Starting phenix.real_space_refine on Fri Jul 3 07:05:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tq8_56127/07_2026/9tq8_56127.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tq8_56127/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9tq8_56127/07_2026/9tq8_56127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tq8_56127/07_2026/9tq8_56127.map" model { file = "/net/cci-nas-00/data/ceres_data/9tq8_56127/07_2026/9tq8_56127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tq8_56127/07_2026/9tq8_56127.cif" } 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-dev-6108/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, 65 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 3, 'ZMR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain breaks: 1 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: 2.22, per 1000 atoms: 0.18 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: 0.84 Conformation dependent library (CDL) restraints added in 457.1 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: 0.38 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: 1.67 Time building geometry restraints manager: 1.15 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: 0.03 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: 1.410 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.140 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.870 ------------------------------------------------------------------------------- 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 : 0.418 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: 0.7265 (mm-30) REVERT: A 156 ARG cc_start: 0.8420 (ttm110) cc_final: 0.7938 (ttm110) REVERT: A 159 MET cc_start: 0.8292 (mtp) cc_final: 0.7623 (mtp) REVERT: A 227 GLN cc_start: 0.8123 (tt0) cc_final: 0.7681 (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: 0.6626 (mtp85) REVERT: A 372 GLU cc_start: 0.7620 (pt0) cc_final: 0.6813 (tt0) REVERT: A 384 ASP cc_start: 0.7683 (t0) cc_final: 0.6910 (t0) REVERT: B 119 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7223 (mm-30) REVERT: B 142 ASP cc_start: 0.8259 (t70) cc_final: 0.8059 (t0) 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: 0.7503 (mtp) REVERT: B 227 GLN cc_start: 0.8129 (tt0) cc_final: 0.7677 (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: 0.7086 (mtp85) REVERT: B 372 GLU cc_start: 0.7568 (pt0) cc_final: 0.6805 (tt0) REVERT: B 384 ASP cc_start: 0.7880 (t0) cc_final: 0.7082 (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: 0.8121 (t0) REVERT: C 156 ARG cc_start: 0.8440 (ttm110) cc_final: 0.7976 (ttm110) REVERT: C 159 MET cc_start: 0.8223 (mtp) cc_final: 0.7539 (mtp) REVERT: C 227 GLN cc_start: 0.8150 (tt0) cc_final: 0.7703 (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: 0.7065 (mtp85) REVERT: C 372 GLU cc_start: 0.7569 (pt0) cc_final: 0.6817 (tt0) REVERT: C 384 ASP cc_start: 0.7860 (t0) cc_final: 0.7059 (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: 0.7521 (mtp) REVERT: D 227 GLN cc_start: 0.8148 (tt0) cc_final: 0.7700 (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: 0.7083 (mtp85) REVERT: D 372 GLU cc_start: 0.7590 (pt0) cc_final: 0.6809 (tt0) REVERT: D 384 ASP cc_start: 0.7855 (t0) cc_final: 0.7061 (t0) outliers start: 9 outliers final: 5 residues processed: 446 average time/residue: 0.0877 time to fit residues: 58.8025 Evaluate side-chains 430 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 425 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 = 0.3878 r_free = 0.3878 target = 0.142188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.111825 restraints weight = 20046.863| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 4.89 r_work: 0.3288 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12612 Z= 0.235 Angle : 0.654 7.641 17156 Z= 0.342 Chirality : 0.052 0.159 1816 Planarity : 0.004 0.042 2192 Dihedral : 5.766 39.978 2040 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 5.39 % Allowed : 24.70 % Favored : 69.91 % 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: -2.20 (0.22), residues: 1540 helix: -2.00 (0.95), residues: 24 sheet: -0.87 (0.25), residues: 560 loop : -1.88 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 301 TYR 0.015 0.002 TYR D 100 PHE 0.017 0.002 PHE A 406 TRP 0.011 0.001 TRP A 296 HIS 0.003 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.23 (12568) covalent geometry : angle 0.64773 / 0.34 (17056) SS BOND : bond 0.00516 / 0.29 ( 32) SS BOND : angle 1.36878 / 0.93 ( 64) hydrogen bonds : bond 0.03163 / 2.15 ( 300) hydrogen bonds : angle 7.23053 / 5.09 ( 732) link_NAG-ASN : bond 0.00265 / 0.18 ( 12) link_NAG-ASN : angle 1.37293 / 0.82 ( 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 514 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 442 time to evaluate : 0.401 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: 0.8107 (mm-30) cc_final: 0.7823 (mm-30) REVERT: A 142 ASP cc_start: 0.8418 (t0) cc_final: 0.8165 (t0) REVERT: A 155 TYR cc_start: 0.8694 (m-80) cc_final: 0.8391 (m-80) REVERT: A 156 ARG cc_start: 0.8635 (ttm110) cc_final: 0.8015 (ttm110) REVERT: A 159 MET cc_start: 0.8393 (mtp) cc_final: 0.7962 (mtp) REVERT: A 254 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7606 (mmtp) REVERT: A 275 HIS cc_start: 0.8854 (t-90) cc_final: 0.8500 (t-90) REVERT: A 287 GLU cc_start: 0.7543 (mp0) cc_final: 0.7078 (mp0) REVERT: A 411 GLU cc_start: 0.8396 (mp0) cc_final: 0.8086 (mp0) REVERT: A 421 CYS cc_start: 0.7195 (m) cc_final: 0.6855 (m) REVERT: B 119 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7837 (mm-30) REVERT: B 142 ASP cc_start: 0.8677 (t70) cc_final: 0.8265 (t0) REVERT: B 155 TYR cc_start: 0.8716 (m-80) cc_final: 0.8399 (m-80) REVERT: B 156 ARG cc_start: 0.8628 (ttm110) cc_final: 0.8021 (ttm110) REVERT: B 159 MET cc_start: 0.8377 (mtp) cc_final: 0.7961 (mtp) REVERT: B 254 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7611 (mmtp) REVERT: B 260 LYS cc_start: 0.9405 (pttm) cc_final: 0.9010 (pptt) REVERT: B 262 LYS cc_start: 0.9079 (ttpp) cc_final: 0.8368 (ttpp) REVERT: B 275 HIS cc_start: 0.8856 (t-90) cc_final: 0.8521 (t-90) REVERT: B 287 GLU cc_start: 0.7587 (mp0) cc_final: 0.7100 (mp0) REVERT: B 421 CYS cc_start: 0.7235 (m) cc_final: 0.6893 (m) REVERT: B 425 GLU cc_start: 0.8572 (tt0) cc_final: 0.8225 (tt0) REVERT: C 119 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7811 (mm-30) REVERT: C 142 ASP cc_start: 0.8619 (t70) cc_final: 0.8186 (t0) REVERT: C 155 TYR cc_start: 0.8707 (m-80) cc_final: 0.8395 (m-80) REVERT: C 156 ARG cc_start: 0.8628 (ttm110) cc_final: 0.8013 (ttm110) REVERT: C 159 MET cc_start: 0.8371 (mtp) cc_final: 0.7932 (mtp) REVERT: C 254 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7627 (mmtp) REVERT: C 260 LYS cc_start: 0.9397 (pttm) cc_final: 0.9000 (pptt) REVERT: C 262 LYS cc_start: 0.9081 (ttpp) cc_final: 0.8377 (ttpp) REVERT: C 275 HIS cc_start: 0.8841 (t-90) cc_final: 0.8520 (t-90) REVERT: C 287 GLU cc_start: 0.7571 (mp0) cc_final: 0.7095 (mp0) REVERT: C 421 CYS cc_start: 0.7248 (m) cc_final: 0.6930 (m) REVERT: C 425 GLU cc_start: 0.8566 (tt0) cc_final: 0.8210 (tt0) REVERT: C 437 TRP cc_start: 0.8710 (p90) cc_final: 0.8466 (p90) REVERT: D 119 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7836 (mm-30) REVERT: D 142 ASP cc_start: 0.8629 (t70) cc_final: 0.8195 (t0) REVERT: D 155 TYR cc_start: 0.8722 (m-80) cc_final: 0.8411 (m-80) REVERT: D 156 ARG cc_start: 0.8634 (ttm110) cc_final: 0.8027 (ttm110) REVERT: D 159 MET cc_start: 0.8405 (mtp) cc_final: 0.7971 (mtp) REVERT: D 254 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7629 (mmtp) REVERT: D 260 LYS cc_start: 0.9400 (pttm) cc_final: 0.9006 (pptt) REVERT: D 262 LYS cc_start: 0.9079 (ttpp) cc_final: 0.8371 (ttpp) REVERT: D 275 HIS cc_start: 0.8837 (t-90) cc_final: 0.8511 (t-90) REVERT: D 287 GLU cc_start: 0.7569 (mp0) cc_final: 0.7091 (mp0) REVERT: D 421 CYS cc_start: 0.7239 (m) cc_final: 0.6913 (m) REVERT: D 425 GLU cc_start: 0.8550 (tt0) cc_final: 0.8196 (tt0) outliers start: 72 outliers final: 43 residues processed: 480 average time/residue: 0.0925 time to fit residues: 64.5936 Evaluate side-chains 460 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 413 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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: 1.9990 chunk 58 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.142159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.111138 restraints weight = 20061.769| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 5.03 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 12612 Z= 0.166 Angle : 0.632 6.857 17156 Z= 0.324 Chirality : 0.051 0.150 1816 Planarity : 0.004 0.032 2192 Dihedral : 5.702 39.398 2038 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 5.69 % Allowed : 27.62 % Favored : 66.69 % 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: -2.03 (0.22), residues: 1540 helix: -2.05 (1.03), residues: 24 sheet: -0.76 (0.24), residues: 576 loop : -1.77 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 301 TYR 0.011 0.002 TYR C 100 PHE 0.012 0.001 PHE C 406 TRP 0.024 0.001 TRP B 296 HIS 0.008 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (12568) covalent geometry : angle 0.62624 / 0.32 (17056) SS BOND : bond 0.00558 / 0.33 ( 32) SS BOND : angle 1.32542 / 0.91 ( 64) hydrogen bonds : bond 0.02751 / 1.87 ( 300) hydrogen bonds : angle 6.76073 / 4.74 ( 732) link_NAG-ASN : bond 0.00184 / 0.12 ( 12) link_NAG-ASN : angle 1.27056 / 0.76 ( 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 508 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 432 time to evaluate : 0.315 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: 0.8510 (m-80) cc_final: 0.8041 (m-80) REVERT: A 156 ARG cc_start: 0.8462 (ttm110) cc_final: 0.7727 (ttm110) REVERT: A 159 MET cc_start: 0.7781 (mtp) cc_final: 0.7129 (mtp) REVERT: A 175 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8762 (mm-30) REVERT: A 214 ASP cc_start: 0.8425 (t0) cc_final: 0.7948 (t0) REVERT: A 254 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7532 (mmtp) REVERT: A 275 HIS cc_start: 0.8476 (t-90) cc_final: 0.8185 (t-90) REVERT: A 284 ASP cc_start: 0.7857 (p0) cc_final: 0.7567 (p0) REVERT: A 287 GLU cc_start: 0.7236 (mp0) cc_final: 0.6828 (mp0) REVERT: A 293 ARG cc_start: 0.7833 (mtm180) cc_final: 0.7468 (mtp-110) REVERT: A 421 CYS cc_start: 0.4557 (m) cc_final: 0.3713 (m) REVERT: A 425 GLU cc_start: 0.7847 (tt0) cc_final: 0.7554 (tt0) REVERT: B 119 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7428 (mm-30) REVERT: B 155 TYR cc_start: 0.8514 (m-80) cc_final: 0.8055 (m-80) REVERT: B 156 ARG cc_start: 0.8447 (ttm110) cc_final: 0.7725 (ttm110) REVERT: B 159 MET cc_start: 0.7759 (mtp) cc_final: 0.7171 (mtp) REVERT: B 175 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8749 (mm-30) REVERT: B 214 ASP cc_start: 0.8422 (t0) cc_final: 0.7897 (t0) REVERT: B 254 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7536 (mmtp) REVERT: B 260 LYS cc_start: 0.9279 (pttm) cc_final: 0.8782 (pptt) REVERT: B 262 LYS cc_start: 0.8981 (ttpp) cc_final: 0.8355 (ttpp) REVERT: B 275 HIS cc_start: 0.8502 (t-90) cc_final: 0.8226 (t-90) REVERT: B 284 ASP cc_start: 0.7838 (p0) cc_final: 0.7571 (p0) REVERT: B 287 GLU cc_start: 0.7231 (mp0) cc_final: 0.6835 (mp0) REVERT: B 411 GLU cc_start: 0.8088 (mp0) cc_final: 0.7762 (mp0) REVERT: B 421 CYS cc_start: 0.4684 (m) cc_final: 0.3839 (m) REVERT: B 425 GLU cc_start: 0.7784 (tt0) cc_final: 0.7554 (tt0) REVERT: C 119 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7388 (mm-30) REVERT: C 155 TYR cc_start: 0.8501 (m-80) cc_final: 0.8025 (m-80) REVERT: C 156 ARG cc_start: 0.8461 (ttm110) cc_final: 0.7840 (ttm170) REVERT: C 159 MET cc_start: 0.7771 (mtp) cc_final: 0.7147 (mtp) REVERT: C 214 ASP cc_start: 0.8430 (t0) cc_final: 0.7907 (t0) REVERT: C 254 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7522 (mmtp) REVERT: C 260 LYS cc_start: 0.9281 (pttm) cc_final: 0.8786 (pptt) REVERT: C 262 LYS cc_start: 0.8980 (ttpp) cc_final: 0.8352 (ttpp) REVERT: C 275 HIS cc_start: 0.8495 (t-90) cc_final: 0.8218 (t-90) REVERT: C 284 ASP cc_start: 0.7808 (p0) cc_final: 0.7559 (p0) REVERT: C 287 GLU cc_start: 0.7212 (mp0) cc_final: 0.6821 (mp0) REVERT: C 411 GLU cc_start: 0.8062 (mp0) cc_final: 0.7693 (mp0) REVERT: C 421 CYS cc_start: 0.4682 (m) cc_final: 0.3858 (m) REVERT: C 425 GLU cc_start: 0.7794 (tt0) cc_final: 0.7571 (tt0) REVERT: C 437 TRP cc_start: 0.8554 (p90) cc_final: 0.8295 (p90) REVERT: D 119 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7407 (mm-30) REVERT: D 155 TYR cc_start: 0.8528 (m-80) cc_final: 0.8075 (m-80) REVERT: D 156 ARG cc_start: 0.8464 (ttm110) cc_final: 0.7840 (ttm170) REVERT: D 159 MET cc_start: 0.7769 (mtp) cc_final: 0.7199 (mtp) REVERT: D 214 ASP cc_start: 0.8427 (t0) cc_final: 0.7906 (t0) REVERT: D 254 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7536 (mmtp) REVERT: D 260 LYS cc_start: 0.9284 (pttm) cc_final: 0.8788 (pptt) REVERT: D 262 LYS cc_start: 0.8975 (ttpp) cc_final: 0.8349 (ttpp) REVERT: D 275 HIS cc_start: 0.8495 (t-90) cc_final: 0.8224 (t-90) REVERT: D 284 ASP cc_start: 0.7796 (p0) cc_final: 0.7544 (p0) REVERT: D 287 GLU cc_start: 0.7203 (mp0) cc_final: 0.6813 (mp0) REVERT: D 411 GLU cc_start: 0.8108 (mp0) cc_final: 0.7749 (mp0) REVERT: D 421 CYS cc_start: 0.4648 (m) cc_final: 0.3802 (m) REVERT: D 425 GLU cc_start: 0.7773 (tt0) cc_final: 0.7556 (tt0) outliers start: 76 outliers final: 41 residues processed: 476 average time/residue: 0.0900 time to fit residues: 62.9548 Evaluate side-chains 475 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 430 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 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 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 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 242 MET 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 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 242 MET 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: 0.9980 chunk 47 optimal weight: 6.9990 chunk 130 optimal weight: 0.4980 chunk 119 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 26 optimal weight: 0.0050 chunk 105 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.144514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.113663 restraints weight = 19822.828| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 5.00 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12612 Z= 0.127 Angle : 0.596 7.006 17156 Z= 0.306 Chirality : 0.050 0.151 1816 Planarity : 0.004 0.034 2192 Dihedral : 5.506 38.893 2036 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 7.04 % Allowed : 26.80 % Favored : 66.17 % 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: -1.92 (0.22), residues: 1540 helix: -1.94 (1.09), residues: 24 sheet: -0.57 (0.24), residues: 568 loop : -1.77 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 430 TYR 0.015 0.001 TYR C 312 PHE 0.012 0.001 PHE D 349 TRP 0.032 0.001 TRP B 296 HIS 0.007 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (12568) covalent geometry : angle 0.58967 / 0.30 (17056) SS BOND : bond 0.00653 / 0.39 ( 32) SS BOND : angle 1.25652 / 0.88 ( 64) hydrogen bonds : bond 0.02262 / 1.53 ( 300) hydrogen bonds : angle 6.45298 / 4.51 ( 732) link_NAG-ASN : bond 0.00176 / 0.12 ( 12) link_NAG-ASN : angle 1.21242 / 0.73 ( 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 539 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 445 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 TYR cc_start: 0.8537 (m-80) cc_final: 0.7953 (m-80) REVERT: A 156 ARG cc_start: 0.8376 (ttm110) cc_final: 0.7742 (ttm170) REVERT: A 159 MET cc_start: 0.7655 (mtp) cc_final: 0.6908 (mtp) REVERT: A 254 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7372 (mmtp) REVERT: A 270 LYS cc_start: 0.9034 (mmmm) cc_final: 0.8617 (tptp) REVERT: A 284 ASP cc_start: 0.7730 (p0) cc_final: 0.7472 (p0) REVERT: A 287 GLU cc_start: 0.7096 (mp0) cc_final: 0.6795 (mp0) REVERT: A 293 ARG cc_start: 0.7773 (mtm180) cc_final: 0.7460 (mtp85) REVERT: A 301 ARG cc_start: 0.8294 (mmm-85) cc_final: 0.8061 (mmm-85) REVERT: A 311 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7898 (mm-30) REVERT: A 349 PHE cc_start: 0.9149 (p90) cc_final: 0.8859 (p90) REVERT: A 373 MET cc_start: 0.8082 (mmm) cc_final: 0.7823 (mmm) REVERT: A 411 GLU cc_start: 0.8208 (mp0) cc_final: 0.7685 (mp0) REVERT: A 425 GLU cc_start: 0.7744 (tt0) cc_final: 0.7445 (tt0) REVERT: B 119 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7474 (mm-30) REVERT: B 142 ASP cc_start: 0.8662 (t0) cc_final: 0.8411 (t0) REVERT: B 155 TYR cc_start: 0.8543 (m-80) cc_final: 0.7972 (m-80) REVERT: B 156 ARG cc_start: 0.8319 (ttm110) cc_final: 0.7705 (ttm170) REVERT: B 159 MET cc_start: 0.7644 (mtp) cc_final: 0.7000 (mtp) REVERT: B 214 ASP cc_start: 0.8518 (t0) cc_final: 0.7956 (t0) REVERT: B 254 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7373 (mmtp) REVERT: B 260 LYS cc_start: 0.9274 (pttm) cc_final: 0.8776 (pptt) REVERT: B 262 LYS cc_start: 0.9029 (ttpp) cc_final: 0.8277 (ttpp) REVERT: B 270 LYS cc_start: 0.9026 (mmmm) cc_final: 0.8604 (tptp) REVERT: B 287 GLU cc_start: 0.7115 (mp0) cc_final: 0.6827 (mp0) REVERT: B 293 ARG cc_start: 0.7794 (mtm180) cc_final: 0.7054 (mtp85) REVERT: B 301 ARG cc_start: 0.8253 (mmm-85) cc_final: 0.8041 (mmm-85) REVERT: B 311 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7900 (mm-30) REVERT: B 349 PHE cc_start: 0.9152 (p90) cc_final: 0.8843 (p90) REVERT: C 119 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7445 (mm-30) REVERT: C 142 ASP cc_start: 0.8557 (t0) cc_final: 0.8292 (t0) REVERT: C 155 TYR cc_start: 0.8536 (m-80) cc_final: 0.7969 (m-80) REVERT: C 156 ARG cc_start: 0.8407 (ttm110) cc_final: 0.7508 (ttp-110) REVERT: C 159 MET cc_start: 0.7699 (mtp) cc_final: 0.7015 (mtp) REVERT: C 214 ASP cc_start: 0.8507 (t0) cc_final: 0.7965 (t0) REVERT: C 254 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7376 (mmtp) REVERT: C 260 LYS cc_start: 0.9289 (pttm) cc_final: 0.8786 (pptt) REVERT: C 262 LYS cc_start: 0.9035 (ttpp) cc_final: 0.8287 (ttpp) REVERT: C 270 LYS cc_start: 0.9049 (mmmm) cc_final: 0.8602 (tptp) REVERT: C 287 GLU cc_start: 0.7092 (mp0) cc_final: 0.6814 (mp0) REVERT: C 301 ARG cc_start: 0.8262 (mmm-85) cc_final: 0.8051 (mmm-85) REVERT: C 311 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7913 (mm-30) REVERT: C 341 ASN cc_start: 0.6951 (t0) cc_final: 0.6730 (t0) REVERT: C 349 PHE cc_start: 0.9152 (p90) cc_final: 0.8856 (p90) REVERT: C 437 TRP cc_start: 0.8640 (p90) cc_final: 0.8347 (p90) REVERT: D 119 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7452 (mm-30) REVERT: D 142 ASP cc_start: 0.8591 (t0) cc_final: 0.8304 (t0) REVERT: D 155 TYR cc_start: 0.8531 (m-80) cc_final: 0.7954 (m-80) REVERT: D 156 ARG cc_start: 0.8320 (ttm110) cc_final: 0.7701 (ttm170) REVERT: D 159 MET cc_start: 0.7692 (mtp) cc_final: 0.7021 (mtp) REVERT: D 214 ASP cc_start: 0.8506 (t0) cc_final: 0.7965 (t0) REVERT: D 254 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7389 (mmtp) REVERT: D 260 LYS cc_start: 0.9272 (pttm) cc_final: 0.8777 (pptt) REVERT: D 262 LYS cc_start: 0.9029 (ttpp) cc_final: 0.8277 (ttpp) REVERT: D 270 LYS cc_start: 0.9048 (mmmm) cc_final: 0.8605 (tptp) REVERT: D 287 GLU cc_start: 0.7092 (mp0) cc_final: 0.6812 (mp0) REVERT: D 301 ARG cc_start: 0.8253 (mmm-85) cc_final: 0.8041 (mmm-85) REVERT: D 311 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7898 (mm-30) REVERT: D 349 PHE cc_start: 0.9170 (p90) cc_final: 0.8867 (p90) outliers start: 94 outliers final: 47 residues processed: 489 average time/residue: 0.0871 time to fit residues: 62.4215 Evaluate side-chains 497 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 446 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 128 GLU 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 446 CYS Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 114 VAL 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 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 316 TYR Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 446 CYS 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 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 444 SER Chi-restraints excluded: chain C residue 446 CYS Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 114 VAL 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 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 413 THR Chi-restraints excluded: chain D residue 446 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 73 optimal weight: 0.0770 chunk 150 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.6740 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.146210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.115120 restraints weight = 19731.196| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 5.10 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12612 Z= 0.120 Angle : 0.620 7.021 17156 Z= 0.316 Chirality : 0.050 0.145 1816 Planarity : 0.004 0.031 2192 Dihedral : 5.241 22.572 2032 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 6.21 % Allowed : 29.57 % Favored : 64.22 % 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: -1.64 (0.22), residues: 1540 helix: -1.79 (1.09), residues: 24 sheet: -0.36 (0.24), residues: 588 loop : -1.62 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 430 TYR 0.018 0.001 TYR A 312 PHE 0.009 0.001 PHE B 465 TRP 0.039 0.001 TRP A 296 HIS 0.005 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (12568) covalent geometry : angle 0.61421 / 0.31 (17056) SS BOND : bond 0.00505 / 0.31 ( 32) SS BOND : angle 1.31611 / 0.92 ( 64) hydrogen bonds : bond 0.02306 / 1.55 ( 300) hydrogen bonds : angle 6.26703 / 4.37 ( 732) link_NAG-ASN : bond 0.00184 / 0.12 ( 12) link_NAG-ASN : angle 1.14142 / 0.69 ( 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 552 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 469 time to evaluate : 0.460 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: symmetry clash REVERT: A 155 TYR cc_start: 0.8532 (m-80) cc_final: 0.7901 (m-80) REVERT: A 156 ARG cc_start: 0.8296 (ttm110) cc_final: 0.7380 (ttp-110) REVERT: A 214 ASP cc_start: 0.8454 (t0) cc_final: 0.7952 (t0) REVERT: A 254 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.7257 (mmtp) REVERT: A 270 LYS cc_start: 0.8973 (mmmm) cc_final: 0.8525 (tptp) REVERT: A 275 HIS cc_start: 0.8492 (t-90) cc_final: 0.7906 (t-90) REVERT: A 293 ARG cc_start: 0.7689 (mtm180) cc_final: 0.6843 (mtp85) REVERT: A 301 ARG cc_start: 0.8263 (mmm-85) cc_final: 0.8022 (mmm-85) REVERT: A 311 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7717 (mm-30) REVERT: A 349 PHE cc_start: 0.9173 (p90) cc_final: 0.8856 (p90) REVERT: A 411 GLU cc_start: 0.8150 (mp0) cc_final: 0.7857 (mp0) REVERT: A 421 CYS cc_start: 0.4097 (m) cc_final: 0.3540 (m) REVERT: A 425 GLU cc_start: 0.7656 (tt0) cc_final: 0.7322 (tt0) REVERT: B 142 ASP cc_start: 0.8539 (t0) cc_final: 0.8226 (t0) REVERT: B 155 TYR cc_start: 0.8560 (m-80) cc_final: 0.7982 (m-80) REVERT: B 156 ARG cc_start: 0.8279 (ttm110) cc_final: 0.7403 (ttp-110) REVERT: B 214 ASP cc_start: 0.8526 (t0) cc_final: 0.7941 (t0) REVERT: B 254 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7244 (mmtp) REVERT: B 260 LYS cc_start: 0.9285 (pttm) cc_final: 0.8795 (pptt) REVERT: B 270 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8608 (tptp) REVERT: B 275 HIS cc_start: 0.8546 (t-90) cc_final: 0.8058 (t-90) REVERT: B 296 TRP cc_start: 0.8141 (t60) cc_final: 0.7869 (t60) REVERT: B 301 ARG cc_start: 0.8236 (mmm-85) cc_final: 0.8005 (mmm-85) REVERT: B 311 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7724 (mm-30) REVERT: B 349 PHE cc_start: 0.9183 (p90) cc_final: 0.8827 (p90) REVERT: B 384 ASP cc_start: 0.8195 (t0) cc_final: 0.7427 (t70) REVERT: B 421 CYS cc_start: 0.4112 (m) cc_final: 0.3541 (m) REVERT: B 425 GLU cc_start: 0.7742 (tt0) cc_final: 0.7422 (tt0) REVERT: C 142 ASP cc_start: 0.8501 (t0) cc_final: 0.8184 (t0) REVERT: C 155 TYR cc_start: 0.8531 (m-80) cc_final: 0.7956 (m-80) REVERT: C 156 ARG cc_start: 0.8270 (ttm110) cc_final: 0.7386 (ttp-110) REVERT: C 209 ASN cc_start: 0.8666 (OUTLIER) cc_final: 0.8445 (m-40) REVERT: C 214 ASP cc_start: 0.8540 (t0) cc_final: 0.7953 (t0) REVERT: C 254 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7250 (mmtp) REVERT: C 270 LYS cc_start: 0.9045 (mmmm) cc_final: 0.8613 (tptp) REVERT: C 275 HIS cc_start: 0.8555 (t-90) cc_final: 0.8063 (t-90) REVERT: C 296 TRP cc_start: 0.8125 (t60) cc_final: 0.7922 (t60) REVERT: C 301 ARG cc_start: 0.8244 (mmm-85) cc_final: 0.8015 (mmm-85) REVERT: C 311 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7728 (mm-30) REVERT: C 341 ASN cc_start: 0.6950 (t0) cc_final: 0.6725 (t0) REVERT: C 349 PHE cc_start: 0.9198 (p90) cc_final: 0.8860 (p90) REVERT: C 384 ASP cc_start: 0.8162 (t0) cc_final: 0.7393 (t70) REVERT: C 421 CYS cc_start: 0.4071 (m) cc_final: 0.3532 (m) REVERT: C 425 GLU cc_start: 0.7691 (tt0) cc_final: 0.7387 (tt0) REVERT: D 142 ASP cc_start: 0.8445 (t0) cc_final: 0.8126 (t0) REVERT: D 155 TYR cc_start: 0.8559 (m-80) cc_final: 0.7992 (m-80) REVERT: D 156 ARG cc_start: 0.8278 (ttm110) cc_final: 0.7395 (ttp-110) REVERT: D 209 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8496 (m-40) REVERT: D 214 ASP cc_start: 0.8537 (t0) cc_final: 0.7952 (t0) REVERT: D 254 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.7262 (mmtp) REVERT: D 260 LYS cc_start: 0.9275 (pttm) cc_final: 0.8795 (pptt) REVERT: D 270 LYS cc_start: 0.9044 (mmmm) cc_final: 0.8600 (tptp) REVERT: D 275 HIS cc_start: 0.8542 (t-90) cc_final: 0.8040 (t-90) REVERT: D 301 ARG cc_start: 0.8249 (mmm-85) cc_final: 0.8042 (mmm-85) REVERT: D 311 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7731 (mm-30) REVERT: D 349 PHE cc_start: 0.9180 (p90) cc_final: 0.8847 (p90) REVERT: D 384 ASP cc_start: 0.8174 (t0) cc_final: 0.7405 (t70) REVERT: D 421 CYS cc_start: 0.4114 (m) cc_final: 0.3552 (m) REVERT: D 425 GLU cc_start: 0.7695 (tt0) cc_final: 0.7384 (tt0) outliers start: 83 outliers final: 57 residues processed: 508 average time/residue: 0.0893 time to fit residues: 66.3178 Evaluate side-chains 496 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 433 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 124 CYS Chi-restraints excluded: chain A residue 128 GLU 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 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 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 189 ASN Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 241 ILE 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 316 TYR 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 124 CYS Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 139 LEU 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 241 ILE 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 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 241 ILE 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 316 TYR Chi-restraints excluded: chain D residue 335 CYS Chi-restraints excluded: chain D residue 413 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.145646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.113839 restraints weight = 19578.878| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 5.14 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12612 Z= 0.134 Angle : 0.663 7.207 17156 Z= 0.339 Chirality : 0.050 0.149 1816 Planarity : 0.004 0.033 2192 Dihedral : 5.297 23.152 2032 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 6.36 % Allowed : 30.46 % Favored : 63.17 % 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: -1.60 (0.22), residues: 1540 helix: -1.76 (1.08), residues: 24 sheet: -0.23 (0.23), residues: 576 loop : -1.65 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 293 TYR 0.020 0.002 TYR B 312 PHE 0.017 0.002 PHE B 422 TRP 0.044 0.001 TRP A 296 HIS 0.004 0.001 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (12568) covalent geometry : angle 0.65363 / 0.34 (17056) SS BOND : bond 0.00445 / 0.25 ( 32) SS BOND : angle 1.76214 / 1.24 ( 64) hydrogen bonds : bond 0.02327 / 1.58 ( 300) hydrogen bonds : angle 6.22686 / 4.33 ( 732) link_NAG-ASN : bond 0.00183 / 0.12 ( 12) link_NAG-ASN : angle 1.13283 / 0.68 ( 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 542 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 457 time to evaluate : 0.503 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: 0.8564 (m-80) cc_final: 0.7945 (m-80) REVERT: A 156 ARG cc_start: 0.8300 (ttm110) cc_final: 0.7408 (ttp-110) REVERT: A 214 ASP cc_start: 0.8477 (t0) cc_final: 0.7978 (t0) REVERT: A 254 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.7275 (mmtp) REVERT: A 270 LYS cc_start: 0.8955 (mmmm) cc_final: 0.8556 (tptp) REVERT: A 301 ARG cc_start: 0.8242 (mmm-85) cc_final: 0.7962 (mmm-85) REVERT: A 311 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7734 (mm-30) REVERT: A 349 PHE cc_start: 0.9152 (p90) cc_final: 0.8808 (p90) REVERT: A 373 MET cc_start: 0.7993 (mmm) cc_final: 0.7730 (mmm) REVERT: A 384 ASP cc_start: 0.8155 (t0) cc_final: 0.7338 (t70) REVERT: A 425 GLU cc_start: 0.7636 (tt0) cc_final: 0.7284 (tt0) REVERT: A 446 CYS cc_start: 0.5224 (m) cc_final: 0.4818 (m) REVERT: B 142 ASP cc_start: 0.8578 (t0) cc_final: 0.8354 (t0) REVERT: B 155 TYR cc_start: 0.8584 (m-80) cc_final: 0.7961 (m-80) REVERT: B 156 ARG cc_start: 0.8291 (ttm110) cc_final: 0.7398 (ttp-110) REVERT: B 159 MET cc_start: 0.7776 (mtp) cc_final: 0.7097 (mtp) REVERT: B 189 ASN cc_start: 0.8370 (OUTLIER) cc_final: 0.8097 (m-40) REVERT: B 209 ASN cc_start: 0.8617 (OUTLIER) cc_final: 0.8175 (m110) REVERT: B 214 ASP cc_start: 0.8534 (t0) cc_final: 0.7995 (t0) REVERT: B 254 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7286 (mmtp) REVERT: B 270 LYS cc_start: 0.9014 (mmmm) cc_final: 0.8598 (tptp) REVERT: B 287 GLU cc_start: 0.7179 (mp0) cc_final: 0.6853 (mp0) REVERT: B 301 ARG cc_start: 0.8255 (mmm-85) cc_final: 0.8021 (mmm-85) REVERT: B 311 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7771 (mm-30) REVERT: B 349 PHE cc_start: 0.9198 (p90) cc_final: 0.8864 (p90) REVERT: B 373 MET cc_start: 0.8052 (mmm) cc_final: 0.7838 (mmm) REVERT: B 425 GLU cc_start: 0.7703 (tt0) cc_final: 0.7397 (tt0) REVERT: B 446 CYS cc_start: 0.5250 (m) cc_final: 0.4842 (m) REVERT: C 142 ASP cc_start: 0.8527 (t0) cc_final: 0.8303 (t0) REVERT: C 155 TYR cc_start: 0.8566 (m-80) cc_final: 0.7942 (m-80) REVERT: C 156 ARG cc_start: 0.8307 (ttm110) cc_final: 0.7404 (ttp-110) REVERT: C 208 TYR cc_start: 0.7707 (t80) cc_final: 0.7494 (t80) REVERT: C 209 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.8275 (m-40) REVERT: C 254 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7286 (mmtp) REVERT: C 259 GLU cc_start: 0.8691 (pm20) cc_final: 0.8262 (pm20) REVERT: C 270 LYS cc_start: 0.8996 (mmmm) cc_final: 0.8593 (tptp) REVERT: C 293 ARG cc_start: 0.7739 (mtp-110) cc_final: 0.7472 (mtm110) REVERT: C 301 ARG cc_start: 0.8243 (mmm-85) cc_final: 0.8008 (mmm-85) REVERT: C 311 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7768 (mm-30) REVERT: C 349 PHE cc_start: 0.9167 (p90) cc_final: 0.8803 (p90) REVERT: C 425 GLU cc_start: 0.7672 (tt0) cc_final: 0.7394 (tt0) REVERT: C 446 CYS cc_start: 0.5186 (m) cc_final: 0.4763 (m) REVERT: D 142 ASP cc_start: 0.8525 (t0) cc_final: 0.8292 (t0) REVERT: D 155 TYR cc_start: 0.8562 (m-80) cc_final: 0.7943 (m-80) REVERT: D 156 ARG cc_start: 0.8292 (ttm110) cc_final: 0.7396 (ttp-110) REVERT: D 159 MET cc_start: 0.7801 (mtp) cc_final: 0.7139 (mtp) REVERT: D 254 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.7279 (mmtp) REVERT: D 270 LYS cc_start: 0.8989 (mmmm) cc_final: 0.8568 (tptp) REVERT: D 287 GLU cc_start: 0.7150 (mp0) cc_final: 0.6812 (mp0) REVERT: D 293 ARG cc_start: 0.7649 (mtm110) cc_final: 0.6791 (mtp85) REVERT: D 301 ARG cc_start: 0.8253 (mmm-85) cc_final: 0.7989 (mmm-85) REVERT: D 311 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7766 (mm-30) REVERT: D 349 PHE cc_start: 0.9174 (p90) cc_final: 0.8827 (p90) REVERT: D 373 MET cc_start: 0.7947 (mmm) cc_final: 0.7741 (mmm) REVERT: D 425 GLU cc_start: 0.7687 (tt0) cc_final: 0.7401 (tt0) REVERT: D 446 CYS cc_start: 0.5173 (m) cc_final: 0.4741 (m) outliers start: 85 outliers final: 61 residues processed: 492 average time/residue: 0.0879 time to fit residues: 62.9722 Evaluate side-chains 517 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 449 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 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 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 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 241 ILE 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 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 131 THR Chi-restraints excluded: chain C residue 139 LEU 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 241 ILE 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 241 ILE 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 316 TYR Chi-restraints excluded: chain D residue 335 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 56 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 151 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3861 r_free = 0.3861 target = 0.143429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.112424 restraints weight = 19654.187| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 4.95 r_work: 0.3329 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12612 Z= 0.186 Angle : 0.701 9.240 17156 Z= 0.361 Chirality : 0.051 0.148 1816 Planarity : 0.004 0.034 2192 Dihedral : 5.389 22.140 2032 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 6.74 % Allowed : 30.76 % Favored : 62.50 % 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: -1.59 (0.22), residues: 1540 helix: -1.93 (1.00), residues: 24 sheet: -0.20 (0.23), residues: 576 loop : -1.66 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 293 TYR 0.020 0.002 TYR A 312 PHE 0.021 0.002 PHE D 422 TRP 0.067 0.002 TRP A 296 HIS 0.016 0.002 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (12568) covalent geometry : angle 0.69359 / 0.36 (17056) SS BOND : bond 0.00703 / 0.42 ( 32) SS BOND : angle 1.62914 / 1.15 ( 64) hydrogen bonds : bond 0.02693 / 1.85 ( 300) hydrogen bonds : angle 6.34150 / 4.41 ( 732) link_NAG-ASN : bond 0.00178 / 0.12 ( 12) link_NAG-ASN : angle 1.20148 / 0.72 ( 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 553 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 463 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: 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: 0.8827 (m-80) cc_final: 0.8230 (m-80) REVERT: A 156 ARG cc_start: 0.8470 (ttm110) cc_final: 0.7675 (ttp-110) REVERT: A 159 MET cc_start: 0.8319 (mtp) cc_final: 0.7816 (mtp) REVERT: A 175 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8952 (mm-30) REVERT: A 209 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.8566 (m-40) REVERT: A 214 ASP cc_start: 0.8582 (t0) cc_final: 0.8111 (t0) REVERT: A 254 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7649 (mmtp) REVERT: A 270 LYS cc_start: 0.9041 (mmmm) cc_final: 0.8605 (tptp) REVERT: A 275 HIS cc_start: 0.8850 (t-90) cc_final: 0.8433 (t-90) REVERT: A 311 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8039 (mm-30) REVERT: A 349 PHE cc_start: 0.9296 (p90) cc_final: 0.8970 (p90) REVERT: A 425 GLU cc_start: 0.8548 (tt0) cc_final: 0.8130 (tt0) REVERT: B 119 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7908 (mm-30) REVERT: B 142 ASP cc_start: 0.8655 (t0) cc_final: 0.8429 (t0) REVERT: B 155 TYR cc_start: 0.8833 (m-80) cc_final: 0.8227 (m-80) REVERT: B 156 ARG cc_start: 0.8483 (ttm110) cc_final: 0.7669 (ttp-110) REVERT: B 159 MET cc_start: 0.8347 (mtp) cc_final: 0.7819 (mtp) REVERT: B 175 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8968 (mm-30) REVERT: B 214 ASP cc_start: 0.8605 (t0) cc_final: 0.8103 (t0) REVERT: B 254 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7662 (mmtp) REVERT: B 270 LYS cc_start: 0.9028 (mmmm) cc_final: 0.8604 (tptp) REVERT: B 275 HIS cc_start: 0.8853 (t-90) cc_final: 0.8442 (t-90) REVERT: B 294 ASP cc_start: 0.8539 (t70) cc_final: 0.7716 (p0) REVERT: B 296 TRP cc_start: 0.8631 (t60) cc_final: 0.8308 (t60) REVERT: B 301 ARG cc_start: 0.8602 (mmm-85) cc_final: 0.8265 (mmm-85) REVERT: B 311 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8052 (mm-30) REVERT: B 349 PHE cc_start: 0.9312 (p90) cc_final: 0.8906 (p90) REVERT: B 384 ASP cc_start: 0.8175 (t0) cc_final: 0.7373 (t70) REVERT: B 425 GLU cc_start: 0.8540 (tt0) cc_final: 0.8028 (tt0) REVERT: C 119 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7927 (mm-30) REVERT: C 142 ASP cc_start: 0.8612 (t0) cc_final: 0.8368 (t0) REVERT: C 155 TYR cc_start: 0.8832 (m-80) cc_final: 0.8236 (m-80) REVERT: C 156 ARG cc_start: 0.8477 (ttm110) cc_final: 0.7658 (ttp-110) REVERT: C 159 MET cc_start: 0.8408 (mtp) cc_final: 0.7884 (mtp) REVERT: C 175 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8976 (mm-30) REVERT: C 209 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.8509 (m-40) REVERT: C 214 ASP cc_start: 0.8628 (t0) cc_final: 0.8137 (t0) REVERT: C 254 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7688 (mmtp) REVERT: C 270 LYS cc_start: 0.9058 (mmmm) cc_final: 0.8622 (tptp) REVERT: C 275 HIS cc_start: 0.8830 (t-90) cc_final: 0.8605 (t-90) REVERT: C 293 ARG cc_start: 0.8141 (mtp-110) cc_final: 0.7771 (mtp-110) REVERT: C 296 TRP cc_start: 0.8792 (t60) cc_final: 0.8449 (t60) REVERT: C 311 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8032 (mm-30) REVERT: C 349 PHE cc_start: 0.9283 (p90) cc_final: 0.8974 (p90) REVERT: C 384 ASP cc_start: 0.8179 (t0) cc_final: 0.7426 (t70) REVERT: C 425 GLU cc_start: 0.8566 (tt0) cc_final: 0.8110 (tt0) REVERT: D 84 LYS cc_start: 0.8778 (mmmm) cc_final: 0.8575 (mmmm) REVERT: D 119 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7907 (mm-30) REVERT: D 142 ASP cc_start: 0.8586 (t0) cc_final: 0.8361 (t0) REVERT: D 155 TYR cc_start: 0.8833 (m-80) cc_final: 0.8237 (m-80) REVERT: D 156 ARG cc_start: 0.8483 (ttm110) cc_final: 0.7661 (ttp-110) REVERT: D 159 MET cc_start: 0.8357 (mtp) cc_final: 0.7841 (mtp) REVERT: D 175 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8959 (mm-30) REVERT: D 214 ASP cc_start: 0.8572 (t0) cc_final: 0.8073 (t0) REVERT: D 254 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7659 (mmtp) REVERT: D 270 LYS cc_start: 0.9029 (mmmm) cc_final: 0.8602 (tptp) REVERT: D 275 HIS cc_start: 0.8827 (t-90) cc_final: 0.8577 (t-90) REVERT: D 301 ARG cc_start: 0.8623 (mmm-85) cc_final: 0.8277 (mmm-85) REVERT: D 311 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8029 (mm-30) REVERT: D 349 PHE cc_start: 0.9324 (p90) cc_final: 0.8929 (p90) REVERT: D 384 ASP cc_start: 0.8186 (t0) cc_final: 0.7433 (t70) REVERT: D 425 GLU cc_start: 0.8568 (tt0) cc_final: 0.8055 (tt0) outliers start: 90 outliers final: 65 residues processed: 500 average time/residue: 0.0924 time to fit residues: 66.8025 Evaluate side-chains 520 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 449 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 139 LEU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 203 VAL 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 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 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 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 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 139 LEU Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 203 VAL 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 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 168 SER 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 80 optimal weight: 0.0030 chunk 114 optimal weight: 10.0000 chunk 19 optimal weight: 0.4980 chunk 136 optimal weight: 0.4980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 ASN D 209 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.145816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.114636 restraints weight = 19545.006| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 5.09 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2911 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= 0.130 Angle : 0.689 10.580 17156 Z= 0.353 Chirality : 0.051 0.150 1816 Planarity : 0.004 0.034 2192 Dihedral : 5.135 23.679 2032 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 5.24 % Allowed : 32.93 % Favored : 61.83 % 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: -1.67 (0.21), residues: 1540 helix: -3.09 (0.60), residues: 48 sheet: 0.02 (0.23), residues: 568 loop : -1.82 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 293 TYR 0.019 0.002 TYR C 208 PHE 0.019 0.001 PHE B 422 TRP 0.079 0.002 TRP A 296 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (12568) covalent geometry : angle 0.68573 / 0.35 (17056) SS BOND : bond 0.00430 / 0.22 ( 32) SS BOND : angle 1.11607 / 0.74 ( 64) hydrogen bonds : bond 0.02155 / 1.54 ( 300) hydrogen bonds : angle 6.25274 / 4.34 ( 732) link_NAG-ASN : bond 0.00197 / 0.13 ( 12) link_NAG-ASN : angle 1.04396 / 0.64 ( 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 533 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 463 time to evaluate : 0.310 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 118 ARG cc_start: 0.7654 (ttt-90) cc_final: 0.6860 (tmt-80) REVERT: A 155 TYR cc_start: 0.8524 (m-80) cc_final: 0.7873 (m-80) REVERT: A 156 ARG cc_start: 0.8241 (ttm110) cc_final: 0.7327 (ttp-110) REVERT: A 214 ASP cc_start: 0.8547 (t0) cc_final: 0.8047 (t0) REVERT: A 254 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.7267 (mmtp) REVERT: A 270 LYS cc_start: 0.8965 (mmmm) cc_final: 0.8526 (tptp) REVERT: A 275 HIS cc_start: 0.8401 (t-90) cc_final: 0.7953 (t-90) REVERT: A 293 ARG cc_start: 0.7554 (mtm110) cc_final: 0.6826 (mtp85) REVERT: A 294 ASP cc_start: 0.7936 (t70) cc_final: 0.7483 (p0) REVERT: A 301 ARG cc_start: 0.8398 (mmm-85) cc_final: 0.7917 (mmm-85) REVERT: A 349 PHE cc_start: 0.9201 (p90) cc_final: 0.8790 (p90) REVERT: A 373 MET cc_start: 0.8056 (mmm) cc_final: 0.7809 (mmm) REVERT: A 376 ASP cc_start: 0.8169 (t0) cc_final: 0.7929 (t0) REVERT: A 384 ASP cc_start: 0.8116 (t0) cc_final: 0.7322 (t70) REVERT: A 425 GLU cc_start: 0.7765 (tt0) cc_final: 0.7359 (tt0) REVERT: B 142 ASP cc_start: 0.8585 (t0) cc_final: 0.8377 (t0) REVERT: B 155 TYR cc_start: 0.8526 (m-80) cc_final: 0.7862 (m-80) REVERT: B 156 ARG cc_start: 0.8255 (ttm110) cc_final: 0.7338 (ttp-110) REVERT: B 214 ASP cc_start: 0.8533 (t0) cc_final: 0.7998 (t0) REVERT: B 254 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.7270 (mmtp) REVERT: B 270 LYS cc_start: 0.8951 (mmmm) cc_final: 0.8529 (tptp) REVERT: B 275 HIS cc_start: 0.8440 (t-90) cc_final: 0.7979 (t-90) REVERT: B 301 ARG cc_start: 0.8195 (mmm-85) cc_final: 0.7870 (mmm-85) REVERT: B 311 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7781 (mm-30) REVERT: B 349 PHE cc_start: 0.9214 (p90) cc_final: 0.8811 (p90) REVERT: B 373 MET cc_start: 0.8078 (mmm) cc_final: 0.7841 (mmm) REVERT: B 425 GLU cc_start: 0.7659 (tt0) cc_final: 0.7279 (tt0) REVERT: C 142 ASP cc_start: 0.8546 (t0) cc_final: 0.8328 (t0) REVERT: C 155 TYR cc_start: 0.8516 (m-80) cc_final: 0.7866 (m-80) REVERT: C 156 ARG cc_start: 0.8256 (ttm110) cc_final: 0.7353 (ttp-110) REVERT: C 209 ASN cc_start: 0.8479 (OUTLIER) cc_final: 0.8202 (m-40) REVERT: C 214 ASP cc_start: 0.8514 (t0) cc_final: 0.7987 (t0) REVERT: C 254 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.7273 (mmtp) REVERT: C 270 LYS cc_start: 0.8952 (mmmm) cc_final: 0.8541 (tptp) REVERT: C 293 ARG cc_start: 0.7704 (mtp-110) cc_final: 0.7488 (mtp-110) REVERT: C 296 TRP cc_start: 0.8462 (t60) cc_final: 0.8191 (t60) REVERT: C 301 ARG cc_start: 0.8418 (mmm-85) cc_final: 0.7928 (mmm-85) REVERT: C 349 PHE cc_start: 0.9188 (p90) cc_final: 0.8776 (p90) REVERT: C 411 GLU cc_start: 0.8145 (mp0) cc_final: 0.7865 (mp0) REVERT: C 425 GLU cc_start: 0.7669 (tt0) cc_final: 0.7330 (tt0) REVERT: C 432 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7998 (tt0) REVERT: D 142 ASP cc_start: 0.8533 (t0) cc_final: 0.8283 (t0) REVERT: D 155 TYR cc_start: 0.8519 (m-80) cc_final: 0.7870 (m-80) REVERT: D 156 ARG cc_start: 0.8275 (ttm110) cc_final: 0.7365 (ttp-110) REVERT: D 214 ASP cc_start: 0.8549 (t0) cc_final: 0.8011 (t0) REVERT: D 254 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.7250 (mmtp) REVERT: D 270 LYS cc_start: 0.8959 (mmmm) cc_final: 0.8531 (tptp) REVERT: D 301 ARG cc_start: 0.8231 (mmm-85) cc_final: 0.7895 (mmm-85) REVERT: D 311 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7723 (mm-30) REVERT: D 349 PHE cc_start: 0.9186 (p90) cc_final: 0.8837 (p90) REVERT: D 376 ASP cc_start: 0.8155 (t0) cc_final: 0.7915 (t0) REVERT: D 384 ASP cc_start: 0.8174 (t0) cc_final: 0.7414 (t70) REVERT: D 425 GLU cc_start: 0.7611 (tt0) cc_final: 0.7282 (tt0) REVERT: D 432 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7950 (tt0) outliers start: 70 outliers final: 56 residues processed: 491 average time/residue: 0.0865 time to fit residues: 61.8973 Evaluate side-chains 512 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 451 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 139 LEU 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 241 ILE 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 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 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 241 ILE Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 258 ILE 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 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 139 LEU 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 241 ILE 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 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 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 241 ILE 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 413 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 62 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 80 optimal weight: 0.0020 chunk 34 optimal weight: 0.7980 chunk 46 optimal weight: 0.0970 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 ASN ** 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 = 0.3909 r_free = 0.3909 target = 0.147351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.116227 restraints weight = 19437.280| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 5.01 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12612 Z= 0.134 Angle : 0.721 9.485 17156 Z= 0.371 Chirality : 0.051 0.163 1816 Planarity : 0.004 0.036 2192 Dihedral : 5.085 27.417 2032 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 4.57 % Allowed : 34.43 % Favored : 61.00 % 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: -1.62 (0.21), residues: 1540 helix: -2.88 (0.63), residues: 48 sheet: 0.08 (0.23), residues: 568 loop : -1.81 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 293 TYR 0.019 0.001 TYR C 312 PHE 0.021 0.001 PHE D 422 TRP 0.087 0.002 TRP A 296 HIS 0.014 0.001 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (12568) covalent geometry : angle 0.71425 / 0.37 (17056) SS BOND : bond 0.00388 / 0.20 ( 32) SS BOND : angle 1.69594 / 1.25 ( 64) hydrogen bonds : bond 0.02160 / 1.52 ( 300) hydrogen bonds : angle 6.12385 / 4.25 ( 732) link_NAG-ASN : bond 0.00175 / 0.11 ( 12) link_NAG-ASN : angle 1.02698 / 0.63 ( 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 516 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 455 time to evaluate : 0.360 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 155 TYR cc_start: 0.8447 (m-80) cc_final: 0.7801 (m-80) REVERT: A 156 ARG cc_start: 0.8240 (ttm110) cc_final: 0.7330 (ttp-110) REVERT: A 209 ASN cc_start: 0.8492 (t0) cc_final: 0.8266 (m-40) REVERT: A 214 ASP cc_start: 0.8487 (t0) cc_final: 0.7991 (t0) REVERT: A 254 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.7239 (mmtp) REVERT: A 264 ILE cc_start: 0.9264 (tt) cc_final: 0.8814 (pt) REVERT: A 270 LYS cc_start: 0.8967 (mmmm) cc_final: 0.8521 (tptp) REVERT: A 293 ARG cc_start: 0.7388 (mtm110) cc_final: 0.6653 (mtp85) REVERT: A 294 ASP cc_start: 0.7845 (t70) cc_final: 0.7642 (t0) REVERT: A 301 ARG cc_start: 0.8369 (mmm-85) cc_final: 0.7892 (mmm-85) REVERT: A 349 PHE cc_start: 0.9197 (p90) cc_final: 0.8797 (p90) REVERT: A 373 MET cc_start: 0.8053 (mmm) cc_final: 0.7788 (mmm) REVERT: A 376 ASP cc_start: 0.8188 (t0) cc_final: 0.7953 (t0) REVERT: A 384 ASP cc_start: 0.8028 (t0) cc_final: 0.7199 (t70) REVERT: A 425 GLU cc_start: 0.7732 (tt0) cc_final: 0.7274 (tt0) REVERT: B 142 ASP cc_start: 0.8574 (t0) cc_final: 0.8369 (t0) REVERT: B 155 TYR cc_start: 0.8490 (m-80) cc_final: 0.7843 (m-80) REVERT: B 156 ARG cc_start: 0.8268 (ttm110) cc_final: 0.7942 (ttp-110) REVERT: B 189 ASN cc_start: 0.8358 (m-40) cc_final: 0.8150 (t0) REVERT: B 214 ASP cc_start: 0.8456 (t0) cc_final: 0.7961 (t0) REVERT: B 254 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.7260 (mmtp) REVERT: B 270 LYS cc_start: 0.8986 (mmmm) cc_final: 0.8545 (tptp) REVERT: B 287 GLU cc_start: 0.7088 (mp0) cc_final: 0.6779 (mp0) REVERT: B 294 ASP cc_start: 0.8102 (t70) cc_final: 0.7816 (t0) REVERT: B 296 TRP cc_start: 0.8220 (t60) cc_final: 0.7967 (t60) REVERT: B 311 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7740 (mm-30) REVERT: B 373 MET cc_start: 0.8068 (mmm) cc_final: 0.7833 (mmm) REVERT: B 376 ASP cc_start: 0.8172 (t0) cc_final: 0.7937 (t0) REVERT: B 384 ASP cc_start: 0.8142 (t0) cc_final: 0.7328 (t70) REVERT: B 425 GLU cc_start: 0.7566 (tt0) cc_final: 0.7274 (tt0) REVERT: C 142 ASP cc_start: 0.8544 (t0) cc_final: 0.8310 (t0) REVERT: C 155 TYR cc_start: 0.8503 (m-80) cc_final: 0.7933 (m-80) REVERT: C 214 ASP cc_start: 0.8514 (t0) cc_final: 0.8022 (t0) REVERT: C 254 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.7277 (mmtp) REVERT: C 270 LYS cc_start: 0.8972 (mmmm) cc_final: 0.8543 (tptp) REVERT: C 287 GLU cc_start: 0.7061 (mp0) cc_final: 0.6777 (mp0) REVERT: C 301 ARG cc_start: 0.8363 (mmm-85) cc_final: 0.7889 (mmm-85) REVERT: C 349 PHE cc_start: 0.9173 (p90) cc_final: 0.8794 (p90) REVERT: C 373 MET cc_start: 0.8075 (mmm) cc_final: 0.7732 (mmm) REVERT: C 376 ASP cc_start: 0.8169 (t0) cc_final: 0.7930 (t0) REVERT: C 384 ASP cc_start: 0.8156 (t0) cc_final: 0.7377 (t70) REVERT: C 425 GLU cc_start: 0.7561 (tt0) cc_final: 0.7285 (tt0) REVERT: D 142 ASP cc_start: 0.8538 (t0) cc_final: 0.8292 (t0) REVERT: D 155 TYR cc_start: 0.8496 (m-80) cc_final: 0.7928 (m-80) REVERT: D 156 ARG cc_start: 0.8249 (ttm110) cc_final: 0.7913 (ttp-110) REVERT: D 214 ASP cc_start: 0.8576 (t0) cc_final: 0.8041 (t0) REVERT: D 254 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.7232 (mmtp) REVERT: D 270 LYS cc_start: 0.8976 (mmmm) cc_final: 0.8532 (tptp) REVERT: D 275 HIS cc_start: 0.8466 (t-90) cc_final: 0.8006 (t-90) REVERT: D 287 GLU cc_start: 0.7097 (mp0) cc_final: 0.6782 (mp0) REVERT: D 293 ARG cc_start: 0.7457 (mtm110) cc_final: 0.6689 (mtp85) REVERT: D 301 ARG cc_start: 0.8194 (mmm-85) cc_final: 0.7868 (mmm-85) REVERT: D 349 PHE cc_start: 0.9140 (p90) cc_final: 0.8793 (p90) REVERT: D 376 ASP cc_start: 0.8166 (t0) cc_final: 0.7933 (t0) REVERT: D 384 ASP cc_start: 0.8120 (t0) cc_final: 0.7335 (t70) REVERT: D 425 GLU cc_start: 0.7622 (tt0) cc_final: 0.7322 (tt0) REVERT: D 432 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7800 (tt0) outliers start: 61 outliers final: 53 residues processed: 486 average time/residue: 0.0826 time to fit residues: 58.9933 Evaluate side-chains 503 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 446 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 139 LEU 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 241 ILE 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 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 241 ILE 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 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 241 ILE 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 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 139 LEU Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 241 ILE 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 413 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 126 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 ASN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.141238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.109423 restraints weight = 19928.143| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 5.10 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 12612 Z= 0.264 Angle : 0.818 9.488 17156 Z= 0.421 Chirality : 0.054 0.249 1816 Planarity : 0.005 0.046 2192 Dihedral : 5.602 28.915 2032 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 5.69 % Allowed : 33.98 % Favored : 60.33 % 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: -1.90 (0.21), residues: 1540 helix: -3.13 (0.52), residues: 48 sheet: -0.01 (0.24), residues: 520 loop : -2.00 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 293 TYR 0.023 0.002 TYR A 312 PHE 0.011 0.002 PHE C 445 TRP 0.117 0.002 TRP A 296 HIS 0.022 0.002 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.26 (12568) covalent geometry : angle 0.79964 / 0.41 (17056) SS BOND : bond 0.00901 / 0.46 ( 32) SS BOND : angle 2.85218 / 1.96 ( 64) hydrogen bonds : bond 0.03075 / 2.18 ( 300) hydrogen bonds : angle 6.43584 / 4.46 ( 732) link_NAG-ASN : bond 0.00207 / 0.14 ( 12) link_NAG-ASN : angle 1.28208 / 0.76 ( 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 547 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 471 time to evaluate : 0.283 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 155 TYR cc_start: 0.8687 (m-80) cc_final: 0.8114 (m-80) REVERT: A 159 MET cc_start: 0.7838 (mtp) cc_final: 0.7240 (mtp) REVERT: A 175 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8871 (mm-30) REVERT: A 214 ASP cc_start: 0.8568 (t0) cc_final: 0.8082 (t0) REVERT: A 253 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.8104 (m-80) REVERT: A 254 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7515 (mmtp) REVERT: A 260 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8731 (pptt) REVERT: A 270 LYS cc_start: 0.9041 (mmmm) cc_final: 0.8603 (tptp) REVERT: A 275 HIS cc_start: 0.8511 (t-90) cc_final: 0.8299 (t-90) REVERT: A 293 ARG cc_start: 0.7837 (mtm110) cc_final: 0.6942 (mtp85) REVERT: A 349 PHE cc_start: 0.9217 (p90) cc_final: 0.8866 (p90) REVERT: A 425 GLU cc_start: 0.7692 (tt0) cc_final: 0.7424 (tt0) REVERT: B 155 TYR cc_start: 0.8677 (m-80) cc_final: 0.8103 (m-80) REVERT: B 159 MET cc_start: 0.7874 (mtp) cc_final: 0.7280 (mtp) REVERT: B 214 ASP cc_start: 0.8455 (t0) cc_final: 0.7956 (t0) REVERT: B 254 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7591 (mmtp) REVERT: B 270 LYS cc_start: 0.9005 (mmmm) cc_final: 0.8582 (tptp) REVERT: B 294 ASP cc_start: 0.8241 (t70) cc_final: 0.7416 (p0) REVERT: B 311 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8099 (mm-30) REVERT: B 349 PHE cc_start: 0.9226 (p90) cc_final: 0.8885 (p90) REVERT: B 384 ASP cc_start: 0.8125 (t0) cc_final: 0.7491 (t0) REVERT: B 425 GLU cc_start: 0.7844 (tt0) cc_final: 0.7487 (tt0) REVERT: C 155 TYR cc_start: 0.8627 (m-80) cc_final: 0.8071 (m-80) REVERT: C 159 MET cc_start: 0.7856 (mtp) cc_final: 0.7285 (mtp) REVERT: C 175 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8856 (mm-30) REVERT: C 209 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8440 (t0) REVERT: C 214 ASP cc_start: 0.8495 (t0) cc_final: 0.8189 (t0) REVERT: C 253 TYR cc_start: 0.8249 (OUTLIER) cc_final: 0.8011 (m-80) REVERT: C 254 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7595 (mmtp) REVERT: C 270 LYS cc_start: 0.9018 (mmmm) cc_final: 0.8595 (tptp) REVERT: C 275 HIS cc_start: 0.8529 (t-90) cc_final: 0.8262 (t-90) REVERT: C 293 ARG cc_start: 0.7652 (ptm160) cc_final: 0.7388 (ptm160) REVERT: C 294 ASP cc_start: 0.8459 (t70) cc_final: 0.8167 (t0) REVERT: C 425 GLU cc_start: 0.7823 (tt0) cc_final: 0.7480 (tt0) REVERT: D 142 ASP cc_start: 0.8637 (t0) cc_final: 0.8434 (t0) REVERT: D 155 TYR cc_start: 0.8666 (m-80) cc_final: 0.8093 (m-80) REVERT: D 159 MET cc_start: 0.7874 (mtp) cc_final: 0.7321 (mtp) REVERT: D 175 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8850 (mm-30) REVERT: D 214 ASP cc_start: 0.8569 (t0) cc_final: 0.8063 (t0) REVERT: D 254 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7583 (mmtp) REVERT: D 270 LYS cc_start: 0.9030 (mmmm) cc_final: 0.8596 (tptp) REVERT: D 275 HIS cc_start: 0.8509 (t-90) cc_final: 0.8297 (t-90) REVERT: D 293 ARG cc_start: 0.7799 (mtm110) cc_final: 0.7266 (mtp85) REVERT: D 349 PHE cc_start: 0.9223 (p90) cc_final: 0.8895 (p90) REVERT: D 384 ASP cc_start: 0.8219 (t0) cc_final: 0.7622 (t0) REVERT: D 425 GLU cc_start: 0.7645 (tt0) cc_final: 0.7359 (tt0) outliers start: 76 outliers final: 52 residues processed: 501 average time/residue: 0.0916 time to fit residues: 67.5573 Evaluate side-chains 508 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 448 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 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 260 LYS 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 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 168 SER 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 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 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 413 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 86 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 ASN ** C 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 = 0.3869 r_free = 0.3869 target = 0.144695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.113062 restraints weight = 19641.672| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 5.16 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12612 Z= 0.164 Angle : 0.813 12.777 17156 Z= 0.417 Chirality : 0.052 0.193 1816 Planarity : 0.005 0.052 2192 Dihedral : 5.607 40.647 2032 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 5.24 % Allowed : 35.48 % Favored : 59.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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 (0.21), residues: 1540 helix: -2.85 (0.58), residues: 48 sheet: -0.15 (0.24), residues: 524 loop : -2.01 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 293 TYR 0.020 0.001 TYR C 312 PHE 0.013 0.001 PHE C 349 TRP 0.110 0.002 TRP D 296 HIS 0.016 0.002 HIS C 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (12568) covalent geometry : angle 0.79776 / 0.41 (17056) SS BOND : bond 0.00712 / 0.37 ( 32) SS BOND : angle 2.61004 / 1.78 ( 64) hydrogen bonds : bond 0.02420 / 1.69 ( 300) hydrogen bonds : angle 6.33377 / 4.37 ( 732) link_NAG-ASN : bond 0.00181 / 0.12 ( 12) link_NAG-ASN : angle 1.07299 / 0.65 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2007.32 seconds wall clock time: 35 minutes 18.82 seconds (2118.82 seconds total)