Starting phenix.real_space_refine on Sat Jun 14 04:50:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zym_60572/06_2025/8zym_60572.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zym_60572/06_2025/8zym_60572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zym_60572/06_2025/8zym_60572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zym_60572/06_2025/8zym_60572.map" model { file = "/net/cci-nas-00/data/ceres_data/8zym_60572/06_2025/8zym_60572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zym_60572/06_2025/8zym_60572.cif" } resolution = 3.23 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= 0.001 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 9984 2.51 5 N 2613 2.21 5 O 3133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15829 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3491 Classifications: {'peptide': 452} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 437} Chain breaks: 1 Chain: "B" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3485 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3485 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 864 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 107} Chain: "E" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 864 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 107} Chain: "F" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 864 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 107} Chain: "G" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 925 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "H" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 925 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "I" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 925 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 9.58, per 1000 atoms: 0.61 Number of scatterers: 15829 At special positions: 0 Unit cell: (148.24, 137.498, 131.052, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 99 16.00 O 3133 8.00 N 2613 7.00 C 9984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 400 " distance=2.04 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 251 " distance=2.03 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 304 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 294 " distance=2.03 Simple disulfide: pdb=" SG CYS A 319 " - pdb=" SG CYS A 328 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 354 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 383 " distance=2.03 Simple disulfide: pdb=" SG CYS A 419 " - pdb=" SG CYS C 110 " distance=2.03 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 400 " distance=2.04 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 251 " distance=2.03 Simple disulfide: pdb=" SG CYS B 274 " - pdb=" SG CYS B 304 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 294 " distance=2.03 Simple disulfide: pdb=" SG CYS B 319 " - pdb=" SG CYS B 328 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 354 " distance=2.03 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 383 " distance=2.03 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS C 400 " distance=2.03 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 251 " distance=2.03 Simple disulfide: pdb=" SG CYS C 274 " - pdb=" SG CYS C 304 " distance=2.03 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 294 " distance=2.03 Simple disulfide: pdb=" SG CYS C 319 " - pdb=" SG CYS C 328 " distance=2.03 Simple disulfide: pdb=" SG CYS C 343 " - pdb=" SG CYS C 354 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 383 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 94 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 94 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.04 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=0, symmetry=0 Time building additional restraints: 3.72 Conformation dependent library (CDL) restraints added in 2.3 seconds 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 37 sheets defined 25.0% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'A' and resid 73 through 100 Processing helix chain 'A' and resid 109 through 121 Processing helix chain 'A' and resid 123 through 135 removed outlier: 4.535A pdb=" N SER A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 163 removed outlier: 3.732A pdb=" N TYR A 159 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 170 removed outlier: 4.223A pdb=" N ILE A 167 " --> pdb=" O GLN A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 202 removed outlier: 4.504A pdb=" N VAL A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 182 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN A 201 " --> pdb=" O GLU A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 225 removed outlier: 3.585A pdb=" N ASN A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 238 removed outlier: 3.544A pdb=" N LYS A 232 " --> pdb=" O THR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 246 removed outlier: 4.000A pdb=" N VAL A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 346 removed outlier: 3.601A pdb=" N ASN A 344 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL A 345 " --> pdb=" O ASN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 480 Processing helix chain 'B' and resid 73 through 100 Processing helix chain 'B' and resid 109 through 121 removed outlier: 3.503A pdb=" N LEU B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 132 removed outlier: 3.585A pdb=" N ILE B 128 " --> pdb=" O GLU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 163 Processing helix chain 'B' and resid 163 through 170 removed outlier: 4.096A pdb=" N ILE B 167 " --> pdb=" O GLN B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 202 removed outlier: 3.819A pdb=" N VAL B 181 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG B 190 " --> pdb=" O GLN B 186 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 224 removed outlier: 3.527A pdb=" N ASN B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 238 removed outlier: 3.543A pdb=" N LYS B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 245 removed outlier: 3.809A pdb=" N VAL B 242 " --> pdb=" O ASN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 346 removed outlier: 3.511A pdb=" N CYS B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN B 344 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL B 345 " --> pdb=" O ASN B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 439 Processing helix chain 'B' and resid 457 through 479 removed outlier: 3.539A pdb=" N ASN B 461 " --> pdb=" O ASN B 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 100 Processing helix chain 'C' and resid 107 through 121 removed outlier: 3.522A pdb=" N SER C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLY C 112 " --> pdb=" O ALA C 108 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA C 114 " --> pdb=" O CYS C 110 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL C 115 " --> pdb=" O SER C 111 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS C 116 " --> pdb=" O GLY C 112 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 118 " --> pdb=" O ALA C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 132 removed outlier: 3.688A pdb=" N ILE C 128 " --> pdb=" O GLU C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 163 removed outlier: 3.630A pdb=" N TYR C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 170 removed outlier: 4.089A pdb=" N ILE C 167 " --> pdb=" O GLN C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 202 removed outlier: 3.844A pdb=" N VAL C 181 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG C 190 " --> pdb=" O GLN C 186 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 225 Processing helix chain 'C' and resid 228 through 238 Processing helix chain 'C' and resid 238 through 246 removed outlier: 3.686A pdb=" N VAL C 242 " --> pdb=" O ASN C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 346 removed outlier: 3.687A pdb=" N ASN C 344 " --> pdb=" O VAL C 340 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL C 345 " --> pdb=" O ASN C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 439 Processing helix chain 'C' and resid 453 through 478 removed outlier: 3.919A pdb=" N GLY C 478 " --> pdb=" O LEU C 474 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 90 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.556A pdb=" N THR H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 46 Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 46 removed outlier: 6.563A pdb=" N GLU A 30 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N VAL A 430 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE A 32 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 137 through 141 removed outlier: 11.001A pdb=" N SER A 147 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N THR A 54 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU A 149 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N VAL A 261 " --> pdb=" O MET A 250 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N MET A 250 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLN A 263 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N SER A 248 " --> pdb=" O GLN A 263 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 294 through 297 Processing sheet with id=AA5, first strand: chain 'A' and resid 320 through 321 Processing sheet with id=AA6, first strand: chain 'A' and resid 365 through 369 removed outlier: 4.138A pdb=" N GLY A 372 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 395 removed outlier: 6.599A pdb=" N ALA A 385 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N THR A 395 " --> pdb=" O CYS A 383 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N CYS A 383 " --> pdb=" O THR A 395 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 320 through 322 removed outlier: 3.562A pdb=" N VAL B 326 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS B 328 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY B 43 " --> pdb=" O CYS B 274 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N CYS B 274 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU B 45 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N THR B 272 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 320 through 322 removed outlier: 3.562A pdb=" N VAL B 326 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS B 328 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 152 through 155 removed outlier: 5.595A pdb=" N LYS B 152 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR B 58 " --> pdb=" O LYS B 152 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU B 154 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL B 261 " --> pdb=" O MET B 250 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N MET B 250 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLN B 263 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N SER B 248 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 139 through 141 Processing sheet with id=AB3, first strand: chain 'B' and resid 294 through 297 Processing sheet with id=AB4, first strand: chain 'B' and resid 365 through 368 Processing sheet with id=AB5, first strand: chain 'B' and resid 391 through 395 removed outlier: 6.630A pdb=" N ALA B 385 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N THR B 395 " --> pdb=" O CYS B 383 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N CYS B 383 " --> pdb=" O THR B 395 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 325 through 327 removed outlier: 7.088A pdb=" N LEU C 45 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP C 302 " --> pdb=" O PHE C 313 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 325 through 327 removed outlier: 7.088A pdb=" N LEU C 45 " --> pdb=" O VAL C 326 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 137 through 141 removed outlier: 11.141A pdb=" N SER C 147 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N THR C 54 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU C 149 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE C 253 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ALA C 259 " --> pdb=" O CYS C 251 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 294 through 297 removed outlier: 5.976A pdb=" N THR C 358 " --> pdb=" O PHE C 449 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N PHE C 449 " --> pdb=" O THR C 358 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 365 through 369 removed outlier: 4.144A pdb=" N GLY C 372 " --> pdb=" O THR C 369 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 391 through 395 removed outlier: 6.625A pdb=" N ALA C 385 " --> pdb=" O ILE C 393 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N THR C 395 " --> pdb=" O CYS C 383 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N CYS C 383 " --> pdb=" O THR C 395 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.585A pdb=" N VAL D 19 " --> pdb=" O ILE D 81 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.542A pdb=" N GLU D 110 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU D 39 " --> pdb=" O TYR D 55 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR D 55 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP D 41 " --> pdb=" O LEU D 53 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.542A pdb=" N GLU D 110 " --> pdb=" O LEU D 11 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.536A pdb=" N VAL E 19 " --> pdb=" O ILE E 81 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.531A pdb=" N GLU E 110 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU E 39 " --> pdb=" O TYR E 55 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TYR E 55 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP E 41 " --> pdb=" O LEU E 53 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.531A pdb=" N GLU E 110 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR E 102 " --> pdb=" O GLN E 96 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 30 through 31 removed outlier: 3.548A pdb=" N LYS E 36 " --> pdb=" O ASN E 31 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.551A pdb=" N VAL F 19 " --> pdb=" O ILE F 81 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.550A pdb=" N GLU F 110 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU F 39 " --> pdb=" O TYR F 55 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR F 55 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP F 41 " --> pdb=" O LEU F 53 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.550A pdb=" N GLU F 110 " --> pdb=" O LEU F 11 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 30 through 31 removed outlier: 3.620A pdb=" N LYS F 36 " --> pdb=" O ASN F 31 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.545A pdb=" N THR G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLN G 16 " --> pdb=" O SER G 84 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 46 through 51 removed outlier: 4.822A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ILE G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ILE G 34 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'H' and resid 46 through 51 removed outlier: 4.892A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ILE H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ILE H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE1, first strand: chain 'I' and resid 57 through 58 removed outlier: 4.846A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ILE I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE I 34 " --> pdb=" O ILE I 50 " (cutoff:3.500A) 747 hydrogen bonds defined for protein. 1917 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.26 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5060 1.34 - 1.46: 3695 1.46 - 1.58: 7217 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 16104 Sorted by residual: bond pdb=" N LEU C 474 " pdb=" CA LEU C 474 " ideal model delta sigma weight residual 1.459 1.491 -0.033 1.28e-02 6.10e+03 6.58e+00 bond pdb=" N ILE C 109 " pdb=" CA ILE C 109 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.08e+00 bond pdb=" N LEU B 464 " pdb=" CA LEU B 464 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 5.96e+00 bond pdb=" CB LYS I 43 " pdb=" CG LYS I 43 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.19e+00 bond pdb=" C ALA C 108 " pdb=" N ILE C 109 " ideal model delta sigma weight residual 1.332 1.314 0.018 1.36e-02 5.41e+03 1.70e+00 ... (remaining 16099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 21528 1.87 - 3.73: 257 3.73 - 5.60: 41 5.60 - 7.47: 8 7.47 - 9.33: 7 Bond angle restraints: 21841 Sorted by residual: angle pdb=" CB LYS I 43 " pdb=" CG LYS I 43 " pdb=" CD LYS I 43 " ideal model delta sigma weight residual 111.30 119.90 -8.60 2.30e+00 1.89e-01 1.40e+01 angle pdb=" C ILE C 109 " pdb=" N CYS C 110 " pdb=" CA CYS C 110 " ideal model delta sigma weight residual 120.38 115.31 5.07 1.37e+00 5.33e-01 1.37e+01 angle pdb=" N LEU B 464 " pdb=" CA LEU B 464 " pdb=" C LEU B 464 " ideal model delta sigma weight residual 111.28 107.33 3.95 1.09e+00 8.42e-01 1.31e+01 angle pdb=" CA LYS I 43 " pdb=" CB LYS I 43 " pdb=" CG LYS I 43 " ideal model delta sigma weight residual 114.10 121.34 -7.24 2.00e+00 2.50e-01 1.31e+01 angle pdb=" CA TRP E 56 " pdb=" CB TRP E 56 " pdb=" CG TRP E 56 " ideal model delta sigma weight residual 113.60 120.45 -6.85 1.90e+00 2.77e-01 1.30e+01 ... (remaining 21836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 8441 17.97 - 35.94: 1063 35.94 - 53.92: 236 53.92 - 71.89: 57 71.89 - 89.86: 18 Dihedral angle restraints: 9815 sinusoidal: 3833 harmonic: 5982 Sorted by residual: dihedral pdb=" CB CYS A 343 " pdb=" SG CYS A 343 " pdb=" SG CYS A 354 " pdb=" CB CYS A 354 " ideal model delta sinusoidal sigma weight residual -86.00 -156.74 70.74 1 1.00e+01 1.00e-02 6.43e+01 dihedral pdb=" CB CYS B 377 " pdb=" SG CYS B 377 " pdb=" SG CYS B 383 " pdb=" CB CYS B 383 " ideal model delta sinusoidal sigma weight residual -86.00 -152.14 66.14 1 1.00e+01 1.00e-02 5.72e+01 dihedral pdb=" CB CYS C 377 " pdb=" SG CYS C 377 " pdb=" SG CYS C 383 " pdb=" CB CYS C 383 " ideal model delta sinusoidal sigma weight residual -86.00 -151.11 65.11 1 1.00e+01 1.00e-02 5.56e+01 ... (remaining 9812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2353 0.083 - 0.165: 193 0.165 - 0.248: 4 0.248 - 0.330: 1 0.330 - 0.413: 2 Chirality restraints: 2553 Sorted by residual: chirality pdb=" CB ILE H 34 " pdb=" CA ILE H 34 " pdb=" CG1 ILE H 34 " pdb=" CG2 ILE H 34 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CB ILE G 34 " pdb=" CA ILE G 34 " pdb=" CG1 ILE G 34 " pdb=" CG2 ILE G 34 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA ILE C 109 " pdb=" N ILE C 109 " pdb=" C ILE C 109 " pdb=" CB ILE C 109 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 2550 not shown) Planarity restraints: 2755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 108 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C ALA C 108 " -0.055 2.00e-02 2.50e+03 pdb=" O ALA C 108 " 0.020 2.00e-02 2.50e+03 pdb=" N ILE C 109 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 94 " 0.025 2.00e-02 2.50e+03 2.14e-02 9.13e+00 pdb=" CG TYR G 94 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR G 94 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR G 94 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR G 94 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR G 94 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR G 94 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR G 94 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 464 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.30e+00 pdb=" C LEU B 464 " 0.036 2.00e-02 2.50e+03 pdb=" O LEU B 464 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA B 465 " -0.012 2.00e-02 2.50e+03 ... (remaining 2752 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 523 2.69 - 3.24: 15620 3.24 - 3.80: 25378 3.80 - 4.35: 33784 4.35 - 4.90: 56324 Nonbonded interactions: 131629 Sorted by model distance: nonbonded pdb=" O MET A 97 " pdb=" OG1 THR A 100 " model vdw 2.139 3.040 nonbonded pdb=" O ILE B 460 " pdb=" OG SER B 463 " model vdw 2.147 3.040 nonbonded pdb=" O MET B 97 " pdb=" OG1 THR B 100 " model vdw 2.149 3.040 nonbonded pdb=" O MET C 97 " pdb=" OG1 THR C 100 " model vdw 2.149 3.040 nonbonded pdb=" OE1 GLN I 6 " pdb=" OG1 THR I 115 " model vdw 2.162 3.040 ... (remaining 131624 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 467 or (resid 468 and (name N or name CA or nam \ e C or name O or name CB )) or resid 469 through 480)) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 39.630 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16137 Z= 0.120 Angle : 0.561 9.332 21907 Z= 0.295 Chirality : 0.044 0.413 2553 Planarity : 0.003 0.033 2755 Dihedral : 16.502 89.860 5876 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.83 % Allowed : 26.42 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.19), residues: 2031 helix: 1.13 (0.25), residues: 447 sheet: -0.82 (0.20), residues: 690 loop : -0.63 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 56 HIS 0.003 0.001 HIS A 278 PHE 0.014 0.001 PHE A 466 TYR 0.052 0.001 TYR G 94 ARG 0.002 0.000 ARG D 67 Details of bonding type rmsd hydrogen bonds : bond 0.15652 ( 724) hydrogen bonds : angle 7.19242 ( 1917) SS BOND : bond 0.00258 ( 33) SS BOND : angle 0.85864 ( 66) covalent geometry : bond 0.00255 (16104) covalent geometry : angle 0.56009 (21841) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 203 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.6116 (mmp) REVERT: A 250 MET cc_start: 0.8705 (tpt) cc_final: 0.8359 (tpt) REVERT: A 331 MET cc_start: 0.7403 (ttm) cc_final: 0.7172 (ttp) REVERT: B 250 MET cc_start: 0.8676 (tpt) cc_final: 0.7913 (tpt) REVERT: B 284 THR cc_start: 0.6304 (OUTLIER) cc_final: 0.6052 (p) REVERT: C 68 LYS cc_start: 0.5402 (OUTLIER) cc_final: 0.4661 (mtmm) REVERT: C 250 MET cc_start: 0.8741 (tpt) cc_final: 0.8383 (tpt) REVERT: C 409 ASP cc_start: 0.7229 (m-30) cc_final: 0.6445 (t0) REVERT: D 85 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7301 (mp10) REVERT: F 85 GLN cc_start: 0.7901 (mm110) cc_final: 0.7460 (mp10) REVERT: G 31 ASN cc_start: 0.7569 (t160) cc_final: 0.7302 (t0) REVERT: H 31 ASN cc_start: 0.7934 (t160) cc_final: 0.7454 (t0) REVERT: H 75 LYS cc_start: 0.8217 (mmtm) cc_final: 0.7762 (mtmt) REVERT: H 103 TYR cc_start: 0.6007 (OUTLIER) cc_final: 0.5466 (t80) REVERT: I 31 ASN cc_start: 0.7781 (t160) cc_final: 0.7325 (t0) outliers start: 70 outliers final: 60 residues processed: 257 average time/residue: 0.2552 time to fit residues: 100.5778 Evaluate side-chains 256 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 191 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 278 HIS Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 33 ASP Chi-restraints excluded: chain I residue 103 TYR Chi-restraints excluded: chain I residue 115 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.0060 chunk 154 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 82 optimal weight: 0.7980 chunk 159 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 185 optimal weight: 0.0570 overall best weight: 1.1116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN B 415 ASN B 426 GLN C 263 GLN C 415 ASN F 85 GLN G 6 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.148691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.121116 restraints weight = 28075.505| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.70 r_work: 0.3650 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16137 Z= 0.155 Angle : 0.579 11.577 21907 Z= 0.305 Chirality : 0.044 0.399 2553 Planarity : 0.004 0.041 2755 Dihedral : 7.137 85.586 2300 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 5.85 % Allowed : 23.47 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.19), residues: 2031 helix: 1.46 (0.25), residues: 453 sheet: -0.73 (0.20), residues: 672 loop : -0.63 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 56 HIS 0.006 0.002 HIS A 278 PHE 0.010 0.001 PHE E 77 TYR 0.022 0.002 TYR G 59 ARG 0.003 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 724) hydrogen bonds : angle 5.83246 ( 1917) SS BOND : bond 0.00318 ( 33) SS BOND : angle 0.89713 ( 66) covalent geometry : bond 0.00356 (16104) covalent geometry : angle 0.57789 (21841) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 208 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7553 (tt0) REVERT: A 250 MET cc_start: 0.8750 (tpt) cc_final: 0.8375 (tpt) REVERT: A 278 HIS cc_start: 0.6824 (OUTLIER) cc_final: 0.6615 (m90) REVERT: A 331 MET cc_start: 0.7764 (ttm) cc_final: 0.7516 (ttp) REVERT: A 464 LEU cc_start: 0.9635 (mm) cc_final: 0.9434 (mp) REVERT: B 250 MET cc_start: 0.8680 (tpt) cc_final: 0.7837 (tpt) REVERT: B 258 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7667 (tp) REVERT: C 278 HIS cc_start: 0.6866 (OUTLIER) cc_final: 0.6288 (m90) REVERT: D 85 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7798 (mp10) REVERT: F 85 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7566 (mp10) REVERT: F 109 LEU cc_start: 0.1230 (OUTLIER) cc_final: 0.0970 (mp) REVERT: G 31 ASN cc_start: 0.7735 (OUTLIER) cc_final: 0.7349 (t0) REVERT: H 31 ASN cc_start: 0.7981 (OUTLIER) cc_final: 0.7572 (t0) REVERT: H 37 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7367 (mm) REVERT: H 75 LYS cc_start: 0.8169 (mmtm) cc_final: 0.7601 (mtmt) REVERT: I 23 THR cc_start: 0.7272 (OUTLIER) cc_final: 0.6967 (p) REVERT: I 31 ASN cc_start: 0.7860 (OUTLIER) cc_final: 0.7314 (t0) outliers start: 107 outliers final: 64 residues processed: 288 average time/residue: 0.2472 time to fit residues: 110.4109 Evaluate side-chains 267 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 192 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 278 HIS Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 400 CYS Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 71 LYS Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 33 ASP Chi-restraints excluded: chain I residue 103 TYR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 118 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 19 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 192 optimal weight: 0.0040 chunk 161 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 172 optimal weight: 0.0670 overall best weight: 0.5330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN B 387 ASN ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.151116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.123825 restraints weight = 27940.646| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.75 r_work: 0.3691 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16137 Z= 0.113 Angle : 0.541 11.777 21907 Z= 0.282 Chirality : 0.043 0.353 2553 Planarity : 0.003 0.045 2755 Dihedral : 6.038 86.777 2236 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.74 % Allowed : 24.07 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.19), residues: 2031 helix: 1.56 (0.25), residues: 453 sheet: -0.62 (0.20), residues: 678 loop : -0.61 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 56 HIS 0.004 0.001 HIS A 278 PHE 0.010 0.001 PHE E 77 TYR 0.020 0.001 TYR H 103 ARG 0.007 0.000 ARG A 468 Details of bonding type rmsd hydrogen bonds : bond 0.03173 ( 724) hydrogen bonds : angle 5.53224 ( 1917) SS BOND : bond 0.00264 ( 33) SS BOND : angle 0.98037 ( 66) covalent geometry : bond 0.00253 (16104) covalent geometry : angle 0.53927 (21841) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 210 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7427 (tt0) REVERT: A 250 MET cc_start: 0.8734 (tpt) cc_final: 0.8314 (tpt) REVERT: A 278 HIS cc_start: 0.6852 (OUTLIER) cc_final: 0.6632 (m90) REVERT: B 250 MET cc_start: 0.8646 (tpt) cc_final: 0.7821 (tpt) REVERT: B 380 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8215 (pttm) REVERT: B 409 ASP cc_start: 0.6983 (m-30) cc_final: 0.6238 (t0) REVERT: C 177 ASN cc_start: 0.6335 (t0) cc_final: 0.5715 (t0) REVERT: C 423 GLN cc_start: 0.6867 (tp40) cc_final: 0.6632 (tp40) REVERT: D 85 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7705 (mp10) REVERT: E 29 VAL cc_start: 0.8454 (OUTLIER) cc_final: 0.8183 (t) REVERT: F 85 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7531 (mp10) REVERT: G 31 ASN cc_start: 0.7704 (OUTLIER) cc_final: 0.7385 (t0) REVERT: H 31 ASN cc_start: 0.8031 (OUTLIER) cc_final: 0.7648 (t0) REVERT: H 37 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7346 (mm) REVERT: H 75 LYS cc_start: 0.8144 (mmtm) cc_final: 0.7802 (mtmt) REVERT: H 103 TYR cc_start: 0.5719 (t80) cc_final: 0.5316 (t80) REVERT: I 23 THR cc_start: 0.7243 (OUTLIER) cc_final: 0.6919 (p) REVERT: I 31 ASN cc_start: 0.7817 (OUTLIER) cc_final: 0.7307 (t0) outliers start: 105 outliers final: 62 residues processed: 292 average time/residue: 0.2431 time to fit residues: 109.4511 Evaluate side-chains 262 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 190 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 400 CYS Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 103 TYR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 118 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 112 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 97 optimal weight: 0.0040 chunk 23 optimal weight: 2.9990 chunk 198 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 183 optimal weight: 0.3980 chunk 84 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 89 optimal weight: 5.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 GLN C 324 ASN ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.151582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.124449 restraints weight = 27560.921| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.71 r_work: 0.3704 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16137 Z= 0.110 Angle : 0.537 12.347 21907 Z= 0.278 Chirality : 0.043 0.324 2553 Planarity : 0.003 0.040 2755 Dihedral : 5.786 87.598 2225 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 5.42 % Allowed : 24.62 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.19), residues: 2031 helix: 1.59 (0.25), residues: 459 sheet: -0.59 (0.21), residues: 660 loop : -0.63 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 56 HIS 0.004 0.001 HIS A 278 PHE 0.010 0.001 PHE E 77 TYR 0.016 0.001 TYR H 94 ARG 0.003 0.000 ARG C 325 Details of bonding type rmsd hydrogen bonds : bond 0.02969 ( 724) hydrogen bonds : angle 5.35693 ( 1917) SS BOND : bond 0.00251 ( 33) SS BOND : angle 0.89970 ( 66) covalent geometry : bond 0.00247 (16104) covalent geometry : angle 0.53559 (21841) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 204 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7328 (tt0) REVERT: A 250 MET cc_start: 0.8750 (tpt) cc_final: 0.8445 (tpt) REVERT: A 278 HIS cc_start: 0.6853 (OUTLIER) cc_final: 0.6636 (m90) REVERT: B 250 MET cc_start: 0.8638 (tpt) cc_final: 0.7819 (tpt) REVERT: B 380 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8183 (pttm) REVERT: B 409 ASP cc_start: 0.6784 (m-30) cc_final: 0.6258 (t0) REVERT: C 177 ASN cc_start: 0.6382 (t0) cc_final: 0.6175 (t0) REVERT: C 179 GLU cc_start: 0.7449 (pt0) cc_final: 0.7063 (pm20) REVERT: E 29 VAL cc_start: 0.8465 (OUTLIER) cc_final: 0.8193 (t) REVERT: F 85 GLN cc_start: 0.7812 (mm-40) cc_final: 0.7529 (mp10) REVERT: G 31 ASN cc_start: 0.7651 (OUTLIER) cc_final: 0.7354 (t0) REVERT: H 31 ASN cc_start: 0.7981 (OUTLIER) cc_final: 0.7601 (t0) REVERT: H 75 LYS cc_start: 0.8116 (mmtm) cc_final: 0.7813 (mtmt) REVERT: H 103 TYR cc_start: 0.5739 (OUTLIER) cc_final: 0.5303 (t80) REVERT: I 23 THR cc_start: 0.7245 (OUTLIER) cc_final: 0.6897 (p) REVERT: I 31 ASN cc_start: 0.7661 (OUTLIER) cc_final: 0.7172 (t0) REVERT: I 37 ILE cc_start: 0.7704 (mm) cc_final: 0.7446 (mm) outliers start: 99 outliers final: 66 residues processed: 281 average time/residue: 0.2535 time to fit residues: 110.2314 Evaluate side-chains 267 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 192 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 103 TYR Chi-restraints excluded: chain I residue 115 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 69 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 142 optimal weight: 7.9990 chunk 197 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.149233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.121739 restraints weight = 28144.226| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.70 r_work: 0.3662 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16137 Z= 0.153 Angle : 0.572 10.342 21907 Z= 0.296 Chirality : 0.044 0.331 2553 Planarity : 0.003 0.041 2755 Dihedral : 5.269 59.922 2212 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 7.06 % Allowed : 22.76 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.19), residues: 2031 helix: 1.62 (0.25), residues: 453 sheet: -0.57 (0.21), residues: 657 loop : -0.63 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 56 HIS 0.005 0.001 HIS A 278 PHE 0.010 0.001 PHE D 77 TYR 0.020 0.002 TYR H 94 ARG 0.008 0.000 ARG A 468 Details of bonding type rmsd hydrogen bonds : bond 0.03184 ( 724) hydrogen bonds : angle 5.35697 ( 1917) SS BOND : bond 0.00318 ( 33) SS BOND : angle 0.99177 ( 66) covalent geometry : bond 0.00356 (16104) covalent geometry : angle 0.57007 (21841) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 194 time to evaluate : 2.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7384 (tt0) REVERT: A 392 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8234 (mp) REVERT: B 250 MET cc_start: 0.8676 (tpt) cc_final: 0.7797 (tpt) REVERT: B 258 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7619 (tp) REVERT: B 380 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8169 (pttm) REVERT: C 179 GLU cc_start: 0.7520 (pt0) cc_final: 0.7100 (pm20) REVERT: D 44 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7203 (tt0) REVERT: D 85 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7785 (mp10) REVERT: E 29 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8248 (t) REVERT: F 85 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7617 (mp10) REVERT: G 31 ASN cc_start: 0.7684 (OUTLIER) cc_final: 0.7367 (t0) REVERT: H 31 ASN cc_start: 0.8026 (OUTLIER) cc_final: 0.7645 (t0) REVERT: H 37 ILE cc_start: 0.7717 (OUTLIER) cc_final: 0.7319 (mm) REVERT: H 75 LYS cc_start: 0.8103 (mmtm) cc_final: 0.7762 (mtmt) REVERT: H 103 TYR cc_start: 0.5772 (OUTLIER) cc_final: 0.5220 (t80) REVERT: I 23 THR cc_start: 0.7269 (OUTLIER) cc_final: 0.6905 (p) REVERT: I 31 ASN cc_start: 0.7762 (OUTLIER) cc_final: 0.7277 (t0) outliers start: 129 outliers final: 88 residues processed: 290 average time/residue: 0.2690 time to fit residues: 121.5126 Evaluate side-chains 290 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 189 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 103 TYR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 118 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 189 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 190 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN A 324 ASN ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.147076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.119381 restraints weight = 27900.626| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.75 r_work: 0.3625 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16137 Z= 0.200 Angle : 0.616 9.011 21907 Z= 0.321 Chirality : 0.045 0.353 2553 Planarity : 0.004 0.041 2755 Dihedral : 5.528 56.899 2212 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 7.49 % Allowed : 22.92 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.19), residues: 2031 helix: 1.41 (0.25), residues: 453 sheet: -0.69 (0.21), residues: 657 loop : -0.70 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 56 HIS 0.005 0.002 HIS A 278 PHE 0.012 0.002 PHE D 68 TYR 0.018 0.002 TYR G 103 ARG 0.002 0.000 ARG G 38 Details of bonding type rmsd hydrogen bonds : bond 0.03498 ( 724) hydrogen bonds : angle 5.48822 ( 1917) SS BOND : bond 0.00389 ( 33) SS BOND : angle 1.07420 ( 66) covalent geometry : bond 0.00468 (16104) covalent geometry : angle 0.61393 (21841) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 197 time to evaluate : 2.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7405 (tt0) REVERT: A 250 MET cc_start: 0.8707 (tpt) cc_final: 0.8401 (tpt) REVERT: A 392 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8248 (mp) REVERT: B 250 MET cc_start: 0.8699 (tpt) cc_final: 0.7815 (tpt) REVERT: B 258 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7820 (tp) REVERT: B 380 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8212 (pttm) REVERT: C 177 ASN cc_start: 0.6218 (t0) cc_final: 0.5386 (t0) REVERT: C 179 GLU cc_start: 0.7569 (pt0) cc_final: 0.7262 (pm20) REVERT: C 278 HIS cc_start: 0.6880 (OUTLIER) cc_final: 0.6306 (m90) REVERT: C 409 ASP cc_start: 0.7254 (m-30) cc_final: 0.6266 (t0) REVERT: D 44 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7246 (tt0) REVERT: D 85 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7785 (mp10) REVERT: F 85 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7627 (mp10) REVERT: G 1 GLN cc_start: 0.6922 (pp30) cc_final: 0.6624 (pp30) REVERT: G 31 ASN cc_start: 0.7835 (OUTLIER) cc_final: 0.7467 (t0) REVERT: H 31 ASN cc_start: 0.7935 (OUTLIER) cc_final: 0.7578 (t0) REVERT: H 37 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.7061 (mm) REVERT: H 75 LYS cc_start: 0.8111 (mmtm) cc_final: 0.7707 (mtmt) REVERT: H 103 TYR cc_start: 0.5786 (OUTLIER) cc_final: 0.5215 (t80) REVERT: I 23 THR cc_start: 0.7293 (OUTLIER) cc_final: 0.6928 (p) REVERT: I 31 ASN cc_start: 0.7951 (OUTLIER) cc_final: 0.7393 (t0) outliers start: 137 outliers final: 99 residues processed: 300 average time/residue: 0.2349 time to fit residues: 109.2323 Evaluate side-chains 303 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 191 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 278 HIS Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 103 TYR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 118 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 146 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN ** I 6 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 = 0.4165 r_free = 0.4165 target = 0.147795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.120332 restraints weight = 27892.194| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.70 r_work: 0.3644 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16137 Z= 0.166 Angle : 0.599 11.722 21907 Z= 0.309 Chirality : 0.044 0.316 2553 Planarity : 0.004 0.040 2755 Dihedral : 5.424 54.150 2212 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 6.78 % Allowed : 23.74 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.19), residues: 2031 helix: 1.42 (0.25), residues: 453 sheet: -0.72 (0.20), residues: 657 loop : -0.71 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 56 HIS 0.004 0.001 HIS A 278 PHE 0.010 0.001 PHE D 77 TYR 0.019 0.002 TYR G 103 ARG 0.006 0.000 ARG A 468 Details of bonding type rmsd hydrogen bonds : bond 0.03291 ( 724) hydrogen bonds : angle 5.41692 ( 1917) SS BOND : bond 0.00356 ( 33) SS BOND : angle 1.09435 ( 66) covalent geometry : bond 0.00388 (16104) covalent geometry : angle 0.59696 (21841) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 200 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7351 (tt0) REVERT: A 250 MET cc_start: 0.8724 (tpt) cc_final: 0.8464 (tpt) REVERT: A 392 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8243 (mp) REVERT: A 438 PHE cc_start: 0.6170 (m-80) cc_final: 0.5934 (m-80) REVERT: B 250 MET cc_start: 0.8681 (tpt) cc_final: 0.7810 (tpt) REVERT: B 258 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7806 (tp) REVERT: B 380 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8227 (pttm) REVERT: C 177 ASN cc_start: 0.6237 (t0) cc_final: 0.5348 (t0) REVERT: C 179 GLU cc_start: 0.7476 (pt0) cc_final: 0.7088 (pm20) REVERT: C 278 HIS cc_start: 0.6855 (OUTLIER) cc_final: 0.6251 (m90) REVERT: C 409 ASP cc_start: 0.7252 (m-30) cc_final: 0.6319 (t0) REVERT: D 44 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7198 (tt0) REVERT: D 85 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7772 (mp10) REVERT: F 44 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7319 (tt0) REVERT: F 85 GLN cc_start: 0.7824 (mm-40) cc_final: 0.7611 (mp10) REVERT: G 1 GLN cc_start: 0.7037 (pp30) cc_final: 0.6774 (pp30) REVERT: G 31 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.7412 (t0) REVERT: H 31 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7697 (t0) REVERT: H 37 ILE cc_start: 0.7486 (OUTLIER) cc_final: 0.7007 (mm) REVERT: H 75 LYS cc_start: 0.8135 (mmtm) cc_final: 0.7743 (mtmt) REVERT: H 103 TYR cc_start: 0.5841 (OUTLIER) cc_final: 0.5080 (t80) REVERT: I 23 THR cc_start: 0.7276 (OUTLIER) cc_final: 0.6915 (p) REVERT: I 31 ASN cc_start: 0.7890 (OUTLIER) cc_final: 0.7422 (t0) outliers start: 124 outliers final: 96 residues processed: 292 average time/residue: 0.2476 time to fit residues: 112.3512 Evaluate side-chains 305 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 195 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 278 HIS Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 103 TYR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 118 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 151 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 193 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 0.0040 chunk 112 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 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 = 0.4191 r_free = 0.4191 target = 0.149855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.122627 restraints weight = 27650.740| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.71 r_work: 0.3677 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16137 Z= 0.123 Angle : 0.571 11.775 21907 Z= 0.293 Chirality : 0.044 0.490 2553 Planarity : 0.003 0.038 2755 Dihedral : 4.996 52.433 2209 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 6.40 % Allowed : 23.91 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.19), residues: 2031 helix: 1.55 (0.24), residues: 456 sheet: -0.69 (0.20), residues: 660 loop : -0.72 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 56 HIS 0.005 0.001 HIS A 278 PHE 0.011 0.001 PHE C 466 TYR 0.016 0.001 TYR G 103 ARG 0.009 0.000 ARG A 468 Details of bonding type rmsd hydrogen bonds : bond 0.02967 ( 724) hydrogen bonds : angle 5.26514 ( 1917) SS BOND : bond 0.00296 ( 33) SS BOND : angle 0.98773 ( 66) covalent geometry : bond 0.00281 (16104) covalent geometry : angle 0.56971 (21841) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 209 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7310 (tt0) REVERT: A 250 MET cc_start: 0.8661 (tpt) cc_final: 0.8387 (tpt) REVERT: A 392 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8219 (mp) REVERT: B 228 THR cc_start: 0.7631 (OUTLIER) cc_final: 0.7428 (p) REVERT: B 250 MET cc_start: 0.8696 (tpt) cc_final: 0.7824 (tpt) REVERT: B 380 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8130 (pttm) REVERT: B 382 LYS cc_start: 0.7400 (pptt) cc_final: 0.7016 (mmmt) REVERT: C 177 ASN cc_start: 0.6118 (t0) cc_final: 0.5407 (t0) REVERT: C 179 GLU cc_start: 0.7496 (pt0) cc_final: 0.7093 (pm20) REVERT: C 250 MET cc_start: 0.8654 (tpt) cc_final: 0.8333 (tpt) REVERT: C 278 HIS cc_start: 0.6813 (OUTLIER) cc_final: 0.6164 (m90) REVERT: C 409 ASP cc_start: 0.7234 (m-30) cc_final: 0.6345 (t0) REVERT: D 44 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.7088 (tt0) REVERT: D 85 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7644 (mp10) REVERT: F 44 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.7260 (tt0) REVERT: G 1 GLN cc_start: 0.7024 (pp30) cc_final: 0.6752 (pp30) REVERT: G 31 ASN cc_start: 0.7701 (OUTLIER) cc_final: 0.7389 (t0) REVERT: H 31 ASN cc_start: 0.7979 (OUTLIER) cc_final: 0.7646 (t0) REVERT: H 37 ILE cc_start: 0.7617 (OUTLIER) cc_final: 0.7132 (mm) REVERT: H 75 LYS cc_start: 0.8156 (mmtm) cc_final: 0.7781 (mtmt) REVERT: H 102 TYR cc_start: 0.6609 (OUTLIER) cc_final: 0.5817 (t80) REVERT: H 103 TYR cc_start: 0.5789 (OUTLIER) cc_final: 0.5244 (t80) REVERT: I 23 THR cc_start: 0.7249 (OUTLIER) cc_final: 0.6890 (p) REVERT: I 31 ASN cc_start: 0.7801 (OUTLIER) cc_final: 0.7355 (t0) outliers start: 117 outliers final: 89 residues processed: 292 average time/residue: 0.2496 time to fit residues: 112.7393 Evaluate side-chains 301 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 197 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 278 HIS Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 103 TYR Chi-restraints excluded: chain I residue 115 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 55 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 139 optimal weight: 9.9990 chunk 157 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 161 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.144013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.116834 restraints weight = 28161.809| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.68 r_work: 0.3570 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 16137 Z= 0.315 Angle : 0.733 10.320 21907 Z= 0.381 Chirality : 0.050 0.556 2553 Planarity : 0.004 0.047 2755 Dihedral : 5.674 52.303 2209 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 7.06 % Allowed : 23.47 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.18), residues: 2031 helix: 1.03 (0.24), residues: 456 sheet: -0.86 (0.21), residues: 627 loop : -0.92 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 56 HIS 0.008 0.002 HIS A 278 PHE 0.022 0.003 PHE A 313 TYR 0.034 0.003 TYR I 32 ARG 0.005 0.001 ARG G 38 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 724) hydrogen bonds : angle 5.71777 ( 1917) SS BOND : bond 0.00521 ( 33) SS BOND : angle 1.21432 ( 66) covalent geometry : bond 0.00741 (16104) covalent geometry : angle 0.73141 (21841) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 193 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7421 (tt0) REVERT: A 250 MET cc_start: 0.8782 (tpt) cc_final: 0.8418 (tpt) REVERT: A 331 MET cc_start: 0.7891 (ttp) cc_final: 0.7521 (tpp) REVERT: B 250 MET cc_start: 0.8734 (tpt) cc_final: 0.7858 (tpt) REVERT: B 258 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7821 (tp) REVERT: B 380 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8323 (pttm) REVERT: C 177 ASN cc_start: 0.6412 (t0) cc_final: 0.5713 (t0) REVERT: C 179 GLU cc_start: 0.7444 (pt0) cc_final: 0.7085 (pm20) REVERT: C 409 ASP cc_start: 0.7413 (m-30) cc_final: 0.6419 (t0) REVERT: D 44 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7322 (tt0) REVERT: F 44 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7493 (tt0) REVERT: G 1 GLN cc_start: 0.7246 (pp30) cc_final: 0.6958 (pp30) REVERT: G 31 ASN cc_start: 0.8028 (OUTLIER) cc_final: 0.7784 (t0) REVERT: H 31 ASN cc_start: 0.8183 (OUTLIER) cc_final: 0.7898 (t0) REVERT: H 37 ILE cc_start: 0.7618 (OUTLIER) cc_final: 0.7200 (mm) REVERT: H 75 LYS cc_start: 0.8222 (mmtm) cc_final: 0.7620 (mtmt) REVERT: H 102 TYR cc_start: 0.6756 (OUTLIER) cc_final: 0.6010 (t80) REVERT: H 103 TYR cc_start: 0.6162 (OUTLIER) cc_final: 0.5427 (t80) REVERT: I 23 THR cc_start: 0.7368 (OUTLIER) cc_final: 0.7009 (p) REVERT: I 31 ASN cc_start: 0.8232 (OUTLIER) cc_final: 0.7761 (t0) REVERT: I 47 TRP cc_start: 0.7817 (t60) cc_final: 0.7476 (t60) REVERT: I 48 LEU cc_start: 0.8363 (mp) cc_final: 0.8146 (mp) outliers start: 129 outliers final: 99 residues processed: 290 average time/residue: 0.2606 time to fit residues: 118.8948 Evaluate side-chains 299 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 188 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 278 HIS Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 103 TYR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 152 optimal weight: 0.0770 chunk 62 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 180 optimal weight: 0.0030 chunk 109 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 64 optimal weight: 0.0970 overall best weight: 0.3146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 GLN ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.150561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.123264 restraints weight = 28053.362| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.75 r_work: 0.3683 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16137 Z= 0.114 Angle : 0.595 12.467 21907 Z= 0.305 Chirality : 0.045 0.459 2553 Planarity : 0.003 0.037 2755 Dihedral : 5.161 53.638 2209 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.05 % Allowed : 26.26 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.19), residues: 2031 helix: 1.46 (0.24), residues: 450 sheet: -0.85 (0.20), residues: 675 loop : -0.73 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 56 HIS 0.003 0.001 HIS A 278 PHE 0.014 0.001 PHE C 466 TYR 0.022 0.001 TYR G 103 ARG 0.004 0.000 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.02937 ( 724) hydrogen bonds : angle 5.29946 ( 1917) SS BOND : bond 0.00286 ( 33) SS BOND : angle 1.01435 ( 66) covalent geometry : bond 0.00256 (16104) covalent geometry : angle 0.59317 (21841) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 204 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7235 (tt0) REVERT: A 250 MET cc_start: 0.8731 (tpt) cc_final: 0.8340 (tpt) REVERT: A 331 MET cc_start: 0.7664 (ttp) cc_final: 0.7262 (tpp) REVERT: B 250 MET cc_start: 0.8673 (tpt) cc_final: 0.7837 (tpt) REVERT: B 380 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8139 (pttm) REVERT: B 382 LYS cc_start: 0.7419 (pptt) cc_final: 0.7023 (mmmt) REVERT: C 177 ASN cc_start: 0.6216 (t0) cc_final: 0.5548 (t0) REVERT: C 179 GLU cc_start: 0.7449 (pt0) cc_final: 0.7052 (pm20) REVERT: C 278 HIS cc_start: 0.6653 (OUTLIER) cc_final: 0.6075 (m90) REVERT: C 409 ASP cc_start: 0.7275 (m-30) cc_final: 0.6316 (t0) REVERT: D 44 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7086 (tt0) REVERT: G 1 GLN cc_start: 0.7180 (pp30) cc_final: 0.6904 (pp30) REVERT: G 31 ASN cc_start: 0.7699 (OUTLIER) cc_final: 0.7362 (t0) REVERT: H 31 ASN cc_start: 0.8018 (OUTLIER) cc_final: 0.7694 (t0) REVERT: H 75 LYS cc_start: 0.8097 (mmtm) cc_final: 0.7756 (mtmt) REVERT: H 102 TYR cc_start: 0.6648 (OUTLIER) cc_final: 0.5971 (t80) REVERT: H 103 TYR cc_start: 0.5816 (OUTLIER) cc_final: 0.5403 (t80) REVERT: I 23 THR cc_start: 0.7262 (OUTLIER) cc_final: 0.6907 (p) REVERT: I 31 ASN cc_start: 0.7825 (OUTLIER) cc_final: 0.7420 (t0) outliers start: 74 outliers final: 60 residues processed: 256 average time/residue: 0.2607 time to fit residues: 102.2596 Evaluate side-chains 266 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 196 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 278 HIS Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 103 TYR Chi-restraints excluded: chain I residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 175 optimal weight: 0.9990 chunk 141 optimal weight: 0.0050 chunk 35 optimal weight: 8.9990 chunk 174 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.148530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.120908 restraints weight = 27910.249| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.72 r_work: 0.3650 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16137 Z= 0.157 Angle : 0.607 11.400 21907 Z= 0.312 Chirality : 0.045 0.469 2553 Planarity : 0.003 0.041 2755 Dihedral : 5.180 53.531 2208 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.21 % Allowed : 26.31 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.19), residues: 2031 helix: 1.44 (0.24), residues: 453 sheet: -0.77 (0.20), residues: 657 loop : -0.69 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 56 HIS 0.004 0.002 HIS A 278 PHE 0.010 0.001 PHE D 68 TYR 0.020 0.002 TYR G 103 ARG 0.004 0.000 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.03179 ( 724) hydrogen bonds : angle 5.30516 ( 1917) SS BOND : bond 0.00329 ( 33) SS BOND : angle 1.00287 ( 66) covalent geometry : bond 0.00367 (16104) covalent geometry : angle 0.60554 (21841) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7467.81 seconds wall clock time: 129 minutes 19.61 seconds (7759.61 seconds total)