Starting phenix.real_space_refine on Mon Jan 20 06:39:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vwp_43593/01_2025/8vwp_43593.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vwp_43593/01_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_43593/01_2025/8vwp_43593.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vwp_43593/01_2025/8vwp_43593.map" model { file = "/net/cci-nas-00/data/ceres_data/8vwp_43593/01_2025/8vwp_43593.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vwp_43593/01_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-5571/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: 9.16, per 1000 atoms: 0.62 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=7, 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 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: 3.30 Conformation dependent library (CDL) restraints added in 2.1 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: 2.80 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: 6.76 Time building geometry restraints manager: 3.87 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: 8821 18.00 - 36.00: 180 36.00 - 53.99: 43 53.99 - 71.99: 17 71.99 - 89.99: 20 Dihedral angle restraints: 9081 sinusoidal: 3229 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 9078 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: 2.02 - 2.60: 45 2.60 - 3.17: 11522 3.17 - 3.75: 20714 3.75 - 4.32: 30478 4.32 - 4.90: 51176 Nonbonded interactions: 113935 Sorted by model distance: nonbonded pdb=" SG CYS C 219 " pdb=" SG CYS C 243 " model vdw 2.024 3.760 nonbonded pdb=" SG CYS B 219 " pdb=" SG CYS B 243 " model vdw 2.024 3.760 nonbonded pdb=" SG CYS D 219 " pdb=" SG CYS D 243 " model vdw 2.024 3.760 nonbonded pdb=" SG CYS C 384 " pdb=" SG CYS C 502 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS D 384 " pdb=" SG CYS D 502 " model vdw 2.027 3.760 ... (remaining 113930 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: 0.12 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: 5.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 36.640 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.880 ------------------------------------------------------------------------------- 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 15152 Z= 0.817 Angle : 1.504 16.930 20644 Z= 1.054 Chirality : 0.094 0.999 2376 Planarity : 0.007 0.130 2636 Dihedral : 10.394 89.988 5308 Min Nonbonded Distance : 2.024 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 *********************** 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 : 1.681 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: 0.3036 time to fit residues: 103.6567 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 : 1.701 ------------------------------------------------------------------------------- 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: 0.9990 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 = 0.3778 r_free = 0.3778 target = 0.150965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.123866 restraints weight = 16895.965| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.01 r_work: 0.3318 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15152 Z= 0.239 Angle : 0.588 6.476 20644 Z= 0.322 Chirality : 0.047 0.140 2376 Planarity : 0.004 0.032 2636 Dihedral : 4.901 22.016 2240 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.50 % Allowed : 4.23 % 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: 0.93 (0.18), residues: 1976 helix: 2.92 (0.28), residues: 296 sheet: 0.84 (0.18), residues: 756 loop : -0.32 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 274 HIS 0.004 0.001 HIS C 194 PHE 0.021 0.002 PHE A 523 TYR 0.015 0.002 TYR A 414 ARG 0.003 0.001 ARG D 398 *********************** 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 176 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 1.746 Fit side-chains REVERT: A 561 ILE cc_start: 0.8873 (mm) cc_final: 0.8662 (tp) REVERT: B 561 ILE cc_start: 0.8868 (mm) cc_final: 0.8656 (tp) REVERT: C 561 ILE cc_start: 0.8874 (mm) cc_final: 0.8664 (tp) REVERT: D 561 ILE cc_start: 0.8868 (mm) cc_final: 0.8661 (tp) outliers start: 21 outliers final: 12 residues processed: 168 average time/residue: 0.3037 time to fit residues: 73.3730 Evaluate side-chains 148 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 1.710 ------------------------------------------------------------------------------- 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: 0.9980 chunk 185 optimal weight: 0.5980 chunk 197 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 199 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 127 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.147361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.122339 restraints weight = 16939.049| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.75 r_work: 0.3309 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15152 Z= 0.229 Angle : 0.544 7.179 20644 Z= 0.295 Chirality : 0.046 0.140 2376 Planarity : 0.004 0.034 2636 Dihedral : 4.393 19.215 2240 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.72 % Allowed : 4.37 % Favored : 93.91 % 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 (0.19), residues: 1976 helix: 3.30 (0.28), residues: 296 sheet: 0.81 (0.18), residues: 764 loop : -0.56 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 318 HIS 0.003 0.001 HIS A 194 PHE 0.016 0.002 PHE B 523 TYR 0.014 0.002 TYR D 414 ARG 0.002 0.000 ARG C 257 *********************** 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 184 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 1.527 Fit side-chains REVERT: A 88 MET cc_start: 0.8271 (mmm) cc_final: 0.7992 (mtp) REVERT: A 128 GLN cc_start: 0.8935 (tp40) cc_final: 0.8676 (tp40) REVERT: B 88 MET cc_start: 0.8268 (mmm) cc_final: 0.7992 (mtp) REVERT: B 128 GLN cc_start: 0.8936 (tp40) cc_final: 0.8675 (tp40) REVERT: B 501 MET cc_start: 0.7909 (tpp) cc_final: 0.7465 (mpp) REVERT: C 88 MET cc_start: 0.8265 (mmm) cc_final: 0.7997 (mtp) REVERT: C 128 GLN cc_start: 0.8934 (tp40) cc_final: 0.8675 (tp40) REVERT: C 501 MET cc_start: 0.7912 (tpp) cc_final: 0.7474 (mpp) REVERT: D 88 MET cc_start: 0.8244 (mmm) cc_final: 0.7981 (mtp) REVERT: D 128 GLN cc_start: 0.8930 (tp40) cc_final: 0.8674 (tp40) REVERT: D 501 MET cc_start: 0.7901 (tpp) cc_final: 0.7451 (mpp) outliers start: 24 outliers final: 19 residues processed: 180 average time/residue: 0.2814 time to fit residues: 75.0441 Evaluate side-chains 162 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 1.644 ------------------------------------------------------------------------------- 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 B residue 604 CYS 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 C residue 604 CYS 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 Chi-restraints excluded: chain D residue 604 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 116 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.146254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.121271 restraints weight = 17014.458| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.75 r_work: 0.3292 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15152 Z= 0.234 Angle : 0.526 4.856 20644 Z= 0.284 Chirality : 0.046 0.149 2376 Planarity : 0.004 0.039 2636 Dihedral : 4.325 17.977 2240 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.15 % Allowed : 5.44 % 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: 0.74 (0.19), residues: 1976 helix: 3.43 (0.28), residues: 296 sheet: 0.76 (0.18), residues: 764 loop : -0.74 (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 B 194 PHE 0.017 0.002 PHE D 523 TYR 0.015 0.002 TYR A 414 ARG 0.002 0.000 ARG B 257 *********************** 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 158 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 1.615 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 154 average time/residue: 0.2743 time to fit residues: 64.8848 Evaluate side-chains 143 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 520 ASP 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: 0.8980 chunk 193 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 165 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 180 optimal weight: 0.0980 chunk 54 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 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 589 ASN B 589 ASN D 589 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.146063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.121093 restraints weight = 17220.560| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.76 r_work: 0.3293 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15152 Z= 0.206 Angle : 0.498 4.829 20644 Z= 0.269 Chirality : 0.045 0.147 2376 Planarity : 0.004 0.039 2636 Dihedral : 4.167 15.764 2240 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.36 % Allowed : 6.59 % Favored : 92.05 % 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 (0.19), residues: 1976 helix: 3.59 (0.28), residues: 292 sheet: 0.76 (0.18), residues: 764 loop : -0.85 (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 B 194 PHE 0.015 0.002 PHE A 523 TYR 0.013 0.001 TYR D 414 ARG 0.001 0.000 ARG B 257 *********************** 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 159 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 1.574 Fit side-chains REVERT: A 128 GLN cc_start: 0.9005 (tp40) cc_final: 0.8637 (tp-100) REVERT: B 128 GLN cc_start: 0.9014 (tp40) cc_final: 0.8648 (tp-100) REVERT: C 128 GLN cc_start: 0.9008 (tp40) cc_final: 0.8640 (tp-100) REVERT: D 128 GLN cc_start: 0.9001 (tp40) cc_final: 0.8632 (tp-100) outliers start: 19 outliers final: 11 residues processed: 155 average time/residue: 0.2421 time to fit residues: 57.3350 Evaluate side-chains 142 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain C residue 219 CYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 520 ASP Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 520 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 139 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 118 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 138 optimal weight: 0.7980 chunk 152 optimal weight: 0.6980 chunk 189 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 589 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.148245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.120483 restraints weight = 17672.059| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.10 r_work: 0.3257 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15152 Z= 0.170 Angle : 0.471 4.860 20644 Z= 0.253 Chirality : 0.045 0.144 2376 Planarity : 0.004 0.042 2636 Dihedral : 4.000 15.030 2240 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.65 % Allowed : 6.66 % 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: 0.73 (0.19), residues: 1976 helix: 3.68 (0.28), residues: 292 sheet: 0.78 (0.18), residues: 764 loop : -0.86 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 318 HIS 0.002 0.001 HIS C 194 PHE 0.013 0.001 PHE B 523 TYR 0.012 0.001 TYR A 414 ARG 0.002 0.000 ARG C 509 *********************** 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 157 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 1.649 Fit side-chains REVERT: A 128 GLN cc_start: 0.8978 (tp40) cc_final: 0.8538 (tp40) REVERT: B 128 GLN cc_start: 0.8964 (tp40) cc_final: 0.8520 (tp40) REVERT: C 128 GLN cc_start: 0.8988 (tp40) cc_final: 0.8551 (tp40) REVERT: D 128 GLN cc_start: 0.8960 (tp40) cc_final: 0.8520 (tp40) outliers start: 23 outliers final: 19 residues processed: 149 average time/residue: 0.2623 time to fit residues: 59.2217 Evaluate side-chains 152 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 1.562 ------------------------------------------------------------------------------- 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 B residue 219 CYS 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 C residue 219 CYS 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 D residue 219 CYS 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 92 optimal weight: 0.8980 chunk 177 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 188 optimal weight: 0.5980 chunk 165 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 175 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 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 = 0.3716 r_free = 0.3716 target = 0.146450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118489 restraints weight = 17590.421| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.10 r_work: 0.3228 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15152 Z= 0.228 Angle : 0.496 4.882 20644 Z= 0.268 Chirality : 0.045 0.142 2376 Planarity : 0.004 0.041 2636 Dihedral : 4.053 15.314 2240 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.15 % Allowed : 6.38 % Favored : 91.48 % 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: 0.63 (0.19), residues: 1976 helix: 3.62 (0.29), residues: 292 sheet: 0.72 (0.18), residues: 764 loop : -0.94 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 274 HIS 0.003 0.001 HIS C 194 PHE 0.014 0.002 PHE C 523 TYR 0.013 0.001 TYR D 414 ARG 0.002 0.000 ARG A 257 *********************** 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 171 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 1.599 Fit side-chains REVERT: A 88 MET cc_start: 0.8339 (tpp) cc_final: 0.8104 (ttp) REVERT: A 128 GLN cc_start: 0.9023 (tp40) cc_final: 0.8632 (tp-100) REVERT: B 88 MET cc_start: 0.8319 (tpp) cc_final: 0.8012 (mtp) REVERT: B 128 GLN cc_start: 0.9011 (tp40) cc_final: 0.8609 (tp-100) REVERT: C 88 MET cc_start: 0.8325 (tpp) cc_final: 0.8021 (mtp) REVERT: C 128 GLN cc_start: 0.9031 (tp40) cc_final: 0.8635 (tp-100) REVERT: D 88 MET cc_start: 0.8302 (tpp) cc_final: 0.8007 (mtp) REVERT: D 128 GLN cc_start: 0.9001 (tp40) cc_final: 0.8602 (tp-100) outliers start: 30 outliers final: 23 residues processed: 159 average time/residue: 0.2644 time to fit residues: 64.0347 Evaluate side-chains 164 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 1.729 ------------------------------------------------------------------------------- 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 219 CYS 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 219 CYS 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 219 CYS 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: 1.9990 chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 80 optimal weight: 0.0070 chunk 82 optimal weight: 0.1980 overall best weight: 0.5600 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.147743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.119854 restraints weight = 17623.163| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.12 r_work: 0.3248 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15152 Z= 0.169 Angle : 0.465 4.854 20644 Z= 0.250 Chirality : 0.044 0.141 2376 Planarity : 0.004 0.040 2636 Dihedral : 3.943 15.176 2240 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.58 % Allowed : 7.23 % Favored : 91.19 % 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: 0.67 (0.19), residues: 1976 helix: 3.74 (0.29), residues: 292 sheet: 0.66 (0.18), residues: 792 loop : -0.91 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 274 HIS 0.002 0.001 HIS C 194 PHE 0.013 0.001 PHE B 523 TYR 0.011 0.001 TYR D 446 ARG 0.001 0.000 ARG D 509 *********************** 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 175 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 1.653 Fit side-chains REVERT: A 88 MET cc_start: 0.8337 (tpp) cc_final: 0.8112 (ttp) REVERT: A 128 GLN cc_start: 0.9002 (tp40) cc_final: 0.8611 (tp-100) REVERT: B 88 MET cc_start: 0.8314 (tpp) cc_final: 0.8104 (ttp) REVERT: B 128 GLN cc_start: 0.8984 (tp40) cc_final: 0.8584 (tp-100) REVERT: C 88 MET cc_start: 0.8320 (tpp) cc_final: 0.8113 (ttp) REVERT: C 128 GLN cc_start: 0.9001 (tp40) cc_final: 0.8606 (tp-100) REVERT: C 501 MET cc_start: 0.8215 (tpp) cc_final: 0.7839 (mpp) REVERT: D 88 MET cc_start: 0.8297 (tpp) cc_final: 0.8019 (mtp) REVERT: D 128 GLN cc_start: 0.8975 (tp40) cc_final: 0.8579 (tp-100) outliers start: 22 outliers final: 22 residues processed: 168 average time/residue: 0.2844 time to fit residues: 70.1336 Evaluate side-chains 174 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 1.696 ------------------------------------------------------------------------------- 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 B residue 219 CYS 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 561 ILE Chi-restraints excluded: chain C residue 219 CYS 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 561 ILE Chi-restraints excluded: chain D residue 219 CYS 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 561 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 199 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 chunk 145 optimal weight: 0.2980 chunk 191 optimal weight: 1.9990 chunk 45 optimal weight: 0.0170 chunk 134 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 overall best weight: 0.4218 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.132791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.103773 restraints weight = 17832.001| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.19 r_work: 0.3060 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15152 Z= 0.144 Angle : 0.448 4.847 20644 Z= 0.241 Chirality : 0.044 0.133 2376 Planarity : 0.004 0.040 2636 Dihedral : 3.776 14.586 2240 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.50 % Allowed : 7.45 % Favored : 91.05 % 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: 0.78 (0.19), residues: 1976 helix: 3.80 (0.29), residues: 292 sheet: 0.76 (0.18), residues: 792 loop : -0.87 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 318 HIS 0.002 0.001 HIS D 194 PHE 0.012 0.001 PHE A 523 TYR 0.010 0.001 TYR A 414 ARG 0.001 0.000 ARG A 509 *********************** 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 186 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 2.058 Fit side-chains REVERT: A 88 MET cc_start: 0.8278 (tpp) cc_final: 0.8037 (ttp) REVERT: A 128 GLN cc_start: 0.8904 (tp40) cc_final: 0.8431 (tp40) REVERT: B 88 MET cc_start: 0.8265 (tpp) cc_final: 0.8036 (ttp) REVERT: B 128 GLN cc_start: 0.8894 (tp40) cc_final: 0.8421 (tp40) REVERT: B 501 MET cc_start: 0.8221 (tpp) cc_final: 0.7761 (mpp) REVERT: C 88 MET cc_start: 0.8267 (tpp) cc_final: 0.8035 (ttp) REVERT: C 128 GLN cc_start: 0.8899 (tp40) cc_final: 0.8424 (tp40) REVERT: C 501 MET cc_start: 0.8220 (tpp) cc_final: 0.7771 (mpp) REVERT: D 88 MET cc_start: 0.8255 (tpp) cc_final: 0.8026 (ttp) REVERT: D 128 GLN cc_start: 0.8898 (tp40) cc_final: 0.8423 (tp40) REVERT: D 501 MET cc_start: 0.8209 (tpp) cc_final: 0.7753 (mpp) outliers start: 21 outliers final: 21 residues processed: 176 average time/residue: 0.2810 time to fit residues: 73.2449 Evaluate side-chains 174 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 1.572 ------------------------------------------------------------------------------- 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 561 ILE Chi-restraints excluded: chain B residue 219 CYS 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 561 ILE Chi-restraints excluded: chain C residue 219 CYS 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 561 ILE Chi-restraints excluded: chain D residue 219 CYS 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 561 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 143 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 50 optimal weight: 0.0870 chunk 106 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.132880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.104211 restraints weight = 17997.827| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.12 r_work: 0.3058 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15152 Z= 0.183 Angle : 0.478 6.093 20644 Z= 0.254 Chirality : 0.045 0.139 2376 Planarity : 0.004 0.039 2636 Dihedral : 3.842 15.005 2240 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.65 % Allowed : 8.38 % Favored : 89.97 % 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: 0.75 (0.19), residues: 1976 helix: 3.75 (0.28), residues: 292 sheet: 0.77 (0.18), residues: 792 loop : -0.91 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 274 HIS 0.003 0.001 HIS C 312 PHE 0.012 0.002 PHE A 523 TYR 0.012 0.001 TYR A 414 ARG 0.001 0.000 ARG D 509 ********************** 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 170 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 1.578 Fit side-chains REVERT: A 88 MET cc_start: 0.8306 (tpp) cc_final: 0.8098 (ttp) REVERT: A 128 GLN cc_start: 0.8934 (tp40) cc_final: 0.8478 (tp40) REVERT: B 88 MET cc_start: 0.8314 (tpp) cc_final: 0.8114 (ttp) REVERT: B 128 GLN cc_start: 0.8927 (tp40) cc_final: 0.8470 (tp40) REVERT: C 88 MET cc_start: 0.8312 (tpp) cc_final: 0.8110 (ttp) REVERT: C 128 GLN cc_start: 0.8931 (tp40) cc_final: 0.8471 (tp40) REVERT: D 128 GLN cc_start: 0.8925 (tp40) cc_final: 0.8467 (tp40) outliers start: 23 outliers final: 20 residues processed: 158 average time/residue: 0.2860 time to fit residues: 66.2399 Evaluate side-chains 165 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 1.752 ------------------------------------------------------------------------------- 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 561 ILE Chi-restraints excluded: chain B residue 219 CYS 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 561 ILE Chi-restraints excluded: chain C residue 219 CYS 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 561 ILE Chi-restraints excluded: chain D residue 219 CYS 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 561 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 160 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 0.4980 chunk 107 optimal weight: 0.0970 chunk 179 optimal weight: 0.7980 chunk 165 optimal weight: 0.8980 chunk 159 optimal weight: 0.3980 chunk 76 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 155 optimal weight: 0.4980 chunk 144 optimal weight: 0.9980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.133520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.104966 restraints weight = 18063.259| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.13 r_work: 0.3070 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15152 Z= 0.153 Angle : 0.460 5.521 20644 Z= 0.244 Chirality : 0.044 0.130 2376 Planarity : 0.003 0.038 2636 Dihedral : 3.749 14.798 2240 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.43 % Allowed : 8.60 % Favored : 89.97 % 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: 0.81 (0.19), residues: 1976 helix: 3.81 (0.28), residues: 292 sheet: 0.89 (0.19), residues: 776 loop : -0.93 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 274 HIS 0.002 0.001 HIS C 194 PHE 0.012 0.001 PHE D 523 TYR 0.010 0.001 TYR D 571 ARG 0.001 0.000 ARG A 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7449.47 seconds wall clock time: 134 minutes 53.65 seconds (8093.65 seconds total)