Starting phenix.real_space_refine on Fri Jun 13 09:32:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vwp_43593/06_2025/8vwp_43593.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vwp_43593/06_2025/8vwp_43593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vwp_43593/06_2025/8vwp_43593.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vwp_43593/06_2025/8vwp_43593.map" model { file = "/net/cci-nas-00/data/ceres_data/8vwp_43593/06_2025/8vwp_43593.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vwp_43593/06_2025/8vwp_43593.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.036 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 96 5.16 5 C 9592 2.51 5 N 2500 2.21 5 O 2632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14820 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3691 Classifications: {'peptide': 503} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 476} Unresolved chain links: 1 Chain breaks: 2 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 314 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 5, 'ASP:plan': 14, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 129 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, B, D Time building chain proxies: 8.34, per 1000 atoms: 0.56 Number of scatterers: 14820 At special positions: 0 Unit cell: (146.85, 146.85, 112.14, 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 96 16.00 O 2632 8.00 N 2500 7.00 C 9592 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS A 604 " distance=2.07 Simple disulfide: pdb=" SG CYS A 219 " - pdb=" SG CYS A 243 " distance=2.02 Simple disulfide: pdb=" SG CYS A 285 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 396 " distance=2.04 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 502 " distance=2.03 Simple disulfide: pdb=" SG CYS A 494 " - pdb=" SG CYS A 506 " distance=2.03 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 577 " distance=2.03 Simple disulfide: pdb=" SG CYS C 188 " - pdb=" SG CYS C 604 " distance=2.07 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS B 604 " distance=2.07 Simple disulfide: pdb=" SG CYS D 188 " - pdb=" SG CYS D 604 " distance=2.07 Simple disulfide: pdb=" SG CYS C 219 " - pdb=" SG CYS C 243 " distance=2.02 Simple disulfide: pdb=" SG CYS B 219 " - pdb=" SG CYS B 243 " distance=2.02 Simple disulfide: pdb=" SG CYS D 219 " - pdb=" SG CYS D 243 " distance=2.02 Simple disulfide: pdb=" SG CYS C 285 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 285 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS D 285 " - pdb=" SG CYS D 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 396 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 396 " distance=2.04 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 396 " distance=2.04 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 502 " distance=2.03 Simple disulfide: pdb=" SG CYS B 384 " - pdb=" SG CYS B 502 " distance=2.03 Simple disulfide: pdb=" SG CYS D 384 " - pdb=" SG CYS D 502 " distance=2.03 Simple disulfide: pdb=" SG CYS C 494 " - pdb=" SG CYS C 506 " distance=2.03 Simple disulfide: pdb=" SG CYS B 494 " - pdb=" SG CYS B 506 " distance=2.03 Simple disulfide: pdb=" SG CYS D 494 " - pdb=" SG CYS D 506 " distance=2.03 Simple disulfide: pdb=" SG CYS C 568 " - pdb=" SG CYS C 577 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 577 " distance=2.03 Simple disulfide: pdb=" SG CYS D 568 " - pdb=" SG CYS D 577 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 189 " " NAG B 701 " - " ASN B 189 " " NAG C 701 " - " ASN C 189 " " NAG D 701 " - " ASN D 189 " Time building additional restraints: 3.20 Conformation dependent library (CDL) restraints added in 1.9 seconds 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3752 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 32 sheets defined 20.3% alpha, 46.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 75 through 99 removed outlier: 3.766A pdb=" N ASN A 83 " --> pdb=" O GLN A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 113 Processing helix chain 'A' and resid 113 through 142 removed outlier: 3.518A pdb=" N THR A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 170 removed outlier: 3.880A pdb=" N ASP A 169 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 391 through 399 Processing helix chain 'A' and resid 400 through 405 removed outlier: 7.185A pdb=" N PHE A 403 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY A 404 " --> pdb=" O MET A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 423 Processing helix chain 'A' and resid 433 through 437 removed outlier: 3.810A pdb=" N SER A 437 " --> pdb=" O PRO A 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 99 removed outlier: 3.766A pdb=" N ASN B 83 " --> pdb=" O GLN B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 113 Processing helix chain 'B' and resid 113 through 142 removed outlier: 3.518A pdb=" N THR B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 170 removed outlier: 3.880A pdb=" N ASP B 169 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'B' and resid 391 through 399 Processing helix chain 'B' and resid 400 through 405 removed outlier: 7.185A pdb=" N PHE B 403 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY B 404 " --> pdb=" O MET B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 423 Processing helix chain 'B' and resid 433 through 437 removed outlier: 3.810A pdb=" N SER B 437 " --> pdb=" O PRO B 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 99 removed outlier: 3.766A pdb=" N ASN C 83 " --> pdb=" O GLN C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 113 Processing helix chain 'C' and resid 113 through 142 removed outlier: 3.518A pdb=" N THR C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 170 removed outlier: 3.880A pdb=" N ASP C 169 " --> pdb=" O ASP C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 391 through 399 Processing helix chain 'C' and resid 400 through 405 removed outlier: 7.185A pdb=" N PHE C 403 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY C 404 " --> pdb=" O MET C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 423 Processing helix chain 'C' and resid 433 through 437 removed outlier: 3.810A pdb=" N SER C 437 " --> pdb=" O PRO C 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 99 removed outlier: 3.766A pdb=" N ASN D 83 " --> pdb=" O GLN D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 113 Processing helix chain 'D' and resid 113 through 142 removed outlier: 3.518A pdb=" N THR D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 170 removed outlier: 3.880A pdb=" N ASP D 169 " --> pdb=" O ASP D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 391 through 399 Processing helix chain 'D' and resid 400 through 405 removed outlier: 7.185A pdb=" N PHE D 403 " --> pdb=" O VAL D 400 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY D 404 " --> pdb=" O MET D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 423 Processing helix chain 'D' and resid 433 through 437 removed outlier: 3.810A pdb=" N SER D 437 " --> pdb=" O PRO D 434 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 178 removed outlier: 5.547A pdb=" N ILE A 561 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG A 584 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER A 563 " --> pdb=" O GLU A 582 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 582 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE A 575 " --> pdb=" O VAL A 600 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 177 through 178 removed outlier: 5.547A pdb=" N ILE A 561 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG A 584 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER A 563 " --> pdb=" O GLU A 582 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 582 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE A 575 " --> pdb=" O VAL A 600 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 218 through 227 removed outlier: 5.516A pdb=" N TYR A 220 " --> pdb=" O ARG A 239 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG A 239 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASN A 222 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU A 237 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR A 232 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU A 255 " --> pdb=" O TYR A 232 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE A 234 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE A 253 " --> pdb=" O PHE A 234 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN A 236 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE A 251 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE A 238 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ARG A 257 " --> pdb=" O PRO A 270 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL A 259 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALA A 268 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 282 through 289 removed outlier: 6.824A pdb=" N SER A 299 " --> pdb=" O ASN A 283 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N CYS A 285 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU A 297 " --> pdb=" O CYS A 285 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL A 287 " --> pdb=" O TRP A 295 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TRP A 295 " --> pdb=" O VAL A 287 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 338 through 339 removed outlier: 7.271A pdb=" N GLN A 364 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ILE A 349 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE A 366 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL A 347 " --> pdb=" O PHE A 366 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU A 368 " --> pdb=" O ASP A 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 338 through 339 Processing sheet with id=AA7, first strand: chain 'A' and resid 443 through 448 removed outlier: 4.315A pdb=" N ARG A 466 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 514 through 516 Processing sheet with id=AA9, first strand: chain 'B' and resid 177 through 178 removed outlier: 5.547A pdb=" N ILE B 561 " --> pdb=" O ARG B 584 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG B 584 " --> pdb=" O ILE B 561 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER B 563 " --> pdb=" O GLU B 582 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU B 582 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE B 575 " --> pdb=" O VAL B 600 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 177 through 178 removed outlier: 5.547A pdb=" N ILE B 561 " --> pdb=" O ARG B 584 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG B 584 " --> pdb=" O ILE B 561 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER B 563 " --> pdb=" O GLU B 582 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU B 582 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE B 575 " --> pdb=" O VAL B 600 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 218 through 227 removed outlier: 5.516A pdb=" N TYR B 220 " --> pdb=" O ARG B 239 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG B 239 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASN B 222 " --> pdb=" O GLU B 237 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU B 237 " --> pdb=" O ASN B 222 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR B 232 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU B 255 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE B 234 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE B 253 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN B 236 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE B 251 " --> pdb=" O GLN B 236 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE B 238 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ARG B 257 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL B 259 " --> pdb=" O ALA B 268 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALA B 268 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 282 through 289 removed outlier: 6.824A pdb=" N SER B 299 " --> pdb=" O ASN B 283 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N CYS B 285 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU B 297 " --> pdb=" O CYS B 285 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL B 287 " --> pdb=" O TRP B 295 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TRP B 295 " --> pdb=" O VAL B 287 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 338 through 339 removed outlier: 7.271A pdb=" N GLN B 364 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ILE B 349 " --> pdb=" O GLN B 364 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE B 366 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL B 347 " --> pdb=" O PHE B 366 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU B 368 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 338 through 339 Processing sheet with id=AB6, first strand: chain 'B' and resid 443 through 448 removed outlier: 4.315A pdb=" N ARG B 466 " --> pdb=" O LEU B 456 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 514 through 516 Processing sheet with id=AB8, first strand: chain 'C' and resid 177 through 178 removed outlier: 5.547A pdb=" N ILE C 561 " --> pdb=" O ARG C 584 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG C 584 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER C 563 " --> pdb=" O GLU C 582 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU C 582 " --> pdb=" O SER C 563 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE C 575 " --> pdb=" O VAL C 600 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 177 through 178 removed outlier: 5.547A pdb=" N ILE C 561 " --> pdb=" O ARG C 584 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG C 584 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER C 563 " --> pdb=" O GLU C 582 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU C 582 " --> pdb=" O SER C 563 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE C 575 " --> pdb=" O VAL C 600 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 218 through 227 removed outlier: 5.516A pdb=" N TYR C 220 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG C 239 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASN C 222 " --> pdb=" O GLU C 237 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU C 237 " --> pdb=" O ASN C 222 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR C 232 " --> pdb=" O LEU C 255 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU C 255 " --> pdb=" O TYR C 232 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE C 234 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE C 253 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN C 236 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE C 251 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE C 238 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ARG C 257 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL C 259 " --> pdb=" O ALA C 268 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALA C 268 " --> pdb=" O VAL C 259 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 282 through 289 removed outlier: 6.824A pdb=" N SER C 299 " --> pdb=" O ASN C 283 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N CYS C 285 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU C 297 " --> pdb=" O CYS C 285 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL C 287 " --> pdb=" O TRP C 295 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TRP C 295 " --> pdb=" O VAL C 287 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 338 through 339 removed outlier: 7.271A pdb=" N GLN C 364 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ILE C 349 " --> pdb=" O GLN C 364 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE C 366 " --> pdb=" O VAL C 347 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL C 347 " --> pdb=" O PHE C 366 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU C 368 " --> pdb=" O ASP C 345 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 338 through 339 Processing sheet with id=AC5, first strand: chain 'C' and resid 443 through 448 removed outlier: 4.315A pdb=" N ARG C 466 " --> pdb=" O LEU C 456 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 514 through 516 Processing sheet with id=AC7, first strand: chain 'D' and resid 177 through 178 removed outlier: 5.547A pdb=" N ILE D 561 " --> pdb=" O ARG D 584 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG D 584 " --> pdb=" O ILE D 561 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER D 563 " --> pdb=" O GLU D 582 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU D 582 " --> pdb=" O SER D 563 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE D 575 " --> pdb=" O VAL D 600 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 177 through 178 removed outlier: 5.547A pdb=" N ILE D 561 " --> pdb=" O ARG D 584 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG D 584 " --> pdb=" O ILE D 561 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER D 563 " --> pdb=" O GLU D 582 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU D 582 " --> pdb=" O SER D 563 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE D 575 " --> pdb=" O VAL D 600 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 218 through 227 removed outlier: 5.516A pdb=" N TYR D 220 " --> pdb=" O ARG D 239 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG D 239 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASN D 222 " --> pdb=" O GLU D 237 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU D 237 " --> pdb=" O ASN D 222 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR D 232 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU D 255 " --> pdb=" O TYR D 232 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE D 234 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE D 253 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN D 236 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE D 251 " --> pdb=" O GLN D 236 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE D 238 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ARG D 257 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL D 259 " --> pdb=" O ALA D 268 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALA D 268 " --> pdb=" O VAL D 259 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 282 through 289 removed outlier: 6.824A pdb=" N SER D 299 " --> pdb=" O ASN D 283 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N CYS D 285 " --> pdb=" O LEU D 297 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU D 297 " --> pdb=" O CYS D 285 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL D 287 " --> pdb=" O TRP D 295 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TRP D 295 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 338 through 339 removed outlier: 7.271A pdb=" N GLN D 364 " --> pdb=" O ILE D 349 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ILE D 349 " --> pdb=" O GLN D 364 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE D 366 " --> pdb=" O VAL D 347 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL D 347 " --> pdb=" O PHE D 366 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU D 368 " --> pdb=" O ASP D 345 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 338 through 339 Processing sheet with id=AD4, first strand: chain 'D' and resid 443 through 448 removed outlier: 4.315A pdb=" N ARG D 466 " --> pdb=" O LEU D 456 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 514 through 516 805 hydrogen bonds defined for protein. 2175 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: 5.49 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3600 1.33 - 1.46: 3676 1.46 - 1.58: 7732 1.58 - 1.71: 8 1.71 - 1.84: 136 Bond restraints: 15152 Sorted by residual: bond pdb=" CB ILE C 607 " pdb=" CG1 ILE C 607 " ideal model delta sigma weight residual 1.530 1.618 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" CB ILE D 607 " pdb=" CG1 ILE D 607 " ideal model delta sigma weight residual 1.530 1.618 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" CB ILE A 607 " pdb=" CG1 ILE A 607 " ideal model delta sigma weight residual 1.530 1.618 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" CB ILE B 607 " pdb=" CG1 ILE B 607 " ideal model delta sigma weight residual 1.530 1.618 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" CA HIS C 312 " pdb=" C HIS C 312 " ideal model delta sigma weight residual 1.528 1.584 -0.056 1.36e-02 5.41e+03 1.70e+01 ... (remaining 15147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 19912 3.39 - 6.77: 664 6.77 - 10.16: 48 10.16 - 13.54: 12 13.54 - 16.93: 8 Bond angle restraints: 20644 Sorted by residual: angle pdb=" N THR D 168 " pdb=" CA THR D 168 " pdb=" C THR D 168 " ideal model delta sigma weight residual 111.71 128.64 -16.93 1.15e+00 7.56e-01 2.17e+02 angle pdb=" N THR B 168 " pdb=" CA THR B 168 " pdb=" C THR B 168 " ideal model delta sigma weight residual 111.71 128.64 -16.93 1.15e+00 7.56e-01 2.17e+02 angle pdb=" N THR C 168 " pdb=" CA THR C 168 " pdb=" C THR C 168 " ideal model delta sigma weight residual 111.71 128.64 -16.93 1.15e+00 7.56e-01 2.17e+02 angle pdb=" N THR A 168 " pdb=" CA THR A 168 " pdb=" C THR A 168 " ideal model delta sigma weight residual 111.71 128.64 -16.93 1.15e+00 7.56e-01 2.17e+02 angle pdb=" N GLU C 407 " pdb=" CA GLU C 407 " pdb=" C GLU C 407 " ideal model delta sigma weight residual 113.15 126.79 -13.64 1.19e+00 7.06e-01 1.31e+02 ... (remaining 20639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 8848 18.00 - 36.00: 204 36.00 - 53.99: 52 53.99 - 71.99: 20 71.99 - 89.99: 20 Dihedral angle restraints: 9144 sinusoidal: 3292 harmonic: 5852 Sorted by residual: dihedral pdb=" C THR B 167 " pdb=" N THR B 167 " pdb=" CA THR B 167 " pdb=" CB THR B 167 " ideal model delta harmonic sigma weight residual -122.00 -148.02 26.02 0 2.50e+00 1.60e-01 1.08e+02 dihedral pdb=" C THR C 167 " pdb=" N THR C 167 " pdb=" CA THR C 167 " pdb=" CB THR C 167 " ideal model delta harmonic sigma weight residual -122.00 -148.02 26.02 0 2.50e+00 1.60e-01 1.08e+02 dihedral pdb=" C THR D 167 " pdb=" N THR D 167 " pdb=" CA THR D 167 " pdb=" CB THR D 167 " ideal model delta harmonic sigma weight residual -122.00 -148.02 26.02 0 2.50e+00 1.60e-01 1.08e+02 ... (remaining 9141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.200: 2324 0.200 - 0.400: 40 0.400 - 0.599: 8 0.599 - 0.799: 0 0.799 - 0.999: 4 Chirality restraints: 2376 Sorted by residual: chirality pdb=" CA THR B 167 " pdb=" N THR B 167 " pdb=" C THR B 167 " pdb=" CB THR B 167 " both_signs ideal model delta sigma weight residual False 2.53 1.53 1.00 2.00e-01 2.50e+01 2.49e+01 chirality pdb=" CA THR D 167 " pdb=" N THR D 167 " pdb=" C THR D 167 " pdb=" CB THR D 167 " both_signs ideal model delta sigma weight residual False 2.53 1.53 1.00 2.00e-01 2.50e+01 2.49e+01 chirality pdb=" CA THR C 167 " pdb=" N THR C 167 " pdb=" C THR C 167 " pdb=" CB THR C 167 " both_signs ideal model delta sigma weight residual False 2.53 1.53 1.00 2.00e-01 2.50e+01 2.49e+01 ... (remaining 2373 not shown) Planarity restraints: 2640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 398 " -0.290 9.50e-02 1.11e+02 1.30e-01 1.04e+01 pdb=" NE ARG C 398 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG C 398 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 398 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 398 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 398 " -0.290 9.50e-02 1.11e+02 1.30e-01 1.04e+01 pdb=" NE ARG A 398 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 398 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 398 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 398 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 398 " -0.290 9.50e-02 1.11e+02 1.30e-01 1.04e+01 pdb=" NE ARG B 398 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B 398 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 398 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 398 " -0.010 2.00e-02 2.50e+03 ... (remaining 2637 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 5007 2.87 - 3.38: 12072 3.38 - 3.88: 23290 3.88 - 4.39: 26759 4.39 - 4.90: 46744 Nonbonded interactions: 113872 Sorted by model distance: nonbonded pdb=" N MET C 313 " pdb=" O MET C 313 " model vdw 2.359 2.496 nonbonded pdb=" N MET B 313 " pdb=" O MET B 313 " model vdw 2.359 2.496 nonbonded pdb=" N MET A 313 " pdb=" O MET A 313 " model vdw 2.359 2.496 nonbonded pdb=" N MET D 313 " pdb=" O MET D 313 " model vdw 2.359 2.496 nonbonded pdb=" N SER A 459 " pdb=" N SER A 460 " model vdw 2.566 2.560 ... (remaining 113867 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 34.660 Find NCS groups from input model: 0.290 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 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 : 0.012 0.088 15184 Z= 0.695 Angle : 1.510 16.930 20712 Z= 1.055 Chirality : 0.094 0.999 2376 Planarity : 0.007 0.130 2636 Dihedral : 10.394 89.988 5308 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.23 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.18), residues: 1976 helix: 1.52 (0.28), residues: 292 sheet: 0.88 (0.19), residues: 724 loop : 0.02 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP D 318 HIS 0.004 0.001 HIS C 596 PHE 0.019 0.004 PHE A 523 TYR 0.035 0.005 TYR D 414 ARG 0.003 0.001 ARG B 592 Details of bonding type rmsd link_NAG-ASN : bond 0.07583 ( 4) link_NAG-ASN : angle 2.24187 ( 12) hydrogen bonds : bond 0.17405 ( 657) hydrogen bonds : angle 7.31580 ( 2175) SS BOND : bond 0.01571 ( 28) SS BOND : angle 2.96046 ( 56) covalent geometry : bond 0.01225 (15152) covalent geometry : angle 1.50379 (20644) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 2.282 Fit side-chains REVERT: A 513 ASP cc_start: 0.8638 (p0) cc_final: 0.8352 (p0) REVERT: B 513 ASP cc_start: 0.8643 (p0) cc_final: 0.8353 (p0) REVERT: C 513 ASP cc_start: 0.8646 (p0) cc_final: 0.8345 (p0) REVERT: D 513 ASP cc_start: 0.8638 (p0) cc_final: 0.8344 (p0) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.3522 time to fit residues: 120.0225 Evaluate side-chains 152 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 156 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 chunk 181 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN B 123 GLN C 123 GLN D 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.150464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.123311 restraints weight = 17041.141| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.01 r_work: 0.3319 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15184 Z= 0.157 Angle : 0.602 7.145 20712 Z= 0.334 Chirality : 0.046 0.141 2376 Planarity : 0.004 0.030 2636 Dihedral : 4.831 21.977 2240 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.72 % Allowed : 4.01 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.18), residues: 1976 helix: 2.85 (0.29), residues: 296 sheet: 0.78 (0.18), residues: 756 loop : -0.33 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 274 HIS 0.002 0.001 HIS D 596 PHE 0.021 0.002 PHE B 523 TYR 0.015 0.002 TYR A 414 ARG 0.002 0.001 ARG D 398 Details of bonding type rmsd link_NAG-ASN : bond 0.00529 ( 4) link_NAG-ASN : angle 0.53829 ( 12) hydrogen bonds : bond 0.05722 ( 657) hydrogen bonds : angle 5.04256 ( 2175) SS BOND : bond 0.00323 ( 28) SS BOND : angle 1.57578 ( 56) covalent geometry : bond 0.00361 (15152) covalent geometry : angle 0.59770 (20644) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 2.113 Fit side-chains REVERT: A 561 ILE cc_start: 0.8869 (mm) cc_final: 0.8664 (tp) REVERT: B 561 ILE cc_start: 0.8864 (mm) cc_final: 0.8660 (tp) REVERT: C 561 ILE cc_start: 0.8869 (mm) cc_final: 0.8666 (tp) REVERT: D 561 ILE cc_start: 0.8863 (mm) cc_final: 0.8661 (tp) outliers start: 24 outliers final: 12 residues processed: 164 average time/residue: 0.3643 time to fit residues: 87.2078 Evaluate side-chains 140 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 2.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 520 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 520 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 10 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 chunk 197 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 199 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.148903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.121822 restraints weight = 17347.526| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.96 r_work: 0.3265 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 15184 Z= 0.148 Angle : 0.547 5.431 20712 Z= 0.298 Chirality : 0.046 0.145 2376 Planarity : 0.004 0.034 2636 Dihedral : 4.437 19.424 2240 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.43 % Allowed : 4.87 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.18), residues: 1976 helix: 3.30 (0.28), residues: 296 sheet: 0.67 (0.18), residues: 764 loop : -0.67 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 318 HIS 0.003 0.001 HIS C 194 PHE 0.016 0.002 PHE B 523 TYR 0.018 0.002 TYR D 414 ARG 0.002 0.000 ARG A 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00370 ( 4) link_NAG-ASN : angle 0.75343 ( 12) hydrogen bonds : bond 0.04319 ( 657) hydrogen bonds : angle 4.44908 ( 2175) SS BOND : bond 0.00400 ( 28) SS BOND : angle 0.97751 ( 56) covalent geometry : bond 0.00352 (15152) covalent geometry : angle 0.54485 (20644) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 1.961 Fit side-chains REVERT: A 88 MET cc_start: 0.8342 (mmm) cc_final: 0.8061 (mtp) REVERT: A 128 GLN cc_start: 0.8989 (tp40) cc_final: 0.8724 (tp40) REVERT: A 501 MET cc_start: 0.7796 (tpp) cc_final: 0.7413 (mpp) REVERT: B 88 MET cc_start: 0.8290 (mmm) cc_final: 0.8016 (mtp) REVERT: B 128 GLN cc_start: 0.8979 (tp40) cc_final: 0.8714 (tp40) REVERT: B 501 MET cc_start: 0.7794 (tpp) cc_final: 0.7414 (mpp) REVERT: C 88 MET cc_start: 0.8305 (mmm) cc_final: 0.8029 (mtp) REVERT: C 128 GLN cc_start: 0.8975 (tp40) cc_final: 0.8716 (tp40) REVERT: C 501 MET cc_start: 0.7801 (tpp) cc_final: 0.7418 (mpp) REVERT: D 88 MET cc_start: 0.8287 (mmm) cc_final: 0.8021 (mtp) REVERT: D 128 GLN cc_start: 0.8976 (tp40) cc_final: 0.8717 (tp40) REVERT: D 501 MET cc_start: 0.7798 (tpp) cc_final: 0.7416 (mpp) outliers start: 20 outliers final: 16 residues processed: 176 average time/residue: 0.3430 time to fit residues: 89.4043 Evaluate side-chains 149 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 520 ASP Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 520 ASP Chi-restraints excluded: chain D residue 562 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 116 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 56 optimal weight: 0.0010 chunk 82 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.148210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.121219 restraints weight = 17426.042| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.96 r_work: 0.3284 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15184 Z= 0.135 Angle : 0.527 6.041 20712 Z= 0.283 Chirality : 0.046 0.150 2376 Planarity : 0.004 0.036 2636 Dihedral : 4.293 17.361 2240 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.43 % Allowed : 5.16 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.19), residues: 1976 helix: 3.38 (0.28), residues: 296 sheet: 0.64 (0.18), residues: 764 loop : -0.80 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 274 HIS 0.003 0.001 HIS C 194 PHE 0.016 0.002 PHE A 523 TYR 0.013 0.001 TYR A 414 ARG 0.002 0.000 ARG C 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 4) link_NAG-ASN : angle 0.82951 ( 12) hydrogen bonds : bond 0.04158 ( 657) hydrogen bonds : angle 4.31972 ( 2175) SS BOND : bond 0.00243 ( 28) SS BOND : angle 0.78664 ( 56) covalent geometry : bond 0.00324 (15152) covalent geometry : angle 0.52615 (20644) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.653 Fit side-chains REVERT: A 128 GLN cc_start: 0.8908 (tp40) cc_final: 0.8423 (tp40) REVERT: B 128 GLN cc_start: 0.8907 (tp40) cc_final: 0.8420 (tp40) REVERT: C 128 GLN cc_start: 0.8902 (tp40) cc_final: 0.8417 (tp40) REVERT: D 128 GLN cc_start: 0.8905 (tp40) cc_final: 0.8422 (tp40) outliers start: 20 outliers final: 12 residues processed: 144 average time/residue: 0.2641 time to fit residues: 58.0130 Evaluate side-chains 140 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 520 ASP Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 520 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 193 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 180 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 159 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 ASN B 589 ASN C 589 ASN D 589 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.148368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.120661 restraints weight = 17504.518| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.05 r_work: 0.3259 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15184 Z= 0.130 Angle : 0.501 4.818 20712 Z= 0.270 Chirality : 0.045 0.137 2376 Planarity : 0.004 0.039 2636 Dihedral : 4.171 15.660 2240 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.72 % Allowed : 4.87 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.19), residues: 1976 helix: 3.59 (0.28), residues: 292 sheet: 0.62 (0.18), residues: 764 loop : -0.94 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 274 HIS 0.003 0.001 HIS C 194 PHE 0.015 0.002 PHE C 523 TYR 0.013 0.001 TYR D 414 ARG 0.001 0.000 ARG C 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 4) link_NAG-ASN : angle 0.95629 ( 12) hydrogen bonds : bond 0.03919 ( 657) hydrogen bonds : angle 4.17980 ( 2175) SS BOND : bond 0.00215 ( 28) SS BOND : angle 0.71598 ( 56) covalent geometry : bond 0.00316 (15152) covalent geometry : angle 0.50018 (20644) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 1.582 Fit side-chains REVERT: A 128 GLN cc_start: 0.8979 (tp40) cc_final: 0.8510 (tp40) REVERT: B 128 GLN cc_start: 0.8976 (tp40) cc_final: 0.8504 (tp40) REVERT: C 128 GLN cc_start: 0.8974 (tp40) cc_final: 0.8503 (tp40) REVERT: D 128 GLN cc_start: 0.8975 (tp40) cc_final: 0.8508 (tp40) outliers start: 24 outliers final: 16 residues processed: 160 average time/residue: 0.2546 time to fit residues: 62.1096 Evaluate side-chains 152 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 520 ASP Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 520 ASP Chi-restraints excluded: chain D residue 562 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 139 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 138 optimal weight: 0.1980 chunk 152 optimal weight: 0.5980 chunk 189 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.148349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.120596 restraints weight = 17540.016| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.05 r_work: 0.3262 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15184 Z= 0.121 Angle : 0.493 4.868 20712 Z= 0.265 Chirality : 0.045 0.141 2376 Planarity : 0.004 0.041 2636 Dihedral : 4.098 14.980 2240 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.15 % Allowed : 6.88 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.19), residues: 1976 helix: 3.65 (0.28), residues: 292 sheet: 0.60 (0.18), residues: 764 loop : -0.95 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 274 HIS 0.002 0.001 HIS C 194 PHE 0.013 0.002 PHE C 523 TYR 0.012 0.001 TYR C 571 ARG 0.002 0.000 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 4) link_NAG-ASN : angle 0.91128 ( 12) hydrogen bonds : bond 0.03805 ( 657) hydrogen bonds : angle 4.11243 ( 2175) SS BOND : bond 0.00207 ( 28) SS BOND : angle 0.67423 ( 56) covalent geometry : bond 0.00290 (15152) covalent geometry : angle 0.49191 (20644) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 1.748 Fit side-chains REVERT: A 88 MET cc_start: 0.8329 (tpp) cc_final: 0.8002 (mtp) REVERT: A 128 GLN cc_start: 0.8989 (tp40) cc_final: 0.8516 (tp40) REVERT: B 88 MET cc_start: 0.8322 (tpp) cc_final: 0.8013 (mtp) REVERT: B 128 GLN cc_start: 0.8989 (tp40) cc_final: 0.8514 (tp40) REVERT: C 88 MET cc_start: 0.8323 (tpp) cc_final: 0.8001 (mtp) REVERT: C 128 GLN cc_start: 0.8986 (tp40) cc_final: 0.8514 (tp40) REVERT: D 88 MET cc_start: 0.8327 (tpp) cc_final: 0.8009 (mtp) REVERT: D 128 GLN cc_start: 0.8986 (tp40) cc_final: 0.8516 (tp40) outliers start: 16 outliers final: 12 residues processed: 148 average time/residue: 0.2573 time to fit residues: 57.8791 Evaluate side-chains 152 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 520 ASP Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 365 MET Chi-restraints excluded: chain D residue 520 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 92 optimal weight: 0.5980 chunk 177 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 188 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 175 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.131872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.102564 restraints weight = 17798.251| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.17 r_work: 0.3030 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15184 Z= 0.117 Angle : 0.482 4.872 20712 Z= 0.259 Chirality : 0.045 0.140 2376 Planarity : 0.004 0.039 2636 Dihedral : 4.035 14.911 2240 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.72 % Allowed : 6.59 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.19), residues: 1976 helix: 3.70 (0.28), residues: 292 sheet: 0.64 (0.18), residues: 764 loop : -0.95 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 274 HIS 0.002 0.001 HIS C 194 PHE 0.013 0.002 PHE A 523 TYR 0.012 0.001 TYR C 571 ARG 0.001 0.000 ARG C 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 4) link_NAG-ASN : angle 0.93371 ( 12) hydrogen bonds : bond 0.03673 ( 657) hydrogen bonds : angle 4.06803 ( 2175) SS BOND : bond 0.00204 ( 28) SS BOND : angle 0.62434 ( 56) covalent geometry : bond 0.00281 (15152) covalent geometry : angle 0.48149 (20644) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 1.621 Fit side-chains REVERT: A 88 MET cc_start: 0.8287 (tpp) cc_final: 0.7967 (mtp) REVERT: A 128 GLN cc_start: 0.8983 (tp40) cc_final: 0.8495 (tp40) REVERT: B 88 MET cc_start: 0.8300 (tpp) cc_final: 0.7989 (mtp) REVERT: B 128 GLN cc_start: 0.8992 (tp40) cc_final: 0.8505 (tp40) REVERT: C 88 MET cc_start: 0.8299 (tpp) cc_final: 0.7985 (mtp) REVERT: C 128 GLN cc_start: 0.8986 (tp40) cc_final: 0.8502 (tp40) REVERT: D 88 MET cc_start: 0.8296 (tpp) cc_final: 0.7985 (mtp) REVERT: D 128 GLN cc_start: 0.8981 (tp40) cc_final: 0.8498 (tp40) outliers start: 24 outliers final: 20 residues processed: 156 average time/residue: 0.2479 time to fit residues: 58.8740 Evaluate side-chains 160 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 520 ASP Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 365 MET Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 520 ASP Chi-restraints excluded: chain D residue 562 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 90 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 50 optimal weight: 0.4980 chunk 128 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.131916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.102589 restraints weight = 17884.730| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.18 r_work: 0.3027 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15184 Z= 0.121 Angle : 0.484 4.836 20712 Z= 0.261 Chirality : 0.045 0.139 2376 Planarity : 0.004 0.039 2636 Dihedral : 4.022 15.070 2240 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.01 % Allowed : 6.88 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.19), residues: 1976 helix: 3.68 (0.28), residues: 292 sheet: 0.56 (0.18), residues: 792 loop : -0.99 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 274 HIS 0.002 0.001 HIS B 194 PHE 0.013 0.002 PHE A 523 TYR 0.011 0.001 TYR C 571 ARG 0.001 0.000 ARG C 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 4) link_NAG-ASN : angle 0.85660 ( 12) hydrogen bonds : bond 0.03655 ( 657) hydrogen bonds : angle 4.04315 ( 2175) SS BOND : bond 0.00201 ( 28) SS BOND : angle 0.64684 ( 56) covalent geometry : bond 0.00293 (15152) covalent geometry : angle 0.48332 (20644) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 1.767 Fit side-chains REVERT: A 88 MET cc_start: 0.8300 (tpp) cc_final: 0.8094 (ttp) REVERT: A 128 GLN cc_start: 0.9012 (tp40) cc_final: 0.8533 (tp40) REVERT: B 88 MET cc_start: 0.8302 (tpp) cc_final: 0.8027 (mtp) REVERT: B 128 GLN cc_start: 0.9018 (tp40) cc_final: 0.8542 (tp40) REVERT: C 88 MET cc_start: 0.8293 (tpp) cc_final: 0.8008 (mtp) REVERT: C 128 GLN cc_start: 0.9015 (tp40) cc_final: 0.8539 (tp40) REVERT: D 88 MET cc_start: 0.8292 (tpp) cc_final: 0.8010 (mtp) REVERT: D 128 GLN cc_start: 0.9012 (tp40) cc_final: 0.8541 (tp40) outliers start: 28 outliers final: 20 residues processed: 171 average time/residue: 0.2762 time to fit residues: 69.8515 Evaluate side-chains 175 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 520 ASP Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 365 MET Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 520 ASP Chi-restraints excluded: chain D residue 562 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 199 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 107 optimal weight: 0.0670 chunk 84 optimal weight: 0.6980 chunk 145 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 chunk 45 optimal weight: 0.0980 chunk 134 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.3539 r_free = 0.3539 target = 0.132503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.103947 restraints weight = 17788.100| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.08 r_work: 0.3065 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15184 Z= 0.103 Angle : 0.465 4.848 20712 Z= 0.250 Chirality : 0.044 0.138 2376 Planarity : 0.004 0.041 2636 Dihedral : 3.909 14.789 2240 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.15 % Allowed : 7.74 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.19), residues: 1976 helix: 3.77 (0.28), residues: 292 sheet: 0.64 (0.18), residues: 792 loop : -0.98 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 274 HIS 0.002 0.001 HIS B 194 PHE 0.012 0.001 PHE C 523 TYR 0.010 0.001 TYR A 414 ARG 0.001 0.000 ARG D 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 4) link_NAG-ASN : angle 0.82465 ( 12) hydrogen bonds : bond 0.03408 ( 657) hydrogen bonds : angle 3.95434 ( 2175) SS BOND : bond 0.00174 ( 28) SS BOND : angle 0.56087 ( 56) covalent geometry : bond 0.00242 (15152) covalent geometry : angle 0.46443 (20644) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 1.835 Fit side-chains REVERT: A 88 MET cc_start: 0.8270 (tpp) cc_final: 0.8057 (ttp) REVERT: A 128 GLN cc_start: 0.8974 (tp40) cc_final: 0.8486 (tp40) REVERT: B 88 MET cc_start: 0.8288 (tpp) cc_final: 0.8077 (ttp) REVERT: B 128 GLN cc_start: 0.8975 (tp40) cc_final: 0.8491 (tp40) REVERT: C 88 MET cc_start: 0.8285 (tpp) cc_final: 0.8076 (ttp) REVERT: C 128 GLN cc_start: 0.8979 (tp40) cc_final: 0.8493 (tp40) REVERT: D 88 MET cc_start: 0.8282 (tpp) cc_final: 0.8074 (ttp) REVERT: D 128 GLN cc_start: 0.8975 (tp40) cc_final: 0.8493 (tp40) outliers start: 16 outliers final: 16 residues processed: 169 average time/residue: 0.2840 time to fit residues: 70.9599 Evaluate side-chains 175 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 520 ASP Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain D residue 365 MET Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 520 ASP Chi-restraints excluded: chain D residue 561 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 143 optimal weight: 0.9980 chunk 57 optimal weight: 0.2980 chunk 50 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.129989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.100516 restraints weight = 17976.847| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.19 r_work: 0.2996 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 15184 Z= 0.187 Angle : 0.555 6.333 20712 Z= 0.297 Chirality : 0.047 0.135 2376 Planarity : 0.004 0.043 2636 Dihedral : 4.209 15.912 2240 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.43 % Allowed : 8.17 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.19), residues: 1976 helix: 3.52 (0.28), residues: 292 sheet: 0.48 (0.18), residues: 776 loop : -1.11 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 274 HIS 0.003 0.002 HIS D 194 PHE 0.014 0.002 PHE A 523 TYR 0.015 0.002 TYR D 571 ARG 0.001 0.000 ARG A 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 4) link_NAG-ASN : angle 0.81577 ( 12) hydrogen bonds : bond 0.04189 ( 657) hydrogen bonds : angle 4.19422 ( 2175) SS BOND : bond 0.00252 ( 28) SS BOND : angle 0.75325 ( 56) covalent geometry : bond 0.00471 (15152) covalent geometry : angle 0.55454 (20644) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 1.782 Fit side-chains REVERT: A 88 MET cc_start: 0.8285 (tpp) cc_final: 0.8083 (ttp) REVERT: A 128 GLN cc_start: 0.8967 (tp40) cc_final: 0.8479 (tp40) REVERT: B 128 GLN cc_start: 0.8966 (tp40) cc_final: 0.8482 (tp40) REVERT: C 88 MET cc_start: 0.8287 (tpp) cc_final: 0.8082 (ttp) REVERT: C 128 GLN cc_start: 0.8973 (tp40) cc_final: 0.8490 (tp40) REVERT: D 88 MET cc_start: 0.8288 (tpp) cc_final: 0.8086 (ttp) REVERT: D 128 GLN cc_start: 0.8965 (tp40) cc_final: 0.8481 (tp40) outliers start: 20 outliers final: 20 residues processed: 155 average time/residue: 0.2957 time to fit residues: 67.6000 Evaluate side-chains 163 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 520 ASP Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain D residue 365 MET Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 520 ASP Chi-restraints excluded: chain D residue 561 ILE Chi-restraints excluded: chain D residue 562 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 160 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 107 optimal weight: 0.0370 chunk 179 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 50 optimal weight: 10.0000 chunk 155 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.131320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.102031 restraints weight = 17956.693| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.18 r_work: 0.3027 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15184 Z= 0.128 Angle : 0.507 5.977 20712 Z= 0.271 Chirality : 0.045 0.135 2376 Planarity : 0.004 0.042 2636 Dihedral : 4.104 15.627 2240 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.15 % Allowed : 8.52 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.19), residues: 1976 helix: 3.58 (0.28), residues: 292 sheet: 0.57 (0.18), residues: 784 loop : -1.11 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 274 HIS 0.002 0.001 HIS A 194 PHE 0.013 0.002 PHE A 523 TYR 0.012 0.001 TYR C 571 ARG 0.001 0.000 ARG D 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00191 ( 4) link_NAG-ASN : angle 0.82604 ( 12) hydrogen bonds : bond 0.03751 ( 657) hydrogen bonds : angle 4.10153 ( 2175) SS BOND : bond 0.00200 ( 28) SS BOND : angle 0.59952 ( 56) covalent geometry : bond 0.00313 (15152) covalent geometry : angle 0.50691 (20644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8510.50 seconds wall clock time: 149 minutes 13.20 seconds (8953.20 seconds total)