Starting phenix.real_space_refine on Mon Jun 23 13:20:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bhq_16066/06_2025/8bhq_16066_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bhq_16066/06_2025/8bhq_16066.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bhq_16066/06_2025/8bhq_16066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bhq_16066/06_2025/8bhq_16066.map" model { file = "/net/cci-nas-00/data/ceres_data/8bhq_16066/06_2025/8bhq_16066_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bhq_16066/06_2025/8bhq_16066_trim.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.005 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 S 85 5.16 5 C 8940 2.51 5 N 2290 2.21 5 O 2485 1.98 5 H 13415 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27215 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'NAG': 1, 'QR3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, B, E, D Time building chain proxies: 13.83, per 1000 atoms: 0.51 Number of scatterers: 27215 At special positions: 0 Unit cell: (93.09, 95.23, 126.26, 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) S 85 16.00 O 2485 8.00 N 2290 7.00 C 8940 6.00 H 13415 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS E 142 " - pdb=" SG CYS E 156 " distance=2.03 Simple disulfide: pdb=" SG CYS D 142 " - pdb=" SG CYS D 156 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 205 " " NAG B 501 " - " ASN B 205 " " NAG C 501 " - " ASN C 205 " " NAG D 501 " - " ASN D 205 " " NAG E 501 " - " ASN E 205 " Time building additional restraints: 7.27 Conformation dependent library (CDL) restraints added in 2.0 seconds 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3190 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 15 sheets defined 42.3% alpha, 37.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'A' and resid 15 through 27 removed outlier: 3.575A pdb=" N THR A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 79 Processing helix chain 'A' and resid 90 through 97 removed outlier: 3.655A pdb=" N LEU A 93 " --> pdb=" O ASN A 90 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER A 95 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 97 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 227 through 233 removed outlier: 3.563A pdb=" N ILE A 231 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 250 removed outlier: 3.555A pdb=" N VAL A 246 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TRP A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 250 " --> pdb=" O VAL A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 280 removed outlier: 3.620A pdb=" N PHE A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 314 Processing helix chain 'A' and resid 317 through 418 removed outlier: 3.573A pdb=" N ALA A 321 " --> pdb=" O GLN A 317 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 393 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Proline residue: A 403 - end of helix Processing helix chain 'B' and resid 15 through 27 removed outlier: 3.576A pdb=" N THR B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 79 Processing helix chain 'B' and resid 90 through 97 removed outlier: 3.655A pdb=" N LEU B 93 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER B 95 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 97 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 227 through 233 removed outlier: 3.563A pdb=" N ILE B 231 " --> pdb=" O GLY B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 250 removed outlier: 3.555A pdb=" N VAL B 246 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TRP B 249 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B 250 " --> pdb=" O VAL B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 280 removed outlier: 3.621A pdb=" N PHE B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU B 280 " --> pdb=" O ALA B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 314 Processing helix chain 'B' and resid 317 through 418 removed outlier: 3.573A pdb=" N ALA B 321 " --> pdb=" O GLN B 317 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS B 393 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Proline residue: B 403 - end of helix Processing helix chain 'C' and resid 15 through 27 removed outlier: 3.574A pdb=" N THR C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 79 Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.654A pdb=" N LEU C 93 " --> pdb=" O ASN C 90 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER C 95 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE C 97 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 181 Processing helix chain 'C' and resid 227 through 233 removed outlier: 3.563A pdb=" N ILE C 231 " --> pdb=" O GLY C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 250 removed outlier: 3.554A pdb=" N VAL C 246 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TRP C 249 " --> pdb=" O GLN C 245 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU C 250 " --> pdb=" O VAL C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 280 removed outlier: 3.620A pdb=" N PHE C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU C 280 " --> pdb=" O ALA C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 314 Processing helix chain 'C' and resid 317 through 418 removed outlier: 3.573A pdb=" N ALA C 321 " --> pdb=" O GLN C 317 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS C 393 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG C 399 " --> pdb=" O ASP C 395 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Proline residue: C 403 - end of helix Processing helix chain 'D' and resid 15 through 27 removed outlier: 3.574A pdb=" N THR D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 79 Processing helix chain 'D' and resid 90 through 97 removed outlier: 3.654A pdb=" N LEU D 93 " --> pdb=" O ASN D 90 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER D 95 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE D 97 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 181 Processing helix chain 'D' and resid 227 through 233 removed outlier: 3.563A pdb=" N ILE D 231 " --> pdb=" O GLY D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 250 removed outlier: 3.556A pdb=" N VAL D 246 " --> pdb=" O ILE D 242 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE D 248 " --> pdb=" O SER D 244 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TRP D 249 " --> pdb=" O GLN D 245 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU D 250 " --> pdb=" O VAL D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 280 removed outlier: 3.620A pdb=" N PHE D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU D 280 " --> pdb=" O ALA D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 314 Processing helix chain 'D' and resid 317 through 418 removed outlier: 3.573A pdb=" N ALA D 321 " --> pdb=" O GLN D 317 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS D 393 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) Proline residue: D 403 - end of helix Processing helix chain 'E' and resid 15 through 27 removed outlier: 3.574A pdb=" N THR E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 79 Processing helix chain 'E' and resid 90 through 97 removed outlier: 3.654A pdb=" N LEU E 93 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER E 95 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE E 97 " --> pdb=" O ALA E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 181 Processing helix chain 'E' and resid 227 through 233 removed outlier: 3.563A pdb=" N ILE E 231 " --> pdb=" O GLY E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 250 removed outlier: 3.555A pdb=" N VAL E 246 " --> pdb=" O ILE E 242 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER E 247 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE E 248 " --> pdb=" O SER E 244 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TRP E 249 " --> pdb=" O GLN E 245 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU E 250 " --> pdb=" O VAL E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 280 removed outlier: 3.620A pdb=" N PHE E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER E 279 " --> pdb=" O SER E 275 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU E 280 " --> pdb=" O ALA E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 314 Processing helix chain 'E' and resid 317 through 418 removed outlier: 3.572A pdb=" N ALA E 321 " --> pdb=" O GLN E 317 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS E 393 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE E 400 " --> pdb=" O LYS E 396 " (cutoff:3.500A) Proline residue: E 403 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 112 removed outlier: 7.280A pdb=" N GLY A 107 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N GLU A 141 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS A 109 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASP A 66 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N PHE A 53 " --> pdb=" O ASP A 66 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N PHE A 68 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ASN A 51 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ALA A 70 " --> pdb=" O TYR A 49 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N TYR A 49 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N THR A 72 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ASP A 47 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N LYS A 74 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 9.766A pdb=" N ARG A 45 " --> pdb=" O LYS A 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 124 removed outlier: 3.650A pdb=" N THR A 133 " --> pdb=" O MET A 121 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASP A 66 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N PHE A 53 " --> pdb=" O ASP A 66 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N PHE A 68 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ASN A 51 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ALA A 70 " --> pdb=" O TYR A 49 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N TYR A 49 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N THR A 72 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ASP A 47 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N LYS A 74 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 9.766A pdb=" N ARG A 45 " --> pdb=" O LYS A 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 102 through 104 removed outlier: 4.485A pdb=" N SER A 162 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR A 214 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY A 198 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS A 223 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU A 196 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 112 removed outlier: 7.281A pdb=" N GLY B 107 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLU B 141 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS B 109 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASP B 66 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N PHE B 53 " --> pdb=" O ASP B 66 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N PHE B 68 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ASN B 51 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ALA B 70 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N TYR B 49 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N THR B 72 " --> pdb=" O ASP B 47 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ASP B 47 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N LYS B 74 " --> pdb=" O ARG B 45 " (cutoff:3.500A) removed outlier: 9.766A pdb=" N ARG B 45 " --> pdb=" O LYS B 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 120 through 124 removed outlier: 3.650A pdb=" N THR B 133 " --> pdb=" O MET B 121 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASP B 66 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N PHE B 53 " --> pdb=" O ASP B 66 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N PHE B 68 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ASN B 51 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ALA B 70 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N TYR B 49 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N THR B 72 " --> pdb=" O ASP B 47 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ASP B 47 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N LYS B 74 " --> pdb=" O ARG B 45 " (cutoff:3.500A) removed outlier: 9.766A pdb=" N ARG B 45 " --> pdb=" O LYS B 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 102 through 104 removed outlier: 4.484A pdb=" N SER B 162 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR B 214 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY B 198 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS B 223 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU B 196 " --> pdb=" O LYS B 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 107 through 112 removed outlier: 7.279A pdb=" N GLY C 107 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLU C 141 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS C 109 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASP C 66 " --> pdb=" O PHE C 53 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N PHE C 53 " --> pdb=" O ASP C 66 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N PHE C 68 " --> pdb=" O ASN C 51 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ASN C 51 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ALA C 70 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N TYR C 49 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N THR C 72 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ASP C 47 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N LYS C 74 " --> pdb=" O ARG C 45 " (cutoff:3.500A) removed outlier: 9.765A pdb=" N ARG C 45 " --> pdb=" O LYS C 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 120 through 124 removed outlier: 3.649A pdb=" N THR C 133 " --> pdb=" O MET C 121 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASP C 66 " --> pdb=" O PHE C 53 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N PHE C 53 " --> pdb=" O ASP C 66 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N PHE C 68 " --> pdb=" O ASN C 51 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ASN C 51 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ALA C 70 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N TYR C 49 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N THR C 72 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ASP C 47 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N LYS C 74 " --> pdb=" O ARG C 45 " (cutoff:3.500A) removed outlier: 9.765A pdb=" N ARG C 45 " --> pdb=" O LYS C 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 102 through 104 removed outlier: 4.484A pdb=" N SER C 162 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR C 214 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY C 198 " --> pdb=" O HIS C 221 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS C 223 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU C 196 " --> pdb=" O LYS C 223 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 107 through 112 removed outlier: 7.279A pdb=" N GLY D 107 " --> pdb=" O GLU D 141 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLU D 141 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS D 109 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASP D 66 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N PHE D 53 " --> pdb=" O ASP D 66 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N PHE D 68 " --> pdb=" O ASN D 51 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ASN D 51 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ALA D 70 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N TYR D 49 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N THR D 72 " --> pdb=" O ASP D 47 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ASP D 47 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N LYS D 74 " --> pdb=" O ARG D 45 " (cutoff:3.500A) removed outlier: 9.766A pdb=" N ARG D 45 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.650A pdb=" N THR D 133 " --> pdb=" O MET D 121 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASP D 66 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N PHE D 53 " --> pdb=" O ASP D 66 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N PHE D 68 " --> pdb=" O ASN D 51 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ASN D 51 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ALA D 70 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N TYR D 49 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N THR D 72 " --> pdb=" O ASP D 47 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ASP D 47 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N LYS D 74 " --> pdb=" O ARG D 45 " (cutoff:3.500A) removed outlier: 9.766A pdb=" N ARG D 45 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 102 through 104 removed outlier: 4.484A pdb=" N SER D 162 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR D 214 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY D 198 " --> pdb=" O HIS D 221 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS D 223 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU D 196 " --> pdb=" O LYS D 223 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 107 through 112 removed outlier: 7.280A pdb=" N GLY E 107 " --> pdb=" O GLU E 141 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLU E 141 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS E 109 " --> pdb=" O SER E 139 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASP E 66 " --> pdb=" O PHE E 53 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N PHE E 53 " --> pdb=" O ASP E 66 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N PHE E 68 " --> pdb=" O ASN E 51 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ASN E 51 " --> pdb=" O PHE E 68 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ALA E 70 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N TYR E 49 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N THR E 72 " --> pdb=" O ASP E 47 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ASP E 47 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N LYS E 74 " --> pdb=" O ARG E 45 " (cutoff:3.500A) removed outlier: 9.767A pdb=" N ARG E 45 " --> pdb=" O LYS E 74 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 120 through 124 removed outlier: 3.650A pdb=" N THR E 133 " --> pdb=" O MET E 121 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASP E 66 " --> pdb=" O PHE E 53 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N PHE E 53 " --> pdb=" O ASP E 66 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N PHE E 68 " --> pdb=" O ASN E 51 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ASN E 51 " --> pdb=" O PHE E 68 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ALA E 70 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N TYR E 49 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N THR E 72 " --> pdb=" O ASP E 47 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ASP E 47 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N LYS E 74 " --> pdb=" O ARG E 45 " (cutoff:3.500A) removed outlier: 9.767A pdb=" N ARG E 45 " --> pdb=" O LYS E 74 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 102 through 104 removed outlier: 4.484A pdb=" N SER E 162 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR E 214 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY E 198 " --> pdb=" O HIS E 221 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS E 223 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU E 196 " --> pdb=" O LYS E 223 " (cutoff:3.500A) 745 hydrogen bonds defined for protein. 2160 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: 10.86 Time building geometry restraints manager: 8.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13415 1.03 - 1.23: 5 1.23 - 1.42: 6120 1.42 - 1.62: 7905 1.62 - 1.81: 150 Bond restraints: 27595 Sorted by residual: bond pdb=" N ASN E 14 " pdb=" H ASN E 14 " ideal model delta sigma weight residual 0.860 0.961 -0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" N ASN D 14 " pdb=" H ASN D 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N ASN A 14 " pdb=" H ASN A 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" N ASN C 14 " pdb=" H ASN C 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" N ASN B 14 " pdb=" H ASN B 14 " ideal model delta sigma weight residual 0.860 0.959 -0.099 2.00e-02 2.50e+03 2.46e+01 ... (remaining 27590 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 48024 1.13 - 2.27: 1408 2.27 - 3.40: 100 3.40 - 4.54: 37 4.54 - 5.67: 16 Bond angle restraints: 49585 Sorted by residual: angle pdb=" C MET E 115 " pdb=" N THR E 116 " pdb=" CA THR E 116 " ideal model delta sigma weight residual 121.70 127.37 -5.67 1.80e+00 3.09e-01 9.92e+00 angle pdb=" C MET A 115 " pdb=" N THR A 116 " pdb=" CA THR A 116 " ideal model delta sigma weight residual 121.70 127.37 -5.67 1.80e+00 3.09e-01 9.91e+00 angle pdb=" C MET B 115 " pdb=" N THR B 116 " pdb=" CA THR B 116 " ideal model delta sigma weight residual 121.70 127.37 -5.67 1.80e+00 3.09e-01 9.91e+00 angle pdb=" C MET C 115 " pdb=" N THR C 116 " pdb=" CA THR C 116 " ideal model delta sigma weight residual 121.70 127.35 -5.65 1.80e+00 3.09e-01 9.84e+00 angle pdb=" C MET D 115 " pdb=" N THR D 116 " pdb=" CA THR D 116 " ideal model delta sigma weight residual 121.70 127.31 -5.61 1.80e+00 3.09e-01 9.71e+00 ... (remaining 49580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.21: 12677 15.21 - 30.42: 369 30.42 - 45.64: 114 45.64 - 60.85: 120 60.85 - 76.06: 10 Dihedral angle restraints: 13290 sinusoidal: 7160 harmonic: 6130 Sorted by residual: dihedral pdb=" CB LYS E 315 " pdb=" CG LYS E 315 " pdb=" CD LYS E 315 " pdb=" CE LYS E 315 " ideal model delta sinusoidal sigma weight residual 60.00 101.84 -41.84 3 1.50e+01 4.44e-03 7.50e+00 dihedral pdb=" CB LYS A 315 " pdb=" CG LYS A 315 " pdb=" CD LYS A 315 " pdb=" CE LYS A 315 " ideal model delta sinusoidal sigma weight residual 60.00 101.79 -41.79 3 1.50e+01 4.44e-03 7.48e+00 dihedral pdb=" CB LYS B 315 " pdb=" CG LYS B 315 " pdb=" CD LYS B 315 " pdb=" CE LYS B 315 " ideal model delta sinusoidal sigma weight residual 60.00 101.79 -41.79 3 1.50e+01 4.44e-03 7.48e+00 ... (remaining 13287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1301 0.025 - 0.050: 532 0.050 - 0.074: 182 0.074 - 0.099: 64 0.099 - 0.124: 81 Chirality restraints: 2160 Sorted by residual: chirality pdb=" C1 NAG D 501 " pdb=" ND2 ASN D 205 " pdb=" C2 NAG D 501 " pdb=" O5 NAG D 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" C1 NAG B 501 " pdb=" ND2 ASN B 205 " pdb=" C2 NAG B 501 " pdb=" O5 NAG B 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-01 2.50e+01 3.69e-01 chirality pdb=" C1 NAG E 501 " pdb=" ND2 ASN E 205 " pdb=" C2 NAG E 501 " pdb=" O5 NAG E 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-01 2.50e+01 3.65e-01 ... (remaining 2157 not shown) Planarity restraints: 4000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 QR3 D 502 " -0.094 2.00e-02 2.50e+03 1.30e-01 1.70e+02 pdb=" C14 QR3 D 502 " -0.064 2.00e-02 2.50e+03 pdb=" C20 QR3 D 502 " -0.067 2.00e-02 2.50e+03 pdb=" N5 QR3 D 502 " 0.225 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 QR3 A 502 " 0.094 2.00e-02 2.50e+03 1.30e-01 1.69e+02 pdb=" C14 QR3 A 502 " 0.064 2.00e-02 2.50e+03 pdb=" C20 QR3 A 502 " 0.066 2.00e-02 2.50e+03 pdb=" N5 QR3 A 502 " -0.224 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 QR3 E 502 " 0.094 2.00e-02 2.50e+03 1.30e-01 1.69e+02 pdb=" C14 QR3 E 502 " 0.064 2.00e-02 2.50e+03 pdb=" C20 QR3 E 502 " 0.066 2.00e-02 2.50e+03 pdb=" N5 QR3 E 502 " -0.224 2.00e-02 2.50e+03 ... (remaining 3997 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 3553 2.28 - 2.86: 60897 2.86 - 3.44: 64854 3.44 - 4.02: 92543 4.02 - 4.60: 142469 Nonbonded interactions: 364316 Sorted by model distance: nonbonded pdb=" OE1 GLU A 253 " pdb=" H GLU A 253 " model vdw 1.695 2.450 nonbonded pdb=" OE1 GLU C 253 " pdb=" H GLU C 253 " model vdw 1.696 2.450 nonbonded pdb=" OE1 GLU B 253 " pdb=" H GLU B 253 " model vdw 1.697 2.450 nonbonded pdb=" OE1 GLU E 253 " pdb=" H GLU E 253 " model vdw 1.697 2.450 nonbonded pdb=" OE1 GLU D 253 " pdb=" H GLU D 253 " model vdw 1.697 2.450 ... (remaining 364311 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 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: 0.490 Extract box with map and model: 1.150 Check model and map are aligned: 0.210 Set scattering table: 0.240 Process input model: 57.940 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 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 : 0.002 0.029 14190 Z= 0.106 Angle : 0.410 5.670 19335 Z= 0.190 Chirality : 0.038 0.124 2160 Planarity : 0.007 0.130 2395 Dihedral : 8.192 76.061 5280 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.21), residues: 1670 helix: 3.31 (0.22), residues: 560 sheet: 0.66 (0.28), residues: 385 loop : 0.42 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 414 HIS 0.003 0.001 HIS D 195 PHE 0.005 0.001 PHE C 68 TYR 0.005 0.001 TYR D 285 ARG 0.002 0.000 ARG A 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00089 ( 5) link_NAG-ASN : angle 1.26311 ( 15) hydrogen bonds : bond 0.27119 ( 670) hydrogen bonds : angle 7.13971 ( 2160) SS BOND : bond 0.00057 ( 5) SS BOND : angle 0.21044 ( 10) covalent geometry : bond 0.00228 (14180) covalent geometry : angle 0.40851 (19310) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 2.390 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: B 23 ASP cc_start: 0.7065 (m-30) cc_final: 0.6861 (m-30) REVERT: E 58 ASP cc_start: 0.7847 (m-30) cc_final: 0.7645 (m-30) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.7736 time to fit residues: 276.3384 Evaluate side-chains 149 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.133607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.115097 restraints weight = 55119.850| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.14 r_work: 0.3284 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14190 Z= 0.215 Angle : 0.607 7.374 19335 Z= 0.318 Chirality : 0.044 0.156 2160 Planarity : 0.005 0.049 2395 Dihedral : 6.599 55.262 2145 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.34 % Allowed : 5.44 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.21), residues: 1670 helix: 2.73 (0.21), residues: 570 sheet: 0.06 (0.25), residues: 495 loop : 0.19 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 414 HIS 0.003 0.001 HIS D 195 PHE 0.018 0.002 PHE D 68 TYR 0.012 0.002 TYR D 285 ARG 0.003 0.000 ARG B 135 Details of bonding type rmsd link_NAG-ASN : bond 0.00088 ( 5) link_NAG-ASN : angle 0.76970 ( 15) hydrogen bonds : bond 0.06643 ( 670) hydrogen bonds : angle 4.78694 ( 2160) SS BOND : bond 0.00864 ( 5) SS BOND : angle 1.02187 ( 10) covalent geometry : bond 0.00491 (14180) covalent geometry : angle 0.60685 (19310) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 158 time to evaluate : 2.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8164 (mmp) cc_final: 0.7861 (mmt) REVERT: B 84 MET cc_start: 0.4844 (ttm) cc_final: 0.4552 (ttm) REVERT: B 151 MET cc_start: 0.7304 (mpp) cc_final: 0.7078 (mpp) REVERT: B 216 MET cc_start: 0.8690 (mmp) cc_final: 0.8392 (mmp) REVERT: C 48 MET cc_start: 0.8336 (mtp) cc_final: 0.8093 (mtp) REVERT: D 78 LEU cc_start: 0.8601 (mt) cc_final: 0.8396 (mt) REVERT: D 84 MET cc_start: 0.4289 (ttm) cc_final: 0.4026 (ttm) REVERT: D 151 MET cc_start: 0.7060 (mpp) cc_final: 0.6818 (mpp) REVERT: D 290 ASP cc_start: 0.8064 (m-30) cc_final: 0.7684 (m-30) REVERT: E 290 ASP cc_start: 0.8015 (m-30) cc_final: 0.7652 (m-30) outliers start: 5 outliers final: 4 residues processed: 160 average time/residue: 0.5964 time to fit residues: 145.7719 Evaluate side-chains 134 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 130 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain D residue 121 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 106 optimal weight: 6.9990 chunk 125 optimal weight: 0.1980 chunk 147 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN C 245 GLN E 245 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.129406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.111179 restraints weight = 54323.498| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.11 r_work: 0.3220 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14190 Z= 0.114 Angle : 0.499 7.733 19335 Z= 0.250 Chirality : 0.040 0.140 2160 Planarity : 0.004 0.046 2395 Dihedral : 5.448 38.724 2145 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.40 % Allowed : 6.51 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.21), residues: 1670 helix: 3.01 (0.21), residues: 570 sheet: 0.25 (0.26), residues: 415 loop : -0.10 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 73 HIS 0.002 0.001 HIS D 195 PHE 0.010 0.001 PHE A 68 TYR 0.008 0.001 TYR B 132 ARG 0.006 0.000 ARG B 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 5) link_NAG-ASN : angle 0.82569 ( 15) hydrogen bonds : bond 0.05188 ( 670) hydrogen bonds : angle 4.29160 ( 2160) SS BOND : bond 0.00487 ( 5) SS BOND : angle 0.92617 ( 10) covalent geometry : bond 0.00244 (14180) covalent geometry : angle 0.49850 (19310) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 150 time to evaluate : 2.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8347 (mtp) cc_final: 0.8026 (mtm) REVERT: A 115 MET cc_start: 0.8293 (mmp) cc_final: 0.8035 (mmp) REVERT: C 48 MET cc_start: 0.8377 (mtp) cc_final: 0.8173 (mtp) REVERT: C 204 GLU cc_start: 0.7756 (pt0) cc_final: 0.7550 (mt-10) REVERT: D 84 MET cc_start: 0.4219 (ttm) cc_final: 0.3935 (ttm) REVERT: D 239 MET cc_start: 0.8612 (mmm) cc_final: 0.8101 (mmp) REVERT: D 267 LEU cc_start: 0.8532 (mt) cc_final: 0.8273 (mt) REVERT: D 290 ASP cc_start: 0.8009 (m-30) cc_final: 0.7636 (m-30) REVERT: E 267 LEU cc_start: 0.8512 (mt) cc_final: 0.8174 (mt) REVERT: E 289 MET cc_start: 0.8001 (ttp) cc_final: 0.7579 (tpp) outliers start: 6 outliers final: 5 residues processed: 151 average time/residue: 0.6598 time to fit residues: 163.0803 Evaluate side-chains 138 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 133 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain D residue 134 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 144 optimal weight: 3.9990 chunk 109 optimal weight: 0.2980 chunk 50 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 245 GLN E 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.125114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.106591 restraints weight = 55498.676| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.15 r_work: 0.3175 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 14190 Z= 0.171 Angle : 0.555 7.661 19335 Z= 0.280 Chirality : 0.042 0.147 2160 Planarity : 0.005 0.049 2395 Dihedral : 5.734 34.413 2145 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.47 % Allowed : 7.18 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.21), residues: 1670 helix: 2.86 (0.21), residues: 575 sheet: 0.22 (0.26), residues: 440 loop : -0.14 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 414 HIS 0.003 0.001 HIS E 195 PHE 0.014 0.002 PHE A 68 TYR 0.013 0.001 TYR B 132 ARG 0.003 0.000 ARG A 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00207 ( 5) link_NAG-ASN : angle 0.87936 ( 15) hydrogen bonds : bond 0.05471 ( 670) hydrogen bonds : angle 4.30159 ( 2160) SS BOND : bond 0.00634 ( 5) SS BOND : angle 1.13783 ( 10) covalent geometry : bond 0.00399 (14180) covalent geometry : angle 0.55429 (19310) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 141 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8370 (mmp) cc_final: 0.8062 (mmp) REVERT: B 289 MET cc_start: 0.8298 (ttp) cc_final: 0.7940 (tpp) REVERT: C 289 MET cc_start: 0.8138 (ttp) cc_final: 0.7697 (tpp) REVERT: D 84 MET cc_start: 0.4148 (ttm) cc_final: 0.3927 (ttm) REVERT: D 267 LEU cc_start: 0.8579 (mt) cc_final: 0.8285 (mt) REVERT: D 290 ASP cc_start: 0.8134 (m-30) cc_final: 0.7824 (m-30) REVERT: E 267 LEU cc_start: 0.8498 (mt) cc_final: 0.8160 (mt) REVERT: E 289 MET cc_start: 0.8217 (ttp) cc_final: 0.7835 (tpp) REVERT: E 290 ASP cc_start: 0.8117 (m-30) cc_final: 0.7718 (m-30) outliers start: 7 outliers final: 7 residues processed: 143 average time/residue: 0.4563 time to fit residues: 102.6457 Evaluate side-chains 133 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 289 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 134 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 245 GLN E 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.125452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.107283 restraints weight = 55222.707| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.11 r_work: 0.3183 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14190 Z= 0.144 Angle : 0.527 8.453 19335 Z= 0.264 Chirality : 0.041 0.145 2160 Planarity : 0.004 0.048 2395 Dihedral : 5.314 31.398 2145 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.40 % Allowed : 7.72 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.21), residues: 1670 helix: 2.96 (0.21), residues: 570 sheet: 0.13 (0.26), residues: 415 loop : -0.31 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 414 HIS 0.003 0.001 HIS A 219 PHE 0.012 0.001 PHE A 68 TYR 0.011 0.001 TYR E 132 ARG 0.009 0.000 ARG D 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00162 ( 5) link_NAG-ASN : angle 0.96333 ( 15) hydrogen bonds : bond 0.05065 ( 670) hydrogen bonds : angle 4.19338 ( 2160) SS BOND : bond 0.01233 ( 5) SS BOND : angle 3.05535 ( 10) covalent geometry : bond 0.00331 (14180) covalent geometry : angle 0.52203 (19310) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 2.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8413 (mmp) cc_final: 0.8103 (mmp) REVERT: B 89 LEU cc_start: 0.6128 (OUTLIER) cc_final: 0.5690 (mp) REVERT: B 267 LEU cc_start: 0.8503 (mt) cc_final: 0.8188 (mt) REVERT: B 289 MET cc_start: 0.8223 (ttp) cc_final: 0.7885 (tpp) REVERT: C 289 MET cc_start: 0.8035 (ttp) cc_final: 0.7609 (tpp) REVERT: D 84 MET cc_start: 0.4355 (ttm) cc_final: 0.4124 (ttm) REVERT: D 267 LEU cc_start: 0.8549 (mt) cc_final: 0.8253 (mt) REVERT: D 290 ASP cc_start: 0.8116 (m-30) cc_final: 0.7842 (m-30) REVERT: E 267 LEU cc_start: 0.8546 (mt) cc_final: 0.8195 (mt) REVERT: E 289 MET cc_start: 0.8191 (ttp) cc_final: 0.7823 (tpp) REVERT: E 290 ASP cc_start: 0.8107 (m-30) cc_final: 0.7719 (m-30) outliers start: 6 outliers final: 4 residues processed: 133 average time/residue: 0.4475 time to fit residues: 96.0372 Evaluate side-chains 137 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain C residue 121 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS C 245 GLN E 245 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.125234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.106908 restraints weight = 55552.730| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.13 r_work: 0.3178 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14190 Z= 0.140 Angle : 0.518 7.831 19335 Z= 0.259 Chirality : 0.041 0.146 2160 Planarity : 0.004 0.048 2395 Dihedral : 5.182 32.548 2145 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.47 % Allowed : 8.19 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.21), residues: 1670 helix: 3.02 (0.21), residues: 570 sheet: 0.09 (0.26), residues: 415 loop : -0.38 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 73 HIS 0.002 0.001 HIS E 195 PHE 0.011 0.001 PHE D 160 TYR 0.011 0.001 TYR E 132 ARG 0.004 0.000 ARG D 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00193 ( 5) link_NAG-ASN : angle 0.92635 ( 15) hydrogen bonds : bond 0.04871 ( 670) hydrogen bonds : angle 4.12417 ( 2160) SS BOND : bond 0.00942 ( 5) SS BOND : angle 2.49114 ( 10) covalent geometry : bond 0.00321 (14180) covalent geometry : angle 0.51441 (19310) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 3.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8452 (mmp) cc_final: 0.8173 (mmp) REVERT: B 89 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5700 (mp) REVERT: B 267 LEU cc_start: 0.8515 (mt) cc_final: 0.8199 (mt) REVERT: B 289 MET cc_start: 0.8222 (ttp) cc_final: 0.7879 (tpp) REVERT: C 289 MET cc_start: 0.8079 (ttp) cc_final: 0.7659 (tpp) REVERT: D 84 MET cc_start: 0.4466 (ttm) cc_final: 0.4214 (ttm) REVERT: D 267 LEU cc_start: 0.8552 (mt) cc_final: 0.8244 (mt) REVERT: D 290 ASP cc_start: 0.8085 (m-30) cc_final: 0.7794 (m-30) REVERT: E 267 LEU cc_start: 0.8504 (mt) cc_final: 0.8143 (mt) REVERT: E 289 MET cc_start: 0.8200 (ttp) cc_final: 0.7834 (tpp) REVERT: E 290 ASP cc_start: 0.8087 (m-30) cc_final: 0.7692 (m-30) outliers start: 7 outliers final: 6 residues processed: 140 average time/residue: 0.4920 time to fit residues: 109.1244 Evaluate side-chains 136 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain C residue 121 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 7 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 160 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 152 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.130242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.111381 restraints weight = 55901.492| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.18 r_work: 0.3241 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 14190 Z= 0.123 Angle : 0.496 7.676 19335 Z= 0.247 Chirality : 0.040 0.143 2160 Planarity : 0.004 0.048 2395 Dihedral : 5.091 32.757 2145 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.40 % Allowed : 8.32 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.21), residues: 1670 helix: 3.15 (0.21), residues: 570 sheet: 0.09 (0.26), residues: 415 loop : -0.38 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 73 HIS 0.002 0.001 HIS E 195 PHE 0.010 0.001 PHE A 68 TYR 0.009 0.001 TYR B 132 ARG 0.003 0.000 ARG D 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00179 ( 5) link_NAG-ASN : angle 0.96667 ( 15) hydrogen bonds : bond 0.04595 ( 670) hydrogen bonds : angle 4.03553 ( 2160) SS BOND : bond 0.00845 ( 5) SS BOND : angle 2.02088 ( 10) covalent geometry : bond 0.00277 (14180) covalent geometry : angle 0.49320 (19310) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 135 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8461 (mmp) cc_final: 0.8193 (mmp) REVERT: B 89 LEU cc_start: 0.6109 (OUTLIER) cc_final: 0.5628 (mp) REVERT: B 216 MET cc_start: 0.8710 (mmp) cc_final: 0.8147 (mmp) REVERT: B 267 LEU cc_start: 0.8542 (mt) cc_final: 0.8198 (mt) REVERT: B 289 MET cc_start: 0.8158 (ttp) cc_final: 0.7817 (tpp) REVERT: C 289 MET cc_start: 0.8069 (ttp) cc_final: 0.7711 (tpp) REVERT: D 84 MET cc_start: 0.4592 (ttm) cc_final: 0.4319 (ttm) REVERT: D 267 LEU cc_start: 0.8540 (mt) cc_final: 0.8218 (mt) REVERT: D 290 ASP cc_start: 0.8035 (m-30) cc_final: 0.7757 (m-30) REVERT: E 267 LEU cc_start: 0.8526 (mt) cc_final: 0.8153 (mt) REVERT: E 289 MET cc_start: 0.8178 (ttp) cc_final: 0.7872 (tpp) REVERT: E 290 ASP cc_start: 0.8194 (m-30) cc_final: 0.7853 (m-30) outliers start: 6 outliers final: 4 residues processed: 138 average time/residue: 0.4989 time to fit residues: 107.5431 Evaluate side-chains 137 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain D residue 289 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 122 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 135 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.128803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.109882 restraints weight = 55938.464| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.19 r_work: 0.3225 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 14190 Z= 0.147 Angle : 0.520 7.768 19335 Z= 0.260 Chirality : 0.041 0.144 2160 Planarity : 0.004 0.048 2395 Dihedral : 5.256 35.926 2145 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.67 % Allowed : 8.79 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.21), residues: 1670 helix: 3.13 (0.21), residues: 570 sheet: 0.07 (0.26), residues: 415 loop : -0.43 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 73 HIS 0.003 0.001 HIS E 195 PHE 0.011 0.001 PHE A 68 TYR 0.011 0.001 TYR E 132 ARG 0.002 0.000 ARG D 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00172 ( 5) link_NAG-ASN : angle 1.09622 ( 15) hydrogen bonds : bond 0.04926 ( 670) hydrogen bonds : angle 4.10244 ( 2160) SS BOND : bond 0.00951 ( 5) SS BOND : angle 2.09158 ( 10) covalent geometry : bond 0.00340 (14180) covalent geometry : angle 0.51762 (19310) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8480 (mmp) cc_final: 0.8189 (mmp) REVERT: B 89 LEU cc_start: 0.6210 (OUTLIER) cc_final: 0.5713 (mp) REVERT: B 216 MET cc_start: 0.8711 (mmp) cc_final: 0.8143 (mmp) REVERT: B 267 LEU cc_start: 0.8538 (mt) cc_final: 0.8192 (mt) REVERT: B 289 MET cc_start: 0.8213 (ttp) cc_final: 0.7859 (tpp) REVERT: C 289 MET cc_start: 0.8119 (ttp) cc_final: 0.7756 (tpp) REVERT: C 290 ASP cc_start: 0.8066 (m-30) cc_final: 0.7601 (m-30) REVERT: D 84 MET cc_start: 0.4566 (ttm) cc_final: 0.4338 (ttm) REVERT: D 267 LEU cc_start: 0.8547 (mt) cc_final: 0.8219 (mt) REVERT: D 290 ASP cc_start: 0.8081 (m-30) cc_final: 0.7826 (m-30) REVERT: E 267 LEU cc_start: 0.8533 (mt) cc_final: 0.8170 (mt) REVERT: E 289 MET cc_start: 0.8265 (ttp) cc_final: 0.7928 (tpp) outliers start: 10 outliers final: 7 residues processed: 139 average time/residue: 0.4857 time to fit residues: 107.4086 Evaluate side-chains 140 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain E residue 412 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 15 optimal weight: 0.0570 chunk 81 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 overall best weight: 1.5102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.129765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.111027 restraints weight = 56569.894| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.15 r_work: 0.3246 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14190 Z= 0.123 Angle : 0.501 7.659 19335 Z= 0.250 Chirality : 0.040 0.144 2160 Planarity : 0.004 0.048 2395 Dihedral : 5.140 36.661 2145 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.40 % Allowed : 8.99 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.21), residues: 1670 helix: 3.21 (0.21), residues: 570 sheet: 0.08 (0.26), residues: 415 loop : -0.41 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 73 HIS 0.002 0.001 HIS E 195 PHE 0.010 0.001 PHE A 68 TYR 0.009 0.001 TYR E 132 ARG 0.002 0.000 ARG D 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00144 ( 5) link_NAG-ASN : angle 1.02507 ( 15) hydrogen bonds : bond 0.04620 ( 670) hydrogen bonds : angle 4.03148 ( 2160) SS BOND : bond 0.00934 ( 5) SS BOND : angle 2.40051 ( 10) covalent geometry : bond 0.00278 (14180) covalent geometry : angle 0.49780 (19310) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 2.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 89 LEU cc_start: 0.6169 (OUTLIER) cc_final: 0.5675 (mp) REVERT: B 216 MET cc_start: 0.8750 (mmp) cc_final: 0.8197 (mmp) REVERT: B 267 LEU cc_start: 0.8509 (mt) cc_final: 0.8172 (mt) REVERT: B 289 MET cc_start: 0.8141 (ttp) cc_final: 0.7795 (tpp) REVERT: C 289 MET cc_start: 0.8062 (ttp) cc_final: 0.7734 (tpp) REVERT: D 84 MET cc_start: 0.4536 (ttm) cc_final: 0.4319 (ttm) REVERT: D 267 LEU cc_start: 0.8529 (mt) cc_final: 0.8197 (mt) REVERT: D 290 ASP cc_start: 0.8089 (m-30) cc_final: 0.7829 (m-30) REVERT: E 267 LEU cc_start: 0.8528 (mt) cc_final: 0.8163 (mt) REVERT: E 289 MET cc_start: 0.8211 (ttp) cc_final: 0.7872 (tpp) outliers start: 6 outliers final: 5 residues processed: 137 average time/residue: 0.5754 time to fit residues: 125.5650 Evaluate side-chains 140 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 121 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 147 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.128781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.110004 restraints weight = 56364.771| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.17 r_work: 0.3214 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14190 Z= 0.180 Angle : 0.555 7.960 19335 Z= 0.279 Chirality : 0.042 0.147 2160 Planarity : 0.005 0.049 2395 Dihedral : 5.531 38.620 2145 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.54 % Allowed : 9.13 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.21), residues: 1670 helix: 2.89 (0.21), residues: 585 sheet: 0.05 (0.26), residues: 415 loop : -0.56 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 114 HIS 0.004 0.001 HIS B 195 PHE 0.013 0.002 PHE A 68 TYR 0.011 0.001 TYR E 132 ARG 0.002 0.000 ARG E 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00157 ( 5) link_NAG-ASN : angle 1.31660 ( 15) hydrogen bonds : bond 0.05380 ( 670) hydrogen bonds : angle 4.22529 ( 2160) SS BOND : bond 0.01185 ( 5) SS BOND : angle 2.71037 ( 10) covalent geometry : bond 0.00423 (14180) covalent geometry : angle 0.55088 (19310) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 2.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8660 (mmp) cc_final: 0.8157 (mmp) REVERT: B 89 LEU cc_start: 0.5993 (OUTLIER) cc_final: 0.5489 (mp) REVERT: B 216 MET cc_start: 0.8781 (mmp) cc_final: 0.8189 (mmp) REVERT: B 289 MET cc_start: 0.8285 (ttp) cc_final: 0.7920 (tpp) REVERT: C 289 MET cc_start: 0.8221 (ttp) cc_final: 0.7863 (tpp) REVERT: C 290 ASP cc_start: 0.8136 (m-30) cc_final: 0.7689 (m-30) REVERT: D 84 MET cc_start: 0.4376 (ttm) cc_final: 0.4148 (ttm) REVERT: D 267 LEU cc_start: 0.8554 (mt) cc_final: 0.8211 (mt) REVERT: E 267 LEU cc_start: 0.8548 (mt) cc_final: 0.8186 (mt) REVERT: E 289 MET cc_start: 0.8338 (ttp) cc_final: 0.8008 (tpp) outliers start: 8 outliers final: 6 residues processed: 140 average time/residue: 0.5005 time to fit residues: 107.7161 Evaluate side-chains 138 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain D residue 289 MET Chi-restraints excluded: chain E residue 412 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 117 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.129585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.110868 restraints weight = 56575.243| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.17 r_work: 0.3224 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 14190 Z= 0.157 Angle : 0.530 7.917 19335 Z= 0.266 Chirality : 0.041 0.145 2160 Planarity : 0.004 0.049 2395 Dihedral : 5.383 41.039 2145 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.40 % Allowed : 9.53 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.21), residues: 1670 helix: 3.09 (0.21), residues: 570 sheet: 0.03 (0.26), residues: 415 loop : -0.58 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 114 HIS 0.003 0.001 HIS E 195 PHE 0.012 0.001 PHE A 68 TYR 0.011 0.001 TYR E 132 ARG 0.003 0.000 ARG A 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00144 ( 5) link_NAG-ASN : angle 1.13033 ( 15) hydrogen bonds : bond 0.05086 ( 670) hydrogen bonds : angle 4.16101 ( 2160) SS BOND : bond 0.01081 ( 5) SS BOND : angle 2.49793 ( 10) covalent geometry : bond 0.00365 (14180) covalent geometry : angle 0.52650 (19310) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12011.61 seconds wall clock time: 209 minutes 22.58 seconds (12562.58 seconds total)