Starting phenix.real_space_refine on Thu Aug 6 01:03:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tq7_56126/08_2026/9tq7_56126.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tq7_56126/08_2026/9tq7_56126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9tq7_56126/08_2026/9tq7_56126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tq7_56126/08_2026/9tq7_56126.map" model { file = "/net/cci-nas-00/data/ceres_data/9tq7_56126/08_2026/9tq7_56126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tq7_56126/08_2026/9tq7_56126.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 88 5.16 5 C 7628 2.51 5 N 2068 2.21 5 O 2364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12156 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2995 Classifications: {'peptide': 387} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 365} Chain: "B" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2995 Classifications: {'peptide': 387} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 365} Chain: "C" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2995 Classifications: {'peptide': 387} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 365} Chain: "D" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2995 Classifications: {'peptide': 387} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 365} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.75, per 1000 atoms: 0.23 Number of scatterers: 12156 At special positions: 0 Unit cell: (117.53, 117.53, 73.584, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 88 16.00 O 2364 8.00 N 2068 7.00 C 7628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 231 " distance=2.04 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 238 " distance=2.05 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 290 " distance=2.02 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 446 " distance=2.04 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.03 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 231 " distance=2.04 Simple disulfide: pdb=" SG CYS B 233 " - pdb=" SG CYS B 238 " distance=2.05 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 290 " distance=2.02 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 446 " distance=2.04 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.03 Simple disulfide: pdb=" SG CYS C 184 " - pdb=" SG CYS C 231 " distance=2.04 Simple disulfide: pdb=" SG CYS C 233 " - pdb=" SG CYS C 238 " distance=2.05 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 290 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 446 " distance=2.04 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.03 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 233 " - pdb=" SG CYS D 238 " distance=2.05 Simple disulfide: pdb=" SG CYS D 279 " - pdb=" SG CYS D 292 " distance=2.03 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 290 " distance=2.02 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 335 " distance=2.03 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 446 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 600 " - " ASN A 88 " " NAG A 601 " - " ASN A 235 " " NAG A 602 " - " ASN A 146 " " NAG B 600 " - " ASN B 88 " " NAG B 601 " - " ASN B 235 " " NAG B 602 " - " ASN B 146 " " NAG C 600 " - " ASN C 88 " " NAG C 601 " - " ASN C 235 " " NAG C 602 " - " ASN C 146 " " NAG D 600 " - " ASN D 88 " " NAG D 601 " - " ASN D 235 " " NAG D 602 " - " ASN D 146 " Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 632.3 milliseconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2776 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 28 sheets defined 8.0% alpha, 36.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 142 through 150 removed outlier: 4.001A pdb=" N GLY A 147 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE A 149 " --> pdb=" O ASN A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 172 removed outlier: 4.011A pdb=" N SER A 172 " --> pdb=" O PRO A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 382 Processing helix chain 'A' and resid 409 through 414 removed outlier: 3.915A pdb=" N THR A 413 " --> pdb=" O HIS A 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 142 through 150 removed outlier: 4.001A pdb=" N GLY B 147 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE B 149 " --> pdb=" O ASN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 4.012A pdb=" N SER B 172 " --> pdb=" O PRO B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 382 Processing helix chain 'B' and resid 409 through 414 removed outlier: 3.915A pdb=" N THR B 413 " --> pdb=" O HIS B 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 142 through 150 removed outlier: 4.001A pdb=" N GLY C 147 " --> pdb=" O HIS C 144 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE C 149 " --> pdb=" O ASN C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 172 removed outlier: 4.011A pdb=" N SER C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 382 Processing helix chain 'C' and resid 409 through 414 removed outlier: 3.914A pdb=" N THR C 413 " --> pdb=" O HIS C 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 142 through 150 removed outlier: 4.001A pdb=" N GLY D 147 " --> pdb=" O HIS D 144 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE D 149 " --> pdb=" O ASN D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 removed outlier: 4.011A pdb=" N SER D 172 " --> pdb=" O PRO D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 382 Processing helix chain 'D' and resid 409 through 414 removed outlier: 3.916A pdb=" N THR D 413 " --> pdb=" O HIS D 409 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 102 removed outlier: 5.344A pdb=" N ILE A 99 " --> pdb=" O CYS A 446 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N CYS A 446 " --> pdb=" O ILE A 99 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.599A pdb=" N PHE A 115 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ALA A 138 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ILE A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLN A 136 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR A 157 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 176 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N SER A 160 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N PHE A 174 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 185 removed outlier: 4.426A pdb=" N SER A 180 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 195 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS A 184 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP A 214 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N TYR A 208 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ILE A 212 " --> pdb=" O TYR A 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 226 Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 226 removed outlier: 7.485A pdb=" N TYR A 253 " --> pdb=" O GLU A 268 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLU A 268 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE A 255 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER A 266 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG A 257 " --> pdb=" O ILE A 264 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 282 through 284 removed outlier: 3.727A pdb=" N THR A 289 " --> pdb=" O TYR A 282 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A 315 " --> pdb=" O TRP A 303 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 352 through 353 removed outlier: 5.863A pdb=" N LYS A 369 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE A 396 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE A 371 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N MET A 373 " --> pdb=" O ASP A 392 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ASP A 392 " --> pdb=" O MET A 373 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TRP A 375 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS A 390 " --> pdb=" O TRP A 375 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 97 through 102 removed outlier: 5.344A pdb=" N ILE B 99 " --> pdb=" O CYS B 446 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N CYS B 446 " --> pdb=" O ILE B 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.599A pdb=" N PHE B 115 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ALA B 138 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ILE B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLN B 136 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR B 157 " --> pdb=" O THR B 135 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 176 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N SER B 160 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N PHE B 174 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 180 through 185 removed outlier: 4.427A pdb=" N SER B 180 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 195 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS B 184 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP B 214 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N TYR B 208 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ILE B 212 " --> pdb=" O TYR B 208 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 224 through 226 Processing sheet with id=AB3, first strand: chain 'B' and resid 224 through 226 removed outlier: 7.484A pdb=" N TYR B 253 " --> pdb=" O GLU B 268 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLU B 268 " --> pdb=" O TYR B 253 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B 255 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER B 266 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG B 257 " --> pdb=" O ILE B 264 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 282 through 284 removed outlier: 3.728A pdb=" N THR B 289 " --> pdb=" O TYR B 282 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 315 " --> pdb=" O TRP B 303 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 352 through 353 removed outlier: 5.862A pdb=" N LYS B 369 " --> pdb=" O ILE B 396 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE B 396 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE B 371 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N MET B 373 " --> pdb=" O ASP B 392 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ASP B 392 " --> pdb=" O MET B 373 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TRP B 375 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS B 390 " --> pdb=" O TRP B 375 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 97 through 102 removed outlier: 5.344A pdb=" N ILE C 99 " --> pdb=" O CYS C 446 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N CYS C 446 " --> pdb=" O ILE C 99 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 115 through 124 removed outlier: 4.600A pdb=" N PHE C 115 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ALA C 138 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ILE C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLN C 136 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR C 157 " --> pdb=" O THR C 135 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER C 176 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N SER C 160 " --> pdb=" O PHE C 174 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N PHE C 174 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 180 through 185 removed outlier: 4.426A pdb=" N SER C 180 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE C 195 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS C 184 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP C 214 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N TYR C 208 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ILE C 212 " --> pdb=" O TYR C 208 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 224 through 226 Processing sheet with id=AC1, first strand: chain 'C' and resid 224 through 226 removed outlier: 7.485A pdb=" N TYR C 253 " --> pdb=" O GLU C 268 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLU C 268 " --> pdb=" O TYR C 253 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE C 255 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N SER C 266 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG C 257 " --> pdb=" O ILE C 264 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 282 through 284 removed outlier: 3.727A pdb=" N THR C 289 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY C 315 " --> pdb=" O TRP C 303 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 352 through 353 removed outlier: 5.863A pdb=" N LYS C 369 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE C 396 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE C 371 " --> pdb=" O VAL C 394 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N MET C 373 " --> pdb=" O ASP C 392 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ASP C 392 " --> pdb=" O MET C 373 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TRP C 375 " --> pdb=" O LYS C 390 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LYS C 390 " --> pdb=" O TRP C 375 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 97 through 102 removed outlier: 5.344A pdb=" N ILE D 99 " --> pdb=" O CYS D 446 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N CYS D 446 " --> pdb=" O ILE D 99 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.599A pdb=" N PHE D 115 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ALA D 138 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ILE D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLN D 136 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR D 157 " --> pdb=" O THR D 135 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 176 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N SER D 160 " --> pdb=" O PHE D 174 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N PHE D 174 " --> pdb=" O SER D 160 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 180 through 185 removed outlier: 4.426A pdb=" N SER D 180 " --> pdb=" O ILE D 195 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE D 195 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS D 184 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP D 214 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N TYR D 208 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ILE D 212 " --> pdb=" O TYR D 208 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 224 through 226 Processing sheet with id=AC8, first strand: chain 'D' and resid 224 through 226 removed outlier: 7.485A pdb=" N TYR D 253 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLU D 268 " --> pdb=" O TYR D 253 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE D 255 " --> pdb=" O SER D 266 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER D 266 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG D 257 " --> pdb=" O ILE D 264 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 282 through 284 removed outlier: 3.727A pdb=" N THR D 289 " --> pdb=" O TYR D 282 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY D 315 " --> pdb=" O TRP D 303 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 352 through 353 removed outlier: 5.863A pdb=" N LYS D 369 " --> pdb=" O ILE D 396 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE D 396 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE D 371 " --> pdb=" O VAL D 394 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N MET D 373 " --> pdb=" O ASP D 392 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ASP D 392 " --> pdb=" O MET D 373 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TRP D 375 " --> pdb=" O LYS D 390 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LYS D 390 " --> pdb=" O TRP D 375 " (cutoff:3.500A) 312 hydrogen bonds defined for protein. 768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3920 1.35 - 1.48: 3412 1.48 - 1.61: 5036 1.61 - 1.74: 0 1.74 - 1.87: 108 Bond restraints: 12476 Sorted by residual: bond pdb=" CB CYS C 421 " pdb=" SG CYS C 421 " ideal model delta sigma weight residual 1.808 1.870 -0.062 3.30e-02 9.18e+02 3.49e+00 bond pdb=" CB CYS A 421 " pdb=" SG CYS A 421 " ideal model delta sigma weight residual 1.808 1.870 -0.062 3.30e-02 9.18e+02 3.48e+00 bond pdb=" CB CYS D 421 " pdb=" SG CYS D 421 " ideal model delta sigma weight residual 1.808 1.869 -0.061 3.30e-02 9.18e+02 3.46e+00 bond pdb=" CB CYS B 421 " pdb=" SG CYS B 421 " ideal model delta sigma weight residual 1.808 1.869 -0.061 3.30e-02 9.18e+02 3.45e+00 bond pdb=" N SER B 82 " pdb=" CA SER B 82 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 ... (remaining 12471 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 16571 2.02 - 4.04: 312 4.04 - 6.05: 29 6.05 - 8.07: 8 8.07 - 10.09: 8 Bond angle restraints: 16928 Sorted by residual: angle pdb=" N CYS B 233 " pdb=" CA CYS B 233 " pdb=" C CYS B 233 " ideal model delta sigma weight residual 108.76 116.48 -7.72 1.58e+00 4.01e-01 2.39e+01 angle pdb=" N CYS A 233 " pdb=" CA CYS A 233 " pdb=" C CYS A 233 " ideal model delta sigma weight residual 108.76 116.45 -7.69 1.58e+00 4.01e-01 2.37e+01 angle pdb=" N CYS C 233 " pdb=" CA CYS C 233 " pdb=" C CYS C 233 " ideal model delta sigma weight residual 108.76 116.45 -7.69 1.58e+00 4.01e-01 2.37e+01 angle pdb=" N CYS D 233 " pdb=" CA CYS D 233 " pdb=" C CYS D 233 " ideal model delta sigma weight residual 108.76 116.45 -7.69 1.58e+00 4.01e-01 2.37e+01 angle pdb=" CA CYS A 233 " pdb=" CB CYS A 233 " pdb=" SG CYS A 233 " ideal model delta sigma weight residual 114.40 124.49 -10.09 2.30e+00 1.89e-01 1.92e+01 ... (remaining 16923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.76: 6453 16.76 - 33.51: 863 33.51 - 50.27: 184 50.27 - 67.02: 28 67.02 - 83.78: 12 Dihedral angle restraints: 7540 sinusoidal: 3172 harmonic: 4368 Sorted by residual: dihedral pdb=" CB CYS D 233 " pdb=" SG CYS D 233 " pdb=" SG CYS D 238 " pdb=" CB CYS D 238 " ideal model delta sinusoidal sigma weight residual 93.00 27.33 65.67 1 1.00e+01 1.00e-02 5.65e+01 dihedral pdb=" CB CYS A 233 " pdb=" SG CYS A 233 " pdb=" SG CYS A 238 " pdb=" CB CYS A 238 " ideal model delta sinusoidal sigma weight residual 93.00 27.34 65.66 1 1.00e+01 1.00e-02 5.64e+01 dihedral pdb=" CB CYS B 233 " pdb=" SG CYS B 233 " pdb=" SG CYS B 238 " pdb=" CB CYS B 238 " ideal model delta sinusoidal sigma weight residual 93.00 27.35 65.65 1 1.00e+01 1.00e-02 5.64e+01 ... (remaining 7537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1281 0.043 - 0.086: 318 0.086 - 0.129: 162 0.129 - 0.172: 27 0.172 - 0.215: 8 Chirality restraints: 1796 Sorted by residual: chirality pdb=" C1 NAG A 600 " pdb=" ND2 ASN A 88 " pdb=" C2 NAG A 600 " pdb=" O5 NAG A 600 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" C1 NAG C 600 " pdb=" ND2 ASN C 88 " pdb=" C2 NAG C 600 " pdb=" O5 NAG C 600 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" C1 NAG B 600 " pdb=" ND2 ASN B 88 " pdb=" C2 NAG B 600 " pdb=" O5 NAG B 600 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1793 not shown) Planarity restraints: 2192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 287 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.48e+00 pdb=" CD GLU B 287 " 0.027 2.00e-02 2.50e+03 pdb=" OE1 GLU B 287 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU B 287 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 287 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.44e+00 pdb=" CD GLU C 287 " -0.027 2.00e-02 2.50e+03 pdb=" OE1 GLU C 287 " 0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU C 287 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 287 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.40e+00 pdb=" CD GLU A 287 " 0.027 2.00e-02 2.50e+03 pdb=" OE1 GLU A 287 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU A 287 " -0.010 2.00e-02 2.50e+03 ... (remaining 2189 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2072 2.76 - 3.30: 12103 3.30 - 3.83: 19346 3.83 - 4.37: 22573 4.37 - 4.90: 41073 Nonbonded interactions: 97167 Sorted by model distance: nonbonded pdb=" O ASP A 284 " pdb=" OD1 ASP A 284 " model vdw 2.227 3.040 nonbonded pdb=" O ASP C 284 " pdb=" OD1 ASP C 284 " model vdw 2.227 3.040 nonbonded pdb=" O ASP B 284 " pdb=" OD1 ASP B 284 " model vdw 2.228 3.040 nonbonded pdb=" O ASP D 284 " pdb=" OD1 ASP D 284 " model vdw 2.228 3.040 nonbonded pdb=" O GLY C 298 " pdb="CA CA C 603 " model vdw 2.254 2.510 ... (remaining 97162 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: 0.02 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 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: 0.030 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.860 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12520 Z= 0.144 Angle : 0.704 10.089 17028 Z= 0.386 Chirality : 0.050 0.215 1796 Planarity : 0.003 0.028 2180 Dihedral : 14.803 83.775 4668 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.35 % Allowed : 32.19 % Favored : 66.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.21), residues: 1540 helix: -2.06 (0.78), residues: 24 sheet: -1.20 (0.23), residues: 580 loop : -1.56 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 173 TYR 0.006 0.001 TYR D 170 PHE 0.008 0.001 PHE C 422 TRP 0.006 0.001 TRP C 219 HIS 0.003 0.001 HIS D 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (12476) covalent geometry : angle 0.68497 / 0.38 (16928) SS BOND : bond 0.00773 / 0.38 ( 32) SS BOND : angle 2.60094 / 1.75 ( 64) hydrogen bonds : bond 0.27637 / 18.61 ( 304) hydrogen bonds : angle 11.86778 / 8.29 ( 768) link_NAG-ASN : bond 0.00300 / 0.21 ( 12) link_NAG-ASN : angle 1.40227 / 0.85 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 487 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.8605 (mt) cc_final: 0.8386 (mt) REVERT: A 214 ASP cc_start: 0.7986 (t0) cc_final: 0.7734 (t0) REVERT: A 275 HIS cc_start: 0.7779 (t-90) cc_final: 0.7046 (t-90) REVERT: A 376 ASP cc_start: 0.8225 (t70) cc_final: 0.7862 (t0) REVERT: A 423 TRP cc_start: 0.8480 (p-90) cc_final: 0.8252 (p-90) REVERT: B 275 HIS cc_start: 0.7892 (t-90) cc_final: 0.7366 (t-90) REVERT: B 376 ASP cc_start: 0.8289 (t70) cc_final: 0.8050 (t70) REVERT: B 415 LEU cc_start: 0.8928 (mt) cc_final: 0.8582 (mp) REVERT: B 418 ILE cc_start: 0.8523 (mm) cc_final: 0.8021 (mm) REVERT: B 436 ILE cc_start: 0.9180 (mm) cc_final: 0.8581 (tt) REVERT: C 158 LEU cc_start: 0.8927 (tt) cc_final: 0.8717 (tt) REVERT: C 275 HIS cc_start: 0.8019 (t-90) cc_final: 0.7494 (t-90) REVERT: C 376 ASP cc_start: 0.8281 (t70) cc_final: 0.8046 (t70) REVERT: C 415 LEU cc_start: 0.8883 (mt) cc_final: 0.8558 (mp) REVERT: C 418 ILE cc_start: 0.8546 (mm) cc_final: 0.8027 (mm) REVERT: D 128 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8518 (mt-10) REVERT: D 275 HIS cc_start: 0.7919 (t-90) cc_final: 0.7420 (t-90) REVERT: D 376 ASP cc_start: 0.8197 (t70) cc_final: 0.7925 (t70) REVERT: D 415 LEU cc_start: 0.8918 (mt) cc_final: 0.8563 (mp) REVERT: D 418 ILE cc_start: 0.8584 (mm) cc_final: 0.8086 (mm) REVERT: D 436 ILE cc_start: 0.9240 (mm) cc_final: 0.8765 (tt) outliers start: 18 outliers final: 11 residues processed: 495 average time/residue: 0.0713 time to fit residues: 55.9563 Evaluate side-chains 452 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 441 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain C residue 161 CYS Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain D residue 161 CYS Chi-restraints excluded: chain D residue 231 CYS Chi-restraints excluded: chain D residue 279 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.0470 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.0484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS A 408 GLN B 144 HIS B 209 ASN B 408 GLN C 144 HIS C 209 ASN C 408 GLN D 209 ASN D 408 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.144563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.120802 restraints weight = 18240.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.126294 restraints weight = 8830.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.130042 restraints weight = 5431.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.132523 restraints weight = 3818.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.134525 restraints weight = 2947.249| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 12520 Z= 0.172 Angle : 0.695 9.426 17028 Z= 0.360 Chirality : 0.052 0.235 1796 Planarity : 0.004 0.026 2180 Dihedral : 6.512 44.055 1923 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 5.61 % Allowed : 24.85 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.21), residues: 1540 helix: -3.19 (0.58), residues: 24 sheet: -0.79 (0.23), residues: 572 loop : -1.43 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 173 TYR 0.010 0.001 TYR A 170 PHE 0.011 0.001 PHE B 445 TRP 0.006 0.001 TRP C 179 HIS 0.003 0.001 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (12476) covalent geometry : angle 0.67898 / 0.35 (16928) SS BOND : bond 0.00741 / 0.37 ( 32) SS BOND : angle 2.22590 / 1.47 ( 64) hydrogen bonds : bond 0.03589 / 2.58 ( 304) hydrogen bonds : angle 7.20490 / 4.98 ( 768) link_NAG-ASN : bond 0.00317 / 0.19 ( 12) link_NAG-ASN : angle 1.60778 / 0.95 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 492 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 ASP cc_start: 0.8361 (t0) cc_final: 0.8115 (t0) REVERT: A 228 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7658 (mm-30) REVERT: A 279 CYS cc_start: 0.6922 (OUTLIER) cc_final: 0.6641 (m) REVERT: A 284 ASP cc_start: 0.8309 (p0) cc_final: 0.8102 (p0) REVERT: A 376 ASP cc_start: 0.8130 (t70) cc_final: 0.7748 (t0) REVERT: A 449 ASP cc_start: 0.8257 (m-30) cc_final: 0.7918 (m-30) REVERT: B 142 ASP cc_start: 0.7419 (t0) cc_final: 0.7218 (t0) REVERT: B 228 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7660 (mm-30) REVERT: B 275 HIS cc_start: 0.8335 (t-90) cc_final: 0.8067 (t-90) REVERT: B 279 CYS cc_start: 0.6772 (OUTLIER) cc_final: 0.6524 (m) REVERT: B 376 ASP cc_start: 0.8102 (t70) cc_final: 0.7737 (t0) REVERT: B 411 GLU cc_start: 0.8172 (mp0) cc_final: 0.7928 (mp0) REVERT: B 415 LEU cc_start: 0.9037 (mt) cc_final: 0.8790 (mp) REVERT: B 436 ILE cc_start: 0.9111 (mm) cc_final: 0.8736 (tt) REVERT: C 268 GLU cc_start: 0.7593 (pm20) cc_final: 0.7217 (pp20) REVERT: C 275 HIS cc_start: 0.8338 (t-90) cc_final: 0.8082 (t-90) REVERT: C 376 ASP cc_start: 0.8102 (t70) cc_final: 0.7734 (t0) REVERT: C 384 ASP cc_start: 0.7904 (t0) cc_final: 0.7372 (t0) REVERT: C 415 LEU cc_start: 0.9033 (mt) cc_final: 0.8799 (mp) REVERT: C 433 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7140 (tm-30) REVERT: D 275 HIS cc_start: 0.8338 (t-90) cc_final: 0.8025 (t-90) REVERT: D 279 CYS cc_start: 0.6772 (OUTLIER) cc_final: 0.6564 (m) REVERT: D 376 ASP cc_start: 0.8090 (t70) cc_final: 0.7719 (t0) REVERT: D 411 GLU cc_start: 0.8189 (mp0) cc_final: 0.7942 (mp0) REVERT: D 415 LEU cc_start: 0.9085 (mt) cc_final: 0.8834 (mp) REVERT: D 436 ILE cc_start: 0.9174 (mm) cc_final: 0.8855 (tt) outliers start: 75 outliers final: 48 residues processed: 519 average time/residue: 0.0775 time to fit residues: 63.1596 Evaluate side-chains 509 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 458 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 219 TRP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 219 TRP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 468 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 69 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS B 144 HIS B 378 ASN C 144 HIS C 378 ASN D 144 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.142691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.118509 restraints weight = 18375.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.123757 restraints weight = 8836.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.127693 restraints weight = 5464.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.130114 restraints weight = 3860.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.132227 restraints weight = 3011.358| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 12520 Z= 0.180 Angle : 0.667 9.413 17028 Z= 0.347 Chirality : 0.050 0.230 1796 Planarity : 0.004 0.062 2180 Dihedral : 6.779 51.482 1915 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 6.81 % Allowed : 24.93 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.21), residues: 1540 helix: -3.24 (0.69), residues: 24 sheet: -0.56 (0.23), residues: 572 loop : -1.41 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 173 TYR 0.013 0.001 TYR B 274 PHE 0.013 0.001 PHE A 445 TRP 0.008 0.001 TRP C 179 HIS 0.004 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (12476) covalent geometry : angle 0.65048 / 0.34 (16928) SS BOND : bond 0.00736 / 0.35 ( 32) SS BOND : angle 2.29192 / 1.49 ( 64) hydrogen bonds : bond 0.03505 / 2.51 ( 304) hydrogen bonds : angle 6.43539 / 4.46 ( 768) link_NAG-ASN : bond 0.00333 / 0.19 ( 12) link_NAG-ASN : angle 1.51523 / 0.88 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 501 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.9121 (m-10) cc_final: 0.8815 (m-80) REVERT: A 214 ASP cc_start: 0.8414 (t0) cc_final: 0.8133 (t0) REVERT: A 228 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7673 (mm-30) REVERT: A 275 HIS cc_start: 0.8430 (t-90) cc_final: 0.8156 (t-90) REVERT: A 277 GLU cc_start: 0.7266 (mt-10) cc_final: 0.7007 (mt-10) REVERT: A 279 CYS cc_start: 0.7012 (OUTLIER) cc_final: 0.6618 (m) REVERT: A 357 VAL cc_start: 0.9276 (t) cc_final: 0.8905 (m) REVERT: A 373 MET cc_start: 0.8049 (mmm) cc_final: 0.7644 (mmm) REVERT: A 376 ASP cc_start: 0.8098 (t0) cc_final: 0.7845 (t0) REVERT: B 123 SER cc_start: 0.8617 (m) cc_final: 0.8375 (t) REVERT: B 142 ASP cc_start: 0.7440 (t0) cc_final: 0.7032 (t0) REVERT: B 279 CYS cc_start: 0.6934 (OUTLIER) cc_final: 0.6584 (m) REVERT: B 284 ASP cc_start: 0.8318 (p0) cc_final: 0.8004 (p0) REVERT: B 287 GLU cc_start: 0.7224 (mp0) cc_final: 0.7005 (mp0) REVERT: B 376 ASP cc_start: 0.8055 (t70) cc_final: 0.7775 (t0) REVERT: B 411 GLU cc_start: 0.8204 (mp0) cc_final: 0.7999 (mp0) REVERT: B 436 ILE cc_start: 0.9094 (mm) cc_final: 0.8718 (tt) REVERT: C 123 SER cc_start: 0.8719 (m) cc_final: 0.8513 (t) REVERT: C 207 LYS cc_start: 0.8925 (mtpp) cc_final: 0.8647 (ttmm) REVERT: C 253 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.7862 (m-80) REVERT: C 275 HIS cc_start: 0.8281 (t-90) cc_final: 0.7940 (t-90) REVERT: C 284 ASP cc_start: 0.8323 (p0) cc_final: 0.7980 (p0) REVERT: C 287 GLU cc_start: 0.7226 (mp0) cc_final: 0.6938 (mp0) REVERT: C 376 ASP cc_start: 0.8092 (t70) cc_final: 0.7849 (t0) REVERT: C 411 GLU cc_start: 0.8155 (mp0) cc_final: 0.7865 (mp0) REVERT: D 123 SER cc_start: 0.8754 (m) cc_final: 0.8493 (t) REVERT: D 275 HIS cc_start: 0.8328 (t-90) cc_final: 0.7983 (t-90) REVERT: D 279 CYS cc_start: 0.6870 (OUTLIER) cc_final: 0.6546 (m) REVERT: D 284 ASP cc_start: 0.8341 (p0) cc_final: 0.7996 (p0) REVERT: D 376 ASP cc_start: 0.8018 (t0) cc_final: 0.7800 (t0) REVERT: D 411 GLU cc_start: 0.8197 (mp0) cc_final: 0.7941 (mp0) REVERT: D 436 ILE cc_start: 0.9246 (mm) cc_final: 0.8975 (tt) outliers start: 91 outliers final: 58 residues processed: 520 average time/residue: 0.0908 time to fit residues: 73.2270 Evaluate side-chains 494 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 432 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 219 TRP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 219 TRP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 253 TYR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 444 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 115 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 44 optimal weight: 0.0040 chunk 141 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 91 optimal weight: 0.3980 chunk 130 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS A 409 HIS B 144 HIS B 409 HIS C 144 HIS C 409 HIS D 144 HIS D 409 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.146305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.122641 restraints weight = 18225.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.127864 restraints weight = 8883.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.131724 restraints weight = 5537.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.134219 restraints weight = 3907.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.136252 restraints weight = 3023.314| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12520 Z= 0.133 Angle : 0.660 9.666 17028 Z= 0.342 Chirality : 0.049 0.219 1796 Planarity : 0.004 0.051 2180 Dihedral : 6.842 52.594 1915 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 5.39 % Allowed : 27.32 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.20), residues: 1540 helix: -4.15 (0.35), residues: 60 sheet: -0.25 (0.23), residues: 528 loop : -1.52 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 173 TYR 0.010 0.001 TYR D 170 PHE 0.019 0.002 PHE C 121 TRP 0.008 0.001 TRP D 179 HIS 0.004 0.001 HIS D 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 (12476) covalent geometry : angle 0.64241 / 0.33 (16928) SS BOND : bond 0.00640 / 0.33 ( 32) SS BOND : angle 2.38482 / 1.55 ( 64) hydrogen bonds : bond 0.03085 / 2.20 ( 304) hydrogen bonds : angle 5.98559 / 4.16 ( 768) link_NAG-ASN : bond 0.00385 / 0.23 ( 12) link_NAG-ASN : angle 1.42104 / 0.82 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 466 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.9077 (m-10) cc_final: 0.8771 (m-80) REVERT: A 214 ASP cc_start: 0.8397 (t0) cc_final: 0.8114 (t0) REVERT: A 256 PHE cc_start: 0.8485 (m-80) cc_final: 0.8197 (m-10) REVERT: A 275 HIS cc_start: 0.8381 (t-90) cc_final: 0.8130 (t-90) REVERT: A 277 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6767 (mt-10) REVERT: A 279 CYS cc_start: 0.6926 (OUTLIER) cc_final: 0.6537 (m) REVERT: A 357 VAL cc_start: 0.9255 (t) cc_final: 0.8837 (m) REVERT: A 373 MET cc_start: 0.8032 (mmm) cc_final: 0.7666 (mmm) REVERT: A 376 ASP cc_start: 0.7999 (t0) cc_final: 0.7715 (t0) REVERT: B 123 SER cc_start: 0.8585 (m) cc_final: 0.8314 (t) REVERT: B 142 ASP cc_start: 0.7395 (t0) cc_final: 0.6996 (t0) REVERT: B 170 TYR cc_start: 0.8965 (m-10) cc_final: 0.8594 (m-80) REVERT: B 256 PHE cc_start: 0.8425 (m-80) cc_final: 0.8158 (m-10) REVERT: B 264 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.8674 (mm) REVERT: B 279 CYS cc_start: 0.6922 (OUTLIER) cc_final: 0.6564 (m) REVERT: B 376 ASP cc_start: 0.7957 (t0) cc_final: 0.7654 (t0) REVERT: B 411 GLU cc_start: 0.8315 (mp0) cc_final: 0.8104 (mp0) REVERT: B 436 ILE cc_start: 0.9100 (mm) cc_final: 0.8733 (tt) REVERT: C 123 SER cc_start: 0.8711 (m) cc_final: 0.8445 (t) REVERT: C 256 PHE cc_start: 0.8486 (m-80) cc_final: 0.8175 (m-10) REVERT: C 275 HIS cc_start: 0.8249 (t-90) cc_final: 0.7951 (t-90) REVERT: C 287 GLU cc_start: 0.7162 (mp0) cc_final: 0.6936 (mp0) REVERT: C 376 ASP cc_start: 0.7994 (t0) cc_final: 0.7675 (t0) REVERT: C 411 GLU cc_start: 0.8210 (mp0) cc_final: 0.7999 (mp0) REVERT: D 123 SER cc_start: 0.8734 (m) cc_final: 0.8456 (t) REVERT: D 256 PHE cc_start: 0.8448 (m-80) cc_final: 0.7917 (m-10) REVERT: D 268 GLU cc_start: 0.7662 (pm20) cc_final: 0.7450 (pp20) REVERT: D 275 HIS cc_start: 0.8270 (t-90) cc_final: 0.8023 (t-90) REVERT: D 279 CYS cc_start: 0.6899 (OUTLIER) cc_final: 0.6580 (m) REVERT: D 376 ASP cc_start: 0.7906 (t0) cc_final: 0.7663 (t0) REVERT: D 411 GLU cc_start: 0.8200 (mp0) cc_final: 0.7991 (mp0) REVERT: D 463 LEU cc_start: 0.8682 (pp) cc_final: 0.8387 (mp) outliers start: 72 outliers final: 46 residues processed: 490 average time/residue: 0.0794 time to fit residues: 61.5120 Evaluate side-chains 460 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 410 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 219 TRP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 219 TRP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 445 PHE Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 444 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 117 optimal weight: 5.9990 chunk 23 optimal weight: 0.0970 chunk 111 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 overall best weight: 1.1180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS B 144 HIS C 144 HIS D 144 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.142983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.118469 restraints weight = 18410.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.123949 restraints weight = 8956.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.127812 restraints weight = 5605.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.130511 restraints weight = 3933.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.132394 restraints weight = 3016.331| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 12520 Z= 0.168 Angle : 0.705 11.421 17028 Z= 0.363 Chirality : 0.049 0.204 1796 Planarity : 0.004 0.064 2180 Dihedral : 6.934 52.727 1915 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 7.34 % Allowed : 26.05 % Favored : 66.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.20), residues: 1540 helix: -4.12 (0.37), residues: 60 sheet: -0.15 (0.23), residues: 540 loop : -1.44 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 368 TYR 0.012 0.001 TYR D 170 PHE 0.015 0.002 PHE D 133 TRP 0.009 0.001 TRP C 179 HIS 0.005 0.001 HIS D 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (12476) covalent geometry : angle 0.68309 / 0.35 (16928) SS BOND : bond 0.00759 / 0.43 ( 32) SS BOND : angle 2.82564 / 1.85 ( 64) hydrogen bonds : bond 0.03234 / 2.30 ( 304) hydrogen bonds : angle 5.81863 / 4.04 ( 768) link_NAG-ASN : bond 0.00330 / 0.19 ( 12) link_NAG-ASN : angle 1.29477 / 0.75 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 450 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.9130 (m-10) cc_final: 0.8827 (m-80) REVERT: A 214 ASP cc_start: 0.8459 (t70) cc_final: 0.8112 (t0) REVERT: A 256 PHE cc_start: 0.8434 (m-80) cc_final: 0.8190 (m-10) REVERT: A 275 HIS cc_start: 0.8406 (t-90) cc_final: 0.8048 (t-90) REVERT: A 277 GLU cc_start: 0.7346 (mt-10) cc_final: 0.7040 (mt-10) REVERT: A 279 CYS cc_start: 0.6942 (OUTLIER) cc_final: 0.6522 (m) REVERT: A 357 VAL cc_start: 0.9297 (t) cc_final: 0.8916 (m) REVERT: A 376 ASP cc_start: 0.8067 (t0) cc_final: 0.7850 (t0) REVERT: A 436 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8766 (tt) REVERT: B 123 SER cc_start: 0.8762 (m) cc_final: 0.8485 (t) REVERT: B 142 ASP cc_start: 0.7680 (t0) cc_final: 0.7377 (t0) REVERT: B 209 ASN cc_start: 0.8127 (m-40) cc_final: 0.7897 (m-40) REVERT: B 256 PHE cc_start: 0.8409 (m-80) cc_final: 0.8184 (m-10) REVERT: B 275 HIS cc_start: 0.8469 (t-90) cc_final: 0.8235 (t-90) REVERT: B 279 CYS cc_start: 0.6910 (OUTLIER) cc_final: 0.6472 (m) REVERT: B 357 VAL cc_start: 0.9295 (t) cc_final: 0.8874 (m) REVERT: B 376 ASP cc_start: 0.8026 (t0) cc_final: 0.7776 (t0) REVERT: B 398 GLU cc_start: 0.7721 (mp0) cc_final: 0.7510 (mp0) REVERT: B 436 ILE cc_start: 0.9161 (mm) cc_final: 0.8760 (tt) REVERT: C 123 SER cc_start: 0.8752 (m) cc_final: 0.8499 (t) REVERT: C 256 PHE cc_start: 0.8440 (m-80) cc_final: 0.8209 (m-10) REVERT: C 284 ASP cc_start: 0.8316 (p0) cc_final: 0.7934 (p0) REVERT: C 287 GLU cc_start: 0.7200 (mp0) cc_final: 0.6876 (mp0) REVERT: C 316 TYR cc_start: 0.8101 (OUTLIER) cc_final: 0.7597 (m-10) REVERT: C 325 ASN cc_start: 0.7951 (t0) cc_final: 0.7575 (p0) REVERT: C 357 VAL cc_start: 0.9292 (t) cc_final: 0.8931 (m) REVERT: C 376 ASP cc_start: 0.8081 (t0) cc_final: 0.7751 (t0) REVERT: C 411 GLU cc_start: 0.8354 (mp0) cc_final: 0.7960 (mp0) REVERT: D 123 SER cc_start: 0.8767 (m) cc_final: 0.8502 (t) REVERT: D 256 PHE cc_start: 0.8414 (m-80) cc_final: 0.8195 (m-10) REVERT: D 279 CYS cc_start: 0.6886 (OUTLIER) cc_final: 0.6520 (m) REVERT: D 357 VAL cc_start: 0.9303 (t) cc_final: 0.8989 (m) REVERT: D 376 ASP cc_start: 0.8036 (t0) cc_final: 0.7762 (t0) REVERT: D 463 LEU cc_start: 0.8808 (pp) cc_final: 0.8442 (mp) outliers start: 98 outliers final: 64 residues processed: 493 average time/residue: 0.0917 time to fit residues: 69.8611 Evaluate side-chains 496 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 427 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 219 TRP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 445 PHE Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 219 TRP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain C residue 316 TYR Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 260 LYS Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 444 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 6 optimal weight: 6.9990 chunk 147 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 101 optimal weight: 0.0870 chunk 141 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS A 409 HIS B 144 HIS C 144 HIS D 144 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.145020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.121090 restraints weight = 18377.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.126528 restraints weight = 9215.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.130330 restraints weight = 5782.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.132779 restraints weight = 4095.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.134516 restraints weight = 3179.534| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12520 Z= 0.146 Angle : 0.721 12.484 17028 Z= 0.369 Chirality : 0.050 0.198 1796 Planarity : 0.004 0.056 2180 Dihedral : 6.968 52.815 1915 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 6.06 % Allowed : 27.69 % Favored : 66.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.20), residues: 1540 helix: -4.11 (0.37), residues: 60 sheet: 0.03 (0.23), residues: 532 loop : -1.40 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 368 TYR 0.011 0.001 TYR D 170 PHE 0.020 0.002 PHE C 121 TRP 0.008 0.001 TRP D 179 HIS 0.006 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (12476) covalent geometry : angle 0.70131 / 0.36 (16928) SS BOND : bond 0.00653 / 0.34 ( 32) SS BOND : angle 2.69552 / 1.76 ( 64) hydrogen bonds : bond 0.03107 / 2.20 ( 304) hydrogen bonds : angle 5.70837 / 3.97 ( 768) link_NAG-ASN : bond 0.00349 / 0.20 ( 12) link_NAG-ASN : angle 1.21739 / 0.71 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 454 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.9097 (m-10) cc_final: 0.8862 (m-80) REVERT: A 214 ASP cc_start: 0.8431 (t70) cc_final: 0.8060 (t0) REVERT: A 256 PHE cc_start: 0.8246 (m-80) cc_final: 0.8014 (m-10) REVERT: A 264 ILE cc_start: 0.9079 (mm) cc_final: 0.8783 (mm) REVERT: A 275 HIS cc_start: 0.8370 (t-90) cc_final: 0.8053 (t-90) REVERT: A 277 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6859 (mt-10) REVERT: A 279 CYS cc_start: 0.6877 (OUTLIER) cc_final: 0.6416 (m) REVERT: A 357 VAL cc_start: 0.9260 (t) cc_final: 0.8892 (m) REVERT: A 376 ASP cc_start: 0.8062 (t0) cc_final: 0.7803 (t0) REVERT: A 436 ILE cc_start: 0.9222 (mt) cc_final: 0.8870 (tt) REVERT: A 449 ASP cc_start: 0.8422 (m-30) cc_final: 0.8108 (m-30) REVERT: A 463 LEU cc_start: 0.8861 (pp) cc_final: 0.8396 (mp) REVERT: B 123 SER cc_start: 0.8794 (m) cc_final: 0.8554 (t) REVERT: B 142 ASP cc_start: 0.7649 (t0) cc_final: 0.7349 (t0) REVERT: B 269 MET cc_start: 0.7844 (mtp) cc_final: 0.7592 (ttp) REVERT: B 275 HIS cc_start: 0.8439 (t-90) cc_final: 0.8150 (t-90) REVERT: B 279 CYS cc_start: 0.6861 (OUTLIER) cc_final: 0.6419 (m) REVERT: B 357 VAL cc_start: 0.9280 (t) cc_final: 0.8865 (m) REVERT: B 373 MET cc_start: 0.8001 (mmm) cc_final: 0.7606 (mmm) REVERT: B 376 ASP cc_start: 0.8012 (t0) cc_final: 0.7730 (t0) REVERT: B 436 ILE cc_start: 0.9196 (mm) cc_final: 0.8831 (tt) REVERT: C 256 PHE cc_start: 0.8401 (m-80) cc_final: 0.8154 (m-10) REVERT: C 284 ASP cc_start: 0.8349 (p0) cc_final: 0.7915 (p0) REVERT: C 287 GLU cc_start: 0.7077 (mp0) cc_final: 0.6741 (mp0) REVERT: C 325 ASN cc_start: 0.7914 (t0) cc_final: 0.7500 (p0) REVERT: C 357 VAL cc_start: 0.9269 (t) cc_final: 0.8875 (m) REVERT: C 376 ASP cc_start: 0.8060 (t0) cc_final: 0.7727 (t0) REVERT: C 411 GLU cc_start: 0.8416 (mp0) cc_final: 0.8115 (mp0) REVERT: D 269 MET cc_start: 0.7870 (mtp) cc_final: 0.7665 (ttp) REVERT: D 279 CYS cc_start: 0.6915 (OUTLIER) cc_final: 0.6488 (m) REVERT: D 357 VAL cc_start: 0.9272 (t) cc_final: 0.8940 (m) REVERT: D 373 MET cc_start: 0.7992 (mmm) cc_final: 0.7630 (mmm) REVERT: D 376 ASP cc_start: 0.7963 (t0) cc_final: 0.7672 (t0) REVERT: D 449 ASP cc_start: 0.8419 (m-30) cc_final: 0.8081 (m-30) REVERT: D 463 LEU cc_start: 0.8755 (pp) cc_final: 0.8456 (mp) outliers start: 81 outliers final: 63 residues processed: 495 average time/residue: 0.0900 time to fit residues: 69.3083 Evaluate side-chains 507 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 441 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 219 TRP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 445 PHE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 219 TRP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 457 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 109 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 150 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 0.0470 chunk 35 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS A 408 GLN B 144 HIS C 144 HIS D 144 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.143054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.119065 restraints weight = 18414.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.124175 restraints weight = 9218.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.128023 restraints weight = 5891.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.130476 restraints weight = 4196.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.132528 restraints weight = 3276.436| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12520 Z= 0.169 Angle : 0.732 12.034 17028 Z= 0.377 Chirality : 0.050 0.196 1796 Planarity : 0.004 0.068 2180 Dihedral : 7.140 56.838 1915 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 5.84 % Allowed : 29.19 % Favored : 64.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.20), residues: 1540 helix: -4.11 (0.38), residues: 60 sheet: -0.13 (0.22), residues: 552 loop : -1.37 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 368 TYR 0.012 0.001 TYR A 316 PHE 0.021 0.002 PHE A 121 TRP 0.009 0.001 TRP D 179 HIS 0.005 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (12476) covalent geometry : angle 0.71196 / 0.37 (16928) SS BOND : bond 0.00739 / 0.40 ( 32) SS BOND : angle 2.76175 / 1.87 ( 64) hydrogen bonds : bond 0.03106 / 2.21 ( 304) hydrogen bonds : angle 5.77278 / 4.01 ( 768) link_NAG-ASN : bond 0.00300 / 0.18 ( 12) link_NAG-ASN : angle 1.18033 / 0.69 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 450 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ASP cc_start: 0.7721 (t0) cc_final: 0.7443 (t0) REVERT: A 170 TYR cc_start: 0.9105 (m-10) cc_final: 0.8854 (m-80) REVERT: A 173 ARG cc_start: 0.7767 (mtm-85) cc_final: 0.7504 (mtm-85) REVERT: A 209 ASN cc_start: 0.7908 (m-40) cc_final: 0.7629 (m-40) REVERT: A 214 ASP cc_start: 0.8451 (t70) cc_final: 0.8078 (t0) REVERT: A 264 ILE cc_start: 0.9122 (mm) cc_final: 0.8858 (mm) REVERT: A 279 CYS cc_start: 0.6805 (OUTLIER) cc_final: 0.6526 (m) REVERT: A 284 ASP cc_start: 0.8335 (p0) cc_final: 0.8068 (p0) REVERT: A 357 VAL cc_start: 0.9300 (t) cc_final: 0.8920 (m) REVERT: A 436 ILE cc_start: 0.9238 (mt) cc_final: 0.8900 (tt) REVERT: A 449 ASP cc_start: 0.8445 (m-30) cc_final: 0.8243 (m-30) REVERT: A 463 LEU cc_start: 0.8895 (pp) cc_final: 0.8438 (mp) REVERT: B 142 ASP cc_start: 0.7842 (t0) cc_final: 0.7559 (t0) REVERT: B 275 HIS cc_start: 0.8412 (t-90) cc_final: 0.8091 (t-90) REVERT: B 279 CYS cc_start: 0.6791 (OUTLIER) cc_final: 0.6503 (m) REVERT: B 284 ASP cc_start: 0.8327 (p0) cc_final: 0.8117 (p0) REVERT: B 357 VAL cc_start: 0.9302 (t) cc_final: 0.8899 (m) REVERT: B 373 MET cc_start: 0.7938 (mmm) cc_final: 0.7581 (mmm) REVERT: B 376 ASP cc_start: 0.8042 (t0) cc_final: 0.7812 (t0) REVERT: B 436 ILE cc_start: 0.9233 (mm) cc_final: 0.8858 (tt) REVERT: C 118 ARG cc_start: 0.8301 (mmm-85) cc_final: 0.8084 (mmm-85) REVERT: C 136 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8508 (mm-40) REVERT: C 230 GLU cc_start: 0.7731 (tt0) cc_final: 0.7523 (tp30) REVERT: C 256 PHE cc_start: 0.8385 (m-80) cc_final: 0.8128 (m-10) REVERT: C 275 HIS cc_start: 0.8268 (t-90) cc_final: 0.7985 (t-90) REVERT: C 284 ASP cc_start: 0.8349 (p0) cc_final: 0.7906 (p0) REVERT: C 287 GLU cc_start: 0.7147 (mp0) cc_final: 0.6853 (mp0) REVERT: C 316 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.7754 (m-10) REVERT: C 357 VAL cc_start: 0.9294 (t) cc_final: 0.8906 (m) REVERT: C 373 MET cc_start: 0.7917 (mmm) cc_final: 0.7566 (mmm) REVERT: C 376 ASP cc_start: 0.8071 (t0) cc_final: 0.7769 (t0) REVERT: C 411 GLU cc_start: 0.8434 (mp0) cc_final: 0.8102 (mp0) REVERT: C 449 ASP cc_start: 0.8395 (m-30) cc_final: 0.8116 (m-30) REVERT: D 275 HIS cc_start: 0.8303 (t-90) cc_final: 0.7996 (t-90) REVERT: D 279 CYS cc_start: 0.6805 (OUTLIER) cc_final: 0.6549 (m) REVERT: D 284 ASP cc_start: 0.8341 (p0) cc_final: 0.8112 (p0) REVERT: D 357 VAL cc_start: 0.9315 (t) cc_final: 0.8975 (m) REVERT: D 373 MET cc_start: 0.7958 (mmm) cc_final: 0.7623 (mmm) REVERT: D 376 ASP cc_start: 0.8018 (t0) cc_final: 0.7758 (t0) REVERT: D 463 LEU cc_start: 0.8811 (pp) cc_final: 0.8488 (mp) outliers start: 78 outliers final: 65 residues processed: 488 average time/residue: 0.0897 time to fit residues: 68.0568 Evaluate side-chains 461 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 392 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 219 TRP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 445 PHE Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 219 TRP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain C residue 316 TYR Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 445 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 43 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 123 optimal weight: 0.0170 chunk 93 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 0.0770 chunk 144 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS B 144 HIS C 144 HIS D 144 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.146488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.122936 restraints weight = 18366.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.128103 restraints weight = 9174.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.132033 restraints weight = 5750.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.134535 restraints weight = 4072.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.136287 restraints weight = 3153.113| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12520 Z= 0.138 Angle : 0.727 11.700 17028 Z= 0.374 Chirality : 0.051 0.202 1796 Planarity : 0.004 0.071 2180 Dihedral : 7.149 59.341 1915 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 5.16 % Allowed : 30.01 % Favored : 64.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.20), residues: 1540 helix: -4.09 (0.39), residues: 60 sheet: -0.06 (0.23), residues: 548 loop : -1.26 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 368 TYR 0.010 0.001 TYR A 316 PHE 0.021 0.002 PHE C 121 TRP 0.009 0.001 TRP D 179 HIS 0.004 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (12476) covalent geometry : angle 0.71317 / 0.37 (16928) SS BOND : bond 0.00725 / 0.41 ( 32) SS BOND : angle 2.33729 / 1.57 ( 64) hydrogen bonds : bond 0.02930 / 2.10 ( 304) hydrogen bonds : angle 5.67121 / 3.94 ( 768) link_NAG-ASN : bond 0.00299 / 0.18 ( 12) link_NAG-ASN : angle 1.15723 / 0.68 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 442 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.9070 (m-10) cc_final: 0.8832 (m-80) REVERT: A 214 ASP cc_start: 0.8390 (t70) cc_final: 0.8069 (t0) REVERT: A 231 CYS cc_start: 0.5934 (OUTLIER) cc_final: 0.5394 (p) REVERT: A 268 GLU cc_start: 0.7864 (pm20) cc_final: 0.7619 (pp20) REVERT: A 275 HIS cc_start: 0.8387 (t-90) cc_final: 0.7953 (t-90) REVERT: A 279 CYS cc_start: 0.6878 (OUTLIER) cc_final: 0.6555 (m) REVERT: A 284 ASP cc_start: 0.8358 (p0) cc_final: 0.8099 (p0) REVERT: A 357 VAL cc_start: 0.9270 (t) cc_final: 0.8898 (m) REVERT: A 436 ILE cc_start: 0.9248 (mt) cc_final: 0.8976 (tp) REVERT: A 463 LEU cc_start: 0.8907 (pp) cc_final: 0.8517 (mp) REVERT: B 142 ASP cc_start: 0.7800 (t0) cc_final: 0.7525 (t0) REVERT: B 173 ARG cc_start: 0.7734 (mtm-85) cc_final: 0.7483 (mtm-85) REVERT: B 268 GLU cc_start: 0.7766 (pm20) cc_final: 0.7502 (pp20) REVERT: B 275 HIS cc_start: 0.8303 (t-90) cc_final: 0.7982 (t-90) REVERT: B 279 CYS cc_start: 0.6828 (OUTLIER) cc_final: 0.6560 (m) REVERT: B 284 ASP cc_start: 0.8358 (p0) cc_final: 0.8060 (p0) REVERT: B 357 VAL cc_start: 0.9257 (t) cc_final: 0.8861 (m) REVERT: B 373 MET cc_start: 0.7935 (mmm) cc_final: 0.7576 (mmm) REVERT: B 376 ASP cc_start: 0.7976 (t0) cc_final: 0.7711 (t0) REVERT: B 436 ILE cc_start: 0.9233 (mm) cc_final: 0.8874 (tt) REVERT: C 118 ARG cc_start: 0.8288 (mmm-85) cc_final: 0.8078 (mmm-85) REVERT: C 136 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8561 (mm-40) REVERT: C 275 HIS cc_start: 0.8201 (t-90) cc_final: 0.7895 (t-90) REVERT: C 284 ASP cc_start: 0.8426 (p0) cc_final: 0.8031 (p0) REVERT: C 287 GLU cc_start: 0.7120 (mp0) cc_final: 0.6820 (mp0) REVERT: C 357 VAL cc_start: 0.9256 (t) cc_final: 0.8843 (m) REVERT: C 373 MET cc_start: 0.7956 (mmm) cc_final: 0.7589 (mmm) REVERT: C 376 ASP cc_start: 0.8053 (t0) cc_final: 0.7743 (t0) REVERT: C 411 GLU cc_start: 0.8484 (mp0) cc_final: 0.8133 (mp0) REVERT: C 463 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8417 (mp) REVERT: D 275 HIS cc_start: 0.8205 (t-90) cc_final: 0.7928 (t-90) REVERT: D 284 ASP cc_start: 0.8396 (p0) cc_final: 0.8089 (p0) REVERT: D 357 VAL cc_start: 0.9311 (t) cc_final: 0.8967 (m) REVERT: D 373 MET cc_start: 0.7956 (mmm) cc_final: 0.7617 (mmm) REVERT: D 376 ASP cc_start: 0.7898 (t0) cc_final: 0.7600 (t0) REVERT: D 463 LEU cc_start: 0.8836 (pp) cc_final: 0.8555 (mp) outliers start: 69 outliers final: 58 residues processed: 476 average time/residue: 0.0883 time to fit residues: 65.5733 Evaluate side-chains 463 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 401 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 219 TRP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 445 PHE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 219 TRP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 443 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 110 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 85 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS B 144 HIS C 144 HIS D 144 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.145748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.121988 restraints weight = 18161.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.127386 restraints weight = 9153.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.131008 restraints weight = 5751.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.133697 restraints weight = 4100.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.135441 restraints weight = 3139.021| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12520 Z= 0.148 Angle : 0.750 11.867 17028 Z= 0.386 Chirality : 0.050 0.196 1796 Planarity : 0.004 0.068 2180 Dihedral : 7.237 59.833 1915 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 5.31 % Allowed : 31.06 % Favored : 63.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.20), residues: 1540 helix: -4.11 (0.38), residues: 60 sheet: 0.00 (0.23), residues: 552 loop : -1.33 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 368 TYR 0.012 0.001 TYR C 276 PHE 0.018 0.001 PHE C 256 TRP 0.008 0.001 TRP D 179 HIS 0.004 0.001 HIS B 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (12476) covalent geometry : angle 0.73413 / 0.38 (16928) SS BOND : bond 0.00703 / 0.39 ( 32) SS BOND : angle 2.55954 / 1.72 ( 64) hydrogen bonds : bond 0.02938 / 2.10 ( 304) hydrogen bonds : angle 5.65810 / 3.93 ( 768) link_NAG-ASN : bond 0.00278 / 0.17 ( 12) link_NAG-ASN : angle 1.12245 / 0.66 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 430 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.9062 (m-10) cc_final: 0.8854 (m-80) REVERT: A 173 ARG cc_start: 0.7709 (mtm-85) cc_final: 0.7046 (mtp180) REVERT: A 214 ASP cc_start: 0.8361 (t70) cc_final: 0.8015 (t0) REVERT: A 231 CYS cc_start: 0.6064 (OUTLIER) cc_final: 0.5536 (p) REVERT: A 275 HIS cc_start: 0.8385 (t-90) cc_final: 0.7946 (t-90) REVERT: A 357 VAL cc_start: 0.9265 (t) cc_final: 0.8906 (m) REVERT: A 436 ILE cc_start: 0.9252 (mt) cc_final: 0.8988 (tp) REVERT: A 463 LEU cc_start: 0.8856 (pp) cc_final: 0.8603 (mp) REVERT: B 142 ASP cc_start: 0.7752 (t0) cc_final: 0.7487 (t0) REVERT: B 173 ARG cc_start: 0.7691 (mtm-85) cc_final: 0.7431 (mtm-85) REVERT: B 275 HIS cc_start: 0.8318 (t-90) cc_final: 0.8015 (t-90) REVERT: B 284 ASP cc_start: 0.8349 (p0) cc_final: 0.8100 (p0) REVERT: B 357 VAL cc_start: 0.9264 (t) cc_final: 0.8882 (m) REVERT: B 368 ARG cc_start: 0.8684 (ttm110) cc_final: 0.8361 (ttm170) REVERT: B 373 MET cc_start: 0.7909 (mmm) cc_final: 0.7571 (mmm) REVERT: B 376 ASP cc_start: 0.8064 (t0) cc_final: 0.7774 (t0) REVERT: B 436 ILE cc_start: 0.9224 (mm) cc_final: 0.8895 (tt) REVERT: C 136 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8545 (mm-40) REVERT: C 231 CYS cc_start: 0.5575 (p) cc_final: 0.5092 (p) REVERT: C 275 HIS cc_start: 0.8212 (t-90) cc_final: 0.7849 (t-90) REVERT: C 284 ASP cc_start: 0.8437 (p0) cc_final: 0.8068 (p0) REVERT: C 287 GLU cc_start: 0.7080 (mp0) cc_final: 0.6854 (mp0) REVERT: C 357 VAL cc_start: 0.9255 (t) cc_final: 0.8848 (m) REVERT: C 373 MET cc_start: 0.7875 (mmm) cc_final: 0.7530 (mmm) REVERT: C 376 ASP cc_start: 0.8102 (t0) cc_final: 0.7799 (t0) REVERT: C 463 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8389 (mp) REVERT: D 275 HIS cc_start: 0.8228 (t-90) cc_final: 0.7902 (t-90) REVERT: D 284 ASP cc_start: 0.8354 (p0) cc_final: 0.8081 (p0) REVERT: D 357 VAL cc_start: 0.9219 (t) cc_final: 0.8848 (m) REVERT: D 368 ARG cc_start: 0.8671 (ttm110) cc_final: 0.8373 (ttm-80) REVERT: D 373 MET cc_start: 0.7933 (mmm) cc_final: 0.7604 (mmm) REVERT: D 376 ASP cc_start: 0.7916 (t0) cc_final: 0.7659 (t0) REVERT: D 463 LEU cc_start: 0.8790 (pp) cc_final: 0.8543 (mp) outliers start: 71 outliers final: 63 residues processed: 467 average time/residue: 0.0830 time to fit residues: 60.6145 Evaluate side-chains 481 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 416 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 219 TRP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 445 PHE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 219 TRP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 443 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 145 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 91 optimal weight: 0.2980 chunk 79 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 149 optimal weight: 0.0570 chunk 93 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 overall best weight: 1.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS B 144 HIS C 144 HIS D 144 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.143832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.119867 restraints weight = 18387.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.125297 restraints weight = 9272.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.128906 restraints weight = 5833.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.131574 restraints weight = 4190.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.133212 restraints weight = 3200.843| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12520 Z= 0.170 Angle : 0.772 11.873 17028 Z= 0.397 Chirality : 0.051 0.207 1796 Planarity : 0.004 0.069 2180 Dihedral : 7.322 59.753 1915 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.94 % Allowed : 31.36 % Favored : 63.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.20), residues: 1540 helix: -4.09 (0.40), residues: 60 sheet: -0.03 (0.23), residues: 552 loop : -1.35 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 368 TYR 0.012 0.001 TYR C 276 PHE 0.023 0.002 PHE C 121 TRP 0.009 0.001 TRP D 179 HIS 0.004 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (12476) covalent geometry : angle 0.75755 / 0.39 (16928) SS BOND : bond 0.00747 / 0.42 ( 32) SS BOND : angle 2.50120 / 1.69 ( 64) hydrogen bonds : bond 0.03028 / 2.18 ( 304) hydrogen bonds : angle 5.70952 / 3.96 ( 768) link_NAG-ASN : bond 0.00245 / 0.14 ( 12) link_NAG-ASN : angle 1.10732 / 0.65 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 432 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ARG cc_start: 0.7728 (mtm-85) cc_final: 0.7351 (mtp-110) REVERT: A 214 ASP cc_start: 0.8375 (t70) cc_final: 0.8024 (t0) REVERT: A 231 CYS cc_start: 0.6127 (OUTLIER) cc_final: 0.5606 (p) REVERT: A 275 HIS cc_start: 0.8400 (t-90) cc_final: 0.7941 (t-90) REVERT: A 284 ASP cc_start: 0.8351 (p0) cc_final: 0.8112 (p0) REVERT: A 357 VAL cc_start: 0.9269 (t) cc_final: 0.8906 (m) REVERT: A 436 ILE cc_start: 0.9280 (mt) cc_final: 0.9018 (tp) REVERT: A 463 LEU cc_start: 0.8849 (pp) cc_final: 0.8606 (mp) REVERT: B 142 ASP cc_start: 0.7898 (t0) cc_final: 0.7628 (t0) REVERT: B 173 ARG cc_start: 0.7744 (mtm-85) cc_final: 0.7366 (mtp-110) REVERT: B 275 HIS cc_start: 0.8327 (t-90) cc_final: 0.7934 (t-90) REVERT: B 284 ASP cc_start: 0.8340 (p0) cc_final: 0.8113 (p0) REVERT: B 357 VAL cc_start: 0.9262 (t) cc_final: 0.8899 (m) REVERT: B 376 ASP cc_start: 0.8071 (t0) cc_final: 0.7855 (t0) REVERT: B 436 ILE cc_start: 0.9218 (mm) cc_final: 0.8888 (tt) REVERT: C 228 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7564 (mm-30) REVERT: C 275 HIS cc_start: 0.8268 (t-90) cc_final: 0.7880 (t-90) REVERT: C 284 ASP cc_start: 0.8361 (p0) cc_final: 0.7987 (p0) REVERT: C 357 VAL cc_start: 0.9271 (t) cc_final: 0.8881 (m) REVERT: C 373 MET cc_start: 0.7869 (mmm) cc_final: 0.7536 (mmm) REVERT: C 376 ASP cc_start: 0.8072 (t0) cc_final: 0.7813 (t0) REVERT: C 463 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8456 (mp) REVERT: D 275 HIS cc_start: 0.8246 (t-90) cc_final: 0.7827 (t-90) REVERT: D 284 ASP cc_start: 0.8345 (p0) cc_final: 0.8111 (p0) REVERT: D 357 VAL cc_start: 0.9271 (t) cc_final: 0.8901 (m) REVERT: D 373 MET cc_start: 0.7871 (mmm) cc_final: 0.7558 (mmm) REVERT: D 376 ASP cc_start: 0.7951 (t0) cc_final: 0.7724 (t0) outliers start: 66 outliers final: 60 residues processed: 468 average time/residue: 0.0809 time to fit residues: 59.3275 Evaluate side-chains 474 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 412 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 CYS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 219 TRP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 445 PHE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 219 TRP Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 279 CYS Chi-restraints excluded: chain D residue 383 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 144 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 116 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 1 optimal weight: 0.3980 chunk 34 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS A 408 GLN B 144 HIS C 144 HIS D 144 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.145595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.121875 restraints weight = 18223.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.127201 restraints weight = 9153.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.131017 restraints weight = 5748.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.133492 restraints weight = 4069.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.135267 restraints weight = 3154.884| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12520 Z= 0.153 Angle : 0.771 11.652 17028 Z= 0.397 Chirality : 0.051 0.193 1796 Planarity : 0.004 0.067 2180 Dihedral : 7.306 59.958 1915 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.87 % Allowed : 31.81 % Favored : 63.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.20), residues: 1540 helix: -4.12 (0.38), residues: 60 sheet: -0.03 (0.23), residues: 544 loop : -1.32 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 368 TYR 0.011 0.001 TYR C 276 PHE 0.017 0.001 PHE C 256 TRP 0.008 0.001 TRP B 457 HIS 0.005 0.001 HIS D 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 (12476) covalent geometry : angle 0.75808 / 0.39 (16928) SS BOND : bond 0.00655 / 0.37 ( 32) SS BOND : angle 2.36081 / 1.61 ( 64) hydrogen bonds : bond 0.02963 / 2.11 ( 304) hydrogen bonds : angle 5.66487 / 3.92 ( 768) link_NAG-ASN : bond 0.00270 / 0.16 ( 12) link_NAG-ASN : angle 1.08427 / 0.64 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2085.44 seconds wall clock time: 36 minutes 52.09 seconds (2212.09 seconds total)