Starting phenix.real_space_refine on Sun Jun 15 01:32:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fsz_29422/06_2025/8fsz_29422.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fsz_29422/06_2025/8fsz_29422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fsz_29422/06_2025/8fsz_29422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fsz_29422/06_2025/8fsz_29422.map" model { file = "/net/cci-nas-00/data/ceres_data/8fsz_29422/06_2025/8fsz_29422.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fsz_29422/06_2025/8fsz_29422.cif" } resolution = 3.79 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= 0.000 sd= 0.003 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 45 5.16 5 C 10990 2.51 5 N 2710 2.21 5 O 2945 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16690 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3273 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Chain: "B" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3273 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 88 Unusual residues: {'NAG': 3, 'Y7H': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 65 Unusual residues: {'NAG': 3, 'Y7H': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'Y7H': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'Y7H': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, D, E Time building chain proxies: 9.95, per 1000 atoms: 0.60 Number of scatterers: 16690 At special positions: 0 Unit cell: (100.1, 97.9, 170.5, 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 45 16.00 O 2945 8.00 N 2710 7.00 C 10990 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " 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 502 " - " ASN A 82 " " NAG A 503 " - " ASN A 148 " " NAG A 504 " - " ASN A 164 " " NAG B 501 " - " ASN B 82 " " NAG B 502 " - " ASN B 148 " " NAG B 503 " - " ASN B 164 " " NAG C 501 " - " ASN C 82 " " NAG C 502 " - " ASN C 148 " " NAG C 503 " - " ASN C 164 " " NAG D 501 " - " ASN D 82 " " NAG D 502 " - " ASN D 148 " " NAG D 503 " - " ASN D 164 " " NAG E 501 " - " ASN E 82 " " NAG E 502 " - " ASN E 148 " " NAG E 503 " - " ASN E 164 " Time building additional restraints: 4.54 Conformation dependent library (CDL) restraints added in 2.2 seconds 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 15 sheets defined 44.6% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 220 through 234 removed outlier: 3.550A pdb=" N SER A 226 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 236 through 241 Processing helix chain 'A' and resid 247 through 262 removed outlier: 4.307A pdb=" N LEU A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 removed outlier: 3.955A pdb=" N ILE A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 310 removed outlier: 4.202A pdb=" N VAL A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS A 310 " --> pdb=" O ARG A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 332 Processing helix chain 'A' and resid 398 through 425 removed outlier: 3.716A pdb=" N ILE A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N HIS A 411 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ARG A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLU A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 462 removed outlier: 4.051A pdb=" N TYR A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ARG A 435 " --> pdb=" O TYR A 431 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 436 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 20 Processing helix chain 'B' and resid 170 through 176 Processing helix chain 'B' and resid 220 through 234 removed outlier: 3.550A pdb=" N SER B 226 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 236 through 241 Processing helix chain 'B' and resid 247 through 262 removed outlier: 4.306A pdb=" N LEU B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 273 removed outlier: 3.955A pdb=" N ILE B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 310 removed outlier: 4.203A pdb=" N VAL B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET B 291 " --> pdb=" O PHE B 287 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS B 310 " --> pdb=" O ARG B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 332 Processing helix chain 'B' and resid 398 through 425 removed outlier: 3.715A pdb=" N ILE B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HIS B 411 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET B 419 " --> pdb=" O LYS B 415 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ARG B 420 " --> pdb=" O ARG B 416 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLU B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL B 422 " --> pdb=" O GLU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 462 removed outlier: 4.050A pdb=" N TYR B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ARG B 435 " --> pdb=" O TYR B 431 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 436 " --> pdb=" O VAL B 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 20 Processing helix chain 'C' and resid 170 through 176 Processing helix chain 'C' and resid 220 through 234 removed outlier: 3.550A pdb=" N SER C 226 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Proline residue: C 230 - end of helix Processing helix chain 'C' and resid 236 through 241 Processing helix chain 'C' and resid 247 through 262 removed outlier: 4.307A pdb=" N LEU C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 273 removed outlier: 3.956A pdb=" N ILE C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE C 268 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 310 removed outlier: 4.203A pdb=" N VAL C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET C 291 " --> pdb=" O PHE C 287 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS C 310 " --> pdb=" O ARG C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 332 Processing helix chain 'C' and resid 398 through 425 removed outlier: 3.716A pdb=" N ILE C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG C 410 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HIS C 411 " --> pdb=" O SER C 407 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE C 412 " --> pdb=" O SER C 408 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ARG C 420 " --> pdb=" O ARG C 416 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLU C 421 " --> pdb=" O ASP C 417 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL C 422 " --> pdb=" O GLU C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 462 removed outlier: 4.050A pdb=" N TYR C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ARG C 435 " --> pdb=" O TYR C 431 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU C 436 " --> pdb=" O VAL C 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 20 Processing helix chain 'D' and resid 170 through 176 Processing helix chain 'D' and resid 220 through 234 removed outlier: 3.550A pdb=" N SER D 226 " --> pdb=" O PHE D 222 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Proline residue: D 230 - end of helix Processing helix chain 'D' and resid 236 through 241 Processing helix chain 'D' and resid 247 through 262 removed outlier: 4.306A pdb=" N LEU D 260 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR D 262 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 273 removed outlier: 3.955A pdb=" N ILE D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE D 268 " --> pdb=" O VAL D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 310 removed outlier: 4.202A pdb=" N VAL D 288 " --> pdb=" O GLY D 284 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET D 291 " --> pdb=" O PHE D 287 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS D 310 " --> pdb=" O ARG D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 332 Processing helix chain 'D' and resid 398 through 425 removed outlier: 3.716A pdb=" N ILE D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG D 410 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N HIS D 411 " --> pdb=" O SER D 407 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE D 412 " --> pdb=" O SER D 408 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET D 419 " --> pdb=" O LYS D 415 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ARG D 420 " --> pdb=" O ARG D 416 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLU D 421 " --> pdb=" O ASP D 417 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL D 422 " --> pdb=" O GLU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 462 removed outlier: 4.051A pdb=" N TYR D 431 " --> pdb=" O LEU D 427 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ARG D 435 " --> pdb=" O TYR D 431 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU D 436 " --> pdb=" O VAL D 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 20 Processing helix chain 'E' and resid 170 through 176 Processing helix chain 'E' and resid 220 through 234 removed outlier: 3.550A pdb=" N SER E 226 " --> pdb=" O PHE E 222 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU E 229 " --> pdb=" O VAL E 225 " (cutoff:3.500A) Proline residue: E 230 - end of helix Processing helix chain 'E' and resid 236 through 241 Processing helix chain 'E' and resid 247 through 262 removed outlier: 4.307A pdb=" N LEU E 260 " --> pdb=" O ILE E 256 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR E 262 " --> pdb=" O LEU E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 273 removed outlier: 3.955A pdb=" N ILE E 267 " --> pdb=" O SER E 263 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE E 268 " --> pdb=" O VAL E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 310 removed outlier: 4.203A pdb=" N VAL E 288 " --> pdb=" O GLY E 284 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET E 291 " --> pdb=" O PHE E 287 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS E 310 " --> pdb=" O ARG E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 332 Processing helix chain 'E' and resid 398 through 425 removed outlier: 3.715A pdb=" N ILE E 409 " --> pdb=" O GLU E 405 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG E 410 " --> pdb=" O LEU E 406 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N HIS E 411 " --> pdb=" O SER E 407 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE E 412 " --> pdb=" O SER E 408 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET E 419 " --> pdb=" O LYS E 415 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ARG E 420 " --> pdb=" O ARG E 416 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLU E 421 " --> pdb=" O ASP E 417 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL E 422 " --> pdb=" O GLU E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 462 removed outlier: 4.051A pdb=" N TYR E 431 " --> pdb=" O LEU E 427 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ARG E 435 " --> pdb=" O TYR E 431 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU E 436 " --> pdb=" O VAL E 432 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 133 removed outlier: 3.909A pdb=" N ASN A 50 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N TYR A 61 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE A 48 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N TRP A 63 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N TYR A 46 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ARG A 65 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ILE A 44 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N TYR A 67 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASP A 42 " --> pdb=" O TYR A 67 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 41 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 89 Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.682A pdb=" N THR A 154 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 129 through 133 removed outlier: 3.909A pdb=" N ASN B 50 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N TYR B 61 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE B 48 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N TRP B 63 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N TYR B 46 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N ARG B 65 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ILE B 44 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N TYR B 67 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASP B 42 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 41 " --> pdb=" O THR B 166 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 85 through 89 Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 100 removed outlier: 3.682A pdb=" N THR B 154 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 129 through 133 removed outlier: 3.909A pdb=" N ASN C 50 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N TYR C 61 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE C 48 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N TRP C 63 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N TYR C 46 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ARG C 65 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ILE C 44 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N TYR C 67 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASP C 42 " --> pdb=" O TYR C 67 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE C 41 " --> pdb=" O THR C 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 85 through 89 Processing sheet with id=AA9, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.682A pdb=" N THR C 154 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 129 through 133 removed outlier: 3.909A pdb=" N ASN D 50 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N TYR D 61 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE D 48 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N TRP D 63 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N TYR D 46 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ARG D 65 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ILE D 44 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N TYR D 67 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASP D 42 " --> pdb=" O TYR D 67 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE D 41 " --> pdb=" O THR D 166 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 85 through 89 Processing sheet with id=AB3, first strand: chain 'D' and resid 98 through 100 removed outlier: 3.682A pdb=" N THR D 154 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 129 through 133 removed outlier: 3.909A pdb=" N ASN E 50 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N TYR E 61 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE E 48 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N TRP E 63 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N TYR E 46 " --> pdb=" O TRP E 63 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ARG E 65 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ILE E 44 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N TYR E 67 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASP E 42 " --> pdb=" O TYR E 67 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE E 41 " --> pdb=" O THR E 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 85 through 89 Processing sheet with id=AB6, first strand: chain 'E' and resid 98 through 100 removed outlier: 3.683A pdb=" N THR E 154 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU E 191 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) 745 hydrogen bonds defined for protein. 2190 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: 4.94 Time building geometry restraints manager: 5.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2692 1.32 - 1.44: 4848 1.44 - 1.56: 9550 1.56 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 17160 Sorted by residual: bond pdb=" CA ARG C 28 " pdb=" C ARG C 28 " ideal model delta sigma weight residual 1.527 1.476 0.051 1.02e-02 9.61e+03 2.50e+01 bond pdb=" CA ARG A 28 " pdb=" C ARG A 28 " ideal model delta sigma weight residual 1.527 1.477 0.050 1.02e-02 9.61e+03 2.43e+01 bond pdb=" CA ARG E 28 " pdb=" C ARG E 28 " ideal model delta sigma weight residual 1.527 1.477 0.050 1.02e-02 9.61e+03 2.41e+01 bond pdb=" CA ARG B 28 " pdb=" C ARG B 28 " ideal model delta sigma weight residual 1.527 1.477 0.050 1.02e-02 9.61e+03 2.38e+01 bond pdb=" CA ARG D 28 " pdb=" C ARG D 28 " ideal model delta sigma weight residual 1.527 1.478 0.049 1.02e-02 9.61e+03 2.34e+01 ... (remaining 17155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 22162 2.27 - 4.55: 1113 4.55 - 6.82: 145 6.82 - 9.09: 30 9.09 - 11.36: 10 Bond angle restraints: 23460 Sorted by residual: angle pdb=" N ARG B 28 " pdb=" CA ARG B 28 " pdb=" C ARG B 28 " ideal model delta sigma weight residual 109.64 102.08 7.56 1.27e+00 6.20e-01 3.54e+01 angle pdb=" N ARG E 28 " pdb=" CA ARG E 28 " pdb=" C ARG E 28 " ideal model delta sigma weight residual 109.64 102.10 7.54 1.27e+00 6.20e-01 3.53e+01 angle pdb=" N ARG C 28 " pdb=" CA ARG C 28 " pdb=" C ARG C 28 " ideal model delta sigma weight residual 109.64 102.10 7.54 1.27e+00 6.20e-01 3.52e+01 angle pdb=" N ARG A 28 " pdb=" CA ARG A 28 " pdb=" C ARG A 28 " ideal model delta sigma weight residual 109.64 102.11 7.53 1.27e+00 6.20e-01 3.52e+01 angle pdb=" N ARG D 28 " pdb=" CA ARG D 28 " pdb=" C ARG D 28 " ideal model delta sigma weight residual 109.64 102.11 7.53 1.27e+00 6.20e-01 3.52e+01 ... (remaining 23455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 9420 17.93 - 35.85: 800 35.85 - 53.78: 130 53.78 - 71.71: 20 71.71 - 89.64: 20 Dihedral angle restraints: 10390 sinusoidal: 4495 harmonic: 5895 Sorted by residual: dihedral pdb=" C PHE D 242 " pdb=" N PHE D 242 " pdb=" CA PHE D 242 " pdb=" CB PHE D 242 " ideal model delta harmonic sigma weight residual -122.60 -131.75 9.15 0 2.50e+00 1.60e-01 1.34e+01 dihedral pdb=" C PHE C 242 " pdb=" N PHE C 242 " pdb=" CA PHE C 242 " pdb=" CB PHE C 242 " ideal model delta harmonic sigma weight residual -122.60 -131.69 9.09 0 2.50e+00 1.60e-01 1.32e+01 dihedral pdb=" C PHE B 242 " pdb=" N PHE B 242 " pdb=" CA PHE B 242 " pdb=" CB PHE B 242 " ideal model delta harmonic sigma weight residual -122.60 -131.68 9.08 0 2.50e+00 1.60e-01 1.32e+01 ... (remaining 10387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2140 0.064 - 0.129: 519 0.129 - 0.193: 76 0.193 - 0.257: 10 0.257 - 0.322: 5 Chirality restraints: 2750 Sorted by residual: chirality pdb=" CA PHE D 242 " pdb=" N PHE D 242 " pdb=" C PHE D 242 " pdb=" CB PHE D 242 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA PHE B 242 " pdb=" N PHE B 242 " pdb=" C PHE B 242 " pdb=" CB PHE B 242 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA PHE C 242 " pdb=" N PHE C 242 " pdb=" C PHE C 242 " pdb=" CB PHE C 242 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 2747 not shown) Planarity restraints: 2865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 106 " 0.028 2.00e-02 2.50e+03 5.75e-02 3.30e+01 pdb=" C VAL D 106 " -0.099 2.00e-02 2.50e+03 pdb=" O VAL D 106 " 0.038 2.00e-02 2.50e+03 pdb=" N GLY D 107 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 106 " 0.028 2.00e-02 2.50e+03 5.73e-02 3.28e+01 pdb=" C VAL C 106 " -0.099 2.00e-02 2.50e+03 pdb=" O VAL C 106 " 0.038 2.00e-02 2.50e+03 pdb=" N GLY C 107 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 106 " 0.028 2.00e-02 2.50e+03 5.73e-02 3.28e+01 pdb=" C VAL B 106 " -0.099 2.00e-02 2.50e+03 pdb=" O VAL B 106 " 0.038 2.00e-02 2.50e+03 pdb=" N GLY B 107 " 0.033 2.00e-02 2.50e+03 ... (remaining 2862 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 6988 2.93 - 3.43: 16217 3.43 - 3.92: 26445 3.92 - 4.41: 28553 4.41 - 4.90: 47523 Nonbonded interactions: 125726 Sorted by model distance: nonbonded pdb=" N TRP B 63 " pdb=" O TRP B 63 " model vdw 2.443 2.496 nonbonded pdb=" N TRP A 63 " pdb=" O TRP A 63 " model vdw 2.443 2.496 nonbonded pdb=" N TRP C 63 " pdb=" O TRP C 63 " model vdw 2.443 2.496 nonbonded pdb=" N TRP E 63 " pdb=" O TRP E 63 " model vdw 2.443 2.496 nonbonded pdb=" N TRP D 63 " pdb=" O TRP D 63 " model vdw 2.444 2.496 ... (remaining 125721 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' and (resid 7 through 465 or resid 502 through 503)) selection = (chain 'B' and (resid 7 through 465 or resid 502 through 503)) selection = (chain 'C' and (resid 7 through 465 or resid 502 through 503)) selection = (chain 'D' and (resid 7 through 465 or resid 502 through 503)) selection = (chain 'E' and (resid 7 through 465 or resid 502 through 503)) } 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 group one per residue 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: 1.960 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: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 38.910 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.060 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 : 0.007 0.056 17180 Z= 0.505 Angle : 1.065 11.364 23515 Z= 0.646 Chirality : 0.057 0.322 2750 Planarity : 0.006 0.057 2850 Dihedral : 13.520 89.636 6535 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.04 (0.18), residues: 1955 helix: -0.14 (0.17), residues: 825 sheet: -0.99 (0.25), residues: 440 loop : -3.08 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP E 331 HIS 0.003 0.001 HIS A 158 PHE 0.029 0.002 PHE D 265 TYR 0.033 0.002 TYR B 262 ARG 0.004 0.001 ARG B 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00152 ( 15) link_NAG-ASN : angle 2.29821 ( 45) hydrogen bonds : bond 0.15046 ( 745) hydrogen bonds : angle 5.39968 ( 2190) SS BOND : bond 0.00034 ( 5) SS BOND : angle 0.24970 ( 10) covalent geometry : bond 0.00739 (17160) covalent geometry : angle 1.06106 (23460) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 2.125 Fit side-chains REVERT: B 291 MET cc_start: 0.7720 (mmt) cc_final: 0.7307 (mmt) REVERT: C 291 MET cc_start: 0.7903 (mmt) cc_final: 0.6875 (mmt) REVERT: D 291 MET cc_start: 0.7705 (mmt) cc_final: 0.7369 (mmt) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.3965 time to fit residues: 78.7726 Evaluate side-chains 47 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.9990 chunk 147 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 177 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 119 HIS A 311 GLN B 66 GLN B 119 HIS B 311 GLN C 66 GLN C 119 HIS C 311 GLN D 66 GLN D 311 GLN E 66 GLN E 311 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.084135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.060344 restraints weight = 66086.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.060089 restraints weight = 50754.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.060282 restraints weight = 37125.644| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17180 Z= 0.173 Angle : 0.612 8.281 23515 Z= 0.309 Chirality : 0.044 0.186 2750 Planarity : 0.005 0.051 2850 Dihedral : 4.625 18.096 2645 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.54 % Allowed : 9.97 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.12 (0.19), residues: 1955 helix: 0.54 (0.18), residues: 850 sheet: -0.57 (0.24), residues: 440 loop : -2.55 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 331 HIS 0.004 0.001 HIS A 119 PHE 0.015 0.001 PHE B 199 TYR 0.017 0.002 TYR C 262 ARG 0.006 0.001 ARG B 424 Details of bonding type rmsd link_NAG-ASN : bond 0.00046 ( 15) link_NAG-ASN : angle 1.61269 ( 45) hydrogen bonds : bond 0.04048 ( 745) hydrogen bonds : angle 4.04543 ( 2190) SS BOND : bond 0.00073 ( 5) SS BOND : angle 0.34222 ( 10) covalent geometry : bond 0.00387 (17160) covalent geometry : angle 0.60832 (23460) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 2.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 262 TYR cc_start: 0.1970 (p90) cc_final: 0.1767 (p90) outliers start: 10 outliers final: 8 residues processed: 55 average time/residue: 0.3288 time to fit residues: 31.2616 Evaluate side-chains 53 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 3.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 262 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 179 optimal weight: 5.9990 chunk 175 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 187 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 163 optimal weight: 8.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.083599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.059938 restraints weight = 65517.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.059584 restraints weight = 45725.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.059600 restraints weight = 35270.533| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17180 Z= 0.142 Angle : 0.557 7.713 23515 Z= 0.280 Chirality : 0.043 0.128 2750 Planarity : 0.004 0.037 2850 Dihedral : 4.294 16.871 2645 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.36 % Allowed : 11.92 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.20), residues: 1955 helix: 0.92 (0.18), residues: 865 sheet: -0.34 (0.25), residues: 435 loop : -2.26 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 331 HIS 0.003 0.001 HIS E 119 PHE 0.027 0.001 PHE A 265 TYR 0.014 0.001 TYR A 67 ARG 0.004 0.000 ARG C 420 Details of bonding type rmsd link_NAG-ASN : bond 0.00065 ( 15) link_NAG-ASN : angle 1.60180 ( 45) hydrogen bonds : bond 0.03562 ( 745) hydrogen bonds : angle 3.79735 ( 2190) SS BOND : bond 0.00053 ( 5) SS BOND : angle 0.47642 ( 10) covalent geometry : bond 0.00324 (17160) covalent geometry : angle 0.55299 (23460) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 46 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.8501 (m-80) REVERT: A 291 MET cc_start: 0.8204 (mmp) cc_final: 0.7676 (mmp) outliers start: 25 outliers final: 12 residues processed: 69 average time/residue: 0.2860 time to fit residues: 33.7429 Evaluate side-chains 55 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 262 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 137 optimal weight: 7.9990 chunk 189 optimal weight: 7.9990 chunk 176 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.080881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.058029 restraints weight = 66961.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.056907 restraints weight = 53524.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.057095 restraints weight = 41993.597| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 17180 Z= 0.259 Angle : 0.695 6.752 23515 Z= 0.349 Chirality : 0.046 0.139 2750 Planarity : 0.005 0.051 2850 Dihedral : 5.244 22.675 2645 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.90 % Allowed : 13.33 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.89 (0.19), residues: 1955 helix: 0.66 (0.18), residues: 855 sheet: -0.47 (0.25), residues: 440 loop : -2.30 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP D 331 HIS 0.005 0.001 HIS E 119 PHE 0.030 0.002 PHE E 265 TYR 0.021 0.002 TYR D 67 ARG 0.004 0.001 ARG C 420 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 15) link_NAG-ASN : angle 1.80206 ( 45) hydrogen bonds : bond 0.04565 ( 745) hydrogen bonds : angle 4.20073 ( 2190) SS BOND : bond 0.00197 ( 5) SS BOND : angle 1.00033 ( 10) covalent geometry : bond 0.00599 (17160) covalent geometry : angle 0.69120 (23460) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 47 time to evaluate : 2.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 TYR cc_start: 0.7572 (OUTLIER) cc_final: 0.6553 (t80) REVERT: B 223 TYR cc_start: 0.7611 (OUTLIER) cc_final: 0.6657 (t80) REVERT: B 400 ARG cc_start: 0.4471 (mmp-170) cc_final: 0.3904 (mmt180) REVERT: C 400 ARG cc_start: 0.4114 (mmp-170) cc_final: 0.3510 (mmt180) REVERT: D 223 TYR cc_start: 0.7676 (OUTLIER) cc_final: 0.6626 (t80) REVERT: E 223 TYR cc_start: 0.7563 (OUTLIER) cc_final: 0.6526 (t80) REVERT: E 291 MET cc_start: 0.8041 (mmm) cc_final: 0.7797 (mmm) outliers start: 35 outliers final: 24 residues processed: 79 average time/residue: 0.3749 time to fit residues: 47.8627 Evaluate side-chains 71 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 43 time to evaluate : 3.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 223 TYR Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 262 TYR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 439 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 94 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.082600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.060477 restraints weight = 67130.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.058809 restraints weight = 56339.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.059167 restraints weight = 43999.705| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17180 Z= 0.118 Angle : 0.549 7.080 23515 Z= 0.272 Chirality : 0.042 0.137 2750 Planarity : 0.004 0.045 2850 Dihedral : 4.648 21.658 2645 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.25 % Allowed : 14.96 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.55 (0.20), residues: 1955 helix: 0.96 (0.19), residues: 865 sheet: -0.31 (0.26), residues: 435 loop : -2.21 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 331 HIS 0.002 0.001 HIS E 119 PHE 0.025 0.001 PHE E 265 TYR 0.011 0.001 TYR D 67 ARG 0.003 0.000 ARG C 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00119 ( 15) link_NAG-ASN : angle 1.45597 ( 45) hydrogen bonds : bond 0.03352 ( 745) hydrogen bonds : angle 3.77520 ( 2190) SS BOND : bond 0.00032 ( 5) SS BOND : angle 0.41578 ( 10) covalent geometry : bond 0.00269 (17160) covalent geometry : angle 0.54569 (23460) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 44 time to evaluate : 1.887 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.8320 (m-80) REVERT: B 235 MET cc_start: 0.7617 (mtm) cc_final: 0.7365 (mtp) REVERT: B 400 ARG cc_start: 0.4395 (mmp-170) cc_final: 0.3902 (mmt180) REVERT: C 400 ARG cc_start: 0.4145 (mmp-170) cc_final: 0.3613 (mmt180) outliers start: 23 outliers final: 17 residues processed: 63 average time/residue: 0.2670 time to fit residues: 28.2283 Evaluate side-chains 61 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 262 TYR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 321 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 90 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 192 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 47 optimal weight: 0.0060 chunk 138 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.9802 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.081921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.059016 restraints weight = 66973.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.058407 restraints weight = 50875.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.058502 restraints weight = 38965.251| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17180 Z= 0.146 Angle : 0.567 9.442 23515 Z= 0.281 Chirality : 0.043 0.136 2750 Planarity : 0.004 0.046 2850 Dihedral : 4.693 24.431 2645 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.33 % Allowed : 14.58 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.20), residues: 1955 helix: 0.92 (0.18), residues: 870 sheet: -0.29 (0.26), residues: 440 loop : -2.16 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 331 HIS 0.003 0.001 HIS E 119 PHE 0.024 0.001 PHE E 265 TYR 0.013 0.001 TYR D 67 ARG 0.003 0.000 ARG B 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00068 ( 15) link_NAG-ASN : angle 1.44567 ( 45) hydrogen bonds : bond 0.03436 ( 745) hydrogen bonds : angle 3.74723 ( 2190) SS BOND : bond 0.00109 ( 5) SS BOND : angle 0.61392 ( 10) covalent geometry : bond 0.00336 (17160) covalent geometry : angle 0.56370 (23460) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 46 time to evaluate : 2.098 Fit side-chains revert: symmetry clash REVERT: A 258 LEU cc_start: 0.6078 (OUTLIER) cc_final: 0.5753 (pp) REVERT: B 235 MET cc_start: 0.7653 (mtm) cc_final: 0.7352 (mtp) REVERT: B 400 ARG cc_start: 0.4449 (mmp-170) cc_final: 0.3956 (mmt180) REVERT: C 223 TYR cc_start: 0.7542 (OUTLIER) cc_final: 0.6664 (t80) REVERT: C 400 ARG cc_start: 0.4095 (mmp-170) cc_final: 0.3576 (mmt180) REVERT: D 258 LEU cc_start: 0.6413 (OUTLIER) cc_final: 0.6156 (pp) outliers start: 43 outliers final: 32 residues processed: 85 average time/residue: 0.2747 time to fit residues: 38.7755 Evaluate side-chains 79 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 44 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 223 TYR Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 262 TYR Chi-restraints excluded: chain E residue 265 PHE Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 439 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 110 optimal weight: 9.9990 chunk 178 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 22 optimal weight: 0.0060 chunk 55 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.083190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.064483 restraints weight = 66522.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.062725 restraints weight = 59290.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.063117 restraints weight = 63307.703| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17180 Z= 0.101 Angle : 0.534 8.040 23515 Z= 0.262 Chirality : 0.042 0.132 2750 Planarity : 0.004 0.044 2850 Dihedral : 4.391 22.877 2645 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.73 % Allowed : 15.93 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.20), residues: 1955 helix: 1.08 (0.19), residues: 870 sheet: -0.19 (0.26), residues: 435 loop : -2.09 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 331 HIS 0.002 0.001 HIS B 118 PHE 0.022 0.001 PHE A 265 TYR 0.009 0.001 TYR A 67 ARG 0.005 0.000 ARG C 420 Details of bonding type rmsd link_NAG-ASN : bond 0.00102 ( 15) link_NAG-ASN : angle 1.31460 ( 45) hydrogen bonds : bond 0.02932 ( 745) hydrogen bonds : angle 3.57834 ( 2190) SS BOND : bond 0.00036 ( 5) SS BOND : angle 0.38929 ( 10) covalent geometry : bond 0.00229 (17160) covalent geometry : angle 0.53173 (23460) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 45 time to evaluate : 1.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.7636 (mtm) cc_final: 0.7297 (mtp) REVERT: B 400 ARG cc_start: 0.4529 (mmp-170) cc_final: 0.4002 (mmt180) REVERT: C 223 TYR cc_start: 0.7404 (OUTLIER) cc_final: 0.6616 (t80) REVERT: C 400 ARG cc_start: 0.4165 (mmp-170) cc_final: 0.3603 (mmt180) REVERT: D 258 LEU cc_start: 0.6464 (OUTLIER) cc_final: 0.6220 (pp) REVERT: E 291 MET cc_start: 0.7568 (mmm) cc_final: 0.7248 (mmp) outliers start: 32 outliers final: 20 residues processed: 73 average time/residue: 0.2549 time to fit residues: 31.3076 Evaluate side-chains 66 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 44 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 223 TYR Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 265 PHE Chi-restraints excluded: chain E residue 280 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 73 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 0.2980 chunk 88 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 110 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.082771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.060282 restraints weight = 66560.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.059352 restraints weight = 54776.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.059634 restraints weight = 41255.758| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17180 Z= 0.114 Angle : 0.549 8.915 23515 Z= 0.267 Chirality : 0.042 0.139 2750 Planarity : 0.004 0.042 2850 Dihedral : 4.374 23.425 2645 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.79 % Allowed : 16.15 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.20), residues: 1955 helix: 1.07 (0.19), residues: 870 sheet: -0.20 (0.26), residues: 440 loop : -2.09 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 331 HIS 0.002 0.001 HIS E 119 PHE 0.023 0.001 PHE E 265 TYR 0.010 0.001 TYR D 67 ARG 0.003 0.000 ARG B 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00064 ( 15) link_NAG-ASN : angle 1.32616 ( 45) hydrogen bonds : bond 0.02981 ( 745) hydrogen bonds : angle 3.55563 ( 2190) SS BOND : bond 0.00073 ( 5) SS BOND : angle 0.48926 ( 10) covalent geometry : bond 0.00263 (17160) covalent geometry : angle 0.54625 (23460) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 47 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 258 LEU cc_start: 0.6163 (OUTLIER) cc_final: 0.5901 (pp) REVERT: B 223 TYR cc_start: 0.7557 (OUTLIER) cc_final: 0.6543 (t80) REVERT: B 235 MET cc_start: 0.7623 (mtm) cc_final: 0.7254 (mtp) REVERT: B 400 ARG cc_start: 0.4494 (mmp-170) cc_final: 0.3764 (mmt180) REVERT: C 223 TYR cc_start: 0.7504 (OUTLIER) cc_final: 0.6657 (t80) REVERT: C 240 VAL cc_start: 0.8099 (t) cc_final: 0.7890 (t) REVERT: C 400 ARG cc_start: 0.4172 (mmp-170) cc_final: 0.3636 (mmt180) REVERT: D 258 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.6234 (pp) REVERT: E 258 LEU cc_start: 0.6164 (OUTLIER) cc_final: 0.5878 (pp) outliers start: 33 outliers final: 23 residues processed: 80 average time/residue: 0.2498 time to fit residues: 33.6216 Evaluate side-chains 74 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 46 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 223 TYR Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 262 TYR Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 265 PHE Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 321 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 124 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 139 optimal weight: 0.0980 chunk 13 optimal weight: 1.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.082802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.064384 restraints weight = 66460.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.062805 restraints weight = 58586.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.063114 restraints weight = 62871.576| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17180 Z= 0.119 Angle : 0.556 10.701 23515 Z= 0.270 Chirality : 0.042 0.131 2750 Planarity : 0.004 0.043 2850 Dihedral : 4.390 23.760 2645 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.95 % Allowed : 16.21 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.35 (0.20), residues: 1955 helix: 1.09 (0.19), residues: 870 sheet: -0.21 (0.26), residues: 440 loop : -2.06 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 331 HIS 0.002 0.001 HIS E 119 PHE 0.022 0.001 PHE A 265 TYR 0.011 0.001 TYR D 67 ARG 0.002 0.000 ARG B 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00060 ( 15) link_NAG-ASN : angle 1.31501 ( 45) hydrogen bonds : bond 0.02993 ( 745) hydrogen bonds : angle 3.54839 ( 2190) SS BOND : bond 0.00068 ( 5) SS BOND : angle 0.45958 ( 10) covalent geometry : bond 0.00275 (17160) covalent geometry : angle 0.55377 (23460) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 47 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 258 LEU cc_start: 0.6391 (OUTLIER) cc_final: 0.6038 (pp) REVERT: B 223 TYR cc_start: 0.7465 (OUTLIER) cc_final: 0.6511 (t80) REVERT: B 235 MET cc_start: 0.7654 (mtm) cc_final: 0.7279 (mtp) REVERT: B 400 ARG cc_start: 0.4566 (mmp-170) cc_final: 0.3793 (mmt180) REVERT: C 223 TYR cc_start: 0.7489 (OUTLIER) cc_final: 0.6669 (t80) REVERT: C 240 VAL cc_start: 0.8049 (t) cc_final: 0.7844 (t) REVERT: C 400 ARG cc_start: 0.4234 (mmp-170) cc_final: 0.3701 (mmt180) REVERT: D 223 TYR cc_start: 0.7611 (OUTLIER) cc_final: 0.6714 (t80) REVERT: D 258 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6428 (pp) REVERT: E 258 LEU cc_start: 0.6354 (OUTLIER) cc_final: 0.6080 (pp) outliers start: 36 outliers final: 26 residues processed: 81 average time/residue: 0.2522 time to fit residues: 34.5878 Evaluate side-chains 77 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 45 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 223 TYR Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 262 TYR Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 265 PHE Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 321 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 182 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 13 optimal weight: 0.2980 chunk 147 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 186 optimal weight: 9.9990 chunk 192 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 136 optimal weight: 0.0000 overall best weight: 0.7586 ------------------------------------------------------------------------------- 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 = 0.3722 r_free = 0.3722 target = 0.083468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.064949 restraints weight = 65889.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.063368 restraints weight = 59660.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.063915 restraints weight = 60462.598| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17180 Z= 0.100 Angle : 0.556 9.919 23515 Z= 0.267 Chirality : 0.042 0.135 2750 Planarity : 0.004 0.043 2850 Dihedral : 4.233 22.597 2645 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.68 % Allowed : 16.53 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.28 (0.20), residues: 1955 helix: 1.18 (0.19), residues: 865 sheet: -0.14 (0.26), residues: 435 loop : -2.08 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 331 HIS 0.002 0.001 HIS B 118 PHE 0.021 0.001 PHE A 265 TYR 0.010 0.001 TYR B 46 ARG 0.002 0.000 ARG B 424 Details of bonding type rmsd link_NAG-ASN : bond 0.00125 ( 15) link_NAG-ASN : angle 1.22845 ( 45) hydrogen bonds : bond 0.02745 ( 745) hydrogen bonds : angle 3.47482 ( 2190) SS BOND : bond 0.00037 ( 5) SS BOND : angle 0.37126 ( 10) covalent geometry : bond 0.00228 (17160) covalent geometry : angle 0.55399 (23460) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 46 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 258 LEU cc_start: 0.6396 (OUTLIER) cc_final: 0.6047 (pp) REVERT: B 223 TYR cc_start: 0.7408 (OUTLIER) cc_final: 0.6583 (t80) REVERT: B 235 MET cc_start: 0.7592 (mtm) cc_final: 0.7178 (mtp) REVERT: B 400 ARG cc_start: 0.4499 (mmp-170) cc_final: 0.3750 (mmt180) REVERT: C 240 VAL cc_start: 0.7929 (t) cc_final: 0.7691 (t) REVERT: C 400 ARG cc_start: 0.4343 (mmp-170) cc_final: 0.3819 (mmt180) REVERT: D 223 TYR cc_start: 0.7570 (OUTLIER) cc_final: 0.6685 (t80) REVERT: D 258 LEU cc_start: 0.6734 (OUTLIER) cc_final: 0.6519 (pp) REVERT: E 258 LEU cc_start: 0.6402 (OUTLIER) cc_final: 0.6137 (pp) outliers start: 31 outliers final: 24 residues processed: 76 average time/residue: 0.2575 time to fit residues: 32.4403 Evaluate side-chains 75 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 46 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 265 PHE Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 321 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 29 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 27 optimal weight: 0.0470 chunk 36 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 181 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.083106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.064588 restraints weight = 65909.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.063222 restraints weight = 58202.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.063517 restraints weight = 62832.688| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17180 Z= 0.112 Angle : 0.558 11.225 23515 Z= 0.270 Chirality : 0.042 0.135 2750 Planarity : 0.004 0.044 2850 Dihedral : 4.263 23.446 2645 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.95 % Allowed : 16.42 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.28 (0.20), residues: 1955 helix: 1.17 (0.19), residues: 865 sheet: -0.17 (0.26), residues: 440 loop : -2.06 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 331 HIS 0.002 0.001 HIS E 119 PHE 0.021 0.001 PHE A 265 TYR 0.010 0.001 TYR A 67 ARG 0.002 0.000 ARG C 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00066 ( 15) link_NAG-ASN : angle 1.27885 ( 45) hydrogen bonds : bond 0.02855 ( 745) hydrogen bonds : angle 3.48008 ( 2190) SS BOND : bond 0.00071 ( 5) SS BOND : angle 0.44742 ( 10) covalent geometry : bond 0.00256 (17160) covalent geometry : angle 0.55541 (23460) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4240.27 seconds wall clock time: 76 minutes 43.11 seconds (4603.11 seconds total)