Starting phenix.real_space_refine on Thu Sep 18 07:00:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vwp_43593/09_2025/8vwp_43593.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vwp_43593/09_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_43593/09_2025/8vwp_43593.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vwp_43593/09_2025/8vwp_43593.map" model { file = "/net/cci-nas-00/data/ceres_data/8vwp_43593/09_2025/8vwp_43593.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vwp_43593/09_2025/8vwp_43593.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 14, 'GLU:plan': 13, 'ASN:plan1': 5, 'ARG:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 1} 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: B, C, D Time building chain proxies: 3.03, per 1000 atoms: 0.20 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 B 188 " - pdb=" SG CYS B 604 " distance=2.07 Simple disulfide: pdb=" SG CYS C 188 " - pdb=" SG CYS C 604 " distance=2.07 Simple disulfide: pdb=" SG CYS D 188 " - pdb=" SG CYS D 604 " distance=2.07 Simple disulfide: pdb=" SG CYS B 219 " - pdb=" SG CYS B 243 " distance=2.02 Simple disulfide: pdb=" SG CYS C 219 " - pdb=" SG CYS C 243 " distance=2.02 Simple disulfide: pdb=" SG CYS D 219 " - pdb=" SG CYS D 243 " distance=2.02 Simple disulfide: pdb=" SG CYS B 285 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 285 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS D 285 " - pdb=" SG CYS D 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 396 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 396 " distance=2.04 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 396 " distance=2.04 Simple disulfide: pdb=" SG CYS B 384 " - pdb=" SG CYS B 502 " distance=2.03 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 502 " distance=2.03 Simple disulfide: pdb=" SG CYS D 384 " - pdb=" SG CYS D 502 " distance=2.03 Simple disulfide: pdb=" SG CYS B 494 " - pdb=" SG CYS B 506 " distance=2.03 Simple disulfide: pdb=" SG CYS C 494 " - pdb=" SG CYS C 506 " distance=2.03 Simple disulfide: pdb=" SG CYS D 494 " - pdb=" SG CYS D 506 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 577 " distance=2.03 Simple disulfide: pdb=" SG CYS C 568 " - pdb=" SG CYS C 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: 1.11 Conformation dependent library (CDL) restraints added in 615.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.71 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: 2.84 Time building geometry restraints manager: 1.54 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 0.010 Normalize map: mean=0, sd=1: 5.480 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.660 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.950 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (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 ARG 0.003 0.001 ARG B 592 TYR 0.035 0.005 TYR D 414 PHE 0.019 0.004 PHE A 523 TRP 0.017 0.004 TRP D 318 HIS 0.004 0.001 HIS C 596 Details of bonding type rmsd covalent geometry : bond 0.01225 (15152) covalent geometry : angle 1.50379 (20644) SS BOND : bond 0.01571 ( 28) SS BOND : angle 2.96046 ( 56) hydrogen bonds : bond 0.17405 ( 657) hydrogen bonds : angle 7.31580 ( 2175) link_NAG-ASN : bond 0.07583 ( 4) link_NAG-ASN : angle 2.24187 ( 12) *********************** 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 : 0.494 Fit side-chains REVERT: A 513 ASP cc_start: 0.8638 (p0) cc_final: 0.8352 (p0) REVERT: B 488 MET cc_start: 0.7985 (ttm) cc_final: 0.7785 (ttm) 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: 0.1435 time to fit residues: 48.9208 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 : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 0.0370 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.0070 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.153036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.126172 restraints weight = 17036.549| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.00 r_work: 0.3357 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1702 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= 0.125 Angle : 0.568 5.732 20712 Z= 0.311 Chirality : 0.046 0.135 2376 Planarity : 0.004 0.030 2636 Dihedral : 4.821 21.230 2240 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.43 % Allowed : 3.94 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.18), residues: 1976 helix: 2.91 (0.28), residues: 296 sheet: 0.86 (0.18), residues: 756 loop : -0.30 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 398 TYR 0.014 0.002 TYR B 132 PHE 0.021 0.002 PHE C 523 TRP 0.006 0.001 TRP D 274 HIS 0.002 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00266 (15152) covalent geometry : angle 0.56342 (20644) SS BOND : bond 0.00324 ( 28) SS BOND : angle 1.40560 ( 56) hydrogen bonds : bond 0.05109 ( 657) hydrogen bonds : angle 4.92612 ( 2175) link_NAG-ASN : bond 0.00551 ( 4) link_NAG-ASN : angle 0.80257 ( 12) *********************** 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 184 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.630 Fit side-chains REVERT: A 561 ILE cc_start: 0.8823 (mm) cc_final: 0.8605 (tp) REVERT: B 561 ILE cc_start: 0.8825 (mm) cc_final: 0.8609 (tp) REVERT: C 561 ILE cc_start: 0.8827 (mm) cc_final: 0.8609 (tp) REVERT: D 561 ILE cc_start: 0.8824 (mm) cc_final: 0.8608 (tp) outliers start: 20 outliers final: 8 residues processed: 176 average time/residue: 0.1344 time to fit residues: 34.2042 Evaluate side-chains 148 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 520 ASP Chi-restraints excluded: chain D residue 85 LEU 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 76 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 195 optimal weight: 0.0170 chunk 10 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.149075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.121818 restraints weight = 17608.737| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.99 r_work: 0.3262 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15184 Z= 0.170 Angle : 0.567 6.112 20712 Z= 0.306 Chirality : 0.047 0.143 2376 Planarity : 0.004 0.034 2636 Dihedral : 4.496 19.707 2240 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.43 % Allowed : 4.80 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.18), residues: 1976 helix: 3.17 (0.28), residues: 296 sheet: 0.76 (0.18), residues: 764 loop : -0.52 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 444 TYR 0.016 0.002 TYR B 414 PHE 0.015 0.002 PHE B 523 TRP 0.004 0.001 TRP D 318 HIS 0.004 0.001 HIS D 596 Details of bonding type rmsd covalent geometry : bond 0.00415 (15152) covalent geometry : angle 0.56518 (20644) SS BOND : bond 0.00570 ( 28) SS BOND : angle 0.93268 ( 56) hydrogen bonds : bond 0.04687 ( 657) hydrogen bonds : angle 4.53509 ( 2175) link_NAG-ASN : bond 0.00406 ( 4) link_NAG-ASN : angle 0.72933 ( 12) *********************** 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 161 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.581 Fit side-chains REVERT: A 88 MET cc_start: 0.8290 (mmm) cc_final: 0.7948 (mtp) REVERT: A 128 GLN cc_start: 0.8961 (tp40) cc_final: 0.8690 (tp40) REVERT: B 88 MET cc_start: 0.8280 (mmm) cc_final: 0.7952 (mtp) REVERT: B 128 GLN cc_start: 0.8958 (tp40) cc_final: 0.8688 (tp40) REVERT: C 88 MET cc_start: 0.8297 (mmm) cc_final: 0.7963 (mtp) REVERT: C 128 GLN cc_start: 0.8958 (tp40) cc_final: 0.8691 (tp40) REVERT: D 88 MET cc_start: 0.8283 (mmm) cc_final: 0.7954 (mtp) REVERT: D 128 GLN cc_start: 0.8957 (tp40) cc_final: 0.8691 (tp40) outliers start: 20 outliers final: 12 residues processed: 157 average time/residue: 0.1357 time to fit residues: 31.1527 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 : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 479 THR Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain B residue 562 THR 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 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 47 optimal weight: 1.9990 chunk 79 optimal weight: 0.0050 chunk 2 optimal weight: 0.9990 chunk 166 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 179 optimal weight: 0.0370 chunk 40 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.150337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.123365 restraints weight = 17574.401| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.98 r_work: 0.3309 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15184 Z= 0.110 Angle : 0.503 4.783 20712 Z= 0.271 Chirality : 0.045 0.146 2376 Planarity : 0.004 0.036 2636 Dihedral : 4.228 17.584 2240 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.86 % Allowed : 5.37 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.18), residues: 1976 helix: 3.47 (0.28), residues: 296 sheet: 0.81 (0.18), residues: 764 loop : -0.71 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 509 TYR 0.013 0.001 TYR C 414 PHE 0.017 0.002 PHE B 523 TRP 0.006 0.001 TRP A 274 HIS 0.002 0.001 HIS D 596 Details of bonding type rmsd covalent geometry : bond 0.00255 (15152) covalent geometry : angle 0.50156 (20644) SS BOND : bond 0.00214 ( 28) SS BOND : angle 0.77895 ( 56) hydrogen bonds : bond 0.03884 ( 657) hydrogen bonds : angle 4.24299 ( 2175) link_NAG-ASN : bond 0.00407 ( 4) link_NAG-ASN : angle 0.81293 ( 12) *********************** 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 156 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.584 Fit side-chains REVERT: A 128 GLN cc_start: 0.8897 (tp40) cc_final: 0.8596 (tp40) REVERT: B 128 GLN cc_start: 0.8894 (tp40) cc_final: 0.8592 (tp40) REVERT: C 128 GLN cc_start: 0.8891 (tp40) cc_final: 0.8591 (tp40) REVERT: D 128 GLN cc_start: 0.8893 (tp40) cc_final: 0.8594 (tp40) outliers start: 12 outliers final: 4 residues processed: 148 average time/residue: 0.1369 time to fit residues: 29.2887 Evaluate side-chains 140 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 136 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain C residue 520 ASP 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 131 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.146469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118601 restraints weight = 17529.430| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.05 r_work: 0.3233 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15184 Z= 0.180 Angle : 0.560 5.019 20712 Z= 0.302 Chirality : 0.047 0.149 2376 Planarity : 0.004 0.041 2636 Dihedral : 4.377 16.933 2240 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.43 % Allowed : 5.37 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.18), residues: 1976 helix: 3.38 (0.28), residues: 292 sheet: 0.62 (0.18), residues: 768 loop : -0.96 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 257 TYR 0.019 0.002 TYR C 414 PHE 0.016 0.002 PHE B 523 TRP 0.005 0.001 TRP D 274 HIS 0.004 0.002 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00449 (15152) covalent geometry : angle 0.55832 (20644) SS BOND : bond 0.00336 ( 28) SS BOND : angle 0.89977 ( 56) hydrogen bonds : bond 0.04510 ( 657) hydrogen bonds : angle 4.36091 ( 2175) link_NAG-ASN : bond 0.00321 ( 4) link_NAG-ASN : angle 0.94727 ( 12) *********************** 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 155 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.608 Fit side-chains REVERT: A 128 GLN cc_start: 0.8951 (tp40) cc_final: 0.8460 (tp40) REVERT: B 128 GLN cc_start: 0.8953 (tp40) cc_final: 0.8458 (tp40) REVERT: C 128 GLN cc_start: 0.8946 (tp40) cc_final: 0.8451 (tp40) REVERT: D 128 GLN cc_start: 0.8951 (tp40) cc_final: 0.8459 (tp40) outliers start: 20 outliers final: 16 residues processed: 151 average time/residue: 0.1247 time to fit residues: 28.8294 Evaluate side-chains 147 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 89 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 195 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 137 optimal weight: 0.7980 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 = 0.3734 r_free = 0.3734 target = 0.147649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.119941 restraints weight = 17350.552| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.05 r_work: 0.3249 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15184 Z= 0.136 Angle : 0.505 4.834 20712 Z= 0.273 Chirality : 0.046 0.145 2376 Planarity : 0.004 0.043 2636 Dihedral : 4.216 15.866 2240 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.50 % Allowed : 6.16 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.19), residues: 1976 helix: 3.51 (0.28), residues: 292 sheet: 0.61 (0.18), residues: 764 loop : -0.96 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 509 TYR 0.013 0.001 TYR B 571 PHE 0.014 0.002 PHE B 523 TRP 0.006 0.001 TRP B 274 HIS 0.003 0.001 HIS B 596 Details of bonding type rmsd covalent geometry : bond 0.00334 (15152) covalent geometry : angle 0.50375 (20644) SS BOND : bond 0.00224 ( 28) SS BOND : angle 0.70203 ( 56) hydrogen bonds : bond 0.03951 ( 657) hydrogen bonds : angle 4.22093 ( 2175) link_NAG-ASN : bond 0.00293 ( 4) link_NAG-ASN : angle 0.94699 ( 12) *********************** 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 161 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.601 Fit side-chains REVERT: A 128 GLN cc_start: 0.8970 (tp40) cc_final: 0.8490 (tp40) REVERT: B 128 GLN cc_start: 0.8972 (tp40) cc_final: 0.8491 (tp40) REVERT: C 128 GLN cc_start: 0.8967 (tp40) cc_final: 0.8488 (tp40) REVERT: D 128 GLN cc_start: 0.8969 (tp40) cc_final: 0.8492 (tp40) outliers start: 21 outliers final: 13 residues processed: 156 average time/residue: 0.1246 time to fit residues: 29.7774 Evaluate side-chains 150 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 69 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 120 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.130178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.100480 restraints weight = 17682.186| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.19 r_work: 0.3010 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15184 Z= 0.164 Angle : 0.528 4.864 20712 Z= 0.286 Chirality : 0.046 0.143 2376 Planarity : 0.004 0.042 2636 Dihedral : 4.283 16.019 2240 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.72 % Allowed : 6.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.19), residues: 1976 helix: 3.44 (0.29), residues: 292 sheet: 0.51 (0.19), residues: 756 loop : -1.11 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 257 TYR 0.014 0.002 TYR A 571 PHE 0.015 0.002 PHE D 523 TRP 0.006 0.001 TRP B 274 HIS 0.003 0.001 HIS B 596 Details of bonding type rmsd covalent geometry : bond 0.00409 (15152) covalent geometry : angle 0.52714 (20644) SS BOND : bond 0.00260 ( 28) SS BOND : angle 0.75755 ( 56) hydrogen bonds : bond 0.04223 ( 657) hydrogen bonds : angle 4.26986 ( 2175) link_NAG-ASN : bond 0.00235 ( 4) link_NAG-ASN : angle 0.97963 ( 12) *********************** 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 166 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.688 Fit side-chains REVERT: A 88 MET cc_start: 0.8273 (tpp) cc_final: 0.8034 (ttp) REVERT: A 128 GLN cc_start: 0.8916 (tp40) cc_final: 0.8415 (tp40) REVERT: B 88 MET cc_start: 0.8291 (tpp) cc_final: 0.8042 (ttp) REVERT: B 128 GLN cc_start: 0.8923 (tp40) cc_final: 0.8423 (tp40) REVERT: C 88 MET cc_start: 0.8298 (tpp) cc_final: 0.8047 (ttp) REVERT: C 128 GLN cc_start: 0.8922 (tp40) cc_final: 0.8423 (tp40) REVERT: D 88 MET cc_start: 0.8295 (tpp) cc_final: 0.8046 (ttp) REVERT: D 128 GLN cc_start: 0.8917 (tp40) cc_final: 0.8420 (tp40) outliers start: 24 outliers final: 20 residues processed: 154 average time/residue: 0.1262 time to fit residues: 29.8712 Evaluate side-chains 159 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU 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 85 LEU 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 85 LEU 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 85 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 86 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 170 optimal weight: 0.0050 chunk 122 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 160 optimal weight: 0.4980 chunk 93 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 = 0.132003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.102542 restraints weight = 17724.827| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.17 r_work: 0.3037 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15184 Z= 0.105 Angle : 0.474 4.850 20712 Z= 0.255 Chirality : 0.044 0.144 2376 Planarity : 0.004 0.038 2636 Dihedral : 4.062 15.393 2240 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.07 % Allowed : 7.16 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.19), residues: 1976 helix: 3.62 (0.29), residues: 292 sheet: 0.55 (0.18), residues: 792 loop : -1.09 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 509 TYR 0.011 0.001 TYR B 571 PHE 0.013 0.001 PHE B 523 TRP 0.006 0.001 TRP B 274 HIS 0.002 0.001 HIS C 194 Details of bonding type rmsd covalent geometry : bond 0.00245 (15152) covalent geometry : angle 0.47338 (20644) SS BOND : bond 0.00184 ( 28) SS BOND : angle 0.58077 ( 56) hydrogen bonds : bond 0.03599 ( 657) hydrogen bonds : angle 4.09508 ( 2175) link_NAG-ASN : bond 0.00269 ( 4) link_NAG-ASN : angle 0.87595 ( 12) *********************** 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 159 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.691 Fit side-chains REVERT: A 88 MET cc_start: 0.8286 (tpp) cc_final: 0.8045 (ttp) REVERT: A 128 GLN cc_start: 0.8957 (tp40) cc_final: 0.8466 (tp40) REVERT: B 88 MET cc_start: 0.8286 (tpp) cc_final: 0.8048 (ttp) REVERT: B 128 GLN cc_start: 0.8960 (tp40) cc_final: 0.8471 (tp40) REVERT: C 88 MET cc_start: 0.8286 (tpp) cc_final: 0.8051 (ttp) REVERT: C 128 GLN cc_start: 0.8956 (tp40) cc_final: 0.8467 (tp40) REVERT: D 88 MET cc_start: 0.8284 (tpp) cc_final: 0.8052 (ttp) REVERT: D 128 GLN cc_start: 0.8955 (tp40) cc_final: 0.8469 (tp40) outliers start: 15 outliers final: 11 residues processed: 152 average time/residue: 0.1269 time to fit residues: 29.4474 Evaluate side-chains 155 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 365 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 45 optimal weight: 0.3980 chunk 87 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 163 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 162 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 114 optimal weight: 1.9990 chunk 152 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.132058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.102587 restraints weight = 17846.823| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.19 r_work: 0.3035 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15184 Z= 0.108 Angle : 0.471 4.845 20712 Z= 0.254 Chirality : 0.045 0.135 2376 Planarity : 0.004 0.039 2636 Dihedral : 3.946 15.243 2240 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.86 % Allowed : 7.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.19), residues: 1976 helix: 3.66 (0.29), residues: 292 sheet: 0.60 (0.18), residues: 792 loop : -1.14 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 509 TYR 0.011 0.001 TYR C 571 PHE 0.013 0.002 PHE B 523 TRP 0.004 0.001 TRP D 318 HIS 0.002 0.001 HIS D 596 Details of bonding type rmsd covalent geometry : bond 0.00257 (15152) covalent geometry : angle 0.47097 (20644) SS BOND : bond 0.00182 ( 28) SS BOND : angle 0.57578 ( 56) hydrogen bonds : bond 0.03517 ( 657) hydrogen bonds : angle 4.01580 ( 2175) link_NAG-ASN : bond 0.00273 ( 4) link_NAG-ASN : angle 0.71782 ( 12) *********************** 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 168 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.652 Fit side-chains REVERT: A 88 MET cc_start: 0.8298 (tpp) cc_final: 0.8079 (ttp) REVERT: A 128 GLN cc_start: 0.8979 (tp40) cc_final: 0.8490 (tp40) REVERT: B 88 MET cc_start: 0.8296 (tpp) cc_final: 0.8087 (ttp) REVERT: B 128 GLN cc_start: 0.8981 (tp40) cc_final: 0.8495 (tp40) REVERT: C 88 MET cc_start: 0.8297 (tpp) cc_final: 0.8090 (ttp) REVERT: C 128 GLN cc_start: 0.8977 (tp40) cc_final: 0.8491 (tp40) REVERT: D 88 MET cc_start: 0.8290 (tpp) cc_final: 0.8087 (ttp) REVERT: D 128 GLN cc_start: 0.8973 (tp40) cc_final: 0.8487 (tp40) outliers start: 12 outliers final: 12 residues processed: 160 average time/residue: 0.1424 time to fit residues: 33.5950 Evaluate side-chains 164 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 561 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 365 MET 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 50 optimal weight: 10.0000 chunk 152 optimal weight: 0.6980 chunk 129 optimal weight: 0.8980 chunk 118 optimal weight: 0.0670 chunk 3 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 196 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 161 optimal weight: 0.0970 chunk 192 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 overall best weight: 0.3074 ------------------------------------------------------------------------------- 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 = 0.3555 r_free = 0.3555 target = 0.133961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.104849 restraints weight = 17664.810| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.17 r_work: 0.3058 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15184 Z= 0.084 Angle : 0.459 6.208 20712 Z= 0.243 Chirality : 0.044 0.141 2376 Planarity : 0.004 0.038 2636 Dihedral : 3.810 14.630 2240 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.57 % Allowed : 8.52 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.19), residues: 1976 helix: 3.79 (0.29), residues: 292 sheet: 0.73 (0.18), residues: 792 loop : -1.09 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 509 TYR 0.009 0.001 TYR A 414 PHE 0.011 0.001 PHE D 523 TRP 0.006 0.001 TRP B 318 HIS 0.004 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00187 (15152) covalent geometry : angle 0.45823 (20644) SS BOND : bond 0.00262 ( 28) SS BOND : angle 0.62495 ( 56) hydrogen bonds : bond 0.03132 ( 657) hydrogen bonds : angle 3.89298 ( 2175) link_NAG-ASN : bond 0.00319 ( 4) link_NAG-ASN : angle 0.73843 ( 12) ********************** 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 168 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 0.605 Fit side-chains REVERT: A 128 GLN cc_start: 0.8979 (tp40) cc_final: 0.8502 (tp40) REVERT: B 128 GLN cc_start: 0.8975 (tp40) cc_final: 0.8498 (tp40) REVERT: C 128 GLN cc_start: 0.8973 (tp40) cc_final: 0.8496 (tp40) REVERT: D 128 GLN cc_start: 0.8974 (tp40) cc_final: 0.8499 (tp40) outliers start: 8 outliers final: 8 residues processed: 160 average time/residue: 0.1417 time to fit residues: 33.3303 Evaluate side-chains 160 residues out of total 1796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 152 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain D residue 365 MET 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 168 optimal weight: 0.7980 chunk 197 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 129 optimal weight: 0.9990 chunk 104 optimal weight: 0.0470 chunk 57 optimal weight: 0.7980 chunk 72 optimal weight: 0.0770 chunk 152 optimal weight: 0.7980 chunk 179 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 overall best weight: 0.4636 ------------------------------------------------------------------------------- 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 = 0.133472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.104354 restraints weight = 17755.688| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.18 r_work: 0.3054 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15184 Z= 0.096 Angle : 0.464 5.126 20712 Z= 0.246 Chirality : 0.044 0.136 2376 Planarity : 0.004 0.036 2636 Dihedral : 3.791 14.807 2240 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.57 % Allowed : 9.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.19), residues: 1976 helix: 3.79 (0.29), residues: 292 sheet: 0.73 (0.18), residues: 792 loop : -1.17 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 509 TYR 0.011 0.001 TYR C 414 PHE 0.012 0.001 PHE B 523 TRP 0.004 0.001 TRP B 318 HIS 0.001 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00223 (15152) covalent geometry : angle 0.46278 (20644) SS BOND : bond 0.00166 ( 28) SS BOND : angle 0.61614 ( 56) hydrogen bonds : bond 0.03233 ( 657) hydrogen bonds : angle 3.89899 ( 2175) link_NAG-ASN : bond 0.00194 ( 4) link_NAG-ASN : angle 0.83659 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3944.79 seconds wall clock time: 68 minutes 10.03 seconds (4090.03 seconds total)