRO D 309 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 335 removed outlier: 3.659A pdb=" N VAL D 328 " --> pdb=" O ASN D 324 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 349 removed outlier: 3.567A pdb=" N LEU D 349 " --> pdb=" O LEU D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 367 removed outlier: 4.054A pdb=" N VAL D 365 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP D 367 " --> pdb=" O ASP D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 3 through 11 removed outlier: 4.091A pdb=" N GLU E 9 " --> pdb=" O HIS E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 54 Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 73 through 83 Processing helix chain 'E' and resid 104 through 122 removed outlier: 4.187A pdb=" N LYS E 108 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Proline residue: E 111 - end of helix Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'E' and resid 132 through 148 Processing helix chain 'E' and resid 149 through 151 No H-bonds generated for 'chain 'E' and resid 149 through 151' Processing helix chain 'E' and resid 159 through 168 removed outlier: 3.576A pdb=" N LYS E 163 " --> pdb=" O GLN E 159 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS E 167 " --> pdb=" O LYS E 163 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER E 168 " --> pdb=" O ILE E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 174 Processing helix chain 'E' and resid 177 through 183 removed outlier: 3.767A pdb=" N ALA E 181 " --> pdb=" O GLU E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 201 removed outlier: 3.616A pdb=" N ALA E 197 " --> pdb=" O GLU E 193 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG E 201 " --> pdb=" O ALA E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 230 removed outlier: 3.620A pdb=" N THR E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU E 216 " --> pdb=" O ARG E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 296 removed outlier: 4.136A pdb=" N VAL E 277 " --> pdb=" O SER E 273 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N TYR E 280 " --> pdb=" O SER E 276 " (cutoff:3.500A) Proline residue: E 285 - end of helix removed outlier: 3.522A pdb=" N ILE E 288 " --> pdb=" O VAL E 284 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU E 294 " --> pdb=" O ASN E 290 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS E 295 " --> pdb=" O LEU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 308 removed outlier: 3.699A pdb=" N MET E 307 " --> pdb=" O SER E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 317 removed outlier: 4.140A pdb=" N LEU E 313 " --> pdb=" O PRO E 309 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU E 314 " --> pdb=" O ALA E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 335 removed outlier: 3.731A pdb=" N VAL E 328 " --> pdb=" O ASN E 324 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA E 335 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 349 removed outlier: 3.543A pdb=" N LEU E 349 " --> pdb=" O LEU E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 367 removed outlier: 4.054A pdb=" N VAL E 365 " --> pdb=" O ASN E 361 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASP E 367 " --> pdb=" O ASP E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'G' and resid 3 through 11 removed outlier: 4.047A pdb=" N GLU G 9 " --> pdb=" O HIS G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 54 Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 73 through 83 Processing helix chain 'G' and resid 104 through 122 removed outlier: 4.189A pdb=" N LYS G 108 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Proline residue: G 111 - end of helix Processing helix chain 'G' and resid 122 through 132 Processing helix chain 'G' and resid 132 through 148 Processing helix chain 'G' and resid 159 through 168 removed outlier: 3.597A pdb=" N LYS G 163 " --> pdb=" O GLN G 159 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS G 167 " --> pdb=" O LYS G 163 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER G 168 " --> pdb=" O ILE G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 174 Processing helix chain 'G' and resid 177 through 183 removed outlier: 3.791A pdb=" N ALA G 181 " --> pdb=" O GLU G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 201 removed outlier: 3.631A pdb=" N ALA G 197 " --> pdb=" O GLU G 193 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG G 201 " --> pdb=" O ALA G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 230 removed outlier: 3.608A pdb=" N THR G 208 " --> pdb=" O SER G 204 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU G 216 " --> pdb=" O ARG G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 282 removed outlier: 4.050A pdb=" N VAL G 277 " --> pdb=" O SER G 273 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR G 280 " --> pdb=" O SER G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 296 removed outlier: 4.242A pdb=" N VAL G 286 " --> pdb=" O ILE G 282 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE G 288 " --> pdb=" O VAL G 284 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU G 294 " --> pdb=" O ASN G 290 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS G 295 " --> pdb=" O LEU G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 308 removed outlier: 3.698A pdb=" N MET G 307 " --> pdb=" O SER G 303 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU G 308 " --> pdb=" O VAL G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 317 removed outlier: 4.152A pdb=" N LEU G 313 " --> pdb=" O PRO G 309 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU G 314 " --> pdb=" O ALA G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 335 removed outlier: 3.670A pdb=" N VAL G 328 " --> pdb=" O ASN G 324 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA G 335 " --> pdb=" O LEU G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 349 removed outlier: 3.546A pdb=" N LEU G 349 " --> pdb=" O LEU G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 367 removed outlier: 4.051A pdb=" N VAL G 365 " --> pdb=" O ASN G 361 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP G 367 " --> pdb=" O ASP G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 374 Processing sheet with id=AA1, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'F' and resid 89 through 91 Processing sheet with id=AA3, first strand: chain 'A' and resid 64 through 66 removed outlier: 4.398A pdb=" N ILE A 259 " --> pdb=" O CYS A 242 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N CYS A 242 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 3.581A pdb=" N LYS A 102 " --> pdb=" O HIS A 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 64 through 66 removed outlier: 4.445A pdb=" N ILE B 259 " --> pdb=" O CYS B 242 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N CYS B 242 " --> pdb=" O ILE B 259 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.663A pdb=" N LYS B 102 " --> pdb=" O HIS B 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AA8, first strand: chain 'C' and resid 89 through 91 removed outlier: 3.610A pdb=" N LYS C 102 " --> pdb=" O HIS C 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AB1, first strand: chain 'D' and resid 89 through 91 removed outlier: 3.614A pdb=" N LYS D 102 " --> pdb=" O HIS D 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 64 through 66 removed outlier: 4.487A pdb=" N ILE E 259 " --> pdb=" O CYS E 242 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N CYS E 242 " --> pdb=" O ILE E 259 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 89 through 91 removed outlier: 3.636A pdb=" N LYS E 102 " --> pdb=" O HIS E 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 64 through 66 Processing sheet with id=AB5, first strand: chain 'G' and resid 89 through 91 removed outlier: 3.669A pdb=" N LYS G 102 " --> pdb=" O HIS G 90 " (cutoff:3.500A) 926 hydrogen bonds defined for protein. 2751 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: 5.38 Time building geometry restraints manager: 8.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6411 1.34 - 1.46: 4543 1.46 - 1.58: 10151 1.58 - 1.69: 0 1.69 - 1.81: 168 Bond restraints: 21273 Sorted by residual: bond pdb=" C VAL B 284 " pdb=" N PRO B 285 " ideal model delta sigma weight residual 1.337 1.352 -0.015 1.24e-02 6.50e+03 1.39e+00 bond pdb=" CA ILE G 323 " pdb=" CB ILE G 323 " ideal model delta sigma weight residual 1.527 1.542 -0.015 1.31e-02 5.83e+03 1.39e+00 bond pdb=" C VAL A 284 " pdb=" N PRO A 285 " ideal model delta sigma weight residual 1.337 1.352 -0.014 1.24e-02 6.50e+03 1.36e+00 bond pdb=" CA ILE D 323 " pdb=" CB ILE D 323 " ideal model delta sigma weight residual 1.530 1.543 -0.012 1.05e-02 9.07e+03 1.36e+00 bond pdb=" CB ASP A 81 " pdb=" CG ASP A 81 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.35e+00 ... (remaining 21268 not shown) Histogram of bond angle deviations from ideal: 99.73 - 106.60: 598 106.60 - 113.47: 11798 113.47 - 120.34: 8021 120.34 - 127.21: 8194 127.21 - 134.08: 264 Bond angle restraints: 28875 Sorted by residual: angle pdb=" N VAL A 277 " pdb=" CA VAL A 277 " pdb=" C VAL A 277 " ideal model delta sigma weight residual 111.90 108.56 3.34 8.10e-01 1.52e+00 1.70e+01 angle pdb=" N VAL B 277 " pdb=" CA VAL B 277 " pdb=" C VAL B 277 " ideal model delta sigma weight residual 111.81 108.52 3.29 8.60e-01 1.35e+00 1.46e+01 angle pdb=" N VAL F 277 " pdb=" CA VAL F 277 " pdb=" C VAL F 277 " ideal model delta sigma weight residual 111.81 108.53 3.28 8.60e-01 1.35e+00 1.46e+01 angle pdb=" N VAL G 277 " pdb=" CA VAL G 277 " pdb=" C VAL G 277 " ideal model delta sigma weight residual 111.81 108.53 3.28 8.60e-01 1.35e+00 1.45e+01 angle pdb=" N VAL D 277 " pdb=" CA VAL D 277 " pdb=" C VAL D 277 " ideal model delta sigma weight residual 111.81 108.58 3.23 8.60e-01 1.35e+00 1.41e+01 ... (remaining 28870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.98: 10233 14.98 - 29.96: 1845 29.96 - 44.94: 584 44.94 - 59.91: 160 59.91 - 74.89: 16 Dihedral angle restraints: 12838 sinusoidal: 5138 harmonic: 7700 Sorted by residual: dihedral pdb=" CA THR F 260 " pdb=" C THR F 260 " pdb=" N CYS F 261 " pdb=" CA CYS F 261 " ideal model delta harmonic sigma weight residual 180.00 149.56 30.44 0 5.00e+00 4.00e-02 3.71e+01 dihedral pdb=" CA THR C 260 " pdb=" C THR C 260 " pdb=" N CYS C 261 " pdb=" CA CYS C 261 " ideal model delta harmonic sigma weight residual 180.00 155.04 24.96 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA THR G 260 " pdb=" C THR G 260 " pdb=" N CYS G 261 " pdb=" CA CYS G 261 " ideal model delta harmonic sigma weight residual 180.00 155.75 24.25 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 12835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2089 0.031 - 0.062: 961 0.062 - 0.093: 257 0.093 - 0.124: 61 0.124 - 0.155: 20 Chirality restraints: 3388 Sorted by residual: chirality pdb=" CB VAL E 234 " pdb=" CA VAL E 234 " pdb=" CG1 VAL E 234 " pdb=" CG2 VAL E 234 " both_signs ideal model delta sigma weight residual False -2.63 -2.78 0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CB VAL C 234 " pdb=" CA VAL C 234 " pdb=" CG1 VAL C 234 " pdb=" CG2 VAL C 234 " both_signs ideal model delta sigma weight residual False -2.63 -2.78 0.15 2.00e-01 2.50e+01 5.89e-01 chirality pdb=" CB VAL A 234 " pdb=" CA VAL A 234 " pdb=" CG1 VAL A 234 " pdb=" CG2 VAL A 234 " both_signs ideal model delta sigma weight residual False -2.63 -2.78 0.15 2.00e-01 2.50e+01 5.87e-01 ... (remaining 3385 not shown) Planarity restraints: 3535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 297 " 0.011 2.00e-02 2.50e+03 1.13e-02 3.19e+00 pdb=" CG TRP G 297 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP G 297 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP G 297 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP G 297 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP G 297 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP G 297 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 297 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 297 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP G 297 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 297 " 0.010 2.00e-02 2.50e+03 9.74e-03 2.37e+00 pdb=" CG TRP F 297 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP F 297 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP F 297 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 297 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 297 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 297 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 297 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 297 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP F 297 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP F 105 " -0.022 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO F 106 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO F 106 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO F 106 " -0.018 5.00e-02 4.00e+02 ... (remaining 3532 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4767 2.78 - 3.31: 19712 3.31 - 3.84: 32644 3.84 - 4.37: 36919 4.37 - 4.90: 63697 Nonbonded interactions: 157739 Sorted by model distance: nonbonded pdb=" OG SER C 113 " pdb=" OH TYR C 226 " model vdw 2.253 2.440 nonbonded pdb=" OG SER A 113 " pdb=" OH TYR A 226 " model vdw 2.257 2.440 nonbonded pdb=" OG SER E 113 " pdb=" OH TYR E 226 " model vdw 2.267 2.440 nonbonded pdb=" OG SER D 113 " pdb=" OH TYR D 226 " model vdw 2.270 2.440 nonbonded pdb=" OG SER F 113 " pdb=" OH TYR F 226 " model vdw 2.271 2.440 ... (remaining 157734 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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' } 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 group one per residue 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: 1.190 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: 6.140 Check model and map are aligned: 0.320 Set scattering table: 0.210 Process input model: 50.920 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 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 : 0.003 0.033 21273 Z= 0.170 Angle : 0.684 11.836 28875 Z= 0.362 Chirality : 0.038 0.155 3388 Planarity : 0.004 0.032 3535 Dihedral : 17.353 74.892 7798 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.35 % Favored : 93.37 % Rotamer: Outliers : 0.21 % Allowed : 33.02 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.18), residues: 2534 helix: 0.59 (0.15), residues: 1414 sheet: None (None), residues: 0 loop : -2.91 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP G 297 HIS 0.004 0.001 HIS A 231 PHE 0.012 0.001 PHE G 40 TYR 0.012 0.001 TYR E 122 ARG 0.003 0.000 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 297 time to evaluate : 2.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 200 GLN cc_start: 0.8272 (mt0) cc_final: 0.7962 (mp10) REVERT: F 318 MET cc_start: 0.5946 (tpp) cc_final: 0.5714 (mmt) REVERT: F 326 LEU cc_start: 0.8881 (tp) cc_final: 0.8498 (mm) REVERT: F 327 ASN cc_start: 0.8192 (m110) cc_final: 0.7982 (m-40) REVERT: A 10 TYR cc_start: 0.7881 (m-80) cc_final: 0.7573 (m-80) REVERT: A 12 LEU cc_start: 0.8051 (tp) cc_final: 0.7812 (tp) REVERT: B 318 MET cc_start: 0.6450 (tpp) cc_final: 0.5947 (mmt) REVERT: C 200 GLN cc_start: 0.7944 (mt0) cc_final: 0.7133 (mp10) REVERT: E 129 GLN cc_start: 0.8198 (mm110) cc_final: 0.7768 (mm110) REVERT: E 161 MET cc_start: 0.3409 (mmm) cc_final: 0.3111 (mmt) REVERT: G 10 TYR cc_start: 0.7644 (m-80) cc_final: 0.7216 (m-80) outliers start: 5 outliers final: 5 residues processed: 300 average time/residue: 0.2669 time to fit residues: 135.5933 Evaluate side-chains 273 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 268 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain D residue 318 MET Chi-restraints excluded: chain G residue 166 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 chunk 105 optimal weight: 0.1980 chunk 65 optimal weight: 0.4980 chunk 128 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 197 optimal weight: 20.0000 chunk 76 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 228 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN E 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21273 Z= 0.195 Angle : 0.613 11.352 28875 Z= 0.295 Chirality : 0.038 0.139 3388 Planarity : 0.004 0.036 3535 Dihedral : 4.713 56.488 2811 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.05 % Allowed : 30.69 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.17), residues: 2534 helix: 0.35 (0.14), residues: 1519 sheet: None (None), residues: 0 loop : -3.09 (0.18), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 297 HIS 0.006 0.001 HIS C 231 PHE 0.012 0.001 PHE C 269 TYR 0.012 0.001 TYR D 280 ARG 0.003 0.000 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 299 time to evaluate : 2.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 200 GLN cc_start: 0.8290 (mt0) cc_final: 0.7942 (mp10) REVERT: F 326 LEU cc_start: 0.8837 (tp) cc_final: 0.8459 (mm) REVERT: F 327 ASN cc_start: 0.8343 (m110) cc_final: 0.8036 (m110) REVERT: A 10 TYR cc_start: 0.7909 (m-80) cc_final: 0.7494 (m-80) REVERT: A 31 GLU cc_start: 0.7481 (pm20) cc_final: 0.7267 (pm20) REVERT: B 31 GLU cc_start: 0.7296 (pm20) cc_final: 0.7077 (pm20) REVERT: C 129 GLN cc_start: 0.8293 (mm110) cc_final: 0.8028 (mm110) REVERT: D 327 ASN cc_start: 0.8347 (OUTLIER) cc_final: 0.8122 (m110) REVERT: E 129 GLN cc_start: 0.8259 (mm110) cc_final: 0.7869 (mm110) REVERT: E 161 MET cc_start: 0.3367 (mmm) cc_final: 0.3084 (mmt) REVERT: G 10 TYR cc_start: 0.7624 (m-80) cc_final: 0.7134 (m-80) REVERT: G 86 ASP cc_start: 0.8344 (m-30) cc_final: 0.7976 (m-30) REVERT: G 161 MET cc_start: 0.3424 (mmm) cc_final: 0.3096 (mmt) outliers start: 72 outliers final: 39 residues processed: 353 average time/residue: 0.2380 time to fit residues: 144.0892 Evaluate side-chains 324 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 284 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 267 SER Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 305 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 9.9990 chunk 71 optimal weight: 30.0000 chunk 190 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 229 optimal weight: 2.9990 chunk 247 optimal weight: 20.0000 chunk 204 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 78 optimal weight: 0.2980 chunk 183 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 ASN G 203 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21273 Z= 0.158 Angle : 0.588 9.812 28875 Z= 0.282 Chirality : 0.039 0.296 3388 Planarity : 0.003 0.035 3535 Dihedral : 4.079 28.601 2800 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.91 % Allowed : 31.54 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.17), residues: 2534 helix: 0.45 (0.15), residues: 1498 sheet: None (None), residues: 0 loop : -3.00 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 345 HIS 0.004 0.001 HIS A 231 PHE 0.010 0.001 PHE F 240 TYR 0.009 0.001 TYR E 280 ARG 0.002 0.000 ARG G 201 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 298 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 31 GLU cc_start: 0.7522 (pm20) cc_final: 0.7268 (pm20) REVERT: F 237 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7880 (tp40) REVERT: F 327 ASN cc_start: 0.8320 (m110) cc_final: 0.7956 (m110) REVERT: A 10 TYR cc_start: 0.7902 (m-80) cc_final: 0.7488 (m-80) REVERT: A 31 GLU cc_start: 0.7496 (pm20) cc_final: 0.7273 (pm20) REVERT: B 31 GLU cc_start: 0.7317 (pm20) cc_final: 0.7086 (pm20) REVERT: B 294 LEU cc_start: 0.8049 (tt) cc_final: 0.7834 (tt) REVERT: C 327 ASN cc_start: 0.8295 (t0) cc_final: 0.8013 (m-40) REVERT: D 31 GLU cc_start: 0.7251 (pm20) cc_final: 0.7019 (pm20) REVERT: D 318 MET cc_start: 0.4975 (tpt) cc_final: 0.4527 (mmt) REVERT: E 129 GLN cc_start: 0.8186 (mm110) cc_final: 0.7817 (mm110) REVERT: E 161 MET cc_start: 0.3444 (mmm) cc_final: 0.2612 (mmm) REVERT: G 10 TYR cc_start: 0.7713 (m-80) cc_final: 0.7282 (m-80) REVERT: G 31 GLU cc_start: 0.7426 (pm20) cc_final: 0.7171 (pm20) REVERT: G 86 ASP cc_start: 0.8271 (m-30) cc_final: 0.7798 (m-30) REVERT: G 161 MET cc_start: 0.3414 (mmm) cc_final: 0.3075 (mmt) outliers start: 45 outliers final: 32 residues processed: 330 average time/residue: 0.2491 time to fit residues: 139.3055 Evaluate side-chains 317 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 284 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 305 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 0.0980 chunk 172 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 109 optimal weight: 0.0770 chunk 153 optimal weight: 8.9990 chunk 230 optimal weight: 6.9990 chunk 243 optimal weight: 1.9990 chunk 120 optimal weight: 0.0070 chunk 218 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 336 ASN ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 ASN E 324 ASN ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21273 Z= 0.149 Angle : 0.572 8.818 28875 Z= 0.273 Chirality : 0.037 0.133 3388 Planarity : 0.003 0.034 3535 Dihedral : 3.958 26.691 2800 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.63 % Allowed : 32.22 % Favored : 65.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.18), residues: 2534 helix: 0.56 (0.15), residues: 1498 sheet: None (None), residues: 0 loop : -2.98 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 345 HIS 0.003 0.000 HIS A 231 PHE 0.009 0.001 PHE F 240 TYR 0.009 0.001 TYR G 122 ARG 0.003 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 299 time to evaluate : 2.315 Fit side-chains revert: symmetry clash REVERT: F 31 GLU cc_start: 0.7417 (pm20) cc_final: 0.7189 (pm20) REVERT: F 237 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7836 (tp40) REVERT: F 327 ASN cc_start: 0.8264 (m110) cc_final: 0.7865 (m110) REVERT: A 10 TYR cc_start: 0.7871 (m-80) cc_final: 0.7453 (m-80) REVERT: A 31 GLU cc_start: 0.7398 (pm20) cc_final: 0.7178 (pm20) REVERT: B 10 TYR cc_start: 0.7816 (m-80) cc_final: 0.7523 (m-80) REVERT: B 31 GLU cc_start: 0.7272 (pm20) cc_final: 0.7034 (pm20) REVERT: C 327 ASN cc_start: 0.8203 (t0) cc_final: 0.7967 (m110) REVERT: D 31 GLU cc_start: 0.7275 (pm20) cc_final: 0.7029 (pm20) REVERT: D 318 MET cc_start: 0.4881 (tpt) cc_final: 0.4416 (mmt) REVERT: D 327 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.8110 (m110) REVERT: E 129 GLN cc_start: 0.8168 (mm110) cc_final: 0.7799 (mm110) REVERT: E 161 MET cc_start: 0.3536 (mmm) cc_final: 0.2684 (mmm) REVERT: E 274 LEU cc_start: 0.9030 (mm) cc_final: 0.8826 (mt) REVERT: G 10 TYR cc_start: 0.7725 (m-80) cc_final: 0.7191 (m-80) REVERT: G 31 GLU cc_start: 0.7458 (pm20) cc_final: 0.7178 (pm20) REVERT: G 86 ASP cc_start: 0.8225 (m-30) cc_final: 0.7654 (m-30) REVERT: G 161 MET cc_start: 0.3410 (mmm) cc_final: 0.3023 (mmt) outliers start: 62 outliers final: 40 residues processed: 348 average time/residue: 0.2469 time to fit residues: 144.7832 Evaluate side-chains 326 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 284 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 267 SER Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 336 ASN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 305 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 3 optimal weight: 0.4980 chunk 181 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 207 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 218 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21273 Z= 0.163 Angle : 0.573 8.246 28875 Z= 0.273 Chirality : 0.038 0.140 3388 Planarity : 0.003 0.036 3535 Dihedral : 3.884 25.886 2800 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.84 % Allowed : 32.60 % Favored : 64.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.18), residues: 2534 helix: 0.59 (0.15), residues: 1498 sheet: None (None), residues: 0 loop : -2.98 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 345 HIS 0.004 0.000 HIS C 231 PHE 0.010 0.001 PHE A 240 TYR 0.010 0.001 TYR G 122 ARG 0.002 0.000 ARG C 201 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 293 time to evaluate : 2.282 Fit side-chains revert: symmetry clash REVERT: F 31 GLU cc_start: 0.7495 (pm20) cc_final: 0.7256 (pm20) REVERT: A 10 TYR cc_start: 0.7920 (m-80) cc_final: 0.7526 (m-80) REVERT: A 31 GLU cc_start: 0.7459 (pm20) cc_final: 0.7216 (pm20) REVERT: A 75 ARG cc_start: 0.7611 (mmm-85) cc_final: 0.7356 (mmt-90) REVERT: B 10 TYR cc_start: 0.7866 (m-80) cc_final: 0.7547 (m-80) REVERT: B 31 GLU cc_start: 0.7354 (pm20) cc_final: 0.7111 (pm20) REVERT: C 86 ASP cc_start: 0.8383 (m-30) cc_final: 0.7799 (m-30) REVERT: C 129 GLN cc_start: 0.8264 (mm110) cc_final: 0.8016 (mm110) REVERT: D 147 LEU cc_start: 0.7435 (pp) cc_final: 0.7214 (pp) REVERT: D 318 MET cc_start: 0.4953 (tpt) cc_final: 0.4473 (mmt) REVERT: E 129 GLN cc_start: 0.8118 (mm110) cc_final: 0.7899 (mm110) REVERT: E 161 MET cc_start: 0.3407 (mmm) cc_final: 0.2605 (mmm) REVERT: G 31 GLU cc_start: 0.7474 (pm20) cc_final: 0.7199 (pm20) REVERT: G 86 ASP cc_start: 0.8251 (m-30) cc_final: 0.7731 (m-30) REVERT: G 161 MET cc_start: 0.3568 (mmm) cc_final: 0.3235 (mmt) outliers start: 67 outliers final: 53 residues processed: 342 average time/residue: 0.2521 time to fit residues: 146.2299 Evaluate side-chains 339 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 286 time to evaluate : 2.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 267 SER Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 305 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 10.0000 chunk 219 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 143 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 243 optimal weight: 4.9990 chunk 202 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 ASN ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21273 Z= 0.225 Angle : 0.602 7.907 28875 Z= 0.291 Chirality : 0.039 0.147 3388 Planarity : 0.004 0.036 3535 Dihedral : 4.054 28.687 2800 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.14 % Allowed : 33.57 % Favored : 63.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.17), residues: 2534 helix: 0.55 (0.14), residues: 1505 sheet: None (None), residues: 0 loop : -3.04 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 345 HIS 0.005 0.001 HIS C 231 PHE 0.012 0.001 PHE B 240 TYR 0.016 0.001 TYR C 226 ARG 0.003 0.000 ARG G 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 284 time to evaluate : 2.167 Fit side-chains revert: symmetry clash REVERT: F 237 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7771 (tp40) REVERT: F 318 MET cc_start: 0.6081 (tpp) cc_final: 0.5634 (tpp) REVERT: A 10 TYR cc_start: 0.7889 (m-80) cc_final: 0.7440 (m-80) REVERT: A 147 LEU cc_start: 0.7519 (pp) cc_final: 0.7276 (pp) REVERT: B 10 TYR cc_start: 0.7921 (m-80) cc_final: 0.7615 (m-80) REVERT: D 147 LEU cc_start: 0.7466 (pp) cc_final: 0.7233 (pp) REVERT: D 318 MET cc_start: 0.4865 (tpt) cc_final: 0.4620 (mmt) REVERT: E 129 GLN cc_start: 0.8189 (mm110) cc_final: 0.7942 (mm-40) REVERT: E 161 MET cc_start: 0.3798 (mmm) cc_final: 0.2915 (mmm) REVERT: E 283 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7015 (mp) REVERT: G 10 TYR cc_start: 0.7746 (m-80) cc_final: 0.7219 (m-80) REVERT: G 86 ASP cc_start: 0.8311 (m-30) cc_final: 0.7966 (m-30) REVERT: G 161 MET cc_start: 0.3513 (mmm) cc_final: 0.3276 (mmt) outliers start: 74 outliers final: 63 residues processed: 340 average time/residue: 0.2466 time to fit residues: 141.3466 Evaluate side-chains 344 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 279 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 267 SER Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 139 ASP Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 305 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 138 optimal weight: 20.0000 chunk 178 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 205 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 242 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21273 Z= 0.195 Angle : 0.589 8.174 28875 Z= 0.281 Chirality : 0.038 0.141 3388 Planarity : 0.003 0.036 3535 Dihedral : 3.952 27.154 2800 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 3.22 % Allowed : 34.04 % Favored : 62.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.17), residues: 2534 helix: 0.57 (0.14), residues: 1505 sheet: None (None), residues: 0 loop : -3.05 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 345 HIS 0.004 0.001 HIS C 231 PHE 0.012 0.001 PHE A 240 TYR 0.016 0.001 TYR G 122 ARG 0.002 0.000 ARG G 212 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 286 time to evaluate : 2.383 Fit side-chains REVERT: F 10 TYR cc_start: 0.7941 (m-80) cc_final: 0.7553 (m-80) REVERT: F 75 ARG cc_start: 0.8191 (mmm160) cc_final: 0.7967 (tpp80) REVERT: F 318 MET cc_start: 0.6146 (tpp) cc_final: 0.5777 (tpp) REVERT: A 9 GLU cc_start: 0.7861 (mp0) cc_final: 0.7433 (mp0) REVERT: A 10 TYR cc_start: 0.7879 (m-80) cc_final: 0.7374 (m-80) REVERT: A 37 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7532 (tp) REVERT: A 147 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7281 (pp) REVERT: B 10 TYR cc_start: 0.7936 (m-80) cc_final: 0.7592 (m-80) REVERT: C 10 TYR cc_start: 0.7907 (m-80) cc_final: 0.7628 (m-80) REVERT: C 86 ASP cc_start: 0.8495 (m-30) cc_final: 0.7989 (m-30) REVERT: D 147 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7283 (pp) REVERT: D 318 MET cc_start: 0.4884 (tpt) cc_final: 0.4598 (mmt) REVERT: E 129 GLN cc_start: 0.8192 (mm110) cc_final: 0.7963 (mm110) REVERT: E 147 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7242 (pp) REVERT: E 161 MET cc_start: 0.3857 (mmm) cc_final: 0.3631 (mmt) REVERT: E 283 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.6889 (mp) REVERT: G 161 MET cc_start: 0.3506 (mmm) cc_final: 0.3248 (mmt) outliers start: 76 outliers final: 54 residues processed: 341 average time/residue: 0.2444 time to fit residues: 140.7695 Evaluate side-chains 339 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 280 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 267 SER Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 305 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 0.8980 chunk 96 optimal weight: 0.0270 chunk 145 optimal weight: 4.9990 chunk 73 optimal weight: 0.0070 chunk 47 optimal weight: 5.9990 chunk 154 optimal weight: 0.6980 chunk 165 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 220 optimal weight: 5.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 ASN E 336 ASN G 336 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21273 Z= 0.145 Angle : 0.571 8.442 28875 Z= 0.271 Chirality : 0.037 0.132 3388 Planarity : 0.003 0.036 3535 Dihedral : 3.768 24.722 2800 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.12 % Allowed : 35.27 % Favored : 62.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.18), residues: 2534 helix: 0.74 (0.15), residues: 1505 sheet: None (None), residues: 0 loop : -3.02 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 345 HIS 0.003 0.001 HIS A 231 PHE 0.010 0.001 PHE B 240 TYR 0.017 0.001 TYR G 122 ARG 0.002 0.000 ARG E 262 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 295 time to evaluate : 2.302 Fit side-chains REVERT: F 10 TYR cc_start: 0.7947 (m-80) cc_final: 0.7512 (m-80) REVERT: F 318 MET cc_start: 0.6166 (tpp) cc_final: 0.5783 (tpp) REVERT: A 37 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7544 (tp) REVERT: A 147 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7317 (pp) REVERT: B 10 TYR cc_start: 0.7942 (m-80) cc_final: 0.7540 (m-80) REVERT: C 10 TYR cc_start: 0.7868 (m-80) cc_final: 0.7557 (m-80) REVERT: C 86 ASP cc_start: 0.8362 (m-30) cc_final: 0.8069 (m-30) REVERT: D 147 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7273 (pp) REVERT: D 318 MET cc_start: 0.4930 (tpt) cc_final: 0.4616 (mmt) REVERT: E 129 GLN cc_start: 0.8191 (mm110) cc_final: 0.7951 (mm-40) REVERT: E 161 MET cc_start: 0.3833 (mmm) cc_final: 0.2970 (mmm) REVERT: E 283 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.6866 (mp) REVERT: G 75 ARG cc_start: 0.8134 (mmm160) cc_final: 0.7920 (tpp80) REVERT: G 161 MET cc_start: 0.3567 (mmm) cc_final: 0.3266 (mmt) outliers start: 50 outliers final: 37 residues processed: 333 average time/residue: 0.2546 time to fit residues: 141.5941 Evaluate side-chains 323 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 282 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 267 SER Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 336 ASN Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 336 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 8.9990 chunk 212 optimal weight: 1.9990 chunk 226 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 177 optimal weight: 7.9990 chunk 69 optimal weight: 20.0000 chunk 204 optimal weight: 0.9990 chunk 214 optimal weight: 20.0000 chunk 225 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 327 ASN ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 336 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21273 Z= 0.230 Angle : 0.612 8.669 28875 Z= 0.292 Chirality : 0.040 0.261 3388 Planarity : 0.004 0.047 3535 Dihedral : 3.940 27.616 2800 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.50 % Allowed : 35.35 % Favored : 62.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.18), residues: 2534 helix: 0.65 (0.14), residues: 1505 sheet: None (None), residues: 0 loop : -3.03 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 105 HIS 0.004 0.001 HIS C 231 PHE 0.013 0.001 PHE C 269 TYR 0.017 0.001 TYR B 122 ARG 0.008 0.000 ARG E 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 278 time to evaluate : 2.420 Fit side-chains REVERT: F 10 TYR cc_start: 0.7958 (m-80) cc_final: 0.7536 (m-80) REVERT: F 318 MET cc_start: 0.6079 (tpp) cc_final: 0.5750 (tpp) REVERT: A 37 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7539 (tp) REVERT: A 147 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7271 (pp) REVERT: D 37 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7690 (tp) REVERT: D 147 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7289 (pp) REVERT: E 129 GLN cc_start: 0.8235 (mm110) cc_final: 0.7985 (mm-40) REVERT: E 161 MET cc_start: 0.3913 (mmm) cc_final: 0.2066 (tpt) REVERT: E 283 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7003 (mp) outliers start: 59 outliers final: 48 residues processed: 323 average time/residue: 0.2380 time to fit residues: 131.6305 Evaluate side-chains 328 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 275 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 267 SER Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 139 ASP Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 336 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 0.7980 chunk 146 optimal weight: 20.0000 chunk 113 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 251 optimal weight: 30.0000 chunk 231 optimal weight: 10.0000 chunk 199 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 154 optimal weight: 0.2980 chunk 122 optimal weight: 8.9990 chunk 158 optimal weight: 10.0000 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21273 Z= 0.294 Angle : 0.661 7.467 28875 Z= 0.320 Chirality : 0.041 0.187 3388 Planarity : 0.004 0.045 3535 Dihedral : 4.270 30.744 2800 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.50 % Allowed : 34.93 % Favored : 62.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.17), residues: 2534 helix: 0.40 (0.14), residues: 1519 sheet: None (None), residues: 0 loop : -3.04 (0.18), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 105 HIS 0.005 0.001 HIS C 231 PHE 0.015 0.002 PHE B 240 TYR 0.022 0.002 TYR C 226 ARG 0.008 0.000 ARG D 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 280 time to evaluate : 2.401 Fit side-chains REVERT: F 10 TYR cc_start: 0.7993 (m-80) cc_final: 0.7568 (m-80) REVERT: F 318 MET cc_start: 0.6079 (tpp) cc_final: 0.5702 (tpp) REVERT: A 37 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7556 (tp) REVERT: A 147 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7302 (pp) REVERT: D 37 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7666 (tp) REVERT: D 147 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7307 (pp) REVERT: E 129 GLN cc_start: 0.8281 (mm110) cc_final: 0.8034 (mm-40) REVERT: E 283 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.6727 (mp) REVERT: G 331 LEU cc_start: 0.8829 (mt) cc_final: 0.8627 (mt) outliers start: 59 outliers final: 52 residues processed: 322 average time/residue: 0.2405 time to fit residues: 131.9506 Evaluate side-chains 334 residues out of total 2359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 277 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 267 SER Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 324 ASN Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 267 SER Chi-restraints excluded: chain G residue 305 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 184 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 205 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 0.0980 chunk 175 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 5 HIS B 5 HIS ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 HIS G 5 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.212191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.141831 restraints weight = 29372.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.144934 restraints weight = 17007.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.146536 restraints weight = 11908.082| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 21273 Z= 0.251 Angle : 0.786 59.107 28875 Z= 0.419 Chirality : 0.042 0.782 3388 Planarity : 0.004 0.106 3535 Dihedral : 4.287 30.655 2800 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.42 % Favored : 92.54 % Rotamer: Outliers : 2.37 % Allowed : 35.23 % Favored : 62.40 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.17), residues: 2534 helix: 0.42 (0.14), residues: 1519 sheet: None (None), residues: 0 loop : -3.04 (0.18), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 105 HIS 0.004 0.001 HIS C 231 PHE 0.013 0.001 PHE B 240 TYR 0.019 0.002 TYR B 122 ARG 0.007 0.000 ARG D 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3747.26 seconds wall clock time: 69 minutes 28.35 seconds (4168.35 seconds total)