Starting phenix.real_space_refine on Fri Sep 27 03:34:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vwp_43593/09_2024/8vwp_43593.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vwp_43593/09_2024/8vwp_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vwp_43593/09_2024/8vwp_43593.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vwp_43593/09_2024/8vwp_43593.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vwp_43593/09_2024/8vwp_43593.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vwp_43593/09_2024/8vwp_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-5461/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: 9.15, 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: 3.56 Conformation dependent library (CDL) restraints added in 2.0 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: 2.51 Creating SS restraints... Processing helix chain 'A' and resid 75 through 99 removed outlier: 3.766A pdb=" N ASN A 83 " --> pdb=" O GLN A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 113 Processing helix chain 'A' and resid 113 through 142 removed outlier: 3.518A pdb=" N THR A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 170 removed outlier: 3.880A pdb=" N ASP A 169 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 391 through 399 Processing helix chain 'A' and resid 400 through 405 removed outlier: 7.185A pdb=" N PHE A 403 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY A 404 " --> pdb=" O MET A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 423 Processing helix chain 'A' and resid 433 through 437 removed outlier: 3.810A pdb=" N SER A 437 " --> pdb=" O PRO A 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 99 removed outlier: 3.766A pdb=" N ASN B 83 " --> pdb=" O GLN B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 113 Processing helix chain 'B' and resid 113 through 142 removed outlier: 3.518A pdb=" N THR B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 170 removed outlier: 3.880A pdb=" N ASP B 169 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'B' and resid 391 through 399 Processing helix chain 'B' and resid 400 through 405 removed outlier: 7.185A pdb=" N PHE B 403 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY B 404 " --> pdb=" O MET B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 423 Processing helix chain 'B' and resid 433 through 437 removed outlier: 3.810A pdb=" N SER B 437 " --> pdb=" O PRO B 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 99 removed outlier: 3.766A pdb=" N ASN C 83 " --> pdb=" O GLN C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 113 Processing helix chain 'C' and resid 113 through 142 removed outlier: 3.518A pdb=" N THR C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 170 removed outlier: 3.880A pdb=" N ASP C 169 " --> pdb=" O ASP C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 391 through 399 Processing helix chain 'C' and resid 400 through 405 removed outlier: 7.185A pdb=" N PHE C 403 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY C 404 " --> pdb=" O MET C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 423 Processing helix chain 'C' and resid 433 through 437 removed outlier: 3.810A pdb=" N SER C 437 " --> pdb=" O PRO C 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 99 removed outlier: 3.766A pdb=" N ASN D 83 " --> pdb=" O GLN D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 113 Processing helix chain 'D' and resid 113 through 142 removed outlier: 3.518A pdb=" N THR D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 170 removed outlier: 3.880A pdb=" N ASP D 169 " --> pdb=" O ASP D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 391 through 399 Processing helix chain 'D' and resid 400 through 405 removed outlier: 7.185A pdb=" N PHE D 403 " --> pdb=" O VAL D 400 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY D 404 " --> pdb=" O MET D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 423 Processing helix chain 'D' and resid 433 through 437 removed outlier: 3.810A pdb=" N SER D 437 " --> pdb=" O PRO D 434 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 178 removed outlier: 5.547A pdb=" N ILE A 561 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG A 584 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER A 563 " --> pdb=" O GLU A 582 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 582 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE A 575 " --> pdb=" O VAL A 600 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 177 through 178 removed outlier: 5.547A pdb=" N ILE A 561 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG A 584 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER A 563 " --> pdb=" O GLU A 582 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 582 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE A 575 " --> pdb=" O VAL A 600 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 218 through 227 removed outlier: 5.516A pdb=" N TYR A 220 " --> pdb=" O ARG A 239 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG A 239 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASN A 222 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU A 237 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR A 232 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU A 255 " --> pdb=" O TYR A 232 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE A 234 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE A 253 " --> pdb=" O PHE A 234 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN A 236 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE A 251 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE A 238 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ARG A 257 " --> pdb=" O PRO A 270 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL A 259 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALA A 268 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 282 through 289 removed outlier: 6.824A pdb=" N SER A 299 " --> pdb=" O ASN A 283 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N CYS A 285 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU A 297 " --> pdb=" O CYS A 285 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL A 287 " --> pdb=" O TRP A 295 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TRP A 295 " --> pdb=" O VAL A 287 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 338 through 339 removed outlier: 7.271A pdb=" N GLN A 364 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ILE A 349 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE A 366 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL A 347 " --> pdb=" O PHE A 366 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU A 368 " --> pdb=" O ASP A 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 338 through 339 Processing sheet with id=AA7, first strand: chain 'A' and resid 443 through 448 removed outlier: 4.315A pdb=" N ARG A 466 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 514 through 516 Processing sheet with id=AA9, first strand: chain 'B' and resid 177 through 178 removed outlier: 5.547A pdb=" N ILE B 561 " --> pdb=" O ARG B 584 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG B 584 " --> pdb=" O ILE B 561 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER B 563 " --> pdb=" O GLU B 582 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU B 582 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE B 575 " --> pdb=" O VAL B 600 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 177 through 178 removed outlier: 5.547A pdb=" N ILE B 561 " --> pdb=" O ARG B 584 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG B 584 " --> pdb=" O ILE B 561 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER B 563 " --> pdb=" O GLU B 582 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU B 582 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE B 575 " --> pdb=" O VAL B 600 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 218 through 227 removed outlier: 5.516A pdb=" N TYR B 220 " --> pdb=" O ARG B 239 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG B 239 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASN B 222 " --> pdb=" O GLU B 237 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU B 237 " --> pdb=" O ASN B 222 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR B 232 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU B 255 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE B 234 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE B 253 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN B 236 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE B 251 " --> pdb=" O GLN B 236 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE B 238 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ARG B 257 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL B 259 " --> pdb=" O ALA B 268 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALA B 268 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 282 through 289 removed outlier: 6.824A pdb=" N SER B 299 " --> pdb=" O ASN B 283 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N CYS B 285 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU B 297 " --> pdb=" O CYS B 285 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL B 287 " --> pdb=" O TRP B 295 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TRP B 295 " --> pdb=" O VAL B 287 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 338 through 339 removed outlier: 7.271A pdb=" N GLN B 364 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ILE B 349 " --> pdb=" O GLN B 364 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE B 366 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL B 347 " --> pdb=" O PHE B 366 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU B 368 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 338 through 339 Processing sheet with id=AB6, first strand: chain 'B' and resid 443 through 448 removed outlier: 4.315A pdb=" N ARG B 466 " --> pdb=" O LEU B 456 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 514 through 516 Processing sheet with id=AB8, first strand: chain 'C' and resid 177 through 178 removed outlier: 5.547A pdb=" N ILE C 561 " --> pdb=" O ARG C 584 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG C 584 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER C 563 " --> pdb=" O GLU C 582 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU C 582 " --> pdb=" O SER C 563 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE C 575 " --> pdb=" O VAL C 600 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 177 through 178 removed outlier: 5.547A pdb=" N ILE C 561 " --> pdb=" O ARG C 584 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG C 584 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER C 563 " --> pdb=" O GLU C 582 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU C 582 " --> pdb=" O SER C 563 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE C 575 " --> pdb=" O VAL C 600 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 218 through 227 removed outlier: 5.516A pdb=" N TYR C 220 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG C 239 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASN C 222 " --> pdb=" O GLU C 237 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU C 237 " --> pdb=" O ASN C 222 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR C 232 " --> pdb=" O LEU C 255 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU C 255 " --> pdb=" O TYR C 232 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE C 234 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE C 253 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN C 236 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE C 251 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE C 238 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ARG C 257 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL C 259 " --> pdb=" O ALA C 268 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALA C 268 " --> pdb=" O VAL C 259 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 282 through 289 removed outlier: 6.824A pdb=" N SER C 299 " --> pdb=" O ASN C 283 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N CYS C 285 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU C 297 " --> pdb=" O CYS C 285 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL C 287 " --> pdb=" O TRP C 295 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TRP C 295 " --> pdb=" O VAL C 287 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 338 through 339 removed outlier: 7.271A pdb=" N GLN C 364 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ILE C 349 " --> pdb=" O GLN C 364 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE C 366 " --> pdb=" O VAL C 347 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL C 347 " --> pdb=" O PHE C 366 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU C 368 " --> pdb=" O ASP C 345 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 338 through 339 Processing sheet with id=AC5, first strand: chain 'C' and resid 443 through 448 removed outlier: 4.315A pdb=" N ARG C 466 " --> pdb=" O LEU C 456 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 514 through 516 Processing sheet with id=AC7, first strand: chain 'D' and resid 177 through 178 removed outlier: 5.547A pdb=" N ILE D 561 " --> pdb=" O ARG D 584 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG D 584 " --> pdb=" O ILE D 561 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER D 563 " --> pdb=" O GLU D 582 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU D 582 " --> pdb=" O SER D 563 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE D 575 " --> pdb=" O VAL D 600 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 177 through 178 removed outlier: 5.547A pdb=" N ILE D 561 " --> pdb=" O ARG D 584 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG D 584 " --> pdb=" O ILE D 561 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER D 563 " --> pdb=" O GLU D 582 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU D 582 " --> pdb=" O SER D 563 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE D 575 " --> pdb=" O VAL D 600 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 218 through 227 removed outlier: 5.516A pdb=" N TYR D 220 " --> pdb=" O ARG D 239 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG D 239 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASN D 222 " --> pdb=" O GLU D 237 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU D 237 " --> pdb=" O ASN D 222 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR D 232 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU D 255 " --> pdb=" O TYR D 232 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE D 234 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE D 253 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN D 236 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE D 251 " --> pdb=" O GLN D 236 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE D 238 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ARG D 257 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL D 259 " --> pdb=" O ALA D 268 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALA D 268 " --> pdb=" O VAL D 259 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 282 through 289 removed outlier: 6.824A pdb=" N SER D 299 " --> pdb=" O ASN D 283 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N CYS D 285 " --> pdb=" O LEU D 297 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU D 297 " --> pdb=" O CYS D 285 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL D 287 " --> pdb=" O TRP D 295 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TRP D 295 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 338 through 339 removed outlier: 7.271A pdb=" N GLN D 364 " --> pdb=" O ILE D 349 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ILE D 349 " --> pdb=" O GLN D 364 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE D 366 " --> pdb=" O VAL D 347 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL D 347 " --> pdb=" O PHE D 366 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU D 368 " --> pdb=" O ASP D 345 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 338 through 339 Processing sheet with id=AD4, first strand: chain 'D' and resid 443 through 448 removed outlier: 4.315A pdb=" N ARG D 466 " --> pdb=" O LEU D 456 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 514 through 516 805 hydrogen bonds defined for protein. 2175 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.76 Time building geometry restraints manager: 4.19 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: 0.00 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: 0.000 Normalize map: mean=0, sd=1: 7.600 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: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 36.670 Find NCS groups from input model: 0.540 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: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.440 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 1.675 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: 0.2957 time to fit residues: 100.9054 Evaluate side-chains 152 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.663 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 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 fitting. rotamer outliers: 21 poor density : 155 time to evaluate : 1.710 Fit side-chains REVERT: A 561 ILE cc_start: 0.8633 (mm) cc_final: 0.8428 (tp) REVERT: B 561 ILE cc_start: 0.8634 (mm) cc_final: 0.8431 (tp) REVERT: C 561 ILE cc_start: 0.8634 (mm) cc_final: 0.8433 (tp) outliers start: 21 outliers final: 12 residues processed: 168 average time/residue: 0.2976 time to fit residues: 71.7232 Evaluate side-chains 147 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 1.678 ------------------------------------------------------------------------------- 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 100 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 123 optimal weight: 0.2980 chunk 50 optimal weight: 4.9990 chunk 181 optimal weight: 0.8980 chunk 196 optimal weight: 0.5980 chunk 162 optimal weight: 0.7980 chunk 180 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 145 optimal weight: 0.0010 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15152 Z= 0.172 Angle : 0.517 7.068 20644 Z= 0.278 Chirality : 0.045 0.137 2376 Planarity : 0.004 0.031 2636 Dihedral : 4.337 18.769 2240 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.93 % Allowed : 5.16 % 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: 1.03 (0.18), residues: 1976 helix: 3.43 (0.28), residues: 296 sheet: 0.94 (0.18), residues: 764 loop : -0.46 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 318 HIS 0.002 0.001 HIS C 596 PHE 0.015 0.002 PHE D 523 TYR 0.012 0.001 TYR D 414 ARG 0.001 0.000 ARG A 509 *********************** 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 170 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 157 time to evaluate : 1.597 Fit side-chains REVERT: B 501 MET cc_start: 0.7440 (tpp) cc_final: 0.7072 (mpp) REVERT: C 501 MET cc_start: 0.7448 (tpp) cc_final: 0.7071 (mpp) REVERT: D 501 MET cc_start: 0.7449 (tpp) cc_final: 0.7078 (mpp) outliers start: 13 outliers final: 7 residues processed: 165 average time/residue: 0.2960 time to fit residues: 70.1384 Evaluate side-chains 143 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 136 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain C residue 520 ASP Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain D residue 520 ASP 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 179 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 193 optimal weight: 0.9980 chunk 95 optimal weight: 0.0020 chunk 173 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15152 Z= 0.214 Angle : 0.519 4.788 20644 Z= 0.280 Chirality : 0.046 0.146 2376 Planarity : 0.004 0.037 2636 Dihedral : 4.231 18.023 2240 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.51 % Allowed : 4.15 % Favored : 93.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.90 (0.19), residues: 1976 helix: 3.41 (0.28), residues: 296 sheet: 0.93 (0.18), residues: 764 loop : -0.66 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 274 HIS 0.003 0.001 HIS A 194 PHE 0.017 0.002 PHE D 523 TYR 0.016 0.002 TYR A 414 ARG 0.001 0.000 ARG A 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 175 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 140 time to evaluate : 1.783 Fit side-chains REVERT: A 501 MET cc_start: 0.7581 (tpp) cc_final: 0.7176 (mpp) REVERT: B 501 MET cc_start: 0.7741 (tpp) cc_final: 0.7466 (mpp) REVERT: C 501 MET cc_start: 0.7747 (tpp) cc_final: 0.7468 (mpp) REVERT: D 501 MET cc_start: 0.7747 (tpp) cc_final: 0.7474 (mpp) outliers start: 35 outliers final: 23 residues processed: 159 average time/residue: 0.2803 time to fit residues: 65.5938 Evaluate side-chains 158 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL 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 90 VAL 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 90 VAL 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 90 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 0.7980 chunk 173 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 ASN ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 ASN ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 ASN ** D 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 589 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15152 Z= 0.211 Angle : 0.498 4.810 20644 Z= 0.269 Chirality : 0.045 0.148 2376 Planarity : 0.004 0.038 2636 Dihedral : 4.114 15.236 2240 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.72 % Allowed : 5.66 % Favored : 92.62 % 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: 0.80 (0.19), residues: 1976 helix: 3.49 (0.28), residues: 292 sheet: 0.88 (0.18), residues: 764 loop : -0.79 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 274 HIS 0.003 0.001 HIS D 194 PHE 0.015 0.002 PHE A 523 TYR 0.013 0.001 TYR D 414 ARG 0.002 0.000 ARG A 398 *********************** 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 166 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 142 time to evaluate : 1.635 Fit side-chains outliers start: 24 outliers final: 12 residues processed: 154 average time/residue: 0.2637 time to fit residues: 61.4773 Evaluate side-chains 143 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 131 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 VAL 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 520 ASP Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain C residue 259 VAL 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 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 65 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 160 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN B 412 ASN C 412 ASN D 412 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15152 Z= 0.235 Angle : 0.508 4.848 20644 Z= 0.274 Chirality : 0.046 0.143 2376 Planarity : 0.004 0.042 2636 Dihedral : 4.153 16.113 2240 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % 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: 0.69 (0.19), residues: 1976 helix: 3.48 (0.28), residues: 292 sheet: 0.80 (0.18), residues: 764 loop : -0.88 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 274 HIS 0.003 0.001 HIS D 194 PHE 0.014 0.002 PHE D 523 TYR 0.013 0.002 TYR A 571 ARG 0.002 0.000 ARG D 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 168 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 138 time to evaluate : 1.728 Fit side-chains outliers start: 30 outliers final: 22 residues processed: 150 average time/residue: 0.2697 time to fit residues: 61.4390 Evaluate side-chains 159 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 137 time to evaluate : 1.725 ------------------------------------------------------------------------------- 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 A residue 562 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain C residue 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 C residue 562 THR Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 365 MET Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 520 ASP Chi-restraints excluded: chain D residue 562 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 141 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 chunk 162 optimal weight: 0.0020 chunk 108 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15152 Z= 0.169 Angle : 0.471 4.833 20644 Z= 0.254 Chirality : 0.044 0.143 2376 Planarity : 0.004 0.041 2636 Dihedral : 3.981 14.650 2240 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.36 % Allowed : 7.23 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.19), residues: 1976 helix: 3.51 (0.29), residues: 292 sheet: 0.76 (0.18), residues: 772 loop : -0.91 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 274 HIS 0.002 0.001 HIS D 194 PHE 0.013 0.001 PHE B 523 TYR 0.011 0.001 TYR D 571 ARG 0.002 0.000 ARG D 509 *********************** 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 159 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 140 time to evaluate : 1.981 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 144 average time/residue: 0.2651 time to fit residues: 58.2638 Evaluate side-chains 147 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 136 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 520 ASP Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 365 MET 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 119 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 151 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3018 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= 0.221 Angle : 0.491 4.855 20644 Z= 0.265 Chirality : 0.045 0.140 2376 Planarity : 0.004 0.042 2636 Dihedral : 4.028 14.985 2240 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.86 % Allowed : 6.95 % 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: 0.61 (0.19), residues: 1976 helix: 3.47 (0.29), residues: 292 sheet: 0.76 (0.18), residues: 772 loop : -0.97 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 274 HIS 0.003 0.001 HIS B 194 PHE 0.013 0.002 PHE C 523 TYR 0.013 0.001 TYR C 571 ARG 0.001 0.000 ARG C 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 166 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 1.762 Fit side-chains outliers start: 26 outliers final: 25 residues processed: 154 average time/residue: 0.2558 time to fit residues: 59.8909 Evaluate side-chains 165 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU 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 85 LEU Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain C residue 219 CYS Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 520 ASP Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 365 MET Chi-restraints excluded: chain D residue 479 THR Chi-restraints excluded: chain D residue 520 ASP Chi-restraints excluded: chain D residue 561 ILE Chi-restraints excluded: chain D residue 562 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 0.9980 chunk 168 optimal weight: 0.0970 chunk 179 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 169 optimal weight: 0.7980 chunk 117 optimal weight: 0.8980 chunk 189 optimal weight: 0.0000 overall best weight: 0.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3093 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= 0.148 Angle : 0.458 4.851 20644 Z= 0.246 Chirality : 0.044 0.134 2376 Planarity : 0.004 0.041 2636 Dihedral : 3.881 14.607 2240 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.00 % Allowed : 8.09 % 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 (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: 0.70 (0.19), residues: 1976 helix: 3.57 (0.29), residues: 292 sheet: 0.78 (0.18), residues: 792 loop : -0.94 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 274 HIS 0.002 0.001 HIS B 194 PHE 0.012 0.001 PHE D 523 TYR 0.013 0.001 TYR A 132 ARG 0.002 0.000 ARG A 398 *********************** 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 159 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 145 time to evaluate : 1.673 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 152 average time/residue: 0.2614 time to fit residues: 60.2746 Evaluate side-chains 149 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 139 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 365 MET 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 85 LEU Chi-restraints excluded: chain D residue 219 CYS 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 115 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 199 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN B 128 GLN C 128 GLN D 128 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 15152 Z= 0.384 Angle : 0.585 6.035 20644 Z= 0.314 Chirality : 0.048 0.138 2376 Planarity : 0.004 0.046 2636 Dihedral : 4.328 16.143 2240 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.15 % Allowed : 7.66 % Favored : 90.19 % 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: 0.29 (0.19), residues: 1976 helix: 3.09 (0.29), residues: 296 sheet: 0.59 (0.19), residues: 764 loop : -1.18 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 480 HIS 0.004 0.002 HIS A 194 PHE 0.015 0.002 PHE D 523 TYR 0.018 0.002 TYR A 571 ARG 0.002 0.000 ARG B 257 ********************** 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 162 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 132 time to evaluate : 1.697 Fit side-chains outliers start: 30 outliers final: 23 residues processed: 147 average time/residue: 0.2657 time to fit residues: 59.0939 Evaluate side-chains 155 residues out of total 1796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 1.692 ------------------------------------------------------------------------------- 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 562 THR Chi-restraints excluded: chain B residue 85 LEU 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 562 THR Chi-restraints excluded: chain C residue 85 LEU 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 562 THR Chi-restraints excluded: chain D residue 85 LEU 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 562 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 chunk 20 optimal weight: 0.0270 chunk 29 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 = 0.3515 r_free = 0.3515 target = 0.131001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.101610 restraints weight = 17858.792| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.20 r_work: 0.3023 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15152 Z= 0.198 Angle : 0.510 6.340 20644 Z= 0.272 Chirality : 0.045 0.134 2376 Planarity : 0.004 0.044 2636 Dihedral : 4.148 15.545 2240 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.36 % Allowed : 9.03 % Favored : 89.61 % 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: 0.41 (0.19), residues: 1976 helix: 3.27 (0.29), residues: 296 sheet: 0.59 (0.18), residues: 784 loop : -1.08 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 274 HIS 0.002 0.001 HIS C 194 PHE 0.013 0.002 PHE D 523 TYR 0.018 0.001 TYR D 464 ARG 0.001 0.000 ARG C 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3050.33 seconds wall clock time: 57 minutes 35.76 seconds (3455.76 seconds total)