Starting phenix.real_space_refine on Sun May 18 08:46:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fsz_29422/05_2025/8fsz_29422.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fsz_29422/05_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_29422/05_2025/8fsz_29422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fsz_29422/05_2025/8fsz_29422.map" model { file = "/net/cci-nas-00/data/ceres_data/8fsz_29422/05_2025/8fsz_29422.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fsz_29422/05_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 9.42, per 1000 atoms: 0.56 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: 3.99 Conformation dependent library (CDL) restraints added in 1.9 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: 1.55 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: 4.38 Time building geometry restraints manager: 4.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 34.670 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.990 ------------------------------------------------------------------------------- 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 : 1.772 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: 0.3315 time to fit residues: 66.0827 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 : 1.883 ------------------------------------------------------------------------------- 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: 4.9990 chunk 113 optimal weight: 7.9990 chunk 177 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.083889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.060308 restraints weight = 66152.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.059931 restraints weight = 50791.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.060189 restraints weight = 37117.804| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17180 Z= 0.180 Angle : 0.617 8.019 23515 Z= 0.311 Chirality : 0.044 0.186 2750 Planarity : 0.005 0.050 2850 Dihedral : 4.663 17.772 2645 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.65 % Allowed : 9.81 % Favored : 89.54 % 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: -1.15 (0.19), residues: 1955 helix: 0.51 (0.18), residues: 850 sheet: -0.57 (0.24), residues: 440 loop : -2.56 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 331 HIS 0.004 0.001 HIS A 119 PHE 0.016 0.001 PHE C 265 TYR 0.018 0.002 TYR C 262 ARG 0.006 0.001 ARG B 424 Details of bonding type rmsd link_NAG-ASN : bond 0.00077 ( 15) link_NAG-ASN : angle 1.62576 ( 45) hydrogen bonds : bond 0.04097 ( 745) hydrogen bonds : angle 4.07957 ( 2190) SS BOND : bond 0.00080 ( 5) SS BOND : angle 0.43911 ( 10) covalent geometry : bond 0.00410 (17160) covalent geometry : angle 0.61369 (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 59 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 291 MET cc_start: 0.8265 (mmm) cc_final: 0.8027 (mmp) outliers start: 12 outliers final: 7 residues processed: 57 average time/residue: 0.2396 time to fit residues: 24.2190 Evaluate side-chains 52 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 2.053 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 179 optimal weight: 6.9990 chunk 175 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 187 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 164 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 163 optimal weight: 0.3980 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.082603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.059525 restraints weight = 65090.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.058839 restraints weight = 50326.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.059042 restraints weight = 38387.152| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17180 Z= 0.173 Angle : 0.591 8.031 23515 Z= 0.297 Chirality : 0.043 0.128 2750 Planarity : 0.004 0.038 2850 Dihedral : 4.455 18.868 2645 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.73 % Allowed : 11.54 % 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: -0.68 (0.20), residues: 1955 helix: 0.87 (0.18), residues: 855 sheet: -0.40 (0.25), residues: 435 loop : -2.22 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 331 HIS 0.003 0.001 HIS A 119 PHE 0.025 0.001 PHE A 265 TYR 0.016 0.002 TYR D 441 ARG 0.005 0.000 ARG B 424 Details of bonding type rmsd link_NAG-ASN : bond 0.00091 ( 15) link_NAG-ASN : angle 1.66213 ( 45) hydrogen bonds : bond 0.03830 ( 745) hydrogen bonds : angle 3.89066 ( 2190) SS BOND : bond 0.00091 ( 5) SS BOND : angle 0.57616 ( 10) covalent geometry : bond 0.00397 (17160) covalent geometry : angle 0.58690 (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 76 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 44 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 400 ARG cc_start: 0.4157 (mmp-170) cc_final: 0.3641 (mmt180) REVERT: C 116 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.8420 (m-80) outliers start: 32 outliers final: 17 residues processed: 73 average time/residue: 0.2456 time to fit residues: 30.8920 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 : 1.922 ------------------------------------------------------------------------------- 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 A residue 262 TYR 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 B residue 291 MET Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 232 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 Chi-restraints excluded: chain E residue 286 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 137 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 chunk 159 optimal weight: 0.9990 chunk 133 optimal weight: 0.1980 chunk 33 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.082928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.059357 restraints weight = 66235.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.058940 restraints weight = 48640.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.059151 restraints weight = 35606.165| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3198 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= 0.138 Angle : 0.557 7.433 23515 Z= 0.275 Chirality : 0.042 0.130 2750 Planarity : 0.004 0.043 2850 Dihedral : 4.414 17.512 2645 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.14 % Allowed : 13.98 % Favored : 84.88 % 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: -0.50 (0.20), residues: 1955 helix: 1.01 (0.18), residues: 865 sheet: -0.33 (0.25), residues: 440 loop : -2.18 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 331 HIS 0.003 0.001 HIS A 119 PHE 0.022 0.001 PHE A 265 TYR 0.020 0.001 TYR B 262 ARG 0.003 0.000 ARG B 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00058 ( 15) link_NAG-ASN : angle 1.52456 ( 45) hydrogen bonds : bond 0.03423 ( 745) hydrogen bonds : angle 3.74562 ( 2190) SS BOND : bond 0.00088 ( 5) SS BOND : angle 0.47489 ( 10) covalent geometry : bond 0.00318 (17160) covalent geometry : angle 0.55348 (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 69 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 1.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.8333 (m-80) REVERT: B 400 ARG cc_start: 0.4176 (mmp-170) cc_final: 0.3703 (mmt180) REVERT: C 265 PHE cc_start: 0.4514 (p90) cc_final: 0.4000 (p90) REVERT: C 400 ARG cc_start: 0.4063 (mmp-170) cc_final: 0.3828 (mmt180) outliers start: 21 outliers final: 14 residues processed: 68 average time/residue: 0.2661 time to fit residues: 29.7585 Evaluate side-chains 62 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 2.064 ------------------------------------------------------------------------------- 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 A residue 262 TYR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 321 LEU 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 D residue 116 TYR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 100 ILE 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: 4.9990 chunk 91 optimal weight: 0.4980 chunk 96 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.082508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.059581 restraints weight = 67058.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.058619 restraints weight = 46667.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.058934 restraints weight = 36360.333| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17180 Z= 0.141 Angle : 0.554 6.903 23515 Z= 0.275 Chirality : 0.042 0.152 2750 Planarity : 0.004 0.040 2850 Dihedral : 4.462 19.274 2645 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.84 % Allowed : 14.20 % Favored : 83.96 % 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: -0.47 (0.20), residues: 1955 helix: 1.03 (0.18), residues: 865 sheet: -0.27 (0.25), residues: 440 loop : -2.19 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 331 HIS 0.003 0.001 HIS E 119 PHE 0.032 0.001 PHE E 265 TYR 0.013 0.001 TYR A 67 ARG 0.004 0.000 ARG E 424 Details of bonding type rmsd link_NAG-ASN : bond 0.00055 ( 15) link_NAG-ASN : angle 1.47480 ( 45) hydrogen bonds : bond 0.03366 ( 745) hydrogen bonds : angle 3.67925 ( 2190) SS BOND : bond 0.00099 ( 5) SS BOND : angle 0.59539 ( 10) covalent geometry : bond 0.00324 (17160) covalent geometry : angle 0.55116 (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 85 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 51 time to evaluate : 2.030 Fit side-chains revert: symmetry clash REVERT: B 235 MET cc_start: 0.7548 (mtm) cc_final: 0.7342 (mtp) REVERT: B 400 ARG cc_start: 0.4424 (mmp-170) cc_final: 0.3922 (mmt180) REVERT: C 400 ARG cc_start: 0.4096 (mmp-170) cc_final: 0.3537 (mmt180) REVERT: E 210 MET cc_start: 0.8533 (tpt) cc_final: 0.8322 (tpt) outliers start: 34 outliers final: 29 residues processed: 81 average time/residue: 0.2733 time to fit residues: 36.4968 Evaluate side-chains 74 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 45 time to evaluate : 2.237 ------------------------------------------------------------------------------- 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 177 ASP Chi-restraints excluded: chain A residue 203 ILE 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 280 THR 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 177 ASP Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 232 ILE 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 Chi-restraints excluded: chain E residue 439 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 90 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 192 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 138 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 179 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.3676 r_free = 0.3676 target = 0.081349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.058774 restraints weight = 67381.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.057456 restraints weight = 62294.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.058031 restraints weight = 42348.794| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 17180 Z= 0.197 Angle : 0.615 6.260 23515 Z= 0.308 Chirality : 0.044 0.141 2750 Planarity : 0.005 0.049 2850 Dihedral : 4.990 26.596 2645 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.82 % Allowed : 13.50 % Favored : 83.69 % 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: -0.65 (0.20), residues: 1955 helix: 0.82 (0.18), residues: 870 sheet: -0.32 (0.26), residues: 440 loop : -2.22 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 331 HIS 0.004 0.001 HIS A 119 PHE 0.028 0.001 PHE E 265 TYR 0.016 0.002 TYR E 67 ARG 0.003 0.000 ARG B 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00145 ( 15) link_NAG-ASN : angle 1.55551 ( 45) hydrogen bonds : bond 0.03848 ( 745) hydrogen bonds : angle 3.88786 ( 2190) SS BOND : bond 0.00150 ( 5) SS BOND : angle 0.81274 ( 10) covalent geometry : bond 0.00454 (17160) covalent geometry : angle 0.61209 (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 97 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 45 time to evaluate : 1.813 Fit side-chains revert: symmetry clash REVERT: A 223 TYR cc_start: 0.7535 (OUTLIER) cc_final: 0.6451 (t80) REVERT: B 223 TYR cc_start: 0.7627 (OUTLIER) cc_final: 0.6672 (t80) REVERT: B 235 MET cc_start: 0.7700 (mtm) cc_final: 0.7330 (mtp) REVERT: B 400 ARG cc_start: 0.4580 (mmp-170) cc_final: 0.4025 (mmt180) REVERT: C 400 ARG cc_start: 0.4380 (mmp-170) cc_final: 0.3764 (mmt180) REVERT: D 223 TYR cc_start: 0.7680 (OUTLIER) cc_final: 0.6638 (t80) REVERT: D 258 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.6355 (pp) REVERT: D 291 MET cc_start: 0.7757 (mmt) cc_final: 0.7412 (mmm) REVERT: D 400 ARG cc_start: 0.4380 (mmp-170) cc_final: 0.3717 (mmt180) REVERT: E 291 MET cc_start: 0.8312 (mmp) cc_final: 0.7849 (mmp) outliers start: 52 outliers final: 38 residues processed: 92 average time/residue: 0.2529 time to fit residues: 37.8152 Evaluate side-chains 86 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 44 time to evaluate : 1.787 ------------------------------------------------------------------------------- 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 203 ILE Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 232 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 57 VAL 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 280 THR Chi-restraints excluded: chain B residue 441 TYR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 117 VAL 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 258 LEU Chi-restraints excluded: chain D residue 262 TYR Chi-restraints excluded: chain D residue 265 PHE 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 258 LEU 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: 0.6980 chunk 178 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 91 optimal weight: 0.4980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.082420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.063710 restraints weight = 66122.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.061892 restraints weight = 59962.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.062310 restraints weight = 65103.429| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17180 Z= 0.120 Angle : 0.551 8.111 23515 Z= 0.272 Chirality : 0.042 0.140 2750 Planarity : 0.004 0.045 2850 Dihedral : 4.624 25.107 2645 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.38 % Allowed : 14.85 % Favored : 82.76 % 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: -0.41 (0.20), residues: 1955 helix: 1.04 (0.19), residues: 870 sheet: -0.27 (0.26), residues: 440 loop : -2.07 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 331 HIS 0.002 0.001 HIS A 119 PHE 0.032 0.001 PHE B 265 TYR 0.011 0.001 TYR D 67 ARG 0.003 0.000 ARG B 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00080 ( 15) link_NAG-ASN : angle 1.39918 ( 45) hydrogen bonds : bond 0.03197 ( 745) hydrogen bonds : angle 3.67619 ( 2190) SS BOND : bond 0.00051 ( 5) SS BOND : angle 0.43808 ( 10) covalent geometry : bond 0.00276 (17160) covalent geometry : angle 0.54855 (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 88 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 44 time to evaluate : 1.824 Fit side-chains revert: symmetry clash REVERT: A 116 TYR cc_start: 0.8539 (OUTLIER) cc_final: 0.8326 (m-80) REVERT: A 291 MET cc_start: 0.7470 (mmm) cc_final: 0.6840 (mmp) REVERT: B 223 TYR cc_start: 0.7530 (OUTLIER) cc_final: 0.6619 (t80) REVERT: B 235 MET cc_start: 0.7684 (mtm) cc_final: 0.7289 (mtp) REVERT: B 400 ARG cc_start: 0.4584 (mmp-170) cc_final: 0.4046 (mmt180) REVERT: C 400 ARG cc_start: 0.4201 (mmp-170) cc_final: 0.3633 (mmt180) REVERT: D 223 TYR cc_start: 0.7585 (OUTLIER) cc_final: 0.6612 (t80) REVERT: D 258 LEU cc_start: 0.6457 (OUTLIER) cc_final: 0.6215 (pp) REVERT: E 262 TYR cc_start: 0.0269 (p90) cc_final: -0.0114 (p90) REVERT: E 291 MET cc_start: 0.8111 (mmp) cc_final: 0.7288 (mmp) outliers start: 44 outliers final: 31 residues processed: 85 average time/residue: 0.2516 time to fit residues: 35.1964 Evaluate side-chains 78 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 43 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 239 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 57 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 280 THR 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 57 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 239 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 57 VAL Chi-restraints excluded: chain E residue 100 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 73 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 71 optimal weight: 0.0770 chunk 88 optimal weight: 0.2980 chunk 44 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 overall best weight: 1.2342 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.082612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.060280 restraints weight = 66468.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.059648 restraints weight = 48268.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.059934 restraints weight = 38464.608| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4012 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 : 0.552 8.939 23515 Z= 0.270 Chirality : 0.042 0.146 2750 Planarity : 0.004 0.041 2850 Dihedral : 4.514 24.360 2645 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.55 % Allowed : 15.12 % 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: 1.07 (0.19), residues: 870 sheet: -0.23 (0.26), residues: 440 loop : -2.06 (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 0.029 0.001 PHE B 265 TYR 0.011 0.001 TYR D 262 ARG 0.002 0.000 ARG B 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00072 ( 15) link_NAG-ASN : angle 1.34899 ( 45) hydrogen bonds : bond 0.03078 ( 745) hydrogen bonds : angle 3.59987 ( 2190) SS BOND : bond 0.00059 ( 5) SS BOND : angle 0.45050 ( 10) covalent geometry : bond 0.00262 (17160) covalent geometry : angle 0.54960 (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 92 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 45 time to evaluate : 1.939 Fit side-chains revert: symmetry clash REVERT: A 116 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.8320 (m-80) REVERT: A 223 TYR cc_start: 0.7449 (OUTLIER) cc_final: 0.6457 (t80) REVERT: B 223 TYR cc_start: 0.7511 (OUTLIER) cc_final: 0.6525 (t80) REVERT: B 235 MET cc_start: 0.7649 (mtm) cc_final: 0.7247 (mtp) REVERT: B 400 ARG cc_start: 0.4529 (mmp-170) cc_final: 0.3984 (mmt180) REVERT: C 240 VAL cc_start: 0.8101 (t) cc_final: 0.7891 (t) REVERT: C 400 ARG cc_start: 0.4304 (mmp-170) cc_final: 0.3734 (mmt180) REVERT: D 223 TYR cc_start: 0.7623 (OUTLIER) cc_final: 0.6721 (t80) REVERT: D 258 LEU cc_start: 0.6568 (OUTLIER) cc_final: 0.6295 (pp) REVERT: E 291 MET cc_start: 0.8161 (mmp) cc_final: 0.7220 (mmp) outliers start: 47 outliers final: 38 residues processed: 91 average time/residue: 0.2472 time to fit residues: 37.3239 Evaluate side-chains 86 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 43 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 236 VAL 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 57 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 117 VAL 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 57 VAL Chi-restraints excluded: chain C residue 100 ILE 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 57 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 262 TYR Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 117 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 124 optimal weight: 6.9990 chunk 167 optimal weight: 8.9990 chunk 169 optimal weight: 0.0030 chunk 90 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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 = 0.083559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.065096 restraints weight = 66166.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.063368 restraints weight = 58621.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.063987 restraints weight = 59602.265| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4038 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= 0.099 Angle : 0.549 10.072 23515 Z= 0.265 Chirality : 0.042 0.133 2750 Planarity : 0.004 0.044 2850 Dihedral : 4.280 22.597 2645 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.90 % Allowed : 16.15 % Favored : 81.95 % 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: -0.16 (0.26), residues: 435 loop : -2.06 (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 0.026 0.001 PHE B 265 TYR 0.017 0.001 TYR E 262 ARG 0.002 0.000 ARG B 424 Details of bonding type rmsd link_NAG-ASN : bond 0.00133 ( 15) link_NAG-ASN : angle 1.24324 ( 45) hydrogen bonds : bond 0.02785 ( 745) hydrogen bonds : angle 3.50337 ( 2190) SS BOND : bond 0.00031 ( 5) SS BOND : angle 0.34895 ( 10) covalent geometry : bond 0.00225 (17160) covalent geometry : angle 0.54672 (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 80 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 45 time to evaluate : 1.876 Fit side-chains revert: symmetry clash REVERT: A 258 LEU cc_start: 0.6372 (OUTLIER) cc_final: 0.6012 (pp) REVERT: B 235 MET cc_start: 0.7614 (mtm) cc_final: 0.7246 (mtp) REVERT: B 400 ARG cc_start: 0.4533 (mmp-170) cc_final: 0.3759 (mmt180) REVERT: C 240 VAL cc_start: 0.7834 (t) cc_final: 0.7615 (t) REVERT: C 400 ARG cc_start: 0.4231 (mmp-170) cc_final: 0.3705 (mmt180) REVERT: D 223 TYR cc_start: 0.7555 (OUTLIER) cc_final: 0.6677 (t80) REVERT: D 258 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6435 (pp) REVERT: E 258 LEU cc_start: 0.6533 (OUTLIER) cc_final: 0.6179 (pp) outliers start: 35 outliers final: 27 residues processed: 79 average time/residue: 0.2503 time to fit residues: 32.8683 Evaluate side-chains 74 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 43 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 236 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 100 ILE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 57 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 116 TYR Chi-restraints excluded: chain D residue 177 ASP 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 57 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 258 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 182 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 186 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.081494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.059053 restraints weight = 66904.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.058505 restraints weight = 52506.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.058688 restraints weight = 39882.230| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 17180 Z= 0.208 Angle : 0.635 10.149 23515 Z= 0.313 Chirality : 0.044 0.159 2750 Planarity : 0.005 0.045 2850 Dihedral : 4.889 28.117 2645 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.66 % Allowed : 15.50 % 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: -0.53 (0.20), residues: 1955 helix: 0.90 (0.18), residues: 880 sheet: -0.25 (0.26), residues: 440 loop : -2.17 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 331 HIS 0.005 0.001 HIS E 119 PHE 0.028 0.001 PHE B 265 TYR 0.021 0.002 TYR E 262 ARG 0.002 0.000 ARG B 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00088 ( 15) link_NAG-ASN : angle 1.47006 ( 45) hydrogen bonds : bond 0.03652 ( 745) hydrogen bonds : angle 3.78189 ( 2190) SS BOND : bond 0.00138 ( 5) SS BOND : angle 0.73267 ( 10) covalent geometry : bond 0.00486 (17160) covalent geometry : angle 0.63253 (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 95 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 46 time to evaluate : 1.965 Fit side-chains REVERT: A 223 TYR cc_start: 0.7586 (OUTLIER) cc_final: 0.6428 (t80) REVERT: A 258 LEU cc_start: 0.6421 (OUTLIER) cc_final: 0.6028 (pp) REVERT: B 223 TYR cc_start: 0.7687 (OUTLIER) cc_final: 0.6868 (t80) REVERT: B 235 MET cc_start: 0.7757 (mtm) cc_final: 0.7324 (mtp) REVERT: B 400 ARG cc_start: 0.4476 (mmp-170) cc_final: 0.3800 (mmt180) REVERT: C 223 TYR cc_start: 0.7588 (OUTLIER) cc_final: 0.6669 (t80) REVERT: C 240 VAL cc_start: 0.7975 (t) cc_final: 0.7730 (t) REVERT: C 400 ARG cc_start: 0.4433 (mmp-170) cc_final: 0.3914 (mmt180) REVERT: D 223 TYR cc_start: 0.7766 (OUTLIER) cc_final: 0.6727 (t80) REVERT: D 258 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6535 (pp) REVERT: D 400 ARG cc_start: 0.4386 (mmp-170) cc_final: 0.3790 (mmt180) REVERT: E 258 LEU cc_start: 0.6423 (OUTLIER) cc_final: 0.6177 (pp) outliers start: 49 outliers final: 35 residues processed: 90 average time/residue: 0.2719 time to fit residues: 39.3430 Evaluate side-chains 88 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 46 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 236 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 100 ILE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 117 VAL 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 57 VAL Chi-restraints excluded: chain C residue 100 ILE 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 57 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 177 ASP 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 265 PHE Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 258 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 29 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 181 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.082490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.064172 restraints weight = 66112.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.062530 restraints weight = 60162.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.063066 restraints weight = 59945.838| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4301 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= 0.124 Angle : 0.573 9.193 23515 Z= 0.280 Chirality : 0.043 0.153 2750 Planarity : 0.004 0.043 2850 Dihedral : 4.630 26.568 2645 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.95 % Allowed : 16.10 % Favored : 81.95 % 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: -0.32 (0.20), residues: 1955 helix: 1.10 (0.19), residues: 870 sheet: -0.25 (0.26), residues: 440 loop : -1.99 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 331 HIS 0.002 0.001 HIS E 119 PHE 0.025 0.001 PHE B 265 TYR 0.013 0.001 TYR E 262 ARG 0.002 0.000 ARG A 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00086 ( 15) link_NAG-ASN : angle 1.34886 ( 45) hydrogen bonds : bond 0.03122 ( 745) hydrogen bonds : angle 3.64129 ( 2190) SS BOND : bond 0.00046 ( 5) SS BOND : angle 0.42712 ( 10) covalent geometry : bond 0.00283 (17160) covalent geometry : angle 0.57043 (23460) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3877.90 seconds wall clock time: 69 minutes 15.11 seconds (4155.11 seconds total)