Starting phenix.real_space_refine on Thu Feb 5 08:39:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j37_61108/02_2026/9j37_61108.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j37_61108/02_2026/9j37_61108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j37_61108/02_2026/9j37_61108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j37_61108/02_2026/9j37_61108.map" model { file = "/net/cci-nas-00/data/ceres_data/9j37_61108/02_2026/9j37_61108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j37_61108/02_2026/9j37_61108.cif" } 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= 0.224 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 115 5.16 5 C 10455 2.51 5 N 2545 2.21 5 O 2855 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15970 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3124 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 3, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 3124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3124 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 3, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 3124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3124 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 3, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 3124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3124 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 3, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "E" Number of atoms: 3124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3124 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 3, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'CLR': 1, 'NAG': 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 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'CLR': 1, 'NAG': 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 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'CLR': 1, 'NAG': 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 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'CLR': 1, 'NAG': 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 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'CLR': 1, 'NAG': 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 Time building chain proxies: 3.32, per 1000 atoms: 0.21 Number of scatterers: 15970 At special positions: 0 Unit cell: (94.08, 93.12, 165.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 115 16.00 O 2855 8.00 N 2545 7.00 C 10455 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 150 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 150 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 164 " 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 601 " - " ASN A 46 " " NAG B 601 " - " ASN B 46 " " NAG C 601 " - " ASN C 46 " " NAG D 601 " - " ASN D 46 " " NAG E 601 " - " ASN E 46 " " NAG F 1 " - " ASN A 133 " " NAG G 1 " - " ASN B 133 " " NAG H 1 " - " ASN C 133 " " NAG I 1 " - " ASN D 133 " " NAG J 1 " - " ASN E 133 " Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 677.4 milliseconds 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3760 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 20 sheets defined 41.9% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 23 through 34 removed outlier: 3.639A pdb=" N ARG A 27 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS A 28 " --> pdb=" O GLU A 24 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 34 " --> pdb=" O TYR A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 237 Processing helix chain 'A' and resid 237 through 249 removed outlier: 3.683A pdb=" N CYS A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 244 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 246 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 253 Processing helix chain 'A' and resid 261 through 274 removed outlier: 4.276A pdb=" N THR A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 278 removed outlier: 3.624A pdb=" N LEU A 278 " --> pdb=" O PHE A 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 275 through 278' Processing helix chain 'A' and resid 291 through 311 removed outlier: 3.770A pdb=" N VAL A 308 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL A 309 " --> pdb=" O GLY A 305 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 319 removed outlier: 3.683A pdb=" N LEU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N TYR A 317 " --> pdb=" O ILE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 335 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.948A pdb=" N LEU A 343 " --> pdb=" O CYS A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 489 removed outlier: 3.748A pdb=" N ALA A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 475 " --> pdb=" O CYS A 471 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 487 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 Processing helix chain 'B' and resid 24 through 34 removed outlier: 3.751A pdb=" N LYS B 28 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 34 " --> pdb=" O TYR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 237 Processing helix chain 'B' and resid 237 through 249 removed outlier: 3.571A pdb=" N CYS B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 244 " --> pdb=" O PRO B 240 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 254 removed outlier: 3.863A pdb=" N LEU B 254 " --> pdb=" O VAL B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 274 removed outlier: 4.234A pdb=" N THR B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 278 removed outlier: 3.618A pdb=" N LEU B 278 " --> pdb=" O PHE B 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 275 through 278' Processing helix chain 'B' and resid 291 through 319 removed outlier: 3.814A pdb=" N VAL B 308 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL B 309 " --> pdb=" O GLY B 305 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 310 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 312 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE B 313 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N TYR B 317 " --> pdb=" O ILE B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 337 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.928A pdb=" N LEU B 343 " --> pdb=" O CYS B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 489 removed outlier: 3.779A pdb=" N ALA B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE B 475 " --> pdb=" O CYS B 471 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL B 477 " --> pdb=" O MET B 473 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 487 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 501 Processing helix chain 'C' and resid 24 through 34 removed outlier: 3.818A pdb=" N LYS C 28 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 237 Processing helix chain 'C' and resid 237 through 249 removed outlier: 3.671A pdb=" N CYS C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE C 244 " --> pdb=" O PRO C 240 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 253 Processing helix chain 'C' and resid 261 through 274 removed outlier: 4.254A pdb=" N THR C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 277 No H-bonds generated for 'chain 'C' and resid 275 through 277' Processing helix chain 'C' and resid 291 through 319 removed outlier: 3.822A pdb=" N VAL C 308 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL C 309 " --> pdb=" O GLY C 305 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 310 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR C 311 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL C 312 " --> pdb=" O VAL C 308 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 313 " --> pdb=" O VAL C 309 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TYR C 317 " --> pdb=" O ILE C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 337 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.941A pdb=" N LEU C 343 " --> pdb=" O CYS C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 489 removed outlier: 3.774A pdb=" N ALA C 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE C 475 " --> pdb=" O CYS C 471 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER C 476 " --> pdb=" O LEU C 472 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL C 477 " --> pdb=" O MET C 473 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU C 487 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 501 Processing helix chain 'D' and resid 24 through 34 removed outlier: 3.768A pdb=" N LYS D 28 " --> pdb=" O GLU D 24 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL D 34 " --> pdb=" O TYR D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 237 Processing helix chain 'D' and resid 237 through 249 removed outlier: 3.704A pdb=" N CYS D 241 " --> pdb=" O LEU D 237 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE D 244 " --> pdb=" O PRO D 240 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA D 246 " --> pdb=" O VAL D 242 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 254 removed outlier: 3.823A pdb=" N LEU D 254 " --> pdb=" O VAL D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 274 removed outlier: 4.165A pdb=" N THR D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 278 removed outlier: 3.606A pdb=" N LEU D 278 " --> pdb=" O PHE D 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 275 through 278' Processing helix chain 'D' and resid 291 through 311 removed outlier: 3.783A pdb=" N VAL D 308 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL D 309 " --> pdb=" O GLY D 305 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL D 310 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR D 311 " --> pdb=" O SER D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 319 removed outlier: 3.843A pdb=" N LEU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR D 317 " --> pdb=" O ILE D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 337 Processing helix chain 'D' and resid 338 through 343 removed outlier: 3.916A pdb=" N LEU D 343 " --> pdb=" O CYS D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 489 removed outlier: 3.766A pdb=" N ALA D 474 " --> pdb=" O LEU D 470 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE D 475 " --> pdb=" O CYS D 471 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER D 476 " --> pdb=" O LEU D 472 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL D 477 " --> pdb=" O MET D 473 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 487 " --> pdb=" O THR D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 501 Processing helix chain 'E' and resid 24 through 34 removed outlier: 3.802A pdb=" N LYS E 28 " --> pdb=" O GLU E 24 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL E 34 " --> pdb=" O TYR E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 237 Processing helix chain 'E' and resid 237 through 249 removed outlier: 3.679A pdb=" N CYS E 241 " --> pdb=" O LEU E 237 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE E 244 " --> pdb=" O PRO E 240 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU E 247 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU E 249 " --> pdb=" O SER E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 253 Processing helix chain 'E' and resid 261 through 274 removed outlier: 4.206A pdb=" N THR E 267 " --> pdb=" O SER E 263 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU E 269 " --> pdb=" O GLY E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 278 removed outlier: 3.634A pdb=" N LEU E 278 " --> pdb=" O PHE E 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 275 through 278' Processing helix chain 'E' and resid 291 through 319 removed outlier: 3.809A pdb=" N VAL E 308 " --> pdb=" O VAL E 304 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL E 309 " --> pdb=" O GLY E 305 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL E 310 " --> pdb=" O LEU E 306 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR E 311 " --> pdb=" O SER E 307 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL E 312 " --> pdb=" O VAL E 308 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE E 313 " --> pdb=" O VAL E 309 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TYR E 317 " --> pdb=" O ILE E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 337 Processing helix chain 'E' and resid 338 through 343 removed outlier: 3.917A pdb=" N LEU E 343 " --> pdb=" O CYS E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 489 removed outlier: 3.739A pdb=" N ALA E 474 " --> pdb=" O LEU E 470 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE E 475 " --> pdb=" O CYS E 471 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER E 476 " --> pdb=" O LEU E 472 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL E 477 " --> pdb=" O MET E 473 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU E 487 " --> pdb=" O THR E 483 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 501 Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 102 Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 102 removed outlier: 7.027A pdb=" N VAL A 71 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASP A 64 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N THR A 73 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE A 62 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN A 75 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N THR A 83 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N THR A 52 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP A 179 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 114 removed outlier: 6.652A pdb=" N THR A 225 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 102 removed outlier: 7.013A pdb=" N VAL B 71 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP B 64 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR B 73 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ILE B 62 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN B 75 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR B 83 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N THR B 52 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP B 179 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 112 through 114 removed outlier: 6.656A pdb=" N THR B 225 " --> pdb=" O VAL B 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 112 through 114 Processing sheet with id=AA9, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB1, first strand: chain 'C' and resid 100 through 102 removed outlier: 7.014A pdb=" N VAL C 71 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASP C 64 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N THR C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ILE C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN C 75 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N THR C 83 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N THR C 52 " --> pdb=" O THR C 83 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP C 179 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 112 through 114 removed outlier: 6.659A pdb=" N THR C 225 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 112 through 114 Processing sheet with id=AB4, first strand: chain 'D' and resid 100 through 102 Processing sheet with id=AB5, first strand: chain 'D' and resid 100 through 102 removed outlier: 7.010A pdb=" N VAL D 71 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASP D 64 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N THR D 73 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ILE D 62 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN D 75 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N THR D 83 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR D 52 " --> pdb=" O THR D 83 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP D 179 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL D 53 " --> pdb=" O ASP D 179 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 112 through 114 removed outlier: 6.651A pdb=" N THR D 225 " --> pdb=" O VAL D 199 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 112 through 114 Processing sheet with id=AB8, first strand: chain 'E' and resid 100 through 102 Processing sheet with id=AB9, first strand: chain 'E' and resid 100 through 102 removed outlier: 7.013A pdb=" N VAL E 71 " --> pdb=" O ASP E 64 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASP E 64 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N THR E 73 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ILE E 62 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN E 75 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N THR E 83 " --> pdb=" O THR E 52 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N THR E 52 " --> pdb=" O THR E 83 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP E 179 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 112 through 114 removed outlier: 6.658A pdb=" N THR E 225 " --> pdb=" O VAL E 199 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 112 through 114 810 hydrogen bonds defined for protein. 2340 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.63 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4875 1.34 - 1.46: 3893 1.46 - 1.58: 7471 1.58 - 1.70: 1 1.70 - 1.81: 170 Bond restraints: 16410 Sorted by residual: bond pdb=" CB PRO D 240 " pdb=" CG PRO D 240 " ideal model delta sigma weight residual 1.492 1.592 -0.100 5.00e-02 4.00e+02 3.98e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.26e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.06e+00 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.00e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 2.99e+00 ... (remaining 16405 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 21917 1.73 - 3.47: 439 3.47 - 5.20: 53 5.20 - 6.94: 2 6.94 - 8.67: 9 Bond angle restraints: 22420 Sorted by residual: angle pdb=" CA PRO D 240 " pdb=" N PRO D 240 " pdb=" CD PRO D 240 " ideal model delta sigma weight residual 112.00 103.33 8.67 1.40e+00 5.10e-01 3.84e+01 angle pdb=" N VAL D 314 " pdb=" CA VAL D 314 " pdb=" C VAL D 314 " ideal model delta sigma weight residual 111.81 108.21 3.60 8.60e-01 1.35e+00 1.75e+01 angle pdb=" C LEU A 238 " pdb=" N ILE A 239 " pdb=" CA ILE A 239 " ideal model delta sigma weight residual 120.24 122.81 -2.57 6.30e-01 2.52e+00 1.66e+01 angle pdb=" N VAL B 314 " pdb=" CA VAL B 314 " pdb=" C VAL B 314 " ideal model delta sigma weight residual 111.81 108.31 3.50 8.60e-01 1.35e+00 1.65e+01 angle pdb=" N VAL E 314 " pdb=" CA VAL E 314 " pdb=" C VAL E 314 " ideal model delta sigma weight residual 111.81 108.32 3.49 8.60e-01 1.35e+00 1.64e+01 ... (remaining 22415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.10: 8521 14.10 - 28.20: 1042 28.20 - 42.30: 388 42.30 - 56.40: 109 56.40 - 70.50: 5 Dihedral angle restraints: 10065 sinusoidal: 4255 harmonic: 5810 Sorted by residual: dihedral pdb=" CB CYS E 150 " pdb=" SG CYS E 150 " pdb=" SG CYS E 164 " pdb=" CB CYS E 164 " ideal model delta sinusoidal sigma weight residual 93.00 64.13 28.87 1 1.00e+01 1.00e-02 1.19e+01 dihedral pdb=" CB CYS B 150 " pdb=" SG CYS B 150 " pdb=" SG CYS B 164 " pdb=" CB CYS B 164 " ideal model delta sinusoidal sigma weight residual 93.00 64.56 28.44 1 1.00e+01 1.00e-02 1.16e+01 dihedral pdb=" CB CYS C 150 " pdb=" SG CYS C 150 " pdb=" SG CYS C 164 " pdb=" CB CYS C 164 " ideal model delta sinusoidal sigma weight residual 93.00 64.74 28.26 1 1.00e+01 1.00e-02 1.14e+01 ... (remaining 10062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1568 0.032 - 0.063: 759 0.063 - 0.095: 187 0.095 - 0.126: 82 0.126 - 0.158: 19 Chirality restraints: 2615 Sorted by residual: chirality pdb=" C1 NAG E 601 " pdb=" ND2 ASN E 46 " pdb=" C2 NAG E 601 " pdb=" O5 NAG E 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.20e-01 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 46 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 46 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.91e-01 ... (remaining 2612 not shown) Planarity restraints: 2755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 239 " -0.082 5.00e-02 4.00e+02 1.19e-01 2.28e+01 pdb=" N PRO D 240 " 0.206 5.00e-02 4.00e+02 pdb=" CA PRO D 240 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO D 240 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 239 " -0.048 5.00e-02 4.00e+02 7.22e-02 8.35e+00 pdb=" N PRO E 240 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO E 240 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 240 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 239 " -0.047 5.00e-02 4.00e+02 7.19e-02 8.28e+00 pdb=" N PRO B 240 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 240 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 240 " -0.040 5.00e-02 4.00e+02 ... (remaining 2752 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2878 2.77 - 3.31: 13831 3.31 - 3.84: 24282 3.84 - 4.37: 27885 4.37 - 4.90: 51414 Nonbonded interactions: 120290 Sorted by model distance: nonbonded pdb=" NZ LYS C 167 " pdb=" OD2 ASP C 219 " model vdw 2.244 3.120 nonbonded pdb=" NZ LYS E 167 " pdb=" OD2 ASP E 219 " model vdw 2.248 3.120 nonbonded pdb=" NZ LYS D 167 " pdb=" OD2 ASP D 219 " model vdw 2.248 3.120 nonbonded pdb=" NZ LYS A 167 " pdb=" OD2 ASP A 219 " model vdw 2.249 3.120 nonbonded pdb=" NZ LYS B 167 " pdb=" OD2 ASP B 219 " model vdw 2.251 3.120 ... (remaining 120285 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.470 Find NCS groups from input model: 0.330 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: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 16430 Z= 0.157 Angle : 0.611 8.673 22475 Z= 0.343 Chirality : 0.041 0.158 2615 Planarity : 0.005 0.119 2745 Dihedral : 14.256 70.499 6290 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 15.95 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.19), residues: 1955 helix: 0.03 (0.20), residues: 745 sheet: 0.14 (0.26), residues: 450 loop : -1.97 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 469 TYR 0.006 0.001 TYR A 140 PHE 0.007 0.001 PHE B 462 TRP 0.007 0.001 TRP E 156 HIS 0.003 0.001 HIS D 163 Details of bonding type rmsd covalent geometry : bond 0.00306 (16410) covalent geometry : angle 0.59800 (22420) SS BOND : bond 0.00187 ( 5) SS BOND : angle 0.69816 ( 10) hydrogen bonds : bond 0.18456 ( 710) hydrogen bonds : angle 7.45036 ( 2340) link_BETA1-4 : bond 0.00573 ( 5) link_BETA1-4 : angle 0.65270 ( 15) link_NAG-ASN : bond 0.00529 ( 10) link_NAG-ASN : angle 3.52201 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 301 MET cc_start: 0.7817 (mmt) cc_final: 0.7354 (mtm) REVERT: E 66 ASP cc_start: 0.8439 (t0) cc_final: 0.8215 (t0) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1179 time to fit residues: 24.3235 Evaluate side-chains 122 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.0970 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.0770 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.2980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.116985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.096773 restraints weight = 17967.141| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.35 r_work: 0.2843 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.0620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16430 Z= 0.115 Angle : 0.547 8.123 22475 Z= 0.277 Chirality : 0.040 0.169 2615 Planarity : 0.005 0.070 2745 Dihedral : 5.756 37.689 2765 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.82 % Allowed : 14.49 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.19), residues: 1955 helix: 0.52 (0.20), residues: 760 sheet: 0.07 (0.25), residues: 450 loop : -1.82 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 469 TYR 0.008 0.001 TYR C 140 PHE 0.006 0.001 PHE D 126 TRP 0.005 0.001 TRP A 82 HIS 0.003 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00225 (16410) covalent geometry : angle 0.53248 (22420) SS BOND : bond 0.00205 ( 5) SS BOND : angle 0.52723 ( 10) hydrogen bonds : bond 0.06060 ( 710) hydrogen bonds : angle 4.95527 ( 2340) link_BETA1-4 : bond 0.00554 ( 5) link_BETA1-4 : angle 0.80769 ( 15) link_NAG-ASN : bond 0.00576 ( 10) link_NAG-ASN : angle 3.42043 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 MET cc_start: 0.8991 (mmm) cc_final: 0.8774 (mmm) REVERT: B 301 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7602 (mmm) REVERT: C 260 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7613 (mt-10) REVERT: D 66 ASP cc_start: 0.8561 (t70) cc_final: 0.8278 (t0) REVERT: D 260 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7365 (mt-10) REVERT: D 301 MET cc_start: 0.7866 (mmt) cc_final: 0.7246 (mtm) outliers start: 31 outliers final: 11 residues processed: 146 average time/residue: 0.1006 time to fit residues: 23.4591 Evaluate side-chains 124 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 281 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 136 optimal weight: 4.9990 chunk 135 optimal weight: 0.6980 chunk 190 optimal weight: 7.9990 chunk 26 optimal weight: 0.0000 chunk 23 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 147 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN B 49 GLN B 236 ASN C 49 GLN C 236 ASN D 49 GLN E 49 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.113793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.092570 restraints weight = 18256.199| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.51 r_work: 0.2778 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16430 Z= 0.136 Angle : 0.579 8.881 22475 Z= 0.286 Chirality : 0.042 0.173 2615 Planarity : 0.005 0.068 2745 Dihedral : 5.469 43.459 2765 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.76 % Allowed : 14.90 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.19), residues: 1955 helix: 0.67 (0.20), residues: 760 sheet: 0.01 (0.25), residues: 450 loop : -1.96 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 469 TYR 0.011 0.001 TYR C 140 PHE 0.011 0.001 PHE A 25 TRP 0.007 0.001 TRP B 89 HIS 0.004 0.001 HIS D 163 Details of bonding type rmsd covalent geometry : bond 0.00311 (16410) covalent geometry : angle 0.56173 (22420) SS BOND : bond 0.00307 ( 5) SS BOND : angle 0.64840 ( 10) hydrogen bonds : bond 0.06340 ( 710) hydrogen bonds : angle 4.61323 ( 2340) link_BETA1-4 : bond 0.00540 ( 5) link_BETA1-4 : angle 0.75753 ( 15) link_NAG-ASN : bond 0.00455 ( 10) link_NAG-ASN : angle 3.83841 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8342 (t0) cc_final: 0.7841 (t0) REVERT: B 63 MET cc_start: 0.9114 (mmm) cc_final: 0.8910 (mmm) REVERT: C 260 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7766 (mt-10) REVERT: D 66 ASP cc_start: 0.8575 (t70) cc_final: 0.8360 (t0) REVERT: D 260 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7457 (mt-10) REVERT: D 301 MET cc_start: 0.7886 (mmt) cc_final: 0.7310 (mtm) outliers start: 30 outliers final: 16 residues processed: 138 average time/residue: 0.1063 time to fit residues: 23.7253 Evaluate side-chains 132 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 281 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 191 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 56 optimal weight: 0.0050 chunk 87 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 189 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.114410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.093893 restraints weight = 18154.278| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.43 r_work: 0.2798 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16430 Z= 0.118 Angle : 0.546 8.573 22475 Z= 0.271 Chirality : 0.040 0.163 2615 Planarity : 0.004 0.062 2745 Dihedral : 5.307 49.427 2765 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.46 % Allowed : 14.78 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.19), residues: 1955 helix: 0.87 (0.20), residues: 760 sheet: 0.09 (0.25), residues: 450 loop : -1.96 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 469 TYR 0.009 0.001 TYR B 140 PHE 0.010 0.001 PHE E 25 TRP 0.006 0.001 TRP D 89 HIS 0.004 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00258 (16410) covalent geometry : angle 0.52959 (22420) SS BOND : bond 0.00304 ( 5) SS BOND : angle 0.67592 ( 10) hydrogen bonds : bond 0.05860 ( 710) hydrogen bonds : angle 4.39368 ( 2340) link_BETA1-4 : bond 0.00484 ( 5) link_BETA1-4 : angle 0.72147 ( 15) link_NAG-ASN : bond 0.00470 ( 10) link_NAG-ASN : angle 3.63051 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 115 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8377 (t0) cc_final: 0.7821 (t0) REVERT: A 301 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7015 (ttp) REVERT: B 301 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7075 (mtm) REVERT: C 68 LYS cc_start: 0.7689 (tptp) cc_final: 0.7476 (tptp) REVERT: C 301 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7034 (ttp) REVERT: D 260 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7498 (mt-10) REVERT: D 301 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7318 (mtm) REVERT: D 473 MET cc_start: 0.6983 (ttp) cc_final: 0.6316 (ttm) outliers start: 42 outliers final: 20 residues processed: 141 average time/residue: 0.1189 time to fit residues: 26.4236 Evaluate side-chains 139 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 301 MET Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 446 ARG Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 281 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 5 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.109471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.089179 restraints weight = 18560.275| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 1.45 r_work: 0.2735 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 16430 Z= 0.184 Angle : 0.650 13.030 22475 Z= 0.314 Chirality : 0.044 0.192 2615 Planarity : 0.005 0.061 2745 Dihedral : 5.559 54.539 2765 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.52 % Allowed : 15.48 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.19), residues: 1955 helix: 0.80 (0.20), residues: 765 sheet: -0.05 (0.25), residues: 450 loop : -2.08 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 469 TYR 0.013 0.002 TYR B 140 PHE 0.016 0.001 PHE E 25 TRP 0.009 0.001 TRP B 89 HIS 0.004 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00453 (16410) covalent geometry : angle 0.62973 (22420) SS BOND : bond 0.00467 ( 5) SS BOND : angle 0.89119 ( 10) hydrogen bonds : bond 0.07263 ( 710) hydrogen bonds : angle 4.63065 ( 2340) link_BETA1-4 : bond 0.00450 ( 5) link_BETA1-4 : angle 0.83156 ( 15) link_NAG-ASN : bond 0.00478 ( 10) link_NAG-ASN : angle 4.40467 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8499 (t0) cc_final: 0.8079 (t0) REVERT: A 68 LYS cc_start: 0.7986 (tptp) cc_final: 0.7469 (tptp) REVERT: A 301 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7095 (ttp) REVERT: B 66 ASP cc_start: 0.8563 (t0) cc_final: 0.8192 (t0) REVERT: B 68 LYS cc_start: 0.7819 (tptp) cc_final: 0.7416 (tptp) REVERT: B 301 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7170 (mtm) REVERT: C 301 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7183 (mtm) REVERT: D 260 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7652 (mt-10) REVERT: D 301 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7443 (mtm) REVERT: E 66 ASP cc_start: 0.8564 (t0) cc_final: 0.8153 (t0) REVERT: E 235 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7450 (mp) REVERT: E 301 MET cc_start: 0.7785 (mmm) cc_final: 0.7499 (mmm) outliers start: 43 outliers final: 24 residues processed: 157 average time/residue: 0.1183 time to fit residues: 29.6510 Evaluate side-chains 157 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 301 MET Chi-restraints excluded: chain D residue 446 ARG Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 281 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 160 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 146 optimal weight: 0.9990 chunk 165 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.110218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.089956 restraints weight = 18468.666| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 1.46 r_work: 0.2739 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 16430 Z= 0.159 Angle : 0.615 12.185 22475 Z= 0.299 Chirality : 0.043 0.183 2615 Planarity : 0.005 0.058 2745 Dihedral : 5.551 56.961 2765 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.64 % Allowed : 16.30 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.19), residues: 1955 helix: 0.92 (0.19), residues: 765 sheet: -0.02 (0.24), residues: 450 loop : -2.13 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 469 TYR 0.011 0.001 TYR B 140 PHE 0.013 0.001 PHE E 25 TRP 0.009 0.001 TRP D 89 HIS 0.004 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00377 (16410) covalent geometry : angle 0.59472 (22420) SS BOND : bond 0.00429 ( 5) SS BOND : angle 0.91206 ( 10) hydrogen bonds : bond 0.06934 ( 710) hydrogen bonds : angle 4.51373 ( 2340) link_BETA1-4 : bond 0.00459 ( 5) link_BETA1-4 : angle 0.80452 ( 15) link_NAG-ASN : bond 0.00480 ( 10) link_NAG-ASN : angle 4.26198 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 127 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7081 (ttp) REVERT: B 66 ASP cc_start: 0.8518 (t0) cc_final: 0.8146 (t0) REVERT: B 68 LYS cc_start: 0.7841 (tptp) cc_final: 0.7421 (tptp) REVERT: B 301 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7083 (mtm) REVERT: C 66 ASP cc_start: 0.8678 (t0) cc_final: 0.8468 (t0) REVERT: C 208 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7592 (ptt90) REVERT: C 301 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7187 (mtm) REVERT: D 260 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7603 (mt-10) REVERT: D 301 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7419 (mtm) REVERT: E 66 ASP cc_start: 0.8503 (t0) cc_final: 0.8017 (t0) REVERT: E 68 LYS cc_start: 0.7963 (tptp) cc_final: 0.6846 (tttm) REVERT: E 80 MET cc_start: 0.8850 (mtm) cc_final: 0.8554 (mtt) REVERT: E 235 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7462 (mp) outliers start: 45 outliers final: 29 residues processed: 155 average time/residue: 0.1280 time to fit residues: 30.9312 Evaluate side-chains 160 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 241 CYS Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 301 MET Chi-restraints excluded: chain D residue 446 ARG Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain E residue 281 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 122 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 17 optimal weight: 0.1980 chunk 90 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.110368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.090167 restraints weight = 18503.750| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.45 r_work: 0.2744 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 16430 Z= 0.151 Angle : 0.609 12.165 22475 Z= 0.295 Chirality : 0.042 0.183 2615 Planarity : 0.004 0.056 2745 Dihedral : 5.521 59.112 2765 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.64 % Allowed : 16.77 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.19), residues: 1955 helix: 1.03 (0.20), residues: 765 sheet: 0.04 (0.25), residues: 450 loop : -2.15 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 469 TYR 0.011 0.001 TYR A 140 PHE 0.012 0.001 PHE A 25 TRP 0.008 0.001 TRP B 89 HIS 0.004 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00355 (16410) covalent geometry : angle 0.58899 (22420) SS BOND : bond 0.00432 ( 5) SS BOND : angle 0.92674 ( 10) hydrogen bonds : bond 0.06809 ( 710) hydrogen bonds : angle 4.46088 ( 2340) link_BETA1-4 : bond 0.00495 ( 5) link_BETA1-4 : angle 0.76030 ( 15) link_NAG-ASN : bond 0.00477 ( 10) link_NAG-ASN : angle 4.25233 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 127 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8417 (t0) cc_final: 0.7930 (t0) REVERT: A 301 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7066 (ttp) REVERT: B 66 ASP cc_start: 0.8581 (t0) cc_final: 0.8190 (t0) REVERT: B 68 LYS cc_start: 0.7824 (tptp) cc_final: 0.6651 (tttm) REVERT: B 301 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7086 (mtm) REVERT: C 66 ASP cc_start: 0.8636 (t0) cc_final: 0.8423 (t0) REVERT: C 208 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7564 (ptt90) REVERT: C 301 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7188 (mtm) REVERT: D 260 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7557 (mt-10) REVERT: D 301 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7417 (mtm) REVERT: E 66 ASP cc_start: 0.8538 (t0) cc_final: 0.8059 (t0) REVERT: E 68 LYS cc_start: 0.7998 (tptp) cc_final: 0.6718 (tttm) REVERT: E 235 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7396 (mp) outliers start: 45 outliers final: 34 residues processed: 157 average time/residue: 0.1270 time to fit residues: 30.9543 Evaluate side-chains 169 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 128 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 241 CYS Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 301 MET Chi-restraints excluded: chain D residue 446 ARG Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain E residue 281 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 117 optimal weight: 0.0050 chunk 18 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.111291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.091102 restraints weight = 18520.931| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 1.44 r_work: 0.2758 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16430 Z= 0.141 Angle : 0.594 12.079 22475 Z= 0.288 Chirality : 0.042 0.177 2615 Planarity : 0.004 0.054 2745 Dihedral : 5.476 59.753 2765 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.52 % Allowed : 16.95 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.19), residues: 1955 helix: 1.15 (0.20), residues: 765 sheet: 0.10 (0.25), residues: 450 loop : -2.13 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 469 TYR 0.010 0.001 TYR C 140 PHE 0.011 0.001 PHE D 25 TRP 0.008 0.001 TRP D 89 HIS 0.004 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00325 (16410) covalent geometry : angle 0.57452 (22420) SS BOND : bond 0.00424 ( 5) SS BOND : angle 0.91972 ( 10) hydrogen bonds : bond 0.06527 ( 710) hydrogen bonds : angle 4.37769 ( 2340) link_BETA1-4 : bond 0.00500 ( 5) link_BETA1-4 : angle 0.72688 ( 15) link_NAG-ASN : bond 0.00464 ( 10) link_NAG-ASN : angle 4.13613 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7070 (ttp) REVERT: B 66 ASP cc_start: 0.8587 (t0) cc_final: 0.8218 (t0) REVERT: B 68 LYS cc_start: 0.7843 (tptp) cc_final: 0.6657 (tttm) REVERT: B 301 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7117 (mtm) REVERT: C 120 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7621 (mt-10) REVERT: C 208 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7552 (ptt90) REVERT: C 301 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7051 (mtm) REVERT: D 260 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7528 (mt-10) REVERT: D 301 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7459 (mtm) outliers start: 43 outliers final: 32 residues processed: 159 average time/residue: 0.1247 time to fit residues: 30.8657 Evaluate side-chains 163 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 241 CYS Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 301 MET Chi-restraints excluded: chain D residue 446 ARG Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain E residue 281 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 62 optimal weight: 0.8980 chunk 115 optimal weight: 0.5980 chunk 59 optimal weight: 6.9990 chunk 90 optimal weight: 0.0770 chunk 73 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 97 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 chunk 170 optimal weight: 3.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.114878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.094254 restraints weight = 18210.123| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.46 r_work: 0.2812 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16430 Z= 0.109 Angle : 0.543 11.605 22475 Z= 0.266 Chirality : 0.040 0.155 2615 Planarity : 0.004 0.052 2745 Dihedral : 5.188 58.892 2765 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.99 % Allowed : 17.30 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.20), residues: 1955 helix: 1.40 (0.20), residues: 765 sheet: 0.33 (0.25), residues: 450 loop : -2.05 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 469 TYR 0.008 0.001 TYR C 140 PHE 0.007 0.001 PHE D 126 TRP 0.007 0.001 TRP B 89 HIS 0.003 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00231 (16410) covalent geometry : angle 0.52709 (22420) SS BOND : bond 0.00323 ( 5) SS BOND : angle 0.83109 ( 10) hydrogen bonds : bond 0.05452 ( 710) hydrogen bonds : angle 4.13010 ( 2340) link_BETA1-4 : bond 0.00518 ( 5) link_BETA1-4 : angle 0.62397 ( 15) link_NAG-ASN : bond 0.00448 ( 10) link_NAG-ASN : angle 3.60902 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.6998 (ttp) REVERT: A 468 ASP cc_start: 0.7613 (t0) cc_final: 0.7324 (t0) REVERT: B 66 ASP cc_start: 0.8553 (t0) cc_final: 0.8130 (t0) REVERT: B 68 LYS cc_start: 0.7809 (tptp) cc_final: 0.6759 (tttm) REVERT: B 301 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.6932 (mtm) REVERT: C 301 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7040 (mtm) REVERT: D 260 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7403 (mt-10) REVERT: D 301 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7284 (mtm) REVERT: D 473 MET cc_start: 0.6953 (ttp) cc_final: 0.6353 (ttm) outliers start: 34 outliers final: 24 residues processed: 146 average time/residue: 0.1225 time to fit residues: 28.1620 Evaluate side-chains 153 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 301 MET Chi-restraints excluded: chain D residue 446 ARG Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 281 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 103 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 104 optimal weight: 0.0870 chunk 14 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 337 ASN C 337 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.114451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.093490 restraints weight = 18294.616| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.51 r_work: 0.2795 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16430 Z= 0.116 Angle : 0.560 11.790 22475 Z= 0.272 Chirality : 0.040 0.158 2615 Planarity : 0.004 0.052 2745 Dihedral : 5.088 58.826 2765 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.76 % Allowed : 17.83 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.20), residues: 1955 helix: 1.47 (0.20), residues: 765 sheet: 0.39 (0.25), residues: 450 loop : -2.03 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 469 TYR 0.009 0.001 TYR B 140 PHE 0.008 0.001 PHE D 126 TRP 0.007 0.001 TRP B 89 HIS 0.003 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00256 (16410) covalent geometry : angle 0.54383 (22420) SS BOND : bond 0.00371 ( 5) SS BOND : angle 0.86151 ( 10) hydrogen bonds : bond 0.05592 ( 710) hydrogen bonds : angle 4.13373 ( 2340) link_BETA1-4 : bond 0.00516 ( 5) link_BETA1-4 : angle 0.61625 ( 15) link_NAG-ASN : bond 0.00420 ( 10) link_NAG-ASN : angle 3.70796 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 LYS cc_start: 0.7809 (tptp) cc_final: 0.6847 (tttm) REVERT: B 301 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.6982 (mtm) REVERT: C 301 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7001 (mtm) REVERT: D 260 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7423 (mt-10) REVERT: D 301 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7321 (mtm) REVERT: D 473 MET cc_start: 0.6963 (ttp) cc_final: 0.6353 (ttm) outliers start: 30 outliers final: 25 residues processed: 146 average time/residue: 0.1227 time to fit residues: 28.1495 Evaluate side-chains 148 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 301 MET Chi-restraints excluded: chain D residue 446 ARG Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 281 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 89 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 179 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 169 optimal weight: 0.0370 chunk 75 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.111149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.090458 restraints weight = 18450.716| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 1.52 r_work: 0.2747 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16430 Z= 0.164 Angle : 0.628 12.189 22475 Z= 0.303 Chirality : 0.043 0.177 2615 Planarity : 0.004 0.053 2745 Dihedral : 5.241 57.169 2765 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.11 % Allowed : 17.60 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.19), residues: 1955 helix: 1.33 (0.20), residues: 765 sheet: 0.22 (0.25), residues: 450 loop : -2.12 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 469 TYR 0.013 0.001 TYR B 140 PHE 0.014 0.001 PHE D 25 TRP 0.008 0.001 TRP D 89 HIS 0.004 0.001 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00398 (16410) covalent geometry : angle 0.60884 (22420) SS BOND : bond 0.00491 ( 5) SS BOND : angle 1.00194 ( 10) hydrogen bonds : bond 0.06690 ( 710) hydrogen bonds : angle 4.38215 ( 2340) link_BETA1-4 : bond 0.00443 ( 5) link_BETA1-4 : angle 0.73585 ( 15) link_NAG-ASN : bond 0.00465 ( 10) link_NAG-ASN : angle 4.26243 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3260.96 seconds wall clock time: 56 minutes 50.01 seconds (3410.01 seconds total)