Starting phenix.real_space_refine on Sun Aug 24 01:04:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fe1_29019/08_2025/8fe1_29019.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fe1_29019/08_2025/8fe1_29019.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fe1_29019/08_2025/8fe1_29019.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fe1_29019/08_2025/8fe1_29019.map" model { file = "/net/cci-nas-00/data/ceres_data/8fe1_29019/08_2025/8fe1_29019.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fe1_29019/08_2025/8fe1_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-2.0-5787/lib/python3.9/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: 32 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 229 Unusual residues: {'IVM': 1, 'NAG': 1, 'PLM': 6, 'PX4': 2} Inner-chain residues flagged as termini: ['pdbres="GLY D 506 "'] Classifications: {'peptide': 1, 'undetermined': 10} Modifications used: {'COO': 1} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 247 Unusual residues: {'D10': 1, 'IVM': 1, 'NAG': 1, 'PLM': 6, 'PX4': 2} Inner-chain residues flagged as termini: ['pdbres="GLY C 503 "'] Classifications: {'peptide': 1, 'undetermined': 11} Modifications used: {'COO': 1} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 226 Unusual residues: {'IVM': 1, 'NAG': 1, 'PLM': 6, 'PX4': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 128 Unusual residues: {'NAG': 2, 'PLM': 5, 'PX4': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.06, per 1000 atoms: 0.20 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: 1.04 Conformation dependent library (CDL) restraints added in 400.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.34 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: 2.31 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2518 1.32 - 1.45: 4092 1.45 - 1.58: 8734 1.58 - 1.71: 287 1.71 - 1.84: 161 Bond restraints: 15792 Sorted by residual: bond pdb=" C34 IVM D 502 " pdb=" C36 IVM D 502 " ideal model delta sigma weight residual 1.500 1.681 -0.181 2.00e-02 2.50e+03 8.21e+01 bond pdb=" C34 IVM B 503 " pdb=" C36 IVM B 503 " ideal model delta sigma weight residual 1.500 1.678 -0.178 2.00e-02 2.50e+03 7.92e+01 bond pdb=" C34 IVM A 503 " pdb=" C36 IVM A 503 " ideal model delta sigma weight residual 1.500 1.678 -0.178 2.00e-02 2.50e+03 7.91e+01 bond pdb=" C34 IVM C 505 " pdb=" C36 IVM C 505 " ideal model delta sigma weight residual 1.500 1.675 -0.175 2.00e-02 2.50e+03 7.67e+01 bond pdb=" C34 IVM A 504 " pdb=" C36 IVM A 504 " ideal model delta sigma weight residual 1.500 1.675 -0.175 2.00e-02 2.50e+03 7.64e+01 ... (remaining 15787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 20311 2.30 - 4.61: 726 4.61 - 6.91: 144 6.91 - 9.21: 52 9.21 - 11.52: 7 Bond angle restraints: 21240 Sorted by residual: angle pdb=" C ASN B 131 " pdb=" N PHE B 132 " pdb=" CA PHE B 132 " ideal model delta sigma weight residual 122.67 115.15 7.52 1.73e+00 3.34e-01 1.89e+01 angle pdb=" N LYS B 128 " pdb=" CA LYS B 128 " pdb=" C LYS B 128 " ideal model delta sigma weight residual 113.12 108.24 4.88 1.25e+00 6.40e-01 1.52e+01 angle pdb=" C17 IVM A 503 " pdb=" C19 IVM A 503 " pdb=" O2 IVM A 503 " ideal model delta sigma weight residual 112.55 101.03 11.52 3.00e+00 1.11e-01 1.47e+01 angle pdb=" C SER E 216 " pdb=" N GLY E 217 " pdb=" CA GLY E 217 " ideal model delta sigma weight residual 122.73 119.22 3.51 9.30e-01 1.16e+00 1.43e+01 angle pdb=" CA GLU D 101 " pdb=" CB GLU D 101 " pdb=" CG GLU D 101 " ideal model delta sigma weight residual 114.10 121.54 -7.44 2.00e+00 2.50e-01 1.38e+01 ... (remaining 21235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.91: 9835 34.91 - 69.82: 217 69.82 - 104.73: 51 104.73 - 139.64: 21 139.64 - 174.55: 2 Dihedral angle restraints: 10126 sinusoidal: 4896 harmonic: 5230 Sorted by residual: dihedral pdb=" O5 PX4 A 505 " pdb=" C7 PX4 A 505 " pdb=" C8 PX4 A 505 " pdb=" O7 PX4 A 505 " ideal model delta sinusoidal sigma weight residual 59.95 -125.50 -174.55 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 PX4 C 502 " pdb=" C7 PX4 C 502 " pdb=" C8 PX4 C 502 " pdb=" O7 PX4 C 502 " ideal model delta sinusoidal sigma weight residual 59.95 -114.05 174.00 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 PX4 C 507 " pdb=" C7 PX4 C 507 " pdb=" C8 PX4 C 507 " pdb=" O7 PX4 C 507 " ideal model delta sinusoidal sigma weight residual 59.95 -161.44 -138.61 1 3.00e+01 1.11e-03 1.87e+01 ... (remaining 10123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.200: 2315 0.200 - 0.400: 22 0.400 - 0.600: 15 0.600 - 0.800: 5 0.800 - 1.000: 8 Chirality restraints: 2365 Sorted by residual: chirality pdb=" C3 IVM A 504 " pdb=" C2 IVM A 504 " pdb=" C4 IVM A 504 " pdb=" C5 IVM A 504 " both_signs ideal model delta sigma weight residual False 2.53 3.52 -1.00 2.00e-01 2.50e+01 2.50e+01 chirality pdb=" C3 IVM C 505 " pdb=" C2 IVM C 505 " pdb=" C4 IVM C 505 " pdb=" C5 IVM C 505 " both_signs ideal model delta sigma weight residual False 2.53 3.52 -0.99 2.00e-01 2.50e+01 2.47e+01 chirality pdb=" C3 IVM A 503 " pdb=" C2 IVM A 503 " pdb=" C4 IVM A 503 " pdb=" C5 IVM A 503 " both_signs ideal model delta sigma weight residual False 2.53 3.47 -0.95 2.00e-01 2.50e+01 2.24e+01 ... (remaining 2362 not shown) Planarity restraints: 2583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 601 " 0.336 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG E 601 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG E 601 " 0.179 2.00e-02 2.50e+03 pdb=" N2 NAG E 601 " -0.501 2.00e-02 2.50e+03 pdb=" O7 NAG E 601 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 335 " 0.013 2.00e-02 2.50e+03 1.83e-02 5.03e+00 pdb=" CG HIS B 335 " -0.038 2.00e-02 2.50e+03 pdb=" ND1 HIS B 335 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 HIS B 335 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 HIS B 335 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS B 335 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS E 254 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" C CYS E 254 " -0.035 2.00e-02 2.50e+03 pdb=" O CYS E 254 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL E 255 " 0.012 2.00e-02 2.50e+03 ... (remaining 2580 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1351 2.75 - 3.29: 14590 3.29 - 3.83: 23829 3.83 - 4.36: 30075 4.36 - 4.90: 51149 Nonbonded interactions: 120994 Sorted by model distance: nonbonded pdb=" OG1 THR A 79 " pdb=" OD1 ASP A 81 " model vdw 2.217 3.040 nonbonded pdb=" OG1 THR C 186 " pdb=" OD1 ASN C 188 " model vdw 2.231 3.040 nonbonded pdb=" OG1 THR C 79 " pdb=" OD1 ASP C 81 " model vdw 2.232 3.040 nonbonded pdb=" OE1 GLU B 193 " pdb=" OH TYR B 221 " model vdw 2.275 3.040 nonbonded pdb=" OE1 GLU A 193 " pdb=" OH TYR A 221 " model vdw 2.276 3.040 ... (remaining 120989 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 336 or resid 398 through 444 or resid 507 throu \ gh 508 or (resid 509 and (name C1 or name C2 or name C3 or name C4 or name C5 or \ name C6 or name C7 or name C8 or name C9 or name O1 or name O2 )) or (resid 510 \ and (name CA or name CB or name C1 or name C2 or name C3 or name C4 or name C5 \ or name C6 or name C7 or name C8 or name C9 or name O1 or name O2 )) or (resid 5 \ 11 and (name CA or name CB or name C1 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name C9 or name CC or name O1 or name O2 ) \ ))) selection = (chain 'B' and (resid 33 through 336 or resid 398 through 444 or resid 506 or (r \ esid 507 and (name CA or name C1 or name C2 or name C3 or name C4 or name C5 or \ name C6 or name C7 or name C8 or name C9 or name O1 or name O2 )) or resid 508 o \ r (resid 509 and (name CA or name CB or name C1 or name C2 or name C3 or name C4 \ or name C5 or name C6 or name C7 or name C8 or name C9 or name O1 or name O2 )) \ or (resid 510 and (name CA or name CB or name C1 or name C2 or name C3 or name \ C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name CC or name O1 \ or name O2 )))) selection = (chain 'C' and (resid 33 through 336 or resid 398 through 444 or (resid 509 and \ (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or na \ me C8 or name C9 or name O1 or name O2 )) or (resid 510 and (name CA or name C1 \ or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or \ name C9 or name O1 or name O2 )) or (resid 511 and (name C1 or name C2 or name C \ 3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name O1 o \ r name O2 )) or (resid 512 and (name CA or name CB or name C1 or name C2 or name \ C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name O1 \ or name O2 )) or resid 513)) selection = (chain 'D' and (resid 33 through 336 or resid 398 through 444 or (resid 507 and \ (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or na \ me C8 or name C9 or name O1 or name O2 )) or (resid 508 and (name CA or name C1 \ or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or \ name C9 or name O1 or name O2 )) or resid 509 through 510 or (resid 511 and (nam \ e CA or name CB or name C1 or name C2 or name C3 or name C4 or name C5 or name C \ 6 or name C7 or name C8 or name C9 or name CC or name O1 or name O2 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.720 Find NCS groups from input model: 0.330 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:8.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.181 15800 Z= 0.784 Angle : 1.047 18.658 21262 Z= 0.463 Chirality : 0.094 1.000 2365 Planarity : 0.008 0.286 2577 Dihedral : 17.018 174.548 6722 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.06 % Allowed : 0.31 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (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 covalent geometry : bond 0.01559 (15792) covalent geometry : angle 1.02645 (21240) SS BOND : bond 0.00837 ( 2) SS BOND : angle 1.58234 ( 4) hydrogen bonds : bond 0.25833 ( 700) hydrogen bonds : angle 7.24366 ( 2328) link_NAG-ASN : bond 0.01238 ( 6) link_NAG-ASN : angle 7.14981 ( 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 : 0.367 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: 0.7745 (pp) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.5441 time to fit residues: 105.5838 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 : 0.399 ------------------------------------------------------------------------------- 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: 6.9990 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... Flipped N/Q/H residues before XYZ refinement: D 290 GLN D 334 GLN E 85 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 = 0.3527 r_free = 0.3527 target = 0.108654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.086675 restraints weight = 27322.025| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.70 r_work: 0.3029 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15800 Z= 0.140 Angle : 0.695 12.000 21262 Z= 0.329 Chirality : 0.046 0.284 2365 Planarity : 0.004 0.039 2577 Dihedral : 13.002 177.927 3240 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.48 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 aren not related in a simple way. whole: 1.15 (0.19), residues: 1747 helix: 2.41 (0.20), residues: 629 sheet: 1.14 (0.26), residues: 388 loop : -0.98 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 115 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 covalent geometry : bond 0.00285 (15792) covalent geometry : angle 0.67461 (21240) SS BOND : bond 0.00230 ( 2) SS BOND : angle 0.83157 ( 4) hydrogen bonds : bond 0.06135 ( 700) hydrogen bonds : angle 4.63585 ( 2328) link_NAG-ASN : bond 0.01082 ( 6) link_NAG-ASN : angle 5.77076 ( 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 180 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.398 Fit side-chains REVERT: A 171 MET cc_start: 0.8942 (mtm) cc_final: 0.8742 (mpp) REVERT: B 33 PRO cc_start: 0.8156 (Cg_exo) cc_final: 0.7665 (Cg_endo) outliers start: 25 outliers final: 6 residues processed: 167 average time/residue: 0.4812 time to fit residues: 89.2097 Evaluate side-chains 129 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 123 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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: 5.9990 chunk 33 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN D 139 ASN D 334 GLN C 334 GLN B 139 ASN E 58 ASN E 159 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.099540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.076844 restraints weight = 28115.128| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.75 r_work: 0.2831 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 15800 Z= 0.294 Angle : 0.754 11.586 21262 Z= 0.368 Chirality : 0.048 0.203 2365 Planarity : 0.004 0.040 2577 Dihedral : 12.126 167.695 3240 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.38 % Allowed : 11.15 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.19), residues: 1747 helix: 2.24 (0.20), residues: 624 sheet: 0.89 (0.25), residues: 395 loop : -1.08 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 333 TYR 0.029 0.002 TYR D 433 PHE 0.021 0.002 PHE D 72 TRP 0.010 0.001 TRP D 430 HIS 0.008 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00706 (15792) covalent geometry : angle 0.73833 (21240) SS BOND : bond 0.00341 ( 2) SS BOND : angle 1.13592 ( 4) hydrogen bonds : bond 0.06172 ( 700) hydrogen bonds : angle 4.60168 ( 2328) link_NAG-ASN : bond 0.01007 ( 6) link_NAG-ASN : angle 5.32343 ( 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 159 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 121 time to evaluate : 0.439 Fit side-chains REVERT: C 138 ASP cc_start: 0.7771 (t0) cc_final: 0.7396 (t0) REVERT: C 333 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7548 (pmm-80) REVERT: C 334 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7962 (mm-40) REVERT: B 197 LYS cc_start: 0.8362 (pmmt) cc_final: 0.8158 (pmtt) REVERT: E 147 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8665 (tm-30) outliers start: 38 outliers final: 16 residues processed: 144 average time/residue: 0.4909 time to fit residues: 78.3792 Evaluate side-chains 135 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 116 SER 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 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 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 147 GLU Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 342 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 89 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 127 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 chunk 171 optimal weight: 0.0370 chunk 40 optimal weight: 0.9980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.102906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.080472 restraints weight = 27237.510| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.76 r_work: 0.2905 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 15800 Z= 0.119 Angle : 0.632 12.074 21262 Z= 0.300 Chirality : 0.044 0.246 2365 Planarity : 0.004 0.054 2577 Dihedral : 10.965 174.226 3240 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.26 % Allowed : 12.91 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.20), residues: 1747 helix: 2.56 (0.20), residues: 625 sheet: 1.09 (0.26), residues: 394 loop : -0.84 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 400 TYR 0.021 0.001 TYR C 325 PHE 0.014 0.001 PHE E 134 TRP 0.009 0.001 TRP D 263 HIS 0.004 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00246 (15792) covalent geometry : angle 0.61530 (21240) SS BOND : bond 0.00258 ( 2) SS BOND : angle 0.56286 ( 4) hydrogen bonds : bond 0.04693 ( 700) hydrogen bonds : angle 4.13558 ( 2328) link_NAG-ASN : bond 0.01085 ( 6) link_NAG-ASN : angle 5.01458 ( 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 172 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.408 Fit side-chains REVERT: D 400 ARG cc_start: 0.8057 (tmm-80) cc_final: 0.7846 (tmm-80) REVERT: C 113 MET cc_start: 0.8470 (ptm) cc_final: 0.8183 (ptm) REVERT: C 138 ASP cc_start: 0.7662 (t0) cc_final: 0.7377 (t0) REVERT: C 334 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7903 (mm-40) REVERT: B 400 ARG cc_start: 0.8293 (tpt-90) cc_final: 0.7866 (mmm160) REVERT: E 147 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8647 (tm-30) outliers start: 36 outliers final: 11 residues processed: 155 average time/residue: 0.4877 time to fit residues: 83.7374 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 : 0.490 ------------------------------------------------------------------------------- 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 42 MET Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 334 GLN Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain E residue 242 CYS Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 342 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 14 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 51 optimal weight: 0.3980 chunk 92 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 140 optimal weight: 0.0470 chunk 79 optimal weight: 3.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN D 139 ASN D 334 GLN B 227 ASN E 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.103392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.081072 restraints weight = 27254.662| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.76 r_work: 0.2916 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15800 Z= 0.118 Angle : 0.614 12.043 21262 Z= 0.290 Chirality : 0.043 0.256 2365 Planarity : 0.003 0.048 2577 Dihedral : 10.165 176.435 3240 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.32 % Allowed : 14.35 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.20), residues: 1747 helix: 2.61 (0.20), residues: 625 sheet: 1.17 (0.26), residues: 391 loop : -0.77 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 409 TYR 0.019 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 covalent geometry : bond 0.00257 (15792) covalent geometry : angle 0.59751 (21240) SS BOND : bond 0.00229 ( 2) SS BOND : angle 0.48300 ( 4) hydrogen bonds : bond 0.04383 ( 700) hydrogen bonds : angle 3.99908 ( 2328) link_NAG-ASN : bond 0.00997 ( 6) link_NAG-ASN : angle 4.96648 ( 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 167 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 0.368 Fit side-chains REVERT: D 400 ARG cc_start: 0.8060 (tmm-80) cc_final: 0.7812 (tmm-80) REVERT: C 138 ASP cc_start: 0.7648 (t0) cc_final: 0.7368 (t0) REVERT: B 320 SER cc_start: 0.9409 (m) cc_final: 0.9133 (m) REVERT: B 400 ARG cc_start: 0.8344 (tpt-90) cc_final: 0.7960 (mmm160) REVERT: E 147 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8604 (tm-30) outliers start: 37 outliers final: 16 residues processed: 152 average time/residue: 0.4320 time to fit residues: 73.3727 Evaluate side-chains 142 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 42 MET 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 204 ASP Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain E residue 242 CYS Chi-restraints excluded: chain E residue 283 SER 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: 0.4980 chunk 77 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 171 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 80 optimal weight: 0.0010 chunk 48 optimal weight: 0.0060 chunk 58 optimal weight: 0.9980 overall best weight: 0.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN D 139 ASN D 334 GLN B 227 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.105453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.083348 restraints weight = 27140.207| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.73 r_work: 0.2946 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2718 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= 0.106 Angle : 0.593 12.242 21262 Z= 0.280 Chirality : 0.043 0.268 2365 Planarity : 0.003 0.046 2577 Dihedral : 9.567 176.635 3240 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.57 % Allowed : 14.85 % 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 aren not related in a simple way. whole: 1.47 (0.20), residues: 1747 helix: 2.63 (0.20), residues: 627 sheet: 1.26 (0.26), residues: 386 loop : -0.69 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 409 TYR 0.017 0.001 TYR C 325 PHE 0.025 0.001 PHE B 319 TRP 0.006 0.001 TRP E 331 HIS 0.002 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00220 (15792) covalent geometry : angle 0.57584 (21240) SS BOND : bond 0.00212 ( 2) SS BOND : angle 0.38281 ( 4) hydrogen bonds : bond 0.04038 ( 700) hydrogen bonds : angle 3.86876 ( 2328) link_NAG-ASN : bond 0.01022 ( 6) link_NAG-ASN : angle 4.89859 ( 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 165 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.364 Fit side-chains REVERT: A 428 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.8274 (t80) REVERT: D 400 ARG cc_start: 0.8081 (tmm-80) cc_final: 0.7840 (tmm-80) REVERT: C 138 ASP cc_start: 0.7647 (t0) cc_final: 0.7371 (t0) REVERT: B 320 SER cc_start: 0.9392 (m) cc_final: 0.9115 (m) REVERT: B 400 ARG cc_start: 0.8267 (tpt-90) cc_final: 0.7885 (mmm160) outliers start: 25 outliers final: 13 residues processed: 159 average time/residue: 0.4154 time to fit residues: 73.8218 Evaluate side-chains 140 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain D residue 42 MET 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 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 E residue 242 CYS Chi-restraints excluded: chain E residue 255 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 32 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 146 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN D 139 ASN D 334 GLN C 334 GLN E 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.102523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.080187 restraints weight = 27313.259| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.76 r_work: 0.2899 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15800 Z= 0.149 Angle : 0.621 12.302 21262 Z= 0.296 Chirality : 0.044 0.251 2365 Planarity : 0.003 0.043 2577 Dihedral : 9.297 174.453 3240 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.19 % Allowed : 14.66 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.20), residues: 1747 helix: 2.56 (0.20), residues: 626 sheet: 1.20 (0.26), residues: 391 loop : -0.68 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 437 TYR 0.019 0.002 TYR C 325 PHE 0.035 0.001 PHE B 319 TRP 0.008 0.001 TRP A 263 HIS 0.005 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00349 (15792) covalent geometry : angle 0.60498 (21240) SS BOND : bond 0.00222 ( 2) SS BOND : angle 0.51515 ( 4) hydrogen bonds : bond 0.04317 ( 700) hydrogen bonds : angle 3.92223 ( 2328) link_NAG-ASN : bond 0.00918 ( 6) link_NAG-ASN : angle 4.85950 ( 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 162 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 428 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8325 (t80) REVERT: D 115 ASP cc_start: 0.8427 (p0) cc_final: 0.8151 (t0) REVERT: C 138 ASP cc_start: 0.7710 (t0) cc_final: 0.7420 (t0) REVERT: B 320 SER cc_start: 0.9345 (m) cc_final: 0.9075 (m) outliers start: 35 outliers final: 17 residues processed: 150 average time/residue: 0.4621 time to fit residues: 77.2905 Evaluate side-chains 138 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 328 VAL 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 C residue 281 ILE Chi-restraints excluded: chain C residue 334 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 219 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 119 optimal weight: 6.9990 chunk 86 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 171 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 334 GLN 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 = 0.3417 r_free = 0.3417 target = 0.102023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.079803 restraints weight = 27748.902| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.73 r_work: 0.2886 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15800 Z= 0.171 Angle : 0.630 11.638 21262 Z= 0.304 Chirality : 0.044 0.242 2365 Planarity : 0.004 0.039 2577 Dihedral : 9.160 172.268 3240 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.07 % Allowed : 15.10 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.20), residues: 1747 helix: 2.60 (0.20), residues: 622 sheet: 1.07 (0.26), residues: 394 loop : -0.63 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 437 TYR 0.020 0.002 TYR C 325 PHE 0.026 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 covalent geometry : bond 0.00406 (15792) covalent geometry : angle 0.61471 (21240) SS BOND : bond 0.00230 ( 2) SS BOND : angle 0.56374 ( 4) hydrogen bonds : bond 0.04400 ( 700) hydrogen bonds : angle 3.96170 ( 2328) link_NAG-ASN : bond 0.00915 ( 6) link_NAG-ASN : angle 4.80620 ( 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 159 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 428 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8337 (t80) REVERT: D 113 MET cc_start: 0.8497 (ppp) cc_final: 0.8193 (pmm) REVERT: D 115 ASP cc_start: 0.8422 (p0) cc_final: 0.8125 (t0) REVERT: D 181 GLU cc_start: 0.8272 (pp20) cc_final: 0.7932 (pp20) REVERT: D 400 ARG cc_start: 0.8087 (tmm-80) cc_final: 0.7881 (tmm-80) REVERT: C 138 ASP cc_start: 0.7723 (t0) cc_final: 0.7492 (t0) REVERT: B 320 SER cc_start: 0.9329 (m) cc_final: 0.9054 (m) REVERT: B 408 LYS cc_start: 0.8586 (mttp) cc_final: 0.8125 (mmmt) outliers start: 33 outliers final: 22 residues processed: 151 average time/residue: 0.4338 time to fit residues: 73.1822 Evaluate side-chains 148 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 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 281 ILE Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 241 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 99 optimal weight: 6.9990 chunk 160 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 109 optimal weight: 0.2980 chunk 53 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 334 GLN E 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.103297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.081174 restraints weight = 27526.054| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.74 r_work: 0.2912 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 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 : 0.003 0.049 15800 Z= 0.123 Angle : 0.612 12.978 21262 Z= 0.293 Chirality : 0.043 0.255 2365 Planarity : 0.003 0.038 2577 Dihedral : 8.928 171.334 3240 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.69 % Allowed : 15.60 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.20), residues: 1747 helix: 2.61 (0.20), residues: 622 sheet: 1.11 (0.26), residues: 394 loop : -0.57 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 437 TYR 0.017 0.001 TYR C 325 PHE 0.032 0.001 PHE B 319 TRP 0.007 0.001 TRP E 284 HIS 0.003 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00280 (15792) covalent geometry : angle 0.59661 (21240) SS BOND : bond 0.00216 ( 2) SS BOND : angle 0.42054 ( 4) hydrogen bonds : bond 0.04129 ( 700) hydrogen bonds : angle 3.87425 ( 2328) link_NAG-ASN : bond 0.00997 ( 6) link_NAG-ASN : angle 4.77822 ( 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 154 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 428 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8340 (t80) REVERT: D 113 MET cc_start: 0.8499 (ppp) cc_final: 0.7723 (ppp) REVERT: D 115 ASP cc_start: 0.8377 (p0) cc_final: 0.8082 (t0) REVERT: D 181 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7964 (pp20) REVERT: D 400 ARG cc_start: 0.8061 (tmm-80) cc_final: 0.7853 (tmm-80) REVERT: C 138 ASP cc_start: 0.7746 (t0) cc_final: 0.7497 (t0) REVERT: C 400 ARG cc_start: 0.8259 (tpp80) cc_final: 0.8015 (tpp80) REVERT: B 320 SER cc_start: 0.9305 (m) cc_final: 0.9054 (m) REVERT: B 408 LYS cc_start: 0.8578 (mttp) cc_final: 0.8116 (mmmt) REVERT: E 269 MET cc_start: 0.8994 (tpp) cc_final: 0.8745 (mmt) outliers start: 27 outliers final: 19 residues processed: 144 average time/residue: 0.4645 time to fit residues: 75.1987 Evaluate side-chains 147 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 328 VAL 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 187 MET Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 334 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 241 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 50 optimal weight: 7.9990 chunk 129 optimal weight: 0.1980 chunk 104 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 119 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.101877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.079453 restraints weight = 27786.800| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.75 r_work: 0.2879 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15800 Z= 0.182 Angle : 0.642 11.989 21262 Z= 0.311 Chirality : 0.044 0.242 2365 Planarity : 0.004 0.039 2577 Dihedral : 9.019 170.179 3240 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.63 % Allowed : 15.85 % 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 aren not related in a simple way. whole: 1.33 (0.20), residues: 1747 helix: 2.44 (0.20), residues: 630 sheet: 1.04 (0.25), residues: 391 loop : -0.64 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 333 TYR 0.020 0.002 TYR D 433 PHE 0.032 0.001 PHE C 319 TRP 0.013 0.001 TRP A 263 HIS 0.005 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00436 (15792) covalent geometry : angle 0.62745 (21240) SS BOND : bond 0.00202 ( 2) SS BOND : angle 0.58390 ( 4) hydrogen bonds : bond 0.04401 ( 700) hydrogen bonds : angle 3.98846 ( 2328) link_NAG-ASN : bond 0.00903 ( 6) link_NAG-ASN : angle 4.76491 ( 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 153 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: D 113 MET cc_start: 0.8477 (ppp) cc_final: 0.7654 (ppp) REVERT: D 115 ASP cc_start: 0.8401 (p0) cc_final: 0.8097 (t0) REVERT: D 400 ARG cc_start: 0.8079 (tmm-80) cc_final: 0.7806 (tmm-80) REVERT: C 138 ASP cc_start: 0.7742 (t0) cc_final: 0.7496 (t0) REVERT: C 400 ARG cc_start: 0.8287 (tpp80) cc_final: 0.8044 (tpp80) REVERT: B 107 LEU cc_start: 0.8089 (mm) cc_final: 0.7018 (pp) REVERT: B 320 SER cc_start: 0.9301 (m) cc_final: 0.9049 (m) REVERT: B 408 LYS cc_start: 0.8582 (mttp) cc_final: 0.8116 (mmmt) REVERT: E 269 MET cc_start: 0.9010 (tpp) cc_final: 0.8764 (mmt) outliers start: 26 outliers final: 20 residues processed: 144 average time/residue: 0.4974 time to fit residues: 79.7917 Evaluate side-chains 143 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 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 219 LEU Chi-restraints excluded: chain E residue 162 LEU 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 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: 0.9990 chunk 5 optimal weight: 3.9990 chunk 158 optimal weight: 0.2980 chunk 38 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 168 ASN C 334 GLN E 234 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.103654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.081715 restraints weight = 27381.583| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.71 r_work: 0.2922 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15800 Z= 0.119 Angle : 0.608 12.338 21262 Z= 0.292 Chirality : 0.043 0.260 2365 Planarity : 0.003 0.038 2577 Dihedral : 8.725 168.948 3240 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.25 % Allowed : 16.29 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.20), residues: 1747 helix: 2.49 (0.20), residues: 628 sheet: 1.10 (0.26), residues: 395 loop : -0.55 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 437 TYR 0.017 0.001 TYR C 325 PHE 0.037 0.001 PHE C 319 TRP 0.009 0.001 TRP A 263 HIS 0.002 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00272 (15792) covalent geometry : angle 0.59229 (21240) SS BOND : bond 0.00184 ( 2) SS BOND : angle 0.38985 ( 4) hydrogen bonds : bond 0.03972 ( 700) hydrogen bonds : angle 3.83708 ( 2328) link_NAG-ASN : bond 0.01010 ( 6) link_NAG-ASN : angle 4.71866 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2923.39 seconds wall clock time: 51 minutes 0.69 seconds (3060.69 seconds total)