Starting phenix.real_space_refine on Sun May 11 23:09:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b65_44247/05_2025/9b65_44247_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b65_44247/05_2025/9b65_44247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b65_44247/05_2025/9b65_44247.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b65_44247/05_2025/9b65_44247.map" model { file = "/net/cci-nas-00/data/ceres_data/9b65_44247/05_2025/9b65_44247_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b65_44247/05_2025/9b65_44247_trim.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 60 5.16 5 C 5416 2.51 5 N 1448 2.21 5 O 1538 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8463 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1659 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 63 Chain: "B" Number of atoms: 2573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2573 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2013 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 256} Chain breaks: 2 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 60 Chain: "S" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Classifications: {'peptide': 1} Time building chain proxies: 5.47, per 1000 atoms: 0.65 Number of scatterers: 8463 At special positions: 0 Unit cell: (103.96, 119.6, 104.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 F 1 9.00 O 1538 8.00 N 1448 7.00 C 5416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.0 seconds 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2084 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 14 sheets defined 32.3% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 6 through 29 removed outlier: 3.510A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.626A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.032A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 254 removed outlier: 3.566A pdb=" N LYS A 248 " --> pdb=" O HIS A 244 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 281 removed outlier: 3.531A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 311 removed outlier: 3.596A pdb=" N ALA A 300 " --> pdb=" O TYR A 296 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 removed outlier: 3.892A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 8 removed outlier: 3.619A pdb=" N ARG B 8 " --> pdb=" O LEU B 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4 through 8' Processing helix chain 'B' and resid 10 through 25 removed outlier: 4.044A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 8 through 22 removed outlier: 3.743A pdb=" N VAL C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 42 removed outlier: 3.921A pdb=" N ASP C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 114 No H-bonds generated for 'chain 'R' and resid 112 through 114' Processing helix chain 'R' and resid 115 through 121 removed outlier: 3.538A pdb=" N ALA R 120 " --> pdb=" O GLN R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 127 removed outlier: 3.753A pdb=" N THR R 125 " --> pdb=" O VAL R 121 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY R 127 " --> pdb=" O SER R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 138 removed outlier: 3.794A pdb=" N LEU R 138 " --> pdb=" O ASN R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 142 Processing helix chain 'R' and resid 154 through 172 removed outlier: 3.809A pdb=" N LEU R 164 " --> pdb=" O ALA R 160 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL R 171 " --> pdb=" O SER R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 177 Processing helix chain 'R' and resid 189 through 220 removed outlier: 3.514A pdb=" N VAL R 204 " --> pdb=" O PHE R 200 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG R 214 " --> pdb=" O THR R 210 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR R 215 " --> pdb=" O ALA R 211 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE R 216 " --> pdb=" O ILE R 212 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE R 218 " --> pdb=" O ARG R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 234 through 247 removed outlier: 4.151A pdb=" N ILE R 245 " --> pdb=" O TRP R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 287 removed outlier: 3.755A pdb=" N ILE R 280 " --> pdb=" O LEU R 276 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL R 285 " --> pdb=" O GLY R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 290 through 311 removed outlier: 3.675A pdb=" N TYR R 294 " --> pdb=" O ILE R 290 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE R 309 " --> pdb=" O ALA R 305 " (cutoff:3.500A) Processing helix chain 'R' and resid 341 through 357 removed outlier: 5.321A pdb=" N LEU R 347 " --> pdb=" O LYS R 343 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE R 348 " --> pdb=" O THR R 344 " (cutoff:3.500A) Processing helix chain 'R' and resid 357 through 366 removed outlier: 3.874A pdb=" N ASP R 366 " --> pdb=" O ILE R 362 " (cutoff:3.500A) Processing helix chain 'R' and resid 378 through 383 Processing helix chain 'R' and resid 384 through 397 removed outlier: 3.994A pdb=" N SER R 390 " --> pdb=" O CYS R 386 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR R 391 " --> pdb=" O LEU R 387 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL R 392 " --> pdb=" O LEU R 388 " (cutoff:3.500A) Proline residue: R 394 - end of helix Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.097A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.777A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'S' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 190 removed outlier: 5.888A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.840A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.400A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.892A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.574A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.172A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.562A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.624A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.587A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.754A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.962A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.594A pdb=" N PHE S 200 " --> pdb=" O CYS S 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 182 through 183 removed outlier: 3.663A pdb=" N ASN S 182 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR S 226 " --> pdb=" O GLN S 219 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 182 through 183 removed outlier: 3.663A pdb=" N ASN S 182 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) 340 hydrogen bonds defined for protein. 963 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: 2.60 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1340 1.31 - 1.43: 2408 1.43 - 1.56: 4805 1.56 - 1.68: 0 1.68 - 1.81: 87 Bond restraints: 8640 Sorted by residual: bond pdb=" N KCA R 501 " pdb=" CAB KCA R 501 " ideal model delta sigma weight residual 1.345 1.462 -0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" C KCA R 501 " pdb=" OAF KCA R 501 " ideal model delta sigma weight residual 1.320 1.391 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" CAB KCA R 501 " pdb=" CAM KCA R 501 " ideal model delta sigma weight residual 1.476 1.526 -0.050 2.00e-02 2.50e+03 6.26e+00 bond pdb=" CAG KCA R 501 " pdb=" OAF KCA R 501 " ideal model delta sigma weight residual 1.430 1.392 0.038 2.00e-02 2.50e+03 3.68e+00 bond pdb=" CAB KCA R 501 " pdb=" OAA KCA R 501 " ideal model delta sigma weight residual 1.223 1.185 0.038 2.00e-02 2.50e+03 3.61e+00 ... (remaining 8635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.03: 11687 4.03 - 8.06: 43 8.06 - 12.09: 1 12.09 - 16.13: 0 16.13 - 20.16: 1 Bond angle restraints: 11732 Sorted by residual: angle pdb=" C SER R 146 " pdb=" N LEU R 147 " pdb=" CA LEU R 147 " ideal model delta sigma weight residual 121.70 129.32 -7.62 1.80e+00 3.09e-01 1.79e+01 angle pdb=" C HIS R 178 " pdb=" N VAL R 179 " pdb=" CA VAL R 179 " ideal model delta sigma weight residual 122.77 118.51 4.26 1.05e+00 9.07e-01 1.65e+01 angle pdb=" N THR R 130 " pdb=" CA THR R 130 " pdb=" C THR R 130 " ideal model delta sigma weight residual 113.56 108.27 5.29 1.39e+00 5.18e-01 1.45e+01 angle pdb=" C ILE R 271 " pdb=" N ASP R 272 " pdb=" CA ASP R 272 " ideal model delta sigma weight residual 120.82 126.25 -5.43 1.47e+00 4.63e-01 1.36e+01 angle pdb=" C GLU C 58 " pdb=" N ASN C 59 " pdb=" CA ASN C 59 " ideal model delta sigma weight residual 121.41 101.25 20.16 5.58e+00 3.21e-02 1.30e+01 ... (remaining 11727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.30: 4997 25.30 - 50.60: 82 50.60 - 75.90: 4 75.90 - 101.20: 1 101.20 - 126.49: 1 Dihedral angle restraints: 5085 sinusoidal: 1861 harmonic: 3224 Sorted by residual: dihedral pdb=" CA TYR S 178 " pdb=" C TYR S 178 " pdb=" N ARG S 179 " pdb=" CA ARG S 179 " ideal model delta harmonic sigma weight residual 180.00 -136.91 -43.09 0 5.00e+00 4.00e-02 7.43e+01 dihedral pdb=" CA HIS R 270 " pdb=" C HIS R 270 " pdb=" N ILE R 271 " pdb=" CA ILE R 271 " ideal model delta harmonic sigma weight residual -180.00 -153.89 -26.11 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA PHE R 174 " pdb=" C PHE R 174 " pdb=" N ILE R 175 " pdb=" CA ILE R 175 " ideal model delta harmonic sigma weight residual 180.00 155.74 24.26 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 5082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 796 0.038 - 0.075: 407 0.075 - 0.113: 133 0.113 - 0.151: 24 0.151 - 0.188: 3 Chirality restraints: 1363 Sorted by residual: chirality pdb=" CA ASP B 5 " pdb=" N ASP B 5 " pdb=" C ASP B 5 " pdb=" CB ASP B 5 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.86e-01 chirality pdb=" CG LEU S 162 " pdb=" CB LEU S 162 " pdb=" CD1 LEU S 162 " pdb=" CD2 LEU S 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.98e-01 chirality pdb=" CA KCA R 501 " pdb=" N KCA R 501 " pdb=" C KCA R 501 " pdb=" CB KCA R 501 " both_signs ideal model delta sigma weight residual False 2.47 2.62 -0.16 2.00e-01 2.50e+01 6.11e-01 ... (remaining 1360 not shown) Planarity restraints: 1470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP S 111 " -0.019 2.00e-02 2.50e+03 1.84e-02 8.49e+00 pdb=" CG TRP S 111 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP S 111 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP S 111 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP S 111 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP S 111 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP S 111 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP S 111 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP S 111 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP S 111 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " -0.016 2.00e-02 2.50e+03 1.85e-02 6.83e+00 pdb=" CG TYR B 59 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 94 " -0.010 2.00e-02 2.50e+03 1.39e-02 3.84e+00 pdb=" CG TYR S 94 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR S 94 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR S 94 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR S 94 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR S 94 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR S 94 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR S 94 " 0.001 2.00e-02 2.50e+03 ... (remaining 1467 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 101 2.58 - 3.16: 7596 3.16 - 3.74: 12648 3.74 - 4.32: 19767 4.32 - 4.90: 31492 Nonbonded interactions: 71604 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.000 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.008 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.038 3.040 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.047 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.130 3.040 ... (remaining 71599 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 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: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.380 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.117 8642 Z= 0.332 Angle : 0.824 20.157 11734 Z= 0.464 Chirality : 0.048 0.188 1363 Planarity : 0.004 0.047 1470 Dihedral : 9.879 126.494 2998 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 29.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.61 % Favored : 92.30 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -4.23 (0.22), residues: 1091 helix: -4.13 (0.17), residues: 314 sheet: -2.01 (0.29), residues: 262 loop : -2.22 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP S 111 HIS 0.014 0.002 HIS S 35 PHE 0.029 0.003 PHE A 354 TYR 0.045 0.003 TYR B 59 ARG 0.008 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.26462 ( 325) hydrogen bonds : angle 11.14333 ( 963) SS BOND : bond 0.00801 ( 1) SS BOND : angle 1.14394 ( 2) covalent geometry : bond 0.00729 ( 8640) covalent geometry : angle 0.82369 (11732) Misc. bond : bond 0.00184 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.864 Fit side-chains REVERT: A 17 LYS cc_start: 0.8113 (mttt) cc_final: 0.7686 (mtpt) REVERT: A 29 LYS cc_start: 0.8429 (ttpp) cc_final: 0.8065 (ttmt) REVERT: A 200 ASP cc_start: 0.8185 (t70) cc_final: 0.7883 (t0) REVERT: A 231 ASP cc_start: 0.7871 (t70) cc_final: 0.7558 (t0) REVERT: A 242 ARG cc_start: 0.4932 (mpt180) cc_final: 0.3666 (ttm-80) REVERT: A 251 ASP cc_start: 0.8222 (t0) cc_final: 0.7930 (t0) REVERT: B 155 ASN cc_start: 0.8204 (t0) cc_final: 0.8001 (t0) REVERT: B 337 LYS cc_start: 0.8526 (mttm) cc_final: 0.8321 (mttt) REVERT: C 20 LYS cc_start: 0.7604 (mtpp) cc_final: 0.7371 (mtmm) REVERT: R 226 ARG cc_start: 0.5958 (mtm110) cc_final: 0.5318 (ttp-110) REVERT: R 240 MET cc_start: 0.5162 (mmp) cc_final: 0.4225 (mmp) REVERT: S 23 SER cc_start: 0.8653 (m) cc_final: 0.8361 (t) REVERT: S 142 SER cc_start: 0.8281 (t) cc_final: 0.7843 (p) REVERT: S 194 SER cc_start: 0.8140 (t) cc_final: 0.7863 (m) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.2725 time to fit residues: 67.6009 Evaluate side-chains 159 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN B 62 HIS B 91 HIS B 110 ASN B 225 HIS B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 295 ASN S 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.170598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.115117 restraints weight = 9122.920| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.30 r_work: 0.3061 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8642 Z= 0.178 Angle : 0.692 15.280 11734 Z= 0.363 Chirality : 0.047 0.166 1363 Planarity : 0.005 0.051 1470 Dihedral : 7.248 122.809 1211 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.95 % Favored : 94.96 % Rotamer: Outliers : 2.05 % Allowed : 7.08 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.39 (0.23), residues: 1091 helix: -3.09 (0.21), residues: 342 sheet: -1.66 (0.27), residues: 280 loop : -1.73 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.005 0.001 HIS B 225 PHE 0.021 0.002 PHE A 354 TYR 0.027 0.002 TYR B 59 ARG 0.007 0.001 ARG R 220 Details of bonding type rmsd hydrogen bonds : bond 0.04690 ( 325) hydrogen bonds : angle 6.11546 ( 963) SS BOND : bond 0.00703 ( 1) SS BOND : angle 1.00267 ( 2) covalent geometry : bond 0.00400 ( 8640) covalent geometry : angle 0.69184 (11732) Misc. bond : bond 0.00051 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8156 (mttt) cc_final: 0.7644 (mtpt) REVERT: A 18 MET cc_start: 0.8716 (ttm) cc_final: 0.8404 (ttm) REVERT: A 29 LYS cc_start: 0.8339 (ttpp) cc_final: 0.7844 (ttmt) REVERT: A 231 ASP cc_start: 0.7946 (t70) cc_final: 0.7589 (t0) REVERT: A 242 ARG cc_start: 0.4598 (mpt180) cc_final: 0.3240 (ttm-80) REVERT: A 243 MET cc_start: 0.7966 (tpp) cc_final: 0.7425 (tpp) REVERT: A 244 HIS cc_start: 0.7662 (OUTLIER) cc_final: 0.7319 (m170) REVERT: A 247 MET cc_start: 0.8160 (mtp) cc_final: 0.7806 (mtt) REVERT: A 251 ASP cc_start: 0.8422 (t0) cc_final: 0.7933 (t0) REVERT: A 306 GLN cc_start: 0.7820 (mm-40) cc_final: 0.7557 (mm-40) REVERT: A 308 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6803 (mp0) REVERT: B 96 ARG cc_start: 0.8751 (mtt-85) cc_final: 0.8493 (mtt-85) REVERT: B 155 ASN cc_start: 0.8228 (t0) cc_final: 0.7738 (t0) REVERT: B 197 ARG cc_start: 0.7958 (mtm110) cc_final: 0.7480 (mtt90) REVERT: B 340 ASN cc_start: 0.8748 (t0) cc_final: 0.8547 (t0) REVERT: C 20 LYS cc_start: 0.7798 (mtpp) cc_final: 0.7497 (mtmm) REVERT: R 109 MET cc_start: 0.3728 (pmt) cc_final: 0.3514 (pmm) REVERT: R 278 PHE cc_start: 0.5965 (t80) cc_final: 0.5732 (t80) REVERT: R 356 TRP cc_start: 0.7233 (m100) cc_final: 0.6382 (m100) REVERT: S 23 SER cc_start: 0.8589 (m) cc_final: 0.8249 (t) REVERT: S 113 GLN cc_start: 0.8122 (mm110) cc_final: 0.7886 (mm-40) REVERT: S 171 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8015 (mt0) outliers start: 18 outliers final: 8 residues processed: 185 average time/residue: 0.2467 time to fit residues: 59.3889 Evaluate side-chains 169 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 159 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain R residue 218 ILE Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 308 MET Chi-restraints excluded: chain R residue 351 VAL Chi-restraints excluded: chain S residue 7 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 63 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 98 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.167501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.112066 restraints weight = 9442.539| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.28 r_work: 0.3032 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8642 Z= 0.169 Angle : 0.650 12.314 11734 Z= 0.337 Chirality : 0.045 0.163 1363 Planarity : 0.004 0.052 1470 Dihedral : 6.908 118.444 1211 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.58 % Favored : 95.33 % Rotamer: Outliers : 2.63 % Allowed : 10.73 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.62 (0.24), residues: 1091 helix: -2.36 (0.24), residues: 334 sheet: -1.30 (0.28), residues: 277 loop : -1.33 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.003 0.001 HIS R 154 PHE 0.018 0.002 PHE A 354 TYR 0.026 0.002 TYR S 178 ARG 0.004 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04213 ( 325) hydrogen bonds : angle 5.63744 ( 963) SS BOND : bond 0.00493 ( 1) SS BOND : angle 1.06053 ( 2) covalent geometry : bond 0.00377 ( 8640) covalent geometry : angle 0.64970 (11732) Misc. bond : bond 0.00041 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 0.948 Fit side-chains REVERT: A 17 LYS cc_start: 0.8250 (mttt) cc_final: 0.7743 (mtpt) REVERT: A 18 MET cc_start: 0.8698 (ttm) cc_final: 0.8373 (ttm) REVERT: A 231 ASP cc_start: 0.8093 (t70) cc_final: 0.7729 (t0) REVERT: A 243 MET cc_start: 0.8021 (tpp) cc_final: 0.7427 (tpp) REVERT: A 244 HIS cc_start: 0.7653 (OUTLIER) cc_final: 0.7323 (m170) REVERT: A 247 MET cc_start: 0.8110 (mtp) cc_final: 0.7760 (mtt) REVERT: A 251 ASP cc_start: 0.8149 (t0) cc_final: 0.7731 (t0) REVERT: A 306 GLN cc_start: 0.7659 (mm-40) cc_final: 0.7265 (mm110) REVERT: A 308 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: B 197 ARG cc_start: 0.7938 (mtm110) cc_final: 0.7683 (mmt-90) REVERT: B 219 ARG cc_start: 0.7795 (ttm170) cc_final: 0.7539 (mtp85) REVERT: B 325 MET cc_start: 0.8556 (tpp) cc_final: 0.8070 (tpp) REVERT: B 337 LYS cc_start: 0.8528 (mttt) cc_final: 0.8087 (mttt) REVERT: B 340 ASN cc_start: 0.8698 (t0) cc_final: 0.8436 (t0) REVERT: C 20 LYS cc_start: 0.7850 (mtpp) cc_final: 0.7523 (mtmm) REVERT: C 42 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7340 (mp0) REVERT: R 109 MET cc_start: 0.3842 (pmt) cc_final: 0.3597 (pmm) REVERT: R 278 PHE cc_start: 0.5845 (t80) cc_final: 0.5580 (t80) REVERT: R 356 TRP cc_start: 0.7231 (m100) cc_final: 0.6294 (m100) REVERT: R 404 LEU cc_start: 0.4987 (mm) cc_final: 0.4780 (mm) REVERT: S 23 SER cc_start: 0.8636 (m) cc_final: 0.8317 (t) REVERT: S 171 GLN cc_start: 0.8422 (mm-40) cc_final: 0.8030 (mt0) outliers start: 23 outliers final: 13 residues processed: 173 average time/residue: 0.2376 time to fit residues: 53.8345 Evaluate side-chains 170 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 308 MET Chi-restraints excluded: chain R residue 351 VAL Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 160 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 13 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 89 optimal weight: 0.4980 chunk 73 optimal weight: 0.0870 chunk 104 optimal weight: 0.0470 chunk 37 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.170602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.115880 restraints weight = 9357.995| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.27 r_work: 0.3081 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8642 Z= 0.119 Angle : 0.591 10.814 11734 Z= 0.307 Chirality : 0.043 0.149 1363 Planarity : 0.004 0.059 1470 Dihedral : 6.533 117.185 1211 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.22 % Favored : 95.69 % Rotamer: Outliers : 3.20 % Allowed : 12.44 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.16 (0.25), residues: 1091 helix: -1.81 (0.26), residues: 336 sheet: -1.07 (0.28), residues: 278 loop : -1.17 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.003 0.001 HIS R 154 PHE 0.013 0.001 PHE R 237 TYR 0.027 0.001 TYR S 178 ARG 0.003 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 325) hydrogen bonds : angle 5.19647 ( 963) SS BOND : bond 0.00322 ( 1) SS BOND : angle 0.88696 ( 2) covalent geometry : bond 0.00256 ( 8640) covalent geometry : angle 0.59091 (11732) Misc. bond : bond 0.00053 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.853 Fit side-chains REVERT: A 17 LYS cc_start: 0.8170 (mttt) cc_final: 0.7777 (mtpt) REVERT: A 18 MET cc_start: 0.8620 (ttm) cc_final: 0.8282 (ttm) REVERT: A 232 LEU cc_start: 0.7289 (mt) cc_final: 0.6989 (mp) REVERT: A 243 MET cc_start: 0.8031 (tpp) cc_final: 0.7495 (tpp) REVERT: A 244 HIS cc_start: 0.7696 (OUTLIER) cc_final: 0.7378 (m170) REVERT: A 247 MET cc_start: 0.8105 (mtp) cc_final: 0.7878 (mtt) REVERT: A 251 ASP cc_start: 0.8046 (t0) cc_final: 0.7839 (t0) REVERT: A 306 GLN cc_start: 0.7530 (mm-40) cc_final: 0.7165 (mm110) REVERT: A 308 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6911 (mp0) REVERT: B 197 ARG cc_start: 0.7878 (mtm110) cc_final: 0.7545 (mpt180) REVERT: B 219 ARG cc_start: 0.7749 (ttm170) cc_final: 0.7543 (mtp85) REVERT: C 14 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7711 (ttpp) REVERT: C 21 MET cc_start: 0.7895 (ttm) cc_final: 0.7683 (ttm) REVERT: R 109 MET cc_start: 0.3587 (pmt) cc_final: 0.3381 (pmm) REVERT: R 164 LEU cc_start: 0.6263 (OUTLIER) cc_final: 0.5975 (tt) REVERT: R 353 ILE cc_start: 0.7348 (mm) cc_final: 0.7026 (mt) REVERT: R 356 TRP cc_start: 0.7180 (m100) cc_final: 0.6282 (m100) REVERT: R 404 LEU cc_start: 0.5107 (mm) cc_final: 0.4905 (mm) REVERT: S 18 ARG cc_start: 0.7784 (mmt-90) cc_final: 0.7521 (tpt170) REVERT: S 23 SER cc_start: 0.8563 (m) cc_final: 0.8253 (t) REVERT: S 73 ASP cc_start: 0.7815 (t0) cc_final: 0.7614 (t70) REVERT: S 77 ASN cc_start: 0.8318 (m-40) cc_final: 0.8116 (m110) REVERT: S 171 GLN cc_start: 0.8313 (mm-40) cc_final: 0.8104 (mt0) outliers start: 28 outliers final: 13 residues processed: 175 average time/residue: 0.2389 time to fit residues: 54.6965 Evaluate side-chains 173 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 308 MET Chi-restraints excluded: chain R residue 351 VAL Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 160 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 64 optimal weight: 0.7980 chunk 45 optimal weight: 0.0980 chunk 100 optimal weight: 0.4980 chunk 84 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 13 GLN S 39 GLN S 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.169046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.113924 restraints weight = 9334.736| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.29 r_work: 0.3053 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8642 Z= 0.139 Angle : 0.603 11.511 11734 Z= 0.311 Chirality : 0.043 0.151 1363 Planarity : 0.004 0.064 1470 Dihedral : 6.427 115.385 1211 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.40 % Favored : 95.51 % Rotamer: Outliers : 2.97 % Allowed : 14.04 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.81 (0.25), residues: 1091 helix: -1.46 (0.27), residues: 334 sheet: -0.95 (0.28), residues: 290 loop : -0.95 (0.31), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS A 195 PHE 0.014 0.001 PHE R 237 TYR 0.026 0.001 TYR S 178 ARG 0.006 0.000 ARG C 27 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 325) hydrogen bonds : angle 5.04982 ( 963) SS BOND : bond 0.00254 ( 1) SS BOND : angle 1.07482 ( 2) covalent geometry : bond 0.00306 ( 8640) covalent geometry : angle 0.60276 (11732) Misc. bond : bond 0.00043 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 0.988 Fit side-chains REVERT: A 17 LYS cc_start: 0.8144 (mttt) cc_final: 0.7755 (mtpt) REVERT: A 18 MET cc_start: 0.8599 (ttm) cc_final: 0.8250 (ttm) REVERT: A 232 LEU cc_start: 0.7252 (mt) cc_final: 0.6860 (mp) REVERT: A 243 MET cc_start: 0.8011 (tpp) cc_final: 0.7461 (tpp) REVERT: A 244 HIS cc_start: 0.7676 (OUTLIER) cc_final: 0.7391 (m170) REVERT: A 247 MET cc_start: 0.8083 (mtp) cc_final: 0.7832 (mtt) REVERT: A 251 ASP cc_start: 0.7921 (t0) cc_final: 0.7699 (t0) REVERT: A 306 GLN cc_start: 0.7468 (mm-40) cc_final: 0.7093 (mm110) REVERT: A 308 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6911 (mp0) REVERT: B 13 GLN cc_start: 0.6802 (pp30) cc_final: 0.6481 (pp30) REVERT: B 197 ARG cc_start: 0.7864 (mtm110) cc_final: 0.7550 (mpt180) REVERT: B 219 ARG cc_start: 0.7738 (ttm170) cc_final: 0.7535 (mtp85) REVERT: C 14 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7674 (ttpp) REVERT: R 109 MET cc_start: 0.3619 (pmt) cc_final: 0.3187 (pmm) REVERT: R 164 LEU cc_start: 0.6296 (OUTLIER) cc_final: 0.6011 (tt) REVERT: R 220 ARG cc_start: 0.7116 (mmm160) cc_final: 0.6635 (mmp80) REVERT: R 240 MET cc_start: 0.5021 (tpp) cc_final: 0.4620 (tpp) REVERT: R 356 TRP cc_start: 0.7198 (m100) cc_final: 0.6199 (m100) REVERT: R 404 LEU cc_start: 0.5010 (mm) cc_final: 0.4796 (mm) REVERT: S 23 SER cc_start: 0.8664 (m) cc_final: 0.8324 (t) REVERT: S 194 SER cc_start: 0.8660 (t) cc_final: 0.8379 (m) outliers start: 26 outliers final: 16 residues processed: 185 average time/residue: 0.2553 time to fit residues: 61.3405 Evaluate side-chains 181 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 308 MET Chi-restraints excluded: chain R residue 351 VAL Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 160 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 76 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN B 259 GLN C 18 GLN S 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.165971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.110929 restraints weight = 9316.480| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.25 r_work: 0.3009 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8642 Z= 0.212 Angle : 0.658 13.549 11734 Z= 0.339 Chirality : 0.045 0.159 1363 Planarity : 0.004 0.067 1470 Dihedral : 6.502 107.226 1211 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.77 % Favored : 95.14 % Rotamer: Outliers : 3.08 % Allowed : 15.75 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.76 (0.25), residues: 1091 helix: -1.38 (0.27), residues: 332 sheet: -0.83 (0.29), residues: 285 loop : -1.03 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.004 0.001 HIS A 195 PHE 0.014 0.002 PHE R 174 TYR 0.024 0.002 TYR S 178 ARG 0.007 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03895 ( 325) hydrogen bonds : angle 5.22938 ( 963) SS BOND : bond 0.00243 ( 1) SS BOND : angle 1.57638 ( 2) covalent geometry : bond 0.00480 ( 8640) covalent geometry : angle 0.65738 (11732) Misc. bond : bond 0.00033 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 0.917 Fit side-chains REVERT: A 17 LYS cc_start: 0.8175 (mttt) cc_final: 0.7886 (mmtp) REVERT: A 231 ASP cc_start: 0.8119 (t70) cc_final: 0.7901 (t0) REVERT: A 243 MET cc_start: 0.8037 (tpp) cc_final: 0.7417 (tpp) REVERT: A 244 HIS cc_start: 0.7539 (OUTLIER) cc_final: 0.7244 (m170) REVERT: A 247 MET cc_start: 0.8158 (mtp) cc_final: 0.7887 (mtt) REVERT: A 251 ASP cc_start: 0.7989 (t0) cc_final: 0.7748 (t0) REVERT: A 306 GLN cc_start: 0.7490 (mm-40) cc_final: 0.7138 (mm110) REVERT: A 308 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6837 (mp0) REVERT: B 13 GLN cc_start: 0.6809 (pp30) cc_final: 0.6527 (pp30) REVERT: B 197 ARG cc_start: 0.7932 (mtm110) cc_final: 0.7597 (mpt180) REVERT: B 219 ARG cc_start: 0.7843 (ttm170) cc_final: 0.7460 (mtp85) REVERT: B 337 LYS cc_start: 0.8609 (mttt) cc_final: 0.8298 (mttt) REVERT: C 14 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7655 (ttpp) REVERT: C 48 ASP cc_start: 0.7833 (p0) cc_final: 0.7622 (p0) REVERT: R 109 MET cc_start: 0.3811 (pmt) cc_final: 0.3546 (pmm) REVERT: R 150 ARG cc_start: 0.6320 (ptp-110) cc_final: 0.5766 (ptp-110) REVERT: R 240 MET cc_start: 0.5067 (tpp) cc_final: 0.4498 (tpp) REVERT: R 278 PHE cc_start: 0.6017 (t80) cc_final: 0.5771 (t80) REVERT: R 336 ARG cc_start: 0.5262 (tpm-80) cc_final: 0.3269 (mmt-90) REVERT: R 356 TRP cc_start: 0.7229 (m100) cc_final: 0.6235 (m100) REVERT: R 405 ARG cc_start: 0.5714 (mtm-85) cc_final: 0.5109 (mtm-85) REVERT: S 23 SER cc_start: 0.8708 (m) cc_final: 0.8390 (t) REVERT: S 194 SER cc_start: 0.8703 (t) cc_final: 0.8409 (m) outliers start: 27 outliers final: 17 residues processed: 184 average time/residue: 0.2612 time to fit residues: 61.8842 Evaluate side-chains 184 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 308 MET Chi-restraints excluded: chain R residue 351 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 160 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 47 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 104 optimal weight: 0.3980 chunk 94 optimal weight: 0.9990 chunk 91 optimal weight: 0.0030 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.168812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.113638 restraints weight = 9454.234| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.30 r_work: 0.3047 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8642 Z= 0.137 Angle : 0.611 12.156 11734 Z= 0.312 Chirality : 0.043 0.150 1363 Planarity : 0.004 0.064 1470 Dihedral : 6.155 102.940 1211 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.40 % Favored : 95.51 % Rotamer: Outliers : 3.08 % Allowed : 16.55 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.67 (0.25), residues: 1091 helix: -1.16 (0.27), residues: 341 sheet: -0.79 (0.29), residues: 288 loop : -1.08 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.002 0.001 HIS R 154 PHE 0.014 0.001 PHE R 237 TYR 0.027 0.001 TYR S 178 ARG 0.008 0.001 ARG R 220 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 325) hydrogen bonds : angle 4.99265 ( 963) SS BOND : bond 0.00316 ( 1) SS BOND : angle 1.17356 ( 2) covalent geometry : bond 0.00300 ( 8640) covalent geometry : angle 0.61082 (11732) Misc. bond : bond 0.00032 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.840 Fit side-chains REVERT: A 17 LYS cc_start: 0.8122 (mttt) cc_final: 0.7845 (mmtp) REVERT: A 231 ASP cc_start: 0.8071 (t70) cc_final: 0.7855 (t0) REVERT: A 247 MET cc_start: 0.8082 (mtp) cc_final: 0.7820 (mtt) REVERT: A 251 ASP cc_start: 0.7958 (t0) cc_final: 0.7738 (t0) REVERT: A 306 GLN cc_start: 0.7448 (mm-40) cc_final: 0.7079 (mm110) REVERT: A 308 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6868 (mp0) REVERT: B 13 GLN cc_start: 0.6780 (pp30) cc_final: 0.6492 (pp30) REVERT: B 181 THR cc_start: 0.7754 (OUTLIER) cc_final: 0.7526 (p) REVERT: B 197 ARG cc_start: 0.7888 (mtm110) cc_final: 0.7570 (mpt180) REVERT: B 219 ARG cc_start: 0.7770 (ttm170) cc_final: 0.7502 (mtp85) REVERT: B 325 MET cc_start: 0.8328 (mmt) cc_final: 0.8025 (tpp) REVERT: B 337 LYS cc_start: 0.8560 (mttt) cc_final: 0.8237 (mttt) REVERT: C 14 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7617 (ttpp) REVERT: R 109 MET cc_start: 0.3735 (pmt) cc_final: 0.3269 (pmm) REVERT: R 220 ARG cc_start: 0.7191 (mmm160) cc_final: 0.6563 (mmp80) REVERT: R 336 ARG cc_start: 0.5185 (tpm-80) cc_final: 0.3244 (mmt-90) REVERT: R 405 ARG cc_start: 0.5836 (mtm-85) cc_final: 0.5234 (mtm-85) REVERT: S 23 SER cc_start: 0.8588 (m) cc_final: 0.8255 (t) REVERT: S 194 SER cc_start: 0.8684 (t) cc_final: 0.8395 (m) outliers start: 27 outliers final: 19 residues processed: 184 average time/residue: 0.2635 time to fit residues: 62.3233 Evaluate side-chains 185 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 308 MET Chi-restraints excluded: chain R residue 351 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 160 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 46 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 53 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.167660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.123617 restraints weight = 9520.536| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.49 r_work: 0.3033 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8642 Z= 0.166 Angle : 0.632 12.158 11734 Z= 0.322 Chirality : 0.044 0.154 1363 Planarity : 0.004 0.075 1470 Dihedral : 6.106 97.575 1211 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.04 % Favored : 94.87 % Rotamer: Outliers : 3.20 % Allowed : 17.01 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.59 (0.25), residues: 1091 helix: -1.06 (0.27), residues: 342 sheet: -0.78 (0.29), residues: 290 loop : -1.02 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 PHE 0.014 0.001 PHE R 237 TYR 0.025 0.001 TYR S 178 ARG 0.008 0.001 ARG C 27 Details of bonding type rmsd hydrogen bonds : bond 0.03632 ( 325) hydrogen bonds : angle 4.99327 ( 963) SS BOND : bond 0.00242 ( 1) SS BOND : angle 1.43019 ( 2) covalent geometry : bond 0.00370 ( 8640) covalent geometry : angle 0.63213 (11732) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.905 Fit side-chains REVERT: A 17 LYS cc_start: 0.8055 (mttt) cc_final: 0.7781 (mmtp) REVERT: A 247 MET cc_start: 0.7951 (mtp) cc_final: 0.7686 (mtt) REVERT: A 251 ASP cc_start: 0.7919 (t0) cc_final: 0.7688 (t0) REVERT: A 306 GLN cc_start: 0.7405 (mm-40) cc_final: 0.7054 (mm110) REVERT: A 308 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6826 (mp0) REVERT: A 337 ASP cc_start: 0.8059 (m-30) cc_final: 0.7850 (m-30) REVERT: B 52 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7708 (mtp85) REVERT: B 197 ARG cc_start: 0.7843 (mtm110) cc_final: 0.7518 (mpt180) REVERT: B 219 ARG cc_start: 0.7764 (ttm170) cc_final: 0.7498 (mtp85) REVERT: C 14 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7548 (ttpp) REVERT: R 150 ARG cc_start: 0.6231 (ptp-110) cc_final: 0.5746 (ptp-110) REVERT: R 220 ARG cc_start: 0.7190 (mmm160) cc_final: 0.6580 (mmp80) REVERT: R 336 ARG cc_start: 0.5174 (tpm-80) cc_final: 0.3294 (mmt-90) REVERT: R 405 ARG cc_start: 0.5547 (mtm-85) cc_final: 0.4903 (mtm-85) REVERT: S 23 SER cc_start: 0.8659 (m) cc_final: 0.8313 (t) REVERT: S 194 SER cc_start: 0.8694 (t) cc_final: 0.8385 (m) outliers start: 28 outliers final: 21 residues processed: 179 average time/residue: 0.2650 time to fit residues: 60.7794 Evaluate side-chains 183 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 308 MET Chi-restraints excluded: chain R residue 351 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 160 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 31 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 82 optimal weight: 0.0970 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.166396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.120658 restraints weight = 9536.999| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.29 r_work: 0.3039 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8642 Z= 0.192 Angle : 0.654 13.067 11734 Z= 0.335 Chirality : 0.045 0.159 1363 Planarity : 0.005 0.078 1470 Dihedral : 6.102 91.817 1211 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.67 % Favored : 95.23 % Rotamer: Outliers : 3.42 % Allowed : 17.01 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.59 (0.25), residues: 1091 helix: -1.09 (0.27), residues: 343 sheet: -0.78 (0.29), residues: 290 loop : -1.02 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS R 154 PHE 0.014 0.002 PHE R 237 TYR 0.025 0.002 TYR S 178 ARG 0.008 0.001 ARG C 27 Details of bonding type rmsd hydrogen bonds : bond 0.03742 ( 325) hydrogen bonds : angle 5.07742 ( 963) SS BOND : bond 0.00271 ( 1) SS BOND : angle 1.50344 ( 2) covalent geometry : bond 0.00433 ( 8640) covalent geometry : angle 0.65335 (11732) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.925 Fit side-chains REVERT: A 17 LYS cc_start: 0.7986 (mttt) cc_final: 0.7698 (mmtp) REVERT: A 244 HIS cc_start: 0.7725 (OUTLIER) cc_final: 0.7306 (m170) REVERT: A 247 MET cc_start: 0.7960 (mtp) cc_final: 0.7673 (mtt) REVERT: A 251 ASP cc_start: 0.7940 (t0) cc_final: 0.7696 (t0) REVERT: A 306 GLN cc_start: 0.7422 (mm-40) cc_final: 0.7063 (mm110) REVERT: A 308 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6772 (mp0) REVERT: A 337 ASP cc_start: 0.7983 (m-30) cc_final: 0.7772 (m-30) REVERT: B 52 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7680 (mtp85) REVERT: B 197 ARG cc_start: 0.7827 (mtm110) cc_final: 0.7491 (mpt180) REVERT: B 219 ARG cc_start: 0.7719 (ttm170) cc_final: 0.7448 (mtp85) REVERT: B 337 LYS cc_start: 0.8556 (mttt) cc_final: 0.8305 (mttt) REVERT: R 109 MET cc_start: 0.3796 (pmt) cc_final: 0.3521 (pmm) REVERT: R 150 ARG cc_start: 0.6246 (ptp-110) cc_final: 0.5752 (ptp-110) REVERT: R 220 ARG cc_start: 0.7177 (mmm160) cc_final: 0.6557 (mmp80) REVERT: R 405 ARG cc_start: 0.5584 (mtm-85) cc_final: 0.4922 (mtm-85) REVERT: S 23 SER cc_start: 0.8666 (m) cc_final: 0.8306 (t) outliers start: 30 outliers final: 22 residues processed: 177 average time/residue: 0.2669 time to fit residues: 60.4860 Evaluate side-chains 187 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 306 VAL Chi-restraints excluded: chain R residue 308 MET Chi-restraints excluded: chain R residue 351 VAL Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 180 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 19 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 95 optimal weight: 0.2980 chunk 70 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 97 optimal weight: 0.0070 chunk 0 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.168810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.123713 restraints weight = 9416.166| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.23 r_work: 0.3084 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8642 Z= 0.136 Angle : 0.620 11.913 11734 Z= 0.315 Chirality : 0.043 0.149 1363 Planarity : 0.004 0.080 1470 Dihedral : 5.853 88.307 1211 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.22 % Favored : 95.69 % Rotamer: Outliers : 2.51 % Allowed : 17.69 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.39 (0.25), residues: 1091 helix: -0.85 (0.28), residues: 340 sheet: -0.68 (0.29), residues: 285 loop : -0.94 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.002 0.001 HIS R 154 PHE 0.014 0.001 PHE R 237 TYR 0.026 0.001 TYR S 178 ARG 0.009 0.001 ARG C 27 Details of bonding type rmsd hydrogen bonds : bond 0.03512 ( 325) hydrogen bonds : angle 4.90959 ( 963) SS BOND : bond 0.00270 ( 1) SS BOND : angle 1.22012 ( 2) covalent geometry : bond 0.00299 ( 8640) covalent geometry : angle 0.61971 (11732) Misc. bond : bond 0.00013 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.863 Fit side-chains REVERT: A 17 LYS cc_start: 0.7983 (mttt) cc_final: 0.7703 (mmtp) REVERT: A 22 ASN cc_start: 0.8099 (m-40) cc_final: 0.7633 (m110) REVERT: A 244 HIS cc_start: 0.7630 (OUTLIER) cc_final: 0.7223 (m170) REVERT: A 247 MET cc_start: 0.7951 (mtp) cc_final: 0.7673 (mtt) REVERT: A 251 ASP cc_start: 0.7896 (t0) cc_final: 0.7647 (t0) REVERT: A 306 GLN cc_start: 0.7408 (mm-40) cc_final: 0.7072 (mm110) REVERT: A 308 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6803 (mp0) REVERT: B 52 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7581 (mtp85) REVERT: B 197 ARG cc_start: 0.7810 (mtm110) cc_final: 0.7518 (mpt180) REVERT: B 219 ARG cc_start: 0.7706 (ttm170) cc_final: 0.7471 (mtp85) REVERT: B 227 SER cc_start: 0.8984 (t) cc_final: 0.8728 (m) REVERT: B 325 MET cc_start: 0.8247 (mmt) cc_final: 0.8020 (tpp) REVERT: B 337 LYS cc_start: 0.8540 (mttt) cc_final: 0.8300 (mttt) REVERT: R 109 MET cc_start: 0.3753 (pmt) cc_final: 0.3285 (pmm) REVERT: S 23 SER cc_start: 0.8585 (m) cc_final: 0.8235 (t) outliers start: 22 outliers final: 18 residues processed: 176 average time/residue: 0.2388 time to fit residues: 55.5629 Evaluate side-chains 179 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 308 MET Chi-restraints excluded: chain R residue 351 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 160 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 17 optimal weight: 0.0970 chunk 26 optimal weight: 0.0020 chunk 93 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 2 optimal weight: 0.3980 chunk 106 optimal weight: 1.9990 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.170627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.116051 restraints weight = 9459.524| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.28 r_work: 0.3084 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8642 Z= 0.119 Angle : 0.603 8.999 11734 Z= 0.308 Chirality : 0.043 0.165 1363 Planarity : 0.004 0.083 1470 Dihedral : 5.620 84.606 1211 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.31 % Favored : 95.60 % Rotamer: Outliers : 2.63 % Allowed : 18.15 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.26), residues: 1091 helix: -0.62 (0.28), residues: 339 sheet: -0.59 (0.29), residues: 284 loop : -0.90 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.002 0.001 HIS R 154 PHE 0.013 0.001 PHE R 237 TYR 0.027 0.001 TYR S 178 ARG 0.009 0.001 ARG C 27 Details of bonding type rmsd hydrogen bonds : bond 0.03365 ( 325) hydrogen bonds : angle 4.77004 ( 963) SS BOND : bond 0.00256 ( 1) SS BOND : angle 1.22079 ( 2) covalent geometry : bond 0.00261 ( 8640) covalent geometry : angle 0.60268 (11732) Misc. bond : bond 0.00009 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5892.11 seconds wall clock time: 102 minutes 23.73 seconds (6143.73 seconds total)