Starting phenix.real_space_refine on Sat May 17 14:10:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zym_60572/05_2025/8zym_60572.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zym_60572/05_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_60572/05_2025/8zym_60572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zym_60572/05_2025/8zym_60572.map" model { file = "/net/cci-nas-00/data/ceres_data/8zym_60572/05_2025/8zym_60572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zym_60572/05_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 8.91, per 1000 atoms: 0.56 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: 3.60 Conformation dependent library (CDL) restraints added in 1.9 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: 2.32 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: 5.73 Time building geometry restraints manager: 4.23 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: 1.470 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: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 35.780 Find NCS groups from input model: 0.500 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: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.740 ------------------------------------------------------------------------------- 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 : 1.801 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: 0.2486 time to fit residues: 98.4536 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 : 1.738 ------------------------------------------------------------------------------- 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 = 28075.504| |-----------------------------------------------------------------------------| 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 : 1.918 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: 0.8376 (tpt) REVERT: A 278 HIS cc_start: 0.6825 (OUTLIER) cc_final: 0.6616 (m90) REVERT: A 331 MET cc_start: 0.7764 (ttm) cc_final: 0.7517 (ttp) REVERT: A 464 LEU cc_start: 0.9637 (mm) cc_final: 0.9437 (mp) REVERT: B 250 MET cc_start: 0.8681 (tpt) cc_final: 0.7837 (tpt) REVERT: B 258 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7666 (tp) REVERT: C 278 HIS cc_start: 0.6867 (OUTLIER) cc_final: 0.6288 (m90) REVERT: D 85 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7797 (mp10) REVERT: F 85 GLN cc_start: 0.7871 (mm-40) cc_final: 0.7565 (mp10) REVERT: F 109 LEU cc_start: 0.1231 (OUTLIER) cc_final: 0.0971 (mp) REVERT: G 31 ASN cc_start: 0.7735 (OUTLIER) cc_final: 0.7350 (t0) REVERT: H 31 ASN cc_start: 0.7981 (OUTLIER) cc_final: 0.7572 (t0) REVERT: H 37 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7367 (mm) REVERT: H 75 LYS cc_start: 0.8169 (mmtm) cc_final: 0.7600 (mtmt) REVERT: I 23 THR cc_start: 0.7272 (OUTLIER) cc_final: 0.6966 (p) REVERT: I 31 ASN cc_start: 0.7859 (OUTLIER) cc_final: 0.7312 (t0) outliers start: 107 outliers final: 64 residues processed: 288 average time/residue: 0.2507 time to fit residues: 111.3985 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 : 1.759 ------------------------------------------------------------------------------- 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: 5.9990 chunk 74 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 203 optimal weight: 0.7980 chunk 192 optimal weight: 0.0270 chunk 161 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 155 optimal weight: 0.5980 chunk 172 optimal weight: 0.0870 overall best weight: 0.4816 ------------------------------------------------------------------------------- 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 H 6 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.151373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.124276 restraints weight = 27617.025| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.70 r_work: 0.3704 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 16137 Z= 0.109 Angle : 0.536 11.875 21907 Z= 0.279 Chirality : 0.043 0.343 2553 Planarity : 0.003 0.046 2755 Dihedral : 5.999 87.012 2236 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.69 % Allowed : 24.12 % 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: -0.24 (0.19), residues: 2031 helix: 1.58 (0.25), residues: 453 sheet: -0.60 (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 0.021 0.001 TYR H 103 ARG 0.007 0.000 ARG A 468 Details of bonding type rmsd hydrogen bonds : bond 0.03095 ( 724) hydrogen bonds : angle 5.49476 ( 1917) SS BOND : bond 0.00265 ( 33) SS BOND : angle 0.95328 ( 66) covalent geometry : bond 0.00242 (16104) covalent geometry : angle 0.53437 (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 317 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 213 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7415 (tt0) REVERT: A 250 MET cc_start: 0.8718 (tpt) cc_final: 0.8319 (tpt) REVERT: A 278 HIS cc_start: 0.6826 (OUTLIER) cc_final: 0.6595 (m90) REVERT: B 250 MET cc_start: 0.8635 (tpt) cc_final: 0.7837 (tpt) REVERT: B 380 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8192 (pttm) REVERT: B 409 ASP cc_start: 0.6957 (m-30) cc_final: 0.6232 (t0) REVERT: C 177 ASN cc_start: 0.6221 (t0) cc_final: 0.5645 (t0) REVERT: D 4 MET cc_start: 0.6000 (mmp) cc_final: 0.5412 (mmp) REVERT: D 85 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7702 (mp10) REVERT: E 29 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.8170 (t) REVERT: F 85 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7565 (mp10) REVERT: G 31 ASN cc_start: 0.7679 (OUTLIER) cc_final: 0.7363 (t0) REVERT: H 31 ASN cc_start: 0.8015 (OUTLIER) cc_final: 0.7675 (t0) REVERT: H 37 ILE cc_start: 0.7804 (OUTLIER) cc_final: 0.7312 (mm) REVERT: H 75 LYS cc_start: 0.8122 (mmtm) cc_final: 0.7811 (mtmt) REVERT: H 103 TYR cc_start: 0.5835 (t80) cc_final: 0.5416 (t80) REVERT: I 23 THR cc_start: 0.7235 (OUTLIER) cc_final: 0.6909 (p) REVERT: I 31 ASN cc_start: 0.7795 (OUTLIER) cc_final: 0.7297 (t0) outliers start: 104 outliers final: 57 residues processed: 294 average time/residue: 0.2372 time to fit residues: 107.4536 Evaluate side-chains 255 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 188 time to evaluate : 1.785 ------------------------------------------------------------------------------- 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 269 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 278 HIS 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 367 VAL Chi-restraints excluded: chain B residue 380 LYS 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: 1.9990 chunk 6 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 198 optimal weight: 0.5980 chunk 82 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 263 GLN ** C 324 ASN ** 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 = 0.4188 r_free = 0.4188 target = 0.149511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.122133 restraints weight = 27638.795| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.70 r_work: 0.3672 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16137 Z= 0.141 Angle : 0.565 11.952 21907 Z= 0.292 Chirality : 0.044 0.347 2553 Planarity : 0.003 0.042 2755 Dihedral : 5.699 86.198 2220 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 6.51 % Allowed : 23.41 % Favored : 70.08 % 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: -0.25 (0.19), residues: 2031 helix: 1.58 (0.25), residues: 453 sheet: -0.64 (0.20), residues: 678 loop : -0.59 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 56 HIS 0.005 0.001 HIS A 278 PHE 0.009 0.001 PHE E 77 TYR 0.018 0.002 TYR H 94 ARG 0.003 0.000 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.03200 ( 724) hydrogen bonds : angle 5.43023 ( 1917) SS BOND : bond 0.00293 ( 33) SS BOND : angle 0.98147 ( 66) covalent geometry : bond 0.00327 (16104) covalent geometry : angle 0.56347 (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 321 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 202 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7370 (tt0) REVERT: A 250 MET cc_start: 0.8779 (tpt) cc_final: 0.8519 (tpt) REVERT: B 250 MET cc_start: 0.8658 (tpt) cc_final: 0.7779 (tpt) REVERT: B 258 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7641 (tp) REVERT: B 380 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8202 (pttm) REVERT: B 409 ASP cc_start: 0.6949 (m-30) cc_final: 0.6262 (t0) REVERT: C 177 ASN cc_start: 0.6364 (t0) cc_final: 0.6150 (t0) REVERT: C 179 GLU cc_start: 0.7492 (pt0) cc_final: 0.7121 (pm20) REVERT: E 29 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8238 (t) REVERT: F 85 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7572 (mp10) REVERT: G 31 ASN cc_start: 0.7727 (OUTLIER) cc_final: 0.7438 (t0) REVERT: G 72 ASP cc_start: 0.6584 (t0) cc_final: 0.6375 (t0) REVERT: H 31 ASN cc_start: 0.8060 (OUTLIER) cc_final: 0.7681 (t0) REVERT: H 37 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7401 (mm) REVERT: H 75 LYS cc_start: 0.8117 (mmtm) cc_final: 0.7776 (mtmt) REVERT: H 103 TYR cc_start: 0.5929 (OUTLIER) cc_final: 0.5419 (t80) REVERT: I 23 THR cc_start: 0.7269 (OUTLIER) cc_final: 0.6919 (p) REVERT: I 31 ASN cc_start: 0.7810 (OUTLIER) cc_final: 0.7316 (t0) outliers start: 119 outliers final: 84 residues processed: 290 average time/residue: 0.2421 time to fit residues: 108.1966 Evaluate side-chains 288 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 194 time to evaluate : 1.718 ------------------------------------------------------------------------------- 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 205 THR Chi-restraints excluded: chain A residue 225 MET 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 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 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 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 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 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 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 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 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 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 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 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: 0.6980 chunk 163 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 197 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 37 optimal weight: 0.0370 chunk 148 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.7464 ------------------------------------------------------------------------------- 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 324 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 = 0.4203 r_free = 0.4203 target = 0.150632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.123245 restraints weight = 28087.487| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.75 r_work: 0.3685 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16137 Z= 0.121 Angle : 0.549 10.928 21907 Z= 0.283 Chirality : 0.043 0.307 2553 Planarity : 0.003 0.039 2755 Dihedral : 5.251 57.193 2216 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 6.51 % Allowed : 23.47 % Favored : 70.02 % 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: -0.24 (0.19), residues: 2031 helix: 1.61 (0.25), residues: 453 sheet: -0.63 (0.20), residues: 678 loop : -0.59 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 56 HIS 0.004 0.001 HIS A 278 PHE 0.010 0.001 PHE A 466 TYR 0.015 0.001 TYR C 260 ARG 0.008 0.000 ARG A 468 Details of bonding type rmsd hydrogen bonds : bond 0.02962 ( 724) hydrogen bonds : angle 5.30276 ( 1917) SS BOND : bond 0.00286 ( 33) SS BOND : angle 0.97809 ( 66) covalent geometry : bond 0.00277 (16104) covalent geometry : angle 0.54758 (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: 119 poor density : 204 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7354 (tt0) REVERT: A 250 MET cc_start: 0.8764 (tpt) cc_final: 0.8555 (tpt) REVERT: A 392 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8252 (mp) REVERT: A 424 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6983 (pm20) REVERT: B 250 MET cc_start: 0.8667 (tpt) cc_final: 0.7839 (tpt) REVERT: B 380 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8191 (pttm) REVERT: C 179 GLU cc_start: 0.7511 (pt0) cc_final: 0.7085 (pm20) REVERT: D 44 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7221 (tt0) REVERT: D 85 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7676 (mp10) REVERT: E 29 VAL cc_start: 0.8481 (OUTLIER) cc_final: 0.8226 (t) REVERT: F 85 GLN cc_start: 0.7844 (mm-40) cc_final: 0.7557 (mp10) REVERT: G 16 GLN cc_start: 0.6729 (OUTLIER) cc_final: 0.6459 (mp10) REVERT: G 31 ASN cc_start: 0.7704 (OUTLIER) cc_final: 0.7403 (t0) REVERT: H 31 ASN cc_start: 0.8020 (OUTLIER) cc_final: 0.7658 (t0) REVERT: H 37 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7296 (mm) REVERT: H 75 LYS cc_start: 0.8082 (mmtm) cc_final: 0.7766 (mtmt) REVERT: H 103 TYR cc_start: 0.5739 (OUTLIER) cc_final: 0.5156 (t80) REVERT: I 23 THR cc_start: 0.7264 (OUTLIER) cc_final: 0.6905 (p) REVERT: I 31 ASN cc_start: 0.7731 (OUTLIER) cc_final: 0.7251 (t0) outliers start: 119 outliers final: 83 residues processed: 292 average time/residue: 0.2520 time to fit residues: 113.1494 Evaluate side-chains 287 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 190 time to evaluate : 1.709 ------------------------------------------------------------------------------- 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 225 MET Chi-restraints excluded: chain A residue 242 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 410 THR Chi-restraints excluded: chain A residue 424 GLU 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 272 THR Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 298 THR 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 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 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 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 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 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 16 GLN 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 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 75 LYS Chi-restraints excluded: chain I residue 103 TYR Chi-restraints excluded: chain I residue 115 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: 2.9990 chunk 156 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 190 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 174 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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** ** 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 = 0.4146 r_free = 0.4146 target = 0.146344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.118411 restraints weight = 28174.283| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.74 r_work: 0.3610 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16137 Z= 0.225 Angle : 0.646 8.611 21907 Z= 0.336 Chirality : 0.046 0.367 2553 Planarity : 0.004 0.044 2755 Dihedral : 5.719 58.120 2216 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 7.71 % Allowed : 22.43 % Favored : 69.86 % 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: -0.49 (0.19), residues: 2031 helix: 1.33 (0.25), residues: 453 sheet: -0.75 (0.20), residues: 657 loop : -0.74 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 56 HIS 0.006 0.002 HIS A 278 PHE 0.016 0.002 PHE D 68 TYR 0.021 0.002 TYR E 101 ARG 0.006 0.001 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.03707 ( 724) hydrogen bonds : angle 5.56703 ( 1917) SS BOND : bond 0.00431 ( 33) SS BOND : angle 1.10491 ( 66) covalent geometry : bond 0.00527 (16104) covalent geometry : angle 0.64380 (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 339 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 198 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7448 (tt0) REVERT: B 250 MET cc_start: 0.8714 (tpt) cc_final: 0.7794 (tpt) REVERT: B 258 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7897 (tp) REVERT: B 380 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8247 (pttm) REVERT: C 177 ASN cc_start: 0.6229 (t0) cc_final: 0.5378 (t0) REVERT: C 179 GLU cc_start: 0.7560 (pt0) cc_final: 0.7237 (pm20) REVERT: C 409 ASP cc_start: 0.7263 (m-30) cc_final: 0.6275 (t0) REVERT: D 44 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7297 (tt0) REVERT: F 44 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7416 (tt0) REVERT: G 1 GLN cc_start: 0.7038 (pp30) cc_final: 0.6774 (pp30) REVERT: G 31 ASN cc_start: 0.7858 (OUTLIER) cc_final: 0.7484 (t0) REVERT: H 31 ASN cc_start: 0.7990 (OUTLIER) cc_final: 0.7659 (t0) REVERT: H 37 ILE cc_start: 0.7617 (OUTLIER) cc_final: 0.7236 (mm) REVERT: H 75 LYS cc_start: 0.8144 (mmtm) cc_final: 0.7718 (mtmt) REVERT: H 103 TYR cc_start: 0.5840 (OUTLIER) cc_final: 0.5353 (t80) REVERT: I 23 THR cc_start: 0.7321 (OUTLIER) cc_final: 0.6957 (p) REVERT: I 31 ASN cc_start: 0.7973 (OUTLIER) cc_final: 0.7415 (t0) outliers start: 141 outliers final: 106 residues processed: 307 average time/residue: 0.2555 time to fit residues: 122.5728 Evaluate side-chains 308 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 191 time to evaluate : 1.696 ------------------------------------------------------------------------------- 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 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 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 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 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 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 378 TYR Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 405 ASN 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 20 THR 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 16 GLN 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 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 53 THR 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 115 THR 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 146 optimal weight: 8.9990 chunk 149 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 169 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.4162 r_free = 0.4162 target = 0.147664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.120548 restraints weight = 28241.553| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.57 r_work: 0.3648 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1427 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= 0.177 Angle : 0.614 11.766 21907 Z= 0.317 Chirality : 0.045 0.326 2553 Planarity : 0.004 0.041 2755 Dihedral : 5.568 51.467 2216 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 7.44 % Allowed : 23.19 % Favored : 69.37 % 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: -0.51 (0.19), residues: 2031 helix: 1.35 (0.25), residues: 453 sheet: -0.80 (0.20), residues: 657 loop : -0.74 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 56 HIS 0.005 0.001 HIS B 278 PHE 0.010 0.001 PHE D 68 TYR 0.021 0.002 TYR G 103 ARG 0.008 0.000 ARG A 468 Details of bonding type rmsd hydrogen bonds : bond 0.03399 ( 724) hydrogen bonds : angle 5.46762 ( 1917) SS BOND : bond 0.00387 ( 33) SS BOND : angle 1.12670 ( 66) covalent geometry : bond 0.00416 (16104) covalent geometry : angle 0.61137 (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 334 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 198 time to evaluate : 1.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7493 (tt0) REVERT: A 250 MET cc_start: 0.8804 (tpt) cc_final: 0.8444 (tpt) REVERT: A 392 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8246 (mp) REVERT: A 438 PHE cc_start: 0.6063 (m-80) cc_final: 0.5818 (m-80) REVERT: B 250 MET cc_start: 0.8723 (tpt) cc_final: 0.7866 (tpt) REVERT: B 258 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7861 (tp) REVERT: B 380 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8248 (pttm) REVERT: C 177 ASN cc_start: 0.6365 (t0) cc_final: 0.5651 (t0) REVERT: C 179 GLU cc_start: 0.7614 (pt0) cc_final: 0.7263 (pm20) REVERT: C 278 HIS cc_start: 0.7003 (OUTLIER) cc_final: 0.6416 (m90) REVERT: C 409 ASP cc_start: 0.7384 (m-30) cc_final: 0.6389 (t0) REVERT: D 44 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7307 (tt0) REVERT: F 85 GLN cc_start: 0.7906 (mm-40) cc_final: 0.7669 (mp10) REVERT: G 1 GLN cc_start: 0.6908 (pp30) cc_final: 0.6649 (pp30) REVERT: G 31 ASN cc_start: 0.7914 (OUTLIER) cc_final: 0.7565 (t0) REVERT: H 31 ASN cc_start: 0.8120 (OUTLIER) cc_final: 0.7794 (t0) REVERT: H 37 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7291 (mm) REVERT: H 75 LYS cc_start: 0.8145 (mmtm) cc_final: 0.7695 (mtmt) REVERT: H 102 TYR cc_start: 0.6791 (OUTLIER) cc_final: 0.5981 (t80) REVERT: H 103 TYR cc_start: 0.5872 (OUTLIER) cc_final: 0.5221 (t80) REVERT: I 23 THR cc_start: 0.7417 (OUTLIER) cc_final: 0.7023 (p) REVERT: I 31 ASN cc_start: 0.8105 (OUTLIER) cc_final: 0.7581 (t0) outliers start: 136 outliers final: 106 residues processed: 300 average time/residue: 0.2374 time to fit residues: 110.5874 Evaluate side-chains 314 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 195 time to evaluate : 2.001 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 112 LYS Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 16 GLN 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 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 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 53 THR 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 115 THR 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 33 ASP 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 151 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 184 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 0.3980 chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** ** 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 = 0.4182 r_free = 0.4182 target = 0.149194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.121587 restraints weight = 27957.421| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.73 r_work: 0.3658 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16137 Z= 0.137 Angle : 0.587 11.657 21907 Z= 0.301 Chirality : 0.045 0.510 2553 Planarity : 0.003 0.039 2755 Dihedral : 5.187 52.229 2213 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 6.51 % Allowed : 23.69 % Favored : 69.80 % 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: -0.41 (0.19), residues: 2031 helix: 1.46 (0.25), residues: 453 sheet: -0.77 (0.20), residues: 660 loop : -0.67 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 56 HIS 0.005 0.001 HIS A 278 PHE 0.011 0.001 PHE C 466 TYR 0.018 0.001 TYR G 103 ARG 0.010 0.000 ARG A 468 Details of bonding type rmsd hydrogen bonds : bond 0.03083 ( 724) hydrogen bonds : angle 5.30893 ( 1917) SS BOND : bond 0.00332 ( 33) SS BOND : angle 1.04119 ( 66) covalent geometry : bond 0.00318 (16104) covalent geometry : angle 0.58493 (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 324 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 205 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7304 (tt0) REVERT: A 250 MET cc_start: 0.8711 (tpt) cc_final: 0.8362 (tpt) REVERT: A 392 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8258 (mp) REVERT: B 250 MET cc_start: 0.8668 (tpt) cc_final: 0.7811 (tpt) REVERT: B 258 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7631 (tp) REVERT: B 380 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8197 (pttm) REVERT: B 382 LYS cc_start: 0.7408 (pptt) cc_final: 0.7020 (mmmt) REVERT: C 177 ASN cc_start: 0.6127 (t0) cc_final: 0.5430 (t0) REVERT: C 179 GLU cc_start: 0.7454 (pt0) cc_final: 0.7061 (pm20) REVERT: C 250 MET cc_start: 0.8676 (tpt) cc_final: 0.8348 (tpt) REVERT: C 278 HIS cc_start: 0.6843 (OUTLIER) cc_final: 0.6205 (m90) REVERT: C 409 ASP cc_start: 0.7244 (m-30) cc_final: 0.6350 (t0) REVERT: D 44 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7138 (tt0) REVERT: F 44 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7281 (tt0) REVERT: F 85 GLN cc_start: 0.7851 (mm-40) cc_final: 0.7625 (mp10) REVERT: G 1 GLN cc_start: 0.7143 (pp30) cc_final: 0.6864 (pp30) REVERT: G 31 ASN cc_start: 0.7772 (OUTLIER) cc_final: 0.7428 (t0) REVERT: H 31 ASN cc_start: 0.8071 (OUTLIER) cc_final: 0.7728 (t0) REVERT: H 37 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7117 (mm) REVERT: H 75 LYS cc_start: 0.8132 (mmtm) cc_final: 0.7756 (mtmt) REVERT: H 103 TYR cc_start: 0.5797 (OUTLIER) cc_final: 0.5262 (t80) REVERT: I 23 THR cc_start: 0.7325 (OUTLIER) cc_final: 0.6954 (p) REVERT: I 31 ASN cc_start: 0.7869 (OUTLIER) cc_final: 0.7406 (t0) outliers start: 119 outliers final: 100 residues processed: 292 average time/residue: 0.2446 time to fit residues: 109.7190 Evaluate side-chains 308 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 195 time to evaluate : 1.870 ------------------------------------------------------------------------------- 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 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 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 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 258 LEU 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 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 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 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 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 20 ILE Chi-restraints excluded: chain G residue 29 LEU 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 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 53 THR 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 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: 0.7980 chunk 1 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 139 optimal weight: 9.9990 chunk 157 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 176 optimal weight: 0.3980 overall best weight: 2.0384 ------------------------------------------------------------------------------- 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** ** 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 = 0.4143 r_free = 0.4143 target = 0.146106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.118294 restraints weight = 27995.338| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.70 r_work: 0.3610 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16137 Z= 0.231 Angle : 0.659 11.032 21907 Z= 0.340 Chirality : 0.047 0.514 2553 Planarity : 0.004 0.045 2755 Dihedral : 5.513 52.479 2213 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 6.84 % Allowed : 23.36 % Favored : 69.80 % 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: -0.60 (0.19), residues: 2031 helix: 1.30 (0.25), residues: 453 sheet: -0.77 (0.21), residues: 627 loop : -0.90 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 56 HIS 0.006 0.002 HIS A 278 PHE 0.015 0.002 PHE D 68 TYR 0.024 0.002 TYR I 32 ARG 0.005 0.000 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.03637 ( 724) hydrogen bonds : angle 5.51304 ( 1917) SS BOND : bond 0.00433 ( 33) SS BOND : angle 1.11480 ( 66) covalent geometry : bond 0.00543 (16104) covalent geometry : angle 0.65703 (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 316 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 191 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7369 (tt0) REVERT: A 250 MET cc_start: 0.8692 (tpt) cc_final: 0.8392 (tpt) REVERT: A 392 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8284 (mp) REVERT: B 250 MET cc_start: 0.8727 (tpt) cc_final: 0.7828 (tpt) REVERT: B 258 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7888 (tp) REVERT: B 380 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8297 (pttm) REVERT: C 177 ASN cc_start: 0.6285 (t0) cc_final: 0.5576 (t0) REVERT: C 179 GLU cc_start: 0.7487 (pt0) cc_final: 0.7124 (pm20) REVERT: C 278 HIS cc_start: 0.6910 (OUTLIER) cc_final: 0.6331 (m90) REVERT: C 409 ASP cc_start: 0.7329 (m-30) cc_final: 0.6398 (t0) REVERT: D 44 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7227 (tt0) REVERT: F 44 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7397 (tt0) REVERT: F 85 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7700 (mp10) REVERT: G 1 GLN cc_start: 0.7202 (pp30) cc_final: 0.6915 (pp30) REVERT: G 31 ASN cc_start: 0.7822 (OUTLIER) cc_final: 0.7595 (t0) REVERT: H 31 ASN cc_start: 0.8051 (OUTLIER) cc_final: 0.7713 (t0) REVERT: H 37 ILE cc_start: 0.7548 (OUTLIER) cc_final: 0.7122 (mm) REVERT: H 75 LYS cc_start: 0.8168 (mmtm) cc_final: 0.7705 (mtmt) REVERT: H 102 TYR cc_start: 0.6681 (OUTLIER) cc_final: 0.5974 (t80) REVERT: H 103 TYR cc_start: 0.6058 (OUTLIER) cc_final: 0.5408 (t80) REVERT: I 23 THR cc_start: 0.7387 (OUTLIER) cc_final: 0.7008 (p) REVERT: I 31 ASN cc_start: 0.7987 (OUTLIER) cc_final: 0.7568 (t0) outliers start: 125 outliers final: 101 residues processed: 288 average time/residue: 0.2357 time to fit residues: 105.6806 Evaluate side-chains 301 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 186 time to evaluate : 1.725 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 53 THR 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 115 THR 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 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 152 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 180 optimal weight: 0.0170 chunk 109 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 61 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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** D 43 GLN ** 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 = 0.4189 r_free = 0.4189 target = 0.149676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.122563 restraints weight = 27776.126| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.70 r_work: 0.3678 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16137 Z= 0.121 Angle : 0.581 12.023 21907 Z= 0.297 Chirality : 0.045 0.451 2553 Planarity : 0.003 0.038 2755 Dihedral : 5.156 53.610 2213 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 5.14 % Allowed : 25.11 % 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: -0.44 (0.19), residues: 2031 helix: 1.51 (0.25), residues: 450 sheet: -0.72 (0.20), residues: 654 loop : -0.78 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 56 HIS 0.003 0.001 HIS A 278 PHE 0.013 0.001 PHE C 466 TYR 0.017 0.001 TYR G 103 ARG 0.004 0.000 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.02962 ( 724) hydrogen bonds : angle 5.27734 ( 1917) SS BOND : bond 0.00302 ( 33) SS BOND : angle 0.96681 ( 66) covalent geometry : bond 0.00278 (16104) covalent geometry : angle 0.57908 (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 293 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 199 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7275 (tt0) REVERT: A 250 MET cc_start: 0.8682 (tpt) cc_final: 0.8356 (tpt) REVERT: A 392 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8201 (mp) REVERT: B 250 MET cc_start: 0.8700 (tpt) cc_final: 0.7847 (tpt) REVERT: B 380 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8146 (pttm) REVERT: B 382 LYS cc_start: 0.7414 (pptt) cc_final: 0.7022 (mmmt) REVERT: C 177 ASN cc_start: 0.6075 (t0) cc_final: 0.5406 (t0) REVERT: C 179 GLU cc_start: 0.7479 (pt0) cc_final: 0.7084 (pm20) REVERT: C 278 HIS cc_start: 0.6660 (OUTLIER) cc_final: 0.6095 (m90) REVERT: C 409 ASP cc_start: 0.7281 (m-30) cc_final: 0.6326 (t0) REVERT: D 44 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7107 (tt0) REVERT: F 85 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7517 (mp10) REVERT: G 31 ASN cc_start: 0.7708 (OUTLIER) cc_final: 0.7378 (t0) REVERT: H 31 ASN cc_start: 0.8041 (OUTLIER) cc_final: 0.7683 (t0) REVERT: H 37 ILE cc_start: 0.7606 (OUTLIER) cc_final: 0.7100 (mm) REVERT: H 75 LYS cc_start: 0.8137 (mmtm) cc_final: 0.7752 (mtmt) REVERT: H 102 TYR cc_start: 0.6683 (OUTLIER) cc_final: 0.6007 (t80) REVERT: H 103 TYR cc_start: 0.5780 (OUTLIER) cc_final: 0.5480 (t80) REVERT: I 23 THR cc_start: 0.7304 (OUTLIER) cc_final: 0.6940 (p) REVERT: I 31 ASN cc_start: 0.7819 (OUTLIER) cc_final: 0.7377 (t0) outliers start: 94 outliers final: 76 residues processed: 268 average time/residue: 0.2476 time to fit residues: 102.4067 Evaluate side-chains 280 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 192 time to evaluate : 1.914 ------------------------------------------------------------------------------- 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 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 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 227 ILE Chi-restraints excluded: chain B residue 239 VAL 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 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 227 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 257 VAL 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 470 SER 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 102 THR Chi-restraints excluded: chain E residue 3 VAL 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 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 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 20 ILE 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 70 SER Chi-restraints excluded: chain I residue 75 LYS 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: 3.9990 chunk 141 optimal weight: 0.0570 chunk 35 optimal weight: 0.7980 chunk 174 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 195 optimal weight: 0.5980 chunk 194 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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** ** 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 = 0.4195 r_free = 0.4195 target = 0.150103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.122923 restraints weight = 27517.740| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.67 r_work: 0.3683 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16137 Z= 0.121 Angle : 0.577 11.655 21907 Z= 0.295 Chirality : 0.044 0.443 2553 Planarity : 0.003 0.036 2755 Dihedral : 5.042 53.336 2212 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 5.03 % Allowed : 25.05 % Favored : 69.91 % 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: -0.41 (0.19), residues: 2031 helix: 1.54 (0.24), residues: 456 sheet: -0.65 (0.20), residues: 651 loop : -0.82 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 56 HIS 0.004 0.001 HIS A 278 PHE 0.016 0.001 PHE A 466 TYR 0.017 0.002 TYR D 38 ARG 0.004 0.000 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.02893 ( 724) hydrogen bonds : angle 5.17902 ( 1917) SS BOND : bond 0.00296 ( 33) SS BOND : angle 0.92480 ( 66) covalent geometry : bond 0.00279 (16104) covalent geometry : angle 0.57554 (21841) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6970.82 seconds wall clock time: 122 minutes 18.88 seconds (7338.88 seconds total)