Starting phenix.real_space_refine on Thu Sep 18 09:38:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zym_60572/09_2025/8zym_60572.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zym_60572/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zym_60572/09_2025/8zym_60572.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zym_60572/09_2025/8zym_60572.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zym_60572/09_2025/8zym_60572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zym_60572/09_2025/8zym_60572.map" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.86, per 1000 atoms: 0.24 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: 1.33 Conformation dependent library (CDL) restraints added in 640.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.67 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: 2.85 Time building geometry restraints manager: 1.73 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: 2.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.400 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.840 ------------------------------------------------------------------------------- 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 : 12.98 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG D 67 TYR 0.052 0.001 TYR G 94 PHE 0.014 0.001 PHE A 466 TRP 0.024 0.001 TRP E 56 HIS 0.003 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00255 (16104) covalent geometry : angle 0.56009 (21841) SS BOND : bond 0.00258 ( 33) SS BOND : angle 0.85864 ( 66) hydrogen bonds : bond 0.15652 ( 724) hydrogen bonds : angle 7.19242 ( 1917) *********************** 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 : 0.659 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: 0.1098 time to fit residues: 43.6550 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 : 0.633 ------------------------------------------------------------------------------- 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 98 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 GLN F 85 GLN G 6 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.145709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.117676 restraints weight = 28308.253| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.69 r_work: 0.3599 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 16137 Z= 0.249 Angle : 0.659 10.091 21907 Z= 0.348 Chirality : 0.047 0.454 2553 Planarity : 0.004 0.042 2755 Dihedral : 7.564 85.034 2300 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 7.88 % Allowed : 22.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.19), residues: 2031 helix: 1.25 (0.25), residues: 453 sheet: -0.72 (0.21), residues: 636 loop : -0.84 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 97 TYR 0.023 0.003 TYR I 32 PHE 0.015 0.002 PHE D 68 TRP 0.020 0.002 TRP E 56 HIS 0.006 0.002 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00581 (16104) covalent geometry : angle 0.65711 (21841) SS BOND : bond 0.00433 ( 33) SS BOND : angle 1.03475 ( 66) hydrogen bonds : bond 0.04498 ( 724) hydrogen bonds : angle 6.02434 ( 1917) *********************** 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 350 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 206 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: A 278 HIS cc_start: 0.6800 (OUTLIER) cc_final: 0.6573 (m90) REVERT: A 331 MET cc_start: 0.7787 (ttm) cc_final: 0.7532 (ttp) REVERT: A 464 LEU cc_start: 0.9635 (mm) cc_final: 0.9428 (mp) REVERT: B 250 MET cc_start: 0.8717 (tpt) cc_final: 0.7848 (tpt) REVERT: B 258 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7920 (tp) REVERT: B 380 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8222 (pttm) REVERT: B 409 ASP cc_start: 0.6947 (m-30) cc_final: 0.6193 (t0) REVERT: C 278 HIS cc_start: 0.6882 (OUTLIER) cc_final: 0.6373 (m90) REVERT: C 409 ASP cc_start: 0.7181 (m-30) cc_final: 0.6205 (t0) REVERT: D 44 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7280 (tt0) REVERT: D 85 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7727 (mp10) REVERT: F 44 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7446 (tt0) REVERT: F 85 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7559 (mp10) REVERT: F 109 LEU cc_start: 0.1241 (OUTLIER) cc_final: 0.0973 (mp) REVERT: G 31 ASN cc_start: 0.7892 (OUTLIER) cc_final: 0.7530 (t0) REVERT: H 31 ASN cc_start: 0.8090 (OUTLIER) cc_final: 0.7694 (t0) REVERT: H 37 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7335 (mm) REVERT: H 75 LYS cc_start: 0.8235 (mmtm) cc_final: 0.7531 (mtpt) REVERT: H 103 TYR cc_start: 0.6129 (OUTLIER) cc_final: 0.5867 (t80) REVERT: I 23 THR cc_start: 0.7336 (OUTLIER) cc_final: 0.7019 (p) REVERT: I 31 ASN cc_start: 0.7975 (OUTLIER) cc_final: 0.7456 (t0) outliers start: 144 outliers final: 92 residues processed: 321 average time/residue: 0.1064 time to fit residues: 53.4117 Evaluate side-chains 298 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 191 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 178 ILE 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 83 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 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 339 GLU 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 278 HIS Chi-restraints excluded: chain C residue 298 THR 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 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 20 THR 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 85 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 20 THR 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 20 THR Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain G residue 37 ILE 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 29 LEU Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 43 LYS 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 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 53 THR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 103 TYR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 118 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 118 optimal weight: 0.3980 chunk 83 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 199 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 120 optimal weight: 0.3980 chunk 74 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 147 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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** B 263 GLN B 415 ASN C 415 ASN ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.149316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.122258 restraints weight = 28395.112| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.60 r_work: 0.3671 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.1005 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= 0.130 Angle : 0.574 11.690 21907 Z= 0.298 Chirality : 0.044 0.338 2553 Planarity : 0.003 0.045 2755 Dihedral : 6.586 86.582 2247 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 6.35 % Allowed : 23.96 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.19), residues: 2031 helix: 1.41 (0.25), residues: 453 sheet: -0.82 (0.20), residues: 678 loop : -0.67 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 38 TYR 0.022 0.002 TYR G 103 PHE 0.013 0.001 PHE F 77 TRP 0.021 0.002 TRP E 56 HIS 0.006 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00297 (16104) covalent geometry : angle 0.57217 (21841) SS BOND : bond 0.00291 ( 33) SS BOND : angle 1.04483 ( 66) hydrogen bonds : bond 0.03456 ( 724) hydrogen bonds : angle 5.66050 ( 1917) *********************** 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 326 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 210 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7396 (tt0) REVERT: A 278 HIS cc_start: 0.6767 (OUTLIER) cc_final: 0.6551 (m90) REVERT: A 331 MET cc_start: 0.7763 (ttm) cc_final: 0.7558 (ttp) REVERT: B 250 MET cc_start: 0.8685 (tpt) cc_final: 0.7862 (tpt) REVERT: B 258 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7657 (tp) REVERT: B 380 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8251 (pttm) REVERT: B 409 ASP cc_start: 0.7004 (m-30) cc_final: 0.6240 (t0) REVERT: C 423 GLN cc_start: 0.6887 (tp40) cc_final: 0.6632 (tp40) REVERT: D 44 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7192 (tt0) REVERT: D 85 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7785 (mp10) REVERT: E 29 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8199 (t) REVERT: F 85 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7617 (mp10) REVERT: G 31 ASN cc_start: 0.7776 (OUTLIER) cc_final: 0.7386 (t0) REVERT: H 31 ASN cc_start: 0.7950 (OUTLIER) cc_final: 0.7567 (t0) REVERT: H 37 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.7322 (mm) REVERT: H 75 LYS cc_start: 0.8186 (mmtm) cc_final: 0.7729 (mtmt) REVERT: H 103 TYR cc_start: 0.5991 (OUTLIER) cc_final: 0.5618 (t80) REVERT: I 23 THR cc_start: 0.7300 (OUTLIER) cc_final: 0.6976 (p) REVERT: I 31 ASN cc_start: 0.7916 (OUTLIER) cc_final: 0.7341 (t0) outliers start: 116 outliers final: 68 residues processed: 296 average time/residue: 0.1071 time to fit residues: 49.3645 Evaluate side-chains 272 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 191 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 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 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 156 LEU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 251 CYS 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 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 332 ASN 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 381 THR Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain E residue 3 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 21 MET Chi-restraints excluded: chain F residue 73 SER 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 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 31 ASN Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 90 THR 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 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 65 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 130 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 203 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 180 optimal weight: 4.9990 chunk 128 optimal weight: 0.0980 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN A 415 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 ASN B 426 GLN C 263 GLN ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.149895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.122322 restraints weight = 28127.452| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.75 r_work: 0.3668 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16137 Z= 0.125 Angle : 0.565 12.210 21907 Z= 0.293 Chirality : 0.044 0.289 2553 Planarity : 0.003 0.042 2755 Dihedral : 6.312 86.799 2239 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 6.89 % Allowed : 23.14 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.19), residues: 2031 helix: 1.47 (0.25), residues: 453 sheet: -0.64 (0.20), residues: 675 loop : -0.73 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.020 0.001 TYR G 103 PHE 0.012 0.001 PHE F 77 TRP 0.018 0.001 TRP E 56 HIS 0.005 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00285 (16104) covalent geometry : angle 0.56395 (21841) SS BOND : bond 0.00284 ( 33) SS BOND : angle 0.94378 ( 66) hydrogen bonds : bond 0.03190 ( 724) hydrogen bonds : angle 5.49273 ( 1917) *********************** 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 329 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 203 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7350 (tt0) REVERT: A 250 MET cc_start: 0.8817 (tpt) cc_final: 0.8326 (tpt) REVERT: B 250 MET cc_start: 0.8670 (tpt) cc_final: 0.7825 (tpt) REVERT: B 258 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7597 (tp) REVERT: B 380 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8238 (pttm) REVERT: B 409 ASP cc_start: 0.7001 (m-30) cc_final: 0.6265 (t0) REVERT: C 278 HIS cc_start: 0.6743 (OUTLIER) cc_final: 0.6055 (m90) REVERT: C 423 GLN cc_start: 0.6833 (tp40) cc_final: 0.6632 (tp40) REVERT: D 44 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7264 (tt0) REVERT: D 85 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7704 (mp10) REVERT: F 85 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7640 (mp10) REVERT: G 31 ASN cc_start: 0.7719 (OUTLIER) cc_final: 0.7343 (t0) REVERT: G 72 ASP cc_start: 0.6547 (t0) cc_final: 0.6333 (t0) REVERT: H 31 ASN cc_start: 0.7915 (OUTLIER) cc_final: 0.7546 (t0) REVERT: H 37 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7360 (mm) REVERT: H 75 LYS cc_start: 0.8157 (mmtm) cc_final: 0.7728 (mtmt) REVERT: H 103 TYR cc_start: 0.5770 (OUTLIER) cc_final: 0.5440 (t80) REVERT: I 23 THR cc_start: 0.7289 (OUTLIER) cc_final: 0.6947 (p) REVERT: I 31 ASN cc_start: 0.7887 (OUTLIER) cc_final: 0.7310 (t0) outliers start: 126 outliers final: 82 residues processed: 301 average time/residue: 0.1118 time to fit residues: 52.3024 Evaluate side-chains 289 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 195 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 242 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 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 220 SER 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 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 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 29 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 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 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 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 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 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 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 135 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 136 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 167 optimal weight: 4.9990 chunk 192 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.149874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.122886 restraints weight = 28169.013| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.61 r_work: 0.3681 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1254 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= 0.131 Angle : 0.561 12.361 21907 Z= 0.291 Chirality : 0.043 0.263 2553 Planarity : 0.003 0.040 2755 Dihedral : 6.060 87.143 2234 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 7.39 % Allowed : 22.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.19), residues: 2031 helix: 1.51 (0.25), residues: 453 sheet: -0.63 (0.20), residues: 675 loop : -0.72 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 468 TYR 0.023 0.001 TYR H 94 PHE 0.010 0.001 PHE F 77 TRP 0.017 0.001 TRP E 56 HIS 0.005 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00303 (16104) covalent geometry : angle 0.55959 (21841) SS BOND : bond 0.00287 ( 33) SS BOND : angle 0.97442 ( 66) hydrogen bonds : bond 0.03137 ( 724) hydrogen bonds : angle 5.41820 ( 1917) *********************** 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 335 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 200 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7352 (tt0) REVERT: A 250 MET cc_start: 0.8805 (tpt) cc_final: 0.8292 (tpt) REVERT: A 392 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8236 (mp) REVERT: B 250 MET cc_start: 0.8673 (tpt) cc_final: 0.7816 (tpt) REVERT: B 258 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7587 (tp) REVERT: C 278 HIS cc_start: 0.6763 (OUTLIER) cc_final: 0.6079 (m90) REVERT: D 44 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7161 (tt0) REVERT: F 44 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.7378 (tt0) REVERT: F 85 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7655 (mp10) REVERT: G 31 ASN cc_start: 0.7722 (OUTLIER) cc_final: 0.7359 (t0) REVERT: H 31 ASN cc_start: 0.8042 (OUTLIER) cc_final: 0.7676 (t0) REVERT: H 37 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7429 (mm) REVERT: H 75 LYS cc_start: 0.8138 (mmtm) cc_final: 0.7734 (mtmt) REVERT: H 103 TYR cc_start: 0.5687 (OUTLIER) cc_final: 0.5466 (t80) REVERT: I 23 THR cc_start: 0.7216 (OUTLIER) cc_final: 0.6884 (p) REVERT: I 31 ASN cc_start: 0.7852 (OUTLIER) cc_final: 0.7369 (t0) outliers start: 135 outliers final: 92 residues processed: 305 average time/residue: 0.1040 time to fit residues: 49.8815 Evaluate side-chains 295 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 191 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 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 363 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 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 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 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 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 417 LEU Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain D residue 3 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 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 E residue 112 LYS Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 31 ASN Chi-restraints excluded: chain G residue 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 65 SER Chi-restraints excluded: chain H residue 70 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 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 87 THR Chi-restraints excluded: chain I residue 103 TYR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 118 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 20 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 136 optimal weight: 0.0870 chunk 167 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 168 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 117 optimal weight: 0.6980 chunk 202 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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 ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.150429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.123156 restraints weight = 27671.709| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.73 r_work: 0.3684 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16137 Z= 0.118 Angle : 0.555 11.078 21907 Z= 0.286 Chirality : 0.044 0.400 2553 Planarity : 0.003 0.038 2755 Dihedral : 5.335 53.898 2227 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.19), residues: 2031 helix: 1.53 (0.25), residues: 459 sheet: -0.60 (0.20), residues: 657 loop : -0.75 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 325 TYR 0.016 0.001 TYR G 103 PHE 0.010 0.001 PHE C 466 TRP 0.017 0.001 TRP E 56 HIS 0.005 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00270 (16104) covalent geometry : angle 0.55320 (21841) SS BOND : bond 0.00308 ( 33) SS BOND : angle 1.02166 ( 66) hydrogen bonds : bond 0.02951 ( 724) hydrogen bonds : angle 5.28708 ( 1917) *********************** 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 323 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 198 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7365 (tt0) REVERT: A 250 MET cc_start: 0.8739 (tpt) cc_final: 0.8269 (tpt) REVERT: A 392 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8235 (mp) REVERT: A 424 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6987 (pm20) REVERT: B 250 MET cc_start: 0.8711 (tpt) cc_final: 0.7854 (tpt) REVERT: B 380 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8186 (pttm) REVERT: C 409 ASP cc_start: 0.7194 (m-30) cc_final: 0.6302 (t0) REVERT: D 44 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7192 (tt0) REVERT: D 85 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7672 (mp10) REVERT: F 44 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7373 (tt0) REVERT: G 1 GLN cc_start: 0.6919 (pp30) cc_final: 0.6610 (pp30) REVERT: G 31 ASN cc_start: 0.7651 (OUTLIER) cc_final: 0.7331 (t0) REVERT: H 31 ASN cc_start: 0.7979 (OUTLIER) cc_final: 0.7621 (t0) REVERT: H 37 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7244 (mm) REVERT: H 75 LYS cc_start: 0.8098 (mmtm) cc_final: 0.7609 (mtmt) REVERT: H 103 TYR cc_start: 0.5582 (OUTLIER) cc_final: 0.5342 (t80) REVERT: I 23 THR cc_start: 0.7233 (OUTLIER) cc_final: 0.6887 (p) REVERT: I 31 ASN cc_start: 0.7820 (OUTLIER) cc_final: 0.7337 (t0) outliers start: 125 outliers final: 88 residues processed: 296 average time/residue: 0.1103 time to fit residues: 50.8742 Evaluate side-chains 288 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 187 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 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 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 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 257 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 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 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 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 3 VAL Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain F residue 109 LEU 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 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 65 SER Chi-restraints excluded: chain H residue 70 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 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 103 TYR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 118 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 60 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 164 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN A 263 GLN ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.149759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.122133 restraints weight = 27950.618| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.76 r_work: 0.3667 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.1404 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= 0.145 Angle : 0.582 12.697 21907 Z= 0.299 Chirality : 0.045 0.432 2553 Planarity : 0.003 0.038 2755 Dihedral : 5.360 54.600 2223 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 7.39 % Allowed : 22.92 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.19), residues: 2031 helix: 1.57 (0.25), residues: 453 sheet: -0.67 (0.20), residues: 657 loop : -0.62 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 468 TYR 0.018 0.002 TYR I 32 PHE 0.009 0.001 PHE F 77 TRP 0.015 0.002 TRP E 56 HIS 0.004 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00338 (16104) covalent geometry : angle 0.57974 (21841) SS BOND : bond 0.00339 ( 33) SS BOND : angle 1.02808 ( 66) hydrogen bonds : bond 0.03107 ( 724) hydrogen bonds : angle 5.30447 ( 1917) *********************** 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 330 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 195 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7394 (tt0) REVERT: A 250 MET cc_start: 0.8765 (tpt) cc_final: 0.8432 (tpt) REVERT: A 392 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8240 (mp) REVERT: A 424 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.7000 (pm20) REVERT: B 250 MET cc_start: 0.8678 (tpt) cc_final: 0.7829 (tpt) REVERT: B 258 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7618 (tp) REVERT: B 380 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8194 (pttm) REVERT: C 250 MET cc_start: 0.8647 (tpt) cc_final: 0.8271 (tpt) REVERT: C 409 ASP cc_start: 0.7235 (m-30) cc_final: 0.6349 (t0) REVERT: D 44 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7141 (tt0) REVERT: D 85 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7781 (mp10) REVERT: F 44 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.7331 (tt0) REVERT: G 1 GLN cc_start: 0.7011 (pp30) cc_final: 0.6722 (pp30) REVERT: G 31 ASN cc_start: 0.7656 (OUTLIER) cc_final: 0.7322 (t0) REVERT: H 31 ASN cc_start: 0.8008 (OUTLIER) cc_final: 0.7642 (t0) REVERT: H 37 ILE cc_start: 0.7513 (OUTLIER) cc_final: 0.7059 (mm) REVERT: H 75 LYS cc_start: 0.8083 (mmtm) cc_final: 0.7739 (mtmt) REVERT: H 102 TYR cc_start: 0.6592 (OUTLIER) cc_final: 0.5794 (t80) REVERT: I 23 THR cc_start: 0.7251 (OUTLIER) cc_final: 0.6898 (p) REVERT: I 31 ASN cc_start: 0.7836 (OUTLIER) cc_final: 0.7383 (t0) outliers start: 135 outliers final: 104 residues processed: 301 average time/residue: 0.1031 time to fit residues: 48.3998 Evaluate side-chains 306 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 188 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 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 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 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 168 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain 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 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 347 ILE Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain F residue 13 VAL 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 65 SER Chi-restraints excluded: chain H residue 70 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 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 118 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 187 optimal weight: 4.9990 chunk 169 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 128 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 104 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 GLN ** C 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.150933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.123444 restraints weight = 28137.801| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.77 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: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16137 Z= 0.119 Angle : 0.568 12.077 21907 Z= 0.290 Chirality : 0.044 0.385 2553 Planarity : 0.003 0.043 2755 Dihedral : 5.116 51.989 2220 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 6.89 % Allowed : 23.63 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.19), residues: 2031 helix: 1.58 (0.25), residues: 459 sheet: -0.63 (0.21), residues: 639 loop : -0.67 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 468 TYR 0.024 0.001 TYR H 103 PHE 0.013 0.001 PHE A 466 TRP 0.017 0.001 TRP E 56 HIS 0.005 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00274 (16104) covalent geometry : angle 0.56615 (21841) SS BOND : bond 0.00294 ( 33) SS BOND : angle 0.97453 ( 66) hydrogen bonds : bond 0.02902 ( 724) hydrogen bonds : angle 5.19195 ( 1917) *********************** 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: 126 poor density : 198 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7351 (tt0) REVERT: A 250 MET cc_start: 0.8715 (tpt) cc_final: 0.8449 (tpt) REVERT: A 392 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8226 (mp) REVERT: A 424 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6998 (pm20) REVERT: B 250 MET cc_start: 0.8656 (tpt) cc_final: 0.7768 (tpt) REVERT: B 380 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8190 (pttm) REVERT: C 250 MET cc_start: 0.8634 (tpt) cc_final: 0.8309 (tpt) REVERT: C 278 HIS cc_start: 0.6744 (OUTLIER) cc_final: 0.6148 (m90) REVERT: C 409 ASP cc_start: 0.7220 (m-30) cc_final: 0.6331 (t0) REVERT: D 44 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7152 (tt0) REVERT: D 85 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7667 (mp10) REVERT: F 44 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7310 (tt0) REVERT: G 1 GLN cc_start: 0.7000 (pp30) cc_final: 0.6708 (pp30) REVERT: G 31 ASN cc_start: 0.7580 (OUTLIER) cc_final: 0.7275 (t0) REVERT: H 31 ASN cc_start: 0.8056 (OUTLIER) cc_final: 0.7755 (t0) REVERT: H 37 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7145 (mm) REVERT: H 75 LYS cc_start: 0.8077 (mmtm) cc_final: 0.7761 (mtmt) REVERT: H 103 TYR cc_start: 0.5527 (t80) cc_final: 0.5255 (t80) REVERT: I 23 THR cc_start: 0.7238 (OUTLIER) cc_final: 0.6883 (p) REVERT: I 31 ASN cc_start: 0.7715 (OUTLIER) cc_final: 0.7279 (t0) outliers start: 126 outliers final: 98 residues processed: 297 average time/residue: 0.1080 time to fit residues: 49.7704 Evaluate side-chains 298 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 187 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 164 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 205 THR 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 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 168 LEU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain 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 175 ILE 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 347 ILE Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain F residue 109 LEU 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 65 SER Chi-restraints excluded: chain H residue 70 SER 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 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 Chi-restraints excluded: chain I residue 118 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 177 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 127 optimal weight: 0.2980 chunk 78 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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** ** C 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.147450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.119616 restraints weight = 27965.969| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.75 r_work: 0.3630 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.1575 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= 0.195 Angle : 0.636 11.257 21907 Z= 0.328 Chirality : 0.046 0.455 2553 Planarity : 0.004 0.042 2755 Dihedral : 5.413 51.630 2218 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 6.95 % Allowed : 23.74 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.19), residues: 2031 helix: 1.51 (0.25), residues: 453 sheet: -0.80 (0.21), residues: 630 loop : -0.68 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 38 TYR 0.021 0.002 TYR I 32 PHE 0.012 0.002 PHE D 68 TRP 0.013 0.002 TRP E 56 HIS 0.005 0.002 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00458 (16104) covalent geometry : angle 0.63368 (21841) SS BOND : bond 0.00457 ( 33) SS BOND : angle 1.12222 ( 66) hydrogen bonds : bond 0.03407 ( 724) hydrogen bonds : angle 5.38302 ( 1917) *********************** 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 318 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 191 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7432 (tt0) REVERT: A 250 MET cc_start: 0.8774 (tpt) cc_final: 0.8532 (tpt) REVERT: A 392 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8255 (mp) REVERT: B 250 MET cc_start: 0.8687 (tpt) cc_final: 0.7822 (tpt) REVERT: B 258 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7803 (tp) REVERT: B 380 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8248 (pttm) REVERT: C 409 ASP cc_start: 0.7316 (m-30) cc_final: 0.6400 (t0) REVERT: D 44 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7168 (tt0) REVERT: F 44 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7406 (tt0) REVERT: G 1 GLN cc_start: 0.7003 (pp30) cc_final: 0.6704 (pp30) REVERT: G 31 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7462 (t0) REVERT: H 31 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7857 (t0) REVERT: H 37 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.7063 (mm) REVERT: H 75 LYS cc_start: 0.8120 (mmtm) cc_final: 0.7750 (mtmt) REVERT: H 103 TYR cc_start: 0.5830 (t80) cc_final: 0.5407 (t80) REVERT: I 23 THR cc_start: 0.7295 (OUTLIER) cc_final: 0.6937 (p) REVERT: I 31 ASN cc_start: 0.7897 (OUTLIER) cc_final: 0.7449 (t0) outliers start: 127 outliers final: 101 residues processed: 288 average time/residue: 0.1021 time to fit residues: 46.2383 Evaluate side-chains 298 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 186 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 168 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 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 175 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 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 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 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 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 65 SER Chi-restraints excluded: chain H residue 70 SER 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 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 Chi-restraints excluded: chain I residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 90 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 190 optimal weight: 0.9980 chunk 165 optimal weight: 0.9980 chunk 119 optimal weight: 0.3980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 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 = 0.4190 r_free = 0.4190 target = 0.149835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.122502 restraints weight = 27531.921| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.71 r_work: 0.3674 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1584 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= 0.131 Angle : 0.598 11.836 21907 Z= 0.305 Chirality : 0.044 0.397 2553 Planarity : 0.003 0.037 2755 Dihedral : 5.227 52.472 2218 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 5.69 % Allowed : 25.05 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.19), residues: 2031 helix: 1.61 (0.25), residues: 453 sheet: -0.79 (0.20), residues: 654 loop : -0.60 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.019 0.001 TYR H 103 PHE 0.013 0.001 PHE C 466 TRP 0.017 0.001 TRP E 56 HIS 0.005 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00303 (16104) covalent geometry : angle 0.59624 (21841) SS BOND : bond 0.00323 ( 33) SS BOND : angle 1.02722 ( 66) hydrogen bonds : bond 0.02987 ( 724) hydrogen bonds : angle 5.23406 ( 1917) ********************** 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 299 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 195 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7314 (tt0) REVERT: A 250 MET cc_start: 0.8737 (tpt) cc_final: 0.8467 (tpt) REVERT: A 392 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8231 (mp) REVERT: B 250 MET cc_start: 0.8662 (tpt) cc_final: 0.7784 (tpt) REVERT: B 380 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8159 (pttm) REVERT: C 278 HIS cc_start: 0.6761 (OUTLIER) cc_final: 0.6149 (m90) REVERT: C 409 ASP cc_start: 0.7284 (m-30) cc_final: 0.6348 (t0) REVERT: D 44 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7209 (tt0) REVERT: F 44 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7299 (tt0) REVERT: G 1 GLN cc_start: 0.7001 (pp30) cc_final: 0.6704 (pp30) REVERT: G 31 ASN cc_start: 0.7671 (OUTLIER) cc_final: 0.7370 (t0) REVERT: H 31 ASN cc_start: 0.8080 (OUTLIER) cc_final: 0.7796 (t0) REVERT: H 37 ILE cc_start: 0.7576 (OUTLIER) cc_final: 0.7121 (mm) REVERT: H 75 LYS cc_start: 0.8108 (mmtm) cc_final: 0.7777 (mtmt) REVERT: H 102 TYR cc_start: 0.6713 (OUTLIER) cc_final: 0.6040 (t80) REVERT: H 103 TYR cc_start: 0.5496 (t80) cc_final: 0.5184 (t80) REVERT: I 23 THR cc_start: 0.7317 (OUTLIER) cc_final: 0.6962 (p) REVERT: I 31 ASN cc_start: 0.7812 (OUTLIER) cc_final: 0.7374 (t0) outliers start: 104 outliers final: 87 residues processed: 277 average time/residue: 0.1115 time to fit residues: 48.4101 Evaluate side-chains 292 residues out of total 1830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 193 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 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 220 SER Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 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 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 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 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 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 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 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 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 65 SER Chi-restraints excluded: chain H residue 70 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 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 70 optimal weight: 9.9990 chunk 111 optimal weight: 0.6980 chunk 193 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 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 = 0.4180 r_free = 0.4180 target = 0.148921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.121465 restraints weight = 27651.871| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.70 r_work: 0.3661 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16137 Z= 0.151 Angle : 0.610 11.668 21907 Z= 0.311 Chirality : 0.045 0.420 2553 Planarity : 0.003 0.039 2755 Dihedral : 5.217 52.472 2216 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 6.02 % Allowed : 24.73 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.19), residues: 2031 helix: 1.60 (0.25), residues: 453 sheet: -0.72 (0.20), residues: 651 loop : -0.68 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 38 TYR 0.019 0.002 TYR I 94 PHE 0.010 0.001 PHE D 68 TRP 0.016 0.002 TRP E 56 HIS 0.004 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00352 (16104) covalent geometry : angle 0.60852 (21841) SS BOND : bond 0.00342 ( 33) SS BOND : angle 1.03987 ( 66) hydrogen bonds : bond 0.03102 ( 724) hydrogen bonds : angle 5.24135 ( 1917) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3392.62 seconds wall clock time: 59 minutes 17.55 seconds (3557.55 seconds total)