Starting phenix.real_space_refine on Wed Mar 4 14:33:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u2m_26315/03_2026/7u2m_26315_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u2m_26315/03_2026/7u2m_26315.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7u2m_26315/03_2026/7u2m_26315.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u2m_26315/03_2026/7u2m_26315.map" model { file = "/net/cci-nas-00/data/ceres_data/7u2m_26315/03_2026/7u2m_26315_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u2m_26315/03_2026/7u2m_26315_trim.cif" } resolution = 2.9 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= 0.002 sd= 1.333 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 105 5.16 5 C 9200 2.51 5 N 2285 2.21 5 O 2565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14155 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2786 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'L2L': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, G, H, I, J Time building chain proxies: 2.45, per 1000 atoms: 0.17 Number of scatterers: 14155 At special positions: 0 Unit cell: (105.537, 106.368, 135.453, 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 105 16.00 O 2565 8.00 N 2285 7.00 C 9200 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 168 " distance=2.04 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.04 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.04 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.04 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG G 1 " - " ASN B 54 " " NAG H 1 " - " ASN C 54 " " NAG I 1 " - " ASN D 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 753.8 milliseconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 25 sheets defined 40.2% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 25 through 35 Processing helix chain 'A' and resid 36 through 40 removed outlier: 4.219A pdb=" N TYR A 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 90 Processing helix chain 'A' and resid 102 through 107 removed outlier: 3.710A pdb=" N ASP A 107 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 243 Processing helix chain 'A' and resid 243 through 256 removed outlier: 3.517A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 286 removed outlier: 3.560A pdb=" N THR A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 327 removed outlier: 3.576A pdb=" N TRP A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 425 removed outlier: 4.330A pdb=" N LYS A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 3.800A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 35 Processing helix chain 'B' and resid 36 through 40 removed outlier: 4.219A pdb=" N TYR B 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 102 through 107 removed outlier: 3.710A pdb=" N ASP B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 243 through 256 removed outlier: 3.517A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 286 removed outlier: 3.560A pdb=" N THR B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N MET B 279 " --> pdb=" O THR B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 327 removed outlier: 3.576A pdb=" N TRP B 302 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 318 " --> pdb=" O LEU B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 425 removed outlier: 4.331A pdb=" N LYS B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU B 394 " --> pdb=" O GLU B 390 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE B 395 " --> pdb=" O MET B 391 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 3.800A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 35 Processing helix chain 'C' and resid 36 through 40 removed outlier: 4.219A pdb=" N TYR C 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 90 Processing helix chain 'C' and resid 102 through 107 removed outlier: 3.710A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 243 Processing helix chain 'C' and resid 243 through 256 removed outlier: 3.517A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 286 removed outlier: 3.559A pdb=" N THR C 278 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET C 279 " --> pdb=" O THR C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 327 removed outlier: 3.575A pdb=" N TRP C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 318 " --> pdb=" O LEU C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 425 removed outlier: 4.331A pdb=" N LYS C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU C 394 " --> pdb=" O GLU C 390 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 395 " --> pdb=" O MET C 391 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG C 398 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP C 403 " --> pdb=" O ALA C 399 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 3.800A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 35 Processing helix chain 'D' and resid 36 through 40 removed outlier: 4.219A pdb=" N TYR D 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 90 Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.710A pdb=" N ASP D 107 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 243 Processing helix chain 'D' and resid 243 through 256 removed outlier: 3.517A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 286 removed outlier: 3.560A pdb=" N THR D 278 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET D 279 " --> pdb=" O THR D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 327 removed outlier: 3.575A pdb=" N TRP D 302 " --> pdb=" O ALA D 298 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 318 " --> pdb=" O LEU D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 425 removed outlier: 4.330A pdb=" N LYS D 393 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU D 394 " --> pdb=" O GLU D 390 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE D 395 " --> pdb=" O MET D 391 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG D 398 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP D 403 " --> pdb=" O ALA D 399 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 3.800A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 35 Processing helix chain 'E' and resid 36 through 40 removed outlier: 4.219A pdb=" N TYR E 40 " --> pdb=" O VAL E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 90 Processing helix chain 'E' and resid 102 through 107 removed outlier: 3.710A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 243 Processing helix chain 'E' and resid 243 through 256 removed outlier: 3.517A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 286 removed outlier: 3.560A pdb=" N THR E 278 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET E 279 " --> pdb=" O THR E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 327 removed outlier: 3.576A pdb=" N TRP E 302 " --> pdb=" O ALA E 298 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA E 318 " --> pdb=" O LEU E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 425 removed outlier: 4.330A pdb=" N LYS E 393 " --> pdb=" O GLU E 389 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU E 394 " --> pdb=" O GLU E 390 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE E 395 " --> pdb=" O MET E 391 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG E 398 " --> pdb=" O LEU E 394 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP E 403 " --> pdb=" O ALA E 399 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG E 407 " --> pdb=" O ASP E 403 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 3.801A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.623A pdb=" N ILE A 136 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP A 84 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 123 removed outlier: 3.508A pdb=" N TRP A 84 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N GLN A 193 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE A 59 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 115 through 116 Processing sheet with id=AA4, first strand: chain 'A' and resid 115 through 116 Processing sheet with id=AA5, first strand: chain 'A' and resid 216 through 217 Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 100 removed outlier: 3.623A pdb=" N ILE B 136 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP B 84 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 122 through 123 removed outlier: 3.508A pdb=" N TRP B 84 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N GLN B 193 " --> pdb=" O CYS B 57 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE B 59 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 115 through 116 Processing sheet with id=AA9, first strand: chain 'B' and resid 115 through 116 Processing sheet with id=AB1, first strand: chain 'B' and resid 216 through 217 Processing sheet with id=AB2, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.622A pdb=" N ILE C 136 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP C 84 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 122 through 123 removed outlier: 3.508A pdb=" N TRP C 84 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N GLN C 193 " --> pdb=" O CYS C 57 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE C 59 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 115 through 116 Processing sheet with id=AB5, first strand: chain 'C' and resid 115 through 116 Processing sheet with id=AB6, first strand: chain 'C' and resid 216 through 217 Processing sheet with id=AB7, first strand: chain 'D' and resid 98 through 100 removed outlier: 3.622A pdb=" N ILE D 136 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP D 84 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 122 through 123 removed outlier: 3.508A pdb=" N TRP D 84 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N GLN D 193 " --> pdb=" O CYS D 57 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE D 59 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 115 through 116 Processing sheet with id=AC1, first strand: chain 'D' and resid 115 through 116 Processing sheet with id=AC2, first strand: chain 'D' and resid 216 through 217 Processing sheet with id=AC3, first strand: chain 'E' and resid 98 through 100 removed outlier: 3.622A pdb=" N ILE E 136 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP E 84 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 122 through 123 removed outlier: 3.508A pdb=" N TRP E 84 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N GLN E 193 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE E 59 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 115 through 116 Processing sheet with id=AC6, first strand: chain 'E' and resid 115 through 116 Processing sheet with id=AC7, first strand: chain 'E' and resid 216 through 217 795 hydrogen bonds defined for protein. 2265 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: 2.59 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4355 1.34 - 1.46: 3586 1.46 - 1.58: 6384 1.58 - 1.70: 0 1.70 - 1.82: 175 Bond restraints: 14500 Sorted by residual: bond pdb=" C LEU D 200 " pdb=" N PRO D 201 " ideal model delta sigma weight residual 1.336 1.316 0.020 1.20e-02 6.94e+03 2.81e+00 bond pdb=" C LEU B 200 " pdb=" N PRO B 201 " ideal model delta sigma weight residual 1.336 1.316 0.020 1.20e-02 6.94e+03 2.72e+00 bond pdb=" C LEU A 200 " pdb=" N PRO A 201 " ideal model delta sigma weight residual 1.336 1.316 0.020 1.20e-02 6.94e+03 2.65e+00 bond pdb=" C LEU E 200 " pdb=" N PRO E 201 " ideal model delta sigma weight residual 1.336 1.317 0.019 1.20e-02 6.94e+03 2.61e+00 bond pdb=" C LEU C 200 " pdb=" N PRO C 201 " ideal model delta sigma weight residual 1.336 1.317 0.019 1.20e-02 6.94e+03 2.51e+00 ... (remaining 14495 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 19119 2.21 - 4.43: 456 4.43 - 6.64: 100 6.64 - 8.85: 0 8.85 - 11.07: 5 Bond angle restraints: 19680 Sorted by residual: angle pdb=" N THR B 128 " pdb=" CA THR B 128 " pdb=" CB THR B 128 " ideal model delta sigma weight residual 114.17 109.93 4.24 1.14e+00 7.69e-01 1.39e+01 angle pdb=" N THR E 128 " pdb=" CA THR E 128 " pdb=" CB THR E 128 " ideal model delta sigma weight residual 114.17 109.94 4.23 1.14e+00 7.69e-01 1.38e+01 angle pdb=" N THR D 128 " pdb=" CA THR D 128 " pdb=" CB THR D 128 " ideal model delta sigma weight residual 114.17 109.95 4.22 1.14e+00 7.69e-01 1.37e+01 angle pdb=" N THR C 128 " pdb=" CA THR C 128 " pdb=" CB THR C 128 " ideal model delta sigma weight residual 114.17 109.95 4.22 1.14e+00 7.69e-01 1.37e+01 angle pdb=" N THR A 128 " pdb=" CA THR A 128 " pdb=" CB THR A 128 " ideal model delta sigma weight residual 114.17 109.96 4.21 1.14e+00 7.69e-01 1.37e+01 ... (remaining 19675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.24: 8600 22.24 - 44.48: 175 44.48 - 66.73: 40 66.73 - 88.97: 35 88.97 - 111.21: 20 Dihedral angle restraints: 8870 sinusoidal: 3755 harmonic: 5115 Sorted by residual: dihedral pdb=" CB CYS C 154 " pdb=" SG CYS C 154 " pdb=" SG CYS C 168 " pdb=" CB CYS C 168 " ideal model delta sinusoidal sigma weight residual 93.00 45.38 47.62 1 1.00e+01 1.00e-02 3.13e+01 dihedral pdb=" CB CYS D 154 " pdb=" SG CYS D 154 " pdb=" SG CYS D 168 " pdb=" CB CYS D 168 " ideal model delta sinusoidal sigma weight residual 93.00 45.40 47.60 1 1.00e+01 1.00e-02 3.13e+01 dihedral pdb=" CB CYS B 154 " pdb=" SG CYS B 154 " pdb=" SG CYS B 168 " pdb=" CB CYS B 168 " ideal model delta sinusoidal sigma weight residual 93.00 45.42 47.58 1 1.00e+01 1.00e-02 3.12e+01 ... (remaining 8867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1676 0.052 - 0.103: 483 0.103 - 0.155: 81 0.155 - 0.206: 10 0.206 - 0.258: 5 Chirality restraints: 2255 Sorted by residual: chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 2252 not shown) Planarity restraints: 2440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 151 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.30e+00 pdb=" C VAL C 151 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL C 151 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU C 152 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 151 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" C VAL E 151 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL E 151 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU E 152 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 151 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.26e+00 pdb=" C VAL D 151 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL D 151 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU D 152 " 0.012 2.00e-02 2.50e+03 ... (remaining 2437 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 170 2.63 - 3.20: 13758 3.20 - 3.76: 20656 3.76 - 4.33: 31807 4.33 - 4.90: 49711 Nonbonded interactions: 116102 Sorted by model distance: nonbonded pdb=" OD2 ASP A 41 " pdb=" OG SER E 27 " model vdw 2.059 3.040 nonbonded pdb=" OG SER D 27 " pdb=" OD2 ASP E 41 " model vdw 2.060 3.040 nonbonded pdb=" OG SER C 27 " pdb=" OD2 ASP D 41 " model vdw 2.064 3.040 nonbonded pdb=" OG SER A 27 " pdb=" OD2 ASP B 41 " model vdw 2.073 3.040 nonbonded pdb=" OG SER B 27 " pdb=" OD2 ASP C 41 " model vdw 2.077 3.040 ... (remaining 116097 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.110 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 : 0.008 0.045 14525 Z= 0.361 Angle : 0.893 11.068 19745 Z= 0.482 Chirality : 0.050 0.258 2255 Planarity : 0.004 0.032 2435 Dihedral : 13.141 111.210 5520 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 29.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.83 (0.18), residues: 1710 helix: -2.67 (0.17), residues: 525 sheet: -2.27 (0.23), residues: 395 loop : -2.48 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 212 TYR 0.023 0.002 TYR B 144 PHE 0.015 0.003 PHE D 258 TRP 0.010 0.002 TRP B 302 HIS 0.005 0.003 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00801 (14500) covalent geometry : angle 0.87828 (19680) SS BOND : bond 0.00383 ( 10) SS BOND : angle 2.35374 ( 20) hydrogen bonds : bond 0.29111 ( 665) hydrogen bonds : angle 10.54496 ( 2265) link_BETA1-4 : bond 0.00139 ( 10) link_BETA1-4 : angle 3.35327 ( 30) link_NAG-ASN : bond 0.00254 ( 5) link_NAG-ASN : angle 2.76225 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 615 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 VAL cc_start: 0.8427 (t) cc_final: 0.8219 (p) REVERT: A 137 SER cc_start: 0.8754 (m) cc_final: 0.8343 (p) REVERT: A 139 ASN cc_start: 0.8500 (p0) cc_final: 0.8134 (p0) REVERT: A 166 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8448 (mm110) REVERT: A 202 GLN cc_start: 0.8606 (mt0) cc_final: 0.8383 (mt0) REVERT: A 286 SER cc_start: 0.9364 (p) cc_final: 0.9117 (p) REVERT: A 317 TYR cc_start: 0.8602 (t80) cc_final: 0.8289 (t80) REVERT: A 395 PHE cc_start: 0.8708 (m-10) cc_final: 0.8474 (m-10) REVERT: B 202 GLN cc_start: 0.8499 (mt0) cc_final: 0.8095 (mt0) REVERT: B 424 THR cc_start: 0.9031 (m) cc_final: 0.8812 (m) REVERT: C 33 LEU cc_start: 0.8736 (tp) cc_final: 0.8487 (tp) REVERT: C 127 VAL cc_start: 0.8460 (t) cc_final: 0.8203 (p) REVERT: C 202 GLN cc_start: 0.8527 (mt0) cc_final: 0.8149 (mt0) REVERT: C 239 TYR cc_start: 0.8832 (m-80) cc_final: 0.8630 (m-80) REVERT: C 395 PHE cc_start: 0.8678 (m-10) cc_final: 0.8460 (m-10) REVERT: D 43 ARG cc_start: 0.8978 (mtm-85) cc_final: 0.8749 (mtm-85) REVERT: D 63 SER cc_start: 0.8466 (t) cc_final: 0.8085 (p) REVERT: D 189 LYS cc_start: 0.8743 (ptpt) cc_final: 0.8540 (tppt) REVERT: D 202 GLN cc_start: 0.8554 (mt0) cc_final: 0.8185 (mt0) REVERT: D 312 SER cc_start: 0.9042 (m) cc_final: 0.8812 (p) REVERT: D 400 LYS cc_start: 0.9221 (ttmm) cc_final: 0.9013 (mmmm) REVERT: E 47 ASN cc_start: 0.9249 (m-40) cc_final: 0.9004 (m-40) REVERT: E 63 SER cc_start: 0.8435 (t) cc_final: 0.8093 (p) REVERT: E 139 ASN cc_start: 0.8580 (p0) cc_final: 0.8265 (p0) REVERT: E 189 LYS cc_start: 0.8688 (ptpt) cc_final: 0.8479 (tppt) REVERT: E 202 GLN cc_start: 0.8562 (mt0) cc_final: 0.8263 (mt0) REVERT: E 222 LYS cc_start: 0.8052 (ptmm) cc_final: 0.7648 (pttt) outliers start: 0 outliers final: 0 residues processed: 615 average time/residue: 0.5214 time to fit residues: 354.3640 Evaluate side-chains 443 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 443 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 77 ASN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN A 141 ASN A 171 GLN A 219 ASN A 231 HIS B 62 ASN B 77 ASN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN B 141 ASN B 171 GLN B 219 ASN B 231 HIS B 242 GLN C 77 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN C 141 ASN C 166 GLN C 231 HIS C 242 GLN C 321 ASN D 62 ASN D 77 ASN D 83 GLN D 141 ASN ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN D 231 HIS D 242 GLN D 321 ASN E 62 ASN E 77 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN E 141 ASN E 171 GLN E 219 ASN E 231 HIS Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.131828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.108296 restraints weight = 22087.145| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.87 r_work: 0.3103 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14525 Z= 0.178 Angle : 0.823 10.552 19745 Z= 0.407 Chirality : 0.050 0.158 2255 Planarity : 0.005 0.043 2435 Dihedral : 11.988 68.098 2200 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.59 % Allowed : 17.18 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.19), residues: 1710 helix: -0.93 (0.19), residues: 615 sheet: -1.16 (0.25), residues: 345 loop : -2.26 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 234 TYR 0.038 0.002 TYR E 317 PHE 0.026 0.002 PHE D 311 TRP 0.008 0.001 TRP A 255 HIS 0.002 0.001 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00399 (14500) covalent geometry : angle 0.80491 (19680) SS BOND : bond 0.00551 ( 10) SS BOND : angle 1.62128 ( 20) hydrogen bonds : bond 0.05758 ( 665) hydrogen bonds : angle 5.87170 ( 2265) link_BETA1-4 : bond 0.00752 ( 10) link_BETA1-4 : angle 4.36425 ( 30) link_NAG-ASN : bond 0.00225 ( 5) link_NAG-ASN : angle 0.86852 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 464 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.8427 (tp) cc_final: 0.8221 (tt) REVERT: A 139 ASN cc_start: 0.8714 (p0) cc_final: 0.8470 (p0) REVERT: A 156 MET cc_start: 0.9396 (OUTLIER) cc_final: 0.9100 (mmm) REVERT: A 204 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8249 (mt) REVERT: A 249 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8019 (mp) REVERT: A 274 THR cc_start: 0.9333 (m) cc_final: 0.9117 (p) REVERT: B 133 LEU cc_start: 0.8460 (tp) cc_final: 0.8148 (tt) REVERT: B 146 ILE cc_start: 0.8770 (pt) cc_final: 0.8562 (tt) REVERT: B 202 GLN cc_start: 0.8849 (mt0) cc_final: 0.8245 (mt0) REVERT: B 249 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.7918 (mp) REVERT: B 274 THR cc_start: 0.9390 (m) cc_final: 0.9186 (p) REVERT: C 133 LEU cc_start: 0.8455 (tp) cc_final: 0.8249 (tt) REVERT: C 202 GLN cc_start: 0.8874 (mt0) cc_final: 0.8370 (mt0) REVERT: C 208 GLU cc_start: 0.7562 (pm20) cc_final: 0.7324 (pm20) REVERT: C 249 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8004 (mp) REVERT: C 316 GLU cc_start: 0.8579 (tm-30) cc_final: 0.7995 (tm-30) REVERT: C 317 TYR cc_start: 0.8680 (t80) cc_final: 0.8321 (t80) REVERT: D 63 SER cc_start: 0.8722 (t) cc_final: 0.8445 (p) REVERT: D 208 GLU cc_start: 0.7541 (pm20) cc_final: 0.7273 (pm20) REVERT: D 229 ARG cc_start: 0.8415 (mtt-85) cc_final: 0.8044 (mtt-85) REVERT: D 316 GLU cc_start: 0.8418 (tm-30) cc_final: 0.7664 (tm-30) REVERT: D 398 ARG cc_start: 0.8124 (mtt90) cc_final: 0.7894 (mmt90) REVERT: E 63 SER cc_start: 0.8607 (t) cc_final: 0.8354 (p) REVERT: E 133 LEU cc_start: 0.8525 (tp) cc_final: 0.8270 (tt) REVERT: E 139 ASN cc_start: 0.8825 (p0) cc_final: 0.8454 (p0) REVERT: E 159 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7854 (tttt) REVERT: E 179 MET cc_start: 0.8833 (mmm) cc_final: 0.8424 (mmm) REVERT: E 202 GLN cc_start: 0.8844 (mt0) cc_final: 0.8338 (mt0) REVERT: E 212 ARG cc_start: 0.8219 (ptp-170) cc_final: 0.7874 (ptp-170) REVERT: E 229 ARG cc_start: 0.8636 (mtt-85) cc_final: 0.8134 (mtt-85) REVERT: E 239 TYR cc_start: 0.8714 (m-80) cc_final: 0.8500 (m-80) REVERT: E 249 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8063 (mp) REVERT: E 289 SER cc_start: 0.9351 (t) cc_final: 0.9140 (p) REVERT: E 316 GLU cc_start: 0.8494 (tm-30) cc_final: 0.7761 (tm-30) outliers start: 70 outliers final: 29 residues processed: 486 average time/residue: 0.4963 time to fit residues: 267.2585 Evaluate side-chains 439 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 403 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 312 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 107 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 121 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 83 GLN A 321 ASN B 47 ASN B 171 GLN B 242 GLN B 321 ASN C 47 ASN C 166 GLN C 242 GLN D 47 ASN D 166 GLN E 47 ASN E 171 GLN E 242 GLN E 321 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.125309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.101043 restraints weight = 22244.770| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.03 r_work: 0.3127 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14525 Z= 0.170 Angle : 0.763 7.653 19745 Z= 0.374 Chirality : 0.049 0.161 2255 Planarity : 0.005 0.049 2435 Dihedral : 8.917 50.191 2200 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 5.77 % Allowed : 19.93 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.20), residues: 1710 helix: 0.13 (0.20), residues: 615 sheet: -0.58 (0.26), residues: 345 loop : -2.05 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 43 TYR 0.030 0.002 TYR E 317 PHE 0.022 0.002 PHE E 311 TRP 0.006 0.001 TRP B 302 HIS 0.003 0.001 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00397 (14500) covalent geometry : angle 0.74422 (19680) SS BOND : bond 0.00594 ( 10) SS BOND : angle 1.68260 ( 20) hydrogen bonds : bond 0.04526 ( 665) hydrogen bonds : angle 5.27230 ( 2265) link_BETA1-4 : bond 0.00505 ( 10) link_BETA1-4 : angle 4.19521 ( 30) link_NAG-ASN : bond 0.00157 ( 5) link_NAG-ASN : angle 0.48851 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 430 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASN cc_start: 0.8715 (p0) cc_final: 0.8476 (p0) REVERT: A 156 MET cc_start: 0.9426 (OUTLIER) cc_final: 0.9024 (mmm) REVERT: A 204 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8327 (mt) REVERT: A 229 ARG cc_start: 0.8776 (mtt-85) cc_final: 0.8561 (mtt-85) REVERT: A 424 THR cc_start: 0.9367 (m) cc_final: 0.9110 (m) REVERT: B 133 LEU cc_start: 0.8548 (tp) cc_final: 0.8252 (tt) REVERT: B 202 GLN cc_start: 0.8878 (mt0) cc_final: 0.8311 (mt0) REVERT: C 173 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7874 (tt0) REVERT: C 208 GLU cc_start: 0.7582 (pm20) cc_final: 0.7280 (pm20) REVERT: C 289 SER cc_start: 0.9276 (t) cc_final: 0.9044 (p) REVERT: C 316 GLU cc_start: 0.8525 (tm-30) cc_final: 0.7774 (tm-30) REVERT: C 424 THR cc_start: 0.9465 (m) cc_final: 0.9238 (m) REVERT: D 63 SER cc_start: 0.8913 (t) cc_final: 0.8693 (p) REVERT: D 204 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8312 (mt) REVERT: D 208 GLU cc_start: 0.7608 (pm20) cc_final: 0.7280 (pm20) REVERT: D 212 ARG cc_start: 0.8294 (ptp-170) cc_final: 0.8085 (ptp-170) REVERT: D 274 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8935 (p) REVERT: D 316 GLU cc_start: 0.8511 (tm-30) cc_final: 0.7810 (tm-30) REVERT: E 63 SER cc_start: 0.8766 (t) cc_final: 0.8525 (p) REVERT: E 133 LEU cc_start: 0.8658 (tp) cc_final: 0.8435 (tt) REVERT: E 139 ASN cc_start: 0.8788 (p0) cc_final: 0.8429 (p0) REVERT: E 156 MET cc_start: 0.9327 (OUTLIER) cc_final: 0.9064 (mmm) REVERT: E 179 MET cc_start: 0.8819 (mmm) cc_final: 0.8466 (mmm) REVERT: E 202 GLN cc_start: 0.8826 (mt0) cc_final: 0.8399 (mt0) REVERT: E 229 ARG cc_start: 0.8688 (mtt-85) cc_final: 0.8084 (mtt-85) REVERT: E 316 GLU cc_start: 0.8535 (tm-30) cc_final: 0.7816 (tm-30) outliers start: 88 outliers final: 42 residues processed: 456 average time/residue: 0.4941 time to fit residues: 249.4775 Evaluate side-chains 444 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 396 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 301 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 140 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 158 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 82 GLN A 242 GLN B 47 ASN B 83 GLN C 47 ASN C 83 GLN C 242 GLN D 47 ASN D 83 GLN D 242 GLN E 47 ASN E 83 GLN E 321 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.125205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.100517 restraints weight = 22182.548| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.04 r_work: 0.3064 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14525 Z= 0.179 Angle : 0.756 9.114 19745 Z= 0.370 Chirality : 0.048 0.163 2255 Planarity : 0.005 0.050 2435 Dihedral : 6.929 45.170 2200 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 6.23 % Allowed : 20.26 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.20), residues: 1710 helix: 0.58 (0.21), residues: 615 sheet: -0.38 (0.27), residues: 345 loop : -1.99 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 43 TYR 0.031 0.002 TYR E 317 PHE 0.020 0.002 PHE E 311 TRP 0.006 0.001 TRP C 422 HIS 0.003 0.001 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00426 (14500) covalent geometry : angle 0.73665 (19680) SS BOND : bond 0.00586 ( 10) SS BOND : angle 1.62620 ( 20) hydrogen bonds : bond 0.04056 ( 665) hydrogen bonds : angle 4.99028 ( 2265) link_BETA1-4 : bond 0.00576 ( 10) link_BETA1-4 : angle 4.24882 ( 30) link_NAG-ASN : bond 0.00138 ( 5) link_NAG-ASN : angle 0.46960 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 407 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASN cc_start: 0.8717 (p0) cc_final: 0.8512 (p0) REVERT: A 156 MET cc_start: 0.9376 (OUTLIER) cc_final: 0.8946 (mtp) REVERT: A 204 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8328 (mt) REVERT: A 249 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8019 (mp) REVERT: A 271 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8818 (tp) REVERT: A 316 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8357 (tm-30) REVERT: A 424 THR cc_start: 0.9360 (m) cc_final: 0.9086 (m) REVERT: B 133 LEU cc_start: 0.8595 (tp) cc_final: 0.8289 (tt) REVERT: B 171 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8412 (pt0) REVERT: B 202 GLN cc_start: 0.8835 (mt0) cc_final: 0.8293 (mt0) REVERT: B 249 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8044 (mp) REVERT: B 424 THR cc_start: 0.9412 (m) cc_final: 0.9147 (m) REVERT: C 105 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7479 (mpm) REVERT: C 173 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: C 208 GLU cc_start: 0.7581 (pm20) cc_final: 0.7313 (pm20) REVERT: C 424 THR cc_start: 0.9469 (m) cc_final: 0.9211 (m) REVERT: D 63 SER cc_start: 0.8888 (t) cc_final: 0.8655 (p) REVERT: D 179 MET cc_start: 0.8811 (mmm) cc_final: 0.8579 (mmm) REVERT: D 189 LYS cc_start: 0.8617 (mmpt) cc_final: 0.8377 (tppt) REVERT: D 204 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8241 (mt) REVERT: D 208 GLU cc_start: 0.7604 (pm20) cc_final: 0.7360 (pm20) REVERT: D 316 GLU cc_start: 0.8604 (tm-30) cc_final: 0.7972 (tm-30) REVERT: E 49 LYS cc_start: 0.9061 (mmtt) cc_final: 0.8856 (mmtt) REVERT: E 62 ASN cc_start: 0.9027 (t0) cc_final: 0.8826 (t0) REVERT: E 63 SER cc_start: 0.8796 (t) cc_final: 0.8582 (p) REVERT: E 83 GLN cc_start: 0.8877 (mt0) cc_final: 0.8649 (mt0) REVERT: E 133 LEU cc_start: 0.8655 (tp) cc_final: 0.8429 (tt) REVERT: E 139 ASN cc_start: 0.8751 (p0) cc_final: 0.8416 (p0) REVERT: E 156 MET cc_start: 0.9317 (OUTLIER) cc_final: 0.9095 (mmm) REVERT: E 179 MET cc_start: 0.8813 (mmm) cc_final: 0.8394 (mmm) REVERT: E 249 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8158 (mp) REVERT: E 274 THR cc_start: 0.9232 (OUTLIER) cc_final: 0.9010 (p) REVERT: E 281 THR cc_start: 0.9494 (t) cc_final: 0.9278 (p) REVERT: E 316 GLU cc_start: 0.8589 (tm-30) cc_final: 0.7843 (tm-30) outliers start: 95 outliers final: 44 residues processed: 432 average time/residue: 0.5149 time to fit residues: 245.6883 Evaluate side-chains 430 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 374 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 423 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 141 optimal weight: 4.9990 chunk 128 optimal weight: 0.0370 chunk 84 optimal weight: 0.0070 chunk 123 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 98 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 26 optimal weight: 0.1980 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN B 47 ASN C 47 ASN C 242 GLN D 47 ASN D 242 GLN E 47 ASN E 321 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.134365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.110544 restraints weight = 21657.359| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.91 r_work: 0.3140 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14525 Z= 0.118 Angle : 0.711 9.274 19745 Z= 0.344 Chirality : 0.046 0.167 2255 Planarity : 0.004 0.046 2435 Dihedral : 5.845 38.983 2200 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 5.97 % Allowed : 21.05 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.20), residues: 1710 helix: 0.78 (0.21), residues: 620 sheet: -0.26 (0.27), residues: 345 loop : -1.88 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 229 TYR 0.031 0.001 TYR E 317 PHE 0.020 0.001 PHE E 311 TRP 0.005 0.001 TRP B 186 HIS 0.001 0.000 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00263 (14500) covalent geometry : angle 0.69487 (19680) SS BOND : bond 0.00396 ( 10) SS BOND : angle 1.24907 ( 20) hydrogen bonds : bond 0.03583 ( 665) hydrogen bonds : angle 4.54239 ( 2265) link_BETA1-4 : bond 0.00594 ( 10) link_BETA1-4 : angle 3.82080 ( 30) link_NAG-ASN : bond 0.00372 ( 5) link_NAG-ASN : angle 0.35307 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 443 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7236 (mpm) REVERT: A 139 ASN cc_start: 0.8773 (p0) cc_final: 0.8541 (p0) REVERT: A 156 MET cc_start: 0.9378 (OUTLIER) cc_final: 0.9082 (mmm) REVERT: A 173 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7365 (mt-10) REVERT: A 202 GLN cc_start: 0.8636 (mt0) cc_final: 0.8382 (mt0) REVERT: A 204 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8342 (mt) REVERT: A 271 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8815 (tp) REVERT: B 105 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.6994 (mpm) REVERT: B 133 LEU cc_start: 0.8513 (tp) cc_final: 0.8233 (tt) REVERT: B 202 GLN cc_start: 0.8787 (mt0) cc_final: 0.8255 (mt0) REVERT: B 204 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8325 (mt) REVERT: B 292 LYS cc_start: 0.8989 (mttt) cc_final: 0.8699 (mttp) REVERT: C 105 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7343 (mpm) REVERT: C 113 ASP cc_start: 0.8929 (p0) cc_final: 0.8701 (p0) REVERT: C 173 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7971 (tt0) REVERT: C 204 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8288 (mt) REVERT: C 208 GLU cc_start: 0.7479 (pm20) cc_final: 0.7235 (pm20) REVERT: C 236 MET cc_start: 0.9223 (mmm) cc_final: 0.8952 (mmt) REVERT: C 412 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8503 (tp) REVERT: C 424 THR cc_start: 0.9432 (m) cc_final: 0.9146 (m) REVERT: D 28 GLU cc_start: 0.8289 (tm-30) cc_final: 0.8086 (tm-30) REVERT: D 63 SER cc_start: 0.8863 (t) cc_final: 0.8639 (p) REVERT: D 189 LYS cc_start: 0.8568 (mmpt) cc_final: 0.8286 (tppt) REVERT: D 208 GLU cc_start: 0.7524 (pm20) cc_final: 0.7106 (pm20) REVERT: D 316 GLU cc_start: 0.8617 (tm-30) cc_final: 0.7930 (tm-30) REVERT: D 412 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8469 (tp) REVERT: E 28 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7852 (tm-30) REVERT: E 48 PHE cc_start: 0.8688 (t80) cc_final: 0.8432 (t80) REVERT: E 49 LYS cc_start: 0.8957 (mmtt) cc_final: 0.8720 (mmtm) REVERT: E 83 GLN cc_start: 0.8737 (mt0) cc_final: 0.8474 (mt0) REVERT: E 133 LEU cc_start: 0.8589 (tp) cc_final: 0.8354 (tt) REVERT: E 139 ASN cc_start: 0.8802 (p0) cc_final: 0.8480 (p0) REVERT: E 156 MET cc_start: 0.9282 (OUTLIER) cc_final: 0.9020 (mmm) REVERT: E 164 ASP cc_start: 0.8690 (p0) cc_final: 0.8345 (p0) REVERT: E 179 MET cc_start: 0.8750 (mmm) cc_final: 0.8326 (mmm) REVERT: E 204 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8301 (mp) REVERT: E 240 LEU cc_start: 0.8866 (tt) cc_final: 0.8604 (tt) REVERT: E 424 THR cc_start: 0.9357 (m) cc_final: 0.9005 (m) outliers start: 91 outliers final: 40 residues processed: 460 average time/residue: 0.4953 time to fit residues: 253.6149 Evaluate side-chains 435 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 382 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 286 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 166 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 0.0000 chunk 109 optimal weight: 0.8980 chunk 136 optimal weight: 0.2980 chunk 128 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 153 optimal weight: 0.3980 chunk 138 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 242 GLN A 326 GLN B 47 ASN C 47 ASN C 242 GLN D 47 ASN D 242 GLN E 47 ASN E 321 ASN E 326 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.134488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.110408 restraints weight = 21581.114| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.94 r_work: 0.3151 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14525 Z= 0.126 Angle : 0.709 7.898 19745 Z= 0.347 Chirality : 0.045 0.140 2255 Planarity : 0.004 0.046 2435 Dihedral : 5.454 30.469 2200 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 5.44 % Allowed : 22.89 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.20), residues: 1710 helix: 0.93 (0.21), residues: 625 sheet: -0.24 (0.26), residues: 345 loop : -1.90 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 268 TYR 0.035 0.002 TYR E 317 PHE 0.019 0.001 PHE B 311 TRP 0.006 0.001 TRP D 422 HIS 0.001 0.000 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00291 (14500) covalent geometry : angle 0.69438 (19680) SS BOND : bond 0.00440 ( 10) SS BOND : angle 1.29125 ( 20) hydrogen bonds : bond 0.03432 ( 665) hydrogen bonds : angle 4.44355 ( 2265) link_BETA1-4 : bond 0.00546 ( 10) link_BETA1-4 : angle 3.67514 ( 30) link_NAG-ASN : bond 0.00209 ( 5) link_NAG-ASN : angle 0.25072 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 418 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7210 (mpm) REVERT: A 139 ASN cc_start: 0.8771 (p0) cc_final: 0.8548 (p0) REVERT: A 156 MET cc_start: 0.9382 (OUTLIER) cc_final: 0.9083 (mmm) REVERT: A 173 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7375 (mt-10) REVERT: A 249 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8027 (mp) REVERT: A 271 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8836 (tp) REVERT: A 279 MET cc_start: 0.8948 (tpt) cc_final: 0.8679 (tpt) REVERT: B 24 MET cc_start: 0.7992 (ptm) cc_final: 0.7768 (ptm) REVERT: B 133 LEU cc_start: 0.8553 (tp) cc_final: 0.8285 (tt) REVERT: B 202 GLN cc_start: 0.8813 (mt0) cc_final: 0.8407 (tt0) REVERT: B 204 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8312 (mt) REVERT: C 105 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7323 (mpm) REVERT: C 120 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8327 (ttmt) REVERT: C 171 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8380 (pt0) REVERT: C 202 GLN cc_start: 0.8687 (mt0) cc_final: 0.8331 (mt0) REVERT: C 208 GLU cc_start: 0.7483 (pm20) cc_final: 0.7229 (pm20) REVERT: C 412 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8491 (tp) REVERT: C 424 THR cc_start: 0.9431 (m) cc_final: 0.9136 (m) REVERT: D 28 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7944 (tm-30) REVERT: D 63 SER cc_start: 0.8885 (t) cc_final: 0.8635 (p) REVERT: D 179 MET cc_start: 0.8765 (mmm) cc_final: 0.8458 (mmm) REVERT: D 189 LYS cc_start: 0.8597 (mmpt) cc_final: 0.8295 (tppt) REVERT: D 208 GLU cc_start: 0.7530 (pm20) cc_final: 0.7116 (pm20) REVERT: D 412 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8491 (tp) REVERT: E 83 GLN cc_start: 0.8770 (mt0) cc_final: 0.8466 (mt0) REVERT: E 96 ASP cc_start: 0.8444 (t0) cc_final: 0.8200 (t0) REVERT: E 133 LEU cc_start: 0.8617 (tp) cc_final: 0.8389 (tt) REVERT: E 139 ASN cc_start: 0.8806 (p0) cc_final: 0.8488 (p0) REVERT: E 156 MET cc_start: 0.9282 (OUTLIER) cc_final: 0.9012 (mmm) REVERT: E 179 MET cc_start: 0.8764 (mmm) cc_final: 0.8454 (mmm) REVERT: E 204 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8320 (mt) REVERT: E 229 ARG cc_start: 0.8718 (mtt-85) cc_final: 0.8449 (mtt180) REVERT: E 240 LEU cc_start: 0.8848 (tt) cc_final: 0.8601 (tt) outliers start: 83 outliers final: 47 residues processed: 437 average time/residue: 0.5220 time to fit residues: 252.5515 Evaluate side-chains 435 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 376 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 423 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 31 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 119 optimal weight: 0.0770 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 chunk 69 optimal weight: 5.9990 overall best weight: 1.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN A 326 GLN B 47 ASN C 47 ASN C 242 GLN D 47 ASN D 242 GLN E 47 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.125707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.101505 restraints weight = 22116.327| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.01 r_work: 0.3034 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14525 Z= 0.181 Angle : 0.715 8.403 19745 Z= 0.355 Chirality : 0.047 0.139 2255 Planarity : 0.004 0.047 2435 Dihedral : 5.369 24.996 2200 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.51 % Allowed : 23.34 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.20), residues: 1710 helix: 1.04 (0.21), residues: 630 sheet: -0.28 (0.26), residues: 345 loop : -1.87 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 268 TYR 0.029 0.002 TYR E 317 PHE 0.018 0.002 PHE A 48 TRP 0.008 0.001 TRP D 422 HIS 0.002 0.001 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00435 (14500) covalent geometry : angle 0.70041 (19680) SS BOND : bond 0.00565 ( 10) SS BOND : angle 1.58239 ( 20) hydrogen bonds : bond 0.03580 ( 665) hydrogen bonds : angle 4.49716 ( 2265) link_BETA1-4 : bond 0.00473 ( 10) link_BETA1-4 : angle 3.63461 ( 30) link_NAG-ASN : bond 0.00107 ( 5) link_NAG-ASN : angle 0.50448 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 392 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7232 (mpm) REVERT: A 139 ASN cc_start: 0.8744 (p0) cc_final: 0.8541 (p0) REVERT: A 156 MET cc_start: 0.9372 (OUTLIER) cc_final: 0.9145 (mmm) REVERT: A 173 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7412 (mt-10) REVERT: A 249 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8048 (mp) REVERT: A 424 THR cc_start: 0.9350 (m) cc_final: 0.9009 (m) REVERT: B 24 MET cc_start: 0.8122 (ptm) cc_final: 0.7862 (ptm) REVERT: B 133 LEU cc_start: 0.8556 (tp) cc_final: 0.8240 (tt) REVERT: B 249 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.7918 (mp) REVERT: B 424 THR cc_start: 0.9434 (m) cc_final: 0.9104 (m) REVERT: C 105 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7342 (mpm) REVERT: C 208 GLU cc_start: 0.7584 (pm20) cc_final: 0.7283 (pm20) REVERT: C 227 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8667 (tt0) REVERT: C 412 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8607 (tp) REVERT: C 424 THR cc_start: 0.9464 (m) cc_final: 0.9181 (m) REVERT: D 63 SER cc_start: 0.8827 (t) cc_final: 0.8503 (p) REVERT: D 94 TYR cc_start: 0.8229 (OUTLIER) cc_final: 0.7630 (t80) REVERT: D 208 GLU cc_start: 0.7484 (pm20) cc_final: 0.7136 (pm20) REVERT: D 412 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8533 (tp) REVERT: E 83 GLN cc_start: 0.8731 (mt0) cc_final: 0.8396 (mt0) REVERT: E 96 ASP cc_start: 0.8487 (t0) cc_final: 0.8201 (t0) REVERT: E 133 LEU cc_start: 0.8606 (tp) cc_final: 0.8331 (tt) REVERT: E 139 ASN cc_start: 0.8812 (p0) cc_final: 0.8511 (p0) REVERT: E 156 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8989 (mmm) REVERT: E 179 MET cc_start: 0.8735 (mmm) cc_final: 0.8389 (mmm) REVERT: E 204 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8217 (mt) REVERT: E 240 LEU cc_start: 0.8744 (tt) cc_final: 0.8500 (tt) REVERT: E 249 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8062 (mp) REVERT: E 424 THR cc_start: 0.9312 (m) cc_final: 0.8963 (m) outliers start: 84 outliers final: 51 residues processed: 410 average time/residue: 0.5068 time to fit residues: 230.3824 Evaluate side-chains 429 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 366 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 423 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 109 optimal weight: 8.9990 chunk 86 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 326 GLN B 47 ASN C 242 GLN D 47 ASN D 242 GLN E 47 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.125097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.101133 restraints weight = 21920.128| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.97 r_work: 0.3102 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14525 Z= 0.186 Angle : 0.753 9.169 19745 Z= 0.375 Chirality : 0.048 0.173 2255 Planarity : 0.004 0.047 2435 Dihedral : 5.333 20.641 2200 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.98 % Allowed : 24.39 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.20), residues: 1710 helix: 1.24 (0.21), residues: 625 sheet: -0.34 (0.26), residues: 345 loop : -1.70 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 229 TYR 0.029 0.002 TYR E 317 PHE 0.024 0.002 PHE A 48 TRP 0.007 0.001 TRP A 302 HIS 0.003 0.001 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00451 (14500) covalent geometry : angle 0.73907 (19680) SS BOND : bond 0.00564 ( 10) SS BOND : angle 1.56488 ( 20) hydrogen bonds : bond 0.03613 ( 665) hydrogen bonds : angle 4.53056 ( 2265) link_BETA1-4 : bond 0.00502 ( 10) link_BETA1-4 : angle 3.56505 ( 30) link_NAG-ASN : bond 0.00107 ( 5) link_NAG-ASN : angle 0.53913 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 386 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7225 (mpm) REVERT: A 173 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7497 (mt-10) REVERT: A 249 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8137 (mp) REVERT: A 424 THR cc_start: 0.9362 (m) cc_final: 0.9023 (m) REVERT: B 24 MET cc_start: 0.8038 (ptm) cc_final: 0.7755 (ptm) REVERT: B 133 LEU cc_start: 0.8613 (tp) cc_final: 0.8330 (tt) REVERT: C 105 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7385 (mpm) REVERT: C 119 GLU cc_start: 0.7954 (tt0) cc_final: 0.7609 (tt0) REVERT: C 208 GLU cc_start: 0.7656 (pm20) cc_final: 0.7399 (pm20) REVERT: C 227 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8675 (tt0) REVERT: C 412 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8627 (tp) REVERT: C 424 THR cc_start: 0.9446 (m) cc_final: 0.9161 (m) REVERT: D 29 PHE cc_start: 0.8760 (t80) cc_final: 0.8538 (t80) REVERT: D 63 SER cc_start: 0.8892 (t) cc_final: 0.8637 (p) REVERT: D 94 TYR cc_start: 0.8247 (OUTLIER) cc_final: 0.7629 (t80) REVERT: D 179 MET cc_start: 0.8849 (mmm) cc_final: 0.8568 (mmm) REVERT: D 208 GLU cc_start: 0.7564 (pm20) cc_final: 0.7257 (pm20) REVERT: D 249 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8150 (mp) REVERT: D 412 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8538 (tp) REVERT: E 49 LYS cc_start: 0.8906 (mmtt) cc_final: 0.8662 (mmtt) REVERT: E 83 GLN cc_start: 0.8836 (mt0) cc_final: 0.8523 (mt0) REVERT: E 96 ASP cc_start: 0.8430 (t0) cc_final: 0.8121 (t0) REVERT: E 133 LEU cc_start: 0.8648 (tp) cc_final: 0.8410 (tt) REVERT: E 139 ASN cc_start: 0.8838 (p0) cc_final: 0.8526 (p0) REVERT: E 156 MET cc_start: 0.9286 (OUTLIER) cc_final: 0.9043 (mmm) REVERT: E 179 MET cc_start: 0.8795 (mmm) cc_final: 0.8499 (mmm) REVERT: E 229 ARG cc_start: 0.8640 (mtp85) cc_final: 0.8107 (mtt-85) REVERT: E 249 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8201 (mp) REVERT: E 424 THR cc_start: 0.9326 (m) cc_final: 0.8972 (m) outliers start: 76 outliers final: 51 residues processed: 400 average time/residue: 0.4896 time to fit residues: 217.4670 Evaluate side-chains 427 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 366 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 423 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 163 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 202 GLN B 47 ASN C 47 ASN C 242 GLN D 47 ASN D 242 GLN E 47 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.131949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.107961 restraints weight = 21682.263| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.89 r_work: 0.3109 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14525 Z= 0.154 Angle : 0.742 8.705 19745 Z= 0.366 Chirality : 0.047 0.133 2255 Planarity : 0.004 0.046 2435 Dihedral : 5.290 20.388 2200 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.46 % Allowed : 25.11 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.20), residues: 1710 helix: 1.35 (0.21), residues: 625 sheet: -0.30 (0.26), residues: 345 loop : -1.67 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 229 TYR 0.029 0.002 TYR E 317 PHE 0.016 0.001 PHE C 311 TRP 0.007 0.001 TRP A 255 HIS 0.001 0.000 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00372 (14500) covalent geometry : angle 0.72833 (19680) SS BOND : bond 0.00502 ( 10) SS BOND : angle 1.43590 ( 20) hydrogen bonds : bond 0.03577 ( 665) hydrogen bonds : angle 4.49788 ( 2265) link_BETA1-4 : bond 0.00586 ( 10) link_BETA1-4 : angle 3.56781 ( 30) link_NAG-ASN : bond 0.00123 ( 5) link_NAG-ASN : angle 0.46858 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 386 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.7258 (mpm) REVERT: A 173 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7420 (mt-10) REVERT: A 239 TYR cc_start: 0.8287 (m-80) cc_final: 0.8025 (m-80) REVERT: B 24 MET cc_start: 0.8004 (ptm) cc_final: 0.7740 (ptm) REVERT: B 133 LEU cc_start: 0.8591 (tp) cc_final: 0.8321 (tt) REVERT: B 202 GLN cc_start: 0.8758 (mt0) cc_final: 0.8445 (mt0) REVERT: C 105 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7394 (mpm) REVERT: C 119 GLU cc_start: 0.7895 (tt0) cc_final: 0.7604 (tt0) REVERT: C 202 GLN cc_start: 0.8703 (mt0) cc_final: 0.8364 (mt0) REVERT: C 208 GLU cc_start: 0.7619 (pm20) cc_final: 0.7359 (pm20) REVERT: C 227 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8675 (tt0) REVERT: C 412 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8597 (tp) REVERT: C 424 THR cc_start: 0.9427 (m) cc_final: 0.9145 (m) REVERT: D 29 PHE cc_start: 0.8728 (t80) cc_final: 0.8502 (t80) REVERT: D 63 SER cc_start: 0.8863 (t) cc_final: 0.8629 (p) REVERT: D 94 TYR cc_start: 0.8278 (OUTLIER) cc_final: 0.7554 (t80) REVERT: D 208 GLU cc_start: 0.7540 (pm20) cc_final: 0.7226 (pm20) REVERT: D 249 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8109 (mp) REVERT: D 412 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8534 (tp) REVERT: E 49 LYS cc_start: 0.8955 (mmtt) cc_final: 0.8610 (mmtt) REVERT: E 83 GLN cc_start: 0.8815 (mt0) cc_final: 0.8508 (mt0) REVERT: E 96 ASP cc_start: 0.8504 (t0) cc_final: 0.8227 (t0) REVERT: E 133 LEU cc_start: 0.8611 (tp) cc_final: 0.8379 (tt) REVERT: E 139 ASN cc_start: 0.8840 (p0) cc_final: 0.8503 (p0) REVERT: E 156 MET cc_start: 0.9269 (OUTLIER) cc_final: 0.9015 (mmm) REVERT: E 179 MET cc_start: 0.8786 (mmm) cc_final: 0.8496 (mmm) REVERT: E 204 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8351 (mt) REVERT: E 229 ARG cc_start: 0.8581 (mtp85) cc_final: 0.8028 (mtt-85) REVERT: E 249 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8202 (mp) outliers start: 68 outliers final: 50 residues processed: 397 average time/residue: 0.5141 time to fit residues: 225.9439 Evaluate side-chains 432 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 372 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 423 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 135 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 80 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 85 optimal weight: 0.0170 chunk 105 optimal weight: 1.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 202 GLN A 326 GLN C 242 GLN D 47 ASN D 242 GLN E 47 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.126973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.102867 restraints weight = 21966.583| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.99 r_work: 0.3140 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14525 Z= 0.146 Angle : 0.749 8.777 19745 Z= 0.370 Chirality : 0.047 0.153 2255 Planarity : 0.004 0.046 2435 Dihedral : 5.171 20.260 2200 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.13 % Allowed : 25.90 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.20), residues: 1710 helix: 1.43 (0.21), residues: 625 sheet: -0.26 (0.26), residues: 345 loop : -1.64 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 229 TYR 0.028 0.002 TYR E 317 PHE 0.020 0.001 PHE B 311 TRP 0.006 0.001 TRP A 255 HIS 0.001 0.000 HIS E 217 Details of bonding type rmsd covalent geometry : bond 0.00351 (14500) covalent geometry : angle 0.73611 (19680) SS BOND : bond 0.00476 ( 10) SS BOND : angle 1.38213 ( 20) hydrogen bonds : bond 0.03571 ( 665) hydrogen bonds : angle 4.43562 ( 2265) link_BETA1-4 : bond 0.00566 ( 10) link_BETA1-4 : angle 3.50245 ( 30) link_NAG-ASN : bond 0.00186 ( 5) link_NAG-ASN : angle 0.44547 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 391 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7926 (pp20) cc_final: 0.7718 (pp20) REVERT: A 105 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7276 (mpm) REVERT: A 236 MET cc_start: 0.9225 (mmm) cc_final: 0.8983 (mmt) REVERT: A 424 THR cc_start: 0.9355 (m) cc_final: 0.9002 (m) REVERT: B 24 MET cc_start: 0.7985 (ptm) cc_final: 0.7748 (ptm) REVERT: B 133 LEU cc_start: 0.8603 (tp) cc_final: 0.8346 (tt) REVERT: B 202 GLN cc_start: 0.8764 (mt0) cc_final: 0.8457 (mt0) REVERT: B 249 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8095 (mp) REVERT: B 424 THR cc_start: 0.9461 (m) cc_final: 0.9130 (m) REVERT: C 105 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7368 (mpm) REVERT: C 119 GLU cc_start: 0.7851 (tt0) cc_final: 0.7631 (tt0) REVERT: C 202 GLN cc_start: 0.8699 (mt0) cc_final: 0.8370 (mt0) REVERT: C 208 GLU cc_start: 0.7610 (pm20) cc_final: 0.7380 (pm20) REVERT: C 316 GLU cc_start: 0.8989 (tm-30) cc_final: 0.8714 (tt0) REVERT: C 424 THR cc_start: 0.9436 (m) cc_final: 0.9147 (m) REVERT: D 28 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7836 (pp20) REVERT: D 29 PHE cc_start: 0.8746 (t80) cc_final: 0.8481 (t80) REVERT: D 63 SER cc_start: 0.8921 (t) cc_final: 0.8695 (p) REVERT: D 94 TYR cc_start: 0.8248 (OUTLIER) cc_final: 0.7561 (t80) REVERT: D 208 GLU cc_start: 0.7570 (pm20) cc_final: 0.7270 (pm20) REVERT: E 49 LYS cc_start: 0.8966 (mmtt) cc_final: 0.8688 (mmtt) REVERT: E 83 GLN cc_start: 0.8813 (mt0) cc_final: 0.8522 (mt0) REVERT: E 96 ASP cc_start: 0.8520 (t0) cc_final: 0.8206 (t0) REVERT: E 133 LEU cc_start: 0.8608 (tp) cc_final: 0.8385 (tt) REVERT: E 139 ASN cc_start: 0.8819 (p0) cc_final: 0.8488 (p0) REVERT: E 156 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.9008 (mmm) REVERT: E 179 MET cc_start: 0.8764 (mmm) cc_final: 0.8492 (mmm) REVERT: E 204 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8341 (mp) REVERT: E 229 ARG cc_start: 0.8553 (mtp85) cc_final: 0.8053 (mtt-85) outliers start: 63 outliers final: 47 residues processed: 402 average time/residue: 0.5285 time to fit residues: 235.1904 Evaluate side-chains 410 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 357 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 423 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 150 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 165 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 57 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 202 GLN C 242 GLN D 47 ASN D 242 GLN E 47 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.132047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.108122 restraints weight = 21800.213| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.95 r_work: 0.3144 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14525 Z= 0.149 Angle : 0.744 9.864 19745 Z= 0.367 Chirality : 0.047 0.161 2255 Planarity : 0.004 0.046 2435 Dihedral : 5.155 20.194 2200 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.61 % Allowed : 26.36 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.20), residues: 1710 helix: 1.33 (0.21), residues: 625 sheet: -0.19 (0.26), residues: 340 loop : -1.49 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 229 TYR 0.027 0.002 TYR E 317 PHE 0.016 0.001 PHE C 311 TRP 0.006 0.001 TRP A 255 HIS 0.002 0.000 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00358 (14500) covalent geometry : angle 0.73052 (19680) SS BOND : bond 0.00501 ( 10) SS BOND : angle 1.38223 ( 20) hydrogen bonds : bond 0.03563 ( 665) hydrogen bonds : angle 4.55327 ( 2265) link_BETA1-4 : bond 0.00576 ( 10) link_BETA1-4 : angle 3.51868 ( 30) link_NAG-ASN : bond 0.00248 ( 5) link_NAG-ASN : angle 0.45956 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5201.50 seconds wall clock time: 89 minutes 15.39 seconds (5355.39 seconds total)