Starting phenix.real_space_refine on Thu Feb 5 00:52:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pkx_71706/02_2026/9pkx_71706.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pkx_71706/02_2026/9pkx_71706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pkx_71706/02_2026/9pkx_71706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pkx_71706/02_2026/9pkx_71706.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pkx_71706/02_2026/9pkx_71706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pkx_71706/02_2026/9pkx_71706.map" } resolution = 2.86 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= 0.001 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 90 5.16 5 C 9060 2.51 5 N 2226 2.21 5 O 2467 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13843 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2730 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 15, 'TRANS': 321} Chain breaks: 1 Chain: "D" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2738 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 15, 'TRANS': 322} Chain breaks: 1 Chain: "C" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2721 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 15, 'TRANS': 320} Chain breaks: 1 Chain: "B" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2768 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Chain: "E" Number of atoms: 2691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2691 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 16, 'TRANS': 314} Chain breaks: 1 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'SY9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'SY9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'SY9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {'NAG': 1, 'SY9': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.75, per 1000 atoms: 0.20 Number of scatterers: 13843 At special positions: 0 Unit cell: (91.56, 92.4, 134.4, 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 90 16.00 O 2467 8.00 N 2226 7.00 C 9060 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 182 " - pdb=" SG CYS E 196 " 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 62 " " NAG B 502 " - " ASN B 62 " " NAG C 502 " - " ASN C 62 " " NAG D 501 " - " ASN D 62 " " NAG E 603 " - " ASN E 241 " Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 553.2 milliseconds 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3230 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 24 sheets defined 39.5% alpha, 41.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 33 through 43 removed outlier: 3.606A pdb=" N PHE A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU A 38 " --> pdb=" O PRO A 34 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASP A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 98 Processing helix chain 'A' and resid 113 through 117 removed outlier: 3.635A pdb=" N ILE A 117 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 Processing helix chain 'A' and resid 251 through 263 removed outlier: 3.673A pdb=" N TRP A 263 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 268 Processing helix chain 'A' and resid 272 through 298 removed outlier: 3.883A pdb=" N ALA A 296 " --> pdb=" O SER A 292 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 334 removed outlier: 3.523A pdb=" N ILE A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 434 removed outlier: 3.615A pdb=" N ASP A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'D' and resid 35 through 42 removed outlier: 3.830A pdb=" N ASP D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS D 40 " --> pdb=" O GLU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 98 Processing helix chain 'D' and resid 113 through 117 removed outlier: 3.790A pdb=" N ILE D 117 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 removed outlier: 3.600A pdb=" N ILE D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 263 removed outlier: 3.519A pdb=" N TRP D 263 " --> pdb=" O VAL D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 272 through 295 removed outlier: 3.514A pdb=" N GLY D 293 " --> pdb=" O THR D 289 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER D 294 " --> pdb=" O GLN D 290 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 333 removed outlier: 3.752A pdb=" N TYR D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA D 327 " --> pdb=" O LEU D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 436 removed outlier: 3.963A pdb=" N VAL D 416 " --> pdb=" O THR D 412 " (cutoff:3.500A) Proline residue: D 419 - end of helix removed outlier: 3.587A pdb=" N ILE D 436 " --> pdb=" O THR D 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 42 Processing helix chain 'C' and resid 95 through 98 removed outlier: 3.593A pdb=" N ALA C 98 " --> pdb=" O PRO C 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 95 through 98' Processing helix chain 'C' and resid 110 through 117 removed outlier: 4.687A pdb=" N ASP C 115 " --> pdb=" O SER C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 251 Processing helix chain 'C' and resid 251 through 263 removed outlier: 3.686A pdb=" N TRP C 263 " --> pdb=" O VAL C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 272 through 295 Processing helix chain 'C' and resid 305 through 334 removed outlier: 3.529A pdb=" N LEU C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 323 " --> pdb=" O PHE C 319 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR C 325 " --> pdb=" O ALA C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 435 removed outlier: 3.936A pdb=" N VAL C 416 " --> pdb=" O THR C 412 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE C 418 " --> pdb=" O SER C 414 " (cutoff:3.500A) Proline residue: C 419 - end of helix removed outlier: 3.530A pdb=" N LYS C 434 " --> pdb=" O TRP C 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 43 Processing helix chain 'B' and resid 95 through 98 Processing helix chain 'B' and resid 113 through 117 removed outlier: 3.573A pdb=" N ILE B 117 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 251 Processing helix chain 'B' and resid 251 through 263 removed outlier: 3.730A pdb=" N TRP B 263 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 268 Processing helix chain 'B' and resid 272 through 298 removed outlier: 3.530A pdb=" N SER B 294 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA B 296 " --> pdb=" O SER B 292 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER B 297 " --> pdb=" O GLY B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 334 Processing helix chain 'B' and resid 400 through 435 removed outlier: 4.119A pdb=" N VAL B 416 " --> pdb=" O THR B 412 " (cutoff:3.500A) Proline residue: B 419 - end of helix Processing helix chain 'E' and resid 55 through 64 removed outlier: 4.172A pdb=" N ILE E 59 " --> pdb=" O SER E 55 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU E 60 " --> pdb=" O THR E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 137 removed outlier: 4.521A pdb=" N LYS E 135 " --> pdb=" O LYS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 272 Processing helix chain 'E' and resid 272 through 284 removed outlier: 3.588A pdb=" N TRP E 284 " --> pdb=" O VAL E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 289 Processing helix chain 'E' and resid 293 through 319 Proline residue: E 299 - end of helix removed outlier: 3.629A pdb=" N ALA E 316 " --> pdb=" O CYS E 312 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER E 317 " --> pdb=" O THR E 313 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU E 318 " --> pdb=" O SER E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 355 removed outlier: 3.616A pdb=" N LEU E 343 " --> pdb=" O GLY E 339 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR E 346 " --> pdb=" O SER E 342 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER E 355 " --> pdb=" O VAL E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 468 through 494 removed outlier: 4.050A pdb=" N ALA E 476 " --> pdb=" O LEU E 472 " (cutoff:3.500A) Proline residue: E 479 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 106 through 108 removed outlier: 4.388A pdb=" N ASN A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ASN A 93 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASN A 62 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL A 61 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLU A 193 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N VAL A 63 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 131 removed outlier: 6.691A pdb=" N VAL A 159 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ALA A 130 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR A 157 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ASN A 93 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASN A 62 " --> pdb=" O ASN A 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 123 Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 123 Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA6, first strand: chain 'D' and resid 106 through 109 removed outlier: 4.567A pdb=" N LEU D 142 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASN D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASN D 93 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASN D 62 " --> pdb=" O ASN D 93 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL D 61 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLU D 193 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N VAL D 63 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.396A pdb=" N VAL D 159 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ALA D 130 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR D 157 " --> pdb=" O ALA D 130 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N PHE D 132 " --> pdb=" O ARG D 155 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ARG D 155 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASN D 93 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASN D 62 " --> pdb=" O ASN D 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 122 through 124 removed outlier: 7.550A pdb=" N CYS D 233 " --> pdb=" O ARG D 220 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ARG D 220 " --> pdb=" O CYS D 233 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLU D 235 " --> pdb=" O ASP D 218 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASP D 218 " --> pdb=" O GLU D 235 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ARG D 237 " --> pdb=" O GLU D 216 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLU D 216 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N HIS D 239 " --> pdb=" O LYS D 214 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AB1, first strand: chain 'C' and resid 106 through 108 removed outlier: 4.410A pdb=" N ASN C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASN C 93 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN C 62 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL C 61 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLU C 193 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL C 63 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 127 through 132 removed outlier: 6.410A pdb=" N VAL C 159 " --> pdb=" O LYS C 128 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA C 130 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR C 157 " --> pdb=" O ALA C 130 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N PHE C 132 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N ARG C 155 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASN C 93 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN C 62 " --> pdb=" O ASN C 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 122 through 124 Processing sheet with id=AB4, first strand: chain 'C' and resid 122 through 124 Processing sheet with id=AB5, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AB6, first strand: chain 'B' and resid 106 through 109 removed outlier: 4.156A pdb=" N LEU B 142 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASN B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN B 93 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASN B 62 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL B 61 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLU B 193 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL B 63 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 127 through 131 removed outlier: 6.553A pdb=" N VAL B 159 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA B 130 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR B 157 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN B 93 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASN B 62 " --> pdb=" O ASN B 93 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 122 through 124 Processing sheet with id=AB9, first strand: chain 'B' and resid 122 through 124 Processing sheet with id=AC1, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AC2, first strand: chain 'E' and resid 126 through 128 removed outlier: 4.656A pdb=" N ASP E 169 " --> pdb=" O PHE E 165 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ASP E 100 " --> pdb=" O SER E 93 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N SER E 93 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ARG E 102 " --> pdb=" O PHE E 91 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE E 91 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASN E 104 " --> pdb=" O ASN E 89 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASN E 112 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU E 81 " --> pdb=" O ASN E 112 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL E 80 " --> pdb=" O GLN E 211 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N MET E 213 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ASP E 82 " --> pdb=" O MET E 213 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 147 through 152 removed outlier: 6.596A pdb=" N GLU E 147 " --> pdb=" O SER E 181 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N SER E 181 " --> pdb=" O GLU E 147 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER E 149 " --> pdb=" O THR E 179 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ASP E 100 " --> pdb=" O SER E 93 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N SER E 93 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ARG E 102 " --> pdb=" O PHE E 91 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE E 91 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASN E 104 " --> pdb=" O ASN E 89 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASN E 112 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU E 81 " --> pdb=" O ASN E 112 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 142 through 144 Processing sheet with id=AC5, first strand: chain 'E' and resid 142 through 144 removed outlier: 4.163A pdb=" N GLU E 256 " --> pdb=" O TYR E 239 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 244 through 245 804 hydrogen bonds defined for protein. 2319 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2167 1.31 - 1.44: 3982 1.44 - 1.56: 7921 1.56 - 1.69: 0 1.69 - 1.81: 149 Bond restraints: 14219 Sorted by residual: bond pdb=" C PRO E 219 " pdb=" O PRO E 219 " ideal model delta sigma weight residual 1.237 1.190 0.048 1.26e-02 6.30e+03 1.44e+01 bond pdb=" C PRO A 120 " pdb=" O PRO A 120 " ideal model delta sigma weight residual 1.233 1.193 0.040 1.16e-02 7.43e+03 1.17e+01 bond pdb=" N PHE A 123 " pdb=" CA PHE A 123 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.18e-02 7.18e+03 8.09e+00 bond pdb=" N ASN A 126 " pdb=" CA ASN A 126 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.18e-02 7.18e+03 7.32e+00 bond pdb=" N GLU E 158 " pdb=" CA GLU E 158 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 7.14e+00 ... (remaining 14214 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 18842 1.74 - 3.48: 416 3.48 - 5.22: 65 5.22 - 6.96: 18 6.96 - 8.71: 3 Bond angle restraints: 19344 Sorted by residual: angle pdb=" N LYS A 128 " pdb=" CA LYS A 128 " pdb=" C LYS A 128 " ideal model delta sigma weight residual 114.31 107.87 6.44 1.29e+00 6.01e-01 2.49e+01 angle pdb=" CA VAL E 155 " pdb=" C VAL E 155 " pdb=" O VAL E 155 " ideal model delta sigma weight residual 121.17 116.81 4.36 1.06e+00 8.90e-01 1.69e+01 angle pdb=" C THR E 156 " pdb=" CA THR E 156 " pdb=" CB THR E 156 " ideal model delta sigma weight residual 110.42 118.44 -8.02 1.99e+00 2.53e-01 1.62e+01 angle pdb=" CA PHE A 123 " pdb=" CB PHE A 123 " pdb=" CG PHE A 123 " ideal model delta sigma weight residual 113.80 117.59 -3.79 1.00e+00 1.00e+00 1.44e+01 angle pdb=" C ASP A 121 " pdb=" CA ASP A 121 " pdb=" CB ASP A 121 " ideal model delta sigma weight residual 111.88 106.57 5.31 1.41e+00 5.03e-01 1.42e+01 ... (remaining 19339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.15: 8313 23.15 - 46.30: 368 46.30 - 69.44: 45 69.44 - 92.59: 10 92.59 - 115.74: 17 Dihedral angle restraints: 8753 sinusoidal: 3775 harmonic: 4978 Sorted by residual: dihedral pdb=" C2 NAG C 502 " pdb=" C1 NAG C 502 " pdb=" O5 NAG C 502 " pdb=" C5 NAG C 502 " ideal model delta sinusoidal sigma weight residual -62.96 52.78 -115.74 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" CA TYR B 102 " pdb=" C TYR B 102 " pdb=" N PRO B 103 " pdb=" CA PRO B 103 " ideal model delta harmonic sigma weight residual -180.00 -160.46 -19.54 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" N2 NAG C 502 " pdb=" C1 NAG C 502 " pdb=" C2 NAG C 502 " pdb=" O5 NAG C 502 " ideal model delta sinusoidal sigma weight residual -178.19 -65.27 -112.92 1 3.00e+01 1.11e-03 1.48e+01 ... (remaining 8750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1796 0.054 - 0.107: 335 0.107 - 0.161: 48 0.161 - 0.215: 11 0.215 - 0.269: 6 Chirality restraints: 2196 Sorted by residual: chirality pdb=" CA ASN E 159 " pdb=" N ASN E 159 " pdb=" C ASN E 159 " pdb=" CB ASN E 159 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C1 NAG E 603 " pdb=" ND2 ASN E 241 " pdb=" C2 NAG E 603 " pdb=" O5 NAG E 603 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA PHE E 152 " pdb=" N PHE E 152 " pdb=" C PHE E 152 " pdb=" CB PHE E 152 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 2193 not shown) Planarity restraints: 2393 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAA SY9 E 601 " -0.004 2.00e-02 2.50e+03 1.55e-01 3.61e+02 pdb=" CAI SY9 E 601 " 0.168 2.00e-02 2.50e+03 pdb=" CAK SY9 E 601 " -0.184 2.00e-02 2.50e+03 pdb=" CAL SY9 E 601 " 0.024 2.00e-02 2.50e+03 pdb=" NAH SY9 E 601 " 0.200 2.00e-02 2.50e+03 pdb=" OAJ SY9 E 601 " -0.204 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAA SY9 A 501 " 0.174 2.00e-02 2.50e+03 1.30e-01 2.53e+02 pdb=" CAI SY9 A 501 " 0.070 2.00e-02 2.50e+03 pdb=" CAK SY9 A 501 " -0.104 2.00e-02 2.50e+03 pdb=" CAL SY9 A 501 " 0.133 2.00e-02 2.50e+03 pdb=" NAH SY9 A 501 " -0.135 2.00e-02 2.50e+03 pdb=" OAJ SY9 A 501 " -0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAA SY9 C 501 " -0.176 2.00e-02 2.50e+03 1.29e-01 2.50e+02 pdb=" CAI SY9 C 501 " -0.063 2.00e-02 2.50e+03 pdb=" CAK SY9 C 501 " 0.093 2.00e-02 2.50e+03 pdb=" CAL SY9 C 501 " -0.132 2.00e-02 2.50e+03 pdb=" NAH SY9 C 501 " 0.152 2.00e-02 2.50e+03 pdb=" OAJ SY9 C 501 " 0.126 2.00e-02 2.50e+03 ... (remaining 2390 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2152 2.76 - 3.30: 13058 3.30 - 3.83: 22267 3.83 - 4.37: 27708 4.37 - 4.90: 47205 Nonbonded interactions: 112390 Sorted by model distance: nonbonded pdb=" OD2 ASP C 110 " pdb=" OG SER C 112 " model vdw 2.230 3.040 nonbonded pdb=" OE1 GLU D 193 " pdb=" OH TYR D 221 " model vdw 2.231 3.040 nonbonded pdb=" OG1 THR B 186 " pdb=" OD1 ASN B 188 " model vdw 2.232 3.040 nonbonded pdb=" O TRP A 267 " pdb=" NH2 ARG B 333 " model vdw 2.254 3.120 nonbonded pdb=" NH1 ARG C 295 " pdb=" OG SER B 294 " model vdw 2.255 3.120 ... (remaining 112385 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 33 through 334 or resid 402 through 435 or resid 502)) selection = (chain 'B' and (resid 33 through 334 or resid 402 through 435 or resid 502)) selection = (chain 'C' and (resid 33 through 435 or resid 502)) selection = (chain 'D' and (resid 33 through 334 or resid 402 through 435 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.840 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 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:8.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 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 : 0.003 0.049 14225 Z= 0.188 Angle : 0.625 8.705 19361 Z= 0.341 Chirality : 0.046 0.269 2196 Planarity : 0.008 0.155 2388 Dihedral : 14.065 115.740 5520 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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 are not related in a simple way. whole: 0.97 (0.20), residues: 1663 helix: 1.26 (0.21), residues: 541 sheet: 1.26 (0.28), residues: 407 loop : -0.13 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 83 TYR 0.016 0.001 TYR A 152 PHE 0.020 0.001 PHE E 152 TRP 0.008 0.001 TRP B 118 HIS 0.009 0.001 HIS E 153 Details of bonding type rmsd covalent geometry : bond 0.00333 (14219) covalent geometry : angle 0.62120 (19344) SS BOND : bond 0.00027 ( 1) SS BOND : angle 0.08061 ( 2) hydrogen bonds : bond 0.23687 ( 669) hydrogen bonds : angle 7.27856 ( 2319) link_NAG-ASN : bond 0.00639 ( 5) link_NAG-ASN : angle 2.67706 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.466 Fit side-chains REVERT: A 311 MET cc_start: 0.8918 (mmt) cc_final: 0.8613 (mmt) REVERT: D 333 ARG cc_start: 0.6234 (tpm170) cc_final: 0.5991 (tpm170) REVERT: C 250 GLN cc_start: 0.8000 (tp-100) cc_final: 0.7748 (mm-40) REVERT: E 155 VAL cc_start: 0.8361 (p) cc_final: 0.8148 (m) REVERT: E 191 MET cc_start: 0.8274 (pmm) cc_final: 0.8059 (pmt) REVERT: E 315 LEU cc_start: 0.8816 (mm) cc_final: 0.8548 (mm) REVERT: E 321 LYS cc_start: 0.8254 (mmtp) cc_final: 0.7993 (mppt) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.6556 time to fit residues: 159.9205 Evaluate side-chains 152 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.0970 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 overall best weight: 3.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN A 290 GLN D 210 GLN D 250 GLN C 225 HIS C 426 ASN E 61 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.091843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.073253 restraints weight = 25827.808| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.78 r_work: 0.2836 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 14225 Z= 0.242 Angle : 0.674 10.435 19361 Z= 0.347 Chirality : 0.046 0.259 2196 Planarity : 0.005 0.051 2388 Dihedral : 9.657 107.333 2254 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.58 % Allowed : 8.45 % Favored : 88.97 % 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 are not related in a simple way. whole: 1.47 (0.21), residues: 1663 helix: 2.11 (0.21), residues: 561 sheet: 1.30 (0.28), residues: 402 loop : -0.13 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 83 TYR 0.023 0.002 TYR B 325 PHE 0.022 0.002 PHE C 428 TRP 0.011 0.001 TRP B 92 HIS 0.005 0.001 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00568 (14219) covalent geometry : angle 0.67013 (19344) SS BOND : bond 0.00266 ( 1) SS BOND : angle 0.63112 ( 2) hydrogen bonds : bond 0.06269 ( 669) hydrogen bonds : angle 4.67369 ( 2319) link_NAG-ASN : bond 0.00286 ( 5) link_NAG-ASN : angle 2.55123 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8021 (mt-10) REVERT: C 250 GLN cc_start: 0.8779 (tp-100) cc_final: 0.7972 (tp-100) REVERT: C 251 MET cc_start: 0.8564 (mtt) cc_final: 0.8294 (mtt) REVERT: E 315 LEU cc_start: 0.8672 (mm) cc_final: 0.8427 (mm) REVERT: E 321 LYS cc_start: 0.8698 (mmtp) cc_final: 0.8212 (mppt) REVERT: E 473 TYR cc_start: 0.7767 (t80) cc_final: 0.7465 (t80) outliers start: 39 outliers final: 10 residues processed: 176 average time/residue: 0.6172 time to fit residues: 118.0180 Evaluate side-chains 162 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 312 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 44 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 121 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN D 210 GLN D 250 GLN D 290 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.093437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.074701 restraints weight = 25918.297| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.83 r_work: 0.2857 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14225 Z= 0.162 Angle : 0.604 9.310 19361 Z= 0.306 Chirality : 0.044 0.261 2196 Planarity : 0.004 0.048 2388 Dihedral : 8.441 106.310 2254 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.64 % Allowed : 9.45 % Favored : 87.91 % 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 are not related in a simple way. whole: 1.62 (0.21), residues: 1663 helix: 2.32 (0.21), residues: 558 sheet: 1.42 (0.28), residues: 402 loop : -0.15 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 333 TYR 0.023 0.001 TYR B 325 PHE 0.019 0.002 PHE A 123 TRP 0.008 0.001 TRP B 92 HIS 0.004 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00370 (14219) covalent geometry : angle 0.60104 (19344) SS BOND : bond 0.00228 ( 1) SS BOND : angle 0.33757 ( 2) hydrogen bonds : bond 0.05188 ( 669) hydrogen bonds : angle 4.23442 ( 2319) link_NAG-ASN : bond 0.00263 ( 5) link_NAG-ASN : angle 2.36414 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 161 time to evaluate : 0.541 Fit side-chains REVERT: A 241 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8051 (mt-10) REVERT: D 51 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8353 (mmp80) REVERT: D 333 ARG cc_start: 0.6604 (tpm170) cc_final: 0.6215 (tpm170) REVERT: C 250 GLN cc_start: 0.8783 (tp-100) cc_final: 0.8146 (mm-40) REVERT: C 251 MET cc_start: 0.8528 (mtt) cc_final: 0.8298 (mtt) REVERT: B 99 TYR cc_start: 0.7654 (p90) cc_final: 0.7362 (p90) REVERT: B 250 GLN cc_start: 0.8989 (tp-100) cc_final: 0.8778 (tp-100) REVERT: B 333 ARG cc_start: 0.8302 (ttm170) cc_final: 0.7901 (ttp80) REVERT: E 117 ARG cc_start: 0.8184 (mtm110) cc_final: 0.7890 (mtm-85) REVERT: E 473 TYR cc_start: 0.7828 (t80) cc_final: 0.7549 (t80) outliers start: 40 outliers final: 19 residues processed: 178 average time/residue: 0.6171 time to fit residues: 119.3183 Evaluate side-chains 171 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 312 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 10.0000 chunk 2 optimal weight: 0.0870 chunk 12 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN D 210 GLN D 250 GLN C 290 GLN B 334 GLN E 61 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.093681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.075039 restraints weight = 25786.469| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.80 r_work: 0.2865 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14225 Z= 0.153 Angle : 0.582 8.030 19361 Z= 0.296 Chirality : 0.043 0.163 2196 Planarity : 0.004 0.052 2388 Dihedral : 6.574 94.460 2254 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.10 % Allowed : 10.77 % Favored : 86.13 % 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 are not related in a simple way. whole: 1.70 (0.21), residues: 1663 helix: 2.42 (0.22), residues: 559 sheet: 1.46 (0.28), residues: 406 loop : -0.13 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 83 TYR 0.024 0.001 TYR B 325 PHE 0.024 0.002 PHE C 428 TRP 0.008 0.001 TRP B 92 HIS 0.004 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00354 (14219) covalent geometry : angle 0.57644 (19344) SS BOND : bond 0.00270 ( 1) SS BOND : angle 0.33424 ( 2) hydrogen bonds : bond 0.04554 ( 669) hydrogen bonds : angle 4.01677 ( 2319) link_NAG-ASN : bond 0.00306 ( 5) link_NAG-ASN : angle 2.98547 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 167 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8035 (mt-10) REVERT: D 51 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8370 (mmp80) REVERT: D 333 ARG cc_start: 0.6732 (tpm170) cc_final: 0.6456 (tpm170) REVERT: C 251 MET cc_start: 0.8525 (mtt) cc_final: 0.8254 (mtt) REVERT: C 295 ARG cc_start: 0.8382 (ttm170) cc_final: 0.8088 (ttm170) REVERT: B 99 TYR cc_start: 0.7750 (p90) cc_final: 0.7509 (p90) REVERT: B 250 GLN cc_start: 0.8944 (tp-100) cc_final: 0.8705 (tp-100) REVERT: B 333 ARG cc_start: 0.8258 (ttm170) cc_final: 0.7725 (ttp80) REVERT: E 315 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8508 (mm) REVERT: E 473 TYR cc_start: 0.7819 (t80) cc_final: 0.7499 (t80) outliers start: 47 outliers final: 20 residues processed: 186 average time/residue: 0.5868 time to fit residues: 118.8100 Evaluate side-chains 170 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 317 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 147 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 151 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 163 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN D 210 GLN D 250 GLN C 290 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.091934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.073621 restraints weight = 26106.322| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.78 r_work: 0.2824 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14225 Z= 0.216 Angle : 0.616 8.363 19361 Z= 0.317 Chirality : 0.045 0.234 2196 Planarity : 0.004 0.049 2388 Dihedral : 6.598 93.218 2254 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.17 % Allowed : 12.35 % Favored : 84.48 % 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 are not related in a simple way. whole: 1.62 (0.21), residues: 1663 helix: 2.36 (0.21), residues: 559 sheet: 1.38 (0.28), residues: 404 loop : -0.15 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 83 TYR 0.027 0.002 TYR B 325 PHE 0.018 0.002 PHE B 425 TRP 0.009 0.001 TRP B 92 HIS 0.005 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00514 (14219) covalent geometry : angle 0.61208 (19344) SS BOND : bond 0.00312 ( 1) SS BOND : angle 0.54116 ( 2) hydrogen bonds : bond 0.04787 ( 669) hydrogen bonds : angle 4.08419 ( 2319) link_NAG-ASN : bond 0.00228 ( 5) link_NAG-ASN : angle 2.69773 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 148 time to evaluate : 0.374 Fit side-chains REVERT: A 241 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8031 (mp0) REVERT: A 288 THR cc_start: 0.9123 (OUTLIER) cc_final: 0.8913 (t) REVERT: D 51 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8386 (mmp80) REVERT: D 333 ARG cc_start: 0.6747 (tpm170) cc_final: 0.6477 (tpm170) REVERT: C 250 GLN cc_start: 0.8848 (tp-100) cc_final: 0.8319 (tm-30) REVERT: C 251 MET cc_start: 0.8609 (mtt) cc_final: 0.8341 (mtt) REVERT: B 333 ARG cc_start: 0.8232 (ttm170) cc_final: 0.7809 (ttp80) REVERT: E 117 ARG cc_start: 0.8223 (mtm110) cc_final: 0.7992 (mtm-85) REVERT: E 262 ARG cc_start: 0.8227 (mtm180) cc_final: 0.7949 (mtm180) REVERT: E 321 LYS cc_start: 0.8656 (mttt) cc_final: 0.7904 (mppt) REVERT: E 473 TYR cc_start: 0.7819 (t80) cc_final: 0.7473 (t80) outliers start: 48 outliers final: 23 residues processed: 173 average time/residue: 0.6180 time to fit residues: 116.1672 Evaluate side-chains 180 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 312 CYS Chi-restraints excluded: chain E residue 317 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 46 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 140 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN D 210 GLN D 250 GLN C 290 GLN B 334 GLN E 61 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.093655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.075373 restraints weight = 25610.846| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.76 r_work: 0.2859 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14225 Z= 0.133 Angle : 0.572 8.994 19361 Z= 0.292 Chirality : 0.043 0.211 2196 Planarity : 0.004 0.046 2388 Dihedral : 6.226 90.632 2254 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.38 % Allowed : 13.47 % Favored : 84.15 % 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 are not related in a simple way. whole: 1.75 (0.21), residues: 1663 helix: 2.45 (0.22), residues: 559 sheet: 1.46 (0.28), residues: 408 loop : -0.08 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 295 TYR 0.024 0.001 TYR B 325 PHE 0.025 0.001 PHE C 428 TRP 0.008 0.001 TRP B 92 HIS 0.003 0.000 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00305 (14219) covalent geometry : angle 0.56780 (19344) SS BOND : bond 0.00334 ( 1) SS BOND : angle 0.29915 ( 2) hydrogen bonds : bond 0.04174 ( 669) hydrogen bonds : angle 3.88992 ( 2319) link_NAG-ASN : bond 0.00363 ( 5) link_NAG-ASN : angle 2.52253 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 0.509 Fit side-chains REVERT: D 333 ARG cc_start: 0.6661 (tpm170) cc_final: 0.6406 (tpm170) REVERT: C 251 MET cc_start: 0.8555 (mtt) cc_final: 0.8322 (mtt) REVERT: C 295 ARG cc_start: 0.8306 (ttm170) cc_final: 0.7921 (ttm170) REVERT: B 99 TYR cc_start: 0.7856 (p90) cc_final: 0.7521 (p90) REVERT: B 333 ARG cc_start: 0.8166 (ttm170) cc_final: 0.7727 (ttp80) REVERT: E 117 ARG cc_start: 0.8212 (mtm110) cc_final: 0.7940 (mtm-85) REVERT: E 321 LYS cc_start: 0.8646 (mttt) cc_final: 0.7910 (mppt) REVERT: E 473 TYR cc_start: 0.7808 (t80) cc_final: 0.7457 (t80) outliers start: 36 outliers final: 19 residues processed: 181 average time/residue: 0.6147 time to fit residues: 120.9697 Evaluate side-chains 181 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 312 CYS Chi-restraints excluded: chain E residue 317 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 158 optimal weight: 1.9990 chunk 109 optimal weight: 0.4980 chunk 41 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 250 GLN A 290 GLN D 210 GLN C 290 GLN B 334 GLN E 151 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.095120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.076651 restraints weight = 25695.495| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.79 r_work: 0.2895 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14225 Z= 0.111 Angle : 0.557 9.231 19361 Z= 0.283 Chirality : 0.042 0.202 2196 Planarity : 0.004 0.049 2388 Dihedral : 5.892 88.871 2254 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.38 % Allowed : 14.86 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.21), residues: 1663 helix: 2.51 (0.22), residues: 560 sheet: 1.44 (0.28), residues: 412 loop : -0.02 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 83 TYR 0.022 0.001 TYR B 325 PHE 0.017 0.001 PHE B 425 TRP 0.008 0.001 TRP B 92 HIS 0.003 0.000 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00246 (14219) covalent geometry : angle 0.55294 (19344) SS BOND : bond 0.00310 ( 1) SS BOND : angle 0.29644 ( 2) hydrogen bonds : bond 0.03693 ( 669) hydrogen bonds : angle 3.71667 ( 2319) link_NAG-ASN : bond 0.00415 ( 5) link_NAG-ASN : angle 2.39866 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 241 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8194 (mm-30) REVERT: A 315 LEU cc_start: 0.9244 (tp) cc_final: 0.8993 (tm) REVERT: D 289 THR cc_start: 0.9320 (OUTLIER) cc_final: 0.9095 (p) REVERT: C 42 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7466 (ptm) REVERT: C 251 MET cc_start: 0.8490 (mtt) cc_final: 0.8237 (mtt) REVERT: B 99 TYR cc_start: 0.7861 (p90) cc_final: 0.7536 (p90) REVERT: B 250 GLN cc_start: 0.8807 (tp-100) cc_final: 0.8537 (tp-100) REVERT: B 333 ARG cc_start: 0.8065 (tmm160) cc_final: 0.7581 (ttp80) REVERT: E 117 ARG cc_start: 0.8164 (mtm110) cc_final: 0.7881 (mtm-85) REVERT: E 321 LYS cc_start: 0.8637 (mttt) cc_final: 0.7947 (mppt) REVERT: E 473 TYR cc_start: 0.7712 (t80) cc_final: 0.7456 (t80) outliers start: 36 outliers final: 15 residues processed: 184 average time/residue: 0.6187 time to fit residues: 124.1823 Evaluate side-chains 174 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 317 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 146 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 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 168 ASN A 250 GLN D 168 ASN D 210 GLN C 290 GLN B 334 GLN E 61 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.091711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.073682 restraints weight = 25956.346| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.78 r_work: 0.2824 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14225 Z= 0.206 Angle : 0.620 9.522 19361 Z= 0.318 Chirality : 0.044 0.225 2196 Planarity : 0.004 0.056 2388 Dihedral : 6.289 87.455 2254 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.97 % Allowed : 14.86 % 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 are not related in a simple way. whole: 1.74 (0.21), residues: 1663 helix: 2.46 (0.22), residues: 559 sheet: 1.46 (0.28), residues: 403 loop : -0.09 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 83 TYR 0.027 0.002 TYR B 325 PHE 0.027 0.002 PHE C 428 TRP 0.009 0.001 TRP B 92 HIS 0.005 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00493 (14219) covalent geometry : angle 0.61645 (19344) SS BOND : bond 0.00342 ( 1) SS BOND : angle 0.55729 ( 2) hydrogen bonds : bond 0.04399 ( 669) hydrogen bonds : angle 3.90900 ( 2319) link_NAG-ASN : bond 0.00209 ( 5) link_NAG-ASN : angle 2.50793 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 153 time to evaluate : 0.559 Fit side-chains REVERT: D 51 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8381 (mmp80) REVERT: D 333 ARG cc_start: 0.6785 (tpm170) cc_final: 0.6494 (tpm170) REVERT: C 42 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7445 (ptm) REVERT: B 333 ARG cc_start: 0.8132 (tmm160) cc_final: 0.7712 (ttp80) REVERT: E 117 ARG cc_start: 0.8320 (mtm110) cc_final: 0.8030 (mtm-85) REVERT: E 321 LYS cc_start: 0.8666 (mttt) cc_final: 0.7971 (mppt) REVERT: E 473 TYR cc_start: 0.7773 (t80) cc_final: 0.7426 (t80) outliers start: 45 outliers final: 19 residues processed: 176 average time/residue: 0.6049 time to fit residues: 115.9023 Evaluate side-chains 173 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 317 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 132 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 139 optimal weight: 0.0980 chunk 60 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 250 GLN D 168 ASN D 210 GLN C 290 GLN B 334 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.093179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.075328 restraints weight = 25601.189| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.74 r_work: 0.2863 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14225 Z= 0.145 Angle : 0.603 9.738 19361 Z= 0.304 Chirality : 0.043 0.398 2196 Planarity : 0.004 0.053 2388 Dihedral : 6.059 86.660 2254 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.11 % Allowed : 15.65 % Favored : 82.23 % 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 are not related in a simple way. whole: 1.80 (0.21), residues: 1663 helix: 2.53 (0.22), residues: 559 sheet: 1.39 (0.28), residues: 413 loop : -0.03 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 83 TYR 0.023 0.001 TYR B 325 PHE 0.019 0.001 PHE E 122 TRP 0.011 0.001 TRP C 263 HIS 0.003 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00342 (14219) covalent geometry : angle 0.59545 (19344) SS BOND : bond 0.00343 ( 1) SS BOND : angle 0.41513 ( 2) hydrogen bonds : bond 0.04001 ( 669) hydrogen bonds : angle 3.79862 ( 2319) link_NAG-ASN : bond 0.00601 ( 5) link_NAG-ASN : angle 3.46280 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: D 51 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8374 (mmp80) REVERT: D 171 MET cc_start: 0.8982 (mtm) cc_final: 0.8778 (mpp) REVERT: D 333 ARG cc_start: 0.6657 (tpm170) cc_final: 0.6354 (tpm170) REVERT: B 333 ARG cc_start: 0.8119 (tmm160) cc_final: 0.7608 (ttp80) REVERT: E 117 ARG cc_start: 0.8312 (mtm110) cc_final: 0.8013 (mtm-85) REVERT: E 321 LYS cc_start: 0.8689 (mttt) cc_final: 0.7984 (mppt) REVERT: E 473 TYR cc_start: 0.7717 (t80) cc_final: 0.7371 (t80) outliers start: 32 outliers final: 21 residues processed: 180 average time/residue: 0.6201 time to fit residues: 121.2200 Evaluate side-chains 173 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 312 CYS Chi-restraints excluded: chain E residue 317 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 79 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 8 optimal weight: 0.0470 chunk 85 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 overall best weight: 1.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 250 GLN D 210 GLN C 290 GLN E 61 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.093302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.075219 restraints weight = 25433.839| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.79 r_work: 0.2868 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14225 Z= 0.135 Angle : 0.596 9.810 19361 Z= 0.301 Chirality : 0.043 0.383 2196 Planarity : 0.004 0.051 2388 Dihedral : 5.945 86.237 2254 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.65 % Allowed : 16.31 % Favored : 82.03 % 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 are not related in a simple way. whole: 1.78 (0.21), residues: 1663 helix: 2.54 (0.22), residues: 559 sheet: 1.43 (0.28), residues: 411 loop : -0.10 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 83 TYR 0.022 0.001 TYR B 325 PHE 0.028 0.001 PHE C 428 TRP 0.013 0.001 TRP C 263 HIS 0.002 0.000 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00319 (14219) covalent geometry : angle 0.58952 (19344) SS BOND : bond 0.00354 ( 1) SS BOND : angle 0.41823 ( 2) hydrogen bonds : bond 0.03872 ( 669) hydrogen bonds : angle 3.74149 ( 2319) link_NAG-ASN : bond 0.00484 ( 5) link_NAG-ASN : angle 3.10826 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3326 Ramachandran restraints generated. 1663 Oldfield, 0 Emsley, 1663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.529 Fit side-chains REVERT: A 315 LEU cc_start: 0.9246 (tp) cc_final: 0.8999 (tm) REVERT: D 171 MET cc_start: 0.8973 (mtm) cc_final: 0.8768 (mpp) REVERT: D 333 ARG cc_start: 0.6731 (tpm170) cc_final: 0.6432 (tpm170) REVERT: C 42 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7427 (ptm) REVERT: C 250 GLN cc_start: 0.8739 (tp-100) cc_final: 0.8315 (tp-100) REVERT: B 99 TYR cc_start: 0.7815 (p90) cc_final: 0.7454 (p90) REVERT: B 333 ARG cc_start: 0.8079 (tmm160) cc_final: 0.7593 (ttp80) REVERT: E 117 ARG cc_start: 0.8301 (mtm110) cc_final: 0.7999 (mtm-85) REVERT: E 321 LYS cc_start: 0.8688 (mttt) cc_final: 0.7999 (mppt) outliers start: 25 outliers final: 18 residues processed: 170 average time/residue: 0.5983 time to fit residues: 111.0978 Evaluate side-chains 176 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain C residue 42 MET Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 312 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 40 optimal weight: 0.0980 chunk 70 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 68 optimal weight: 0.3980 chunk 88 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 250 GLN D 210 GLN C 168 ASN C 290 GLN E 290 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.096676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.078371 restraints weight = 25579.368| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.77 r_work: 0.2904 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14225 Z= 0.110 Angle : 0.572 9.908 19361 Z= 0.288 Chirality : 0.042 0.290 2196 Planarity : 0.004 0.050 2388 Dihedral : 5.683 85.827 2254 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.65 % Allowed : 16.12 % Favored : 82.23 % 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 are not related in a simple way. whole: 1.86 (0.21), residues: 1663 helix: 2.64 (0.22), residues: 559 sheet: 1.48 (0.28), residues: 411 loop : -0.08 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 83 TYR 0.020 0.001 TYR B 99 PHE 0.019 0.001 PHE E 122 TRP 0.012 0.001 TRP C 263 HIS 0.003 0.000 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00252 (14219) covalent geometry : angle 0.56705 (19344) SS BOND : bond 0.00326 ( 1) SS BOND : angle 0.35960 ( 2) hydrogen bonds : bond 0.03438 ( 669) hydrogen bonds : angle 3.61082 ( 2319) link_NAG-ASN : bond 0.00549 ( 5) link_NAG-ASN : angle 2.79798 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3469.66 seconds wall clock time: 60 minutes 1.95 seconds (3601.95 seconds total)