Starting phenix.real_space_refine on Sat Aug 23 12:17:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o5u_70148/08_2025/9o5u_70148.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o5u_70148/08_2025/9o5u_70148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o5u_70148/08_2025/9o5u_70148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o5u_70148/08_2025/9o5u_70148.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o5u_70148/08_2025/9o5u_70148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o5u_70148/08_2025/9o5u_70148.map" } resolution = 2.75 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= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 7128 2.51 5 N 2036 2.21 5 O 2320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11612 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2889 Classifications: {'peptide': 386} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 368} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D Time building chain proxies: 2.60, per 1000 atoms: 0.22 Number of scatterers: 11612 At special positions: 0 Unit cell: (122.778, 122.778, 63.902, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 2320 8.00 N 2036 7.00 C 7128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 82 " - pdb=" SG CYS A 416 " distance=2.02 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 122 " distance=2.03 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 224 " distance=2.02 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 231 " distance=2.04 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 288 " distance=2.02 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 286 " distance=2.03 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 440 " distance=2.03 Simple disulfide: pdb=" SG CYS B 82 " - pdb=" SG CYS B 416 " distance=2.02 Simple disulfide: pdb=" SG CYS C 82 " - pdb=" SG CYS C 416 " distance=2.02 Simple disulfide: pdb=" SG CYS D 82 " - pdb=" SG CYS D 416 " distance=2.02 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 122 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 122 " distance=2.03 Simple disulfide: pdb=" SG CYS D 117 " - pdb=" SG CYS D 122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 224 " distance=2.02 Simple disulfide: pdb=" SG CYS C 177 " - pdb=" SG CYS C 224 " distance=2.02 Simple disulfide: pdb=" SG CYS D 177 " - pdb=" SG CYS D 224 " distance=2.02 Simple disulfide: pdb=" SG CYS B 226 " - pdb=" SG CYS B 231 " distance=2.04 Simple disulfide: pdb=" SG CYS C 226 " - pdb=" SG CYS C 231 " distance=2.04 Simple disulfide: pdb=" SG CYS D 226 " - pdb=" SG CYS D 231 " distance=2.04 Simple disulfide: pdb=" SG CYS B 274 " - pdb=" SG CYS B 288 " distance=2.02 Simple disulfide: pdb=" SG CYS C 274 " - pdb=" SG CYS C 288 " distance=2.02 Simple disulfide: pdb=" SG CYS D 274 " - pdb=" SG CYS D 288 " distance=2.02 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 286 " distance=2.03 Simple disulfide: pdb=" SG CYS C 276 " - pdb=" SG CYS C 286 " distance=2.03 Simple disulfide: pdb=" SG CYS D 276 " - pdb=" SG CYS D 286 " distance=2.03 Simple disulfide: pdb=" SG CYS B 315 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS C 315 " - pdb=" SG CYS C 333 " distance=2.03 Simple disulfide: pdb=" SG CYS D 315 " - pdb=" SG CYS D 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 420 " - pdb=" SG CYS B 440 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 440 " distance=2.03 Simple disulfide: pdb=" SG CYS D 420 " - pdb=" SG CYS D 440 " distance=2.03 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 501 " - " ASN A 281 " " NAG B 501 " - " ASN B 281 " " NAG C 501 " - " ASN C 281 " " NAG D 501 " - " ASN D 281 " Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 621.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 24 sheets defined 0.0% alpha, 45.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 93 removed outlier: 6.794A pdb=" N ILE A 438 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N MET A 92 " --> pdb=" O SER A 436 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER A 436 " --> pdb=" O MET A 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 117 removed outlier: 4.478A pdb=" N HIS A 108 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ALA A 131 " --> pdb=" O HIS A 108 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ASN A 110 " --> pdb=" O HIS A 129 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N HIS A 129 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLU A 112 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LEU A 127 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU A 151 " --> pdb=" O HIS A 168 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 178 removed outlier: 4.006A pdb=" N THR A 191 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N TYR A 201 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LEU A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 217 through 219 Processing sheet with id=AA5, first strand: chain 'A' and resid 217 through 219 removed outlier: 4.132A pdb=" N ASP A 237 " --> pdb=" O GLN A 247 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN A 247 " --> pdb=" O ASP A 237 " (cutoff:3.500A) removed outlier: 11.000A pdb=" N SER A 246 " --> pdb=" O GLY A 266 " (cutoff:3.500A) removed outlier: 11.154A pdb=" N GLY A 266 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ALA A 248 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR A 264 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS A 254 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ILE A 258 " --> pdb=" O LYS A 254 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N ALA A 309 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN A 263 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL A 311 " --> pdb=" O ASN A 263 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N SER A 265 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N LEU A 313 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N THR A 283 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ALA A 278 " --> pdb=" O THR A 283 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N MET A 285 " --> pdb=" O CYS A 276 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N CYS A 276 " --> pdb=" O MET A 285 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ALA A 287 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N CYS A 274 " --> pdb=" O ALA A 287 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 351 removed outlier: 5.835A pdb=" N PHE A 359 " --> pdb=" O PRO A 378 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL A 371 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N THR A 399 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A 375 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ILE A 395 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLY A 377 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 393 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 86 through 93 removed outlier: 6.794A pdb=" N ILE B 438 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N MET B 92 " --> pdb=" O SER B 436 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER B 436 " --> pdb=" O MET B 92 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 108 through 117 removed outlier: 4.478A pdb=" N HIS B 108 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ALA B 131 " --> pdb=" O HIS B 108 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ASN B 110 " --> pdb=" O HIS B 129 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N HIS B 129 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLU B 112 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LEU B 127 " --> pdb=" O GLU B 112 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU B 151 " --> pdb=" O HIS B 168 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 173 through 178 removed outlier: 4.006A pdb=" N THR B 191 " --> pdb=" O ASP B 194 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N TYR B 201 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LEU B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 217 through 219 Processing sheet with id=AB2, first strand: chain 'B' and resid 217 through 219 removed outlier: 4.132A pdb=" N ASP B 237 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN B 247 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 11.000A pdb=" N SER B 246 " --> pdb=" O GLY B 266 " (cutoff:3.500A) removed outlier: 11.154A pdb=" N GLY B 266 " --> pdb=" O SER B 246 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ALA B 248 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR B 264 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS B 254 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ILE B 258 " --> pdb=" O LYS B 254 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N ALA B 309 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN B 263 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL B 311 " --> pdb=" O ASN B 263 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N SER B 265 " --> pdb=" O VAL B 311 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N LEU B 313 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N THR B 283 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ALA B 278 " --> pdb=" O THR B 283 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N MET B 285 " --> pdb=" O CYS B 276 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N CYS B 276 " --> pdb=" O MET B 285 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ALA B 287 " --> pdb=" O CYS B 274 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N CYS B 274 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 348 through 351 removed outlier: 5.835A pdb=" N PHE B 359 " --> pdb=" O PRO B 378 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL B 371 " --> pdb=" O THR B 399 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N THR B 399 " --> pdb=" O VAL B 371 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL B 375 " --> pdb=" O ILE B 395 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ILE B 395 " --> pdb=" O VAL B 375 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLY B 377 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU B 393 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 86 through 93 removed outlier: 6.794A pdb=" N ILE C 438 " --> pdb=" O PHE C 90 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N MET C 92 " --> pdb=" O SER C 436 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER C 436 " --> pdb=" O MET C 92 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 108 through 117 removed outlier: 4.478A pdb=" N HIS C 108 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ALA C 131 " --> pdb=" O HIS C 108 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ASN C 110 " --> pdb=" O HIS C 129 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N HIS C 129 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLU C 112 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LEU C 127 " --> pdb=" O GLU C 112 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU C 151 " --> pdb=" O HIS C 168 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 173 through 178 removed outlier: 4.006A pdb=" N THR C 191 " --> pdb=" O ASP C 194 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N TYR C 201 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LEU C 205 " --> pdb=" O TYR C 201 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 217 through 219 Processing sheet with id=AB8, first strand: chain 'C' and resid 217 through 219 removed outlier: 4.132A pdb=" N ASP C 237 " --> pdb=" O GLN C 247 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN C 247 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 11.000A pdb=" N SER C 246 " --> pdb=" O GLY C 266 " (cutoff:3.500A) removed outlier: 11.154A pdb=" N GLY C 266 " --> pdb=" O SER C 246 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ALA C 248 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR C 264 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS C 254 " --> pdb=" O ILE C 258 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ILE C 258 " --> pdb=" O LYS C 254 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N ALA C 309 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN C 263 " --> pdb=" O ALA C 309 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL C 311 " --> pdb=" O ASN C 263 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N SER C 265 " --> pdb=" O VAL C 311 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N LEU C 313 " --> pdb=" O SER C 265 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N THR C 283 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ALA C 278 " --> pdb=" O THR C 283 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N MET C 285 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N CYS C 276 " --> pdb=" O MET C 285 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ALA C 287 " --> pdb=" O CYS C 274 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N CYS C 274 " --> pdb=" O ALA C 287 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 348 through 351 removed outlier: 5.835A pdb=" N PHE C 359 " --> pdb=" O PRO C 378 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL C 371 " --> pdb=" O THR C 399 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N THR C 399 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL C 375 " --> pdb=" O ILE C 395 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ILE C 395 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLY C 377 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU C 393 " --> pdb=" O GLY C 377 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 86 through 93 removed outlier: 6.794A pdb=" N ILE D 438 " --> pdb=" O PHE D 90 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N MET D 92 " --> pdb=" O SER D 436 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER D 436 " --> pdb=" O MET D 92 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 108 through 117 removed outlier: 4.478A pdb=" N HIS D 108 " --> pdb=" O ALA D 131 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ALA D 131 " --> pdb=" O HIS D 108 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ASN D 110 " --> pdb=" O HIS D 129 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N HIS D 129 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLU D 112 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LEU D 127 " --> pdb=" O GLU D 112 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU D 151 " --> pdb=" O HIS D 168 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 173 through 178 removed outlier: 4.006A pdb=" N THR D 191 " --> pdb=" O ASP D 194 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N TYR D 201 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LEU D 205 " --> pdb=" O TYR D 201 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 217 through 219 Processing sheet with id=AC5, first strand: chain 'D' and resid 217 through 219 removed outlier: 4.132A pdb=" N ASP D 237 " --> pdb=" O GLN D 247 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN D 247 " --> pdb=" O ASP D 237 " (cutoff:3.500A) removed outlier: 11.000A pdb=" N SER D 246 " --> pdb=" O GLY D 266 " (cutoff:3.500A) removed outlier: 11.154A pdb=" N GLY D 266 " --> pdb=" O SER D 246 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ALA D 248 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR D 264 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS D 254 " --> pdb=" O ILE D 258 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ILE D 258 " --> pdb=" O LYS D 254 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N ALA D 309 " --> pdb=" O VAL D 261 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN D 263 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL D 311 " --> pdb=" O ASN D 263 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N SER D 265 " --> pdb=" O VAL D 311 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N LEU D 313 " --> pdb=" O SER D 265 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N THR D 283 " --> pdb=" O ALA D 278 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ALA D 278 " --> pdb=" O THR D 283 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N MET D 285 " --> pdb=" O CYS D 276 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N CYS D 276 " --> pdb=" O MET D 285 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ALA D 287 " --> pdb=" O CYS D 274 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N CYS D 274 " --> pdb=" O ALA D 287 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 348 through 351 removed outlier: 5.835A pdb=" N PHE D 359 " --> pdb=" O PRO D 378 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL D 371 " --> pdb=" O THR D 399 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N THR D 399 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL D 375 " --> pdb=" O ILE D 395 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ILE D 395 " --> pdb=" O VAL D 375 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLY D 377 " --> pdb=" O LEU D 393 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU D 393 " --> pdb=" O GLY D 377 " (cutoff:3.500A) 364 hydrogen bonds defined for protein. 972 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.16 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 3944 1.36 - 1.49: 3096 1.49 - 1.62: 4616 1.62 - 1.75: 4 1.75 - 1.89: 188 Bond restraints: 11848 Sorted by residual: bond pdb=" CB CYS C 315 " pdb=" SG CYS C 315 " ideal model delta sigma weight residual 1.808 1.885 -0.077 3.30e-02 9.18e+02 5.49e+00 bond pdb=" CB CYS B 315 " pdb=" SG CYS B 315 " ideal model delta sigma weight residual 1.808 1.885 -0.077 3.30e-02 9.18e+02 5.49e+00 bond pdb=" CB CYS A 315 " pdb=" SG CYS A 315 " ideal model delta sigma weight residual 1.808 1.885 -0.077 3.30e-02 9.18e+02 5.49e+00 bond pdb=" CB CYS D 315 " pdb=" SG CYS D 315 " ideal model delta sigma weight residual 1.808 1.885 -0.077 3.30e-02 9.18e+02 5.49e+00 bond pdb=" CB CYS B 333 " pdb=" SG CYS B 333 " ideal model delta sigma weight residual 1.808 1.735 0.073 3.30e-02 9.18e+02 4.93e+00 ... (remaining 11843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 14780 2.10 - 4.21: 1088 4.21 - 6.31: 160 6.31 - 8.42: 8 8.42 - 10.52: 16 Bond angle restraints: 16052 Sorted by residual: angle pdb=" N ILE C 414 " pdb=" CA ILE C 414 " pdb=" C ILE C 414 " ideal model delta sigma weight residual 110.82 102.08 8.74 9.70e-01 1.06e+00 8.13e+01 angle pdb=" N ILE D 414 " pdb=" CA ILE D 414 " pdb=" C ILE D 414 " ideal model delta sigma weight residual 110.82 102.08 8.74 9.70e-01 1.06e+00 8.13e+01 angle pdb=" N ILE B 414 " pdb=" CA ILE B 414 " pdb=" C ILE B 414 " ideal model delta sigma weight residual 110.82 102.08 8.74 9.70e-01 1.06e+00 8.13e+01 angle pdb=" N ILE A 414 " pdb=" CA ILE A 414 " pdb=" C ILE A 414 " ideal model delta sigma weight residual 110.82 102.08 8.74 9.70e-01 1.06e+00 8.13e+01 angle pdb=" CA PRO C 159 " pdb=" N PRO C 159 " pdb=" CD PRO C 159 " ideal model delta sigma weight residual 112.00 101.78 10.22 1.40e+00 5.10e-01 5.33e+01 ... (remaining 16047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 6784 17.51 - 35.02: 288 35.02 - 52.53: 72 52.53 - 70.03: 28 70.03 - 87.54: 8 Dihedral angle restraints: 7180 sinusoidal: 2836 harmonic: 4344 Sorted by residual: dihedral pdb=" CG ARG C 149 " pdb=" CD ARG C 149 " pdb=" NE ARG C 149 " pdb=" CZ ARG C 149 " ideal model delta sinusoidal sigma weight residual 180.00 135.76 44.24 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG D 149 " pdb=" CD ARG D 149 " pdb=" NE ARG D 149 " pdb=" CZ ARG D 149 " ideal model delta sinusoidal sigma weight residual 180.00 135.76 44.24 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG B 149 " pdb=" CD ARG B 149 " pdb=" NE ARG B 149 " pdb=" CZ ARG B 149 " ideal model delta sinusoidal sigma weight residual 180.00 135.76 44.24 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 7177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1312 0.070 - 0.139: 384 0.139 - 0.208: 72 0.208 - 0.278: 4 0.278 - 0.347: 8 Chirality restraints: 1780 Sorted by residual: chirality pdb=" CB VAL B 197 " pdb=" CA VAL B 197 " pdb=" CG1 VAL B 197 " pdb=" CG2 VAL B 197 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CB VAL A 197 " pdb=" CA VAL A 197 " pdb=" CG1 VAL A 197 " pdb=" CG2 VAL A 197 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CB VAL C 197 " pdb=" CA VAL C 197 " pdb=" CG1 VAL C 197 " pdb=" CG2 VAL C 197 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 1777 not shown) Planarity restraints: 2120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 158 " 0.082 5.00e-02 4.00e+02 1.17e-01 2.21e+01 pdb=" N PRO B 159 " -0.203 5.00e-02 4.00e+02 pdb=" CA PRO B 159 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 159 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 158 " -0.082 5.00e-02 4.00e+02 1.17e-01 2.21e+01 pdb=" N PRO A 159 " 0.203 5.00e-02 4.00e+02 pdb=" CA PRO A 159 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 159 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 158 " -0.082 5.00e-02 4.00e+02 1.17e-01 2.21e+01 pdb=" N PRO D 159 " 0.203 5.00e-02 4.00e+02 pdb=" CA PRO D 159 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO D 159 " -0.063 5.00e-02 4.00e+02 ... (remaining 2117 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1360 2.75 - 3.29: 10980 3.29 - 3.82: 20192 3.82 - 4.36: 26044 4.36 - 4.90: 45512 Nonbonded interactions: 104088 Sorted by model distance: nonbonded pdb=" O ASN A 203 " pdb=" OD1 ASN A 203 " model vdw 2.211 3.040 nonbonded pdb=" O ASN D 203 " pdb=" OD1 ASN D 203 " model vdw 2.211 3.040 nonbonded pdb=" O ASN C 203 " pdb=" OD1 ASN C 203 " model vdw 2.211 3.040 nonbonded pdb=" O ASN B 203 " pdb=" OD1 ASN B 203 " model vdw 2.211 3.040 nonbonded pdb=" O ASP A 337 " pdb=" OD1 ASP A 337 " model vdw 2.266 3.040 ... (remaining 104083 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.730 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 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 : 0.007 0.098 11884 Z= 0.287 Angle : 1.234 12.137 16128 Z= 0.732 Chirality : 0.069 0.347 1780 Planarity : 0.009 0.117 2116 Dihedral : 11.687 87.540 4332 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.20), residues: 1536 helix: -3.58 (0.77), residues: 24 sheet: 0.65 (0.22), residues: 564 loop : -0.45 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 296 TYR 0.018 0.004 TYR B 98 PHE 0.041 0.006 PHE D 160 TRP 0.018 0.006 TRP B 172 HIS 0.006 0.002 HIS D 129 Details of bonding type rmsd covalent geometry : bond 0.00665 (11848) covalent geometry : angle 1.19629 (16052) SS BOND : bond 0.00802 ( 32) SS BOND : angle 4.53406 ( 64) hydrogen bonds : bond 0.11183 ( 356) hydrogen bonds : angle 7.93764 ( 972) link_NAG-ASN : bond 0.00362 ( 4) link_NAG-ASN : angle 4.78182 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.480 Fit side-chains REVERT: A 150 MET cc_start: 0.8006 (mtt) cc_final: 0.7312 (pp-130) REVERT: A 257 LYS cc_start: 0.8309 (mtmm) cc_final: 0.7691 (ttmm) REVERT: A 371 VAL cc_start: 0.7357 (t) cc_final: 0.7124 (p) REVERT: B 150 MET cc_start: 0.8043 (mtt) cc_final: 0.7338 (pp-130) REVERT: B 257 LYS cc_start: 0.8292 (mtmm) cc_final: 0.7674 (ttmm) REVERT: B 371 VAL cc_start: 0.7365 (t) cc_final: 0.7139 (p) REVERT: C 150 MET cc_start: 0.8035 (mtt) cc_final: 0.7317 (pp-130) REVERT: C 257 LYS cc_start: 0.8308 (mtmm) cc_final: 0.7689 (ttmm) REVERT: C 371 VAL cc_start: 0.7375 (t) cc_final: 0.7146 (p) REVERT: D 150 MET cc_start: 0.8016 (mtt) cc_final: 0.7299 (pp-130) REVERT: D 257 LYS cc_start: 0.8314 (mtmm) cc_final: 0.7699 (ttmm) REVERT: D 371 VAL cc_start: 0.7374 (t) cc_final: 0.7138 (p) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.6642 time to fit residues: 117.7794 Evaluate side-chains 136 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN A 291 ASN B 291 ASN C 291 ASN D 255 GLN D 291 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.137174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.113336 restraints weight = 13136.549| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.84 r_work: 0.3224 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 11884 Z= 0.274 Angle : 0.740 6.352 16128 Z= 0.413 Chirality : 0.052 0.149 1780 Planarity : 0.006 0.042 2116 Dihedral : 6.025 26.165 1768 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.88 % Allowed : 8.15 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.21), residues: 1536 helix: -3.50 (0.68), residues: 48 sheet: 0.33 (0.21), residues: 580 loop : -0.97 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 149 TYR 0.010 0.002 TYR B 98 PHE 0.018 0.003 PHE D 114 TRP 0.013 0.002 TRP D 172 HIS 0.004 0.001 HIS C 168 Details of bonding type rmsd covalent geometry : bond 0.00638 (11848) covalent geometry : angle 0.73121 (16052) SS BOND : bond 0.00435 ( 32) SS BOND : angle 1.84590 ( 64) hydrogen bonds : bond 0.05914 ( 356) hydrogen bonds : angle 6.72050 ( 972) link_NAG-ASN : bond 0.00144 ( 4) link_NAG-ASN : angle 1.69089 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.502 Fit side-chains REVERT: A 150 MET cc_start: 0.8285 (mtt) cc_final: 0.7398 (pmt) REVERT: A 415 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7912 (mt-10) REVERT: B 150 MET cc_start: 0.8241 (mtt) cc_final: 0.7405 (pmt) REVERT: B 415 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7906 (mt-10) REVERT: C 150 MET cc_start: 0.8257 (mtt) cc_final: 0.7413 (pmt) REVERT: C 415 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7903 (mt-10) REVERT: D 150 MET cc_start: 0.8300 (mtt) cc_final: 0.7410 (pmt) REVERT: D 415 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7922 (mt-10) outliers start: 24 outliers final: 8 residues processed: 180 average time/residue: 0.5397 time to fit residues: 106.6052 Evaluate side-chains 152 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 415 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 70 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 84 optimal weight: 20.0000 chunk 123 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.137250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.113640 restraints weight = 13298.010| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.84 r_work: 0.3235 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11884 Z= 0.228 Angle : 0.668 6.091 16128 Z= 0.370 Chirality : 0.049 0.145 1780 Planarity : 0.005 0.028 2116 Dihedral : 5.982 27.598 1768 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.51 % Allowed : 9.40 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.21), residues: 1536 helix: -4.43 (0.28), residues: 24 sheet: 0.12 (0.21), residues: 572 loop : -1.18 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 149 TYR 0.007 0.001 TYR A 201 PHE 0.017 0.003 PHE B 160 TRP 0.012 0.002 TRP A 172 HIS 0.004 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00535 (11848) covalent geometry : angle 0.65812 (16052) SS BOND : bond 0.00357 ( 32) SS BOND : angle 1.80190 ( 64) hydrogen bonds : bond 0.05151 ( 356) hydrogen bonds : angle 6.55638 ( 972) link_NAG-ASN : bond 0.00167 ( 4) link_NAG-ASN : angle 1.94527 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.495 Fit side-chains REVERT: A 150 MET cc_start: 0.8245 (mtt) cc_final: 0.7397 (pmt) REVERT: A 415 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7479 (mt-10) REVERT: B 150 MET cc_start: 0.8205 (mtt) cc_final: 0.7400 (pmt) REVERT: B 415 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7506 (mt-10) REVERT: C 150 MET cc_start: 0.8197 (mtt) cc_final: 0.7404 (pmt) REVERT: C 415 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7479 (mt-10) REVERT: D 150 MET cc_start: 0.8250 (mtt) cc_final: 0.7402 (pmt) REVERT: D 415 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7479 (mt-10) outliers start: 32 outliers final: 12 residues processed: 164 average time/residue: 0.6282 time to fit residues: 112.0212 Evaluate side-chains 152 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 415 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 12 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.139072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.115400 restraints weight = 13284.649| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.87 r_work: 0.3234 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11884 Z= 0.180 Angle : 0.633 5.871 16128 Z= 0.347 Chirality : 0.048 0.141 1780 Planarity : 0.004 0.026 2116 Dihedral : 5.795 26.547 1768 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.57 % Allowed : 11.60 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.21), residues: 1536 helix: -4.34 (0.30), residues: 24 sheet: -0.10 (0.21), residues: 572 loop : -1.25 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 149 TYR 0.005 0.001 TYR A 137 PHE 0.014 0.002 PHE B 114 TRP 0.010 0.002 TRP A 172 HIS 0.003 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00422 (11848) covalent geometry : angle 0.62200 (16052) SS BOND : bond 0.00225 ( 32) SS BOND : angle 1.78235 ( 64) hydrogen bonds : bond 0.04596 ( 356) hydrogen bonds : angle 6.39406 ( 972) link_NAG-ASN : bond 0.00188 ( 4) link_NAG-ASN : angle 1.86025 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.486 Fit side-chains REVERT: A 150 MET cc_start: 0.8209 (mtt) cc_final: 0.7462 (pmt) REVERT: A 291 ASN cc_start: 0.8813 (t0) cc_final: 0.8556 (t0) REVERT: A 415 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7664 (mt-10) REVERT: B 150 MET cc_start: 0.8227 (mtt) cc_final: 0.7461 (pmt) REVERT: B 291 ASN cc_start: 0.8804 (t0) cc_final: 0.8544 (t0) REVERT: B 415 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7637 (mt-10) REVERT: C 150 MET cc_start: 0.8195 (mtt) cc_final: 0.7475 (pmt) REVERT: C 291 ASN cc_start: 0.8813 (t0) cc_final: 0.8553 (t0) REVERT: C 415 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7629 (mt-10) REVERT: D 150 MET cc_start: 0.8254 (mtt) cc_final: 0.7472 (pmt) REVERT: D 291 ASN cc_start: 0.8831 (t0) cc_final: 0.8572 (t0) REVERT: D 415 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7633 (mt-10) outliers start: 20 outliers final: 12 residues processed: 160 average time/residue: 0.6071 time to fit residues: 106.1060 Evaluate side-chains 160 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 177 CYS Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 177 CYS Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 415 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 89 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 1 optimal weight: 0.0970 chunk 113 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.137498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.113851 restraints weight = 13260.381| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.87 r_work: 0.3216 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 11884 Z= 0.217 Angle : 0.651 5.576 16128 Z= 0.355 Chirality : 0.048 0.145 1780 Planarity : 0.004 0.028 2116 Dihedral : 5.865 27.833 1768 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.82 % Allowed : 11.60 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.21), residues: 1536 helix: None (None), residues: 0 sheet: -0.08 (0.21), residues: 564 loop : -1.24 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 149 TYR 0.007 0.001 TYR A 137 PHE 0.015 0.002 PHE A 114 TRP 0.010 0.002 TRP D 172 HIS 0.003 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00513 (11848) covalent geometry : angle 0.64321 (16052) SS BOND : bond 0.00275 ( 32) SS BOND : angle 1.57669 ( 64) hydrogen bonds : bond 0.04760 ( 356) hydrogen bonds : angle 6.45771 ( 972) link_NAG-ASN : bond 0.00143 ( 4) link_NAG-ASN : angle 1.87706 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 0.491 Fit side-chains REVERT: A 150 MET cc_start: 0.8229 (mtt) cc_final: 0.7452 (pmt) REVERT: A 291 ASN cc_start: 0.8902 (t0) cc_final: 0.8624 (t0) REVERT: A 415 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7789 (mt-10) REVERT: B 150 MET cc_start: 0.8217 (mtt) cc_final: 0.7446 (pmt) REVERT: B 291 ASN cc_start: 0.8893 (t0) cc_final: 0.8611 (t0) REVERT: B 415 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7800 (mt-10) REVERT: C 150 MET cc_start: 0.8223 (mtt) cc_final: 0.7458 (pmt) REVERT: C 291 ASN cc_start: 0.8900 (t0) cc_final: 0.8617 (t0) REVERT: C 415 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7761 (mt-10) REVERT: D 150 MET cc_start: 0.8239 (mtt) cc_final: 0.7453 (pmt) REVERT: D 291 ASN cc_start: 0.8926 (t0) cc_final: 0.8643 (t0) REVERT: D 415 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7743 (mt-10) outliers start: 36 outliers final: 24 residues processed: 184 average time/residue: 0.5733 time to fit residues: 115.4003 Evaluate side-chains 180 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 416 CYS Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 177 CYS Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 177 CYS Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 416 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 145 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 146 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 0.0470 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 203 ASN B 108 HIS B 203 ASN C 108 HIS C 203 ASN D 108 HIS D 203 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.142230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.118910 restraints weight = 13072.368| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.86 r_work: 0.3278 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11884 Z= 0.128 Angle : 0.576 5.959 16128 Z= 0.312 Chirality : 0.046 0.135 1780 Planarity : 0.004 0.023 2116 Dihedral : 5.470 24.107 1768 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.88 % Allowed : 12.85 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.21), residues: 1536 helix: None (None), residues: 0 sheet: -0.24 (0.21), residues: 572 loop : -1.17 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 149 TYR 0.005 0.001 TYR D 137 PHE 0.012 0.002 PHE B 114 TRP 0.010 0.001 TRP A 172 HIS 0.003 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00301 (11848) covalent geometry : angle 0.56692 (16052) SS BOND : bond 0.00142 ( 32) SS BOND : angle 1.49989 ( 64) hydrogen bonds : bond 0.03976 ( 356) hydrogen bonds : angle 6.18002 ( 972) link_NAG-ASN : bond 0.00276 ( 4) link_NAG-ASN : angle 1.79700 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.488 Fit side-chains REVERT: A 150 MET cc_start: 0.8220 (mtt) cc_final: 0.7455 (pmt) REVERT: A 291 ASN cc_start: 0.8714 (t0) cc_final: 0.8458 (t0) REVERT: A 307 LYS cc_start: 0.8880 (mttt) cc_final: 0.7830 (mmpt) REVERT: B 150 MET cc_start: 0.8225 (mtt) cc_final: 0.7454 (pmt) REVERT: B 291 ASN cc_start: 0.8704 (t0) cc_final: 0.8446 (t0) REVERT: B 307 LYS cc_start: 0.8870 (mttt) cc_final: 0.7821 (mmpt) REVERT: C 150 MET cc_start: 0.8194 (mtt) cc_final: 0.7460 (pmt) REVERT: C 291 ASN cc_start: 0.8714 (t0) cc_final: 0.8454 (t0) REVERT: C 307 LYS cc_start: 0.8875 (mttt) cc_final: 0.7828 (mmpt) REVERT: D 150 MET cc_start: 0.8234 (mtt) cc_final: 0.7455 (pmt) REVERT: D 291 ASN cc_start: 0.8719 (t0) cc_final: 0.8460 (t0) REVERT: D 307 LYS cc_start: 0.8884 (mttt) cc_final: 0.7851 (mmpt) outliers start: 24 outliers final: 12 residues processed: 164 average time/residue: 0.6263 time to fit residues: 111.4787 Evaluate side-chains 164 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 387 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 99 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 79 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS B 108 HIS C 108 HIS D 108 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.137572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.113769 restraints weight = 13280.806| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.87 r_work: 0.3208 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 11884 Z= 0.231 Angle : 0.659 6.508 16128 Z= 0.355 Chirality : 0.049 0.146 1780 Planarity : 0.004 0.031 2116 Dihedral : 5.854 27.504 1768 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.19 % Allowed : 13.17 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.21), residues: 1536 helix: None (None), residues: 0 sheet: -0.18 (0.21), residues: 572 loop : -1.34 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 149 TYR 0.007 0.001 TYR B 137 PHE 0.015 0.002 PHE A 114 TRP 0.009 0.002 TRP A 172 HIS 0.003 0.001 HIS D 168 Details of bonding type rmsd covalent geometry : bond 0.00553 (11848) covalent geometry : angle 0.64895 (16052) SS BOND : bond 0.00279 ( 32) SS BOND : angle 1.73923 ( 64) hydrogen bonds : bond 0.04689 ( 356) hydrogen bonds : angle 6.42529 ( 972) link_NAG-ASN : bond 0.00147 ( 4) link_NAG-ASN : angle 1.86894 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.552 Fit side-chains REVERT: A 150 MET cc_start: 0.8233 (mtt) cc_final: 0.7462 (pmt) REVERT: B 150 MET cc_start: 0.8214 (mtt) cc_final: 0.7456 (pmt) REVERT: C 150 MET cc_start: 0.8198 (mtt) cc_final: 0.7461 (pmt) REVERT: D 150 MET cc_start: 0.8257 (mtt) cc_final: 0.7465 (pmt) outliers start: 28 outliers final: 24 residues processed: 164 average time/residue: 0.5794 time to fit residues: 103.7449 Evaluate side-chains 172 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 416 CYS Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 177 CYS Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 177 CYS Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 416 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 90 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 120 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 chunk 107 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS B 108 HIS C 108 HIS D 108 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.141279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.117638 restraints weight = 13021.870| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.87 r_work: 0.3267 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11884 Z= 0.141 Angle : 0.583 5.769 16128 Z= 0.315 Chirality : 0.046 0.137 1780 Planarity : 0.004 0.023 2116 Dihedral : 5.491 24.474 1768 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.19 % Allowed : 13.48 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.21), residues: 1536 helix: None (None), residues: 0 sheet: -0.24 (0.21), residues: 564 loop : -1.26 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 149 TYR 0.006 0.001 TYR B 137 PHE 0.012 0.002 PHE C 114 TRP 0.010 0.002 TRP A 172 HIS 0.003 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00330 (11848) covalent geometry : angle 0.57370 (16052) SS BOND : bond 0.00177 ( 32) SS BOND : angle 1.53612 ( 64) hydrogen bonds : bond 0.04076 ( 356) hydrogen bonds : angle 6.20946 ( 972) link_NAG-ASN : bond 0.00257 ( 4) link_NAG-ASN : angle 1.84153 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.474 Fit side-chains REVERT: A 150 MET cc_start: 0.8200 (mtt) cc_final: 0.7463 (pmt) REVERT: A 291 ASN cc_start: 0.8829 (t0) cc_final: 0.8570 (t0) REVERT: B 150 MET cc_start: 0.8180 (mtt) cc_final: 0.7463 (pmt) REVERT: B 291 ASN cc_start: 0.8828 (t0) cc_final: 0.8565 (t0) REVERT: C 150 MET cc_start: 0.8174 (mtt) cc_final: 0.7461 (pmt) REVERT: C 291 ASN cc_start: 0.8816 (t0) cc_final: 0.8551 (t0) REVERT: D 150 MET cc_start: 0.8214 (mtt) cc_final: 0.7464 (pmt) REVERT: D 291 ASN cc_start: 0.8821 (t0) cc_final: 0.8556 (t0) outliers start: 28 outliers final: 20 residues processed: 172 average time/residue: 0.5420 time to fit residues: 102.1776 Evaluate side-chains 176 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 416 CYS Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 416 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 25 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.141184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.117520 restraints weight = 12994.485| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.87 r_work: 0.3266 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11884 Z= 0.147 Angle : 0.585 5.585 16128 Z= 0.315 Chirality : 0.047 0.138 1780 Planarity : 0.003 0.022 2116 Dihedral : 5.432 24.302 1768 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.57 % Allowed : 14.73 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.21), residues: 1536 helix: None (None), residues: 0 sheet: -0.20 (0.22), residues: 564 loop : -1.26 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 149 TYR 0.006 0.001 TYR D 137 PHE 0.012 0.002 PHE D 114 TRP 0.010 0.001 TRP B 172 HIS 0.003 0.001 HIS D 168 Details of bonding type rmsd covalent geometry : bond 0.00347 (11848) covalent geometry : angle 0.57740 (16052) SS BOND : bond 0.00165 ( 32) SS BOND : angle 1.42182 ( 64) hydrogen bonds : bond 0.04079 ( 356) hydrogen bonds : angle 6.19915 ( 972) link_NAG-ASN : bond 0.00239 ( 4) link_NAG-ASN : angle 1.83314 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.477 Fit side-chains REVERT: A 150 MET cc_start: 0.8175 (mtt) cc_final: 0.7460 (pmt) REVERT: A 291 ASN cc_start: 0.8842 (t0) cc_final: 0.8597 (t0) REVERT: B 150 MET cc_start: 0.8162 (mtt) cc_final: 0.7460 (pmt) REVERT: B 291 ASN cc_start: 0.8843 (t0) cc_final: 0.8597 (t0) REVERT: C 150 MET cc_start: 0.8157 (mtt) cc_final: 0.7475 (pmt) REVERT: C 291 ASN cc_start: 0.8830 (t0) cc_final: 0.8580 (t0) REVERT: D 150 MET cc_start: 0.8207 (mtt) cc_final: 0.7467 (pmt) REVERT: D 291 ASN cc_start: 0.8842 (t0) cc_final: 0.8593 (t0) outliers start: 20 outliers final: 20 residues processed: 164 average time/residue: 0.5607 time to fit residues: 100.8397 Evaluate side-chains 172 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 416 CYS Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 416 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 80 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.141373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.117614 restraints weight = 13175.356| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.88 r_work: 0.3258 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11884 Z= 0.148 Angle : 0.586 5.597 16128 Z= 0.315 Chirality : 0.047 0.138 1780 Planarity : 0.003 0.023 2116 Dihedral : 5.419 24.229 1768 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.57 % Allowed : 14.73 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.21), residues: 1536 helix: None (None), residues: 0 sheet: -0.13 (0.22), residues: 556 loop : -1.25 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 149 TYR 0.006 0.001 TYR C 137 PHE 0.012 0.002 PHE B 114 TRP 0.009 0.001 TRP C 172 HIS 0.002 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00350 (11848) covalent geometry : angle 0.57856 (16052) SS BOND : bond 0.00171 ( 32) SS BOND : angle 1.37012 ( 64) hydrogen bonds : bond 0.04076 ( 356) hydrogen bonds : angle 6.17995 ( 972) link_NAG-ASN : bond 0.00251 ( 4) link_NAG-ASN : angle 1.81959 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.489 Fit side-chains REVERT: A 92 MET cc_start: 0.5446 (mpt) cc_final: 0.4982 (mpp) REVERT: A 150 MET cc_start: 0.8204 (mtt) cc_final: 0.7470 (pmt) REVERT: A 291 ASN cc_start: 0.8840 (t0) cc_final: 0.8586 (t0) REVERT: B 92 MET cc_start: 0.5409 (mpt) cc_final: 0.4949 (mpp) REVERT: B 150 MET cc_start: 0.8182 (mtt) cc_final: 0.7461 (pmt) REVERT: B 291 ASN cc_start: 0.8836 (t0) cc_final: 0.8581 (t0) REVERT: C 92 MET cc_start: 0.5369 (mpt) cc_final: 0.4923 (mpp) REVERT: C 150 MET cc_start: 0.8164 (mtt) cc_final: 0.7479 (pmt) REVERT: C 291 ASN cc_start: 0.8823 (t0) cc_final: 0.8565 (t0) REVERT: D 92 MET cc_start: 0.5396 (mpt) cc_final: 0.4942 (mpp) REVERT: D 150 MET cc_start: 0.8216 (mtt) cc_final: 0.7475 (pmt) REVERT: D 291 ASN cc_start: 0.8837 (t0) cc_final: 0.8583 (t0) outliers start: 20 outliers final: 20 residues processed: 160 average time/residue: 0.5677 time to fit residues: 99.0914 Evaluate side-chains 172 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 416 CYS Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 416 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 138 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 146 optimal weight: 0.0000 chunk 131 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN B 203 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.148083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.125683 restraints weight = 13218.972| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.80 r_work: 0.3374 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11884 Z= 0.124 Angle : 0.562 5.708 16128 Z= 0.302 Chirality : 0.046 0.135 1780 Planarity : 0.003 0.023 2116 Dihedral : 5.234 22.980 1768 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.80 % Allowed : 14.81 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.21), residues: 1536 helix: None (None), residues: 0 sheet: -0.11 (0.22), residues: 556 loop : -1.22 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 149 TYR 0.005 0.001 TYR D 137 PHE 0.011 0.002 PHE D 114 TRP 0.010 0.001 TRP A 172 HIS 0.002 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00292 (11848) covalent geometry : angle 0.55557 (16052) SS BOND : bond 0.00149 ( 32) SS BOND : angle 1.22280 ( 64) hydrogen bonds : bond 0.03845 ( 356) hydrogen bonds : angle 6.08988 ( 972) link_NAG-ASN : bond 0.00290 ( 4) link_NAG-ASN : angle 1.80539 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4054.84 seconds wall clock time: 70 minutes 13.50 seconds (4213.50 seconds total)