Starting phenix.real_space_refine on Mon Aug 25 10:10:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bhq_16066/08_2025/8bhq_16066_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bhq_16066/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8bhq_16066/08_2025/8bhq_16066_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bhq_16066/08_2025/8bhq_16066_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bhq_16066/08_2025/8bhq_16066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bhq_16066/08_2025/8bhq_16066.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: B, C, D, E Time building chain proxies: 5.25, per 1000 atoms: 0.19 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 B 142 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS D 142 " - pdb=" SG CYS D 156 " distance=2.03 Simple disulfide: pdb=" SG CYS E 142 " - pdb=" SG CYS E 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: 1.89 Conformation dependent library (CDL) restraints added in 624.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.48 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: 4.68 Time building geometry restraints manager: 2.60 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.990 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: 0.130 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.590 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.470 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.002 0.000 ARG A 86 TYR 0.005 0.001 TYR D 285 PHE 0.005 0.001 PHE C 68 TRP 0.003 0.000 TRP D 414 HIS 0.003 0.001 HIS D 195 Details of bonding type rmsd covalent geometry : bond 0.00228 (14180) covalent geometry : angle 0.40851 (19310) SS BOND : bond 0.00057 ( 5) SS BOND : angle 0.21044 ( 10) hydrogen bonds : bond 0.27119 ( 670) hydrogen bonds : angle 7.13971 ( 2160) link_NAG-ASN : bond 0.00089 ( 5) link_NAG-ASN : angle 1.26311 ( 15) *********************** 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 : 0.654 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: 0.6862 (m-30) REVERT: E 58 ASP cc_start: 0.7847 (m-30) cc_final: 0.7644 (m-30) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.2969 time to fit residues: 104.7160 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 : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0770 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- 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 = 0.3654 r_free = 0.3654 target = 0.133365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.114857 restraints weight = 55167.086| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.13 r_work: 0.3273 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14190 Z= 0.215 Angle : 0.623 7.673 19335 Z= 0.323 Chirality : 0.044 0.153 2160 Planarity : 0.005 0.049 2395 Dihedral : 6.584 53.653 2145 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.34 % Allowed : 5.57 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.21), residues: 1670 helix: 2.69 (0.21), residues: 570 sheet: 0.11 (0.25), residues: 490 loop : 0.14 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 40 TYR 0.012 0.002 TYR D 285 PHE 0.018 0.002 PHE D 68 TRP 0.011 0.001 TRP C 414 HIS 0.004 0.001 HIS D 195 Details of bonding type rmsd covalent geometry : bond 0.00501 (14180) covalent geometry : angle 0.62221 (19310) SS BOND : bond 0.00826 ( 5) SS BOND : angle 1.06594 ( 10) hydrogen bonds : bond 0.06601 ( 670) hydrogen bonds : angle 4.81225 ( 2160) link_NAG-ASN : bond 0.00107 ( 5) link_NAG-ASN : angle 0.84299 ( 15) *********************** 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 : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8178 (mmp) cc_final: 0.7873 (mmt) REVERT: B 151 MET cc_start: 0.7339 (mpp) cc_final: 0.7116 (mpp) REVERT: B 216 MET cc_start: 0.8691 (mmp) cc_final: 0.8402 (mmp) REVERT: C 48 MET cc_start: 0.8348 (mtp) cc_final: 0.8092 (mtp) REVERT: D 78 LEU cc_start: 0.8593 (mt) cc_final: 0.8390 (mt) REVERT: D 84 MET cc_start: 0.4513 (ttt) cc_final: 0.4302 (ttm) REVERT: D 151 MET cc_start: 0.6973 (mpp) cc_final: 0.6710 (mpp) REVERT: D 290 ASP cc_start: 0.8098 (m-30) cc_final: 0.7733 (m-30) REVERT: E 290 ASP cc_start: 0.8011 (m-30) cc_final: 0.7657 (m-30) outliers start: 5 outliers final: 4 residues processed: 160 average time/residue: 0.2129 time to fit residues: 51.9287 Evaluate side-chains 132 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 128 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 25 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.3561 r_free = 0.3561 target = 0.126787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.108475 restraints weight = 54794.861| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.12 r_work: 0.3185 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3610 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= 0.148 Angle : 0.529 8.209 19335 Z= 0.267 Chirality : 0.041 0.145 2160 Planarity : 0.004 0.046 2395 Dihedral : 5.693 38.729 2145 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.54 % Allowed : 6.64 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.21), residues: 1670 helix: 2.87 (0.21), residues: 570 sheet: 0.24 (0.26), residues: 415 loop : -0.15 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 40 TYR 0.011 0.001 TYR B 132 PHE 0.012 0.001 PHE A 68 TRP 0.007 0.001 TRP C 414 HIS 0.003 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00334 (14180) covalent geometry : angle 0.52790 (19310) SS BOND : bond 0.00570 ( 5) SS BOND : angle 1.04941 ( 10) hydrogen bonds : bond 0.05727 ( 670) hydrogen bonds : angle 4.37872 ( 2160) link_NAG-ASN : bond 0.00159 ( 5) link_NAG-ASN : angle 0.96933 ( 15) *********************** 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 151 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8310 (mmp) cc_final: 0.8026 (mmp) REVERT: B 267 LEU cc_start: 0.8542 (mt) cc_final: 0.8276 (mt) REVERT: B 289 MET cc_start: 0.8174 (ttp) cc_final: 0.7790 (tpp) REVERT: C 289 MET cc_start: 0.8071 (ttp) cc_final: 0.7627 (tpp) REVERT: D 239 MET cc_start: 0.8677 (mmm) cc_final: 0.8452 (mmp) REVERT: D 267 LEU cc_start: 0.8583 (mt) cc_final: 0.8320 (mt) REVERT: D 290 ASP cc_start: 0.8086 (m-30) cc_final: 0.7706 (m-30) REVERT: E 267 LEU cc_start: 0.8581 (mt) cc_final: 0.8269 (mt) REVERT: E 289 MET cc_start: 0.8142 (ttp) cc_final: 0.7724 (tpp) outliers start: 8 outliers final: 6 residues processed: 145 average time/residue: 0.2112 time to fit residues: 47.3182 Evaluate side-chains 135 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 129 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 289 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 55 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 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 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 = 0.3515 r_free = 0.3515 target = 0.123525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.105203 restraints weight = 55300.469| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.12 r_work: 0.3159 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14190 Z= 0.200 Angle : 0.581 8.269 19335 Z= 0.294 Chirality : 0.042 0.149 2160 Planarity : 0.005 0.051 2395 Dihedral : 5.839 33.948 2145 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.21), residues: 1670 helix: 2.72 (0.21), residues: 570 sheet: 0.13 (0.26), residues: 415 loop : -0.34 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 40 TYR 0.014 0.001 TYR B 132 PHE 0.015 0.002 PHE B 68 TRP 0.006 0.001 TRP C 414 HIS 0.004 0.001 HIS E 195 Details of bonding type rmsd covalent geometry : bond 0.00471 (14180) covalent geometry : angle 0.57776 (19310) SS BOND : bond 0.00882 ( 5) SS BOND : angle 2.43452 ( 10) hydrogen bonds : bond 0.05790 ( 670) hydrogen bonds : angle 4.41234 ( 2160) link_NAG-ASN : bond 0.00206 ( 5) link_NAG-ASN : angle 1.08003 ( 15) *********************** 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 138 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8425 (mmp) cc_final: 0.7996 (mmp) REVERT: B 151 MET cc_start: 0.7496 (mpp) cc_final: 0.7228 (mpp) REVERT: B 289 MET cc_start: 0.8357 (ttp) cc_final: 0.8011 (tpp) REVERT: C 289 MET cc_start: 0.8181 (ttp) cc_final: 0.7753 (tpp) REVERT: D 84 MET cc_start: 0.4177 (ttm) cc_final: 0.3968 (ttm) REVERT: D 267 LEU cc_start: 0.8589 (mt) cc_final: 0.8296 (mt) REVERT: D 290 ASP cc_start: 0.8171 (m-30) cc_final: 0.7891 (m-30) REVERT: E 267 LEU cc_start: 0.8563 (mt) cc_final: 0.8209 (mt) REVERT: E 289 MET cc_start: 0.8291 (ttp) cc_final: 0.7888 (tpp) outliers start: 6 outliers final: 6 residues processed: 133 average time/residue: 0.1789 time to fit residues: 39.2066 Evaluate side-chains 132 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 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 D residue 134 LEU 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 96 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.124865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.106687 restraints weight = 55448.159| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.11 r_work: 0.3165 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14190 Z= 0.149 Angle : 0.534 8.275 19335 Z= 0.268 Chirality : 0.041 0.147 2160 Planarity : 0.005 0.049 2395 Dihedral : 5.359 31.133 2145 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.47 % Allowed : 7.72 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.21), residues: 1670 helix: 2.83 (0.21), residues: 570 sheet: 0.07 (0.26), residues: 415 loop : -0.38 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 40 TYR 0.011 0.001 TYR E 132 PHE 0.012 0.001 PHE B 68 TRP 0.005 0.001 TRP D 73 HIS 0.003 0.001 HIS E 195 Details of bonding type rmsd covalent geometry : bond 0.00340 (14180) covalent geometry : angle 0.52914 (19310) SS BOND : bond 0.01077 ( 5) SS BOND : angle 3.11966 ( 10) hydrogen bonds : bond 0.05215 ( 670) hydrogen bonds : angle 4.26300 ( 2160) link_NAG-ASN : bond 0.00162 ( 5) link_NAG-ASN : angle 0.98593 ( 15) *********************** 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 136 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8452 (mmp) cc_final: 0.8114 (mmp) REVERT: B 89 LEU cc_start: 0.6120 (OUTLIER) cc_final: 0.5648 (mp) REVERT: B 289 MET cc_start: 0.8241 (ttp) cc_final: 0.7915 (tpp) REVERT: D 267 LEU cc_start: 0.8598 (mt) cc_final: 0.8302 (mt) REVERT: D 290 ASP cc_start: 0.8109 (m-30) cc_final: 0.7840 (m-30) REVERT: E 267 LEU cc_start: 0.8552 (mt) cc_final: 0.8189 (mt) REVERT: E 289 MET cc_start: 0.8216 (ttp) cc_final: 0.7826 (tpp) outliers start: 7 outliers final: 6 residues processed: 132 average time/residue: 0.1824 time to fit residues: 39.0560 Evaluate side-chains 130 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 77 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 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 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3505 r_free = 0.3505 target = 0.122625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.104372 restraints weight = 56383.626| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.12 r_work: 0.3151 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 14190 Z= 0.198 Angle : 0.580 8.243 19335 Z= 0.293 Chirality : 0.042 0.150 2160 Planarity : 0.005 0.051 2395 Dihedral : 5.642 34.137 2145 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.74 % Allowed : 8.05 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.21), residues: 1670 helix: 2.71 (0.22), residues: 570 sheet: -0.05 (0.25), residues: 430 loop : -0.67 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 79 TYR 0.011 0.001 TYR E 132 PHE 0.014 0.002 PHE A 68 TRP 0.005 0.001 TRP C 414 HIS 0.004 0.001 HIS E 195 Details of bonding type rmsd covalent geometry : bond 0.00466 (14180) covalent geometry : angle 0.57561 (19310) SS BOND : bond 0.01288 ( 5) SS BOND : angle 3.01586 ( 10) hydrogen bonds : bond 0.05777 ( 670) hydrogen bonds : angle 4.38287 ( 2160) link_NAG-ASN : bond 0.00191 ( 5) link_NAG-ASN : angle 1.19144 ( 15) *********************** 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 136 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8519 (mmp) cc_final: 0.8084 (mmp) REVERT: A 239 MET cc_start: 0.8666 (mmm) cc_final: 0.8116 (mmp) REVERT: B 89 LEU cc_start: 0.6090 (OUTLIER) cc_final: 0.5535 (mp) REVERT: B 289 MET cc_start: 0.8294 (ttp) cc_final: 0.7955 (tpp) REVERT: C 290 ASP cc_start: 0.8136 (m-30) cc_final: 0.7656 (m-30) REVERT: E 267 LEU cc_start: 0.8595 (mt) cc_final: 0.8227 (mt) REVERT: E 289 MET cc_start: 0.8296 (ttp) cc_final: 0.7904 (tpp) outliers start: 11 outliers final: 5 residues processed: 131 average time/residue: 0.1978 time to fit residues: 40.3496 Evaluate side-chains 130 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 289 MET Chi-restraints excluded: chain E residue 412 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 99 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 146 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 139 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 = 0.3613 r_free = 0.3613 target = 0.130184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.111342 restraints weight = 55839.023| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.18 r_work: 0.3226 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.4537 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= 0.139 Angle : 0.518 8.008 19335 Z= 0.259 Chirality : 0.040 0.146 2160 Planarity : 0.004 0.050 2395 Dihedral : 5.182 32.476 2145 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.34 % Allowed : 9.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.21), residues: 1670 helix: 2.88 (0.22), residues: 570 sheet: -0.01 (0.26), residues: 415 loop : -0.51 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 120 TYR 0.010 0.001 TYR E 132 PHE 0.011 0.001 PHE B 68 TRP 0.006 0.001 TRP A 73 HIS 0.003 0.001 HIS E 195 Details of bonding type rmsd covalent geometry : bond 0.00318 (14180) covalent geometry : angle 0.51481 (19310) SS BOND : bond 0.01036 ( 5) SS BOND : angle 2.35630 ( 10) hydrogen bonds : bond 0.04949 ( 670) hydrogen bonds : angle 4.18515 ( 2160) link_NAG-ASN : bond 0.00164 ( 5) link_NAG-ASN : angle 0.98603 ( 15) *********************** 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 133 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.8548 (mmm) cc_final: 0.8063 (mmp) REVERT: B 89 LEU cc_start: 0.6088 (OUTLIER) cc_final: 0.5566 (mp) REVERT: B 289 MET cc_start: 0.8186 (ttp) cc_final: 0.7848 (tpp) REVERT: D 267 LEU cc_start: 0.8601 (mt) cc_final: 0.8268 (mt) REVERT: E 267 LEU cc_start: 0.8558 (mt) cc_final: 0.8203 (mt) outliers start: 5 outliers final: 3 residues processed: 130 average time/residue: 0.1928 time to fit residues: 40.2486 Evaluate side-chains 131 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 127 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 101 optimal weight: 2.9990 chunk 146 optimal weight: 0.3980 chunk 161 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 131 optimal weight: 0.0980 chunk 68 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 219 HIS E 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.134279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.115712 restraints weight = 55586.320| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.14 r_work: 0.3287 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 14190 Z= 0.086 Angle : 0.458 7.001 19335 Z= 0.228 Chirality : 0.039 0.144 2160 Planarity : 0.004 0.048 2395 Dihedral : 4.843 35.388 2145 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.20 % Allowed : 9.53 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.21), residues: 1670 helix: 3.23 (0.21), residues: 570 sheet: 0.08 (0.26), residues: 415 loop : -0.29 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 120 TYR 0.007 0.001 TYR D 285 PHE 0.007 0.001 PHE A 409 TRP 0.008 0.001 TRP A 73 HIS 0.001 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00182 (14180) covalent geometry : angle 0.45572 (19310) SS BOND : bond 0.00713 ( 5) SS BOND : angle 1.79368 ( 10) hydrogen bonds : bond 0.03805 ( 670) hydrogen bonds : angle 3.86201 ( 2160) link_NAG-ASN : bond 0.00155 ( 5) link_NAG-ASN : angle 0.88604 ( 15) *********************** 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 139 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 136 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8548 (mmp) cc_final: 0.8257 (mmt) REVERT: A 239 MET cc_start: 0.8520 (mmm) cc_final: 0.8028 (mmp) REVERT: B 89 LEU cc_start: 0.6142 (OUTLIER) cc_final: 0.5684 (mp) REVERT: B 289 MET cc_start: 0.7952 (ttp) cc_final: 0.7628 (tpp) REVERT: D 267 LEU cc_start: 0.8578 (mt) cc_final: 0.8215 (mt) REVERT: D 290 ASP cc_start: 0.8116 (m-30) cc_final: 0.7780 (m-30) REVERT: E 267 LEU cc_start: 0.8574 (mt) cc_final: 0.8201 (mt) outliers start: 3 outliers final: 2 residues processed: 138 average time/residue: 0.1883 time to fit residues: 41.7614 Evaluate side-chains 132 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 129 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 120 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.127159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.108303 restraints weight = 56313.330| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.18 r_work: 0.3182 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 14190 Z= 0.246 Angle : 0.607 8.142 19335 Z= 0.307 Chirality : 0.043 0.152 2160 Planarity : 0.005 0.051 2395 Dihedral : 5.908 38.438 2145 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.27 % Allowed : 9.87 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.21), residues: 1670 helix: 2.83 (0.21), residues: 575 sheet: -0.02 (0.25), residues: 455 loop : -0.68 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 79 TYR 0.013 0.001 TYR E 132 PHE 0.016 0.002 PHE A 68 TRP 0.005 0.001 TRP B 114 HIS 0.005 0.001 HIS E 195 Details of bonding type rmsd covalent geometry : bond 0.00588 (14180) covalent geometry : angle 0.60331 (19310) SS BOND : bond 0.01356 ( 5) SS BOND : angle 2.66946 ( 10) hydrogen bonds : bond 0.05987 ( 670) hydrogen bonds : angle 4.36816 ( 2160) link_NAG-ASN : bond 0.00192 ( 5) link_NAG-ASN : angle 1.53465 ( 15) *********************** 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 130 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8631 (mmp) cc_final: 0.7931 (mmt) REVERT: A 239 MET cc_start: 0.8641 (mmm) cc_final: 0.8075 (mmp) REVERT: A 290 ASP cc_start: 0.8146 (m-30) cc_final: 0.7677 (m-30) REVERT: B 89 LEU cc_start: 0.6108 (OUTLIER) cc_final: 0.5553 (mp) REVERT: B 290 ASP cc_start: 0.8092 (m-30) cc_final: 0.7678 (m-30) REVERT: C 290 ASP cc_start: 0.8081 (m-30) cc_final: 0.7634 (m-30) REVERT: E 267 LEU cc_start: 0.8586 (mt) cc_final: 0.8232 (mt) REVERT: E 289 MET cc_start: 0.8410 (ttp) cc_final: 0.8061 (tpp) outliers start: 4 outliers final: 3 residues processed: 130 average time/residue: 0.2304 time to fit residues: 45.5038 Evaluate side-chains 130 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 412 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 57 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 23 optimal weight: 0.1980 chunk 43 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.130844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.112037 restraints weight = 55717.433| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.18 r_work: 0.3225 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 14190 Z= 0.101 Angle : 0.485 7.885 19335 Z= 0.241 Chirality : 0.040 0.142 2160 Planarity : 0.004 0.048 2395 Dihedral : 5.084 41.605 2145 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.13 % Allowed : 10.00 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.21), residues: 1670 helix: 3.14 (0.21), residues: 570 sheet: 0.04 (0.26), residues: 415 loop : -0.44 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 120 TYR 0.007 0.001 TYR D 285 PHE 0.009 0.001 PHE B 68 TRP 0.007 0.001 TRP A 73 HIS 0.002 0.001 HIS C 221 Details of bonding type rmsd covalent geometry : bond 0.00221 (14180) covalent geometry : angle 0.48282 (19310) SS BOND : bond 0.00792 ( 5) SS BOND : angle 2.00539 ( 10) hydrogen bonds : bond 0.04322 ( 670) hydrogen bonds : angle 3.99282 ( 2160) link_NAG-ASN : bond 0.00172 ( 5) link_NAG-ASN : angle 0.88098 ( 15) ********************** 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 132 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8612 (mmp) cc_final: 0.8035 (mmt) REVERT: A 239 MET cc_start: 0.8557 (mmm) cc_final: 0.8074 (mmp) REVERT: B 89 LEU cc_start: 0.6193 (OUTLIER) cc_final: 0.5675 (mp) REVERT: B 289 MET cc_start: 0.8110 (ttp) cc_final: 0.7744 (tpp) REVERT: C 290 ASP cc_start: 0.7973 (m-30) cc_final: 0.7591 (m-30) REVERT: D 267 LEU cc_start: 0.8553 (mt) cc_final: 0.8198 (mt) REVERT: D 290 ASP cc_start: 0.8183 (m-30) cc_final: 0.7913 (m-30) REVERT: E 267 LEU cc_start: 0.8542 (mt) cc_final: 0.8170 (mt) REVERT: E 289 MET cc_start: 0.8163 (ttp) cc_final: 0.7834 (tpp) outliers start: 2 outliers final: 1 residues processed: 132 average time/residue: 0.2045 time to fit residues: 42.4266 Evaluate side-chains 131 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 89 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 112 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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 = 0.3627 r_free = 0.3627 target = 0.131477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.112933 restraints weight = 55502.159| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.14 r_work: 0.3248 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 14190 Z= 0.118 Angle : 0.496 7.311 19335 Z= 0.247 Chirality : 0.040 0.143 2160 Planarity : 0.004 0.049 2395 Dihedral : 5.235 39.972 2145 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.13 % Allowed : 10.07 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.21), residues: 1670 helix: 3.20 (0.21), residues: 570 sheet: 0.05 (0.26), residues: 415 loop : -0.44 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 120 TYR 0.009 0.001 TYR E 132 PHE 0.009 0.001 PHE A 68 TRP 0.006 0.001 TRP A 73 HIS 0.002 0.001 HIS E 195 Details of bonding type rmsd covalent geometry : bond 0.00267 (14180) covalent geometry : angle 0.49321 (19310) SS BOND : bond 0.00893 ( 5) SS BOND : angle 2.03760 ( 10) hydrogen bonds : bond 0.04478 ( 670) hydrogen bonds : angle 3.98586 ( 2160) link_NAG-ASN : bond 0.00144 ( 5) link_NAG-ASN : angle 1.01371 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4935.80 seconds wall clock time: 84 minutes 22.78 seconds (5062.78 seconds total)