Starting phenix.real_space_refine on Sat Sep 12 18:10:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6x3s_22031/09_2026/6x3s_22031.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x3s_22031/09_2026/6x3s_22031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6x3s_22031/09_2026/6x3s_22031.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6x3s_22031/09_2026/6x3s_22031.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x3s_22031/09_2026/6x3s_22031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x3s_22031/09_2026/6x3s_22031.map" model { file = "/net/cci-nas-00/data/ceres_data/6x3s_22031/09_2026/6x3s_22031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x3s_22031/09_2026/6x3s_22031.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 97 5.16 5 C 11245 2.51 5 N 2828 2.21 5 O 3237 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17407 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "B" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "C" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "D" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "E" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2729 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "I" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 802 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "J" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 907 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 914 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} 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 chiralities: 3 Chain: "G" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "H" 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 chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'J94': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'J94': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.89, per 1000 atoms: 0.22 Number of scatterers: 17407 At special positions: 0 Unit cell: (138.278, 128.282, 136.612, 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 97 16.00 O 3237 8.00 N 2828 7.00 C 11245 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.04 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 165 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " 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 ALPHA1-2 " MAN G 4 " - " MAN G 5 " " MAN G 5 " - " MAN G 6 " " MAN G 8 " - " MAN G 9 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " ALPHA1-6 " BMA G 3 " - " MAN G 7 " " MAN G 7 " - " MAN G 8 " 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 M 1 " - " NAG M 2 " NAG-ASN " NAG A 404 " - " ASN A 80 " " NAG C 404 " - " ASN C 80 " " NAG D 401 " - " ASN D 111 " " NAG F 1 " - " ASN A 149 " " NAG G 1 " - " ASN B 111 " " NAG H 1 " - " ASN C 149 " " NAG M 1 " - " ASN E 208 " Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 725.4 milliseconds 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4020 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 27 sheets defined 31.8% alpha, 38.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 Processing helix chain 'A' and resid 84 through 90 removed outlier: 3.865A pdb=" N ASP A 89 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 238 removed outlier: 4.669A pdb=" N MET A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Proline residue: A 228 - end of helix Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 246 through 272 removed outlier: 3.985A pdb=" N ARG A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 306 removed outlier: 3.578A pdb=" N MET A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 339 removed outlier: 3.565A pdb=" N ALA A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Proline residue: A 325 - end of helix Processing helix chain 'B' and resid 11 through 23 removed outlier: 3.701A pdb=" N PHE B 15 " --> pdb=" O ASN B 11 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 76 removed outlier: 4.019A pdb=" N LYS B 76 " --> pdb=" O GLU B 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 73 through 76' Processing helix chain 'B' and resid 87 through 92 Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 223 through 244 removed outlier: 4.911A pdb=" N LEU B 232 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 245 through 247 No H-bonds generated for 'chain 'B' and resid 245 through 247' Processing helix chain 'B' and resid 251 through 274 removed outlier: 3.604A pdb=" N ARG B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 311 Processing helix chain 'B' and resid 314 through 346 removed outlier: 3.657A pdb=" N ALA B 319 " --> pdb=" O PRO B 315 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Proline residue: B 330 - end of helix removed outlier: 3.623A pdb=" N ASN B 346 " --> pdb=" O ALA B 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 21 Processing helix chain 'C' and resid 84 through 90 removed outlier: 3.821A pdb=" N ASP C 89 " --> pdb=" O ARG C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 238 removed outlier: 4.794A pdb=" N MET C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Proline residue: C 228 - end of helix removed outlier: 3.554A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 241 No H-bonds generated for 'chain 'C' and resid 239 through 241' Processing helix chain 'C' and resid 246 through 272 removed outlier: 3.723A pdb=" N ARG C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU C 270 " --> pdb=" O THR C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 305 Processing helix chain 'C' and resid 309 through 339 Proline residue: C 325 - end of helix Processing helix chain 'D' and resid 12 through 23 removed outlier: 4.292A pdb=" N LEU D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 removed outlier: 3.769A pdb=" N LYS D 76 " --> pdb=" O GLU D 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 73 through 76' Processing helix chain 'D' and resid 87 through 92 removed outlier: 3.586A pdb=" N SER D 92 " --> pdb=" O ASN D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 223 through 230 removed outlier: 4.100A pdb=" N ILE D 228 " --> pdb=" O GLY D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.622A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 247 No H-bonds generated for 'chain 'D' and resid 245 through 247' Processing helix chain 'D' and resid 251 through 277 removed outlier: 3.559A pdb=" N LEU D 264 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 311 removed outlier: 3.714A pdb=" N PHE D 289 " --> pdb=" O ALA D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 346 removed outlier: 3.505A pdb=" N ALA D 318 " --> pdb=" O GLN D 314 " (cutoff:3.500A) Proline residue: D 330 - end of helix Processing helix chain 'E' and resid 26 through 35 removed outlier: 3.511A pdb=" N LEU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 106 removed outlier: 4.156A pdb=" N MET E 102 " --> pdb=" O ASN E 99 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL E 103 " --> pdb=" O SER E 100 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLY E 104 " --> pdb=" O ASN E 101 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS E 105 " --> pdb=" O MET E 102 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE E 106 " --> pdb=" O VAL E 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 99 through 106' Processing helix chain 'E' and resid 234 through 240 removed outlier: 4.183A pdb=" N ILE E 238 " --> pdb=" O GLY E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 252 Processing helix chain 'E' and resid 252 through 257 removed outlier: 4.369A pdb=" N TRP E 256 " --> pdb=" O TRP E 252 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE E 257 " --> pdb=" O VAL E 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 252 through 257' Processing helix chain 'E' and resid 261 through 286 removed outlier: 4.065A pdb=" N ILE E 282 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA E 283 " --> pdb=" O LEU E 279 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG E 284 " --> pdb=" O SER E 280 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER E 286 " --> pdb=" O ILE E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 324 removed outlier: 3.512A pdb=" N LEU E 298 " --> pdb=" O THR E 294 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER E 323 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 354 removed outlier: 4.074A pdb=" N LYS E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET E 331 " --> pdb=" O ARG E 327 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP E 332 " --> pdb=" O ALA E 328 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE E 337 " --> pdb=" O SER E 333 " (cutoff:3.500A) Proline residue: E 340 - end of helix Processing helix chain 'J' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 83 removed outlier: 4.251A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP A 56 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL A 50 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR A 58 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 46 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TYR A 62 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ILE A 44 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLN A 64 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ILE A 42 " --> pdb=" O GLN A 64 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ALA A 66 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N MET A 40 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N ARG A 68 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N VAL A 38 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.896A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR A 131 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL A 106 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ARG A 129 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP A 56 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL A 50 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR A 58 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 46 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TYR A 62 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ILE A 44 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLN A 64 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ILE A 42 " --> pdb=" O GLN A 64 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ALA A 66 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N MET A 40 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N ARG A 68 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N VAL A 38 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 97 removed outlier: 3.976A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP A 190 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 86 removed outlier: 4.632A pdb=" N LEU B 119 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 108 through 109 removed outlier: 7.004A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N VAL B 180 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE B 45 " --> pdb=" O VAL B 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.155A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLY B 208 " --> pdb=" O GLN B 204 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLN B 204 " --> pdb=" O GLY B 208 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N TYR B 210 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE B 202 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 212 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N SER B 200 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR B 214 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL B 198 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N HIS B 216 " --> pdb=" O GLN B 196 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN B 196 " --> pdb=" O HIS B 216 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N HIS B 218 " --> pdb=" O LEU B 194 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 81 through 83 removed outlier: 4.356A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASP C 56 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N VAL C 50 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR C 58 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TYR C 62 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ILE C 44 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLN C 64 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ILE C 42 " --> pdb=" O GLN C 64 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ALA C 66 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N MET C 40 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N ARG C 68 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N VAL C 38 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.891A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL C 106 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ARG C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASP C 56 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N VAL C 50 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR C 58 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TYR C 62 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ILE C 44 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLN C 64 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ILE C 42 " --> pdb=" O GLN C 64 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ALA C 66 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N MET C 40 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N ARG C 68 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N VAL C 38 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.787A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP C 190 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 83 through 86 removed outlier: 4.417A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N GLU D 59 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 108 through 109 removed outlier: 7.180A pdb=" N GLU D 59 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N VAL D 180 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE D 45 " --> pdb=" O VAL D 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.055A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS D 218 " --> pdb=" O GLY D 195 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LYS D 220 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LEU D 193 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 59 through 66 removed outlier: 6.523A pdb=" N VAL E 59 " --> pdb=" O PHE E 77 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N PHE E 77 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER E 61 " --> pdb=" O ASP E 75 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N THR E 73 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N VAL E 65 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLU E 71 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ARG E 144 " --> pdb=" O ALA E 121 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ALA E 121 " --> pdb=" O ARG E 144 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR E 146 " --> pdb=" O ALA E 119 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ALA E 119 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASP E 148 " --> pdb=" O LYS E 117 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 95 through 98 removed outlier: 3.805A pdb=" N LEU E 131 " --> pdb=" O LEU E 98 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TYR E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU E 52 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N THR E 51 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLN E 182 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE E 53 " --> pdb=" O GLN E 182 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 111 through 113 removed outlier: 4.613A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AB8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.515A pdb=" N MET I 11 " --> pdb=" O GLU I 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'I' and resid 45 through 48 removed outlier: 6.398A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR I 96 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AC2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.541A pdb=" N MET J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 10 through 12 removed outlier: 4.159A pdb=" N TYR J 107 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.411A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR L 96 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.411A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AC8, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.101A pdb=" N GLU K 10 " --> pdb=" O THR K 115 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N MET K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.101A pdb=" N GLU K 10 " --> pdb=" O THR K 115 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TYR K 107 " --> pdb=" O ARG K 98 " (cutoff:3.500A) 896 hydrogen bonds defined for protein. 2571 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: 3.25 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4870 1.33 - 1.45: 3507 1.45 - 1.57: 9309 1.57 - 1.69: 0 1.69 - 1.81: 167 Bond restraints: 17853 Sorted by residual: bond pdb=" C09 J94 A 405 " pdb=" O10 J94 A 405 " ideal model delta sigma weight residual 1.351 1.224 0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" C09 J94 C 405 " pdb=" O10 J94 C 405 " ideal model delta sigma weight residual 1.351 1.225 0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" C25 J94 A 405 " pdb=" O24 J94 A 405 " ideal model delta sigma weight residual 1.350 1.225 0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" C25 J94 C 405 " pdb=" O24 J94 C 405 " ideal model delta sigma weight residual 1.350 1.225 0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C13 J94 A 405 " pdb=" O12 J94 A 405 " ideal model delta sigma weight residual 1.349 1.226 0.123 2.00e-02 2.50e+03 3.78e+01 ... (remaining 17848 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 24013 2.54 - 5.08: 249 5.08 - 7.62: 29 7.62 - 10.17: 3 10.17 - 12.71: 2 Bond angle restraints: 24296 Sorted by residual: angle pdb=" C ALA D 152 " pdb=" N CYS D 153 " pdb=" CA CYS D 153 " ideal model delta sigma weight residual 122.15 109.44 12.71 3.47e+00 8.31e-02 1.34e+01 angle pdb=" C SER E 164 " pdb=" N CYS E 165 " pdb=" CA CYS E 165 " ideal model delta sigma weight residual 122.38 111.99 10.39 2.90e+00 1.19e-01 1.28e+01 angle pdb=" CA CYS E 165 " pdb=" CB CYS E 165 " pdb=" SG CYS E 165 " ideal model delta sigma weight residual 114.40 122.37 -7.97 2.30e+00 1.89e-01 1.20e+01 angle pdb=" CA ASN E 208 " pdb=" C ASN E 208 " pdb=" O ASN E 208 " ideal model delta sigma weight residual 121.94 118.28 3.66 1.15e+00 7.56e-01 1.01e+01 angle pdb=" CA ASN B 111 " pdb=" C ASN B 111 " pdb=" O ASN B 111 " ideal model delta sigma weight residual 121.78 118.36 3.42 1.12e+00 7.97e-01 9.31e+00 ... (remaining 24291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.15: 9881 25.15 - 50.30: 432 50.30 - 75.44: 37 75.44 - 100.59: 11 100.59 - 125.74: 2 Dihedral angle restraints: 10363 sinusoidal: 4107 harmonic: 6256 Sorted by residual: dihedral pdb=" CB CYS E 151 " pdb=" SG CYS E 151 " pdb=" SG CYS E 165 " pdb=" CB CYS E 165 " ideal model delta sinusoidal sigma weight residual -86.00 -21.06 -64.94 1 1.00e+01 1.00e-02 5.53e+01 dihedral pdb=" CA CYS C 150 " pdb=" C CYS C 150 " pdb=" N THR C 151 " pdb=" CA THR C 151 " ideal model delta harmonic sigma weight residual -180.00 -155.08 -24.92 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA VAL D 64 " pdb=" C VAL D 64 " pdb=" N PHE D 65 " pdb=" CA PHE D 65 " ideal model delta harmonic sigma weight residual 180.00 157.27 22.73 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 10360 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.159: 2785 0.159 - 0.319: 11 0.319 - 0.478: 0 0.478 - 0.637: 1 0.637 - 0.797: 3 Chirality restraints: 2800 Sorted by residual: chirality pdb=" C1 MAN G 9 " pdb=" O2 MAN G 8 " pdb=" C2 MAN G 9 " pdb=" O5 MAN G 9 " both_signs ideal model delta sigma weight residual False 2.40 1.60 0.80 2.00e-02 2.50e+03 1.59e+03 chirality pdb=" C1 MAN G 7 " pdb=" O6 BMA G 3 " pdb=" C2 MAN G 7 " pdb=" O5 MAN G 7 " both_signs ideal model delta sigma weight residual False 2.40 1.64 0.76 2.00e-02 2.50e+03 1.43e+03 chirality pdb=" C1 MAN G 5 " pdb=" O2 MAN G 4 " pdb=" C2 MAN G 5 " pdb=" O5 MAN G 5 " both_signs ideal model delta sigma weight residual False 2.40 1.70 0.70 2.00e-02 2.50e+03 1.21e+03 ... (remaining 2797 not shown) Planarity restraints: 2992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " 0.144 2.00e-02 2.50e+03 1.18e-01 1.74e+02 pdb=" C7 NAG H 2 " -0.039 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " 0.107 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " -0.187 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 2 " -0.129 2.00e-02 2.50e+03 1.06e-01 1.42e+02 pdb=" C7 NAG G 2 " 0.035 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " -0.096 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " 0.171 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " -0.102 2.00e-02 2.50e+03 8.38e-02 8.79e+01 pdb=" C7 NAG M 2 " 0.028 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " -0.077 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " 0.133 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " 0.017 2.00e-02 2.50e+03 ... (remaining 2989 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 338 2.68 - 3.23: 16202 3.23 - 3.79: 27024 3.79 - 4.34: 37543 4.34 - 4.90: 63222 Nonbonded interactions: 144329 Sorted by model distance: nonbonded pdb=" O SER B 241 " pdb=" OG SER B 244 " model vdw 2.119 3.040 nonbonded pdb=" O VAL D 307 " pdb=" OG1 THR D 311 " model vdw 2.128 3.040 nonbonded pdb=" OH TYR B 26 " pdb=" OD2 ASP B 72 " model vdw 2.193 3.040 nonbonded pdb=" OG1 THR D 99 " pdb=" OH TYR D 169 " model vdw 2.227 3.040 nonbonded pdb=" OG SER I 7 " pdb=" OG SER I 22 " model vdw 2.260 3.040 ... (remaining 144324 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 10 through 347) } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'I' selection = (chain 'L' and resid 1 through 105) } ncs_group { reference = chain 'J' selection = (chain 'K' and resid 2 through 117) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 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: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.010 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 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 : 0.006 0.127 17882 Z= 0.279 Angle : 0.689 16.264 24374 Z= 0.344 Chirality : 0.053 0.797 2800 Planarity : 0.005 0.118 2985 Dihedral : 13.752 125.739 6316 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.05 % Allowed : 5.89 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -2.03 (0.16), residues: 2103 helix: -0.08 (0.20), residues: 584 sheet: -1.41 (0.18), residues: 654 loop : -2.08 (0.18), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 255 TYR 0.019 0.001 TYR A 299 PHE 0.021 0.001 PHE D 258 TRP 0.009 0.001 TRP D 70 HIS 0.003 0.001 HIS B 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.28 (17853) covalent geometry : angle 0.65620 / 0.34 (24296) SS BOND : bond 0.00261 / 0.16 ( 9) SS BOND : angle 2.00868 / 1.27 ( 18) hydrogen bonds : bond 0.10150 / 7.15 ( 799) hydrogen bonds : angle 5.33553 / 3.71 ( 2571) link_ALPHA1-2 : bond 0.01676 / 0.85 ( 3) link_ALPHA1-2 : angle 6.67382 / 3.69 ( 9) link_ALPHA1-3 : bond 0.00264 / 0.14 ( 1) link_ALPHA1-3 : angle 0.71493 / 0.38 ( 3) link_ALPHA1-6 : bond 0.00576 / 0.30 ( 2) link_ALPHA1-6 : angle 4.83009 / 2.79 ( 6) link_BETA1-4 : bond 0.01154 / 0.59 ( 7) link_BETA1-4 : angle 4.24515 / 2.64 ( 21) link_NAG-ASN : bond 0.00209 / 0.13 ( 7) link_NAG-ASN : angle 2.21126 / 1.62 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 430 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7402 (mm-30) REVERT: C 139 ASP cc_start: 0.6325 (t70) cc_final: 0.5382 (t0) REVERT: C 299 TYR cc_start: 0.8093 (t80) cc_final: 0.7661 (t80) REVERT: D 15 PHE cc_start: 0.7545 (t80) cc_final: 0.7333 (t80) REVERT: E 314 TYR cc_start: 0.8458 (t80) cc_final: 0.8084 (t80) outliers start: 1 outliers final: 0 residues processed: 431 average time/residue: 0.1564 time to fit residues: 99.0276 Evaluate side-chains 360 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.0030 chunk 200 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.1980 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 GLN A 90 GLN A 113 ASN A 303 ASN A 309 GLN B 68 GLN B 110 HIS B 116 ASN B 190 GLN B 242 GLN B 308 ASN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN C 265 ASN C 309 GLN D 68 GLN D 88 ASN D 116 ASN D 308 ASN E 33 ASN E 80 GLN E 128 ASN E 135 ASN ** E 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 347 ASN J 6 GLN J 55 ASN K 3 GLN K 6 GLN K 77 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.132894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.105833 restraints weight = 25798.502| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.07 r_work: 0.3142 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17882 Z= 0.109 Angle : 0.562 11.506 24374 Z= 0.281 Chirality : 0.042 0.173 2800 Planarity : 0.004 0.063 2985 Dihedral : 6.004 119.406 2376 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.27 % Allowed : 12.06 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -0.96 (0.17), residues: 2103 helix: 0.99 (0.21), residues: 588 sheet: -0.87 (0.19), residues: 626 loop : -1.53 (0.19), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 86 TYR 0.025 0.001 TYR I 49 PHE 0.017 0.001 PHE E 346 TRP 0.012 0.001 TRP A 319 HIS 0.004 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (17853) covalent geometry : angle 0.55513 / 0.28 (24296) SS BOND : bond 0.00370 / 0.22 ( 9) SS BOND : angle 1.59536 / 1.08 ( 18) hydrogen bonds : bond 0.03665 / 2.44 ( 799) hydrogen bonds : angle 4.40419 / 3.01 ( 2571) link_ALPHA1-2 : bond 0.00692 / 0.36 ( 3) link_ALPHA1-2 : angle 1.55656 / 0.87 ( 9) link_ALPHA1-3 : bond 0.00288 / 0.15 ( 1) link_ALPHA1-3 : angle 1.57812 / 0.82 ( 3) link_ALPHA1-6 : bond 0.00610 / 0.31 ( 2) link_ALPHA1-6 : angle 1.88211 / 0.96 ( 6) link_BETA1-4 : bond 0.00498 / 0.31 ( 7) link_BETA1-4 : angle 1.73748 / 1.13 ( 21) link_NAG-ASN : bond 0.00342 / 0.23 ( 7) link_NAG-ASN : angle 1.72507 / 1.26 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 386 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 ARG cc_start: 0.7678 (ppt170) cc_final: 0.7315 (ppt170) REVERT: B 89 LEU cc_start: 0.8381 (tt) cc_final: 0.8099 (mm) REVERT: B 170 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8166 (mm-30) REVERT: C 61 MET cc_start: 0.9374 (ptp) cc_final: 0.9172 (ptt) REVERT: C 139 ASP cc_start: 0.7017 (t70) cc_final: 0.6252 (t70) REVERT: C 141 ARG cc_start: 0.8486 (mtm180) cc_final: 0.8226 (mtm180) REVERT: C 244 TYR cc_start: 0.6322 (p90) cc_final: 0.6111 (p90) REVERT: C 261 MET cc_start: 0.8846 (mmm) cc_final: 0.8463 (mmm) REVERT: C 299 TYR cc_start: 0.8037 (t80) cc_final: 0.7576 (t80) REVERT: C 306 PHE cc_start: 0.7191 (t80) cc_final: 0.6913 (t80) REVERT: C 309 GLN cc_start: 0.6412 (OUTLIER) cc_final: 0.5647 (mt0) REVERT: D 24 ASP cc_start: 0.8230 (t0) cc_final: 0.7586 (p0) REVERT: D 106 LYS cc_start: 0.8528 (tptp) cc_final: 0.8310 (tppt) REVERT: D 112 MET cc_start: 0.8527 (tpp) cc_final: 0.8283 (tpp) REVERT: E 45 ASP cc_start: 0.7476 (m-30) cc_final: 0.6984 (m-30) REVERT: E 71 GLU cc_start: 0.7259 (pt0) cc_final: 0.6916 (pt0) REVERT: E 85 ARG cc_start: 0.8057 (mtm-85) cc_final: 0.7725 (ptp90) REVERT: I 53 ASN cc_start: 0.8889 (m110) cc_final: 0.8540 (m-40) REVERT: J 61 ASP cc_start: 0.8212 (t0) cc_final: 0.8010 (t0) REVERT: L 17 GLU cc_start: 0.7086 (pt0) cc_final: 0.6573 (pt0) REVERT: K 40 ARG cc_start: 0.8395 (mmm-85) cc_final: 0.8184 (mmm-85) outliers start: 24 outliers final: 11 residues processed: 395 average time/residue: 0.1415 time to fit residues: 84.3963 Evaluate side-chains 363 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 351 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain K residue 75 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 129 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 112 optimal weight: 0.0370 chunk 113 optimal weight: 4.9990 chunk 196 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN A 267 HIS ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN C 309 GLN D 229 GLN D 346 ASN E 135 ASN E 156 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.132213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.103251 restraints weight = 26105.011| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.21 r_work: 0.3137 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17882 Z= 0.162 Angle : 0.570 12.813 24374 Z= 0.284 Chirality : 0.043 0.170 2800 Planarity : 0.004 0.066 2985 Dihedral : 6.220 123.755 2376 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.86 % Allowed : 15.08 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -0.54 (0.18), residues: 2103 helix: 1.33 (0.21), residues: 590 sheet: -0.61 (0.20), residues: 623 loop : -1.27 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 312 TYR 0.023 0.001 TYR I 49 PHE 0.027 0.001 PHE E 346 TRP 0.013 0.001 TRP A 319 HIS 0.003 0.001 HIS B 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (17853) covalent geometry : angle 0.56173 / 0.28 (24296) SS BOND : bond 0.00201 / 0.12 ( 9) SS BOND : angle 1.95209 / 1.31 ( 18) hydrogen bonds : bond 0.03719 / 2.45 ( 799) hydrogen bonds : angle 4.31592 / 2.94 ( 2571) link_ALPHA1-2 : bond 0.00503 / 0.26 ( 3) link_ALPHA1-2 : angle 1.65887 / 0.96 ( 9) link_ALPHA1-3 : bond 0.00041 / 0.02 ( 1) link_ALPHA1-3 : angle 1.78116 / 0.92 ( 3) link_ALPHA1-6 : bond 0.00376 / 0.19 ( 2) link_ALPHA1-6 : angle 1.71024 / 0.96 ( 6) link_BETA1-4 : bond 0.00467 / 0.25 ( 7) link_BETA1-4 : angle 1.55917 / 1.10 ( 21) link_NAG-ASN : bond 0.00151 / 0.10 ( 7) link_NAG-ASN : angle 1.79372 / 1.34 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 355 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 40 GLU cc_start: 0.8902 (tp30) cc_final: 0.8606 (tp30) REVERT: B 69 SER cc_start: 0.9296 (t) cc_final: 0.8985 (m) REVERT: B 89 LEU cc_start: 0.8394 (tt) cc_final: 0.8112 (mm) REVERT: B 204 GLN cc_start: 0.8764 (tp40) cc_final: 0.8546 (tp40) REVERT: C 139 ASP cc_start: 0.7099 (t70) cc_final: 0.6187 (t0) REVERT: C 244 TYR cc_start: 0.6366 (p90) cc_final: 0.6154 (p90) REVERT: C 261 MET cc_start: 0.8814 (mmm) cc_final: 0.8390 (mmm) REVERT: C 299 TYR cc_start: 0.7849 (t80) cc_final: 0.7432 (t80) REVERT: C 309 GLN cc_start: 0.6476 (OUTLIER) cc_final: 0.5597 (mt0) REVERT: D 24 ASP cc_start: 0.8246 (t0) cc_final: 0.7448 (p0) REVERT: D 40 GLU cc_start: 0.8903 (tt0) cc_final: 0.8365 (pt0) REVERT: D 106 LYS cc_start: 0.8656 (tptp) cc_final: 0.8448 (tppt) REVERT: E 45 ASP cc_start: 0.7468 (m-30) cc_final: 0.6933 (m-30) REVERT: E 71 GLU cc_start: 0.7250 (pt0) cc_final: 0.6857 (pt0) REVERT: E 85 ARG cc_start: 0.8108 (mtm-85) cc_final: 0.7649 (ptp90) REVERT: I 53 ASN cc_start: 0.8936 (m110) cc_final: 0.8516 (m-40) REVERT: J 61 ASP cc_start: 0.8318 (t0) cc_final: 0.8076 (t0) REVERT: L 17 GLU cc_start: 0.7137 (pt0) cc_final: 0.6612 (pt0) REVERT: K 40 ARG cc_start: 0.8346 (mmm-85) cc_final: 0.8133 (mmm-85) REVERT: K 73 ASP cc_start: 0.6581 (t70) cc_final: 0.6362 (t70) outliers start: 35 outliers final: 22 residues processed: 372 average time/residue: 0.1398 time to fit residues: 78.9607 Evaluate side-chains 356 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 333 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain K residue 75 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 184 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN A 267 HIS C 224 GLN D 110 HIS D 346 ASN E 135 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.128479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.099305 restraints weight = 26131.859| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.16 r_work: 0.3061 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17882 Z= 0.175 Angle : 0.575 12.669 24374 Z= 0.286 Chirality : 0.043 0.162 2800 Planarity : 0.004 0.068 2985 Dihedral : 6.259 123.713 2376 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.71 % Allowed : 15.45 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -0.36 (0.18), residues: 2103 helix: 1.44 (0.21), residues: 590 sheet: -0.49 (0.20), residues: 627 loop : -1.15 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 265 TYR 0.025 0.002 TYR I 49 PHE 0.033 0.002 PHE E 346 TRP 0.011 0.001 TRP A 319 HIS 0.002 0.001 HIS B 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (17853) covalent geometry : angle 0.56768 / 0.28 (24296) SS BOND : bond 0.00247 / 0.14 ( 9) SS BOND : angle 1.91938 / 1.28 ( 18) hydrogen bonds : bond 0.03727 / 2.45 ( 799) hydrogen bonds : angle 4.29350 / 2.93 ( 2571) link_ALPHA1-2 : bond 0.00424 / 0.22 ( 3) link_ALPHA1-2 : angle 1.68792 / 0.97 ( 9) link_ALPHA1-3 : bond 0.00003 / 0.00 ( 1) link_ALPHA1-3 : angle 1.83359 / 0.94 ( 3) link_ALPHA1-6 : bond 0.00263 / 0.13 ( 2) link_ALPHA1-6 : angle 1.83666 / 1.02 ( 6) link_BETA1-4 : bond 0.00392 / 0.22 ( 7) link_BETA1-4 : angle 1.51084 / 1.05 ( 21) link_NAG-ASN : bond 0.00159 / 0.10 ( 7) link_NAG-ASN : angle 1.81737 / 1.36 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 343 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 SER cc_start: 0.9276 (t) cc_final: 0.8981 (m) REVERT: B 89 LEU cc_start: 0.8387 (tt) cc_final: 0.8126 (mm) REVERT: B 286 MET cc_start: 0.8632 (ttp) cc_final: 0.8366 (ttp) REVERT: C 261 MET cc_start: 0.8890 (mmm) cc_final: 0.8458 (mmm) REVERT: C 299 TYR cc_start: 0.7948 (t80) cc_final: 0.7438 (t80) REVERT: D 15 PHE cc_start: 0.7531 (t80) cc_final: 0.7310 (t80) REVERT: D 24 ASP cc_start: 0.8213 (t0) cc_final: 0.7450 (p0) REVERT: D 40 GLU cc_start: 0.8866 (tt0) cc_final: 0.8407 (pt0) REVERT: D 106 LYS cc_start: 0.8639 (tptp) cc_final: 0.8438 (tppt) REVERT: D 242 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7028 (mt0) REVERT: E 45 ASP cc_start: 0.7465 (m-30) cc_final: 0.6971 (m-30) REVERT: E 71 GLU cc_start: 0.7268 (pt0) cc_final: 0.6928 (pt0) REVERT: E 85 ARG cc_start: 0.8176 (mtm-85) cc_final: 0.7955 (mtm-85) REVERT: E 229 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8566 (mt) REVERT: I 53 ASN cc_start: 0.8943 (m110) cc_final: 0.8559 (m-40) REVERT: J 61 ASP cc_start: 0.8342 (t0) cc_final: 0.8104 (t0) REVERT: L 17 GLU cc_start: 0.7110 (pt0) cc_final: 0.6628 (pt0) REVERT: K 65 GLN cc_start: 0.8375 (pp30) cc_final: 0.8073 (pp30) REVERT: K 73 ASP cc_start: 0.6628 (t70) cc_final: 0.6380 (t70) outliers start: 51 outliers final: 30 residues processed: 370 average time/residue: 0.1333 time to fit residues: 74.9019 Evaluate side-chains 367 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 335 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 75 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 163 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 77 optimal weight: 0.3980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN A 267 HIS C 224 GLN D 346 ASN E 135 ASN ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.129260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.101339 restraints weight = 25998.350| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.11 r_work: 0.3065 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17882 Z= 0.164 Angle : 0.566 12.602 24374 Z= 0.282 Chirality : 0.043 0.163 2800 Planarity : 0.004 0.069 2985 Dihedral : 6.262 123.914 2376 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.13 % Allowed : 16.41 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -0.21 (0.18), residues: 2103 helix: 1.62 (0.21), residues: 589 sheet: -0.41 (0.20), residues: 634 loop : -1.11 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 265 TYR 0.023 0.001 TYR L 49 PHE 0.045 0.002 PHE E 346 TRP 0.012 0.001 TRP A 319 HIS 0.002 0.001 HIS E 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (17853) covalent geometry : angle 0.55880 / 0.28 (24296) SS BOND : bond 0.00240 / 0.13 ( 9) SS BOND : angle 1.83119 / 1.21 ( 18) hydrogen bonds : bond 0.03654 / 2.40 ( 799) hydrogen bonds : angle 4.23461 / 2.89 ( 2571) link_ALPHA1-2 : bond 0.00390 / 0.20 ( 3) link_ALPHA1-2 : angle 1.69800 / 0.98 ( 9) link_ALPHA1-3 : bond 0.00097 / 0.05 ( 1) link_ALPHA1-3 : angle 1.74339 / 0.90 ( 3) link_ALPHA1-6 : bond 0.00305 / 0.15 ( 2) link_ALPHA1-6 : angle 1.81679 / 1.01 ( 6) link_BETA1-4 : bond 0.00392 / 0.22 ( 7) link_BETA1-4 : angle 1.47075 / 1.02 ( 21) link_NAG-ASN : bond 0.00146 / 0.10 ( 7) link_NAG-ASN : angle 1.78677 / 1.33 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 336 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 SER cc_start: 0.9285 (t) cc_final: 0.8984 (m) REVERT: B 89 LEU cc_start: 0.8380 (tt) cc_final: 0.8121 (mm) REVERT: B 204 GLN cc_start: 0.8843 (tp40) cc_final: 0.8579 (tp40) REVERT: B 286 MET cc_start: 0.8621 (ttp) cc_final: 0.8364 (ttp) REVERT: C 261 MET cc_start: 0.8882 (mmm) cc_final: 0.8417 (mmm) REVERT: C 299 TYR cc_start: 0.7911 (t80) cc_final: 0.7452 (t80) REVERT: D 15 PHE cc_start: 0.7493 (t80) cc_final: 0.7281 (t80) REVERT: D 24 ASP cc_start: 0.8203 (t0) cc_final: 0.7439 (p0) REVERT: D 40 GLU cc_start: 0.8815 (tt0) cc_final: 0.8379 (pt0) REVERT: D 242 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.6987 (mt0) REVERT: D 346 ASN cc_start: 0.4857 (m-40) cc_final: 0.4533 (m110) REVERT: E 45 ASP cc_start: 0.7429 (m-30) cc_final: 0.6920 (m-30) REVERT: E 71 GLU cc_start: 0.7341 (pt0) cc_final: 0.7031 (pt0) REVERT: E 85 ARG cc_start: 0.8186 (mtm-85) cc_final: 0.7949 (mtm-85) REVERT: E 229 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8565 (mt) REVERT: I 45 LYS cc_start: 0.8891 (mmtm) cc_final: 0.8641 (mmmt) REVERT: I 53 ASN cc_start: 0.8936 (m110) cc_final: 0.8539 (m-40) REVERT: J 61 ASP cc_start: 0.8368 (t0) cc_final: 0.8151 (t0) REVERT: L 17 GLU cc_start: 0.7117 (pt0) cc_final: 0.6639 (pt0) REVERT: K 46 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7798 (mt-10) REVERT: K 65 GLN cc_start: 0.8414 (pp30) cc_final: 0.8048 (pp30) outliers start: 59 outliers final: 42 residues processed: 368 average time/residue: 0.1331 time to fit residues: 75.2688 Evaluate side-chains 371 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 327 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 75 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 56 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 176 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 chunk 30 optimal weight: 30.0000 chunk 158 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN A 267 HIS E 135 ASN E 154 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.126588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.099239 restraints weight = 25960.113| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.13 r_work: 0.3029 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17882 Z= 0.226 Angle : 0.613 12.746 24374 Z= 0.305 Chirality : 0.045 0.191 2800 Planarity : 0.004 0.072 2985 Dihedral : 6.421 124.721 2376 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.45 % Allowed : 17.10 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -0.23 (0.18), residues: 2103 helix: 1.58 (0.21), residues: 590 sheet: -0.41 (0.20), residues: 626 loop : -1.10 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 265 TYR 0.024 0.002 TYR I 49 PHE 0.049 0.002 PHE E 346 TRP 0.013 0.001 TRP A 319 HIS 0.003 0.001 HIS B 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.23 (17853) covalent geometry : angle 0.60416 / 0.30 (24296) SS BOND : bond 0.00272 / 0.17 ( 9) SS BOND : angle 2.20320 / 1.42 ( 18) hydrogen bonds : bond 0.03992 / 2.62 ( 799) hydrogen bonds : angle 4.38027 / 2.98 ( 2571) link_ALPHA1-2 : bond 0.00330 / 0.17 ( 3) link_ALPHA1-2 : angle 1.88933 / 1.08 ( 9) link_ALPHA1-3 : bond 0.00128 / 0.07 ( 1) link_ALPHA1-3 : angle 1.87422 / 0.97 ( 3) link_ALPHA1-6 : bond 0.00166 / 0.08 ( 2) link_ALPHA1-6 : angle 2.09132 / 1.17 ( 6) link_BETA1-4 : bond 0.00435 / 0.24 ( 7) link_BETA1-4 : angle 1.50021 / 1.05 ( 21) link_NAG-ASN : bond 0.00235 / 0.13 ( 7) link_NAG-ASN : angle 2.03037 / 1.52 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 333 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 SER cc_start: 0.9318 (t) cc_final: 0.8992 (m) REVERT: B 89 LEU cc_start: 0.8387 (tt) cc_final: 0.8126 (mm) REVERT: B 286 MET cc_start: 0.8672 (ttp) cc_final: 0.8438 (ttp) REVERT: C 261 MET cc_start: 0.8924 (mmm) cc_final: 0.8439 (mmm) REVERT: C 299 TYR cc_start: 0.8015 (t80) cc_final: 0.7466 (t80) REVERT: D 40 GLU cc_start: 0.8777 (tt0) cc_final: 0.8382 (pt0) REVERT: D 242 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7071 (mt0) REVERT: E 71 GLU cc_start: 0.7287 (pt0) cc_final: 0.6922 (pt0) REVERT: E 229 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8553 (mt) REVERT: I 53 ASN cc_start: 0.8945 (m110) cc_final: 0.8543 (m-40) REVERT: L 17 GLU cc_start: 0.7182 (pt0) cc_final: 0.6720 (pt0) REVERT: K 65 GLN cc_start: 0.8446 (pp30) cc_final: 0.8074 (pp30) outliers start: 65 outliers final: 46 residues processed: 373 average time/residue: 0.1345 time to fit residues: 76.7740 Evaluate side-chains 372 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 324 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 75 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 37 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 82 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 30 optimal weight: 30.0000 chunk 85 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 191 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 HIS E 33 ASN E 135 ASN ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.130261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.102115 restraints weight = 25900.740| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.11 r_work: 0.3101 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17882 Z= 0.123 Angle : 0.556 12.590 24374 Z= 0.277 Chirality : 0.042 0.258 2800 Planarity : 0.004 0.073 2985 Dihedral : 6.228 123.006 2376 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.66 % Allowed : 18.43 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -0.04 (0.18), residues: 2103 helix: 1.71 (0.21), residues: 591 sheet: -0.26 (0.21), residues: 618 loop : -1.00 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 265 TYR 0.026 0.001 TYR L 49 PHE 0.037 0.001 PHE E 346 TRP 0.013 0.001 TRP A 319 HIS 0.002 0.000 HIS D 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (17853) covalent geometry : angle 0.54902 / 0.28 (24296) SS BOND : bond 0.00197 / 0.11 ( 9) SS BOND : angle 1.82259 / 1.18 ( 18) hydrogen bonds : bond 0.03530 / 2.32 ( 799) hydrogen bonds : angle 4.19505 / 2.86 ( 2571) link_ALPHA1-2 : bond 0.00436 / 0.22 ( 3) link_ALPHA1-2 : angle 1.61149 / 0.93 ( 9) link_ALPHA1-3 : bond 0.00271 / 0.14 ( 1) link_ALPHA1-3 : angle 1.49662 / 0.78 ( 3) link_ALPHA1-6 : bond 0.00358 / 0.19 ( 2) link_ALPHA1-6 : angle 1.63701 / 0.91 ( 6) link_BETA1-4 : bond 0.00391 / 0.23 ( 7) link_BETA1-4 : angle 1.44676 / 0.99 ( 21) link_NAG-ASN : bond 0.00174 / 0.12 ( 7) link_NAG-ASN : angle 1.71190 / 1.25 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 348 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 GLU cc_start: 0.8786 (tp30) cc_final: 0.8586 (tp30) REVERT: B 69 SER cc_start: 0.9217 (t) cc_final: 0.8938 (m) REVERT: B 89 LEU cc_start: 0.8416 (tt) cc_final: 0.8155 (mm) REVERT: B 204 GLN cc_start: 0.8820 (tp40) cc_final: 0.8562 (tp40) REVERT: B 286 MET cc_start: 0.8641 (ttp) cc_final: 0.8395 (ttp) REVERT: C 261 MET cc_start: 0.8896 (mmm) cc_final: 0.8423 (mmm) REVERT: C 299 TYR cc_start: 0.7895 (t80) cc_final: 0.7448 (t80) REVERT: D 24 ASP cc_start: 0.8203 (t0) cc_final: 0.7501 (p0) REVERT: D 40 GLU cc_start: 0.8756 (tt0) cc_final: 0.8360 (pt0) REVERT: D 219 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8856 (mt) REVERT: D 242 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7015 (mt0) REVERT: E 45 ASP cc_start: 0.7404 (m-30) cc_final: 0.7062 (m-30) REVERT: E 71 GLU cc_start: 0.7324 (pt0) cc_final: 0.6895 (pt0) REVERT: E 85 ARG cc_start: 0.8171 (mtm-85) cc_final: 0.7914 (mtm-85) REVERT: E 308 PHE cc_start: 0.8502 (t80) cc_final: 0.8092 (t80) REVERT: I 45 LYS cc_start: 0.8943 (mmtm) cc_final: 0.8668 (mmmt) REVERT: I 53 ASN cc_start: 0.8892 (m110) cc_final: 0.8485 (m-40) REVERT: L 17 GLU cc_start: 0.7087 (pt0) cc_final: 0.6660 (pt0) REVERT: K 46 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7770 (mt-10) REVERT: K 65 GLN cc_start: 0.8467 (pp30) cc_final: 0.8085 (pp30) outliers start: 50 outliers final: 34 residues processed: 378 average time/residue: 0.1386 time to fit residues: 79.8208 Evaluate side-chains 368 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 332 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 312 ARG Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 75 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 160 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 89 optimal weight: 0.0060 chunk 131 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 HIS C 224 GLN E 135 ASN ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.129067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.100502 restraints weight = 25854.938| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.05 r_work: 0.3076 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17882 Z= 0.141 Angle : 0.565 12.592 24374 Z= 0.281 Chirality : 0.043 0.225 2800 Planarity : 0.004 0.074 2985 Dihedral : 6.227 123.697 2376 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.08 % Allowed : 18.22 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 0.04 (0.18), residues: 2103 helix: 1.72 (0.21), residues: 591 sheet: -0.18 (0.21), residues: 618 loop : -0.94 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 61 TYR 0.025 0.001 TYR L 49 PHE 0.031 0.001 PHE B 304 TRP 0.015 0.001 TRP A 319 HIS 0.002 0.001 HIS B 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (17853) covalent geometry : angle 0.55747 / 0.28 (24296) SS BOND : bond 0.00204 / 0.11 ( 9) SS BOND : angle 1.83141 / 1.19 ( 18) hydrogen bonds : bond 0.03546 / 2.34 ( 799) hydrogen bonds : angle 4.18301 / 2.85 ( 2571) link_ALPHA1-2 : bond 0.00393 / 0.20 ( 3) link_ALPHA1-2 : angle 1.72119 / 0.99 ( 9) link_ALPHA1-3 : bond 0.00199 / 0.10 ( 1) link_ALPHA1-3 : angle 1.55499 / 0.81 ( 3) link_ALPHA1-6 : bond 0.00276 / 0.14 ( 2) link_ALPHA1-6 : angle 1.73876 / 0.97 ( 6) link_BETA1-4 : bond 0.00431 / 0.25 ( 7) link_BETA1-4 : angle 1.45148 / 1.01 ( 21) link_NAG-ASN : bond 0.00161 / 0.11 ( 7) link_NAG-ASN : angle 1.74173 / 1.29 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 339 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 SER cc_start: 0.9199 (t) cc_final: 0.8946 (m) REVERT: B 89 LEU cc_start: 0.8378 (tt) cc_final: 0.8098 (mm) REVERT: B 204 GLN cc_start: 0.8837 (tp40) cc_final: 0.8619 (tp40) REVERT: B 286 MET cc_start: 0.8607 (ttp) cc_final: 0.8365 (ttp) REVERT: C 261 MET cc_start: 0.8927 (mmm) cc_final: 0.8445 (mmm) REVERT: C 299 TYR cc_start: 0.8030 (t80) cc_final: 0.7501 (t80) REVERT: D 24 ASP cc_start: 0.8169 (t0) cc_final: 0.7509 (p0) REVERT: D 40 GLU cc_start: 0.8689 (tt0) cc_final: 0.8335 (pt0) REVERT: D 242 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7045 (mt0) REVERT: E 45 ASP cc_start: 0.7406 (m-30) cc_final: 0.7204 (m-30) REVERT: E 71 GLU cc_start: 0.7309 (pt0) cc_final: 0.7038 (pt0) REVERT: E 229 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8574 (mt) REVERT: I 45 LYS cc_start: 0.8961 (mmtm) cc_final: 0.8704 (mmmt) REVERT: I 53 ASN cc_start: 0.8914 (m110) cc_final: 0.8646 (m-40) REVERT: I 79 GLN cc_start: 0.7466 (mp10) cc_final: 0.7005 (mp10) REVERT: L 17 GLU cc_start: 0.7079 (pt0) cc_final: 0.6668 (pt0) REVERT: K 46 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7791 (mt-10) REVERT: K 65 GLN cc_start: 0.8493 (pp30) cc_final: 0.8095 (pp30) outliers start: 58 outliers final: 45 residues processed: 373 average time/residue: 0.1381 time to fit residues: 78.7031 Evaluate side-chains 376 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 329 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 312 ARG Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 75 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 205 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 70 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 HIS E 135 ASN E 154 GLN E 200 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.126189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.098669 restraints weight = 26103.272| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.13 r_work: 0.3015 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 17882 Z= 0.254 Angle : 0.650 12.799 24374 Z= 0.323 Chirality : 0.046 0.219 2800 Planarity : 0.005 0.078 2985 Dihedral : 6.514 125.366 2376 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.08 % Allowed : 18.37 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -0.11 (0.18), residues: 2103 helix: 1.58 (0.21), residues: 590 sheet: -0.30 (0.20), residues: 626 loop : -0.98 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 61 TYR 0.033 0.002 TYR E 314 PHE 0.033 0.002 PHE E 346 TRP 0.018 0.002 TRP A 319 HIS 0.004 0.001 HIS B 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.25 (17853) covalent geometry : angle 0.64083 / 0.32 (24296) SS BOND : bond 0.00311 / 0.19 ( 9) SS BOND : angle 2.35914 / 1.52 ( 18) hydrogen bonds : bond 0.04102 / 2.69 ( 799) hydrogen bonds : angle 4.45566 / 3.03 ( 2571) link_ALPHA1-2 : bond 0.00272 / 0.14 ( 3) link_ALPHA1-2 : angle 2.02375 / 1.16 ( 9) link_ALPHA1-3 : bond 0.00181 / 0.10 ( 1) link_ALPHA1-3 : angle 1.93785 / 1.00 ( 3) link_ALPHA1-6 : bond 0.00193 / 0.10 ( 2) link_ALPHA1-6 : angle 2.15356 / 1.21 ( 6) link_BETA1-4 : bond 0.00447 / 0.25 ( 7) link_BETA1-4 : angle 1.50642 / 1.06 ( 21) link_NAG-ASN : bond 0.00294 / 0.17 ( 7) link_NAG-ASN : angle 2.14119 / 1.61 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 335 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 89 LEU cc_start: 0.8391 (tt) cc_final: 0.8121 (mm) REVERT: C 213 LYS cc_start: 0.8631 (ttmm) cc_final: 0.8392 (tttt) REVERT: C 261 MET cc_start: 0.8933 (mmm) cc_final: 0.8431 (mmm) REVERT: C 299 TYR cc_start: 0.8034 (t80) cc_final: 0.7440 (t80) REVERT: D 40 GLU cc_start: 0.8787 (tt0) cc_final: 0.8381 (pt0) REVERT: D 219 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8805 (mt) REVERT: D 242 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7080 (mt0) REVERT: E 71 GLU cc_start: 0.7280 (pt0) cc_final: 0.6902 (pt0) REVERT: E 229 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8576 (mt) REVERT: E 239 GLN cc_start: 0.8461 (tp-100) cc_final: 0.7941 (tp-100) REVERT: E 324 GLN cc_start: 0.5724 (mp10) cc_final: 0.5500 (mp10) REVERT: I 53 ASN cc_start: 0.8950 (m110) cc_final: 0.8561 (m-40) REVERT: I 79 GLN cc_start: 0.7397 (mp10) cc_final: 0.6863 (mp10) REVERT: J 10 GLU cc_start: 0.7187 (pm20) cc_final: 0.6838 (mm-30) REVERT: J 35 TYR cc_start: 0.9082 (m-80) cc_final: 0.8861 (m-80) REVERT: L 17 GLU cc_start: 0.7175 (pt0) cc_final: 0.6749 (pt0) REVERT: K 48 ILE cc_start: 0.9139 (mt) cc_final: 0.8910 (mm) REVERT: K 65 GLN cc_start: 0.8525 (pp30) cc_final: 0.8165 (pp30) outliers start: 58 outliers final: 47 residues processed: 370 average time/residue: 0.1352 time to fit residues: 76.0425 Evaluate side-chains 380 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 330 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 312 ARG Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 75 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 26 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 168 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 HIS C 54 ASN C 224 GLN E 33 ASN E 135 ASN ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.129587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.102285 restraints weight = 25851.801| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.98 r_work: 0.3084 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17882 Z= 0.119 Angle : 0.575 12.849 24374 Z= 0.286 Chirality : 0.043 0.208 2800 Planarity : 0.004 0.080 2985 Dihedral : 6.263 123.024 2376 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.44 % Allowed : 18.96 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 0.05 (0.18), residues: 2103 helix: 1.69 (0.21), residues: 592 sheet: -0.18 (0.21), residues: 618 loop : -0.89 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 61 TYR 0.034 0.001 TYR E 314 PHE 0.026 0.001 PHE E 346 TRP 0.018 0.001 TRP A 319 HIS 0.003 0.001 HIS E 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (17853) covalent geometry : angle 0.56838 / 0.28 (24296) SS BOND : bond 0.00211 / 0.12 ( 9) SS BOND : angle 1.80419 / 1.18 ( 18) hydrogen bonds : bond 0.03539 / 2.32 ( 799) hydrogen bonds : angle 4.21418 / 2.87 ( 2571) link_ALPHA1-2 : bond 0.00454 / 0.23 ( 3) link_ALPHA1-2 : angle 1.60705 / 0.93 ( 9) link_ALPHA1-3 : bond 0.00344 / 0.18 ( 1) link_ALPHA1-3 : angle 1.45975 / 0.76 ( 3) link_ALPHA1-6 : bond 0.00413 / 0.21 ( 2) link_ALPHA1-6 : angle 1.56452 / 0.87 ( 6) link_BETA1-4 : bond 0.00386 / 0.23 ( 7) link_BETA1-4 : angle 1.45475 / 0.99 ( 21) link_NAG-ASN : bond 0.00190 / 0.14 ( 7) link_NAG-ASN : angle 1.73791 / 1.28 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 339 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 SER cc_start: 0.9190 (t) cc_final: 0.8949 (m) REVERT: B 89 LEU cc_start: 0.8375 (tt) cc_final: 0.8114 (mm) REVERT: B 304 PHE cc_start: 0.8419 (t80) cc_final: 0.8178 (t80) REVERT: C 261 MET cc_start: 0.8904 (mmm) cc_final: 0.8425 (mmm) REVERT: C 299 TYR cc_start: 0.8015 (t80) cc_final: 0.7547 (t80) REVERT: C 319 TRP cc_start: 0.6559 (t60) cc_final: 0.5867 (t60) REVERT: D 24 ASP cc_start: 0.8161 (t0) cc_final: 0.7514 (p0) REVERT: D 40 GLU cc_start: 0.8709 (tt0) cc_final: 0.8376 (pt0) REVERT: D 219 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8844 (mt) REVERT: D 242 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7034 (mt0) REVERT: E 71 GLU cc_start: 0.7268 (pt0) cc_final: 0.6895 (pt0) REVERT: E 229 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8559 (mt) REVERT: E 276 MET cc_start: 0.8836 (mmm) cc_final: 0.8417 (tpt) REVERT: I 53 ASN cc_start: 0.8889 (m110) cc_final: 0.8585 (m-40) REVERT: I 79 GLN cc_start: 0.7436 (mp10) cc_final: 0.6945 (mp10) REVERT: J 10 GLU cc_start: 0.7187 (pm20) cc_final: 0.6843 (mm-30) REVERT: J 35 TYR cc_start: 0.8991 (m-80) cc_final: 0.8782 (m-80) REVERT: L 17 GLU cc_start: 0.7061 (pt0) cc_final: 0.6652 (pt0) REVERT: L 61 ARG cc_start: 0.7118 (ptt-90) cc_final: 0.6494 (ptt90) REVERT: K 46 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7768 (mt-10) REVERT: K 65 GLN cc_start: 0.8521 (pp30) cc_final: 0.8170 (pp30) outliers start: 46 outliers final: 37 residues processed: 364 average time/residue: 0.1341 time to fit residues: 74.9844 Evaluate side-chains 374 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 334 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 310 PHE Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 75 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 21 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 194 optimal weight: 20.0000 chunk 145 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 HIS C 224 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.130574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.103233 restraints weight = 25892.995| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.98 r_work: 0.3102 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17882 Z= 0.114 Angle : 0.552 12.581 24374 Z= 0.273 Chirality : 0.042 0.197 2800 Planarity : 0.004 0.078 2985 Dihedral : 6.136 122.655 2376 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.18 % Allowed : 19.17 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: 0.16 (0.18), residues: 2103 helix: 1.75 (0.21), residues: 594 sheet: -0.07 (0.21), residues: 612 loop : -0.84 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 61 TYR 0.030 0.001 TYR E 314 PHE 0.024 0.001 PHE B 304 TRP 0.017 0.001 TRP A 319 HIS 0.009 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (17853) covalent geometry : angle 0.54594 / 0.27 (24296) SS BOND : bond 0.00215 / 0.12 ( 9) SS BOND : angle 1.66434 / 1.13 ( 18) hydrogen bonds : bond 0.03314 / 2.18 ( 799) hydrogen bonds : angle 4.09323 / 2.79 ( 2571) link_ALPHA1-2 : bond 0.00427 / 0.22 ( 3) link_ALPHA1-2 : angle 1.64165 / 0.94 ( 9) link_ALPHA1-3 : bond 0.00414 / 0.22 ( 1) link_ALPHA1-3 : angle 1.44109 / 0.75 ( 3) link_ALPHA1-6 : bond 0.00366 / 0.19 ( 2) link_ALPHA1-6 : angle 1.60085 / 0.89 ( 6) link_BETA1-4 : bond 0.00414 / 0.23 ( 7) link_BETA1-4 : angle 1.43886 / 1.00 ( 21) link_NAG-ASN : bond 0.00171 / 0.12 ( 7) link_NAG-ASN : angle 1.60924 / 1.17 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5005.57 seconds wall clock time: 86 minutes 27.41 seconds (5187.41 seconds total)