Starting phenix.real_space_refine on Fri Jul 3 19:42:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fe1_29019/07_2026/8fe1_29019.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fe1_29019/07_2026/8fe1_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 { model { file = "/net/cci-nas-00/data/ceres_data/8fe1_29019/07_2026/8fe1_29019.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fe1_29019/07_2026/8fe1_29019.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fe1_29019/07_2026/8fe1_29019.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fe1_29019/07_2026/8fe1_29019.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8fe1_29019/07_2026/8fe1_29019.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fe1_29019/07_2026/8fe1_29019.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 22 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: 38 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: 30 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: 36 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: 29 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.99, per 1000 atoms: 0.19 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: 1.19 Conformation dependent library (CDL) restraints added in 692.4 milliseconds 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: 0.55 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: 2.43 Time building geometry restraints manager: 1.65 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 - 24.09: 9358 24.09 - 48.18: 496 48.18 - 72.27: 66 72.27 - 96.36: 31 96.36 - 120.45: 33 Dihedral angle restraints: 9984 sinusoidal: 4754 harmonic: 5230 Sorted by residual: dihedral pdb=" CA LEU D 166 " pdb=" C LEU D 166 " pdb=" N LYS D 167 " pdb=" CA LYS D 167 " ideal model delta harmonic sigma weight residual 180.00 159.72 20.28 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" C27 IVM B 503 " pdb=" C25 IVM B 503 " pdb=" C26 IVM B 503 " pdb=" O7 IVM B 503 " ideal model delta sinusoidal sigma weight residual 52.31 -68.14 120.45 1 3.00e+01 1.11e-03 1.61e+01 dihedral pdb=" CA LEU E 188 " pdb=" C LEU E 188 " pdb=" N PHE E 189 " pdb=" CA PHE E 189 " ideal model delta harmonic sigma weight residual -180.00 -159.97 -20.03 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 9981 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: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 12.990 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 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:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 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 : 16.497 120.447 6580 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (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 ARG 0.006 0.000 ARG C 51 TYR 0.025 0.001 TYR B 152 PHE 0.029 0.002 PHE E 144 TRP 0.019 0.001 TRP D 430 HIS 0.024 0.002 HIS B 335 Details of bonding type rmsd/Z covalent geometry : bond 0.01559 / 0.78 (15792) covalent geometry : angle 1.02645 / 0.46 (21240) SS BOND : bond 0.00837 / 0.60 ( 2) SS BOND : angle 1.58234 / 1.01 ( 4) hydrogen bonds : bond 0.25833 / 17.41 ( 700) hydrogen bonds : angle 7.24366 / 4.98 ( 2328) link_NAG-ASN : bond 0.01238 / 0.74 ( 6) link_NAG-ASN : angle 7.14981 / 4.71 ( 18) *********************** 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 : 0.590 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: 0.6009 time to fit residues: 117.2426 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 : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.0010 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 90 GLN D 290 GLN D 334 GLN 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 = 0.3527 r_free = 0.3527 target = 0.108582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.086611 restraints weight = 27311.809| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.70 r_work: 0.3029 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15800 Z= 0.140 Angle : 0.697 12.092 21262 Z= 0.330 Chirality : 0.046 0.280 2365 Planarity : 0.004 0.038 2577 Dihedral : 11.205 102.393 3098 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.57 % Allowed : 8.33 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.19), residues: 1747 helix: 2.40 (0.20), residues: 625 sheet: 1.13 (0.26), residues: 388 loop : -0.94 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 117 TYR 0.017 0.001 TYR C 325 PHE 0.017 0.001 PHE D 319 TRP 0.011 0.001 TRP D 430 HIS 0.003 0.001 HIS A 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (15792) covalent geometry : angle 0.67715 / 0.32 (21240) SS BOND : bond 0.00202 / 0.14 ( 2) SS BOND : angle 0.99967 / 0.81 ( 4) hydrogen bonds : bond 0.05962 / 3.99 ( 700) hydrogen bonds : angle 4.58727 / 3.15 ( 2328) link_NAG-ASN : bond 0.01070 / 0.62 ( 6) link_NAG-ASN : angle 5.76029 / 3.96 ( 18) *********************** 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 186 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.567 Fit side-chains REVERT: A 334 GLN cc_start: 0.8238 (mm110) cc_final: 0.7932 (mm110) REVERT: D 400 ARG cc_start: 0.8064 (tmm-80) cc_final: 0.7776 (tmm-80) REVERT: B 33 PRO cc_start: 0.8141 (Cg_exo) cc_final: 0.7646 (Cg_endo) REVERT: B 400 ARG cc_start: 0.8399 (tpt-90) cc_final: 0.8076 (tpt-90) outliers start: 25 outliers final: 6 residues processed: 173 average time/residue: 0.5215 time to fit residues: 100.1252 Evaluate side-chains 130 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 C residue 281 ILE 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 67 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN D 334 GLN B 139 ASN E 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.103816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.081401 restraints weight = 27773.956| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.76 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: 0.8698 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15800 Z= 0.162 Angle : 0.651 11.856 21262 Z= 0.312 Chirality : 0.044 0.234 2365 Planarity : 0.004 0.036 2577 Dihedral : 9.847 97.989 3098 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.01 % Allowed : 10.78 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.20), residues: 1747 helix: 2.53 (0.20), residues: 625 sheet: 1.19 (0.25), residues: 391 loop : -0.92 (0.21), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 237 TYR 0.020 0.002 TYR C 433 PHE 0.017 0.001 PHE E 134 TRP 0.009 0.001 TRP D 430 HIS 0.005 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (15792) covalent geometry : angle 0.63389 / 0.31 (21240) SS BOND : bond 0.00280 / 0.20 ( 2) SS BOND : angle 0.75064 / 0.40 ( 4) hydrogen bonds : bond 0.05440 / 3.66 ( 700) hydrogen bonds : angle 4.29269 / 2.95 ( 2328) link_NAG-ASN : bond 0.00975 / 0.55 ( 6) link_NAG-ASN : angle 5.11538 / 3.43 ( 18) *********************** 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 165 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.586 Fit side-chains REVERT: A 334 GLN cc_start: 0.8248 (mm110) cc_final: 0.7915 (mm110) REVERT: D 400 ARG cc_start: 0.8146 (tmm-80) cc_final: 0.7877 (tmm-80) REVERT: C 32 MET cc_start: 0.9385 (tpt) cc_final: 0.9141 (tpp) REVERT: C 138 ASP cc_start: 0.7702 (t0) cc_final: 0.7263 (t0) REVERT: C 171 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8706 (mpp) REVERT: B 187 MET cc_start: 0.8774 (mmm) cc_final: 0.8419 (mmt) REVERT: B 197 LYS cc_start: 0.8158 (pmmt) cc_final: 0.7949 (pmtt) REVERT: B 400 ARG cc_start: 0.8509 (tpt-90) cc_final: 0.8241 (tpt-90) outliers start: 32 outliers final: 11 residues processed: 150 average time/residue: 0.5283 time to fit residues: 88.2227 Evaluate side-chains 134 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 42 MET Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain E residue 283 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 89 optimal weight: 0.2980 chunk 8 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN D 139 ASN D 334 GLN C 334 GLN B 131 ASN E 159 ASN E 215 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.102162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.079788 restraints weight = 27759.878| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.75 r_work: 0.2884 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15800 Z= 0.176 Angle : 0.646 11.624 21262 Z= 0.309 Chirality : 0.045 0.241 2365 Planarity : 0.004 0.059 2577 Dihedral : 8.861 85.225 3098 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.82 % Allowed : 12.22 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.20), residues: 1747 helix: 2.50 (0.20), residues: 625 sheet: 1.11 (0.25), residues: 395 loop : -0.84 (0.21), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 295 TYR 0.021 0.002 TYR C 433 PHE 0.016 0.001 PHE E 134 TRP 0.008 0.001 TRP D 430 HIS 0.004 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (15792) covalent geometry : angle 0.62980 / 0.31 (21240) SS BOND : bond 0.00264 / 0.19 ( 2) SS BOND : angle 0.65759 / 0.38 ( 4) hydrogen bonds : bond 0.04806 / 3.22 ( 700) hydrogen bonds : angle 4.15584 / 2.85 ( 2328) link_NAG-ASN : bond 0.00963 / 0.55 ( 6) link_NAG-ASN : angle 4.91671 / 3.30 ( 18) *********************** 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 175 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 130 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: D 400 ARG cc_start: 0.8161 (tmm-80) cc_final: 0.7855 (tmm-80) REVERT: C 32 MET cc_start: 0.9333 (tpt) cc_final: 0.9124 (tpp) REVERT: C 138 ASP cc_start: 0.7680 (t0) cc_final: 0.7363 (t0) REVERT: C 333 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.6865 (pmm-80) outliers start: 45 outliers final: 17 residues processed: 158 average time/residue: 0.4971 time to fit residues: 87.6493 Evaluate side-chains 141 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 261 LEU 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 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 227 ASN 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 282 LEU Chi-restraints excluded: chain E residue 283 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 14 optimal weight: 4.9990 chunk 148 optimal weight: 0.6980 chunk 159 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 140 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN D 139 ASN D 334 GLN E 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.102717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.080532 restraints weight = 27303.902| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.75 r_work: 0.2909 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15800 Z= 0.125 Angle : 0.610 12.078 21262 Z= 0.290 Chirality : 0.044 0.236 2365 Planarity : 0.003 0.045 2577 Dihedral : 8.207 78.365 3098 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.32 % Allowed : 14.10 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.20), residues: 1747 helix: 2.58 (0.20), residues: 626 sheet: 1.16 (0.26), residues: 394 loop : -0.74 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 409 TYR 0.020 0.001 TYR C 325 PHE 0.016 0.001 PHE B 319 TRP 0.007 0.001 TRP B 430 HIS 0.003 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (15792) covalent geometry : angle 0.59365 / 0.29 (21240) SS BOND : bond 0.00245 / 0.17 ( 2) SS BOND : angle 0.52977 / 0.29 ( 4) hydrogen bonds : bond 0.04437 / 2.98 ( 700) hydrogen bonds : angle 4.00955 / 2.75 ( 2328) link_NAG-ASN : bond 0.01001 / 0.58 ( 6) link_NAG-ASN : angle 4.80911 / 3.24 ( 18) *********************** 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 170 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 0.620 Fit side-chains REVERT: A 428 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.8278 (t80) REVERT: D 400 ARG cc_start: 0.8158 (tmm-80) cc_final: 0.7891 (tmm-80) REVERT: C 32 MET cc_start: 0.9346 (tpt) cc_final: 0.9124 (tpp) REVERT: C 138 ASP cc_start: 0.7642 (t0) cc_final: 0.7345 (t0) REVERT: B 250 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.7580 (mp10) REVERT: B 320 SER cc_start: 0.9404 (m) cc_final: 0.9131 (m) outliers start: 37 outliers final: 16 residues processed: 156 average time/residue: 0.5374 time to fit residues: 92.9931 Evaluate side-chains 144 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 244 MET 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 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 B residue 250 GLN Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 242 CYS Chi-restraints excluded: chain E residue 342 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 167 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 171 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 48 optimal weight: 0.4980 chunk 58 optimal weight: 0.7980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 139 ASN D 334 GLN C 334 GLN 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 = 0.3396 r_free = 0.3396 target = 0.100677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.078279 restraints weight = 27600.893| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.72 r_work: 0.2854 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15800 Z= 0.213 Angle : 0.658 11.688 21262 Z= 0.318 Chirality : 0.045 0.214 2365 Planarity : 0.004 0.046 2577 Dihedral : 8.180 80.538 3098 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.07 % Allowed : 14.35 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.20), residues: 1747 helix: 2.41 (0.20), residues: 627 sheet: 1.04 (0.25), residues: 391 loop : -0.82 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 437 TYR 0.022 0.002 TYR D 433 PHE 0.021 0.002 PHE B 319 TRP 0.008 0.001 TRP E 284 HIS 0.006 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.21 (15792) covalent geometry : angle 0.64302 / 0.32 (21240) SS BOND : bond 0.00303 / 0.21 ( 2) SS BOND : angle 0.75001 / 0.49 ( 4) hydrogen bonds : bond 0.04843 / 3.24 ( 700) hydrogen bonds : angle 4.16178 / 2.86 ( 2328) link_NAG-ASN : bond 0.00948 / 0.54 ( 6) link_NAG-ASN : angle 4.84613 / 3.25 ( 18) *********************** 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: 49 poor density : 125 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: A 428 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8345 (t80) REVERT: D 400 ARG cc_start: 0.8216 (tmm-80) cc_final: 0.7936 (tmm-80) REVERT: C 32 MET cc_start: 0.9321 (tpt) cc_final: 0.9079 (tpp) REVERT: C 138 ASP cc_start: 0.7731 (t0) cc_final: 0.7464 (t0) REVERT: B 250 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.7566 (mp10) REVERT: B 320 SER cc_start: 0.9403 (m) cc_final: 0.9123 (m) REVERT: B 323 LEU cc_start: 0.9329 (mp) cc_final: 0.9108 (mp) REVERT: E 231 ASP cc_start: 0.8239 (t0) cc_final: 0.7830 (t0) outliers start: 49 outliers final: 23 residues processed: 159 average time/residue: 0.5123 time to fit residues: 91.1576 Evaluate side-chains 145 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 323 LEU Chi-restraints excluded: chain A residue 428 PHE 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 244 MET 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 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 227 ASN Chi-restraints excluded: chain B residue 250 GLN 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 241 ASN 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 32 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 114 optimal weight: 0.3980 chunk 112 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 334 GLN E 58 ASN E 159 ASN E 234 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.102724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.080569 restraints weight = 27449.757| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.73 r_work: 0.2896 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15800 Z= 0.124 Angle : 0.614 12.272 21262 Z= 0.295 Chirality : 0.043 0.234 2365 Planarity : 0.003 0.042 2577 Dihedral : 7.658 81.678 3098 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.51 % Allowed : 14.97 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.20), residues: 1747 helix: 2.60 (0.20), residues: 623 sheet: 1.08 (0.26), residues: 391 loop : -0.68 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 437 TYR 0.019 0.001 TYR C 325 PHE 0.022 0.001 PHE B 319 TRP 0.007 0.001 TRP B 430 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (15792) covalent geometry : angle 0.59821 / 0.29 (21240) SS BOND : bond 0.00228 / 0.16 ( 2) SS BOND : angle 0.48431 / 0.26 ( 4) hydrogen bonds : bond 0.04316 / 2.89 ( 700) hydrogen bonds : angle 3.97680 / 2.73 ( 2328) link_NAG-ASN : bond 0.01004 / 0.59 ( 6) link_NAG-ASN : angle 4.73329 / 3.19 ( 18) *********************** 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 174 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.645 Fit side-chains REVERT: A 187 MET cc_start: 0.8620 (mmm) cc_final: 0.8409 (mmt) REVERT: A 428 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.8315 (t80) REVERT: D 400 ARG cc_start: 0.8175 (tmm-80) cc_final: 0.7885 (tmm-80) REVERT: C 32 MET cc_start: 0.9326 (tpt) cc_final: 0.9084 (tpp) REVERT: C 138 ASP cc_start: 0.7675 (t0) cc_final: 0.7437 (t0) REVERT: B 320 SER cc_start: 0.9413 (m) cc_final: 0.9132 (m) outliers start: 40 outliers final: 22 residues processed: 163 average time/residue: 0.5086 time to fit residues: 92.9534 Evaluate side-chains 149 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 244 MET 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 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 B residue 227 ASN Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 178 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 119 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 334 GLN ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 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 = 0.3398 r_free = 0.3398 target = 0.100912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.078423 restraints weight = 27905.005| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.75 r_work: 0.2857 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15800 Z= 0.208 Angle : 0.647 11.470 21262 Z= 0.316 Chirality : 0.045 0.221 2365 Planarity : 0.004 0.040 2577 Dihedral : 7.725 82.586 3098 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.63 % Allowed : 14.97 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.20), residues: 1747 helix: 2.50 (0.20), residues: 623 sheet: 0.97 (0.25), residues: 391 loop : -0.75 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 437 TYR 0.022 0.002 TYR D 433 PHE 0.035 0.001 PHE B 319 TRP 0.010 0.001 TRP E 284 HIS 0.005 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 (15792) covalent geometry : angle 0.63260 / 0.31 (21240) SS BOND : bond 0.00235 / 0.17 ( 2) SS BOND : angle 0.65812 / 0.45 ( 4) hydrogen bonds : bond 0.04673 / 3.13 ( 700) hydrogen bonds : angle 4.10600 / 2.82 ( 2328) link_NAG-ASN : bond 0.00908 / 0.52 ( 6) link_NAG-ASN : angle 4.74826 / 3.20 ( 18) *********************** 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: 42 poor density : 122 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 428 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8337 (t80) REVERT: D 181 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8000 (pp20) REVERT: D 400 ARG cc_start: 0.8175 (tmm-80) cc_final: 0.7883 (tmm-80) REVERT: C 32 MET cc_start: 0.9309 (tpt) cc_final: 0.9064 (tpp) REVERT: C 138 ASP cc_start: 0.7776 (t0) cc_final: 0.7536 (t0) REVERT: C 333 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.6863 (pmm-80) REVERT: B 250 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.7481 (mp10) REVERT: B 320 SER cc_start: 0.9352 (m) cc_final: 0.9080 (m) REVERT: B 408 LYS cc_start: 0.8605 (mttp) cc_final: 0.8155 (mmmt) REVERT: E 477 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7535 (mp) outliers start: 42 outliers final: 26 residues processed: 153 average time/residue: 0.4781 time to fit residues: 82.2410 Evaluate side-chains 154 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 244 MET 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 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 227 ASN Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 241 ASN 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 Chi-restraints excluded: chain E residue 477 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 99 optimal weight: 6.9990 chunk 160 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 chunk 130 optimal weight: 0.0870 chunk 109 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN E 159 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 = 0.3430 r_free = 0.3430 target = 0.102382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.080270 restraints weight = 27244.561| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.76 r_work: 0.2903 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15800 Z= 0.112 Angle : 0.605 11.872 21262 Z= 0.292 Chirality : 0.043 0.242 2365 Planarity : 0.003 0.038 2577 Dihedral : 7.356 83.417 3098 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.94 % Allowed : 15.66 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.20), residues: 1747 helix: 2.60 (0.20), residues: 623 sheet: 1.03 (0.26), residues: 391 loop : -0.63 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 437 TYR 0.018 0.001 TYR C 325 PHE 0.019 0.001 PHE B 319 TRP 0.008 0.001 TRP B 430 HIS 0.002 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (15792) covalent geometry : angle 0.58975 / 0.29 (21240) SS BOND : bond 0.00222 / 0.16 ( 2) SS BOND : angle 0.41263 / 0.22 ( 4) hydrogen bonds : bond 0.04164 / 2.79 ( 700) hydrogen bonds : angle 3.91984 / 2.69 ( 2328) link_NAG-ASN : bond 0.01037 / 0.61 ( 6) link_NAG-ASN : angle 4.69080 / 3.17 ( 18) *********************** 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 161 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 80 MET cc_start: 0.9360 (mtt) cc_final: 0.9047 (mtm) REVERT: A 428 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.8339 (t80) REVERT: D 113 MET cc_start: 0.8512 (ppp) cc_final: 0.8259 (ppp) REVERT: D 181 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.8006 (pp20) REVERT: D 400 ARG cc_start: 0.8184 (tmm-80) cc_final: 0.7875 (tmm-80) REVERT: C 32 MET cc_start: 0.9308 (tpt) cc_final: 0.9063 (tpp) REVERT: C 138 ASP cc_start: 0.7736 (t0) cc_final: 0.7510 (t0) REVERT: B 127 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8653 (tm-30) REVERT: B 320 SER cc_start: 0.9365 (m) cc_final: 0.9089 (m) REVERT: E 231 ASP cc_start: 0.8195 (t0) cc_final: 0.7799 (t0) REVERT: E 477 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7493 (mp) outliers start: 31 outliers final: 19 residues processed: 152 average time/residue: 0.4871 time to fit residues: 82.8007 Evaluate side-chains 149 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 428 PHE 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 244 MET Chi-restraints excluded: chain C residue 261 LEU 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 B residue 250 GLN Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 241 ASN 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 477 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 50 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 37 optimal weight: 0.0050 chunk 119 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 168 ASN C 334 GLN ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.102466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.080302 restraints weight = 27651.816| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.74 r_work: 0.2897 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15800 Z= 0.138 Angle : 0.618 11.684 21262 Z= 0.298 Chirality : 0.043 0.240 2365 Planarity : 0.003 0.039 2577 Dihedral : 7.269 83.969 3098 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.75 % Allowed : 16.17 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.20), residues: 1747 helix: 2.59 (0.20), residues: 623 sheet: 1.01 (0.26), residues: 391 loop : -0.67 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 437 TYR 0.019 0.002 TYR D 433 PHE 0.036 0.001 PHE B 319 TRP 0.007 0.001 TRP A 263 HIS 0.004 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (15792) covalent geometry : angle 0.60305 / 0.29 (21240) SS BOND : bond 0.00196 / 0.14 ( 2) SS BOND : angle 0.42049 / 0.26 ( 4) hydrogen bonds : bond 0.04196 / 2.81 ( 700) hydrogen bonds : angle 3.94049 / 2.70 ( 2328) link_NAG-ASN : bond 0.00954 / 0.56 ( 6) link_NAG-ASN : angle 4.67126 / 3.16 ( 18) ********************** 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 157 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: A 80 MET cc_start: 0.9375 (mtt) cc_final: 0.9054 (mtm) REVERT: A 428 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8325 (t80) REVERT: D 113 MET cc_start: 0.8515 (ppp) cc_final: 0.8249 (ppp) REVERT: D 181 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7980 (pp20) REVERT: D 400 ARG cc_start: 0.8181 (tmm-80) cc_final: 0.7860 (tmm-80) REVERT: C 32 MET cc_start: 0.9307 (tpt) cc_final: 0.9056 (tpp) REVERT: C 138 ASP cc_start: 0.7756 (t0) cc_final: 0.7506 (t0) REVERT: C 400 ARG cc_start: 0.8252 (tpp80) cc_final: 0.8027 (tpp80) REVERT: B 127 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8627 (tm-30) REVERT: B 320 SER cc_start: 0.9325 (m) cc_final: 0.9064 (m) REVERT: B 408 LYS cc_start: 0.8574 (mttp) cc_final: 0.8118 (mmmt) REVERT: E 231 ASP cc_start: 0.8186 (t0) cc_final: 0.7788 (t0) REVERT: E 477 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7502 (mp) outliers start: 28 outliers final: 21 residues processed: 151 average time/residue: 0.5420 time to fit residues: 91.6755 Evaluate side-chains 150 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 428 PHE 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 244 MET Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 261 LEU 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 227 ASN Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 241 ASN 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 477 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 11 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 114 optimal weight: 0.0270 chunk 148 optimal weight: 3.9990 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 334 GLN ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.102552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.080309 restraints weight = 27393.344| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.74 r_work: 0.2898 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 15800 Z= 0.163 Angle : 0.814 59.074 21262 Z= 0.445 Chirality : 0.044 0.390 2365 Planarity : 0.004 0.113 2577 Dihedral : 7.267 83.972 3098 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.63 % Allowed : 16.17 % Favored : 82.21 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.20), residues: 1747 helix: 2.59 (0.20), residues: 623 sheet: 1.01 (0.26), residues: 391 loop : -0.67 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 437 TYR 0.018 0.002 TYR D 433 PHE 0.033 0.001 PHE B 319 TRP 0.007 0.001 TRP B 430 HIS 0.004 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (15792) covalent geometry : angle 0.80341 / 0.44 (21240) SS BOND : bond 0.00201 / 0.14 ( 2) SS BOND : angle 0.41361 / 0.26 ( 4) hydrogen bonds : bond 0.04191 / 2.81 ( 700) hydrogen bonds : angle 3.94669 / 2.71 ( 2328) link_NAG-ASN : bond 0.00956 / 0.56 ( 6) link_NAG-ASN : angle 4.67122 / 3.16 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3293.75 seconds wall clock time: 57 minutes 19.20 seconds (3439.20 seconds total)