Starting phenix.real_space_refine on Tue Aug 26 09:10:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sgo_40462/08_2025/8sgo_40462_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sgo_40462/08_2025/8sgo_40462.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sgo_40462/08_2025/8sgo_40462.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sgo_40462/08_2025/8sgo_40462.map" model { file = "/net/cci-nas-00/data/ceres_data/8sgo_40462/08_2025/8sgo_40462_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sgo_40462/08_2025/8sgo_40462_trim.cif" } resolution = 2.65 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: 6 Type Number sf(0) Gaussians P 7 5.49 5 S 98 5.16 5 C 11499 2.51 5 N 2836 2.21 5 O 3302 1.98 5 H 16960 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34702 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 5473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 5473 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "B" Number of atoms: 5454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5454 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "C" Number of atoms: 5473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 5473 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "D" Number of atoms: 5454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5454 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "E" Number of atoms: 5443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5443 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "I" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1573 Classifications: {'peptide': 105} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "J" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1784 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1595 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1798 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: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: 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: "N" 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: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'ABU': 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: "B" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 138 Unusual residues: {'PTY': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "C" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 120 Unusual residues: {'ABU': 1, 'NAG': 1, 'PTY': 1, 'Q3G': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'A8W': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.21, per 1000 atoms: 0.21 Number of scatterers: 34702 At special positions: 0 Unit cell: (160.41, 132.606, 120.842, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 98 16.00 P 7 15.00 O 3302 8.00 N 2836 7.00 C 11499 6.00 H 16960 1.00 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 165 " distance=2.05 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 " " MAN G 7 " - " MAN G 10 " 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 M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A 401 " - " ASN A 80 " " NAG C 401 " - " ASN C 80 " " NAG G 1 " - " ASN B 111 " " NAG H 1 " - " ASN C 149 " " NAG M 1 " - " ASN D 111 " " NAG N 1 " - " ASN E 208 " Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 896.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 46 helices and 31 sheets defined 32.0% alpha, 40.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 7 through 21 Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.565A pdb=" N ASP A 89 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 226 removed outlier: 3.503A pdb=" N TYR A 226 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 238 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 269 removed outlier: 3.900A pdb=" N ARG A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 307 removed outlier: 4.671A pdb=" N PHE A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 340 removed outlier: 4.105A pdb=" N ALA A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 322 " --> pdb=" O ARG A 318 " (cutoff:3.500A) Proline residue: A 325 - end of helix Processing helix chain 'B' and resid 11 through 23 Processing helix chain 'B' and resid 72 through 76 removed outlier: 3.660A pdb=" N LYS B 76 " --> pdb=" O GLU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 223 through 230 Processing helix chain 'B' and resid 230 through 244 removed outlier: 3.891A pdb=" N SER B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 277 removed outlier: 3.600A pdb=" N ARG B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 311 Processing helix chain 'B' and resid 314 through 346 removed outlier: 3.974A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Proline residue: B 330 - end of helix removed outlier: 3.701A 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 70 through 73 removed outlier: 3.645A pdb=" N SER C 73 " --> pdb=" O LYS C 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 70 through 73' Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 225 through 238 removed outlier: 3.874A pdb=" N SER C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 3.529A 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 270 removed outlier: 4.083A pdb=" N ARG C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 305 Processing helix chain 'C' and resid 309 through 339 removed outlier: 3.715A pdb=" N ALA C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Proline residue: C 325 - end of helix Processing helix chain 'D' and resid 11 through 24 Processing helix chain 'D' and resid 72 through 76 removed outlier: 3.525A pdb=" N LEU D 75 " --> pdb=" O ASP D 72 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS D 76 " --> pdb=" O GLU D 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 72 through 76' Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.570A pdb=" N SER D 92 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 230 through 243 Processing helix chain 'D' and resid 244 through 246 No H-bonds generated for 'chain 'D' and resid 244 through 246' Processing helix chain 'D' and resid 251 through 276 removed outlier: 3.815A pdb=" N ARG D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N SER D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 311 Processing helix chain 'D' and resid 314 through 346 removed outlier: 4.171A pdb=" N ILE D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) Proline residue: D 330 - end of helix Processing helix chain 'E' and resid 26 through 35 Processing helix chain 'E' and resid 102 through 106 removed outlier: 3.782A pdb=" N LYS E 105 " --> pdb=" O MET E 102 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE E 106 " --> pdb=" O VAL E 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 102 through 106' Processing helix chain 'E' and resid 234 through 240 Processing helix chain 'E' and resid 240 through 253 Processing helix chain 'E' and resid 254 through 256 No H-bonds generated for 'chain 'E' and resid 254 through 256' Processing helix chain 'E' and resid 261 through 287 removed outlier: 3.648A pdb=" N ARG E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU E 287 " --> pdb=" O ALA E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 324 removed outlier: 3.586A pdb=" N PHE E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER E 323 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 357 removed outlier: 3.869A pdb=" N ASP E 332 " --> pdb=" O ALA E 328 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 3.718A 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 87 through 91 removed outlier: 4.121A pdb=" N THR J 91 " --> pdb=" O SER J 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.653A pdb=" N GLN K 65 " --> pdb=" O PRO K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 83 removed outlier: 4.713A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP A 43 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 83 removed outlier: 4.713A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP A 43 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.782A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.782A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N TYR A 205 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS A 197 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ARG A 207 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N THR A 195 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER A 209 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU A 193 " --> pdb=" O SER A 209 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N SER A 211 " --> pdb=" O TYR A 191 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR A 191 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LYS A 213 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 83 through 86 removed outlier: 4.132A pdb=" N LEU B 119 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE B 46 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 108 through 109 removed outlier: 7.068A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE B 46 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.210A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.210A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N TYR B 210 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE B 202 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL B 212 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER B 200 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR B 214 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL B 198 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N HIS B 216 " --> pdb=" O GLN B 196 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLN B 196 " --> pdb=" O HIS B 216 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N HIS B 218 " --> pdb=" O LEU B 194 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.525A pdb=" N LEU C 83 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL C 36 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N TYR C 167 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL C 38 " --> pdb=" O TYR C 167 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.525A pdb=" N LEU C 83 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N THR C 176 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE C 42 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.858A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.858A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL C 199 " --> pdb=" O GLY C 203 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N TYR C 205 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS C 197 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG C 207 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N THR C 195 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER C 209 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU C 193 " --> pdb=" O SER C 209 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N SER C 211 " --> pdb=" O TYR C 191 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TYR C 191 " --> pdb=" O SER C 211 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS C 213 " --> pdb=" O VAL C 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 83 through 86 removed outlier: 4.337A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLU D 59 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL D 53 " --> pdb=" O GLU D 59 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N THR D 61 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N PHE D 65 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N VAL D 47 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ARG D 67 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE D 45 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR D 39 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N GLU D 170 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL D 41 " --> pdb=" O GLU D 170 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 108 through 109 removed outlier: 6.568A pdb=" N GLU D 59 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL D 53 " --> pdb=" O GLU D 59 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N THR D 61 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N PHE D 65 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N VAL D 47 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ARG D 67 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE D 45 " --> pdb=" O ARG D 67 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.228A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.228A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 61 through 66 removed outlier: 3.605A pdb=" N SER E 61 " --> pdb=" O ASP E 75 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR E 73 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N VAL E 65 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU E 71 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ARG E 144 " --> pdb=" O ALA E 121 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ALA E 121 " --> pdb=" O ARG E 144 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR E 146 " --> pdb=" O ALA E 119 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ALA E 119 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASP E 148 " --> pdb=" O LYS E 117 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 95 through 98 removed outlier: 4.621A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR E 58 " --> pdb=" O PHE E 77 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU E 52 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS E 184 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N MET E 57 " --> pdb=" O LYS E 184 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N SER E 186 " --> pdb=" O MET E 57 " (cutoff:3.500A) removed outlier: 9.657A pdb=" N VAL E 59 " --> pdb=" O SER E 186 " (cutoff:3.500A) removed outlier: 10.125A pdb=" N VAL E 188 " --> pdb=" O VAL E 59 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 111 through 113 removed outlier: 3.653A pdb=" N PHE E 227 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.416A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.751A pdb=" N THR I 96 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.638A pdb=" N LEU J 81 " --> pdb=" O LEU J 20 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.160A pdb=" N GLU J 10 " --> pdb=" O THR J 115 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N MET J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ARG J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.160A pdb=" N GLU J 10 " --> pdb=" O THR J 115 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR J 107 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC9, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.530A pdb=" N MET L 11 " --> pdb=" O LYS L 102 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.443A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR L 96 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.589A pdb=" N VAL K 18 " --> pdb=" O LEU K 83 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.620A pdb=" N GLU K 10 " --> pdb=" O SER K 113 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR K 94 " --> pdb=" O THR K 112 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N MET K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ARG K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.620A pdb=" N GLU K 10 " --> pdb=" O SER K 113 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR K 94 " --> pdb=" O THR K 112 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR K 107 " --> pdb=" O ARG K 98 " (cutoff:3.500A) 886 hydrogen bonds defined for protein. 2538 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: 8.44 Time building geometry restraints manager: 3.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.00: 16951 1.00 - 1.21: 19 1.21 - 1.41: 7440 1.41 - 1.62: 10555 1.62 - 1.82: 167 Bond restraints: 35132 Sorted by residual: bond pdb=" NE2 GLN A 148 " pdb="HE22 GLN A 148 " ideal model delta sigma weight residual 0.860 0.796 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" NE2 GLN B 242 " pdb="HE22 GLN B 242 " ideal model delta sigma weight residual 0.860 0.803 0.057 2.00e-02 2.50e+03 8.16e+00 bond pdb=" ND2 ASN E 347 " pdb="HD22 ASN E 347 " ideal model delta sigma weight residual 0.860 0.807 0.053 2.00e-02 2.50e+03 7.11e+00 bond pdb=" C5 PTY B 403 " pdb=" O14 PTY B 403 " ideal model delta sigma weight residual 1.409 1.456 -0.047 2.00e-02 2.50e+03 5.42e+00 bond pdb=" C5 PTY D 401 " pdb=" O14 PTY D 401 " ideal model delta sigma weight residual 1.409 1.454 -0.045 2.00e-02 2.50e+03 5.13e+00 ... (remaining 35127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.36: 62880 5.36 - 10.72: 35 10.72 - 16.09: 2 16.09 - 21.45: 4 21.45 - 26.81: 5 Bond angle restraints: 62926 Sorted by residual: angle pdb=" CG ASN E 347 " pdb=" ND2 ASN E 347 " pdb="HD22 ASN E 347 " ideal model delta sigma weight residual 120.00 146.81 -26.81 3.00e+00 1.11e-01 7.99e+01 angle pdb="HD21 ASN E 347 " pdb=" ND2 ASN E 347 " pdb="HD22 ASN E 347 " ideal model delta sigma weight residual 120.00 95.08 24.92 3.00e+00 1.11e-01 6.90e+01 angle pdb=" CD GLN B 242 " pdb=" NE2 GLN B 242 " pdb="HE22 GLN B 242 " ideal model delta sigma weight residual 120.00 144.39 -24.39 3.00e+00 1.11e-01 6.61e+01 angle pdb="HE21 GLN B 242 " pdb=" NE2 GLN B 242 " pdb="HE22 GLN B 242 " ideal model delta sigma weight residual 120.00 96.98 23.02 3.00e+00 1.11e-01 5.89e+01 angle pdb=" CG ASN E 347 " pdb=" ND2 ASN E 347 " pdb="HD21 ASN E 347 " ideal model delta sigma weight residual 120.00 97.16 22.84 3.00e+00 1.11e-01 5.80e+01 ... (remaining 62921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.10: 16580 34.10 - 68.21: 518 68.21 - 102.31: 62 102.31 - 136.41: 11 136.41 - 170.52: 7 Dihedral angle restraints: 17178 sinusoidal: 9490 harmonic: 7688 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 -20.66 -65.34 1 1.00e+01 1.00e-02 5.59e+01 dihedral pdb=" CA CYS E 165 " pdb=" C CYS E 165 " pdb=" N PRO E 166 " pdb=" CA PRO E 166 " ideal model delta harmonic sigma weight residual -180.00 -155.84 -24.16 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" C3 PTY D 401 " pdb=" O11 PTY D 401 " pdb=" P1 PTY D 401 " pdb=" O12 PTY D 401 " ideal model delta sinusoidal sigma weight residual 300.23 129.71 170.52 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 17175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2330 0.057 - 0.114: 436 0.114 - 0.170: 48 0.170 - 0.227: 3 0.227 - 0.284: 4 Chirality restraints: 2821 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 2818 not shown) Planarity restraints: 5029 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 148 " 0.067 2.00e-02 2.50e+03 9.78e-02 1.43e+02 pdb=" CD GLN A 148 " -0.037 2.00e-02 2.50e+03 pdb=" OE1 GLN A 148 " 0.005 2.00e-02 2.50e+03 pdb=" NE2 GLN A 148 " -0.161 2.00e-02 2.50e+03 pdb="HE21 GLN A 148 " -0.031 2.00e-02 2.50e+03 pdb="HE22 GLN A 148 " 0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 242 " 0.052 2.00e-02 2.50e+03 9.25e-02 1.28e+02 pdb=" CD GLN B 242 " -0.005 2.00e-02 2.50e+03 pdb=" OE1 GLN B 242 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN B 242 " -0.159 2.00e-02 2.50e+03 pdb="HE21 GLN B 242 " -0.037 2.00e-02 2.50e+03 pdb="HE22 GLN B 242 " 0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 347 " 0.047 2.00e-02 2.50e+03 8.98e-02 1.21e+02 pdb=" CG ASN E 347 " 0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN E 347 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN E 347 " -0.156 2.00e-02 2.50e+03 pdb="HD21 ASN E 347 " -0.039 2.00e-02 2.50e+03 pdb="HD22 ASN E 347 " 0.143 2.00e-02 2.50e+03 ... (remaining 5026 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 1134 2.14 - 2.76: 64752 2.76 - 3.37: 94082 3.37 - 3.99: 128601 3.99 - 4.60: 201569 Nonbonded interactions: 490138 Sorted by model distance: nonbonded pdb=" H GLY K 100 " pdb=" O ALA K 104 " model vdw 1.531 2.450 nonbonded pdb=" O ILE I 2 " pdb=" HG1 THR I 96 " model vdw 1.536 2.450 nonbonded pdb=" HH TYR I 36 " pdb=" O ALA J 104 " model vdw 1.548 2.450 nonbonded pdb=" O MET C 55 " pdb=" H CYS C 136 " model vdw 1.550 2.450 nonbonded pdb=" OE1 GLU C 155 " pdb="HH21 ARG C 207 " model vdw 1.552 2.450 ... (remaining 490133 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' and resid 7 through 402) } ncs_group { reference = (chain 'B' and (resid 10 through 401 or (resid 402 and (name C1 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C \ 3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or nam \ e C36 or name C37 or name C38 or name C5 or name C6 or name C8 or name N1 or nam \ e O10 or name O11 or name O12 or name O13 or name O14 or name O30 or name O4 or \ name O7 or name P1 )))) selection = chain 'D' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'M' } 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: 0.010 Normalize map: mean=0, sd=1: 1.480 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: 0.210 Extract box with map and model: 0.350 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 31.590 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 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 : 0.005 0.047 18203 Z= 0.242 Angle : 0.736 11.611 24726 Z= 0.355 Chirality : 0.046 0.284 2821 Planarity : 0.005 0.046 2998 Dihedral : 16.639 170.517 7097 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 aren not related in a simple way. whole: -2.96 (0.16), residues: 2103 helix: -0.54 (0.20), residues: 584 sheet: -2.57 (0.17), residues: 672 loop : -2.30 (0.18), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 197 TYR 0.025 0.002 TYR D 294 PHE 0.017 0.002 PHE A 98 TRP 0.014 0.001 TRP A 92 HIS 0.008 0.001 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00536 (18172) covalent geometry : angle 0.72794 (24642) SS BOND : bond 0.00593 ( 9) SS BOND : angle 1.47483 ( 18) hydrogen bonds : bond 0.13406 ( 768) hydrogen bonds : angle 6.90234 ( 2538) link_ALPHA1-2 : bond 0.00227 ( 3) link_ALPHA1-2 : angle 1.93697 ( 9) link_ALPHA1-3 : bond 0.00243 ( 2) link_ALPHA1-3 : angle 2.29256 ( 6) link_ALPHA1-6 : bond 0.00157 ( 2) link_ALPHA1-6 : angle 2.42640 ( 6) link_BETA1-4 : bond 0.00303 ( 9) link_BETA1-4 : angle 2.09621 ( 27) link_NAG-ASN : bond 0.00287 ( 6) link_NAG-ASN : angle 2.14883 ( 18) *********************** 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 342 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.9238 (ptp) cc_final: 0.9034 (ptt) REVERT: A 260 THR cc_start: 0.9007 (m) cc_final: 0.8736 (p) REVERT: B 286 MET cc_start: 0.8335 (ttp) cc_final: 0.8103 (ttp) REVERT: E 239 GLN cc_start: 0.8470 (tp40) cc_final: 0.8017 (tm-30) REVERT: E 331 MET cc_start: 0.7004 (ttm) cc_final: 0.6628 (ttm) REVERT: I 11 MET cc_start: 0.7629 (ppp) cc_final: 0.7200 (ppp) REVERT: J 46 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7776 (mt-10) REVERT: J 67 LYS cc_start: 0.8182 (tttt) cc_final: 0.7847 (ttmm) REVERT: L 105 LEU cc_start: 0.8136 (tp) cc_final: 0.7911 (tp) REVERT: K 28 ASN cc_start: 0.8620 (m-40) cc_final: 0.8380 (m-40) REVERT: K 31 ASP cc_start: 0.8428 (m-30) cc_final: 0.8033 (m-30) REVERT: K 80 TYR cc_start: 0.8989 (m-80) cc_final: 0.8755 (m-80) outliers start: 0 outliers final: 1 residues processed: 342 average time/residue: 1.2780 time to fit residues: 485.3604 Evaluate side-chains 216 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 215 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN B 116 ASN D 56 HIS ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN L 53 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.090459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.060524 restraints weight = 92127.511| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.29 r_work: 0.2672 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18203 Z= 0.237 Angle : 0.626 7.727 24726 Z= 0.322 Chirality : 0.045 0.231 2821 Planarity : 0.005 0.065 2998 Dihedral : 14.835 178.009 3159 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.96 % Allowed : 11.26 % Favored : 87.79 % 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 aren not related in a simple way. whole: -1.42 (0.17), residues: 2103 helix: 1.16 (0.21), residues: 596 sheet: -1.86 (0.17), residues: 709 loop : -1.53 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 318 TYR 0.016 0.002 TYR E 172 PHE 0.016 0.002 PHE D 101 TRP 0.008 0.001 TRP D 341 HIS 0.005 0.001 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00541 (18172) covalent geometry : angle 0.61610 (24642) SS BOND : bond 0.00575 ( 9) SS BOND : angle 1.39880 ( 18) hydrogen bonds : bond 0.04731 ( 768) hydrogen bonds : angle 5.16357 ( 2538) link_ALPHA1-2 : bond 0.00158 ( 3) link_ALPHA1-2 : angle 1.90140 ( 9) link_ALPHA1-3 : bond 0.00677 ( 2) link_ALPHA1-3 : angle 1.35868 ( 6) link_ALPHA1-6 : bond 0.00153 ( 2) link_ALPHA1-6 : angle 2.17402 ( 6) link_BETA1-4 : bond 0.00378 ( 9) link_BETA1-4 : angle 2.51488 ( 27) link_NAG-ASN : bond 0.00280 ( 6) link_NAG-ASN : angle 1.73278 ( 18) *********************** 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 240 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 222 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8627 (mp0) cc_final: 0.8411 (mp0) REVERT: A 153 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8721 (mm-30) REVERT: A 182 GLU cc_start: 0.8061 (pm20) cc_final: 0.7858 (pm20) REVERT: A 260 THR cc_start: 0.9345 (m) cc_final: 0.9009 (p) REVERT: B 40 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8102 (tm-30) REVERT: C 227 MET cc_start: 0.8599 (mmm) cc_final: 0.8364 (mmt) REVERT: D 106 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8994 (tptm) REVERT: E 239 GLN cc_start: 0.8819 (tp40) cc_final: 0.8118 (tm-30) REVERT: E 258 ASN cc_start: 0.8687 (t0) cc_final: 0.8418 (t0) REVERT: I 42 GLN cc_start: 0.8494 (mt0) cc_final: 0.8081 (mt0) REVERT: K 10 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7399 (mm-30) REVERT: K 28 ASN cc_start: 0.9039 (m-40) cc_final: 0.8633 (m-40) REVERT: K 31 ASP cc_start: 0.9071 (m-30) cc_final: 0.8615 (m-30) REVERT: K 80 TYR cc_start: 0.9253 (m-80) cc_final: 0.9001 (m-80) outliers start: 18 outliers final: 3 residues processed: 231 average time/residue: 1.2898 time to fit residues: 331.0040 Evaluate side-chains 212 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 207 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain L residue 12 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 46 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 186 optimal weight: 1.9990 chunk 182 optimal weight: 5.9990 chunk 2 optimal weight: 0.2980 chunk 121 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN D 56 HIS ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.091044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.061132 restraints weight = 91166.225| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.29 r_work: 0.2679 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18203 Z= 0.150 Angle : 0.547 6.956 24726 Z= 0.281 Chirality : 0.043 0.160 2821 Planarity : 0.004 0.071 2998 Dihedral : 13.063 175.350 3157 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.59 % Allowed : 11.84 % 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 aren not related in a simple way. whole: -0.51 (0.18), residues: 2103 helix: 2.05 (0.21), residues: 592 sheet: -1.35 (0.18), residues: 687 loop : -1.10 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 85 TYR 0.014 0.001 TYR C 299 PHE 0.012 0.001 PHE A 98 TRP 0.007 0.001 TRP K 103 HIS 0.005 0.001 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00340 (18172) covalent geometry : angle 0.53882 (24642) SS BOND : bond 0.00462 ( 9) SS BOND : angle 1.08019 ( 18) hydrogen bonds : bond 0.03930 ( 768) hydrogen bonds : angle 4.69828 ( 2538) link_ALPHA1-2 : bond 0.00292 ( 3) link_ALPHA1-2 : angle 1.63417 ( 9) link_ALPHA1-3 : bond 0.00647 ( 2) link_ALPHA1-3 : angle 1.36107 ( 6) link_ALPHA1-6 : bond 0.00207 ( 2) link_ALPHA1-6 : angle 1.81868 ( 6) link_BETA1-4 : bond 0.00319 ( 9) link_BETA1-4 : angle 2.12070 ( 27) link_NAG-ASN : bond 0.00157 ( 6) link_NAG-ASN : angle 1.47546 ( 18) *********************** 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 250 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 220 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8642 (mp0) cc_final: 0.8430 (mp0) REVERT: A 153 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8686 (mm-30) REVERT: A 245 ASP cc_start: 0.8502 (m-30) cc_final: 0.7970 (m-30) REVERT: A 260 THR cc_start: 0.9343 (m) cc_final: 0.8997 (p) REVERT: C 227 MET cc_start: 0.8610 (mmm) cc_final: 0.8405 (mmt) REVERT: D 294 TYR cc_start: 0.8707 (t80) cc_final: 0.8411 (t80) REVERT: E 239 GLN cc_start: 0.8760 (tp40) cc_final: 0.8259 (tm-30) REVERT: E 258 ASN cc_start: 0.8664 (t0) cc_final: 0.8387 (t0) REVERT: I 11 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7857 (ppp) REVERT: J 73 ASP cc_start: 0.8919 (t70) cc_final: 0.8434 (t70) REVERT: L 39 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8572 (mttt) REVERT: K 10 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7479 (mm-30) REVERT: K 80 TYR cc_start: 0.9250 (m-80) cc_final: 0.9018 (m-80) REVERT: K 101 LEU cc_start: 0.8509 (mp) cc_final: 0.8047 (tp) outliers start: 30 outliers final: 12 residues processed: 235 average time/residue: 1.2797 time to fit residues: 336.5357 Evaluate side-chains 224 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 210 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 39 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 114 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 152 optimal weight: 0.9990 chunk 176 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 56 HIS L 1 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.090929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.060922 restraints weight = 91300.105| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 2.29 r_work: 0.2672 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18203 Z= 0.147 Angle : 0.535 6.942 24726 Z= 0.274 Chirality : 0.042 0.204 2821 Planarity : 0.004 0.075 2998 Dihedral : 12.149 169.429 3157 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.38 % Allowed : 12.53 % Favored : 86.09 % 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 aren not related in a simple way. whole: -0.03 (0.19), residues: 2103 helix: 2.48 (0.21), residues: 584 sheet: -1.08 (0.19), residues: 685 loop : -0.81 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 85 TYR 0.015 0.001 TYR C 299 PHE 0.012 0.001 PHE A 98 TRP 0.007 0.001 TRP K 103 HIS 0.005 0.001 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00334 (18172) covalent geometry : angle 0.52698 (24642) SS BOND : bond 0.00407 ( 9) SS BOND : angle 1.16176 ( 18) hydrogen bonds : bond 0.03649 ( 768) hydrogen bonds : angle 4.52409 ( 2538) link_ALPHA1-2 : bond 0.00236 ( 3) link_ALPHA1-2 : angle 1.65661 ( 9) link_ALPHA1-3 : bond 0.00677 ( 2) link_ALPHA1-3 : angle 1.29839 ( 6) link_ALPHA1-6 : bond 0.00146 ( 2) link_ALPHA1-6 : angle 1.94632 ( 6) link_BETA1-4 : bond 0.00307 ( 9) link_BETA1-4 : angle 1.88750 ( 27) link_NAG-ASN : bond 0.00118 ( 6) link_NAG-ASN : angle 1.54765 ( 18) *********************** 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 246 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 220 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASN cc_start: 0.7113 (t0) cc_final: 0.6558 (t0) REVERT: A 260 THR cc_start: 0.9345 (m) cc_final: 0.8986 (p) REVERT: D 294 TYR cc_start: 0.8720 (t80) cc_final: 0.8379 (t80) REVERT: E 239 GLN cc_start: 0.8742 (tp40) cc_final: 0.8283 (tm-30) REVERT: E 313 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7836 (tm-30) REVERT: J 73 ASP cc_start: 0.8924 (t70) cc_final: 0.8502 (t70) REVERT: K 10 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7518 (mm-30) REVERT: K 80 TYR cc_start: 0.9255 (m-80) cc_final: 0.9014 (m-80) REVERT: K 101 LEU cc_start: 0.8499 (mp) cc_final: 0.8016 (tp) outliers start: 26 outliers final: 13 residues processed: 231 average time/residue: 1.2010 time to fit residues: 310.4046 Evaluate side-chains 217 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 204 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain L residue 12 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 120 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 175 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN D 56 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.090409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.060320 restraints weight = 91138.732| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 2.28 r_work: 0.2657 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18203 Z= 0.167 Angle : 0.542 7.068 24726 Z= 0.278 Chirality : 0.042 0.206 2821 Planarity : 0.005 0.081 2998 Dihedral : 11.528 166.602 3157 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.38 % Allowed : 13.49 % Favored : 85.13 % 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 aren not related in a simple way. whole: 0.24 (0.19), residues: 2103 helix: 2.66 (0.21), residues: 585 sheet: -0.92 (0.19), residues: 672 loop : -0.62 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 85 TYR 0.014 0.001 TYR A 157 PHE 0.014 0.001 PHE A 98 TRP 0.007 0.001 TRP K 103 HIS 0.005 0.001 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00382 (18172) covalent geometry : angle 0.53473 (24642) SS BOND : bond 0.00432 ( 9) SS BOND : angle 1.13761 ( 18) hydrogen bonds : bond 0.03636 ( 768) hydrogen bonds : angle 4.45147 ( 2538) link_ALPHA1-2 : bond 0.00207 ( 3) link_ALPHA1-2 : angle 1.70655 ( 9) link_ALPHA1-3 : bond 0.00592 ( 2) link_ALPHA1-3 : angle 1.34222 ( 6) link_ALPHA1-6 : bond 0.00140 ( 2) link_ALPHA1-6 : angle 1.95607 ( 6) link_BETA1-4 : bond 0.00296 ( 9) link_BETA1-4 : angle 1.76406 ( 27) link_NAG-ASN : bond 0.00148 ( 6) link_NAG-ASN : angle 1.61356 ( 18) *********************** 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 243 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASN cc_start: 0.6990 (t0) cc_final: 0.6548 (t0) REVERT: A 260 THR cc_start: 0.9348 (m) cc_final: 0.8974 (p) REVERT: A 319 TRP cc_start: 0.7708 (t60) cc_final: 0.7359 (t60) REVERT: D 294 TYR cc_start: 0.8761 (t80) cc_final: 0.8374 (t80) REVERT: E 239 GLN cc_start: 0.8751 (tp40) cc_final: 0.8305 (tm-30) REVERT: E 258 ASN cc_start: 0.8773 (t0) cc_final: 0.8565 (t0) REVERT: E 296 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7728 (tpt) REVERT: I 102 LYS cc_start: 0.8663 (mmmt) cc_final: 0.8405 (tptm) REVERT: J 73 ASP cc_start: 0.8920 (t70) cc_final: 0.8486 (t70) REVERT: K 10 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7531 (mm-30) REVERT: K 11 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8883 (tm) REVERT: K 80 TYR cc_start: 0.9263 (m-80) cc_final: 0.9059 (m-80) REVERT: K 101 LEU cc_start: 0.8529 (mp) cc_final: 0.8187 (mt) outliers start: 26 outliers final: 12 residues processed: 229 average time/residue: 1.2042 time to fit residues: 308.8570 Evaluate side-chains 221 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 207 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain E residue 296 MET Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain K residue 11 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 176 optimal weight: 0.0270 chunk 92 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 156 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 64 optimal weight: 7.9990 overall best weight: 1.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 56 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.089804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.060261 restraints weight = 90775.586| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 2.25 r_work: 0.2648 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18203 Z= 0.180 Angle : 0.552 7.028 24726 Z= 0.284 Chirality : 0.043 0.218 2821 Planarity : 0.004 0.087 2998 Dihedral : 10.898 165.437 3157 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.49 % Allowed : 13.70 % Favored : 84.81 % 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 aren not related in a simple way. whole: 0.40 (0.19), residues: 2103 helix: 2.73 (0.21), residues: 585 sheet: -0.76 (0.19), residues: 672 loop : -0.54 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 85 TYR 0.014 0.001 TYR A 157 PHE 0.014 0.001 PHE A 98 TRP 0.008 0.001 TRP E 252 HIS 0.006 0.001 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00413 (18172) covalent geometry : angle 0.54489 (24642) SS BOND : bond 0.00449 ( 9) SS BOND : angle 1.37682 ( 18) hydrogen bonds : bond 0.03646 ( 768) hydrogen bonds : angle 4.42924 ( 2538) link_ALPHA1-2 : bond 0.00210 ( 3) link_ALPHA1-2 : angle 1.75320 ( 9) link_ALPHA1-3 : bond 0.00523 ( 2) link_ALPHA1-3 : angle 1.30784 ( 6) link_ALPHA1-6 : bond 0.00128 ( 2) link_ALPHA1-6 : angle 2.01933 ( 6) link_BETA1-4 : bond 0.00322 ( 9) link_BETA1-4 : angle 1.76300 ( 27) link_NAG-ASN : bond 0.00162 ( 6) link_NAG-ASN : angle 1.64277 ( 18) *********************** 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 245 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 217 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASN cc_start: 0.6919 (t0) cc_final: 0.6605 (t0) REVERT: A 260 THR cc_start: 0.9364 (m) cc_final: 0.9011 (p) REVERT: A 319 TRP cc_start: 0.7729 (t60) cc_final: 0.7397 (t60) REVERT: D 294 TYR cc_start: 0.8756 (t80) cc_final: 0.8382 (t80) REVERT: E 239 GLN cc_start: 0.8740 (tp40) cc_final: 0.8309 (tm-30) REVERT: E 296 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7654 (tpt) REVERT: I 102 LYS cc_start: 0.8633 (mmmt) cc_final: 0.8339 (tptm) REVERT: J 30 LYS cc_start: 0.9253 (ttmt) cc_final: 0.9014 (tttt) REVERT: J 73 ASP cc_start: 0.8883 (t70) cc_final: 0.8410 (t70) REVERT: K 11 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8833 (tm) REVERT: K 101 LEU cc_start: 0.8595 (mp) cc_final: 0.8081 (tp) outliers start: 28 outliers final: 11 residues processed: 229 average time/residue: 1.2557 time to fit residues: 321.8483 Evaluate side-chains 218 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 205 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain E residue 296 MET Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain K residue 11 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 46 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 HIS C 265 ASN D 56 HIS D 229 GLN E 258 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.089533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.059330 restraints weight = 90640.946| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 2.28 r_work: 0.2635 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2503 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 18203 Z= 0.202 Angle : 0.569 7.760 24726 Z= 0.292 Chirality : 0.043 0.223 2821 Planarity : 0.005 0.097 2998 Dihedral : 10.538 164.586 3157 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.22 % Allowed : 14.29 % Favored : 84.49 % 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 aren not related in a simple way. whole: 0.45 (0.19), residues: 2103 helix: 2.72 (0.21), residues: 587 sheet: -0.68 (0.19), residues: 672 loop : -0.53 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 85 TYR 0.015 0.001 TYR A 157 PHE 0.014 0.001 PHE D 157 TRP 0.010 0.001 TRP E 252 HIS 0.008 0.001 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00465 (18172) covalent geometry : angle 0.56124 (24642) SS BOND : bond 0.00688 ( 9) SS BOND : angle 1.40929 ( 18) hydrogen bonds : bond 0.03735 ( 768) hydrogen bonds : angle 4.45521 ( 2538) link_ALPHA1-2 : bond 0.00181 ( 3) link_ALPHA1-2 : angle 1.77282 ( 9) link_ALPHA1-3 : bond 0.00483 ( 2) link_ALPHA1-3 : angle 1.33381 ( 6) link_ALPHA1-6 : bond 0.00211 ( 2) link_ALPHA1-6 : angle 2.00759 ( 6) link_BETA1-4 : bond 0.00331 ( 9) link_BETA1-4 : angle 1.81020 ( 27) link_NAG-ASN : bond 0.00199 ( 6) link_NAG-ASN : angle 1.69347 ( 18) *********************** 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 233 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8606 (mp0) cc_final: 0.8381 (mp0) REVERT: A 243 ASN cc_start: 0.6921 (t0) cc_final: 0.6581 (t0) REVERT: A 260 THR cc_start: 0.9379 (m) cc_final: 0.9010 (p) REVERT: A 319 TRP cc_start: 0.7729 (t60) cc_final: 0.7409 (t60) REVERT: D 294 TYR cc_start: 0.8804 (t80) cc_final: 0.8377 (t80) REVERT: E 239 GLN cc_start: 0.8736 (tp40) cc_final: 0.8328 (tm-30) REVERT: E 296 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7709 (tpt) REVERT: I 102 LYS cc_start: 0.8657 (mmmt) cc_final: 0.8383 (tptm) REVERT: J 30 LYS cc_start: 0.9253 (ttmt) cc_final: 0.9042 (tttt) REVERT: J 73 ASP cc_start: 0.8920 (t70) cc_final: 0.8504 (t70) REVERT: K 11 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8834 (tm) REVERT: K 101 LEU cc_start: 0.8593 (mp) cc_final: 0.8269 (mt) outliers start: 23 outliers final: 14 residues processed: 221 average time/residue: 1.2725 time to fit residues: 313.8793 Evaluate side-chains 218 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain E residue 296 MET Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain K residue 11 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 70 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 204 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 56 HIS D 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.089789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.059442 restraints weight = 90949.369| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 2.31 r_work: 0.2623 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2493 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18203 Z= 0.197 Angle : 0.569 8.866 24726 Z= 0.292 Chirality : 0.043 0.224 2821 Planarity : 0.005 0.102 2998 Dihedral : 10.384 164.092 3157 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.17 % Allowed : 14.98 % Favored : 83.86 % 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 aren not related in a simple way. whole: 0.54 (0.19), residues: 2103 helix: 2.78 (0.21), residues: 587 sheet: -0.60 (0.19), residues: 672 loop : -0.50 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG E 85 TYR 0.015 0.001 TYR A 157 PHE 0.014 0.001 PHE D 157 TRP 0.011 0.001 TRP E 252 HIS 0.006 0.001 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00453 (18172) covalent geometry : angle 0.56140 (24642) SS BOND : bond 0.00641 ( 9) SS BOND : angle 1.25910 ( 18) hydrogen bonds : bond 0.03719 ( 768) hydrogen bonds : angle 4.44410 ( 2538) link_ALPHA1-2 : bond 0.00172 ( 3) link_ALPHA1-2 : angle 1.74625 ( 9) link_ALPHA1-3 : bond 0.00531 ( 2) link_ALPHA1-3 : angle 1.31995 ( 6) link_ALPHA1-6 : bond 0.00196 ( 2) link_ALPHA1-6 : angle 2.00068 ( 6) link_BETA1-4 : bond 0.00320 ( 9) link_BETA1-4 : angle 1.78702 ( 27) link_NAG-ASN : bond 0.00186 ( 6) link_NAG-ASN : angle 1.69558 ( 18) *********************** 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 229 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8655 (mp0) cc_final: 0.8401 (mp0) REVERT: A 243 ASN cc_start: 0.6901 (t0) cc_final: 0.6549 (t0) REVERT: A 260 THR cc_start: 0.9372 (m) cc_final: 0.9011 (p) REVERT: A 319 TRP cc_start: 0.7737 (t60) cc_final: 0.7423 (t60) REVERT: D 294 TYR cc_start: 0.8806 (t80) cc_final: 0.8398 (t80) REVERT: E 239 GLN cc_start: 0.8752 (tp40) cc_final: 0.8332 (tm-30) REVERT: E 258 ASN cc_start: 0.8720 (t0) cc_final: 0.8082 (t0) REVERT: E 296 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7746 (tpt) REVERT: I 102 LYS cc_start: 0.8648 (mmmt) cc_final: 0.8381 (tptm) REVERT: J 30 LYS cc_start: 0.9279 (ttmt) cc_final: 0.9054 (tttt) REVERT: J 73 ASP cc_start: 0.8914 (t70) cc_final: 0.8583 (t0) REVERT: K 10 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7577 (mm-30) REVERT: K 11 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8837 (tm) REVERT: K 101 LEU cc_start: 0.8606 (mp) cc_final: 0.8127 (tp) outliers start: 22 outliers final: 14 residues processed: 218 average time/residue: 1.2218 time to fit residues: 298.5510 Evaluate side-chains 219 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 203 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain E residue 296 MET Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain K residue 11 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 31 optimal weight: 0.0770 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 132 optimal weight: 0.0670 chunk 157 optimal weight: 0.8980 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN D 56 HIS D 229 GLN J 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.090581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.061152 restraints weight = 90351.507| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 2.26 r_work: 0.2672 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 18203 Z= 0.102 Angle : 0.530 10.509 24726 Z= 0.271 Chirality : 0.042 0.208 2821 Planarity : 0.004 0.108 2998 Dihedral : 9.977 163.608 3157 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.01 % Allowed : 15.08 % Favored : 83.91 % 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 aren not related in a simple way. whole: 0.67 (0.19), residues: 2103 helix: 2.93 (0.21), residues: 587 sheet: -0.55 (0.19), residues: 680 loop : -0.42 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG E 85 TYR 0.018 0.001 TYR C 299 PHE 0.010 0.001 PHE D 157 TRP 0.010 0.001 TRP E 252 HIS 0.002 0.001 HIS D 110 Details of bonding type rmsd covalent geometry : bond 0.00232 (18172) covalent geometry : angle 0.52499 (24642) SS BOND : bond 0.00521 ( 9) SS BOND : angle 0.82073 ( 18) hydrogen bonds : bond 0.03373 ( 768) hydrogen bonds : angle 4.23665 ( 2538) link_ALPHA1-2 : bond 0.00356 ( 3) link_ALPHA1-2 : angle 1.57236 ( 9) link_ALPHA1-3 : bond 0.00799 ( 2) link_ALPHA1-3 : angle 1.16884 ( 6) link_ALPHA1-6 : bond 0.00284 ( 2) link_ALPHA1-6 : angle 1.81702 ( 6) link_BETA1-4 : bond 0.00333 ( 9) link_BETA1-4 : angle 1.54256 ( 27) link_NAG-ASN : bond 0.00122 ( 6) link_NAG-ASN : angle 1.48404 ( 18) *********************** 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 232 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 213 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8563 (mp0) cc_final: 0.8284 (mp0) REVERT: A 243 ASN cc_start: 0.6902 (t0) cc_final: 0.6567 (t0) REVERT: A 260 THR cc_start: 0.9372 (m) cc_final: 0.9024 (p) REVERT: A 319 TRP cc_start: 0.7755 (t60) cc_final: 0.7413 (t60) REVERT: D 294 TYR cc_start: 0.8737 (t80) cc_final: 0.8343 (t80) REVERT: E 178 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8675 (mt-10) REVERT: E 239 GLN cc_start: 0.8728 (tp40) cc_final: 0.8324 (tm-30) REVERT: E 258 ASN cc_start: 0.8741 (t0) cc_final: 0.8458 (t0) REVERT: I 102 LYS cc_start: 0.8683 (mmmt) cc_final: 0.8421 (tptm) REVERT: J 30 LYS cc_start: 0.9268 (ttmt) cc_final: 0.9026 (tttt) REVERT: J 73 ASP cc_start: 0.8859 (t70) cc_final: 0.8535 (t0) REVERT: K 10 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7517 (mm-30) REVERT: K 11 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8823 (tm) REVERT: K 80 TYR cc_start: 0.9216 (m-80) cc_final: 0.9012 (m-80) REVERT: K 101 LEU cc_start: 0.8535 (mp) cc_final: 0.8035 (tp) outliers start: 19 outliers final: 11 residues processed: 223 average time/residue: 1.2175 time to fit residues: 305.4564 Evaluate side-chains 218 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 206 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain K residue 11 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 78 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 203 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 144 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 56 HIS E 152 GLN L 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.090605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.061108 restraints weight = 90697.096| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 2.26 r_work: 0.2673 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2542 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18203 Z= 0.117 Angle : 0.531 11.558 24726 Z= 0.271 Chirality : 0.042 0.216 2821 Planarity : 0.004 0.109 2998 Dihedral : 9.610 164.002 3157 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.69 % Allowed : 15.67 % Favored : 83.64 % 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 aren not related in a simple way. whole: 0.75 (0.19), residues: 2103 helix: 2.93 (0.21), residues: 591 sheet: -0.47 (0.19), residues: 680 loop : -0.36 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG E 85 TYR 0.016 0.001 TYR C 299 PHE 0.011 0.001 PHE D 157 TRP 0.014 0.001 TRP E 252 HIS 0.003 0.001 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00268 (18172) covalent geometry : angle 0.52574 (24642) SS BOND : bond 0.00518 ( 9) SS BOND : angle 0.82727 ( 18) hydrogen bonds : bond 0.03256 ( 768) hydrogen bonds : angle 4.17141 ( 2538) link_ALPHA1-2 : bond 0.00278 ( 3) link_ALPHA1-2 : angle 1.62260 ( 9) link_ALPHA1-3 : bond 0.00741 ( 2) link_ALPHA1-3 : angle 1.19834 ( 6) link_ALPHA1-6 : bond 0.00197 ( 2) link_ALPHA1-6 : angle 1.94461 ( 6) link_BETA1-4 : bond 0.00326 ( 9) link_BETA1-4 : angle 1.52759 ( 27) link_NAG-ASN : bond 0.00078 ( 6) link_NAG-ASN : angle 1.45836 ( 18) ********************** 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 224 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 211 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASN cc_start: 0.6894 (t0) cc_final: 0.6555 (t0) REVERT: A 260 THR cc_start: 0.9384 (m) cc_final: 0.9030 (p) REVERT: A 319 TRP cc_start: 0.7727 (t60) cc_final: 0.7471 (t60) REVERT: D 294 TYR cc_start: 0.8701 (t80) cc_final: 0.8343 (t80) REVERT: E 178 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8680 (mt-10) REVERT: E 239 GLN cc_start: 0.8767 (tp40) cc_final: 0.8393 (tm-30) REVERT: E 258 ASN cc_start: 0.8787 (t0) cc_final: 0.8544 (t0) REVERT: I 102 LYS cc_start: 0.8673 (mmmt) cc_final: 0.8418 (tptm) REVERT: J 30 LYS cc_start: 0.9265 (ttmt) cc_final: 0.9027 (tttt) REVERT: J 73 ASP cc_start: 0.8854 (t70) cc_final: 0.8560 (t0) REVERT: K 10 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7488 (mm-30) REVERT: K 11 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8830 (tm) REVERT: K 101 LEU cc_start: 0.8589 (mp) cc_final: 0.8078 (tp) outliers start: 13 outliers final: 11 residues processed: 219 average time/residue: 1.1935 time to fit residues: 292.8772 Evaluate side-chains 215 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 203 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain K residue 11 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 159 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 chunk 100 optimal weight: 0.0020 chunk 22 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 56 HIS E 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.090575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.061118 restraints weight = 90608.518| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.26 r_work: 0.2668 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2538 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18203 Z= 0.131 Angle : 0.537 9.156 24726 Z= 0.274 Chirality : 0.042 0.222 2821 Planarity : 0.005 0.109 2998 Dihedral : 9.390 166.684 3157 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.74 % Allowed : 15.99 % Favored : 83.27 % 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 aren not related in a simple way. whole: 0.78 (0.19), residues: 2103 helix: 2.93 (0.21), residues: 593 sheet: -0.43 (0.19), residues: 682 loop : -0.37 (0.23), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG E 85 TYR 0.015 0.001 TYR C 299 PHE 0.012 0.001 PHE D 157 TRP 0.019 0.001 TRP E 252 HIS 0.004 0.001 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00302 (18172) covalent geometry : angle 0.53080 (24642) SS BOND : bond 0.00491 ( 9) SS BOND : angle 0.90720 ( 18) hydrogen bonds : bond 0.03300 ( 768) hydrogen bonds : angle 4.17514 ( 2538) link_ALPHA1-2 : bond 0.00270 ( 3) link_ALPHA1-2 : angle 1.64701 ( 9) link_ALPHA1-3 : bond 0.00722 ( 2) link_ALPHA1-3 : angle 1.18298 ( 6) link_ALPHA1-6 : bond 0.00190 ( 2) link_ALPHA1-6 : angle 1.97611 ( 6) link_BETA1-4 : bond 0.00330 ( 9) link_BETA1-4 : angle 1.55477 ( 27) link_NAG-ASN : bond 0.00096 ( 6) link_NAG-ASN : angle 1.50375 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11264.59 seconds wall clock time: 190 minutes 46.03 seconds (11446.03 seconds total)