Starting phenix.real_space_refine on Thu Mar 5 00:07:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x3s_22031/03_2026/6x3s_22031.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x3s_22031/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6x3s_22031/03_2026/6x3s_22031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x3s_22031/03_2026/6x3s_22031.map" model { file = "/net/cci-nas-00/data/ceres_data/6x3s_22031/03_2026/6x3s_22031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x3s_22031/03_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-dev-5986/lib/python3.9/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 dihedrals: 9 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 dihedrals: 27 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.92, per 1000 atoms: 0.23 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: 1.70 Conformation dependent library (CDL) restraints added in 887.1 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: 0.61 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: 3.14 Time building geometry restraints manager: 2.26 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 - 30.18: 10507 30.18 - 60.35: 251 60.35 - 90.53: 48 90.53 - 120.70: 16 120.70 - 150.88: 6 Dihedral angle restraints: 10828 sinusoidal: 4572 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 10825 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: 2.310 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: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.000 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 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 : 15.454 150.879 6781 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 covalent geometry : bond 0.00582 (17853) covalent geometry : angle 0.65620 (24296) SS BOND : bond 0.00261 ( 9) SS BOND : angle 2.00868 ( 18) hydrogen bonds : bond 0.10150 ( 799) hydrogen bonds : angle 5.33553 ( 2571) link_ALPHA1-2 : bond 0.01676 ( 3) link_ALPHA1-2 : angle 6.67382 ( 9) link_ALPHA1-3 : bond 0.00264 ( 1) link_ALPHA1-3 : angle 0.71493 ( 3) link_ALPHA1-6 : bond 0.00576 ( 2) link_ALPHA1-6 : angle 4.83009 ( 6) link_BETA1-4 : bond 0.01154 ( 7) link_BETA1-4 : angle 4.24515 ( 21) link_NAG-ASN : bond 0.00209 ( 7) link_NAG-ASN : angle 2.21126 ( 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 : 0.795 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: 0.1491 time to fit residues: 93.7768 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 : 0.642 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 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: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.132973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.105081 restraints weight = 25875.233| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.21 r_work: 0.3134 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17882 Z= 0.111 Angle : 0.565 11.500 24374 Z= 0.281 Chirality : 0.042 0.173 2800 Planarity : 0.004 0.063 2985 Dihedral : 11.317 155.183 2841 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.22 % Allowed : 12.21 % Favored : 86.56 % 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: -0.95 (0.17), residues: 2103 helix: 1.00 (0.21), residues: 588 sheet: -0.85 (0.19), residues: 625 loop : -1.52 (0.19), residues: 890 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 0.018 0.001 PHE E 346 TRP 0.012 0.001 TRP A 319 HIS 0.003 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00239 (17853) covalent geometry : angle 0.55616 (24296) SS BOND : bond 0.00292 ( 9) SS BOND : angle 1.58435 ( 18) hydrogen bonds : bond 0.03663 ( 799) hydrogen bonds : angle 4.37714 ( 2571) link_ALPHA1-2 : bond 0.00404 ( 3) link_ALPHA1-2 : angle 1.98069 ( 9) link_ALPHA1-3 : bond 0.00941 ( 1) link_ALPHA1-3 : angle 1.72153 ( 3) link_ALPHA1-6 : bond 0.00416 ( 2) link_ALPHA1-6 : angle 1.45164 ( 6) link_BETA1-4 : bond 0.00619 ( 7) link_BETA1-4 : angle 2.07827 ( 21) link_NAG-ASN : bond 0.00330 ( 7) link_NAG-ASN : angle 1.70636 ( 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 409 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 386 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 ARG cc_start: 0.7620 (ppt170) cc_final: 0.7249 (ppt170) REVERT: B 89 LEU cc_start: 0.8393 (tt) cc_final: 0.8106 (mm) REVERT: B 170 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8187 (mm-30) REVERT: C 139 ASP cc_start: 0.6993 (t70) cc_final: 0.6212 (t70) REVERT: C 141 ARG cc_start: 0.8490 (mtm180) cc_final: 0.8226 (mtm180) REVERT: C 244 TYR cc_start: 0.6269 (p90) cc_final: 0.6056 (p90) REVERT: C 261 MET cc_start: 0.8827 (mmm) cc_final: 0.8445 (mmm) REVERT: C 299 TYR cc_start: 0.7986 (t80) cc_final: 0.7534 (t80) REVERT: C 306 PHE cc_start: 0.7155 (t80) cc_final: 0.6858 (t80) REVERT: C 309 GLN cc_start: 0.6413 (OUTLIER) cc_final: 0.5653 (mt0) REVERT: D 24 ASP cc_start: 0.8228 (t0) cc_final: 0.7563 (p0) REVERT: D 106 LYS cc_start: 0.8539 (tptp) cc_final: 0.8312 (tppt) REVERT: D 112 MET cc_start: 0.8558 (tpp) cc_final: 0.8317 (tpp) REVERT: E 45 ASP cc_start: 0.7458 (m-30) cc_final: 0.7240 (m-30) REVERT: E 71 GLU cc_start: 0.7257 (pt0) cc_final: 0.6894 (pt0) REVERT: E 85 ARG cc_start: 0.8032 (mtm-85) cc_final: 0.7801 (ptp90) REVERT: I 53 ASN cc_start: 0.8897 (m110) cc_final: 0.8498 (m-40) REVERT: J 61 ASP cc_start: 0.8199 (t0) cc_final: 0.7987 (t0) REVERT: L 17 GLU cc_start: 0.7133 (pt0) cc_final: 0.6618 (pt0) REVERT: K 40 ARG cc_start: 0.8366 (mmm-85) cc_final: 0.8153 (mmm-85) outliers start: 23 outliers final: 11 residues processed: 395 average time/residue: 0.1334 time to fit residues: 78.7784 Evaluate side-chains 362 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 350 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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: 0.0030 chunk 146 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 chunk 145 optimal weight: 8.9990 chunk 53 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 196 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 HIS ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN C 309 GLN D 216 HIS 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 = 0.3609 r_free = 0.3609 target = 0.132030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.105882 restraints weight = 25846.425| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.28 r_work: 0.3092 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17882 Z= 0.107 Angle : 0.536 12.871 24374 Z= 0.266 Chirality : 0.042 0.180 2800 Planarity : 0.004 0.065 2985 Dihedral : 10.474 154.803 2841 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.43 % Allowed : 14.34 % Favored : 84.23 % 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: -0.45 (0.18), residues: 2103 helix: 1.41 (0.21), residues: 589 sheet: -0.51 (0.20), residues: 598 loop : -1.26 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 312 TYR 0.023 0.001 TYR I 49 PHE 0.026 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 covalent geometry : bond 0.00238 (17853) covalent geometry : angle 0.52791 (24296) SS BOND : bond 0.00190 ( 9) SS BOND : angle 1.51905 ( 18) hydrogen bonds : bond 0.03393 ( 799) hydrogen bonds : angle 4.16786 ( 2571) link_ALPHA1-2 : bond 0.00490 ( 3) link_ALPHA1-2 : angle 1.66645 ( 9) link_ALPHA1-3 : bond 0.00870 ( 1) link_ALPHA1-3 : angle 1.59725 ( 3) link_ALPHA1-6 : bond 0.00442 ( 2) link_ALPHA1-6 : angle 1.68286 ( 6) link_BETA1-4 : bond 0.00498 ( 7) link_BETA1-4 : angle 2.03787 ( 21) link_NAG-ASN : bond 0.00215 ( 7) link_NAG-ASN : angle 1.62497 ( 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: 27 poor density : 363 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 40 GLU cc_start: 0.8716 (tp30) cc_final: 0.8510 (tp30) REVERT: B 89 LEU cc_start: 0.8358 (tt) cc_final: 0.8115 (mm) REVERT: C 244 TYR cc_start: 0.6269 (p90) cc_final: 0.6050 (p90) REVERT: C 261 MET cc_start: 0.8915 (mmm) cc_final: 0.8504 (mmm) REVERT: C 299 TYR cc_start: 0.7946 (t80) cc_final: 0.7519 (t80) REVERT: C 309 GLN cc_start: 0.6698 (OUTLIER) cc_final: 0.5790 (mt0) REVERT: D 24 ASP cc_start: 0.8118 (t0) cc_final: 0.7457 (p0) REVERT: D 40 GLU cc_start: 0.8794 (tt0) cc_final: 0.8397 (pt0) REVERT: E 45 ASP cc_start: 0.7478 (m-30) cc_final: 0.7186 (m-30) REVERT: E 71 GLU cc_start: 0.7282 (pt0) cc_final: 0.6931 (pt0) REVERT: E 85 ARG cc_start: 0.8072 (mtm-85) cc_final: 0.7854 (ptp90) REVERT: E 162 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7950 (tt0) REVERT: I 45 LYS cc_start: 0.8964 (mmtm) cc_final: 0.8702 (mmmt) REVERT: I 53 ASN cc_start: 0.8938 (m110) cc_final: 0.8668 (m-40) REVERT: J 61 ASP cc_start: 0.8279 (t0) cc_final: 0.8073 (t0) REVERT: L 17 GLU cc_start: 0.7033 (pt0) cc_final: 0.6539 (pt0) REVERT: K 65 GLN cc_start: 0.8388 (pp30) cc_final: 0.8063 (pp30) outliers start: 27 outliers final: 13 residues processed: 375 average time/residue: 0.1323 time to fit residues: 75.1382 Evaluate side-chains 350 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 336 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP 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 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 229 GLN Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 278 THR 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 184 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 90 GLN A 267 HIS C 224 GLN 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 = 0.3586 r_free = 0.3586 target = 0.130139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.101958 restraints weight = 26076.182| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.15 r_work: 0.3075 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17882 Z= 0.158 Angle : 0.560 12.868 24374 Z= 0.279 Chirality : 0.043 0.176 2800 Planarity : 0.004 0.066 2985 Dihedral : 10.208 155.380 2841 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.34 % Allowed : 15.24 % Favored : 82.42 % 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: -0.24 (0.18), residues: 2103 helix: 1.55 (0.21), residues: 589 sheet: -0.34 (0.20), residues: 611 loop : -1.14 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 265 TYR 0.025 0.001 TYR I 49 PHE 0.034 0.001 PHE E 346 TRP 0.013 0.001 TRP A 319 HIS 0.002 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00367 (17853) covalent geometry : angle 0.55201 (24296) SS BOND : bond 0.00189 ( 9) SS BOND : angle 1.76359 ( 18) hydrogen bonds : bond 0.03530 ( 799) hydrogen bonds : angle 4.19339 ( 2571) link_ALPHA1-2 : bond 0.00384 ( 3) link_ALPHA1-2 : angle 1.82699 ( 9) link_ALPHA1-3 : bond 0.00743 ( 1) link_ALPHA1-3 : angle 1.58206 ( 3) link_ALPHA1-6 : bond 0.00255 ( 2) link_ALPHA1-6 : angle 2.10885 ( 6) link_BETA1-4 : bond 0.00428 ( 7) link_BETA1-4 : angle 1.81355 ( 21) link_NAG-ASN : bond 0.00149 ( 7) link_NAG-ASN : angle 1.75007 ( 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 389 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 345 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7812 (ttm110) REVERT: B 69 SER cc_start: 0.9281 (t) cc_final: 0.8998 (m) REVERT: B 89 LEU cc_start: 0.8362 (tt) cc_final: 0.8085 (mm) REVERT: B 286 MET cc_start: 0.8580 (ttp) cc_final: 0.8300 (ttp) REVERT: C 141 ARG cc_start: 0.8684 (mtm110) cc_final: 0.8390 (mtm180) REVERT: C 261 MET cc_start: 0.8880 (mmm) cc_final: 0.8429 (mmm) REVERT: C 299 TYR cc_start: 0.7953 (t80) cc_final: 0.7479 (t80) REVERT: C 306 PHE cc_start: 0.7239 (t80) cc_final: 0.6839 (t80) REVERT: D 24 ASP cc_start: 0.8157 (t0) cc_final: 0.7427 (p0) REVERT: D 40 GLU cc_start: 0.8887 (tt0) cc_final: 0.8411 (pt0) REVERT: D 242 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7029 (mt0) REVERT: E 45 ASP cc_start: 0.7437 (m-30) cc_final: 0.6913 (m-30) REVERT: E 71 GLU cc_start: 0.7302 (pt0) cc_final: 0.6878 (pt0) REVERT: E 85 ARG cc_start: 0.8131 (mtm-85) cc_final: 0.7904 (mtm-85) REVERT: E 245 THR cc_start: 0.8989 (p) cc_final: 0.8783 (m) REVERT: E 276 MET cc_start: 0.8952 (mmm) cc_final: 0.8504 (tpt) REVERT: I 45 LYS cc_start: 0.8872 (mmtm) cc_final: 0.8643 (mmmt) REVERT: I 53 ASN cc_start: 0.8935 (m110) cc_final: 0.8559 (m-40) REVERT: J 61 ASP cc_start: 0.8292 (t0) cc_final: 0.8076 (t0) REVERT: L 17 GLU cc_start: 0.7095 (pt0) cc_final: 0.6606 (pt0) REVERT: K 3 GLN cc_start: 0.7664 (tp40) cc_final: 0.7404 (tt0) REVERT: K 46 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7817 (mt-10) REVERT: K 65 GLN cc_start: 0.8425 (pp30) cc_final: 0.8034 (pp30) outliers start: 44 outliers final: 26 residues processed: 369 average time/residue: 0.1261 time to fit residues: 71.3853 Evaluate side-chains 359 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 331 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 332 ASN Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 37 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 145 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 108 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 E residue 92 THR Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 279 LEU 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 J residue 32 THR Chi-restraints excluded: chain L residue 5 THR 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: 0.8980 chunk 64 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 chunk 4 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 267 HIS C 224 GLN D 116 ASN D 346 ASN E 135 ASN ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.131035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.103812 restraints weight = 25869.134| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.13 r_work: 0.3092 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17882 Z= 0.124 Angle : 0.537 12.757 24374 Z= 0.267 Chirality : 0.042 0.181 2800 Planarity : 0.004 0.068 2985 Dihedral : 9.987 155.987 2841 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.81 % Allowed : 15.99 % Favored : 81.20 % 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: -0.06 (0.18), residues: 2103 helix: 1.65 (0.21), residues: 593 sheet: -0.18 (0.21), residues: 598 loop : -1.04 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 265 TYR 0.023 0.001 TYR L 49 PHE 0.041 0.001 PHE E 346 TRP 0.011 0.001 TRP A 319 HIS 0.002 0.000 HIS E 156 Details of bonding type rmsd covalent geometry : bond 0.00282 (17853) covalent geometry : angle 0.52952 (24296) SS BOND : bond 0.00213 ( 9) SS BOND : angle 1.57353 ( 18) hydrogen bonds : bond 0.03366 ( 799) hydrogen bonds : angle 4.09479 ( 2571) link_ALPHA1-2 : bond 0.00411 ( 3) link_ALPHA1-2 : angle 1.77942 ( 9) link_ALPHA1-3 : bond 0.00964 ( 1) link_ALPHA1-3 : angle 1.35292 ( 3) link_ALPHA1-6 : bond 0.00262 ( 2) link_ALPHA1-6 : angle 1.95074 ( 6) link_BETA1-4 : bond 0.00430 ( 7) link_BETA1-4 : angle 1.62160 ( 21) link_NAG-ASN : bond 0.00173 ( 7) link_NAG-ASN : angle 1.65722 ( 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 401 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 348 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7789 (ttm110) REVERT: B 69 SER cc_start: 0.9262 (t) cc_final: 0.8991 (m) REVERT: B 89 LEU cc_start: 0.8307 (tt) cc_final: 0.8029 (mm) REVERT: B 286 MET cc_start: 0.8573 (ttp) cc_final: 0.8286 (ttp) REVERT: C 299 TYR cc_start: 0.7891 (t80) cc_final: 0.7425 (t80) REVERT: D 15 PHE cc_start: 0.7471 (t80) cc_final: 0.7251 (t80) REVERT: D 24 ASP cc_start: 0.8115 (t0) cc_final: 0.7402 (p0) REVERT: D 40 GLU cc_start: 0.8825 (tt0) cc_final: 0.8395 (pt0) REVERT: D 242 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.6948 (mt0) REVERT: D 346 ASN cc_start: 0.4974 (m-40) cc_final: 0.4666 (m110) REVERT: E 45 ASP cc_start: 0.7416 (m-30) cc_final: 0.6856 (m-30) REVERT: E 71 GLU cc_start: 0.7317 (pt0) cc_final: 0.6893 (pt0) REVERT: E 85 ARG cc_start: 0.8161 (mtm-85) cc_final: 0.7911 (mtm-85) REVERT: E 162 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7853 (tt0) REVERT: E 229 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8540 (mt) REVERT: I 45 LYS cc_start: 0.8910 (mmtm) cc_final: 0.8641 (mmmt) REVERT: I 53 ASN cc_start: 0.8924 (m110) cc_final: 0.8577 (m-40) REVERT: I 79 GLN cc_start: 0.7360 (mp10) cc_final: 0.6867 (mp10) REVERT: L 17 GLU cc_start: 0.7097 (pt0) cc_final: 0.6602 (pt0) REVERT: K 3 GLN cc_start: 0.7605 (tp40) cc_final: 0.7348 (tt0) REVERT: K 46 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7802 (mt-10) REVERT: K 65 GLN cc_start: 0.8439 (pp30) cc_final: 0.8022 (pp30) outliers start: 53 outliers final: 36 residues processed: 378 average time/residue: 0.1250 time to fit residues: 72.3729 Evaluate side-chains 368 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 329 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 195 THR Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 37 ARG 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 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 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 147 GLU 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 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 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 J residue 32 THR Chi-restraints excluded: chain L residue 5 THR 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: 6.9990 chunk 165 optimal weight: 0.3980 chunk 116 optimal weight: 0.0370 chunk 99 optimal weight: 10.0000 chunk 176 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 199 optimal weight: 10.0000 chunk 186 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 30 optimal weight: 0.0370 chunk 158 optimal weight: 8.9990 overall best weight: 1.4940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 267 HIS B 204 GLN C 224 GLN C 309 GLN E 135 ASN ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.130310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.102285 restraints weight = 25928.823| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.12 r_work: 0.3069 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2010 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= 0.143 Angle : 0.550 13.043 24374 Z= 0.273 Chirality : 0.043 0.188 2800 Planarity : 0.004 0.070 2985 Dihedral : 9.935 155.808 2841 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.03 % Allowed : 16.57 % Favored : 80.40 % 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: 0.06 (0.18), residues: 2103 helix: 1.72 (0.21), residues: 594 sheet: -0.15 (0.21), residues: 611 loop : -0.92 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 265 TYR 0.024 0.001 TYR I 49 PHE 0.041 0.001 PHE E 346 TRP 0.012 0.001 TRP A 319 HIS 0.002 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00330 (17853) covalent geometry : angle 0.54223 (24296) SS BOND : bond 0.00299 ( 9) SS BOND : angle 1.71072 ( 18) hydrogen bonds : bond 0.03452 ( 799) hydrogen bonds : angle 4.11044 ( 2571) link_ALPHA1-2 : bond 0.00370 ( 3) link_ALPHA1-2 : angle 1.87051 ( 9) link_ALPHA1-3 : bond 0.00972 ( 1) link_ALPHA1-3 : angle 1.35710 ( 3) link_ALPHA1-6 : bond 0.00284 ( 2) link_ALPHA1-6 : angle 2.09114 ( 6) link_BETA1-4 : bond 0.00426 ( 7) link_BETA1-4 : angle 1.52998 ( 21) link_NAG-ASN : bond 0.00156 ( 7) link_NAG-ASN : angle 1.75267 ( 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: 57 poor density : 341 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 TYR cc_start: 0.8376 (p90) cc_final: 0.8069 (p90) REVERT: A 77 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8898 (pt) REVERT: B 37 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7847 (ttm110) REVERT: B 69 SER cc_start: 0.9286 (t) cc_final: 0.8997 (m) REVERT: B 89 LEU cc_start: 0.8305 (tt) cc_final: 0.8041 (mm) REVERT: B 286 MET cc_start: 0.8578 (ttp) cc_final: 0.8300 (ttp) REVERT: C 261 MET cc_start: 0.8687 (mmm) cc_final: 0.8454 (mmm) REVERT: C 299 TYR cc_start: 0.7901 (t80) cc_final: 0.7404 (t80) REVERT: C 309 GLN cc_start: 0.6102 (OUTLIER) cc_final: 0.5674 (mt0) REVERT: D 24 ASP cc_start: 0.8123 (t0) cc_final: 0.7363 (p0) REVERT: D 40 GLU cc_start: 0.8800 (tt0) cc_final: 0.8373 (pt0) REVERT: D 242 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.6964 (mt0) REVERT: E 45 ASP cc_start: 0.7394 (m-30) cc_final: 0.7068 (m-30) REVERT: E 71 GLU cc_start: 0.7332 (pt0) cc_final: 0.6900 (pt0) REVERT: E 229 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8560 (mt) REVERT: I 45 LYS cc_start: 0.8928 (mmtm) cc_final: 0.8657 (mmmt) REVERT: I 53 ASN cc_start: 0.8915 (m110) cc_final: 0.8565 (m-40) REVERT: I 79 GLN cc_start: 0.7351 (mp10) cc_final: 0.7106 (mp10) REVERT: L 17 GLU cc_start: 0.7167 (pt0) cc_final: 0.6697 (pt0) REVERT: K 46 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7815 (mt-10) REVERT: K 65 GLN cc_start: 0.8463 (pp30) cc_final: 0.8041 (pp30) outliers start: 57 outliers final: 43 residues processed: 375 average time/residue: 0.1253 time to fit residues: 71.5672 Evaluate side-chains 373 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 325 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 77 ILE Chi-restraints excluded: chain A residue 160 THR 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 37 ARG Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 204 GLN 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 139 ASP Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 194 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 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 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 69 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 37 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 267 HIS C 309 GLN D 110 HIS E 135 ASN E 154 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.125562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.097336 restraints weight = 26068.796| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.11 r_work: 0.3016 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 17882 Z= 0.299 Angle : 0.674 13.287 24374 Z= 0.335 Chirality : 0.048 0.262 2800 Planarity : 0.005 0.074 2985 Dihedral : 10.261 155.188 2841 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.35 % Allowed : 17.26 % Favored : 79.39 % 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: -0.18 (0.18), residues: 2103 helix: 1.57 (0.21), residues: 590 sheet: -0.33 (0.20), residues: 625 loop : -1.07 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 85 TYR 0.028 0.002 TYR E 314 PHE 0.044 0.002 PHE E 346 TRP 0.015 0.002 TRP A 319 HIS 0.004 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00709 (17853) covalent geometry : angle 0.66361 (24296) SS BOND : bond 0.00319 ( 9) SS BOND : angle 2.44452 ( 18) hydrogen bonds : bond 0.04249 ( 799) hydrogen bonds : angle 4.50142 ( 2571) link_ALPHA1-2 : bond 0.00332 ( 3) link_ALPHA1-2 : angle 2.19951 ( 9) link_ALPHA1-3 : bond 0.00353 ( 1) link_ALPHA1-3 : angle 1.70974 ( 3) link_ALPHA1-6 : bond 0.00859 ( 2) link_ALPHA1-6 : angle 2.75813 ( 6) link_BETA1-4 : bond 0.00435 ( 7) link_BETA1-4 : angle 1.54654 ( 21) link_NAG-ASN : bond 0.00372 ( 7) link_NAG-ASN : angle 2.31487 ( 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 395 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 332 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 LYS cc_start: 0.8350 (mttp) cc_final: 0.8006 (mmtm) REVERT: A 236 SER cc_start: 0.9124 (t) cc_final: 0.8452 (p) REVERT: B 37 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7792 (ttm110) REVERT: B 89 LEU cc_start: 0.8399 (tt) cc_final: 0.8129 (mm) REVERT: B 124 ASP cc_start: 0.8555 (t70) cc_final: 0.8248 (t0) REVERT: B 286 MET cc_start: 0.8679 (ttp) cc_final: 0.8441 (ttp) REVERT: C 261 MET cc_start: 0.8712 (mmm) cc_final: 0.8428 (mmm) REVERT: C 299 TYR cc_start: 0.8056 (t80) cc_final: 0.7362 (t80) REVERT: C 309 GLN cc_start: 0.6652 (OUTLIER) cc_final: 0.5893 (mt0) REVERT: D 40 GLU cc_start: 0.8789 (tt0) cc_final: 0.8361 (pt0) REVERT: D 242 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7095 (mt0) REVERT: E 71 GLU cc_start: 0.7311 (pt0) cc_final: 0.6914 (pt0) REVERT: E 229 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8561 (mt) REVERT: I 53 ASN cc_start: 0.8961 (m110) cc_final: 0.8497 (m-40) REVERT: I 79 GLN cc_start: 0.7379 (mp10) cc_final: 0.7053 (mp10) REVERT: J 35 TYR cc_start: 0.9136 (m-80) cc_final: 0.8930 (m-80) REVERT: L 17 GLU cc_start: 0.7272 (pt0) cc_final: 0.6825 (pt0) REVERT: K 3 GLN cc_start: 0.7744 (tp40) cc_final: 0.7497 (tt0) REVERT: K 48 ILE cc_start: 0.9174 (mt) cc_final: 0.8951 (mm) REVERT: K 65 GLN cc_start: 0.8528 (pp30) cc_final: 0.8143 (pp30) outliers start: 63 outliers final: 44 residues processed: 371 average time/residue: 0.1294 time to fit residues: 73.0473 Evaluate side-chains 371 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 323 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 195 THR Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 37 ARG Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 145 ASP 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 139 ASP Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 151 THR 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 108 VAL 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 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 74 THR Chi-restraints excluded: chain J residue 32 THR 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: 0.7980 chunk 59 optimal weight: 4.9990 chunk 89 optimal weight: 0.0170 chunk 131 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 103 optimal weight: 0.0570 chunk 176 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS C 309 GLN E 33 ASN E 135 ASN ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.131352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.105206 restraints weight = 25851.039| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.22 r_work: 0.3117 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2163 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= 0.107 Angle : 0.557 13.170 24374 Z= 0.277 Chirality : 0.042 0.210 2800 Planarity : 0.004 0.075 2985 Dihedral : 9.944 156.256 2841 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.07 % Allowed : 18.43 % Favored : 79.50 % 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: 0.08 (0.18), residues: 2103 helix: 1.73 (0.21), residues: 595 sheet: -0.15 (0.21), residues: 617 loop : -0.90 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 265 TYR 0.030 0.001 TYR E 314 PHE 0.036 0.001 PHE E 346 TRP 0.013 0.001 TRP D 70 HIS 0.002 0.000 HIS E 156 Details of bonding type rmsd covalent geometry : bond 0.00231 (17853) covalent geometry : angle 0.54969 (24296) SS BOND : bond 0.00190 ( 9) SS BOND : angle 1.68457 ( 18) hydrogen bonds : bond 0.03416 ( 799) hydrogen bonds : angle 4.14820 ( 2571) link_ALPHA1-2 : bond 0.00426 ( 3) link_ALPHA1-2 : angle 1.75699 ( 9) link_ALPHA1-3 : bond 0.01214 ( 1) link_ALPHA1-3 : angle 1.18960 ( 3) link_ALPHA1-6 : bond 0.00307 ( 2) link_ALPHA1-6 : angle 1.70322 ( 6) link_BETA1-4 : bond 0.00403 ( 7) link_BETA1-4 : angle 1.54654 ( 21) link_NAG-ASN : bond 0.00199 ( 7) link_NAG-ASN : angle 1.65521 ( 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 383 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 344 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 SER cc_start: 0.8995 (t) cc_final: 0.8317 (p) REVERT: B 37 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7857 (ttm110) REVERT: B 69 SER cc_start: 0.9221 (t) cc_final: 0.8981 (m) REVERT: B 89 LEU cc_start: 0.8349 (tt) cc_final: 0.8084 (mm) REVERT: B 286 MET cc_start: 0.8625 (ttp) cc_final: 0.8356 (ttp) REVERT: C 261 MET cc_start: 0.8767 (mmm) cc_final: 0.8490 (mmm) REVERT: C 299 TYR cc_start: 0.7923 (t80) cc_final: 0.7417 (t80) REVERT: C 309 GLN cc_start: 0.6630 (OUTLIER) cc_final: 0.6135 (mt0) REVERT: C 319 TRP cc_start: 0.6606 (t60) cc_final: 0.5907 (t60) REVERT: D 24 ASP cc_start: 0.8156 (t0) cc_final: 0.7442 (p0) REVERT: D 40 GLU cc_start: 0.8748 (tt0) cc_final: 0.8340 (pt0) REVERT: D 242 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.6958 (mt0) REVERT: E 71 GLU cc_start: 0.7299 (pt0) cc_final: 0.6899 (pt0) REVERT: E 229 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8554 (mt) REVERT: E 239 GLN cc_start: 0.8427 (tp-100) cc_final: 0.7936 (tp-100) REVERT: E 276 MET cc_start: 0.8823 (mmm) cc_final: 0.8441 (tpt) REVERT: I 45 LYS cc_start: 0.8947 (mmtm) cc_final: 0.8611 (mmmt) REVERT: I 53 ASN cc_start: 0.8911 (m110) cc_final: 0.8506 (m-40) REVERT: I 70 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.7616 (p0) REVERT: I 79 GLN cc_start: 0.7235 (mp10) cc_final: 0.6909 (mp10) REVERT: J 35 TYR cc_start: 0.9034 (m-80) cc_final: 0.8824 (m-80) REVERT: L 17 GLU cc_start: 0.7190 (pt0) cc_final: 0.6785 (pt0) REVERT: K 46 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7799 (mt-10) REVERT: K 65 GLN cc_start: 0.8519 (pp30) cc_final: 0.8133 (pp30) outliers start: 39 outliers final: 28 residues processed: 367 average time/residue: 0.1221 time to fit residues: 68.7718 Evaluate side-chains 360 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 327 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 318 ARG Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 37 ARG 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 331 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 139 ASP 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 C residue 309 GLN Chi-restraints excluded: chain D residue 84 LEU 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 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 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 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: 7.9990 chunk 49 optimal weight: 0.5980 chunk 119 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS C 224 GLN C 309 GLN E 135 ASN E 154 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.125614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.099052 restraints weight = 26208.107| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.99 r_work: 0.3023 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 17882 Z= 0.307 Angle : 0.682 12.906 24374 Z= 0.339 Chirality : 0.048 0.230 2800 Planarity : 0.005 0.077 2985 Dihedral : 10.246 155.311 2841 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.50 % Allowed : 18.59 % 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: -0.11 (0.18), residues: 2103 helix: 1.59 (0.21), residues: 589 sheet: -0.29 (0.20), residues: 626 loop : -0.99 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 61 TYR 0.032 0.002 TYR E 314 PHE 0.034 0.002 PHE B 304 TRP 0.017 0.002 TRP A 319 HIS 0.004 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00731 (17853) covalent geometry : angle 0.67215 (24296) SS BOND : bond 0.00329 ( 9) SS BOND : angle 2.50359 ( 18) hydrogen bonds : bond 0.04263 ( 799) hydrogen bonds : angle 4.53109 ( 2571) link_ALPHA1-2 : bond 0.00371 ( 3) link_ALPHA1-2 : angle 2.29442 ( 9) link_ALPHA1-3 : bond 0.00550 ( 1) link_ALPHA1-3 : angle 1.84278 ( 3) link_ALPHA1-6 : bond 0.01048 ( 2) link_ALPHA1-6 : angle 2.63272 ( 6) link_BETA1-4 : bond 0.00428 ( 7) link_BETA1-4 : angle 1.54973 ( 21) link_NAG-ASN : bond 0.00404 ( 7) link_NAG-ASN : angle 2.29022 ( 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 376 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 329 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 SER cc_start: 0.9033 (t) cc_final: 0.8390 (p) REVERT: B 37 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7870 (ttm110) REVERT: B 89 LEU cc_start: 0.8402 (tt) cc_final: 0.8147 (mm) REVERT: B 124 ASP cc_start: 0.8463 (t70) cc_final: 0.8217 (t0) REVERT: C 261 MET cc_start: 0.8808 (mmm) cc_final: 0.8522 (mmm) REVERT: C 299 TYR cc_start: 0.8134 (t80) cc_final: 0.7504 (t80) REVERT: C 309 GLN cc_start: 0.6736 (OUTLIER) cc_final: 0.6086 (mt0) REVERT: D 40 GLU cc_start: 0.8681 (tt0) cc_final: 0.8341 (pt0) REVERT: D 242 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7106 (mt0) REVERT: E 71 GLU cc_start: 0.7241 (pt0) cc_final: 0.6892 (pt0) REVERT: E 85 ARG cc_start: 0.8071 (mtm-85) cc_final: 0.7865 (ptp90) REVERT: E 229 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8569 (mt) REVERT: E 239 GLN cc_start: 0.8561 (tp-100) cc_final: 0.8119 (tp-100) REVERT: I 53 ASN cc_start: 0.8982 (m110) cc_final: 0.8590 (m-40) REVERT: I 79 GLN cc_start: 0.7576 (mp10) cc_final: 0.7080 (mp10) REVERT: L 17 GLU cc_start: 0.7238 (pt0) cc_final: 0.6814 (pt0) REVERT: K 3 GLN cc_start: 0.7772 (tp40) cc_final: 0.7551 (tt0) REVERT: K 48 ILE cc_start: 0.9170 (mt) cc_final: 0.8969 (mm) REVERT: K 65 GLN cc_start: 0.8552 (pp30) cc_final: 0.8186 (pp30) outliers start: 47 outliers final: 37 residues processed: 359 average time/residue: 0.1354 time to fit residues: 73.3406 Evaluate side-chains 359 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 318 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 195 THR Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 37 ARG 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 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 151 THR 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 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 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 250 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 I residue 15 VAL Chi-restraints excluded: chain L residue 5 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 168 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS C 309 GLN E 33 ASN E 135 ASN E 154 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.130544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.101219 restraints weight = 25656.250| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.19 r_work: 0.3101 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2235 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= 0.124 Angle : 0.580 13.271 24374 Z= 0.287 Chirality : 0.043 0.205 2800 Planarity : 0.004 0.079 2985 Dihedral : 10.012 155.898 2841 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.34 % Allowed : 18.80 % Favored : 78.86 % 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: 0.08 (0.18), residues: 2103 helix: 1.72 (0.21), residues: 592 sheet: -0.16 (0.21), residues: 618 loop : -0.89 (0.20), 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 0.022 0.001 PHE B 304 TRP 0.017 0.001 TRP A 319 HIS 0.002 0.001 HIS I 87 Details of bonding type rmsd covalent geometry : bond 0.00279 (17853) covalent geometry : angle 0.57282 (24296) SS BOND : bond 0.00185 ( 9) SS BOND : angle 1.85540 ( 18) hydrogen bonds : bond 0.03585 ( 799) hydrogen bonds : angle 4.24936 ( 2571) link_ALPHA1-2 : bond 0.00381 ( 3) link_ALPHA1-2 : angle 1.83855 ( 9) link_ALPHA1-3 : bond 0.01012 ( 1) link_ALPHA1-3 : angle 1.25420 ( 3) link_ALPHA1-6 : bond 0.00287 ( 2) link_ALPHA1-6 : angle 1.77843 ( 6) link_BETA1-4 : bond 0.00389 ( 7) link_BETA1-4 : angle 1.49844 ( 21) link_NAG-ASN : bond 0.00189 ( 7) link_NAG-ASN : angle 1.77531 ( 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 376 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 332 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 SER cc_start: 0.9002 (t) cc_final: 0.8368 (p) REVERT: B 37 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7895 (ttm110) REVERT: B 69 SER cc_start: 0.9237 (t) cc_final: 0.8978 (m) REVERT: B 89 LEU cc_start: 0.8384 (tt) cc_final: 0.8112 (mm) REVERT: B 286 MET cc_start: 0.8646 (ttp) cc_final: 0.8404 (ttp) REVERT: B 304 PHE cc_start: 0.8348 (t80) cc_final: 0.8099 (t80) REVERT: C 261 MET cc_start: 0.8814 (mmm) cc_final: 0.8527 (mmm) REVERT: C 299 TYR cc_start: 0.7913 (t80) cc_final: 0.7374 (t80) REVERT: C 309 GLN cc_start: 0.6493 (OUTLIER) cc_final: 0.6075 (mt0) REVERT: C 319 TRP cc_start: 0.6605 (t60) cc_final: 0.5931 (t60) REVERT: D 24 ASP cc_start: 0.8246 (t0) cc_final: 0.7592 (p0) REVERT: D 40 GLU cc_start: 0.8766 (tt0) cc_final: 0.8378 (pt0) REVERT: D 242 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.6957 (mt0) REVERT: E 71 GLU cc_start: 0.7276 (pt0) cc_final: 0.6886 (pt0) REVERT: E 85 ARG cc_start: 0.8111 (mtm-85) cc_final: 0.7907 (ptp90) REVERT: E 229 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8563 (mt) REVERT: E 239 GLN cc_start: 0.8479 (tp-100) cc_final: 0.7962 (tp-100) REVERT: E 276 MET cc_start: 0.8836 (mmm) cc_final: 0.8402 (tpt) REVERT: I 53 ASN cc_start: 0.8912 (m110) cc_final: 0.8510 (m-40) REVERT: I 79 GLN cc_start: 0.7459 (mp10) cc_final: 0.6853 (mp10) REVERT: L 17 GLU cc_start: 0.7194 (pt0) cc_final: 0.6767 (pt0) REVERT: L 61 ARG cc_start: 0.7155 (ptt-90) cc_final: 0.6408 (ptt90) REVERT: K 3 GLN cc_start: 0.7696 (tp40) cc_final: 0.7451 (tt0) REVERT: K 46 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7841 (mt-10) REVERT: K 65 GLN cc_start: 0.8607 (pp30) cc_final: 0.8238 (pp30) outliers start: 44 outliers final: 37 residues processed: 362 average time/residue: 0.1285 time to fit residues: 70.9045 Evaluate side-chains 369 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 328 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 195 THR Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 37 ARG 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 331 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 84 LEU 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 21 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS E 135 ASN E 154 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.127674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.099187 restraints weight = 25955.192| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.03 r_work: 0.3049 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17882 Z= 0.204 Angle : 0.617 13.211 24374 Z= 0.306 Chirality : 0.045 0.208 2800 Planarity : 0.005 0.078 2985 Dihedral : 10.071 155.590 2841 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.50 % Allowed : 18.85 % 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: 0.05 (0.18), residues: 2103 helix: 1.69 (0.21), residues: 590 sheet: -0.20 (0.20), residues: 625 loop : -0.87 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 61 TYR 0.034 0.002 TYR E 314 PHE 0.030 0.002 PHE E 346 TRP 0.020 0.001 TRP A 319 HIS 0.003 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00482 (17853) covalent geometry : angle 0.60884 (24296) SS BOND : bond 0.00256 ( 9) SS BOND : angle 2.13927 ( 18) hydrogen bonds : bond 0.03831 ( 799) hydrogen bonds : angle 4.35037 ( 2571) link_ALPHA1-2 : bond 0.00304 ( 3) link_ALPHA1-2 : angle 2.05057 ( 9) link_ALPHA1-3 : bond 0.00715 ( 1) link_ALPHA1-3 : angle 1.47731 ( 3) link_ALPHA1-6 : bond 0.00456 ( 2) link_ALPHA1-6 : angle 2.18806 ( 6) link_BETA1-4 : bond 0.00408 ( 7) link_BETA1-4 : angle 1.48077 ( 21) link_NAG-ASN : bond 0.00241 ( 7) link_NAG-ASN : angle 1.99083 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4870.92 seconds wall clock time: 83 minutes 54.18 seconds (5034.18 seconds total)