Starting phenix.real_space_refine on Thu Aug 6 01:21:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tq8_56127/08_2026/9tq8_56127.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tq8_56127/08_2026/9tq8_56127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9tq8_56127/08_2026/9tq8_56127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tq8_56127/08_2026/9tq8_56127.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9tq8_56127/08_2026/9tq8_56127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tq8_56127/08_2026/9tq8_56127.map" } resolution = 3.48 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 88 5.16 5 C 7676 2.51 5 N 2084 2.21 5 O 2392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12244 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2995 Classifications: {'peptide': 387} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 365} Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 66 Unusual residues: {' CA': 1, 'NAG': 3, 'ZMR': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B, C, D Time building chain proxies: 2.71, per 1000 atoms: 0.22 Number of scatterers: 12244 At special positions: 0 Unit cell: (119.574, 119.574, 71.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 88 16.00 O 2392 8.00 N 2084 7.00 C 7676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 238 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 290 " distance=1.49 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 446 " distance=1.53 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.03 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.03 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.03 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 184 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 233 " - pdb=" SG CYS B 238 " distance=2.03 Simple disulfide: pdb=" SG CYS C 233 " - pdb=" SG CYS C 238 " distance=2.03 Simple disulfide: pdb=" SG CYS D 233 " - pdb=" SG CYS D 238 " distance=2.03 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS D 279 " - pdb=" SG CYS D 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 290 " distance=1.49 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 290 " distance=1.49 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 290 " distance=1.49 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 446 " distance=1.53 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 446 " distance=1.53 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 446 " distance=1.53 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 146 " " NAG A 602 " - " ASN A 235 " " NAG A 603 " - " ASN A 88 " " NAG B 601 " - " ASN B 146 " " NAG B 602 " - " ASN B 235 " " NAG B 603 " - " ASN B 88 " " NAG C 601 " - " ASN C 146 " " NAG C 602 " - " ASN C 235 " " NAG C 603 " - " ASN C 88 " " NAG D 601 " - " ASN D 146 " " NAG D 602 " - " ASN D 235 " " NAG D 603 " - " ASN D 88 " Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 460.4 milliseconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2776 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 28 sheets defined 4.1% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 168 through 172 removed outlier: 3.898A pdb=" N SER A 172 " --> pdb=" O PRO A 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.898A pdb=" N SER B 172 " --> pdb=" O PRO B 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 142 through 146 Processing helix chain 'C' and resid 168 through 172 removed outlier: 3.898A pdb=" N SER C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 142 through 146 Processing helix chain 'D' and resid 168 through 172 removed outlier: 3.897A pdb=" N SER D 172 " --> pdb=" O PRO D 169 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 3.602A pdb=" N ALA A 98 " --> pdb=" O CYS A 446 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N SER A 444 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LYS A 102 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N SER A 442 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 426 " --> pdb=" O SER A 441 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 117 removed outlier: 7.304A pdb=" N VAL A 116 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN A 136 " --> pdb=" O VAL A 116 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 115 through 117 removed outlier: 7.304A pdb=" N VAL A 116 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN A 136 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 176 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N SER A 160 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N PHE A 174 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 183 removed outlier: 4.092A pdb=" N SER A 180 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP A 214 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N TYR A 208 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ILE A 212 " --> pdb=" O TYR A 208 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 225 removed outlier: 3.720A pdb=" N THR A 240 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE A 256 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS A 265 " --> pdb=" O ARG A 257 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 280 through 284 removed outlier: 3.687A pdb=" N VAL A 291 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR A 289 " --> pdb=" O TYR A 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 359 through 361 removed outlier: 6.986A pdb=" N LYS A 369 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLY A 395 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE A 371 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS A 389 " --> pdb=" O TRP A 375 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 96 through 102 removed outlier: 3.602A pdb=" N ALA B 98 " --> pdb=" O CYS B 446 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER B 444 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LYS B 102 " --> pdb=" O SER B 442 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N SER B 442 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 426 " --> pdb=" O SER B 441 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 115 through 117 removed outlier: 7.304A pdb=" N VAL B 116 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN B 136 " --> pdb=" O VAL B 116 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 115 through 117 removed outlier: 7.304A pdb=" N VAL B 116 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN B 136 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER B 176 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N SER B 160 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N PHE B 174 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 180 through 183 removed outlier: 4.093A pdb=" N SER B 180 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP B 214 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N TYR B 208 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ILE B 212 " --> pdb=" O TYR B 208 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 224 through 225 removed outlier: 3.720A pdb=" N THR B 240 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE B 256 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS B 265 " --> pdb=" O ARG B 257 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 280 through 284 removed outlier: 3.688A pdb=" N VAL B 291 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR B 289 " --> pdb=" O TYR B 282 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 359 through 361 removed outlier: 6.986A pdb=" N LYS B 369 " --> pdb=" O GLY B 395 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLY B 395 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE B 371 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS B 389 " --> pdb=" O TRP B 375 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 96 through 102 removed outlier: 3.602A pdb=" N ALA C 98 " --> pdb=" O CYS C 446 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER C 444 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LYS C 102 " --> pdb=" O SER C 442 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N SER C 442 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C 426 " --> pdb=" O SER C 441 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 115 through 117 removed outlier: 7.304A pdb=" N VAL C 116 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN C 136 " --> pdb=" O VAL C 116 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 115 through 117 removed outlier: 7.304A pdb=" N VAL C 116 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN C 136 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER C 176 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N SER C 160 " --> pdb=" O PHE C 174 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N PHE C 174 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 180 through 183 removed outlier: 4.093A pdb=" N SER C 180 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP C 214 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N TYR C 208 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ILE C 212 " --> pdb=" O TYR C 208 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 224 through 225 removed outlier: 3.720A pdb=" N THR C 240 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE C 256 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS C 265 " --> pdb=" O ARG C 257 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 280 through 284 removed outlier: 3.687A pdb=" N VAL C 291 " --> pdb=" O SER C 280 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR C 289 " --> pdb=" O TYR C 282 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 359 through 361 removed outlier: 6.986A pdb=" N LYS C 369 " --> pdb=" O GLY C 395 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLY C 395 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE C 371 " --> pdb=" O ILE C 393 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS C 389 " --> pdb=" O TRP C 375 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 96 through 102 removed outlier: 3.602A pdb=" N ALA D 98 " --> pdb=" O CYS D 446 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER D 444 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LYS D 102 " --> pdb=" O SER D 442 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N SER D 442 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 426 " --> pdb=" O SER D 441 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 115 through 117 removed outlier: 7.304A pdb=" N VAL D 116 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN D 136 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 115 through 117 removed outlier: 7.304A pdb=" N VAL D 116 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN D 136 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER D 176 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N SER D 160 " --> pdb=" O PHE D 174 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N PHE D 174 " --> pdb=" O SER D 160 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 180 through 183 removed outlier: 4.093A pdb=" N SER D 180 " --> pdb=" O ILE D 195 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP D 214 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N TYR D 208 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ILE D 212 " --> pdb=" O TYR D 208 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 224 through 225 removed outlier: 3.720A pdb=" N THR D 240 " --> pdb=" O PHE D 256 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE D 256 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS D 265 " --> pdb=" O ARG D 257 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 280 through 284 removed outlier: 3.687A pdb=" N VAL D 291 " --> pdb=" O SER D 280 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR D 289 " --> pdb=" O TYR D 282 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 359 through 361 removed outlier: 6.985A pdb=" N LYS D 369 " --> pdb=" O GLY D 395 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLY D 395 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE D 371 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS D 389 " --> pdb=" O TRP D 375 " (cutoff:3.500A) 300 hydrogen bonds defined for protein. 732 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: 1.87 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3944 1.35 - 1.48: 3452 1.48 - 1.61: 5064 1.61 - 1.74: 0 1.74 - 1.87: 108 Bond restraints: 12568 Sorted by residual: bond pdb=" CA CYS C 421 " pdb=" CB CYS C 421 " ideal model delta sigma weight residual 1.533 1.567 -0.034 1.60e-02 3.91e+03 4.44e+00 bond pdb=" CA CYS D 421 " pdb=" CB CYS D 421 " ideal model delta sigma weight residual 1.533 1.567 -0.034 1.60e-02 3.91e+03 4.44e+00 bond pdb=" CA CYS B 421 " pdb=" CB CYS B 421 " ideal model delta sigma weight residual 1.533 1.566 -0.033 1.60e-02 3.91e+03 4.33e+00 bond pdb=" CA CYS A 421 " pdb=" CB CYS A 421 " ideal model delta sigma weight residual 1.533 1.566 -0.033 1.60e-02 3.91e+03 4.31e+00 bond pdb=" CB CYS B 421 " pdb=" SG CYS B 421 " ideal model delta sigma weight residual 1.808 1.869 -0.061 3.30e-02 9.18e+02 3.40e+00 ... (remaining 12563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 16790 2.04 - 4.07: 240 4.07 - 6.11: 14 6.11 - 8.14: 8 8.14 - 10.18: 4 Bond angle restraints: 17056 Sorted by residual: angle pdb=" N CYS B 281 " pdb=" CA CYS B 281 " pdb=" CB CYS B 281 " ideal model delta sigma weight residual 110.46 103.15 7.31 1.55e+00 4.16e-01 2.22e+01 angle pdb=" N CYS C 281 " pdb=" CA CYS C 281 " pdb=" CB CYS C 281 " ideal model delta sigma weight residual 110.46 103.16 7.30 1.55e+00 4.16e-01 2.22e+01 angle pdb=" N CYS A 281 " pdb=" CA CYS A 281 " pdb=" CB CYS A 281 " ideal model delta sigma weight residual 110.46 103.17 7.29 1.55e+00 4.16e-01 2.21e+01 angle pdb=" N CYS D 281 " pdb=" CA CYS D 281 " pdb=" CB CYS D 281 " ideal model delta sigma weight residual 110.46 103.18 7.28 1.55e+00 4.16e-01 2.21e+01 angle pdb=" CA CYS D 446 " pdb=" CB CYS D 446 " pdb=" SG CYS D 446 " ideal model delta sigma weight residual 114.40 124.58 -10.18 2.30e+00 1.89e-01 1.96e+01 ... (remaining 17051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 6605 17.01 - 34.01: 839 34.01 - 51.02: 172 51.02 - 68.03: 32 68.03 - 85.04: 12 Dihedral angle restraints: 7660 sinusoidal: 3292 harmonic: 4368 Sorted by residual: dihedral pdb=" CB CYS B 421 " pdb=" SG CYS B 421 " pdb=" SG CYS B 446 " pdb=" CB CYS B 446 " ideal model delta sinusoidal sigma weight residual -86.00 -171.04 85.04 1 1.00e+01 1.00e-02 8.77e+01 dihedral pdb=" CB CYS D 421 " pdb=" SG CYS D 421 " pdb=" SG CYS D 446 " pdb=" CB CYS D 446 " ideal model delta sinusoidal sigma weight residual -86.00 -171.01 85.01 1 1.00e+01 1.00e-02 8.76e+01 dihedral pdb=" CB CYS C 421 " pdb=" SG CYS C 421 " pdb=" SG CYS C 446 " pdb=" CB CYS C 446 " ideal model delta sinusoidal sigma weight residual -86.00 -170.98 84.98 1 1.00e+01 1.00e-02 8.76e+01 ... (remaining 7657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1389 0.046 - 0.091: 255 0.091 - 0.137: 161 0.137 - 0.182: 5 0.182 - 0.228: 6 Chirality restraints: 1816 Sorted by residual: chirality pdb=" CA CYS D 446 " pdb=" N CYS D 446 " pdb=" C CYS D 446 " pdb=" CB CYS D 446 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA CYS B 446 " pdb=" N CYS B 446 " pdb=" C CYS B 446 " pdb=" CB CYS B 446 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA CYS A 446 " pdb=" N CYS A 446 " pdb=" C CYS A 446 " pdb=" CB CYS A 446 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1813 not shown) Planarity restraints: 2204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 280 " -0.010 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" C SER D 280 " 0.036 2.00e-02 2.50e+03 pdb=" O SER D 280 " -0.014 2.00e-02 2.50e+03 pdb=" N CYS D 281 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 280 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.40e+00 pdb=" C SER A 280 " -0.036 2.00e-02 2.50e+03 pdb=" O SER A 280 " 0.014 2.00e-02 2.50e+03 pdb=" N CYS A 281 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 280 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.34e+00 pdb=" C SER B 280 " -0.036 2.00e-02 2.50e+03 pdb=" O SER B 280 " 0.014 2.00e-02 2.50e+03 pdb=" N CYS B 281 " 0.012 2.00e-02 2.50e+03 ... (remaining 2201 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 32 2.41 - 3.03: 8230 3.03 - 3.65: 17691 3.65 - 4.28: 25795 4.28 - 4.90: 45599 Nonbonded interactions: 97347 Sorted by model distance: nonbonded pdb=" CA CYS C 421 " pdb=" SG CYS C 446 " model vdw 1.782 3.064 nonbonded pdb=" CA CYS A 421 " pdb=" SG CYS A 446 " model vdw 1.783 3.064 nonbonded pdb=" CA CYS D 421 " pdb=" SG CYS D 446 " model vdw 1.783 3.064 nonbonded pdb=" CA CYS B 421 " pdb=" SG CYS B 446 " model vdw 1.783 3.064 nonbonded pdb=" OG SER D 101 " pdb=" OG SER D 444 " model vdw 1.933 3.040 ... (remaining 97342 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.600 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 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 : 0.013 0.538 12612 Z= 0.669 Angle : 1.040 53.317 17156 Z= 0.517 Chirality : 0.048 0.228 1816 Planarity : 0.003 0.025 2192 Dihedral : 14.492 75.262 4788 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 0.67 % Allowed : 26.87 % Favored : 72.46 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 9.52 % 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 are not related in a simple way. whole: -2.31 (0.22), residues: 1540 helix: -1.40 (1.06), residues: 24 sheet: -1.04 (0.25), residues: 556 loop : -1.91 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 293 TYR 0.012 0.001 TYR D 312 PHE 0.015 0.001 PHE B 445 TRP 0.005 0.001 TRP B 423 HIS 0.004 0.001 HIS B 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (12568) covalent geometry : angle 0.59921 / 0.32 (17056) SS BOND : bond 0.25966 / 15.61 ( 32) SS BOND : angle 13.90825 / 10.42 ( 64) hydrogen bonds : bond 0.23724 / 16.26 ( 300) hydrogen bonds : angle 9.93275 / 6.95 ( 732) link_NAG-ASN : bond 0.00219 / 0.14 ( 12) link_NAG-ASN : angle 1.22532 / 0.75 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 444 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7264 (mm-30) REVERT: A 156 ARG cc_start: 0.8420 (ttm110) cc_final: 0.7937 (ttm110) REVERT: A 159 MET cc_start: 0.8292 (mtp) cc_final: 0.7621 (mtp) REVERT: A 227 GLN cc_start: 0.8123 (tt0) cc_final: 0.7686 (tt0) REVERT: A 287 GLU cc_start: 0.6922 (mp0) cc_final: 0.6542 (mp0) REVERT: A 293 ARG cc_start: 0.7470 (mtm110) cc_final: 0.6632 (mtp85) REVERT: A 301 ARG cc_start: 0.8245 (tpp80) cc_final: 0.7732 (mmm-85) REVERT: A 372 GLU cc_start: 0.7620 (pt0) cc_final: 0.6809 (tt0) REVERT: A 384 ASP cc_start: 0.7683 (t0) cc_final: 0.6909 (t0) REVERT: B 119 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7223 (mm-30) REVERT: B 156 ARG cc_start: 0.8443 (ttm110) cc_final: 0.7981 (ttm110) REVERT: B 159 MET cc_start: 0.8218 (mtp) cc_final: 0.7501 (mtp) REVERT: B 227 GLN cc_start: 0.8129 (tt0) cc_final: 0.7682 (tt0) REVERT: B 287 GLU cc_start: 0.7040 (mp0) cc_final: 0.6626 (mp0) REVERT: B 293 ARG cc_start: 0.7451 (mtm110) cc_final: 0.7090 (mtp85) REVERT: B 301 ARG cc_start: 0.8237 (tpp80) cc_final: 0.7360 (mmm-85) REVERT: B 372 GLU cc_start: 0.7568 (pt0) cc_final: 0.6802 (tt0) REVERT: B 384 ASP cc_start: 0.7880 (t0) cc_final: 0.7081 (t0) REVERT: C 119 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7196 (mm-30) REVERT: C 142 ASP cc_start: 0.8339 (t70) cc_final: 0.8122 (t0) REVERT: C 156 ARG cc_start: 0.8440 (ttm110) cc_final: 0.7975 (ttm110) REVERT: C 159 MET cc_start: 0.8223 (mtp) cc_final: 0.7537 (mtp) REVERT: C 227 GLN cc_start: 0.8150 (tt0) cc_final: 0.7708 (tt0) REVERT: C 287 GLU cc_start: 0.7007 (mp0) cc_final: 0.6587 (mp0) REVERT: C 293 ARG cc_start: 0.7416 (mtm110) cc_final: 0.7070 (mtp85) REVERT: C 301 ARG cc_start: 0.8222 (tpp80) cc_final: 0.7344 (mmm-85) REVERT: C 372 GLU cc_start: 0.7569 (pt0) cc_final: 0.6814 (tt0) REVERT: C 384 ASP cc_start: 0.7860 (t0) cc_final: 0.7058 (t0) REVERT: D 119 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7212 (mm-30) REVERT: D 142 ASP cc_start: 0.8290 (t70) cc_final: 0.8066 (t0) REVERT: D 156 ARG cc_start: 0.8441 (ttm110) cc_final: 0.7978 (ttm110) REVERT: D 159 MET cc_start: 0.8232 (mtp) cc_final: 0.7519 (mtp) REVERT: D 227 GLN cc_start: 0.8148 (tt0) cc_final: 0.7705 (tt0) REVERT: D 287 GLU cc_start: 0.7013 (mp0) cc_final: 0.6588 (mp0) REVERT: D 293 ARG cc_start: 0.7441 (mtm110) cc_final: 0.7087 (mtp85) REVERT: D 301 ARG cc_start: 0.8198 (tpp80) cc_final: 0.7333 (mmm-85) REVERT: D 372 GLU cc_start: 0.7590 (pt0) cc_final: 0.6806 (tt0) REVERT: D 384 ASP cc_start: 0.7855 (t0) cc_final: 0.7060 (t0) outliers start: 9 outliers final: 5 residues processed: 446 average time/residue: 0.0995 time to fit residues: 66.7194 Evaluate side-chains 432 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 427 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 TYR Chi-restraints excluded: chain C residue 316 TYR Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain D residue 316 TYR Chi-restraints excluded: chain D residue 439 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN A 295 ASN B 209 ASN B 295 ASN C 209 ASN C 295 ASN D 209 ASN D 295 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.142416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.112340 restraints weight = 20208.109| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 4.88 r_work: 0.3294 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12612 Z= 0.235 Angle : 0.652 7.870 17156 Z= 0.341 Chirality : 0.052 0.160 1816 Planarity : 0.004 0.029 2192 Dihedral : 5.752 39.724 2040 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 5.39 % Allowed : 24.33 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 are not related in a simple way. whole: -2.14 (0.22), residues: 1540 helix: -1.99 (0.96), residues: 24 sheet: -0.81 (0.25), residues: 552 loop : -1.85 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 327 TYR 0.014 0.002 TYR D 100 PHE 0.017 0.002 PHE A 406 TRP 0.013 0.001 TRP A 296 HIS 0.004 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.23 (12568) covalent geometry : angle 0.64559 / 0.34 (17056) SS BOND : bond 0.00553 / 0.33 ( 32) SS BOND : angle 1.39069 / 0.95 ( 64) hydrogen bonds : bond 0.03236 / 2.22 ( 300) hydrogen bonds : angle 7.27952 / 5.12 ( 732) link_NAG-ASN : bond 0.00194 / 0.13 ( 12) link_NAG-ASN : angle 1.38344 / 0.83 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 445 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7835 (mm-30) REVERT: A 155 TYR cc_start: 0.8692 (m-80) cc_final: 0.8392 (m-80) REVERT: A 156 ARG cc_start: 0.8671 (ttm110) cc_final: 0.8048 (ttm110) REVERT: A 159 MET cc_start: 0.8393 (mtp) cc_final: 0.7952 (mtp) REVERT: A 254 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7622 (mmtp) REVERT: A 275 HIS cc_start: 0.8852 (t-90) cc_final: 0.8500 (t-90) REVERT: A 287 GLU cc_start: 0.7545 (mp0) cc_final: 0.7077 (mp0) REVERT: A 411 GLU cc_start: 0.8393 (mp0) cc_final: 0.8114 (mp0) REVERT: A 421 CYS cc_start: 0.7211 (m) cc_final: 0.6847 (m) REVERT: B 119 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7847 (mm-30) REVERT: B 142 ASP cc_start: 0.8495 (t0) cc_final: 0.8231 (t0) REVERT: B 155 TYR cc_start: 0.8715 (m-80) cc_final: 0.8400 (m-80) REVERT: B 156 ARG cc_start: 0.8640 (ttm110) cc_final: 0.8030 (ttm110) REVERT: B 159 MET cc_start: 0.8369 (mtp) cc_final: 0.7942 (mtp) REVERT: B 254 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7627 (mmtp) REVERT: B 260 LYS cc_start: 0.9409 (pttm) cc_final: 0.9021 (pptt) REVERT: B 262 LYS cc_start: 0.9090 (ttpp) cc_final: 0.8392 (ttpp) REVERT: B 275 HIS cc_start: 0.8845 (t-90) cc_final: 0.8513 (t-90) REVERT: B 287 GLU cc_start: 0.7639 (mp0) cc_final: 0.7159 (mp0) REVERT: B 301 ARG cc_start: 0.8598 (tpp80) cc_final: 0.8005 (mmm-85) REVERT: B 421 CYS cc_start: 0.7231 (m) cc_final: 0.6877 (m) REVERT: B 425 GLU cc_start: 0.8566 (tt0) cc_final: 0.8221 (tt0) REVERT: C 119 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7768 (mm-30) REVERT: C 142 ASP cc_start: 0.8627 (t70) cc_final: 0.8200 (t0) REVERT: C 155 TYR cc_start: 0.8707 (m-80) cc_final: 0.8398 (m-80) REVERT: C 156 ARG cc_start: 0.8637 (ttm110) cc_final: 0.8020 (ttm110) REVERT: C 159 MET cc_start: 0.8374 (mtp) cc_final: 0.7930 (mtp) REVERT: C 254 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7640 (mmtp) REVERT: C 260 LYS cc_start: 0.9395 (pttm) cc_final: 0.9003 (pptt) REVERT: C 262 LYS cc_start: 0.9082 (ttpp) cc_final: 0.8381 (ttpp) REVERT: C 275 HIS cc_start: 0.8835 (t-90) cc_final: 0.8513 (t-90) REVERT: C 287 GLU cc_start: 0.7578 (mp0) cc_final: 0.7097 (mp0) REVERT: C 301 ARG cc_start: 0.8581 (tpp80) cc_final: 0.8045 (mmm-85) REVERT: C 421 CYS cc_start: 0.7279 (m) cc_final: 0.6944 (m) REVERT: C 437 TRP cc_start: 0.8702 (p90) cc_final: 0.8465 (p90) REVERT: D 119 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7791 (mm-30) REVERT: D 142 ASP cc_start: 0.8635 (t70) cc_final: 0.8231 (t0) REVERT: D 155 TYR cc_start: 0.8715 (m-80) cc_final: 0.8408 (m-80) REVERT: D 156 ARG cc_start: 0.8640 (ttm110) cc_final: 0.8028 (ttm110) REVERT: D 159 MET cc_start: 0.8392 (mtp) cc_final: 0.7946 (mtp) REVERT: D 254 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7643 (mmtp) REVERT: D 260 LYS cc_start: 0.9403 (pttm) cc_final: 0.9014 (pptt) REVERT: D 262 LYS cc_start: 0.9080 (ttpp) cc_final: 0.8381 (ttpp) REVERT: D 275 HIS cc_start: 0.8828 (t-90) cc_final: 0.8500 (t-90) REVERT: D 287 GLU cc_start: 0.7568 (mp0) cc_final: 0.7086 (mp0) REVERT: D 301 ARG cc_start: 0.8611 (tpp80) cc_final: 0.8034 (mmm-85) REVERT: D 421 CYS cc_start: 0.7295 (m) cc_final: 0.6948 (m) outliers start: 72 outliers final: 43 residues processed: 483 average time/residue: 0.1129 time to fit residues: 78.8957 Evaluate side-chains 472 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 425 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 316 TYR Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 189 ASN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 316 TYR Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 316 TYR Chi-restraints excluded: chain D residue 335 CYS Chi-restraints excluded: chain D residue 448 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN B 209 ASN C 209 ASN D 209 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.144720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.114703 restraints weight = 20080.393| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 4.91 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12612 Z= 0.141 Angle : 0.624 7.287 17156 Z= 0.320 Chirality : 0.050 0.151 1816 Planarity : 0.004 0.047 2192 Dihedral : 5.653 38.753 2038 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 5.76 % Allowed : 26.57 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 are not related in a simple way. whole: -1.97 (0.22), residues: 1540 helix: -1.94 (1.08), residues: 24 sheet: -0.61 (0.24), residues: 564 loop : -1.81 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 301 TYR 0.011 0.001 TYR D 100 PHE 0.012 0.001 PHE B 406 TRP 0.024 0.001 TRP B 296 HIS 0.007 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (12568) covalent geometry : angle 0.61938 / 0.32 (17056) SS BOND : bond 0.00562 / 0.34 ( 32) SS BOND : angle 1.20419 / 0.83 ( 64) hydrogen bonds : bond 0.02592 / 1.76 ( 300) hydrogen bonds : angle 6.75175 / 4.73 ( 732) link_NAG-ASN : bond 0.00190 / 0.13 ( 12) link_NAG-ASN : angle 1.21663 / 0.73 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 444 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 TYR cc_start: 0.8502 (m-80) cc_final: 0.8033 (m-80) REVERT: A 156 ARG cc_start: 0.8415 (ttm110) cc_final: 0.7684 (ttm110) REVERT: A 159 MET cc_start: 0.7739 (mtp) cc_final: 0.7100 (mtp) REVERT: A 175 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8704 (mm-30) REVERT: A 214 ASP cc_start: 0.8409 (t0) cc_final: 0.7933 (t0) REVERT: A 254 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7477 (mmtp) REVERT: A 275 HIS cc_start: 0.8448 (t-90) cc_final: 0.8162 (t-90) REVERT: A 284 ASP cc_start: 0.7844 (p0) cc_final: 0.7557 (p0) REVERT: A 287 GLU cc_start: 0.7188 (mp0) cc_final: 0.6813 (mp0) REVERT: A 293 ARG cc_start: 0.7789 (mtm180) cc_final: 0.7368 (mtp-110) REVERT: A 349 PHE cc_start: 0.9174 (p90) cc_final: 0.8889 (p90) REVERT: A 421 CYS cc_start: 0.4490 (m) cc_final: 0.3623 (m) REVERT: A 425 GLU cc_start: 0.7820 (tt0) cc_final: 0.7529 (tt0) REVERT: B 119 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7441 (mm-30) REVERT: B 142 ASP cc_start: 0.8451 (t0) cc_final: 0.8217 (t70) REVERT: B 155 TYR cc_start: 0.8523 (m-80) cc_final: 0.8060 (m-80) REVERT: B 156 ARG cc_start: 0.8412 (ttm110) cc_final: 0.7816 (ttm170) REVERT: B 159 MET cc_start: 0.7741 (mtp) cc_final: 0.7105 (mtp) REVERT: B 214 ASP cc_start: 0.8401 (t0) cc_final: 0.7878 (t0) REVERT: B 254 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7491 (mmtp) REVERT: B 260 LYS cc_start: 0.9275 (pttm) cc_final: 0.8778 (pptt) REVERT: B 262 LYS cc_start: 0.8969 (ttpp) cc_final: 0.8343 (ttpp) REVERT: B 275 HIS cc_start: 0.8480 (t-90) cc_final: 0.8194 (t-90) REVERT: B 287 GLU cc_start: 0.7242 (mp0) cc_final: 0.6840 (mp0) REVERT: B 301 ARG cc_start: 0.8267 (tpp80) cc_final: 0.7594 (mmm-85) REVERT: B 384 ASP cc_start: 0.8073 (t0) cc_final: 0.7136 (t0) REVERT: B 411 GLU cc_start: 0.8089 (mp0) cc_final: 0.7768 (mp0) REVERT: B 421 CYS cc_start: 0.4618 (m) cc_final: 0.3761 (m) REVERT: B 425 GLU cc_start: 0.7755 (tt0) cc_final: 0.7525 (tt0) REVERT: C 85 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8793 (mm) REVERT: C 119 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7419 (mm-30) REVERT: C 155 TYR cc_start: 0.8519 (m-80) cc_final: 0.8049 (m-80) REVERT: C 156 ARG cc_start: 0.8438 (ttm110) cc_final: 0.7831 (ttm170) REVERT: C 159 MET cc_start: 0.7726 (mtp) cc_final: 0.7103 (mtp) REVERT: C 214 ASP cc_start: 0.8411 (t0) cc_final: 0.7892 (t0) REVERT: C 254 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7487 (mmtp) REVERT: C 260 LYS cc_start: 0.9280 (pttm) cc_final: 0.8786 (pptt) REVERT: C 262 LYS cc_start: 0.8969 (ttpp) cc_final: 0.8347 (ttpp) REVERT: C 275 HIS cc_start: 0.8474 (t-90) cc_final: 0.8192 (t-90) REVERT: C 284 ASP cc_start: 0.7803 (p0) cc_final: 0.7558 (p0) REVERT: C 287 GLU cc_start: 0.7155 (mp0) cc_final: 0.6791 (mp0) REVERT: C 411 GLU cc_start: 0.8077 (mp0) cc_final: 0.7719 (mp0) REVERT: C 421 CYS cc_start: 0.4611 (m) cc_final: 0.3770 (m) REVERT: C 425 GLU cc_start: 0.7753 (tt0) cc_final: 0.7395 (tt0) REVERT: C 437 TRP cc_start: 0.8485 (p90) cc_final: 0.8231 (p90) REVERT: D 119 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7413 (mm-30) REVERT: D 155 TYR cc_start: 0.8521 (m-80) cc_final: 0.8068 (m-80) REVERT: D 156 ARG cc_start: 0.8441 (ttm110) cc_final: 0.7826 (ttm170) REVERT: D 159 MET cc_start: 0.7716 (mtp) cc_final: 0.7100 (mtp) REVERT: D 214 ASP cc_start: 0.8398 (t0) cc_final: 0.7874 (t0) REVERT: D 254 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7497 (mmtp) REVERT: D 260 LYS cc_start: 0.9286 (pttm) cc_final: 0.8788 (pptt) REVERT: D 262 LYS cc_start: 0.8960 (ttpp) cc_final: 0.8335 (ttpp) REVERT: D 275 HIS cc_start: 0.8458 (t-90) cc_final: 0.8186 (t-90) REVERT: D 284 ASP cc_start: 0.7778 (p0) cc_final: 0.7524 (p0) REVERT: D 287 GLU cc_start: 0.7148 (mp0) cc_final: 0.6786 (mp0) REVERT: D 301 ARG cc_start: 0.8276 (tpp80) cc_final: 0.7600 (mmm-85) REVERT: D 421 CYS cc_start: 0.4597 (m) cc_final: 0.3740 (m) REVERT: D 425 GLU cc_start: 0.7741 (tt0) cc_final: 0.7517 (tt0) outliers start: 77 outliers final: 37 residues processed: 486 average time/residue: 0.1043 time to fit residues: 74.6721 Evaluate side-chains 480 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 438 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 189 ASN Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 335 CYS Chi-restraints excluded: chain D residue 448 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 62 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN B 209 ASN C 209 ASN D 209 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.140374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.110297 restraints weight = 20155.849| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 4.92 r_work: 0.3260 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 12612 Z= 0.259 Angle : 0.660 5.959 17156 Z= 0.342 Chirality : 0.051 0.152 1816 Planarity : 0.004 0.048 2192 Dihedral : 5.717 22.822 2032 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 8.08 % Allowed : 26.57 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 are not related in a simple way. whole: -2.00 (0.22), residues: 1540 helix: -2.35 (0.91), residues: 24 sheet: -0.54 (0.24), residues: 556 loop : -1.87 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 301 TYR 0.016 0.002 TYR C 312 PHE 0.014 0.002 PHE C 349 TRP 0.033 0.002 TRP B 296 HIS 0.007 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.26 (12568) covalent geometry : angle 0.65117 / 0.34 (17056) SS BOND : bond 0.00725 / 0.42 ( 32) SS BOND : angle 1.56573 / 1.10 ( 64) hydrogen bonds : bond 0.02936 / 2.02 ( 300) hydrogen bonds : angle 6.67494 / 4.68 ( 732) link_NAG-ASN : bond 0.00262 / 0.18 ( 12) link_NAG-ASN : angle 1.50460 / 0.89 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 441 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8730 (mm) REVERT: A 155 TYR cc_start: 0.8828 (m-80) cc_final: 0.8310 (m-80) REVERT: A 159 MET cc_start: 0.8384 (mtp) cc_final: 0.7975 (mtp) REVERT: A 214 ASP cc_start: 0.8506 (t0) cc_final: 0.8046 (t0) REVERT: A 253 TYR cc_start: 0.8694 (OUTLIER) cc_final: 0.8303 (m-80) REVERT: A 254 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7775 (mmtp) REVERT: A 270 LYS cc_start: 0.9118 (mmmm) cc_final: 0.8698 (tptp) REVERT: A 275 HIS cc_start: 0.8929 (t-90) cc_final: 0.8614 (t-90) REVERT: A 284 ASP cc_start: 0.7871 (p0) cc_final: 0.7648 (p0) REVERT: A 287 GLU cc_start: 0.7613 (mp0) cc_final: 0.7188 (mp0) REVERT: A 293 ARG cc_start: 0.8373 (mtm180) cc_final: 0.8073 (mtp-110) REVERT: A 301 ARG cc_start: 0.8789 (mmm-85) cc_final: 0.8413 (mmm-85) REVERT: A 411 GLU cc_start: 0.8450 (mp0) cc_final: 0.7665 (mp0) REVERT: A 425 GLU cc_start: 0.8619 (tt0) cc_final: 0.8167 (tt0) REVERT: B 119 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7856 (mm-30) REVERT: B 142 ASP cc_start: 0.8632 (t0) cc_final: 0.8355 (t0) REVERT: B 155 TYR cc_start: 0.8862 (m-80) cc_final: 0.8347 (m-80) REVERT: B 159 MET cc_start: 0.8361 (mtp) cc_final: 0.7917 (mtp) REVERT: B 214 ASP cc_start: 0.8608 (t0) cc_final: 0.8088 (t0) REVERT: B 253 TYR cc_start: 0.8637 (OUTLIER) cc_final: 0.8289 (m-80) REVERT: B 254 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7802 (mmtp) REVERT: B 259 GLU cc_start: 0.9026 (pm20) cc_final: 0.8724 (pm20) REVERT: B 260 LYS cc_start: 0.9418 (pttm) cc_final: 0.9192 (mmmt) REVERT: B 270 LYS cc_start: 0.9120 (mmmm) cc_final: 0.8687 (tptp) REVERT: B 275 HIS cc_start: 0.8935 (t-90) cc_final: 0.8609 (t-90) REVERT: B 287 GLU cc_start: 0.7679 (mp0) cc_final: 0.7210 (mp0) REVERT: B 293 ARG cc_start: 0.8301 (mtm180) cc_final: 0.7648 (mtp85) REVERT: B 301 ARG cc_start: 0.8636 (tpp80) cc_final: 0.8006 (mmm-85) REVERT: B 318 CYS cc_start: 0.7354 (m) cc_final: 0.6919 (t) REVERT: C 119 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7877 (mm-30) REVERT: C 142 ASP cc_start: 0.8716 (t0) cc_final: 0.8508 (t0) REVERT: C 155 TYR cc_start: 0.8834 (m-80) cc_final: 0.8329 (m-80) REVERT: C 159 MET cc_start: 0.8397 (mtp) cc_final: 0.7994 (mtp) REVERT: C 214 ASP cc_start: 0.8601 (t0) cc_final: 0.8083 (t0) REVERT: C 253 TYR cc_start: 0.8674 (OUTLIER) cc_final: 0.8319 (m-80) REVERT: C 254 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7796 (mmtp) REVERT: C 259 GLU cc_start: 0.9040 (pm20) cc_final: 0.8771 (pm20) REVERT: C 260 LYS cc_start: 0.9428 (pttm) cc_final: 0.9207 (mmmt) REVERT: C 270 LYS cc_start: 0.9142 (mmmm) cc_final: 0.8695 (tptp) REVERT: C 275 HIS cc_start: 0.8929 (t-90) cc_final: 0.8614 (t-90) REVERT: C 284 ASP cc_start: 0.7769 (p0) cc_final: 0.7562 (p0) REVERT: C 287 GLU cc_start: 0.7552 (mp0) cc_final: 0.7186 (mp0) REVERT: C 411 GLU cc_start: 0.8321 (mp0) cc_final: 0.8118 (mp0) REVERT: D 85 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8621 (mm) REVERT: D 119 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7899 (mm-30) REVERT: D 142 ASP cc_start: 0.8704 (t0) cc_final: 0.8445 (t0) REVERT: D 155 TYR cc_start: 0.8835 (m-80) cc_final: 0.8336 (m-80) REVERT: D 159 MET cc_start: 0.8403 (mtp) cc_final: 0.8026 (mtp) REVERT: D 214 ASP cc_start: 0.8613 (t0) cc_final: 0.8096 (t0) REVERT: D 253 TYR cc_start: 0.8678 (OUTLIER) cc_final: 0.8328 (m-80) REVERT: D 254 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7816 (mmtp) REVERT: D 259 GLU cc_start: 0.9035 (pm20) cc_final: 0.8744 (pm20) REVERT: D 260 LYS cc_start: 0.9418 (pttm) cc_final: 0.9189 (mmmt) REVERT: D 270 LYS cc_start: 0.9126 (mmmm) cc_final: 0.8688 (tptp) REVERT: D 275 HIS cc_start: 0.8933 (t-90) cc_final: 0.8622 (t-90) REVERT: D 284 ASP cc_start: 0.7794 (p0) cc_final: 0.7590 (p0) REVERT: D 287 GLU cc_start: 0.7561 (mp0) cc_final: 0.7194 (mp0) REVERT: D 301 ARG cc_start: 0.8660 (tpp80) cc_final: 0.8041 (mmm-85) REVERT: D 318 CYS cc_start: 0.7437 (m) cc_final: 0.6974 (t) REVERT: D 411 GLU cc_start: 0.8356 (mp0) cc_final: 0.7518 (mp0) outliers start: 108 outliers final: 59 residues processed: 493 average time/residue: 0.1001 time to fit residues: 71.8406 Evaluate side-chains 486 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 417 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 253 TYR Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 253 TYR Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 446 CYS Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 189 ASN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 253 TYR Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 446 CYS Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 253 TYR Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 335 CYS Chi-restraints excluded: chain D residue 413 THR Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 448 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 73 optimal weight: 0.8980 chunk 150 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 143 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN B 209 ASN C 209 ASN D 209 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.142896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.112027 restraints weight = 19721.241| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 5.06 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12612 Z= 0.129 Angle : 0.629 6.513 17156 Z= 0.323 Chirality : 0.050 0.146 1816 Planarity : 0.004 0.036 2192 Dihedral : 5.555 22.406 2032 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 7.49 % Allowed : 27.84 % Favored : 64.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 are not related in a simple way. whole: -1.87 (0.22), residues: 1540 helix: -2.16 (0.97), residues: 24 sheet: -0.42 (0.24), residues: 564 loop : -1.81 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 156 TYR 0.014 0.001 TYR C 312 PHE 0.013 0.001 PHE C 349 TRP 0.025 0.001 TRP B 296 HIS 0.004 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (12568) covalent geometry : angle 0.62309 / 0.32 (17056) SS BOND : bond 0.00709 / 0.44 ( 32) SS BOND : angle 1.30705 / 0.91 ( 64) hydrogen bonds : bond 0.02405 / 1.63 ( 300) hydrogen bonds : angle 6.45477 / 4.51 ( 732) link_NAG-ASN : bond 0.00207 / 0.14 ( 12) link_NAG-ASN : angle 1.21298 / 0.72 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 471 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 TYR cc_start: 0.8574 (m-80) cc_final: 0.7915 (m-80) REVERT: A 156 ARG cc_start: 0.8297 (ttm110) cc_final: 0.7392 (ttp-110) REVERT: A 159 MET cc_start: 0.7703 (mtp) cc_final: 0.6998 (mtp) REVERT: A 175 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8794 (mm-30) REVERT: A 254 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7386 (mmtp) REVERT: A 270 LYS cc_start: 0.9079 (mmmm) cc_final: 0.8637 (tptp) REVERT: A 275 HIS cc_start: 0.8501 (t-90) cc_final: 0.8289 (t-90) REVERT: A 287 GLU cc_start: 0.7235 (mp0) cc_final: 0.6857 (mp0) REVERT: A 293 ARG cc_start: 0.7917 (mtm180) cc_final: 0.7181 (mtp85) REVERT: A 301 ARG cc_start: 0.8396 (mmm-85) cc_final: 0.8013 (mmm-85) REVERT: A 411 GLU cc_start: 0.8152 (mp0) cc_final: 0.7820 (mp0) REVERT: A 421 CYS cc_start: 0.4031 (m) cc_final: 0.3472 (m) REVERT: A 425 GLU cc_start: 0.7723 (tt0) cc_final: 0.7424 (tt0) REVERT: B 142 ASP cc_start: 0.8492 (t0) cc_final: 0.8166 (t0) REVERT: B 156 ARG cc_start: 0.8313 (ttm110) cc_final: 0.7411 (ttp-110) REVERT: B 159 MET cc_start: 0.7686 (mtp) cc_final: 0.7002 (mtp) REVERT: B 175 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8740 (mm-30) REVERT: B 189 ASN cc_start: 0.8297 (OUTLIER) cc_final: 0.8054 (m-40) REVERT: B 209 ASN cc_start: 0.8673 (OUTLIER) cc_final: 0.8211 (m-40) REVERT: B 214 ASP cc_start: 0.8477 (t0) cc_final: 0.7959 (t0) REVERT: B 254 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7382 (mmtp) REVERT: B 262 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8467 (ptpp) REVERT: B 270 LYS cc_start: 0.9042 (mmmm) cc_final: 0.8607 (tptp) REVERT: B 287 GLU cc_start: 0.7311 (mp0) cc_final: 0.6902 (mp0) REVERT: B 294 ASP cc_start: 0.8270 (t70) cc_final: 0.7463 (p0) REVERT: B 296 TRP cc_start: 0.8216 (t60) cc_final: 0.7966 (t60) REVERT: B 301 ARG cc_start: 0.8172 (tpp80) cc_final: 0.7626 (mmm-85) REVERT: B 384 ASP cc_start: 0.8280 (t0) cc_final: 0.7415 (t70) REVERT: B 421 CYS cc_start: 0.4094 (m) cc_final: 0.3548 (m) REVERT: B 425 GLU cc_start: 0.7862 (tt0) cc_final: 0.7492 (tt0) REVERT: C 142 ASP cc_start: 0.8525 (t0) cc_final: 0.8232 (t0) REVERT: C 155 TYR cc_start: 0.8557 (m-80) cc_final: 0.7874 (m-80) REVERT: C 156 ARG cc_start: 0.8530 (ttm110) cc_final: 0.8004 (ttm170) REVERT: C 159 MET cc_start: 0.7680 (mtp) cc_final: 0.7013 (mtp) REVERT: C 175 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8749 (mm-30) REVERT: C 189 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7978 (m-40) REVERT: C 209 ASN cc_start: 0.8639 (OUTLIER) cc_final: 0.8201 (m-40) REVERT: C 214 ASP cc_start: 0.8501 (t0) cc_final: 0.7961 (t0) REVERT: C 254 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7375 (mmtp) REVERT: C 262 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8433 (ptpp) REVERT: C 270 LYS cc_start: 0.9055 (mmmm) cc_final: 0.8614 (tptp) REVERT: C 287 GLU cc_start: 0.7226 (mp0) cc_final: 0.6887 (mp0) REVERT: C 293 ARG cc_start: 0.7909 (mtm180) cc_final: 0.7360 (mtp85) REVERT: C 294 ASP cc_start: 0.8268 (t70) cc_final: 0.7323 (p0) REVERT: C 296 TRP cc_start: 0.8260 (t60) cc_final: 0.7983 (t60) REVERT: C 384 ASP cc_start: 0.8214 (t0) cc_final: 0.7727 (t70) REVERT: C 421 CYS cc_start: 0.4071 (m) cc_final: 0.3502 (m) REVERT: C 425 GLU cc_start: 0.7795 (tt0) cc_final: 0.7441 (tt0) REVERT: D 142 ASP cc_start: 0.8594 (t0) cc_final: 0.8338 (t0) REVERT: D 156 ARG cc_start: 0.8546 (ttm110) cc_final: 0.8026 (ttm170) REVERT: D 159 MET cc_start: 0.7696 (mtp) cc_final: 0.7021 (mtp) REVERT: D 175 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8760 (mm-30) REVERT: D 189 ASN cc_start: 0.8211 (OUTLIER) cc_final: 0.7991 (m-40) REVERT: D 209 ASN cc_start: 0.8656 (OUTLIER) cc_final: 0.8185 (m-40) REVERT: D 214 ASP cc_start: 0.8415 (t0) cc_final: 0.7916 (t0) REVERT: D 254 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7403 (mmtp) REVERT: D 262 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8438 (ptpp) REVERT: D 270 LYS cc_start: 0.9086 (mmmm) cc_final: 0.8634 (tptp) REVERT: D 287 GLU cc_start: 0.7130 (mp0) cc_final: 0.6825 (mp0) REVERT: D 293 ARG cc_start: 0.7845 (mtm180) cc_final: 0.7225 (mtp85) REVERT: D 301 ARG cc_start: 0.8209 (tpp80) cc_final: 0.7542 (mmm-85) REVERT: D 318 CYS cc_start: 0.7044 (m) cc_final: 0.6341 (t) REVERT: D 384 ASP cc_start: 0.8222 (t0) cc_final: 0.7374 (t0) REVERT: D 421 CYS cc_start: 0.4119 (m) cc_final: 0.3531 (m) REVERT: D 425 GLU cc_start: 0.7815 (tt0) cc_final: 0.7450 (tt0) outliers start: 100 outliers final: 49 residues processed: 505 average time/residue: 0.0915 time to fit residues: 67.6025 Evaluate side-chains 510 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 448 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 189 ASN Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 209 ASN Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 335 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 21 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 0.0980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN B 209 ASN C 209 ASN D 209 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.141446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.110529 restraints weight = 19677.282| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 4.96 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12612 Z= 0.190 Angle : 0.685 6.469 17156 Z= 0.354 Chirality : 0.051 0.147 1816 Planarity : 0.004 0.031 2192 Dihedral : 5.584 22.079 2032 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 7.04 % Allowed : 30.84 % Favored : 62.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 are not related in a simple way. whole: -1.94 (0.21), residues: 1540 helix: -2.09 (0.96), residues: 24 sheet: -0.44 (0.24), residues: 564 loop : -1.88 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 156 TYR 0.017 0.002 TYR B 208 PHE 0.016 0.002 PHE B 174 TRP 0.043 0.002 TRP A 296 HIS 0.012 0.002 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (12568) covalent geometry : angle 0.67471 / 0.35 (17056) SS BOND : bond 0.00541 / 0.30 ( 32) SS BOND : angle 1.90338 / 1.36 ( 64) hydrogen bonds : bond 0.02656 / 1.81 ( 300) hydrogen bonds : angle 6.36123 / 4.45 ( 732) link_NAG-ASN : bond 0.00192 / 0.13 ( 12) link_NAG-ASN : angle 1.28348 / 0.77 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 458 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 TYR cc_start: 0.8625 (m-80) cc_final: 0.7979 (m-80) REVERT: A 156 ARG cc_start: 0.8345 (ttm110) cc_final: 0.7408 (ttp-110) REVERT: A 159 MET cc_start: 0.7702 (mtp) cc_final: 0.7071 (mtp) REVERT: A 175 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8853 (mm-30) REVERT: A 254 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7451 (mmtp) REVERT: A 270 LYS cc_start: 0.9075 (mmmm) cc_final: 0.8585 (tptp) REVERT: A 275 HIS cc_start: 0.8520 (t-90) cc_final: 0.8254 (t-90) REVERT: A 284 ASP cc_start: 0.7823 (p0) cc_final: 0.7536 (p0) REVERT: A 287 GLU cc_start: 0.7337 (mp0) cc_final: 0.6891 (mp0) REVERT: A 293 ARG cc_start: 0.7983 (mtm180) cc_final: 0.7236 (mtp85) REVERT: A 296 TRP cc_start: 0.8443 (t60) cc_final: 0.8230 (t60) REVERT: A 301 ARG cc_start: 0.8450 (mmm-85) cc_final: 0.8049 (mmm-85) REVERT: A 425 GLU cc_start: 0.7799 (tt0) cc_final: 0.7477 (tt0) REVERT: A 446 CYS cc_start: 0.5259 (m) cc_final: 0.4790 (m) REVERT: B 142 ASP cc_start: 0.8569 (t0) cc_final: 0.8316 (t0) REVERT: B 159 MET cc_start: 0.7655 (mtp) cc_final: 0.7016 (mtp) REVERT: B 175 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8838 (mm-30) REVERT: B 189 ASN cc_start: 0.8340 (OUTLIER) cc_final: 0.8111 (m-40) REVERT: B 209 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8217 (m110) REVERT: B 214 ASP cc_start: 0.8560 (t0) cc_final: 0.8060 (t0) REVERT: B 254 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7441 (mmtp) REVERT: B 270 LYS cc_start: 0.8973 (mmmm) cc_final: 0.8524 (tptp) REVERT: B 287 GLU cc_start: 0.7352 (mp0) cc_final: 0.6934 (mp0) REVERT: B 301 ARG cc_start: 0.8260 (tpp80) cc_final: 0.7614 (mmm-85) REVERT: B 425 GLU cc_start: 0.7782 (tt0) cc_final: 0.7438 (tt0) REVERT: B 446 CYS cc_start: 0.5239 (m) cc_final: 0.4760 (m) REVERT: C 159 MET cc_start: 0.7701 (mtp) cc_final: 0.7064 (mtp) REVERT: C 175 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8824 (mm-30) REVERT: C 189 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.8088 (m-40) REVERT: C 209 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8176 (m110) REVERT: C 214 ASP cc_start: 0.8554 (t0) cc_final: 0.8055 (t0) REVERT: C 254 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7423 (mmtp) REVERT: C 270 LYS cc_start: 0.8991 (mmmm) cc_final: 0.8536 (tptp) REVERT: C 284 ASP cc_start: 0.7759 (p0) cc_final: 0.7282 (p0) REVERT: C 287 GLU cc_start: 0.7395 (mp0) cc_final: 0.6827 (mp0) REVERT: C 425 GLU cc_start: 0.7768 (tt0) cc_final: 0.7487 (tt0) REVERT: C 446 CYS cc_start: 0.5292 (m) cc_final: 0.4841 (m) REVERT: D 159 MET cc_start: 0.7716 (mtp) cc_final: 0.7091 (mtp) REVERT: D 175 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8819 (mm-30) REVERT: D 209 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8202 (m110) REVERT: D 214 ASP cc_start: 0.8549 (t0) cc_final: 0.8047 (t0) REVERT: D 254 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7452 (mmtp) REVERT: D 260 LYS cc_start: 0.9062 (mmtt) cc_final: 0.8854 (mmmt) REVERT: D 270 LYS cc_start: 0.9016 (mmmm) cc_final: 0.8528 (tptp) REVERT: D 284 ASP cc_start: 0.7771 (p0) cc_final: 0.7323 (p0) REVERT: D 287 GLU cc_start: 0.7374 (mp0) cc_final: 0.6803 (mp0) REVERT: D 296 TRP cc_start: 0.8468 (t60) cc_final: 0.8219 (t60) REVERT: D 301 ARG cc_start: 0.8246 (tpp80) cc_final: 0.7591 (mmm-85) REVERT: D 411 GLU cc_start: 0.8178 (mp0) cc_final: 0.7755 (mp0) REVERT: D 425 GLU cc_start: 0.7758 (tt0) cc_final: 0.7419 (tt0) REVERT: D 446 CYS cc_start: 0.5279 (m) cc_final: 0.4821 (m) outliers start: 94 outliers final: 57 residues processed: 494 average time/residue: 0.1055 time to fit residues: 75.6340 Evaluate side-chains 517 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 451 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 189 ASN Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 209 ASN Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 316 TYR Chi-restraints excluded: chain D residue 335 CYS Chi-restraints excluded: chain D residue 413 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 56 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 134 optimal weight: 0.5980 chunk 151 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN B 144 HIS B 209 ASN C 209 ASN D 209 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.143696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.112319 restraints weight = 19612.141| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 5.08 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12612 Z= 0.145 Angle : 0.690 8.353 17156 Z= 0.357 Chirality : 0.050 0.145 1816 Planarity : 0.004 0.055 2192 Dihedral : 5.509 24.322 2032 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 5.91 % Allowed : 32.19 % Favored : 61.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 are not related in a simple way. whole: -2.04 (0.21), residues: 1540 helix: -3.27 (0.56), residues: 48 sheet: -0.31 (0.24), residues: 556 loop : -1.99 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 156 TYR 0.020 0.002 TYR B 208 PHE 0.013 0.001 PHE C 349 TRP 0.035 0.001 TRP D 296 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (12568) covalent geometry : angle 0.68262 / 0.35 (17056) SS BOND : bond 0.00676 / 0.41 ( 32) SS BOND : angle 1.66124 / 1.19 ( 64) hydrogen bonds : bond 0.02568 / 1.74 ( 300) hydrogen bonds : angle 6.31068 / 4.39 ( 732) link_NAG-ASN : bond 0.00190 / 0.12 ( 12) link_NAG-ASN : angle 1.17002 / 0.71 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 462 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8865 (mmmm) cc_final: 0.8594 (tmmt) REVERT: A 118 ARG cc_start: 0.7669 (ttt-90) cc_final: 0.6907 (tmt-80) REVERT: A 119 GLU cc_start: 0.7970 (mm-30) cc_final: 0.6194 (mm-30) REVERT: A 155 TYR cc_start: 0.8616 (m-80) cc_final: 0.7932 (m-80) REVERT: A 156 ARG cc_start: 0.8299 (ttm110) cc_final: 0.7376 (ttp-110) REVERT: A 175 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8794 (mm-30) REVERT: A 209 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8420 (t0) REVERT: A 214 ASP cc_start: 0.8538 (t0) cc_final: 0.8057 (t0) REVERT: A 254 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7419 (mmtp) REVERT: A 270 LYS cc_start: 0.9018 (mmmm) cc_final: 0.8530 (tptp) REVERT: A 284 ASP cc_start: 0.7830 (p0) cc_final: 0.7537 (p0) REVERT: A 287 GLU cc_start: 0.7246 (mp0) cc_final: 0.6902 (mp0) REVERT: A 293 ARG cc_start: 0.7970 (mtm180) cc_final: 0.7200 (mtp85) REVERT: A 301 ARG cc_start: 0.8380 (mmm-85) cc_final: 0.7983 (mmm-85) REVERT: A 311 GLU cc_start: 0.8439 (tp30) cc_final: 0.8183 (tp30) REVERT: A 384 ASP cc_start: 0.8194 (t0) cc_final: 0.7712 (t70) REVERT: A 421 CYS cc_start: 0.4200 (m) cc_final: 0.3720 (m) REVERT: A 425 GLU cc_start: 0.7831 (tt0) cc_final: 0.7487 (tt0) REVERT: B 142 ASP cc_start: 0.8529 (t0) cc_final: 0.8200 (t0) REVERT: B 155 TYR cc_start: 0.8608 (m-80) cc_final: 0.7903 (m-80) REVERT: B 175 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8777 (mm-30) REVERT: B 186 ASP cc_start: 0.8409 (p0) cc_final: 0.8186 (p0) REVERT: B 189 ASN cc_start: 0.8401 (m110) cc_final: 0.8128 (m-40) REVERT: B 209 ASN cc_start: 0.8519 (OUTLIER) cc_final: 0.8263 (m-40) REVERT: B 214 ASP cc_start: 0.8578 (t0) cc_final: 0.8047 (t0) REVERT: B 254 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7442 (mmtp) REVERT: B 270 LYS cc_start: 0.8988 (mmmm) cc_final: 0.8588 (tptp) REVERT: B 287 GLU cc_start: 0.7264 (mp0) cc_final: 0.6917 (mp0) REVERT: B 293 ARG cc_start: 0.7723 (mtm110) cc_final: 0.7401 (mtp85) REVERT: B 294 ASP cc_start: 0.8312 (t70) cc_final: 0.7492 (p0) REVERT: B 301 ARG cc_start: 0.8182 (tpp80) cc_final: 0.7582 (mmm-85) REVERT: B 311 GLU cc_start: 0.8414 (tp30) cc_final: 0.8165 (tp30) REVERT: B 384 ASP cc_start: 0.8315 (t0) cc_final: 0.7449 (t70) REVERT: B 421 CYS cc_start: 0.4301 (m) cc_final: 0.3823 (m) REVERT: B 425 GLU cc_start: 0.7788 (tt0) cc_final: 0.7501 (tt0) REVERT: C 155 TYR cc_start: 0.8605 (m-80) cc_final: 0.7904 (m-80) REVERT: C 175 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8760 (mm-30) REVERT: C 189 ASN cc_start: 0.8426 (m110) cc_final: 0.8106 (m-40) REVERT: C 209 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.8285 (m-40) REVERT: C 214 ASP cc_start: 0.8522 (t0) cc_final: 0.8018 (t0) REVERT: C 254 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7414 (mmtp) REVERT: C 270 LYS cc_start: 0.9007 (mmmm) cc_final: 0.8592 (tptp) REVERT: C 284 ASP cc_start: 0.7754 (p0) cc_final: 0.7283 (p0) REVERT: C 287 GLU cc_start: 0.7325 (mp0) cc_final: 0.6916 (mp0) REVERT: C 311 GLU cc_start: 0.8423 (tp30) cc_final: 0.8172 (tp30) REVERT: C 373 MET cc_start: 0.7976 (mmm) cc_final: 0.7748 (mmm) REVERT: C 384 ASP cc_start: 0.8256 (t0) cc_final: 0.7787 (t70) REVERT: C 421 CYS cc_start: 0.4420 (m) cc_final: 0.3970 (m) REVERT: C 425 GLU cc_start: 0.7786 (tt0) cc_final: 0.7472 (tt0) REVERT: D 155 TYR cc_start: 0.8603 (m-80) cc_final: 0.7904 (m-80) REVERT: D 175 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8769 (mm-30) REVERT: D 214 ASP cc_start: 0.8560 (t0) cc_final: 0.8057 (t0) REVERT: D 254 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7452 (mmtm) REVERT: D 260 LYS cc_start: 0.9096 (mmtt) cc_final: 0.8786 (mmmt) REVERT: D 270 LYS cc_start: 0.9028 (mmmm) cc_final: 0.8590 (tptp) REVERT: D 293 ARG cc_start: 0.7689 (mtm110) cc_final: 0.7249 (mtp85) REVERT: D 301 ARG cc_start: 0.8115 (tpp80) cc_final: 0.7537 (mmm-85) REVERT: D 311 GLU cc_start: 0.8413 (tp30) cc_final: 0.8172 (tp30) REVERT: D 384 ASP cc_start: 0.8266 (t0) cc_final: 0.7797 (t70) REVERT: D 421 CYS cc_start: 0.4395 (m) cc_final: 0.4112 (m) REVERT: D 425 GLU cc_start: 0.7790 (tt0) cc_final: 0.7481 (tt0) outliers start: 79 outliers final: 59 residues processed: 496 average time/residue: 0.1073 time to fit residues: 77.6510 Evaluate side-chains 506 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 440 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 316 TYR Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 209 ASN Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 253 TYR Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 316 TYR Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 253 TYR Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 335 CYS Chi-restraints excluded: chain D residue 413 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 136 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.145003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.113577 restraints weight = 19672.183| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 5.09 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12612 Z= 0.146 Angle : 0.732 9.431 17156 Z= 0.376 Chirality : 0.051 0.150 1816 Planarity : 0.004 0.047 2192 Dihedral : 5.439 30.323 2032 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 5.39 % Allowed : 33.91 % Favored : 60.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 are not related in a simple way. whole: -2.05 (0.21), residues: 1540 helix: -3.18 (0.58), residues: 48 sheet: -0.31 (0.24), residues: 556 loop : -2.03 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 156 TYR 0.021 0.002 TYR C 208 PHE 0.022 0.001 PHE C 422 TRP 0.035 0.001 TRP D 296 HIS 0.015 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (12568) covalent geometry : angle 0.72022 / 0.37 (17056) SS BOND : bond 0.00722 / 0.43 ( 32) SS BOND : angle 2.12002 / 1.56 ( 64) hydrogen bonds : bond 0.02584 / 1.72 ( 300) hydrogen bonds : angle 6.27051 / 4.36 ( 732) link_NAG-ASN : bond 0.00173 / 0.11 ( 12) link_NAG-ASN : angle 1.14979 / 0.70 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 449 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.8953 (mmmm) cc_final: 0.8633 (tmmt) REVERT: A 155 TYR cc_start: 0.8617 (m-80) cc_final: 0.7957 (m-80) REVERT: A 175 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8834 (mm-30) REVERT: A 254 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.7301 (mmtp) REVERT: A 270 LYS cc_start: 0.9009 (mmmm) cc_final: 0.8572 (tptp) REVERT: A 275 HIS cc_start: 0.8530 (t-90) cc_final: 0.8108 (t-90) REVERT: A 296 TRP cc_start: 0.8363 (t60) cc_final: 0.8087 (t60) REVERT: A 311 GLU cc_start: 0.8437 (tp30) cc_final: 0.8180 (tp30) REVERT: A 373 MET cc_start: 0.8060 (mmm) cc_final: 0.7779 (mmm) REVERT: A 425 GLU cc_start: 0.7808 (tt0) cc_final: 0.7398 (tt0) REVERT: B 118 ARG cc_start: 0.7627 (ttt-90) cc_final: 0.6862 (tmt-80) REVERT: B 142 ASP cc_start: 0.8510 (t0) cc_final: 0.8259 (t0) REVERT: B 150 LYS cc_start: 0.8781 (tptp) cc_final: 0.8535 (tptp) REVERT: B 155 TYR cc_start: 0.8586 (m-80) cc_final: 0.7958 (m-80) REVERT: B 159 MET cc_start: 0.7689 (mtp) cc_final: 0.7065 (mtp) REVERT: B 175 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8820 (mm-30) REVERT: B 189 ASN cc_start: 0.8486 (m110) cc_final: 0.8170 (m-40) REVERT: B 209 ASN cc_start: 0.8525 (m-40) cc_final: 0.8167 (m-40) REVERT: B 214 ASP cc_start: 0.8521 (t0) cc_final: 0.8026 (t0) REVERT: B 254 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7458 (mmtm) REVERT: B 270 LYS cc_start: 0.8991 (mmmm) cc_final: 0.8564 (tptp) REVERT: B 293 ARG cc_start: 0.7647 (mtm110) cc_final: 0.7201 (mtp85) REVERT: B 311 GLU cc_start: 0.8428 (tp30) cc_final: 0.8169 (tp30) REVERT: B 373 MET cc_start: 0.7996 (mmm) cc_final: 0.7782 (mmm) REVERT: B 425 GLU cc_start: 0.7778 (tt0) cc_final: 0.7421 (tt0) REVERT: C 155 TYR cc_start: 0.8592 (m-80) cc_final: 0.7911 (m-80) REVERT: C 159 MET cc_start: 0.7713 (mtp) cc_final: 0.7158 (mtp) REVERT: C 189 ASN cc_start: 0.8530 (m110) cc_final: 0.8219 (m-40) REVERT: C 209 ASN cc_start: 0.8516 (m-40) cc_final: 0.8158 (m-40) REVERT: C 214 ASP cc_start: 0.8526 (t0) cc_final: 0.8027 (t0) REVERT: C 254 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7430 (mmtm) REVERT: C 270 LYS cc_start: 0.9000 (mmmm) cc_final: 0.8574 (tptp) REVERT: C 284 ASP cc_start: 0.7622 (p0) cc_final: 0.7154 (p0) REVERT: C 287 GLU cc_start: 0.7273 (mp0) cc_final: 0.6845 (mp0) REVERT: C 311 GLU cc_start: 0.8404 (tp30) cc_final: 0.8129 (tp30) REVERT: C 373 MET cc_start: 0.8016 (mmm) cc_final: 0.7814 (mmm) REVERT: C 411 GLU cc_start: 0.8123 (mp0) cc_final: 0.7792 (mp0) REVERT: C 425 GLU cc_start: 0.7692 (tt0) cc_final: 0.7365 (tt0) REVERT: D 118 ARG cc_start: 0.7524 (ttt-90) cc_final: 0.6791 (tmt-80) REVERT: D 155 TYR cc_start: 0.8591 (m-80) cc_final: 0.7917 (m-80) REVERT: D 175 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8782 (mm-30) REVERT: D 186 ASP cc_start: 0.8502 (p0) cc_final: 0.8299 (p0) REVERT: D 214 ASP cc_start: 0.8508 (t0) cc_final: 0.8012 (t0) REVERT: D 254 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.7357 (mmtm) REVERT: D 260 LYS cc_start: 0.9159 (mmtt) cc_final: 0.8794 (mmmt) REVERT: D 270 LYS cc_start: 0.9021 (mmmm) cc_final: 0.8572 (tptp) REVERT: D 294 ASP cc_start: 0.8215 (t70) cc_final: 0.7525 (p0) REVERT: D 296 TRP cc_start: 0.8250 (t60) cc_final: 0.7919 (t60) REVERT: D 311 GLU cc_start: 0.8425 (tp30) cc_final: 0.8163 (tp30) REVERT: D 373 MET cc_start: 0.7986 (mmm) cc_final: 0.7743 (mmm) REVERT: D 425 GLU cc_start: 0.7823 (tt0) cc_final: 0.7450 (tt0) outliers start: 72 outliers final: 60 residues processed: 479 average time/residue: 0.1084 time to fit residues: 75.7172 Evaluate side-chains 506 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 442 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 253 TYR Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 316 TYR Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 253 TYR Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 253 TYR Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 316 TYR Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 253 TYR Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 335 CYS Chi-restraints excluded: chain D residue 413 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 62 optimal weight: 0.8980 chunk 1 optimal weight: 0.4980 chunk 28 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 122 optimal weight: 0.0170 chunk 143 optimal weight: 0.7980 chunk 80 optimal weight: 0.0570 chunk 34 optimal weight: 0.9990 chunk 46 optimal weight: 0.0770 overall best weight: 0.2894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS A 209 ASN ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 ASN C 209 ASN ** D 297 HIS ** 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 = 0.3899 r_free = 0.3899 target = 0.146609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.116055 restraints weight = 19401.373| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 5.03 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12612 Z= 0.134 Angle : 0.718 8.483 17156 Z= 0.369 Chirality : 0.050 0.146 1816 Planarity : 0.005 0.052 2192 Dihedral : 5.228 28.667 2032 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 5.01 % Allowed : 33.91 % Favored : 61.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 are not related in a simple way. whole: -1.85 (0.21), residues: 1540 helix: -2.95 (0.62), residues: 48 sheet: -0.25 (0.23), residues: 580 loop : -1.87 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 301 TYR 0.017 0.001 TYR A 208 PHE 0.029 0.002 PHE D 422 TRP 0.033 0.001 TRP D 296 HIS 0.013 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (12568) covalent geometry : angle 0.71306 / 0.37 (17056) SS BOND : bond 0.00607 / 0.30 ( 32) SS BOND : angle 1.47319 / 1.05 ( 64) hydrogen bonds : bond 0.02215 / 1.52 ( 300) hydrogen bonds : angle 6.10805 / 4.26 ( 732) link_NAG-ASN : bond 0.00191 / 0.12 ( 12) link_NAG-ASN : angle 1.06396 / 0.66 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 464 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.9010 (mmmm) cc_final: 0.8673 (tmmt) REVERT: A 118 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.6873 (tmt-80) REVERT: A 155 TYR cc_start: 0.8568 (m-80) cc_final: 0.7997 (m-80) REVERT: A 214 ASP cc_start: 0.8550 (t0) cc_final: 0.8051 (t0) REVERT: A 227 GLN cc_start: 0.8537 (tt0) cc_final: 0.8279 (tt0) REVERT: A 254 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.7259 (mmtp) REVERT: A 270 LYS cc_start: 0.8985 (mmmm) cc_final: 0.8522 (tptp) REVERT: A 275 HIS cc_start: 0.8450 (t-90) cc_final: 0.7916 (t-90) REVERT: A 284 ASP cc_start: 0.7706 (p0) cc_final: 0.7175 (p0) REVERT: A 287 GLU cc_start: 0.7086 (mp0) cc_final: 0.6751 (mp0) REVERT: A 301 ARG cc_start: 0.8419 (mmm-85) cc_final: 0.7913 (mmm-85) REVERT: A 311 GLU cc_start: 0.8431 (tp30) cc_final: 0.8164 (tp30) REVERT: A 349 PHE cc_start: 0.9183 (p90) cc_final: 0.8753 (p90) REVERT: A 373 MET cc_start: 0.8130 (mmm) cc_final: 0.7863 (mmm) REVERT: A 425 GLU cc_start: 0.7704 (tt0) cc_final: 0.7270 (tt0) REVERT: A 432 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7826 (tt0) REVERT: B 118 ARG cc_start: 0.7516 (ttt-90) cc_final: 0.6757 (tmt-80) REVERT: B 142 ASP cc_start: 0.8509 (t0) cc_final: 0.8184 (t0) REVERT: B 155 TYR cc_start: 0.8540 (m-80) cc_final: 0.7972 (m-80) REVERT: B 189 ASN cc_start: 0.8544 (m110) cc_final: 0.8132 (m-40) REVERT: B 214 ASP cc_start: 0.8547 (t0) cc_final: 0.8021 (t0) REVERT: B 270 LYS cc_start: 0.8956 (mmmm) cc_final: 0.8500 (tptp) REVERT: B 275 HIS cc_start: 0.8460 (t-90) cc_final: 0.8156 (t-90) REVERT: B 293 ARG cc_start: 0.7454 (mtm110) cc_final: 0.7055 (mtp85) REVERT: B 294 ASP cc_start: 0.8171 (t70) cc_final: 0.7511 (p0) REVERT: B 301 ARG cc_start: 0.8254 (mmm-85) cc_final: 0.7472 (mmm-85) REVERT: B 311 GLU cc_start: 0.8411 (tp30) cc_final: 0.8135 (tp30) REVERT: B 373 MET cc_start: 0.8060 (mmm) cc_final: 0.7782 (mmm) REVERT: B 384 ASP cc_start: 0.8075 (t0) cc_final: 0.7215 (t0) REVERT: B 422 PHE cc_start: 0.8890 (p90) cc_final: 0.8595 (p90) REVERT: B 425 GLU cc_start: 0.7700 (tt0) cc_final: 0.7344 (tt0) REVERT: C 118 ARG cc_start: 0.7540 (ttt-90) cc_final: 0.6762 (tmt-80) REVERT: C 189 ASN cc_start: 0.8556 (m110) cc_final: 0.8145 (m-40) REVERT: C 214 ASP cc_start: 0.8493 (t0) cc_final: 0.7992 (t0) REVERT: C 270 LYS cc_start: 0.8959 (mmmm) cc_final: 0.8512 (tptp) REVERT: C 311 GLU cc_start: 0.8385 (tp30) cc_final: 0.8120 (tp30) REVERT: C 373 MET cc_start: 0.8063 (mmm) cc_final: 0.7856 (mmm) REVERT: C 384 ASP cc_start: 0.8089 (t0) cc_final: 0.7222 (t0) REVERT: C 425 GLU cc_start: 0.7688 (tt0) cc_final: 0.7323 (tt0) REVERT: D 118 ARG cc_start: 0.7498 (ttt-90) cc_final: 0.6746 (tmt-80) REVERT: D 214 ASP cc_start: 0.8494 (t0) cc_final: 0.7996 (t0) REVERT: D 259 GLU cc_start: 0.8585 (pm20) cc_final: 0.8301 (pm20) REVERT: D 260 LYS cc_start: 0.9151 (mmtt) cc_final: 0.8811 (mmmt) REVERT: D 270 LYS cc_start: 0.8943 (mmmm) cc_final: 0.8480 (tptp) REVERT: D 275 HIS cc_start: 0.8455 (t-90) cc_final: 0.8208 (t-90) REVERT: D 287 GLU cc_start: 0.7090 (mp0) cc_final: 0.6751 (mp0) REVERT: D 293 ARG cc_start: 0.7406 (mtm110) cc_final: 0.7054 (mtp85) REVERT: D 301 ARG cc_start: 0.8196 (mmm-85) cc_final: 0.7354 (mmm-85) REVERT: D 311 GLU cc_start: 0.8414 (tp30) cc_final: 0.8134 (tp30) REVERT: D 373 MET cc_start: 0.8064 (mmm) cc_final: 0.7818 (mmm) REVERT: D 384 ASP cc_start: 0.8056 (t0) cc_final: 0.7155 (t0) REVERT: D 425 GLU cc_start: 0.7639 (tt0) cc_final: 0.7284 (tt0) outliers start: 67 outliers final: 52 residues processed: 496 average time/residue: 0.0994 time to fit residues: 72.6984 Evaluate side-chains 493 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 439 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 253 TYR Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 316 TYR Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 253 TYR Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 253 TYR Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 316 TYR Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 335 CYS Chi-restraints excluded: chain D residue 413 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 126 optimal weight: 0.4980 chunk 23 optimal weight: 0.0370 chunk 42 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 HIS ** 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 = 0.3884 r_free = 0.3884 target = 0.145549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.114200 restraints weight = 19804.856| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 5.19 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12612 Z= 0.148 Angle : 0.754 8.543 17156 Z= 0.389 Chirality : 0.051 0.143 1816 Planarity : 0.005 0.050 2192 Dihedral : 5.236 29.177 2032 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.94 % Allowed : 35.63 % Favored : 59.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 are not related in a simple way. whole: -1.83 (0.21), residues: 1540 helix: -2.81 (0.61), residues: 48 sheet: -0.05 (0.23), residues: 564 loop : -1.98 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 301 TYR 0.020 0.001 TYR C 312 PHE 0.022 0.002 PHE D 349 TRP 0.080 0.002 TRP A 296 HIS 0.024 0.002 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (12568) covalent geometry : angle 0.74742 / 0.39 (17056) SS BOND : bond 0.00593 / 0.32 ( 32) SS BOND : angle 1.64125 / 1.20 ( 64) hydrogen bonds : bond 0.02458 / 1.70 ( 300) hydrogen bonds : angle 6.02243 / 4.17 ( 732) link_NAG-ASN : bond 0.00160 / 0.11 ( 12) link_NAG-ASN : angle 1.07610 / 0.66 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 449 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.9013 (mmmm) cc_final: 0.8673 (tmmt) REVERT: A 118 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.6869 (tmt-80) REVERT: A 175 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8831 (mm-30) REVERT: A 214 ASP cc_start: 0.8465 (t0) cc_final: 0.7979 (t0) REVERT: A 227 GLN cc_start: 0.8649 (tt0) cc_final: 0.8398 (tt0) REVERT: A 254 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.7282 (mmtp) REVERT: A 259 GLU cc_start: 0.8717 (pm20) cc_final: 0.8512 (pm20) REVERT: A 264 ILE cc_start: 0.9278 (tt) cc_final: 0.8812 (pt) REVERT: A 275 HIS cc_start: 0.8416 (t-90) cc_final: 0.8027 (t-90) REVERT: A 284 ASP cc_start: 0.7720 (p0) cc_final: 0.7227 (p0) REVERT: A 287 GLU cc_start: 0.7121 (mp0) cc_final: 0.6771 (mp0) REVERT: A 293 ARG cc_start: 0.7643 (mtp85) cc_final: 0.7205 (mtp85) REVERT: A 294 ASP cc_start: 0.8040 (t70) cc_final: 0.7759 (t0) REVERT: A 301 ARG cc_start: 0.8378 (mmm-85) cc_final: 0.7904 (mmm-85) REVERT: A 311 GLU cc_start: 0.8458 (tp30) cc_final: 0.8155 (tp30) REVERT: A 349 PHE cc_start: 0.9199 (p90) cc_final: 0.8817 (p90) REVERT: A 384 ASP cc_start: 0.8016 (t0) cc_final: 0.7146 (t0) REVERT: A 425 GLU cc_start: 0.7708 (tt0) cc_final: 0.7286 (tt0) REVERT: A 432 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7809 (tt0) REVERT: B 118 ARG cc_start: 0.7520 (ttt-90) cc_final: 0.6724 (tmt-80) REVERT: B 142 ASP cc_start: 0.8509 (t0) cc_final: 0.8199 (t0) REVERT: B 214 ASP cc_start: 0.8493 (t0) cc_final: 0.7992 (t0) REVERT: B 270 LYS cc_start: 0.8999 (mmmm) cc_final: 0.8467 (tptp) REVERT: B 296 TRP cc_start: 0.8389 (t60) cc_final: 0.8071 (t60) REVERT: B 301 ARG cc_start: 0.8268 (mmm-85) cc_final: 0.7440 (mmm-85) REVERT: B 311 GLU cc_start: 0.8413 (tp30) cc_final: 0.8127 (tp30) REVERT: B 373 MET cc_start: 0.8037 (mmm) cc_final: 0.7813 (mmm) REVERT: B 384 ASP cc_start: 0.8033 (t0) cc_final: 0.7124 (t0) REVERT: B 425 GLU cc_start: 0.7737 (tt0) cc_final: 0.7341 (tt0) REVERT: C 85 LEU cc_start: 0.8873 (mm) cc_final: 0.8403 (mm) REVERT: C 118 ARG cc_start: 0.7431 (ttt-90) cc_final: 0.6658 (tmt-80) REVERT: C 159 MET cc_start: 0.7721 (mtp) cc_final: 0.7105 (mtp) REVERT: C 214 ASP cc_start: 0.8466 (t0) cc_final: 0.7964 (t0) REVERT: C 228 GLU cc_start: 0.8370 (tt0) cc_final: 0.8060 (tt0) REVERT: C 270 LYS cc_start: 0.8977 (mmmm) cc_final: 0.8435 (tptp) REVERT: C 294 ASP cc_start: 0.8023 (t70) cc_final: 0.7414 (p0) REVERT: C 311 GLU cc_start: 0.8408 (tp30) cc_final: 0.8116 (tp30) REVERT: C 411 GLU cc_start: 0.8095 (mp0) cc_final: 0.7651 (mp0) REVERT: C 425 GLU cc_start: 0.7706 (tt0) cc_final: 0.7320 (tt0) REVERT: D 118 ARG cc_start: 0.7526 (ttt-90) cc_final: 0.6724 (tmt-80) REVERT: D 159 MET cc_start: 0.7782 (mtp) cc_final: 0.7150 (mtp) REVERT: D 228 GLU cc_start: 0.8369 (tt0) cc_final: 0.8066 (tt0) REVERT: D 259 GLU cc_start: 0.8583 (pm20) cc_final: 0.8378 (pm20) REVERT: D 260 LYS cc_start: 0.9173 (mmtt) cc_final: 0.8840 (mmmt) REVERT: D 270 LYS cc_start: 0.9002 (mmmm) cc_final: 0.8435 (tptp) REVERT: D 287 GLU cc_start: 0.7113 (mp0) cc_final: 0.6779 (mp0) REVERT: D 301 ARG cc_start: 0.8205 (mmm-85) cc_final: 0.7417 (mmm-85) REVERT: D 311 GLU cc_start: 0.8417 (tp30) cc_final: 0.8114 (tp30) REVERT: D 373 MET cc_start: 0.8098 (mmm) cc_final: 0.7868 (mmm) REVERT: D 425 GLU cc_start: 0.7687 (tt0) cc_final: 0.7313 (tt0) outliers start: 66 outliers final: 59 residues processed: 480 average time/residue: 0.1018 time to fit residues: 72.5904 Evaluate side-chains 509 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 448 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 253 TYR Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 316 TYR Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 253 TYR Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 316 TYR Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 253 TYR Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 316 TYR Chi-restraints excluded: chain D residue 335 CYS Chi-restraints excluded: chain D residue 413 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 86 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 57 optimal weight: 0.2980 chunk 82 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 HIS ** 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 = 0.3842 r_free = 0.3842 target = 0.142574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.111585 restraints weight = 19730.179| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 5.04 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12612 Z= 0.194 Angle : 0.799 13.042 17156 Z= 0.411 Chirality : 0.052 0.158 1816 Planarity : 0.005 0.053 2192 Dihedral : 5.429 31.079 2032 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 4.64 % Allowed : 36.00 % Favored : 59.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 are not related in a simple way. whole: -1.93 (0.20), residues: 1540 helix: -2.85 (0.57), residues: 48 sheet: -0.04 (0.23), residues: 532 loop : -2.05 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 293 TYR 0.022 0.002 TYR C 312 PHE 0.022 0.002 PHE D 349 TRP 0.075 0.002 TRP A 296 HIS 0.021 0.002 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (12568) covalent geometry : angle 0.78784 / 0.41 (17056) SS BOND : bond 0.00673 / 0.33 ( 32) SS BOND : angle 2.19624 / 1.56 ( 64) hydrogen bonds : bond 0.02690 / 1.87 ( 300) hydrogen bonds : angle 6.26171 / 4.33 ( 732) link_NAG-ASN : bond 0.00162 / 0.11 ( 12) link_NAG-ASN : angle 1.12048 / 0.68 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2432.83 seconds wall clock time: 42 minutes 42.43 seconds (2562.43 seconds total)