Starting phenix.real_space_refine on Sun Aug 24 03:48:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fsz_29422/08_2025/8fsz_29422.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fsz_29422/08_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_29422/08_2025/8fsz_29422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fsz_29422/08_2025/8fsz_29422.map" model { file = "/net/cci-nas-00/data/ceres_data/8fsz_29422/08_2025/8fsz_29422.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fsz_29422/08_2025/8fsz_29422.cif" } resolution = 3.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.99, per 1000 atoms: 0.18 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: 1.05 Conformation dependent library (CDL) restraints added in 491.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.33 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: 1.96 Time building geometry restraints manager: 1.39 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: 1.550 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.760 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.930 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.004 0.001 ARG B 28 TYR 0.033 0.002 TYR B 262 PHE 0.029 0.002 PHE D 265 TRP 0.053 0.003 TRP E 331 HIS 0.003 0.001 HIS A 158 Details of bonding type rmsd covalent geometry : bond 0.00739 (17160) covalent geometry : angle 1.06106 (23460) SS BOND : bond 0.00034 ( 5) SS BOND : angle 0.24970 ( 10) hydrogen bonds : bond 0.15046 ( 745) hydrogen bonds : angle 5.39968 ( 2190) link_NAG-ASN : bond 0.00152 ( 15) link_NAG-ASN : angle 2.29821 ( 45) *********************** 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 : 0.423 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: 0.1331 time to fit residues: 26.6294 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 : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 311 GLN C 66 GLN C 311 GLN D 66 GLN D 311 GLN E 66 GLN E 311 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.083475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.059844 restraints weight = 65787.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.059518 restraints weight = 48499.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.059554 restraints weight = 37314.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.060027 restraints weight = 34327.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.060041 restraints weight = 28984.530| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17180 Z= 0.202 Angle : 0.638 7.955 23515 Z= 0.323 Chirality : 0.045 0.196 2750 Planarity : 0.005 0.057 2850 Dihedral : 4.772 18.215 2645 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.60 % Allowed : 10.35 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.19), residues: 1955 helix: 0.55 (0.18), residues: 860 sheet: -0.55 (0.25), residues: 440 loop : -2.50 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 424 TYR 0.021 0.002 TYR C 262 PHE 0.016 0.001 PHE C 199 TRP 0.042 0.002 TRP D 331 HIS 0.004 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00448 (17160) covalent geometry : angle 0.63432 (23460) SS BOND : bond 0.00058 ( 5) SS BOND : angle 0.48219 ( 10) hydrogen bonds : bond 0.04127 ( 745) hydrogen bonds : angle 4.06845 ( 2190) link_NAG-ASN : bond 0.00178 ( 15) link_NAG-ASN : angle 1.66047 ( 45) *********************** 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 58 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 56 average time/residue: 0.0882 time to fit residues: 8.7914 Evaluate side-chains 52 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 262 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 22 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 131 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 chunk 1 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.083188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.060576 restraints weight = 66817.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.059473 restraints weight = 56759.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.059664 restraints weight = 42492.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.059925 restraints weight = 36429.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.060047 restraints weight = 32979.535| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17180 Z= 0.147 Angle : 0.561 7.720 23515 Z= 0.282 Chirality : 0.043 0.125 2750 Planarity : 0.004 0.039 2850 Dihedral : 4.352 17.637 2645 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.63 % Allowed : 11.82 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.20), residues: 1955 helix: 0.91 (0.18), residues: 865 sheet: -0.39 (0.25), residues: 435 loop : -2.26 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 306 TYR 0.014 0.001 TYR A 67 PHE 0.025 0.001 PHE A 265 TRP 0.030 0.002 TRP D 331 HIS 0.003 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00336 (17160) covalent geometry : angle 0.55751 (23460) SS BOND : bond 0.00055 ( 5) SS BOND : angle 0.47723 ( 10) hydrogen bonds : bond 0.03663 ( 745) hydrogen bonds : angle 3.83839 ( 2190) link_NAG-ASN : bond 0.00064 ( 15) link_NAG-ASN : angle 1.61477 ( 45) *********************** 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 75 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 45 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 MET cc_start: 0.8231 (mmp) cc_final: 0.7624 (mmp) REVERT: C 116 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.8393 (m-80) REVERT: E 116 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.8336 (m-80) outliers start: 30 outliers final: 16 residues processed: 72 average time/residue: 0.1002 time to fit residues: 12.1907 Evaluate side-chains 60 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain 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 116 TYR Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 116 TYR Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 262 TYR Chi-restraints excluded: chain E residue 439 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 88 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 171 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 113 optimal weight: 9.9990 chunk 137 optimal weight: 7.9990 chunk 172 optimal weight: 4.9990 chunk 141 optimal weight: 0.0570 chunk 59 optimal weight: 4.9990 chunk 89 optimal weight: 0.3980 chunk 10 optimal weight: 4.9990 overall best weight: 0.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.084108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.064770 restraints weight = 66228.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.063553 restraints weight = 57579.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.063844 restraints weight = 59133.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.063805 restraints weight = 39731.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.064307 restraints weight = 33661.831| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17180 Z= 0.101 Angle : 0.525 7.630 23515 Z= 0.258 Chirality : 0.042 0.131 2750 Planarity : 0.004 0.040 2850 Dihedral : 4.172 15.364 2645 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.98 % Allowed : 13.82 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.20), residues: 1955 helix: 1.10 (0.19), residues: 865 sheet: -0.18 (0.25), residues: 435 loop : -2.13 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 306 TYR 0.021 0.001 TYR B 262 PHE 0.027 0.001 PHE E 265 TRP 0.021 0.001 TRP B 331 HIS 0.002 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00226 (17160) covalent geometry : angle 0.52159 (23460) SS BOND : bond 0.00042 ( 5) SS BOND : angle 0.34078 ( 10) hydrogen bonds : bond 0.03082 ( 745) hydrogen bonds : angle 3.64879 ( 2190) link_NAG-ASN : bond 0.00081 ( 15) link_NAG-ASN : angle 1.43799 ( 45) *********************** 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 62 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 265 PHE cc_start: 0.4416 (p90) cc_final: 0.3926 (p90) REVERT: E 291 MET cc_start: 0.8083 (mmm) cc_final: 0.6698 (mmm) outliers start: 18 outliers final: 4 residues processed: 61 average time/residue: 0.1020 time to fit residues: 10.8871 Evaluate side-chains 48 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 286 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 60 optimal weight: 7.9990 chunk 192 optimal weight: 5.9990 chunk 95 optimal weight: 0.0370 chunk 15 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 2 optimal weight: 0.5980 chunk 119 optimal weight: 0.8980 chunk 157 optimal weight: 8.9990 overall best weight: 1.7062 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.083115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.059677 restraints weight = 66367.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.059529 restraints weight = 46991.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.059756 restraints weight = 35095.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.059951 restraints weight = 31359.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.060043 restraints weight = 29014.916| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3247 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= 0.132 Angle : 0.541 6.919 23515 Z= 0.268 Chirality : 0.042 0.126 2750 Planarity : 0.004 0.039 2850 Dihedral : 4.249 16.116 2645 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.98 % Allowed : 14.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.20), residues: 1955 helix: 1.14 (0.18), residues: 865 sheet: -0.12 (0.26), residues: 435 loop : -2.16 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 306 TYR 0.013 0.001 TYR D 67 PHE 0.023 0.001 PHE E 265 TRP 0.022 0.001 TRP E 331 HIS 0.003 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00303 (17160) covalent geometry : angle 0.53756 (23460) SS BOND : bond 0.00095 ( 5) SS BOND : angle 0.52354 ( 10) hydrogen bonds : bond 0.03233 ( 745) hydrogen bonds : angle 3.61771 ( 2190) link_NAG-ASN : bond 0.00052 ( 15) link_NAG-ASN : angle 1.46001 ( 45) *********************** 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 68 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 400 ARG cc_start: 0.4213 (mmp-170) cc_final: 0.3738 (mmt180) REVERT: C 265 PHE cc_start: 0.4395 (p90) cc_final: 0.3916 (p90) REVERT: C 400 ARG cc_start: 0.4168 (mmp-170) cc_final: 0.3934 (mmt180) outliers start: 18 outliers final: 13 residues processed: 65 average time/residue: 0.1066 time to fit residues: 11.4708 Evaluate side-chains 61 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 203 ILE 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 321 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 262 TYR Chi-restraints excluded: chain E residue 321 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 161 optimal weight: 8.9990 chunk 174 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 179 optimal weight: 20.0000 chunk 167 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.083463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.059484 restraints weight = 66580.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.059470 restraints weight = 46046.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.059993 restraints weight = 32850.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.060374 restraints weight = 26822.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.060495 restraints weight = 23231.550| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3419 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= 0.114 Angle : 0.530 9.552 23515 Z= 0.260 Chirality : 0.042 0.145 2750 Planarity : 0.004 0.041 2850 Dihedral : 4.210 17.418 2645 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.19 % Allowed : 14.96 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.20), residues: 1955 helix: 1.20 (0.19), residues: 865 sheet: -0.08 (0.26), residues: 435 loop : -2.11 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 306 TYR 0.011 0.001 TYR A 67 PHE 0.020 0.001 PHE E 265 TRP 0.019 0.001 TRP D 331 HIS 0.002 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00260 (17160) covalent geometry : angle 0.52707 (23460) SS BOND : bond 0.00062 ( 5) SS BOND : angle 0.39484 ( 10) hydrogen bonds : bond 0.02994 ( 745) hydrogen bonds : angle 3.52967 ( 2190) link_NAG-ASN : bond 0.00061 ( 15) link_NAG-ASN : angle 1.38332 ( 45) *********************** 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 69 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 47 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: B 400 ARG cc_start: 0.4204 (mmp-170) cc_final: 0.3760 (mmt180) REVERT: C 400 ARG cc_start: 0.4163 (mmp-170) cc_final: 0.3953 (mmt180) REVERT: D 235 MET cc_start: 0.7614 (mtm) cc_final: 0.7310 (mtm) outliers start: 22 outliers final: 19 residues processed: 67 average time/residue: 0.1228 time to fit residues: 13.6943 Evaluate side-chains 63 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 203 ILE 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 C residue 203 ILE Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 177 ASP 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 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 22 optimal weight: 0.9980 chunk 152 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 173 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 86 optimal weight: 0.2980 chunk 1 optimal weight: 0.4980 chunk 95 optimal weight: 10.0000 chunk 17 optimal weight: 0.5980 chunk 125 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.084098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.059712 restraints weight = 65947.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.060364 restraints weight = 41912.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.060984 restraints weight = 28476.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.061258 restraints weight = 23287.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.061373 restraints weight = 21134.833| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3488 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= 0.094 Angle : 0.518 7.085 23515 Z= 0.254 Chirality : 0.042 0.133 2750 Planarity : 0.004 0.040 2850 Dihedral : 4.035 17.192 2645 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.41 % Allowed : 15.61 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.20), residues: 1955 helix: 1.27 (0.19), residues: 865 sheet: -0.07 (0.26), residues: 435 loop : -2.09 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 420 TYR 0.010 0.001 TYR A 46 PHE 0.018 0.001 PHE E 265 TRP 0.015 0.001 TRP B 331 HIS 0.002 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00210 (17160) covalent geometry : angle 0.51507 (23460) SS BOND : bond 0.00030 ( 5) SS BOND : angle 0.31674 ( 10) hydrogen bonds : bond 0.02732 ( 745) hydrogen bonds : angle 3.42885 ( 2190) link_NAG-ASN : bond 0.00130 ( 15) link_NAG-ASN : angle 1.27600 ( 45) *********************** 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 71 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 45 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 400 ARG cc_start: 0.4199 (mmp-170) cc_final: 0.3769 (mmt180) REVERT: C 400 ARG cc_start: 0.4248 (mmp-170) cc_final: 0.3797 (mmt180) outliers start: 26 outliers final: 17 residues processed: 68 average time/residue: 0.1039 time to fit residues: 11.9385 Evaluate side-chains 61 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 203 ILE 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 262 TYR Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 321 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 19 optimal weight: 1.9990 chunk 194 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 191 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 1 optimal weight: 0.0370 chunk 65 optimal weight: 5.9990 overall best weight: 2.1864 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.082455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.059263 restraints weight = 66250.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.059187 restraints weight = 48830.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.058943 restraints weight = 38483.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.059235 restraints weight = 34960.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.059343 restraints weight = 30692.174| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17180 Z= 0.158 Angle : 0.595 11.548 23515 Z= 0.289 Chirality : 0.043 0.131 2750 Planarity : 0.004 0.039 2850 Dihedral : 4.443 22.266 2645 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.73 % Allowed : 15.88 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.20), residues: 1955 helix: 1.19 (0.18), residues: 865 sheet: -0.14 (0.26), residues: 440 loop : -2.12 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 306 TYR 0.015 0.001 TYR D 67 PHE 0.021 0.001 PHE E 265 TRP 0.024 0.002 TRP D 331 HIS 0.003 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00364 (17160) covalent geometry : angle 0.59216 (23460) SS BOND : bond 0.00111 ( 5) SS BOND : angle 0.63542 ( 10) hydrogen bonds : bond 0.03316 ( 745) hydrogen bonds : angle 3.57536 ( 2190) link_NAG-ASN : bond 0.00058 ( 15) link_NAG-ASN : angle 1.44393 ( 45) *********************** 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 78 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 46 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 258 LEU cc_start: 0.6287 (OUTLIER) cc_final: 0.5944 (pp) REVERT: B 400 ARG cc_start: 0.4432 (mmp-170) cc_final: 0.3960 (mmt180) REVERT: C 400 ARG cc_start: 0.4187 (mmp-170) cc_final: 0.3672 (mmt180) REVERT: D 223 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.6686 (t80) REVERT: E 258 LEU cc_start: 0.6218 (OUTLIER) cc_final: 0.5960 (pp) REVERT: E 400 ARG cc_start: 0.4052 (mmp-170) cc_final: 0.3585 (mmt180) outliers start: 32 outliers final: 25 residues processed: 76 average time/residue: 0.1132 time to fit residues: 13.9969 Evaluate side-chains 72 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 44 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 116 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 203 ILE Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 265 PHE Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 321 LEU 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 137 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 170 optimal weight: 0.8980 chunk 168 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 149 optimal weight: 0.0870 chunk 108 optimal weight: 6.9990 chunk 148 optimal weight: 6.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.083721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.060883 restraints weight = 66187.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.060889 restraints weight = 48172.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.060743 restraints weight = 38442.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.060929 restraints weight = 34553.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.061104 restraints weight = 30541.031| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3758 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 9.692 23515 Z= 0.264 Chirality : 0.042 0.180 2750 Planarity : 0.004 0.039 2850 Dihedral : 4.221 21.228 2645 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.30 % Allowed : 16.53 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.20), residues: 1955 helix: 1.28 (0.19), residues: 865 sheet: -0.08 (0.26), residues: 435 loop : -2.06 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 424 TYR 0.010 0.001 TYR A 67 PHE 0.018 0.001 PHE E 265 TRP 0.015 0.001 TRP B 331 HIS 0.002 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00222 (17160) covalent geometry : angle 0.54671 (23460) SS BOND : bond 0.00021 ( 5) SS BOND : angle 0.30685 ( 10) hydrogen bonds : bond 0.02787 ( 745) hydrogen bonds : angle 3.44071 ( 2190) link_NAG-ASN : bond 0.00131 ( 15) link_NAG-ASN : angle 1.28990 ( 45) *********************** 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 70 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 46 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: B 400 ARG cc_start: 0.4455 (mmp-170) cc_final: 0.3982 (mmt180) REVERT: C 240 VAL cc_start: 0.8063 (t) cc_final: 0.7848 (t) REVERT: C 400 ARG cc_start: 0.4228 (mmp-170) cc_final: 0.3735 (mmt180) REVERT: E 258 LEU cc_start: 0.6234 (OUTLIER) cc_final: 0.5983 (pp) REVERT: E 400 ARG cc_start: 0.4125 (mmp-170) cc_final: 0.3649 (mmt180) outliers start: 24 outliers final: 19 residues processed: 68 average time/residue: 0.1167 time to fit residues: 12.5910 Evaluate side-chains 66 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 203 ILE 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 258 LEU Chi-restraints excluded: chain B residue 262 TYR 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 100 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 258 LEU Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 321 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 35 optimal weight: 10.0000 chunk 171 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 159 optimal weight: 0.5980 chunk 174 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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 = 0.3677 r_free = 0.3677 target = 0.081314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.062774 restraints weight = 66246.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.061090 restraints weight = 62305.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.061593 restraints weight = 63934.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.061673 restraints weight = 41396.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.061977 restraints weight = 34902.259| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 17180 Z= 0.231 Angle : 0.664 10.190 23515 Z= 0.328 Chirality : 0.045 0.163 2750 Planarity : 0.005 0.048 2850 Dihedral : 4.989 28.845 2645 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.52 % Allowed : 16.31 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.20), residues: 1955 helix: 0.88 (0.18), residues: 880 sheet: -0.18 (0.26), residues: 440 loop : -2.19 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 420 TYR 0.020 0.002 TYR C 67 PHE 0.024 0.001 PHE E 265 TRP 0.031 0.002 TRP A 331 HIS 0.005 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00537 (17160) covalent geometry : angle 0.66168 (23460) SS BOND : bond 0.00167 ( 5) SS BOND : angle 0.80908 ( 10) hydrogen bonds : bond 0.03854 ( 745) hydrogen bonds : angle 3.82378 ( 2190) link_NAG-ASN : bond 0.00116 ( 15) link_NAG-ASN : angle 1.51200 ( 45) ********************** 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 74 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 46 time to evaluate : 0.485 Fit side-chains REVERT: A 258 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.6039 (pp) REVERT: B 400 ARG cc_start: 0.4530 (mmp-170) cc_final: 0.3780 (mmt180) REVERT: C 400 ARG cc_start: 0.4430 (mmp-170) cc_final: 0.3889 (mmt180) REVERT: D 240 VAL cc_start: 0.8221 (t) cc_final: 0.7988 (t) outliers start: 28 outliers final: 26 residues processed: 73 average time/residue: 0.1034 time to fit residues: 12.3442 Evaluate side-chains 71 residues out of total 1845 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 44 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 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 258 LEU Chi-restraints excluded: chain B residue 262 TYR 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 100 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 258 LEU Chi-restraints excluded: chain E residue 265 PHE Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 321 LEU 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 109 optimal weight: 10.0000 chunk 125 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.082561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.063934 restraints weight = 66328.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.062370 restraints weight = 60494.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.063026 restraints weight = 58125.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.062974 restraints weight = 40128.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.063539 restraints weight = 34122.706| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4114 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= 0.134 Angle : 0.585 9.504 23515 Z= 0.286 Chirality : 0.043 0.156 2750 Planarity : 0.004 0.044 2850 Dihedral : 4.708 27.127 2645 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.36 % Allowed : 16.48 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.20), residues: 1955 helix: 1.08 (0.19), residues: 870 sheet: -0.17 (0.26), residues: 435 loop : -2.03 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 306 TYR 0.013 0.001 TYR D 67 PHE 0.020 0.001 PHE E 265 TRP 0.021 0.001 TRP A 331 HIS 0.003 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00308 (17160) covalent geometry : angle 0.58221 (23460) SS BOND : bond 0.00054 ( 5) SS BOND : angle 0.45485 ( 10) hydrogen bonds : bond 0.03268 ( 745) hydrogen bonds : angle 3.66855 ( 2190) link_NAG-ASN : bond 0.00072 ( 15) link_NAG-ASN : angle 1.40339 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1903.80 seconds wall clock time: 33 minutes 53.29 seconds (2033.29 seconds total)