Starting phenix.real_space_refine on Sat Jun 14 06:52:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fe1_29019/06_2025/8fe1_29019.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fe1_29019/06_2025/8fe1_29019.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fe1_29019/06_2025/8fe1_29019.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fe1_29019/06_2025/8fe1_29019.map" model { file = "/net/cci-nas-00/data/ceres_data/8fe1_29019/06_2025/8fe1_29019.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fe1_29019/06_2025/8fe1_29019.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 10225 2.51 5 N 2357 2.21 5 O 2767 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15445 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2887 Classifications: {'peptide': 355} Link IDs: {'PTRANS': 15, 'TRANS': 339} Chain breaks: 1 Chain: "D" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2886 Classifications: {'peptide': 355} Link IDs: {'PTRANS': 16, 'TRANS': 338} Chain breaks: 1 Chain: "C" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2895 Classifications: {'peptide': 356} Link IDs: {'PTRANS': 16, 'TRANS': 339} Chain breaks: 1 Chain: "B" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2887 Classifications: {'peptide': 355} Link IDs: {'PTRANS': 16, 'TRANS': 338} Chain breaks: 1 Chain: "E" Number of atoms: 2800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2800 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 18, 'TRANS': 327} Chain breaks: 1 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 250 Unusual residues: {'IVM': 2, 'NAG': 1, 'PLM': 5, 'PX4': 1} Inner-chain residues flagged as termini: ['pdbres="GLY A 506 "'] Classifications: {'peptide': 1, 'undetermined': 9} Modifications used: {'COO': 1} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 229 Unusual residues: {'IVM': 1, 'NAG': 1, 'PLM': 6, 'PX4': 2} Inner-chain residues flagged as termini: ['pdbres="GLY D 506 "'] Classifications: {'peptide': 1, 'undetermined': 10} Modifications used: {'COO': 1} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 247 Unusual residues: {'D10': 1, 'IVM': 1, 'NAG': 1, 'PLM': 6, 'PX4': 2} Inner-chain residues flagged as termini: ['pdbres="GLY C 503 "'] Classifications: {'peptide': 1, 'undetermined': 11} Modifications used: {'COO': 1} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 226 Unusual residues: {'IVM': 1, 'NAG': 1, 'PLM': 6, 'PX4': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 128 Unusual residues: {'NAG': 2, 'PLM': 5, 'PX4': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 10.45, per 1000 atoms: 0.68 Number of scatterers: 15445 At special positions: 0 Unit cell: (89.88, 92.4, 138.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 2767 8.00 N 2357 7.00 C 10225 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 182 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 242 " - pdb=" SG CYS E 254 " distance=2.04 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 504 " - " ASN C 62 " " NAG D 501 " - " ASN D 62 " " NAG E 601 " - " ASN E 241 " " NAG E 603 " - " ASN E 54 " Time building additional restraints: 3.75 Conformation dependent library (CDL) restraints added in 1.8 seconds 3494 Ramachandran restraints generated. 1747 Oldfield, 0 Emsley, 1747 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3398 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 23 sheets defined 40.4% alpha, 37.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 33 through 42 removed outlier: 3.591A pdb=" N PHE A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 38 " --> pdb=" O PRO A 34 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 116 removed outlier: 3.824A pdb=" N ASP A 115 " --> pdb=" O SER A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 Processing helix chain 'A' and resid 251 through 264 removed outlier: 3.573A pdb=" N ILE A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 272 through 295 removed outlier: 3.561A pdb=" N ARG A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 334 removed outlier: 3.716A pdb=" N TYR A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 444 removed outlier: 3.914A pdb=" N VAL A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Proline residue: A 419 - end of helix removed outlier: 3.542A pdb=" N TYR A 433 " --> pdb=" O TYR A 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 41 removed outlier: 3.539A pdb=" N PHE D 37 " --> pdb=" O PRO D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 98 Processing helix chain 'D' and resid 110 through 117 removed outlier: 4.681A pdb=" N ASP D 115 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER D 116 " --> pdb=" O MET D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 Processing helix chain 'D' and resid 251 through 264 removed outlier: 3.524A pdb=" N VAL D 264 " --> pdb=" O ILE D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 268 Processing helix chain 'D' and resid 272 through 295 removed outlier: 3.648A pdb=" N SER D 294 " --> pdb=" O GLN D 290 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 334 removed outlier: 3.611A pdb=" N ILE D 309 " --> pdb=" O LYS D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 444 removed outlier: 3.532A pdb=" N LYS D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP D 411 " --> pdb=" O ALA D 407 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL D 416 " --> pdb=" O THR D 412 " (cutoff:3.500A) Proline residue: D 419 - end of helix Processing helix chain 'C' and resid 33 through 41 Processing helix chain 'C' and resid 110 through 117 removed outlier: 3.527A pdb=" N MET C 113 " --> pdb=" O ASP C 110 " (cutoff:3.500A) removed outlier: 4.054A 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 264 removed outlier: 3.611A pdb=" N VAL C 264 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 267 No H-bonds generated for 'chain 'C' and resid 265 through 267' Processing helix chain 'C' and resid 272 through 296 removed outlier: 3.798A pdb=" N ALA C 296 " --> pdb=" O SER C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 334 removed outlier: 3.536A pdb=" N ILE C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 444 removed outlier: 3.547A pdb=" N ILE C 410 " --> pdb=" O ARG C 406 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP C 411 " --> pdb=" O ALA C 407 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL C 416 " --> pdb=" O THR C 412 " (cutoff:3.500A) Proline residue: C 419 - end of helix Processing helix chain 'B' and resid 33 through 41 removed outlier: 3.619A pdb=" N ASP B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 41 " --> pdb=" O PHE B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 117 Processing helix chain 'B' and resid 244 through 251 removed outlier: 3.791A pdb=" N ILE B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 264 removed outlier: 3.895A pdb=" N VAL B 264 " --> pdb=" O ILE B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 268 Processing helix chain 'B' and resid 272 through 295 removed outlier: 3.725A pdb=" N ARG B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 305 through 338 removed outlier: 3.587A pdb=" N ILE B 309 " --> pdb=" O LYS B 305 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN B 334 " --> pdb=" O PHE B 330 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N HIS B 335 " --> pdb=" O ILE B 331 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LYS B 336 " --> pdb=" O ALA B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 443 removed outlier: 4.028A 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 58 through 64 Processing helix chain 'E' and resid 130 through 137 removed outlier: 3.831A pdb=" N LYS E 135 " --> pdb=" O LYS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 191 Processing helix chain 'E' and resid 265 through 272 removed outlier: 3.678A pdb=" N MET E 270 " --> pdb=" O GLY E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 285 removed outlier: 3.601A pdb=" N LEU E 285 " --> pdb=" O VAL E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 293 through 319 Proline residue: E 299 - end of helix removed outlier: 3.589A pdb=" N SER E 317 " --> pdb=" O THR E 313 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU E 318 " --> pdb=" O SER E 314 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU E 319 " --> pdb=" O LEU E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 355 removed outlier: 3.759A pdb=" N ILE E 330 " --> pdb=" O LYS E 326 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TRP E 331 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU E 343 " --> pdb=" O GLY E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 493 removed outlier: 3.549A pdb=" N ASP E 471 " --> pdb=" O ALA E 467 " (cutoff:3.500A) removed outlier: 3.630A 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 107 through 108 removed outlier: 3.620A pdb=" N LEU A 107 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE A 144 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP A 92 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASN A 93 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ASN A 62 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL A 61 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLU A 193 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 6.069A 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: 6.693A pdb=" N VAL A 159 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ALA A 130 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR A 157 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP A 92 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASN A 93 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 6.085A 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 124 removed outlier: 7.621A pdb=" N CYS A 233 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ARG A 220 " --> pdb=" O CYS A 233 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLU A 235 " --> pdb=" O ASP A 218 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASP A 218 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ARG A 237 " --> pdb=" O GLU A 216 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLU A 216 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N HIS A 239 " --> pdb=" O LYS A 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA5, first strand: chain 'D' and resid 107 through 108 removed outlier: 3.643A pdb=" N ILE D 144 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG D 83 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N SER D 74 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ASN D 85 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N PHE D 72 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N PHE D 87 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ASN D 70 " --> pdb=" O PHE D 87 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ARG D 89 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N PHE D 68 " --> pdb=" O ARG D 89 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N GLN D 91 " --> pdb=" O ASN D 66 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ASN D 66 " --> pdb=" O GLN D 91 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N ASN D 93 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 10.126A pdb=" N THR D 64 " --> pdb=" O ASN D 93 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL D 61 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLU D 193 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL D 63 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 127 through 131 removed outlier: 6.700A pdb=" N VAL D 159 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA D 130 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N THR D 157 " --> pdb=" O ALA D 130 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG D 83 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N SER D 74 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ASN D 85 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N PHE D 72 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N PHE D 87 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ASN D 70 " --> pdb=" O PHE D 87 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ARG D 89 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N PHE D 68 " --> pdb=" O ARG D 89 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N GLN D 91 " --> pdb=" O ASN D 66 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ASN D 66 " --> pdb=" O GLN D 91 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N ASN D 93 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 10.126A pdb=" N THR D 64 " --> pdb=" O ASN D 93 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 122 through 124 Processing sheet with id=AA8, first strand: chain 'D' and resid 122 through 124 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 109 removed outlier: 4.615A pdb=" N LEU C 142 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASN C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP C 81 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE C 75 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N PHE C 87 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ILE C 69 " --> pdb=" O PHE C 87 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ARG C 89 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ILE C 67 " --> pdb=" O ARG C 89 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLN C 91 " --> pdb=" O CYS C 65 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N CYS C 65 " --> pdb=" O GLN C 91 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N ASN C 93 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N VAL C 63 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL C 61 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N GLU C 193 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 6.460A 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 131 removed outlier: 6.412A pdb=" N VAL C 159 " --> pdb=" O LYS C 128 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA C 130 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N THR C 157 " --> pdb=" O ALA C 130 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP C 81 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE C 75 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N PHE C 87 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ILE C 69 " --> pdb=" O PHE C 87 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ARG C 89 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ILE C 67 " --> pdb=" O ARG C 89 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLN C 91 " --> pdb=" O CYS C 65 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N CYS C 65 " --> pdb=" O GLN C 91 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N ASN C 93 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N VAL C 63 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N GLN C 201 " --> pdb=" O CYS C 65 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE C 67 " --> pdb=" O GLN C 201 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 123 through 124 Processing sheet with id=AB4, first strand: chain 'C' and resid 123 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: 3.667A pdb=" N ILE B 144 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU B 142 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP B 92 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASN B 93 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN B 62 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL B 61 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU B 193 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 5.949A 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 132 removed outlier: 6.201A pdb=" N GLU B 127 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ALA B 161 " --> pdb=" O GLU B 127 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY B 129 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR B 157 " --> pdb=" O ASN B 131 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP B 92 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASN B 93 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 6.605A 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 removed outlier: 3.604A pdb=" N ASP B 218 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 224 through 226 Processing sheet with id=AC2, first strand: chain 'E' and resid 147 through 151 removed outlier: 6.788A pdb=" N THR E 179 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ALA E 150 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N SER E 177 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASP E 100 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE E 94 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N PHE E 106 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE E 88 " --> pdb=" O PHE E 106 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ARG E 108 " --> pdb=" O ILE E 86 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ILE E 86 " --> pdb=" O ARG E 108 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ARG E 110 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL E 84 " --> pdb=" O ARG E 110 " (cutoff:3.500A) removed outlier: 9.194A pdb=" N ASN E 112 " --> pdb=" O ASP E 82 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N ASP E 82 " --> pdb=" O ASN E 112 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 160 through 164 removed outlier: 6.518A pdb=" N ASP E 100 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE E 94 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N PHE E 106 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE E 88 " --> pdb=" O PHE E 106 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ARG E 108 " --> pdb=" O ILE E 86 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ILE E 86 " --> pdb=" O ARG E 108 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ARG E 110 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL E 84 " --> pdb=" O ARG E 110 " (cutoff:3.500A) removed outlier: 9.194A pdb=" N ASN E 112 " --> pdb=" O ASP E 82 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N ASP E 82 " --> pdb=" O ASN E 112 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N GLN E 221 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE E 86 " --> pdb=" O GLN E 221 " (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 244 through 246 812 hydrogen bonds defined for protein. 2328 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.93 Time building geometry restraints manager: 4.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2518 1.32 - 1.45: 4092 1.45 - 1.58: 8734 1.58 - 1.71: 287 1.71 - 1.84: 161 Bond restraints: 15792 Sorted by residual: bond pdb=" C34 IVM D 502 " pdb=" C36 IVM D 502 " ideal model delta sigma weight residual 1.500 1.681 -0.181 2.00e-02 2.50e+03 8.21e+01 bond pdb=" C34 IVM B 503 " pdb=" C36 IVM B 503 " ideal model delta sigma weight residual 1.500 1.678 -0.178 2.00e-02 2.50e+03 7.92e+01 bond pdb=" C34 IVM A 503 " pdb=" C36 IVM A 503 " ideal model delta sigma weight residual 1.500 1.678 -0.178 2.00e-02 2.50e+03 7.91e+01 bond pdb=" C34 IVM C 505 " pdb=" C36 IVM C 505 " ideal model delta sigma weight residual 1.500 1.675 -0.175 2.00e-02 2.50e+03 7.67e+01 bond pdb=" C34 IVM A 504 " pdb=" C36 IVM A 504 " ideal model delta sigma weight residual 1.500 1.675 -0.175 2.00e-02 2.50e+03 7.64e+01 ... (remaining 15787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 20311 2.30 - 4.61: 726 4.61 - 6.91: 144 6.91 - 9.21: 52 9.21 - 11.52: 7 Bond angle restraints: 21240 Sorted by residual: angle pdb=" C ASN B 131 " pdb=" N PHE B 132 " pdb=" CA PHE B 132 " ideal model delta sigma weight residual 122.67 115.15 7.52 1.73e+00 3.34e-01 1.89e+01 angle pdb=" N LYS B 128 " pdb=" CA LYS B 128 " pdb=" C LYS B 128 " ideal model delta sigma weight residual 113.12 108.24 4.88 1.25e+00 6.40e-01 1.52e+01 angle pdb=" C17 IVM A 503 " pdb=" C19 IVM A 503 " pdb=" O2 IVM A 503 " ideal model delta sigma weight residual 112.55 101.03 11.52 3.00e+00 1.11e-01 1.47e+01 angle pdb=" C SER E 216 " pdb=" N GLY E 217 " pdb=" CA GLY E 217 " ideal model delta sigma weight residual 122.73 119.22 3.51 9.30e-01 1.16e+00 1.43e+01 angle pdb=" CA GLU D 101 " pdb=" CB GLU D 101 " pdb=" CG GLU D 101 " ideal model delta sigma weight residual 114.10 121.54 -7.44 2.00e+00 2.50e-01 1.38e+01 ... (remaining 21235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.91: 9835 34.91 - 69.82: 217 69.82 - 104.73: 51 104.73 - 139.64: 21 139.64 - 174.55: 2 Dihedral angle restraints: 10126 sinusoidal: 4896 harmonic: 5230 Sorted by residual: dihedral pdb=" O5 PX4 A 505 " pdb=" C7 PX4 A 505 " pdb=" C8 PX4 A 505 " pdb=" O7 PX4 A 505 " ideal model delta sinusoidal sigma weight residual 59.95 -125.50 -174.55 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 PX4 C 502 " pdb=" C7 PX4 C 502 " pdb=" C8 PX4 C 502 " pdb=" O7 PX4 C 502 " ideal model delta sinusoidal sigma weight residual 59.95 -114.05 174.00 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 PX4 C 507 " pdb=" C7 PX4 C 507 " pdb=" C8 PX4 C 507 " pdb=" O7 PX4 C 507 " ideal model delta sinusoidal sigma weight residual 59.95 -161.44 -138.61 1 3.00e+01 1.11e-03 1.87e+01 ... (remaining 10123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.200: 2315 0.200 - 0.400: 22 0.400 - 0.600: 15 0.600 - 0.800: 5 0.800 - 1.000: 8 Chirality restraints: 2365 Sorted by residual: chirality pdb=" C3 IVM A 504 " pdb=" C2 IVM A 504 " pdb=" C4 IVM A 504 " pdb=" C5 IVM A 504 " both_signs ideal model delta sigma weight residual False 2.53 3.52 -1.00 2.00e-01 2.50e+01 2.50e+01 chirality pdb=" C3 IVM C 505 " pdb=" C2 IVM C 505 " pdb=" C4 IVM C 505 " pdb=" C5 IVM C 505 " both_signs ideal model delta sigma weight residual False 2.53 3.52 -0.99 2.00e-01 2.50e+01 2.47e+01 chirality pdb=" C3 IVM A 503 " pdb=" C2 IVM A 503 " pdb=" C4 IVM A 503 " pdb=" C5 IVM A 503 " both_signs ideal model delta sigma weight residual False 2.53 3.47 -0.95 2.00e-01 2.50e+01 2.24e+01 ... (remaining 2362 not shown) Planarity restraints: 2583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 601 " 0.336 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG E 601 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG E 601 " 0.179 2.00e-02 2.50e+03 pdb=" N2 NAG E 601 " -0.501 2.00e-02 2.50e+03 pdb=" O7 NAG E 601 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 335 " 0.013 2.00e-02 2.50e+03 1.83e-02 5.03e+00 pdb=" CG HIS B 335 " -0.038 2.00e-02 2.50e+03 pdb=" ND1 HIS B 335 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 HIS B 335 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 HIS B 335 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS B 335 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS E 254 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" C CYS E 254 " -0.035 2.00e-02 2.50e+03 pdb=" O CYS E 254 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL E 255 " 0.012 2.00e-02 2.50e+03 ... (remaining 2580 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1351 2.75 - 3.29: 14590 3.29 - 3.83: 23829 3.83 - 4.36: 30075 4.36 - 4.90: 51149 Nonbonded interactions: 120994 Sorted by model distance: nonbonded pdb=" OG1 THR A 79 " pdb=" OD1 ASP A 81 " model vdw 2.217 3.040 nonbonded pdb=" OG1 THR C 186 " pdb=" OD1 ASN C 188 " model vdw 2.231 3.040 nonbonded pdb=" OG1 THR C 79 " pdb=" OD1 ASP C 81 " model vdw 2.232 3.040 nonbonded pdb=" OE1 GLU B 193 " pdb=" OH TYR B 221 " model vdw 2.275 3.040 nonbonded pdb=" OE1 GLU A 193 " pdb=" OH TYR A 221 " model vdw 2.276 3.040 ... (remaining 120989 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 336 or resid 398 through 444 or resid 507 throu \ gh 508 or (resid 509 and (name C1 or name C2 or name C3 or name C4 or name C5 or \ name C6 or name C7 or name C8 or name C9 or name O1 or name O2 )) or (resid 510 \ and (name CA or name CB or name C1 or name C2 or name C3 or name C4 or name C5 \ or name C6 or name C7 or name C8 or name C9 or name O1 or name O2 )) or (resid 5 \ 11 and (name CA or name CB or name C1 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name C9 or name CC or name O1 or name O2 ) \ ))) selection = (chain 'B' and (resid 33 through 336 or resid 398 through 444 or resid 506 or (r \ esid 507 and (name CA or name C1 or name C2 or name C3 or name C4 or name C5 or \ name C6 or name C7 or name C8 or name C9 or name O1 or name O2 )) or resid 508 o \ r (resid 509 and (name CA or name CB or name C1 or name C2 or name C3 or name C4 \ or name C5 or name C6 or name C7 or name C8 or name C9 or name O1 or name O2 )) \ or (resid 510 and (name CA or name CB or name C1 or name C2 or name C3 or name \ C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name CC or name O1 \ or name O2 )))) selection = (chain 'C' and (resid 33 through 336 or resid 398 through 444 or (resid 509 and \ (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or na \ me C8 or name C9 or name O1 or name O2 )) or (resid 510 and (name CA or name C1 \ or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or \ name C9 or name O1 or name O2 )) or (resid 511 and (name C1 or name C2 or name C \ 3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name O1 o \ r name O2 )) or (resid 512 and (name CA or name CB or name C1 or name C2 or name \ C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name O1 \ or name O2 )) or resid 513)) selection = (chain 'D' and (resid 33 through 336 or resid 398 through 444 or (resid 507 and \ (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or na \ me C8 or name C9 or name O1 or name O2 )) or (resid 508 and (name CA or name C1 \ or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or \ name C9 or name O1 or name O2 )) or resid 509 through 510 or (resid 511 and (nam \ e CA or name CB or name C1 or name C2 or name C3 or name C4 or name C5 or name C \ 6 or name C7 or name C8 or name C9 or name CC or name O1 or name O2 )))) } 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: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 36.420 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 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 : 0.016 0.181 15800 Z= 0.784 Angle : 1.047 18.658 21262 Z= 0.463 Chirality : 0.094 1.000 2365 Planarity : 0.008 0.286 2577 Dihedral : 17.018 174.548 6722 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.06 % Allowed : 0.31 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.19), residues: 1747 helix: 1.58 (0.20), residues: 606 sheet: 0.58 (0.25), residues: 401 loop : -0.96 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 430 HIS 0.024 0.002 HIS B 335 PHE 0.029 0.002 PHE E 144 TYR 0.025 0.001 TYR B 152 ARG 0.006 0.000 ARG C 51 Details of bonding type rmsd link_NAG-ASN : bond 0.01238 ( 6) link_NAG-ASN : angle 7.14981 ( 18) hydrogen bonds : bond 0.25833 ( 700) hydrogen bonds : angle 7.24366 ( 2328) SS BOND : bond 0.00837 ( 2) SS BOND : angle 1.58234 ( 4) covalent geometry : bond 0.01559 (15792) covalent geometry : angle 1.02645 (21240) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3494 Ramachandran restraints generated. 1747 Oldfield, 0 Emsley, 1747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3494 Ramachandran restraints generated. 1747 Oldfield, 0 Emsley, 1747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 1.785 Fit side-chains REVERT: A 311 MET cc_start: 0.9248 (mmt) cc_final: 0.9020 (mmt) REVERT: A 399 MET cc_start: 0.8158 (mmp) cc_final: 0.7893 (mpp) REVERT: B 107 LEU cc_start: 0.8138 (mt) cc_final: 0.7737 (pp) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 1.3242 time to fit residues: 258.2753 Evaluate side-chains 126 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 158 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 290 GLN D 334 GLN B 139 ASN E 85 ASN E 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.101185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.078326 restraints weight = 27752.408| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.71 r_work: 0.2867 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 15800 Z= 0.303 Angle : 0.809 11.359 21262 Z= 0.393 Chirality : 0.050 0.215 2365 Planarity : 0.005 0.039 2577 Dihedral : 13.276 174.531 3240 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.94 % Allowed : 8.77 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.19), residues: 1747 helix: 2.06 (0.19), residues: 631 sheet: 0.82 (0.25), residues: 389 loop : -1.22 (0.21), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 430 HIS 0.009 0.001 HIS A 133 PHE 0.020 0.002 PHE D 72 TYR 0.028 0.002 TYR C 433 ARG 0.007 0.001 ARG E 117 Details of bonding type rmsd link_NAG-ASN : bond 0.01078 ( 6) link_NAG-ASN : angle 5.85597 ( 18) hydrogen bonds : bond 0.06374 ( 700) hydrogen bonds : angle 4.80697 ( 2328) SS BOND : bond 0.00309 ( 2) SS BOND : angle 1.15399 ( 4) covalent geometry : bond 0.00716 (15792) covalent geometry : angle 0.79064 (21240) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3494 Ramachandran restraints generated. 1747 Oldfield, 0 Emsley, 1747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3494 Ramachandran restraints generated. 1747 Oldfield, 0 Emsley, 1747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 1.850 Fit side-chains revert: symmetry clash REVERT: D 39 ASP cc_start: 0.8271 (m-30) cc_final: 0.8020 (p0) REVERT: D 400 ARG cc_start: 0.8148 (tmm-80) cc_final: 0.7850 (tmm-80) REVERT: C 113 MET cc_start: 0.8574 (ptm) cc_final: 0.8199 (ptm) REVERT: C 115 ASP cc_start: 0.8653 (p0) cc_final: 0.8432 (OUTLIER) REVERT: B 400 ARG cc_start: 0.8395 (tpt-90) cc_final: 0.8182 (tpt-90) REVERT: E 239 TYR cc_start: 0.7808 (t80) cc_final: 0.7511 (t80) outliers start: 31 outliers final: 10 residues processed: 157 average time/residue: 1.3522 time to fit residues: 234.4831 Evaluate side-chains 129 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 227 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 76 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 334 GLN B 139 ASN E 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.103400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.080939 restraints weight = 27189.528| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.77 r_work: 0.2914 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15800 Z= 0.126 Angle : 0.636 12.104 21262 Z= 0.302 Chirality : 0.044 0.250 2365 Planarity : 0.004 0.058 2577 Dihedral : 11.648 168.561 3240 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.01 % Allowed : 11.34 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.20), residues: 1747 helix: 2.53 (0.20), residues: 625 sheet: 1.02 (0.26), residues: 392 loop : -0.96 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 263 HIS 0.003 0.001 HIS A 133 PHE 0.014 0.001 PHE C 319 TYR 0.020 0.001 TYR C 325 ARG 0.004 0.000 ARG E 83 Details of bonding type rmsd link_NAG-ASN : bond 0.01068 ( 6) link_NAG-ASN : angle 5.11810 ( 18) hydrogen bonds : bond 0.05121 ( 700) hydrogen bonds : angle 4.25224 ( 2328) SS BOND : bond 0.00263 ( 2) SS BOND : angle 0.57214 ( 4) covalent geometry : bond 0.00266 (15792) covalent geometry : angle 0.61884 (21240) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3494 Ramachandran restraints generated. 1747 Oldfield, 0 Emsley, 1747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3494 Ramachandran restraints generated. 1747 Oldfield, 0 Emsley, 1747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 1.902 Fit side-chains REVERT: D 32 MET cc_start: 0.8866 (tmm) cc_final: 0.8597 (tmm) REVERT: D 39 ASP cc_start: 0.8228 (m-30) cc_final: 0.7999 (p0) REVERT: D 400 ARG cc_start: 0.8150 (tmm-80) cc_final: 0.7864 (tmm-80) REVERT: C 32 MET cc_start: 0.9363 (tpt) cc_final: 0.9144 (tpp) REVERT: C 113 MET cc_start: 0.8476 (ptm) cc_final: 0.8153 (ptm) REVERT: C 333 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7463 (pmm-80) REVERT: C 334 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7907 (mm-40) REVERT: B 323 LEU cc_start: 0.9397 (tp) cc_final: 0.9177 (mm) REVERT: E 147 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8626 (tm-30) outliers start: 32 outliers final: 9 residues processed: 167 average time/residue: 1.2171 time to fit residues: 226.7080 Evaluate side-chains 138 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 334 GLN Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 242 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 166 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 120 optimal weight: 0.4980 chunk 17 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN D 334 GLN B 131 ASN B 139 ASN B 227 ASN E 215 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.102757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.080539 restraints weight = 27129.703| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.75 r_work: 0.2906 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15800 Z= 0.136 Angle : 0.629 11.978 21262 Z= 0.297 Chirality : 0.044 0.251 2365 Planarity : 0.004 0.051 2577 Dihedral : 10.839 174.425 3240 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.32 % Allowed : 13.03 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.20), residues: 1747 helix: 2.57 (0.20), residues: 625 sheet: 1.05 (0.26), residues: 395 loop : -0.86 (0.21), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 430 HIS 0.003 0.001 HIS A 133 PHE 0.016 0.001 PHE C 422 TYR 0.019 0.002 TYR C 325 ARG 0.002 0.000 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00971 ( 6) link_NAG-ASN : angle 5.09373 ( 18) hydrogen bonds : bond 0.04704 ( 700) hydrogen bonds : angle 4.10292 ( 2328) SS BOND : bond 0.00275 ( 2) SS BOND : angle 0.55324 ( 4) covalent geometry : bond 0.00309 (15792) covalent geometry : angle 0.61162 (21240) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3494 Ramachandran restraints generated. 1747 Oldfield, 0 Emsley, 1747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3494 Ramachandran restraints generated. 1747 Oldfield, 0 Emsley, 1747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 1.653 Fit side-chains REVERT: D 39 ASP cc_start: 0.8266 (m-30) cc_final: 0.8024 (p0) REVERT: D 400 ARG cc_start: 0.8166 (tmm-80) cc_final: 0.7907 (tmm-80) REVERT: B 323 LEU cc_start: 0.9388 (tp) cc_final: 0.9179 (mm) outliers start: 37 outliers final: 20 residues processed: 157 average time/residue: 1.2042 time to fit residues: 210.3984 Evaluate side-chains 140 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 198 MET Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 342 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 129 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN D 139 ASN D 334 GLN B 227 ASN E 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.102451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.080076 restraints weight = 27847.328| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.76 r_work: 0.2891 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15800 Z= 0.155 Angle : 0.628 12.135 21262 Z= 0.298 Chirality : 0.044 0.242 2365 Planarity : 0.004 0.049 2577 Dihedral : 10.342 175.502 3240 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.76 % Allowed : 14.04 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.20), residues: 1747 helix: 2.57 (0.20), residues: 626 sheet: 1.08 (0.26), residues: 389 loop : -0.85 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 430 HIS 0.004 0.001 HIS A 133 PHE 0.014 0.001 PHE B 123 TYR 0.019 0.002 TYR C 325 ARG 0.003 0.000 ARG E 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00938 ( 6) link_NAG-ASN : angle 5.01632 ( 18) hydrogen bonds : bond 0.04629 ( 700) hydrogen bonds : angle 4.07935 ( 2328) SS BOND : bond 0.00223 ( 2) SS BOND : angle 0.55990 ( 4) covalent geometry : bond 0.00361 (15792) covalent geometry : angle 0.61138 (21240) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3494 Ramachandran restraints generated. 1747 Oldfield, 0 Emsley, 1747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3494 Ramachandran restraints generated. 1747 Oldfield, 0 Emsley, 1747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 127 time to evaluate : 1.782 Fit side-chains REVERT: A 122 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8714 (tt) REVERT: D 39 ASP cc_start: 0.8296 (m-30) cc_final: 0.8032 (p0) REVERT: D 400 ARG cc_start: 0.8188 (tmm-80) cc_final: 0.7924 (tmm-80) REVERT: C 32 MET cc_start: 0.9268 (tpt) cc_final: 0.9039 (tpp) REVERT: B 400 ARG cc_start: 0.8260 (tpt-90) cc_final: 0.7897 (mmm160) outliers start: 44 outliers final: 20 residues processed: 159 average time/residue: 1.1451 time to fit residues: 204.0433 Evaluate side-chains 146 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 242 CYS Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 477 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 34 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 172 optimal weight: 0.5980 chunk 120 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 18 optimal weight: 0.2980 chunk 148 optimal weight: 20.0000 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN D 334 GLN C 334 GLN ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN E 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.101357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.078833 restraints weight = 27776.622| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.75 r_work: 0.2865 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15800 Z= 0.190 Angle : 0.651 12.143 21262 Z= 0.313 Chirality : 0.045 0.233 2365 Planarity : 0.004 0.049 2577 Dihedral : 10.016 174.539 3240 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.94 % Allowed : 14.72 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.20), residues: 1747 helix: 2.54 (0.20), residues: 625 sheet: 0.93 (0.26), residues: 395 loop : -0.84 (0.21), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 430 HIS 0.006 0.001 HIS A 133 PHE 0.014 0.001 PHE B 123 TYR 0.020 0.002 TYR C 325 ARG 0.003 0.000 ARG E 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00915 ( 6) link_NAG-ASN : angle 4.97049 ( 18) hydrogen bonds : bond 0.04738 ( 700) hydrogen bonds : angle 4.10784 ( 2328) SS BOND : bond 0.00234 ( 2) SS BOND : angle 0.65823 ( 4) covalent geometry : bond 0.00453 (15792) covalent geometry : angle 0.63510 (21240) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3494 Ramachandran restraints generated. 1747 Oldfield, 0 Emsley, 1747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3494 Ramachandran restraints generated. 1747 Oldfield, 0 Emsley, 1747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 127 time to evaluate : 1.642 Fit side-chains REVERT: A 122 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8831 (tt) REVERT: D 39 ASP cc_start: 0.8320 (m-30) cc_final: 0.7960 (m-30) REVERT: D 181 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8022 (pp20) REVERT: D 400 ARG cc_start: 0.8200 (tmm-80) cc_final: 0.7907 (tmm-80) REVERT: C 32 MET cc_start: 0.9261 (tpt) cc_final: 0.8966 (tpp) REVERT: B 320 SER cc_start: 0.9379 (m) cc_final: 0.9108 (m) REVERT: B 400 ARG cc_start: 0.8247 (tpt-90) cc_final: 0.7845 (mmm160) REVERT: B 431 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8815 (mp) outliers start: 47 outliers final: 26 residues processed: 162 average time/residue: 1.1930 time to fit residues: 215.5722 Evaluate side-chains 155 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 334 GLN Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 198 MET Chi-restraints excluded: chain E residue 242 CYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 342 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 107 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 3 optimal weight: 0.0870 chunk 132 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 35 optimal weight: 0.0010 chunk 6 optimal weight: 3.9990 chunk 159 optimal weight: 0.4980 overall best weight: 0.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN D 334 GLN B 227 ASN E 58 ASN E 234 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.104092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.081898 restraints weight = 27575.860| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.75 r_work: 0.2922 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 15800 Z= 0.110 Angle : 0.609 12.488 21262 Z= 0.291 Chirality : 0.043 0.259 2365 Planarity : 0.003 0.045 2577 Dihedral : 9.465 174.381 3240 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.51 % Allowed : 15.29 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.20), residues: 1747 helix: 2.76 (0.20), residues: 616 sheet: 1.10 (0.26), residues: 389 loop : -0.70 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 430 HIS 0.005 0.001 HIS C 335 PHE 0.027 0.001 PHE B 319 TYR 0.018 0.001 TYR C 325 ARG 0.002 0.000 ARG C 400 Details of bonding type rmsd link_NAG-ASN : bond 0.01061 ( 6) link_NAG-ASN : angle 4.89598 ( 18) hydrogen bonds : bond 0.04124 ( 700) hydrogen bonds : angle 3.88514 ( 2328) SS BOND : bond 0.00165 ( 2) SS BOND : angle 0.36214 ( 4) covalent geometry : bond 0.00227 (15792) covalent geometry : angle 0.59254 (21240) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3494 Ramachandran restraints generated. 1747 Oldfield, 0 Emsley, 1747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3494 Ramachandran restraints generated. 1747 Oldfield, 0 Emsley, 1747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 1.761 Fit side-chains REVERT: A 122 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8745 (tt) REVERT: A 171 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8761 (mpp) REVERT: D 39 ASP cc_start: 0.8275 (m-30) cc_final: 0.7903 (m-30) REVERT: D 181 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7939 (pp20) REVERT: D 400 ARG cc_start: 0.8170 (tmm-80) cc_final: 0.7887 (tmm-80) REVERT: C 32 MET cc_start: 0.9268 (tpt) cc_final: 0.8991 (tpp) REVERT: B 320 SER cc_start: 0.9393 (m) cc_final: 0.9119 (m) REVERT: B 400 ARG cc_start: 0.8243 (tpt-90) cc_final: 0.7845 (mmm160) outliers start: 40 outliers final: 20 residues processed: 173 average time/residue: 1.1346 time to fit residues: 220.8814 Evaluate side-chains 150 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 198 MET Chi-restraints excluded: chain E residue 242 CYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 342 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 168 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 165 optimal weight: 0.0570 chunk 18 optimal weight: 4.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN C 334 GLN B 227 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.102283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.080150 restraints weight = 27279.407| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.75 r_work: 0.2899 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15800 Z= 0.138 Angle : 0.619 11.821 21262 Z= 0.296 Chirality : 0.044 0.251 2365 Planarity : 0.003 0.042 2577 Dihedral : 9.236 173.189 3240 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.13 % Allowed : 15.98 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.20), residues: 1747 helix: 2.65 (0.20), residues: 622 sheet: 1.05 (0.26), residues: 391 loop : -0.73 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 430 HIS 0.004 0.001 HIS A 133 PHE 0.040 0.001 PHE B 319 TYR 0.018 0.002 TYR D 433 ARG 0.006 0.000 ARG C 437 Details of bonding type rmsd link_NAG-ASN : bond 0.00944 ( 6) link_NAG-ASN : angle 4.87360 ( 18) hydrogen bonds : bond 0.04224 ( 700) hydrogen bonds : angle 3.91999 ( 2328) SS BOND : bond 0.00191 ( 2) SS BOND : angle 0.47999 ( 4) covalent geometry : bond 0.00321 (15792) covalent geometry : angle 0.60290 (21240) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3494 Ramachandran restraints generated. 1747 Oldfield, 0 Emsley, 1747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3494 Ramachandran restraints generated. 1747 Oldfield, 0 Emsley, 1747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 1.761 Fit side-chains REVERT: A 122 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8828 (tt) REVERT: D 39 ASP cc_start: 0.8285 (m-30) cc_final: 0.7914 (m-30) REVERT: D 181 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7951 (pp20) REVERT: D 400 ARG cc_start: 0.8181 (tmm-80) cc_final: 0.7902 (tmm-80) REVERT: C 32 MET cc_start: 0.9273 (tpt) cc_final: 0.8988 (tpp) REVERT: C 333 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.6916 (pmm-80) REVERT: B 320 SER cc_start: 0.9352 (m) cc_final: 0.9093 (m) outliers start: 34 outliers final: 24 residues processed: 156 average time/residue: 1.1443 time to fit residues: 200.1101 Evaluate side-chains 152 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 334 GLN Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 198 MET Chi-restraints excluded: chain E residue 242 CYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 342 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 6 optimal weight: 0.0000 chunk 166 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 162 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN B 227 ASN E 234 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.104163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.082109 restraints weight = 27495.433| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.74 r_work: 0.2931 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 15800 Z= 0.110 Angle : 0.609 12.003 21262 Z= 0.291 Chirality : 0.043 0.266 2365 Planarity : 0.003 0.040 2577 Dihedral : 8.931 172.375 3240 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.82 % Allowed : 16.35 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.20), residues: 1747 helix: 2.69 (0.20), residues: 622 sheet: 1.12 (0.26), residues: 385 loop : -0.67 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 331 HIS 0.006 0.001 HIS C 335 PHE 0.016 0.001 PHE B 319 TYR 0.017 0.001 TYR C 325 ARG 0.006 0.000 ARG C 437 Details of bonding type rmsd link_NAG-ASN : bond 0.01018 ( 6) link_NAG-ASN : angle 4.88321 ( 18) hydrogen bonds : bond 0.03950 ( 700) hydrogen bonds : angle 3.83097 ( 2328) SS BOND : bond 0.00194 ( 2) SS BOND : angle 0.39824 ( 4) covalent geometry : bond 0.00242 (15792) covalent geometry : angle 0.59210 (21240) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3494 Ramachandran restraints generated. 1747 Oldfield, 0 Emsley, 1747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3494 Ramachandran restraints generated. 1747 Oldfield, 0 Emsley, 1747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 1.737 Fit side-chains REVERT: A 122 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8777 (tt) REVERT: A 428 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.8323 (t80) REVERT: D 39 ASP cc_start: 0.8246 (m-30) cc_final: 0.7865 (m-30) REVERT: D 113 MET cc_start: 0.8592 (ptm) cc_final: 0.8303 (ptt) REVERT: D 400 ARG cc_start: 0.8169 (tmm-80) cc_final: 0.7858 (tmm-80) REVERT: C 32 MET cc_start: 0.9260 (tpt) cc_final: 0.8956 (tpp) REVERT: B 320 SER cc_start: 0.9343 (m) cc_final: 0.9083 (m) REVERT: E 269 MET cc_start: 0.8961 (tpp) cc_final: 0.8747 (mmt) outliers start: 29 outliers final: 21 residues processed: 155 average time/residue: 1.1117 time to fit residues: 193.8469 Evaluate side-chains 148 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 198 MET Chi-restraints excluded: chain E residue 242 CYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 342 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 122 optimal weight: 0.0770 chunk 119 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 169 optimal weight: 0.9990 chunk 96 optimal weight: 0.4980 chunk 38 optimal weight: 6.9990 overall best weight: 0.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 334 GLN B 227 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.104019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.081866 restraints weight = 27339.987| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.77 r_work: 0.2930 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 15800 Z= 0.113 Angle : 0.609 11.962 21262 Z= 0.291 Chirality : 0.043 0.267 2365 Planarity : 0.004 0.039 2577 Dihedral : 8.830 171.718 3240 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.01 % Allowed : 16.23 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.20), residues: 1747 helix: 2.70 (0.20), residues: 623 sheet: 1.14 (0.26), residues: 385 loop : -0.64 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 331 HIS 0.002 0.001 HIS A 133 PHE 0.035 0.001 PHE B 319 TYR 0.015 0.001 TYR C 325 ARG 0.006 0.000 ARG C 437 Details of bonding type rmsd link_NAG-ASN : bond 0.00996 ( 6) link_NAG-ASN : angle 4.88125 ( 18) hydrogen bonds : bond 0.03883 ( 700) hydrogen bonds : angle 3.81652 ( 2328) SS BOND : bond 0.00192 ( 2) SS BOND : angle 0.35837 ( 4) covalent geometry : bond 0.00248 (15792) covalent geometry : angle 0.59202 (21240) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3494 Ramachandran restraints generated. 1747 Oldfield, 0 Emsley, 1747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3494 Ramachandran restraints generated. 1747 Oldfield, 0 Emsley, 1747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 1.737 Fit side-chains REVERT: A 122 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8758 (tt) REVERT: A 428 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.8343 (t80) REVERT: D 39 ASP cc_start: 0.8260 (m-30) cc_final: 0.7872 (m-30) REVERT: D 181 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7918 (pp20) REVERT: D 400 ARG cc_start: 0.8139 (tmm-80) cc_final: 0.7830 (tmm-80) REVERT: C 32 MET cc_start: 0.9269 (tpt) cc_final: 0.8989 (tpp) REVERT: B 320 SER cc_start: 0.9347 (m) cc_final: 0.9096 (m) REVERT: E 231 ASP cc_start: 0.8194 (t0) cc_final: 0.7811 (t0) outliers start: 32 outliers final: 22 residues processed: 155 average time/residue: 1.1074 time to fit residues: 192.9406 Evaluate side-chains 150 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 334 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 198 MET Chi-restraints excluded: chain E residue 242 CYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 342 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 159 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 334 GLN B 227 ASN E 234 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.103960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.081849 restraints weight = 27154.573| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.77 r_work: 0.2931 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.204 15800 Z= 0.182 Angle : 0.814 59.164 21262 Z= 0.443 Chirality : 0.043 0.268 2365 Planarity : 0.004 0.039 2577 Dihedral : 8.831 171.711 3240 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.63 % Allowed : 16.60 % Favored : 81.77 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.20), residues: 1747 helix: 2.69 (0.20), residues: 623 sheet: 1.14 (0.26), residues: 385 loop : -0.63 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 331 HIS 0.003 0.001 HIS B 335 PHE 0.033 0.001 PHE C 319 TYR 0.016 0.001 TYR C 325 ARG 0.005 0.000 ARG C 437 Details of bonding type rmsd link_NAG-ASN : bond 0.01273 ( 6) link_NAG-ASN : angle 5.00674 ( 18) hydrogen bonds : bond 0.03898 ( 700) hydrogen bonds : angle 3.82436 ( 2328) SS BOND : bond 0.00186 ( 2) SS BOND : angle 0.37356 ( 4) covalent geometry : bond 0.00374 (15792) covalent geometry : angle 0.80120 (21240) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7615.42 seconds wall clock time: 131 minutes 37.87 seconds (7897.87 seconds total)