Starting phenix.real_space_refine on Tue Aug 26 09:35:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sid_40506/08_2025/8sid_40506_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sid_40506/08_2025/8sid_40506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sid_40506/08_2025/8sid_40506_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sid_40506/08_2025/8sid_40506_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sid_40506/08_2025/8sid_40506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sid_40506/08_2025/8sid_40506.map" } resolution = 2.71 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 8 5.49 5 S 98 5.16 5 C 11520 2.51 5 N 2837 2.21 5 O 3310 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 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34733 Number of models: 1 Model: "" Number of chains: 18 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: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {'ABU': 1, 'NAG': 1, 'ZWY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 142 Unusual residues: {'PTY': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Unusual residues: {'ABU': 1, 'NAG': 1, 'Q3G': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 175 Unusual residues: {'POV': 1, 'PTY': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 27 Time building chain proxies: 6.01, per 1000 atoms: 0.17 Number of scatterers: 34733 At special positions: 0 Unit cell: (133.675, 160.41, 100.524, 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 8 15.00 O 3310 8.00 N 2837 7.00 C 11520 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=2.04 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 153 " distance=2.04 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 165 " distance=2.05 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=2.04 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: 2.82 Conformation dependent library (CDL) restraints added in 867.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 47 helices and 32 sheets defined 32.1% alpha, 40.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 7 through 21 Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.564A pdb=" N ASP A 89 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 226 removed outlier: 3.545A 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 271 removed outlier: 3.884A pdb=" N ARG A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR A 271 " --> pdb=" O HIS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 306 Processing helix chain 'A' and resid 309 through 340 removed outlier: 4.142A pdb=" N ALA A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) removed outlier: 3.742A 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: 3.657A 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 removed outlier: 3.570A pdb=" N ILE B 228 " --> pdb=" O GLY B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 243 Processing helix chain 'B' and resid 244 through 247 Processing helix chain 'B' and resid 251 through 276 removed outlier: 3.667A pdb=" N ARG B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG B 274 " --> pdb=" O SER B 270 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N SER B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 311 Processing helix chain 'B' and resid 314 through 346 removed outlier: 3.981A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Proline residue: B 330 - end of helix removed outlier: 3.737A 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: 3.626A 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: 3.969A pdb=" N SER C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 3.521A 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 247 through 270 removed outlier: 3.553A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU C 270 " --> pdb=" O THR C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 305 Processing helix chain 'C' and resid 309 through 339 removed outlier: 3.538A 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: 3.574A pdb=" N LEU D 75 " --> pdb=" O ASP D 72 " (cutoff:3.500A) removed outlier: 3.974A 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: 3.670A 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: 3.794A pdb=" N ARG D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) removed outlier: 4.153A 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: 4.174A pdb=" N ILE D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 3.706A 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: 3.771A pdb=" N LYS E 105 " --> pdb=" O MET E 102 " (cutoff:3.500A) removed outlier: 3.842A 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 257 Processing helix chain 'E' and resid 261 through 287 removed outlier: 3.722A pdb=" N ARG E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU E 287 " --> pdb=" O ALA E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 324 removed outlier: 3.553A pdb=" N PHE E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER E 323 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 357 removed outlier: 3.694A pdb=" N ALA E 328 " --> pdb=" O GLN E 324 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 3.661A 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: 4.155A pdb=" N THR J 91 " --> pdb=" O SER J 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.692A 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: 4.744A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 43 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 130 through 132 removed outlier: 6.683A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 43 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.528A 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: 3.826A 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: 3.826A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP A 190 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 83 through 86 removed outlier: 4.096A pdb=" N LEU B 119 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 3.535A 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: 7.112A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 3.535A 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: 4.208A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.411A 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: 4.208A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N TYR B 210 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE B 202 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 212 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N SER B 200 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR B 214 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL B 198 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N HIS B 216 " --> pdb=" O GLN B 196 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLN B 196 " --> pdb=" O HIS B 216 " (cutoff:3.500A) removed outlier: 6.686A 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: 3.667A pdb=" N LEU C 83 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP C 56 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL C 50 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR C 58 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TYR C 62 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ILE C 44 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLN C 64 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ILE C 42 " --> pdb=" O GLN C 64 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ALA C 66 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N MET C 40 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ARG C 68 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N VAL C 38 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.667A pdb=" N LEU C 83 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP C 56 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL C 50 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR C 58 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TYR C 62 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ILE C 44 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLN C 64 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ILE C 42 " --> pdb=" O GLN C 64 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ALA C 66 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N MET C 40 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ARG C 68 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N VAL C 38 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N THR C 176 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 6.784A 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: 3.857A 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: 3.857A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLY C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL C 199 " --> pdb=" O GLY C 203 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N TYR C 205 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS C 197 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG C 207 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR C 195 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N SER C 209 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU C 193 " --> pdb=" O SER C 209 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER C 211 " --> pdb=" O TYR C 191 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR C 191 " --> pdb=" O SER C 211 " (cutoff:3.500A) removed outlier: 6.667A 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: 4.257A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU D 59 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL D 53 " --> pdb=" O GLU D 59 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR D 61 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N PHE D 65 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N VAL D 47 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ARG D 67 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE D 45 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N THR D 39 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N GLU D 170 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.039A 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: 6.633A pdb=" N GLU D 59 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL D 53 " --> pdb=" O GLU D 59 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR D 61 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N PHE D 65 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N VAL D 47 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ARG D 67 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 5.288A 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: 4.210A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.449A 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: 4.210A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.886A 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: 3.572A pdb=" N SER E 61 " --> pdb=" O ASP E 75 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR E 73 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL E 65 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLU E 71 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ARG E 144 " --> pdb=" O ALA E 121 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ALA E 121 " --> pdb=" O ARG E 144 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR E 146 " --> pdb=" O ALA E 119 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ALA E 119 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 6.997A 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: 4.622A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU E 52 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS E 184 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N MET E 57 " --> pdb=" O LYS E 184 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N SER E 186 " --> pdb=" O MET E 57 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 111 through 113 removed outlier: 3.518A pdb=" N PHE E 227 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.622A 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: 3.511A pdb=" N TYR I 86 " --> pdb=" O THR I 101 " (cutoff:3.500A) removed outlier: 6.432A 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: 3.511A pdb=" N TYR I 86 " --> pdb=" O THR I 101 " (cutoff:3.500A) removed outlier: 3.756A 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 Processing sheet with id=AC6, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AC7, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.071A pdb=" N GLU J 10 " --> pdb=" O THR J 115 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N MET J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ARG J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.071A pdb=" N GLU J 10 " --> pdb=" O THR J 115 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR J 107 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.616A pdb=" N THR L 101 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR L 86 " --> pdb=" O THR L 101 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.616A pdb=" N THR L 101 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR L 86 " --> pdb=" O THR L 101 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR L 96 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.578A pdb=" N VAL K 18 " --> pdb=" O LEU K 83 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.679A pdb=" N GLU K 10 " --> pdb=" O SER K 113 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR K 94 " --> pdb=" O THR K 112 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N MET K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.679A pdb=" N GLU K 10 " --> pdb=" O SER K 113 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR K 94 " --> pdb=" O THR K 112 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR K 107 " --> pdb=" O ARG K 98 " (cutoff:3.500A) 875 hydrogen bonds defined for protein. 2493 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: 8.46 Time building geometry restraints manager: 4.02 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: 22 1.21 - 1.42: 7601 1.42 - 1.62: 10421 1.62 - 1.83: 167 Bond restraints: 35162 Sorted by residual: bond pdb=" C29 POV D 401 " pdb="C210 POV D 401 " ideal model delta sigma weight residual 1.333 1.530 -0.197 2.00e-02 2.50e+03 9.71e+01 bond pdb=" O20 ZWY A 403 " pdb=" S21 ZWY A 403 " ideal model delta sigma weight residual 1.628 1.562 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" NE2 GLN A 148 " pdb="HE22 GLN A 148 " ideal model delta sigma weight residual 0.860 0.798 0.062 2.00e-02 2.50e+03 9.64e+00 bond pdb=" ND2 ASN E 347 " pdb="HD22 ASN E 347 " ideal model delta sigma weight residual 0.860 0.810 0.050 2.00e-02 2.50e+03 6.29e+00 bond pdb=" C5 PTY B 401 " pdb=" O14 PTY B 401 " ideal model delta sigma weight residual 1.409 1.455 -0.046 2.00e-02 2.50e+03 5.32e+00 ... (remaining 35157 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.31: 62927 6.31 - 12.63: 26 12.63 - 18.94: 2 18.94 - 25.26: 4 25.26 - 31.57: 4 Bond angle restraints: 62963 Sorted by residual: angle pdb=" CD GLN B 242 " pdb=" NE2 GLN B 242 " pdb="HE22 GLN B 242 " ideal model delta sigma weight residual 120.00 151.57 -31.57 3.00e+00 1.11e-01 1.11e+02 angle pdb="HE21 GLN B 242 " pdb=" NE2 GLN B 242 " pdb="HE22 GLN B 242 " ideal model delta sigma weight residual 120.00 89.88 30.12 3.00e+00 1.11e-01 1.01e+02 angle pdb=" CG ASN E 347 " pdb=" ND2 ASN E 347 " pdb="HD22 ASN E 347 " ideal model delta sigma weight residual 120.00 148.42 -28.42 3.00e+00 1.11e-01 8.98e+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 94.01 25.99 3.00e+00 1.11e-01 7.51e+01 angle pdb=" CD GLN B 242 " pdb=" NE2 GLN B 242 " pdb="HE21 GLN B 242 " ideal model delta sigma weight residual 120.00 95.65 24.35 3.00e+00 1.11e-01 6.59e+01 ... (remaining 62958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.00: 16541 33.00 - 66.00: 571 66.00 - 98.99: 67 98.99 - 131.99: 18 131.99 - 164.99: 3 Dihedral angle restraints: 17200 sinusoidal: 9512 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 -16.76 -69.24 1 1.00e+01 1.00e-02 6.20e+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 -156.17 -23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" C3 PTY B 402 " pdb=" O11 PTY B 402 " pdb=" P1 PTY B 402 " pdb=" O12 PTY B 402 " ideal model delta sinusoidal sigma weight residual 300.23 135.24 164.99 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 17197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2281 0.055 - 0.111: 463 0.111 - 0.166: 70 0.166 - 0.222: 3 0.222 - 0.277: 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 -2.55 0.28 2.00e-01 2.50e+01 1.92e+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 -2.52 0.25 2.00e-01 2.50e+01 1.56e+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 -2.51 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 2818 not shown) Planarity restraints: 5033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 ZWY A 403 " -0.184 2.00e-02 2.50e+03 1.53e-01 2.94e+02 pdb=" C13 ZWY A 403 " 0.228 2.00e-02 2.50e+03 pdb=" C14 ZWY A 403 " 0.095 2.00e-02 2.50e+03 pdb=" C15 ZWY A 403 " 0.012 2.00e-02 2.50e+03 pdb=" C19 ZWY A 403 " -0.151 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 148 " 0.062 2.00e-02 2.50e+03 9.66e-02 1.40e+02 pdb=" CD GLN A 148 " -0.026 2.00e-02 2.50e+03 pdb=" OE1 GLN A 148 " 0.004 2.00e-02 2.50e+03 pdb=" NE2 GLN A 148 " -0.162 2.00e-02 2.50e+03 pdb="HE21 GLN A 148 " -0.034 2.00e-02 2.50e+03 pdb="HE22 GLN A 148 " 0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 347 " 0.043 2.00e-02 2.50e+03 8.77e-02 1.15e+02 pdb=" CG ASN E 347 " 0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN E 347 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN E 347 " -0.153 2.00e-02 2.50e+03 pdb="HD21 ASN E 347 " -0.039 2.00e-02 2.50e+03 pdb="HD22 ASN E 347 " 0.139 2.00e-02 2.50e+03 ... (remaining 5030 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1424 2.16 - 2.77: 66554 2.77 - 3.38: 93810 3.38 - 3.99: 128955 3.99 - 4.60: 201027 Nonbonded interactions: 491770 Sorted by model distance: nonbonded pdb=" H GLY K 100 " pdb=" O ALA K 104 " model vdw 1.550 2.450 nonbonded pdb=" OE1 GLU C 155 " pdb="HH21 ARG C 207 " model vdw 1.554 2.450 nonbonded pdb=" OG1 THR D 99 " pdb=" HH TYR D 169 " model vdw 1.557 2.450 nonbonded pdb=" HH TYR I 36 " pdb=" O ALA J 104 " model vdw 1.578 2.450 nonbonded pdb="HE22 GLN L 6 " pdb=" O TYR L 86 " model vdw 1.579 2.450 ... (remaining 491765 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 402) selection = (chain 'C' and resid 7 through 402) } ncs_group { reference = (chain 'B' and (resid 10 through 347 or resid 402 through 403)) selection = (chain 'D' and (resid 10 through 347 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 C3 or name C3 \ 0 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or nam \ e C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or \ name C44 or name C5 or name C6 or name C8 or name N1 or name 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 ) \ ) or (resid 403 and (name C1 or name C11 or name 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 C24 or name C25 or name C26 or name \ C27 or name C28 or name C3 or name C30 or name C31 or name C32 or name C33 or na \ me C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 o \ r name C41 or name C42 or name C43 or name C44 or name C5 or name C6 or name C8 \ or name N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O \ 30 or name O4 or name O7 or name P1 )))) } 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: 0.000 Normalize map: mean=0, sd=1: 1.620 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: 0.130 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 31.270 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.197 18233 Z= 0.260 Angle : 0.746 12.669 24763 Z= 0.352 Chirality : 0.046 0.277 2821 Planarity : 0.005 0.153 3002 Dihedral : 16.848 164.988 7119 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % 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: -2.81 (0.16), residues: 2103 helix: -0.14 (0.20), residues: 573 sheet: -2.58 (0.17), residues: 680 loop : -2.31 (0.18), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 50 TYR 0.023 0.002 TYR D 294 PHE 0.019 0.002 PHE E 77 TRP 0.013 0.001 TRP E 134 HIS 0.007 0.002 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00566 (18202) covalent geometry : angle 0.73823 (24679) SS BOND : bond 0.00725 ( 9) SS BOND : angle 1.70843 ( 18) hydrogen bonds : bond 0.11522 ( 770) hydrogen bonds : angle 6.13684 ( 2493) link_ALPHA1-2 : bond 0.00277 ( 3) link_ALPHA1-2 : angle 2.26364 ( 9) link_ALPHA1-3 : bond 0.00344 ( 2) link_ALPHA1-3 : angle 2.21276 ( 6) link_ALPHA1-6 : bond 0.00067 ( 2) link_ALPHA1-6 : angle 2.38119 ( 6) link_BETA1-4 : bond 0.00297 ( 9) link_BETA1-4 : angle 1.95935 ( 27) link_NAG-ASN : bond 0.00304 ( 6) link_NAG-ASN : angle 2.15695 ( 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 384 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLN cc_start: 0.8057 (tp40) cc_final: 0.7754 (tm-30) REVERT: B 241 SER cc_start: 0.9136 (t) cc_final: 0.8873 (p) REVERT: C 171 ASP cc_start: 0.7459 (m-30) cc_final: 0.7149 (t0) REVERT: C 265 ASN cc_start: 0.6954 (t0) cc_final: 0.6698 (t0) REVERT: J 89 GLU cc_start: 0.7875 (pp20) cc_final: 0.7376 (pp20) REVERT: L 9 LYS cc_start: 0.8231 (tptt) cc_final: 0.7791 (tptp) REVERT: L 56 THR cc_start: 0.8766 (m) cc_final: 0.8464 (p) outliers start: 0 outliers final: 0 residues processed: 384 average time/residue: 1.2534 time to fit residues: 535.8357 Evaluate side-chains 209 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 HIS I 6 GLN I 53 ASN J 5 GLN J 82 GLN L 38 GLN K 39 GLN K 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.090568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.063845 restraints weight = 98266.910| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.34 r_work: 0.2804 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18233 Z= 0.167 Angle : 0.617 7.579 24763 Z= 0.311 Chirality : 0.044 0.334 2821 Planarity : 0.005 0.046 3002 Dihedral : 13.846 176.876 3179 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.86 % Allowed : 11.84 % Favored : 86.30 % 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: -1.36 (0.18), residues: 2103 helix: 1.47 (0.21), residues: 579 sheet: -1.92 (0.18), residues: 695 loop : -1.59 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 185 TYR 0.014 0.001 TYR A 299 PHE 0.012 0.001 PHE A 98 TRP 0.008 0.001 TRP A 67 HIS 0.008 0.001 HIS E 163 Details of bonding type rmsd covalent geometry : bond 0.00381 (18202) covalent geometry : angle 0.60729 (24679) SS BOND : bond 0.00529 ( 9) SS BOND : angle 1.08431 ( 18) hydrogen bonds : bond 0.04017 ( 770) hydrogen bonds : angle 4.84714 ( 2493) link_ALPHA1-2 : bond 0.00381 ( 3) link_ALPHA1-2 : angle 1.81127 ( 9) link_ALPHA1-3 : bond 0.01035 ( 2) link_ALPHA1-3 : angle 1.38374 ( 6) link_ALPHA1-6 : bond 0.00249 ( 2) link_ALPHA1-6 : angle 2.43429 ( 6) link_BETA1-4 : bond 0.00252 ( 9) link_BETA1-4 : angle 2.47274 ( 27) link_NAG-ASN : bond 0.00212 ( 6) link_NAG-ASN : angle 1.66524 ( 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 249 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 214 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLN cc_start: 0.8307 (tp40) cc_final: 0.7844 (tm-30) REVERT: A 227 MET cc_start: 0.8857 (mmm) cc_final: 0.8371 (ttt) REVERT: A 294 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.7749 (mpt) REVERT: B 241 SER cc_start: 0.9190 (t) cc_final: 0.8961 (p) REVERT: C 171 ASP cc_start: 0.7529 (m-30) cc_final: 0.7183 (t0) REVERT: C 265 ASN cc_start: 0.7210 (t0) cc_final: 0.7008 (t0) REVERT: C 286 MET cc_start: 0.8554 (mtp) cc_final: 0.8324 (mtp) REVERT: C 312 ARG cc_start: 0.6742 (ttm-80) cc_final: 0.6504 (ttm-80) REVERT: D 112 MET cc_start: 0.8624 (tpt) cc_final: 0.8421 (tpt) REVERT: D 131 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8386 (ptp) REVERT: D 294 TYR cc_start: 0.8844 (t80) cc_final: 0.8599 (t80) REVERT: E 70 MET cc_start: 0.8835 (mmm) cc_final: 0.8590 (mmt) REVERT: E 239 GLN cc_start: 0.8986 (tt0) cc_final: 0.8682 (tt0) REVERT: E 276 MET cc_start: 0.9371 (tpt) cc_final: 0.9116 (tpt) REVERT: J 73 ASP cc_start: 0.8236 (t70) cc_final: 0.7864 (t70) REVERT: J 107 TYR cc_start: 0.8861 (m-80) cc_final: 0.8607 (m-80) REVERT: L 9 LYS cc_start: 0.8345 (tptt) cc_final: 0.7730 (tptp) REVERT: L 13 MET cc_start: 0.8126 (mtt) cc_final: 0.7915 (mtp) REVERT: L 39 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8268 (mmtm) REVERT: L 56 THR cc_start: 0.8861 (m) cc_final: 0.8514 (p) REVERT: K 73 ASP cc_start: 0.8304 (t70) cc_final: 0.7859 (t0) outliers start: 35 outliers final: 13 residues processed: 233 average time/residue: 1.1196 time to fit residues: 294.6814 Evaluate side-chains 210 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 194 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain K residue 55 ASN Chi-restraints excluded: chain K residue 77 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 93 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 59 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 201 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.089395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.062700 restraints weight = 98110.194| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.32 r_work: 0.2773 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 18233 Z= 0.199 Angle : 0.586 9.599 24763 Z= 0.300 Chirality : 0.043 0.204 2821 Planarity : 0.004 0.081 3002 Dihedral : 11.836 176.595 3179 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.12 % Allowed : 13.17 % Favored : 84.71 % 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: -0.52 (0.18), residues: 2103 helix: 2.10 (0.21), residues: 586 sheet: -1.44 (0.18), residues: 713 loop : -1.03 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 185 TYR 0.015 0.001 TYR A 299 PHE 0.014 0.001 PHE A 306 TRP 0.008 0.001 TRP E 351 HIS 0.007 0.002 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00457 (18202) covalent geometry : angle 0.57813 (24679) SS BOND : bond 0.00530 ( 9) SS BOND : angle 1.21582 ( 18) hydrogen bonds : bond 0.03932 ( 770) hydrogen bonds : angle 4.61019 ( 2493) link_ALPHA1-2 : bond 0.00164 ( 3) link_ALPHA1-2 : angle 1.91896 ( 9) link_ALPHA1-3 : bond 0.00374 ( 2) link_ALPHA1-3 : angle 1.62138 ( 6) link_ALPHA1-6 : bond 0.00044 ( 2) link_ALPHA1-6 : angle 2.00865 ( 6) link_BETA1-4 : bond 0.00362 ( 9) link_BETA1-4 : angle 2.00819 ( 27) link_NAG-ASN : bond 0.00174 ( 6) link_NAG-ASN : angle 1.77330 ( 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 246 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 206 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8308 (tt0) REVERT: A 224 GLN cc_start: 0.8342 (tp40) cc_final: 0.7939 (tm-30) REVERT: A 227 MET cc_start: 0.8763 (mmm) cc_final: 0.8290 (ttt) REVERT: A 244 TYR cc_start: 0.7913 (p90) cc_final: 0.7445 (p90) REVERT: A 294 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.7721 (mpt) REVERT: B 63 ASP cc_start: 0.8706 (t0) cc_final: 0.8455 (t0) REVERT: C 49 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.7100 (mtm) REVERT: C 55 MET cc_start: 0.9331 (mmt) cc_final: 0.9091 (mmt) REVERT: C 171 ASP cc_start: 0.7567 (m-30) cc_final: 0.7145 (t0) REVERT: C 265 ASN cc_start: 0.7257 (t0) cc_final: 0.7030 (t0) REVERT: C 312 ARG cc_start: 0.6782 (ttm-80) cc_final: 0.6523 (ttm-80) REVERT: D 266 MET cc_start: 0.8681 (mmm) cc_final: 0.8440 (tpp) REVERT: D 294 TYR cc_start: 0.8923 (t80) cc_final: 0.8655 (t80) REVERT: E 70 MET cc_start: 0.8947 (mmm) cc_final: 0.8628 (mmt) REVERT: E 239 GLN cc_start: 0.8892 (tt0) cc_final: 0.8551 (tt0) REVERT: E 276 MET cc_start: 0.9349 (tpt) cc_final: 0.9135 (tpt) REVERT: J 13 LYS cc_start: 0.7061 (mmpt) cc_final: 0.6790 (mmpt) REVERT: J 73 ASP cc_start: 0.8302 (t70) cc_final: 0.7869 (t0) REVERT: J 107 TYR cc_start: 0.8900 (m-80) cc_final: 0.8624 (m-80) REVERT: L 9 LYS cc_start: 0.8386 (tptt) cc_final: 0.7763 (tptp) REVERT: L 56 THR cc_start: 0.8985 (m) cc_final: 0.8676 (p) REVERT: K 73 ASP cc_start: 0.8278 (t70) cc_final: 0.7759 (t0) outliers start: 40 outliers final: 17 residues processed: 227 average time/residue: 1.2070 time to fit residues: 309.4907 Evaluate side-chains 212 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 55 ASN Chi-restraints excluded: chain K residue 77 ASN Chi-restraints excluded: chain K residue 85 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 128 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 161 optimal weight: 8.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 56 HIS ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.088325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.060942 restraints weight = 97338.278| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 2.34 r_work: 0.2725 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 18233 Z= 0.216 Angle : 0.581 6.189 24763 Z= 0.298 Chirality : 0.043 0.237 2821 Planarity : 0.004 0.048 3002 Dihedral : 10.752 169.220 3179 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.50 % Allowed : 13.81 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.19), residues: 2103 helix: 2.41 (0.21), residues: 589 sheet: -0.99 (0.19), residues: 670 loop : -0.94 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 185 TYR 0.016 0.002 TYR E 172 PHE 0.030 0.001 PHE A 306 TRP 0.008 0.001 TRP J 103 HIS 0.009 0.002 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00491 (18202) covalent geometry : angle 0.57356 (24679) SS BOND : bond 0.00542 ( 9) SS BOND : angle 1.32311 ( 18) hydrogen bonds : bond 0.03777 ( 770) hydrogen bonds : angle 4.54109 ( 2493) link_ALPHA1-2 : bond 0.00252 ( 3) link_ALPHA1-2 : angle 1.89981 ( 9) link_ALPHA1-3 : bond 0.00696 ( 2) link_ALPHA1-3 : angle 1.32375 ( 6) link_ALPHA1-6 : bond 0.00228 ( 2) link_ALPHA1-6 : angle 2.05329 ( 6) link_BETA1-4 : bond 0.00251 ( 9) link_BETA1-4 : angle 1.91516 ( 27) link_NAG-ASN : bond 0.00341 ( 6) link_NAG-ASN : angle 1.66197 ( 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 253 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 206 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLN cc_start: 0.8479 (tp40) cc_final: 0.7989 (tm-30) REVERT: A 227 MET cc_start: 0.8744 (mmm) cc_final: 0.8238 (ttt) REVERT: A 294 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.7792 (mpt) REVERT: B 21 ARG cc_start: 0.8555 (ttm110) cc_final: 0.8185 (ttp80) REVERT: B 63 ASP cc_start: 0.8779 (t70) cc_final: 0.8539 (t0) REVERT: C 49 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.7268 (mtm) REVERT: C 171 ASP cc_start: 0.7491 (m-30) cc_final: 0.7087 (t0) REVERT: C 312 ARG cc_start: 0.6820 (ttm-80) cc_final: 0.6513 (ttm-80) REVERT: D 266 MET cc_start: 0.8805 (mmm) cc_final: 0.8524 (tpp) REVERT: D 294 TYR cc_start: 0.8872 (t80) cc_final: 0.8605 (t80) REVERT: E 70 MET cc_start: 0.9043 (mmm) cc_final: 0.8572 (mmt) REVERT: E 189 GLU cc_start: 0.8743 (pt0) cc_final: 0.8420 (pt0) REVERT: E 239 GLN cc_start: 0.8982 (tt0) cc_final: 0.8589 (tt0) REVERT: J 73 ASP cc_start: 0.8416 (t70) cc_final: 0.7929 (t0) REVERT: L 9 LYS cc_start: 0.8423 (tptt) cc_final: 0.7804 (tptp) REVERT: L 45 LYS cc_start: 0.8909 (mmmm) cc_final: 0.8576 (mppt) REVERT: L 56 THR cc_start: 0.9032 (m) cc_final: 0.8714 (p) REVERT: K 3 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7758 (tm-30) REVERT: K 73 ASP cc_start: 0.8266 (t70) cc_final: 0.7779 (t0) outliers start: 47 outliers final: 24 residues processed: 233 average time/residue: 1.1303 time to fit residues: 296.1797 Evaluate side-chains 216 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 55 ASN Chi-restraints excluded: chain K residue 77 ASN Chi-restraints excluded: chain K residue 85 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 114 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 160 optimal weight: 8.9990 chunk 174 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.088880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.061505 restraints weight = 97142.037| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.34 r_work: 0.2738 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18233 Z= 0.149 Angle : 0.538 7.291 24763 Z= 0.274 Chirality : 0.042 0.214 2821 Planarity : 0.004 0.072 3002 Dihedral : 10.290 168.134 3179 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.70 % Allowed : 15.03 % 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: 0.15 (0.19), residues: 2103 helix: 2.66 (0.21), residues: 588 sheet: -0.93 (0.19), residues: 669 loop : -0.80 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 249 TYR 0.014 0.001 TYR E 314 PHE 0.009 0.001 PHE E 113 TRP 0.007 0.001 TRP A 67 HIS 0.005 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00339 (18202) covalent geometry : angle 0.53122 (24679) SS BOND : bond 0.00521 ( 9) SS BOND : angle 1.04905 ( 18) hydrogen bonds : bond 0.03570 ( 770) hydrogen bonds : angle 4.39915 ( 2493) link_ALPHA1-2 : bond 0.00077 ( 3) link_ALPHA1-2 : angle 1.73015 ( 9) link_ALPHA1-3 : bond 0.00780 ( 2) link_ALPHA1-3 : angle 1.29342 ( 6) link_ALPHA1-6 : bond 0.00096 ( 2) link_ALPHA1-6 : angle 1.93390 ( 6) link_BETA1-4 : bond 0.00250 ( 9) link_BETA1-4 : angle 1.73139 ( 27) link_NAG-ASN : bond 0.00184 ( 6) link_NAG-ASN : angle 1.75320 ( 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 229 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 197 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLN cc_start: 0.8420 (tp40) cc_final: 0.7949 (tm-30) REVERT: A 227 MET cc_start: 0.8720 (mmm) cc_final: 0.8228 (ttt) REVERT: A 294 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.7801 (mpt) REVERT: B 21 ARG cc_start: 0.8607 (ttm110) cc_final: 0.8223 (ttp80) REVERT: B 63 ASP cc_start: 0.8766 (t70) cc_final: 0.8522 (t0) REVERT: B 279 LYS cc_start: 0.8355 (mttt) cc_final: 0.7704 (mmpt) REVERT: C 49 MET cc_start: 0.7420 (mtp) cc_final: 0.7203 (mtm) REVERT: C 171 ASP cc_start: 0.7458 (m-30) cc_final: 0.7077 (t0) REVERT: D 266 MET cc_start: 0.8820 (mmm) cc_final: 0.8594 (tpp) REVERT: D 294 TYR cc_start: 0.8856 (t80) cc_final: 0.8622 (t80) REVERT: E 70 MET cc_start: 0.8998 (mmm) cc_final: 0.8593 (mmt) REVERT: E 189 GLU cc_start: 0.8783 (pt0) cc_final: 0.8466 (pt0) REVERT: E 239 GLN cc_start: 0.8915 (tt0) cc_final: 0.8440 (tt0) REVERT: J 13 LYS cc_start: 0.7199 (mmpt) cc_final: 0.6994 (mmpt) REVERT: J 46 GLU cc_start: 0.8677 (tt0) cc_final: 0.8397 (mt-10) REVERT: J 73 ASP cc_start: 0.8473 (t70) cc_final: 0.8009 (t0) REVERT: L 9 LYS cc_start: 0.8384 (tptt) cc_final: 0.7775 (tptp) REVERT: L 45 LYS cc_start: 0.8914 (mmmm) cc_final: 0.8575 (mppt) REVERT: L 56 THR cc_start: 0.9054 (m) cc_final: 0.8755 (p) REVERT: K 73 ASP cc_start: 0.8234 (t70) cc_final: 0.7743 (t0) REVERT: K 96 CYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7146 (p) outliers start: 32 outliers final: 18 residues processed: 215 average time/residue: 1.1686 time to fit residues: 283.9410 Evaluate side-chains 206 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain K residue 77 ASN Chi-restraints excluded: chain K residue 89 GLU Chi-restraints excluded: chain K residue 96 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 100 optimal weight: 0.0770 chunk 133 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 HIS ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.088376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.061036 restraints weight = 97019.854| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.34 r_work: 0.2729 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18233 Z= 0.184 Angle : 0.544 6.637 24763 Z= 0.278 Chirality : 0.042 0.219 2821 Planarity : 0.004 0.072 3002 Dihedral : 10.063 165.944 3179 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.65 % Allowed : 15.24 % Favored : 83.11 % 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: 2.71 (0.21), residues: 588 sheet: -0.83 (0.19), residues: 669 loop : -0.77 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 312 TYR 0.014 0.001 TYR E 314 PHE 0.011 0.001 PHE E 113 TRP 0.008 0.001 TRP A 168 HIS 0.006 0.001 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00419 (18202) covalent geometry : angle 0.53624 (24679) SS BOND : bond 0.00661 ( 9) SS BOND : angle 1.12310 ( 18) hydrogen bonds : bond 0.03594 ( 770) hydrogen bonds : angle 4.40113 ( 2493) link_ALPHA1-2 : bond 0.00236 ( 3) link_ALPHA1-2 : angle 1.85753 ( 9) link_ALPHA1-3 : bond 0.00891 ( 2) link_ALPHA1-3 : angle 1.36041 ( 6) link_ALPHA1-6 : bond 0.00081 ( 2) link_ALPHA1-6 : angle 2.03901 ( 6) link_BETA1-4 : bond 0.00298 ( 9) link_BETA1-4 : angle 1.79053 ( 27) link_NAG-ASN : bond 0.00190 ( 6) link_NAG-ASN : angle 1.72703 ( 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 220 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLN cc_start: 0.8434 (tp40) cc_final: 0.7955 (tm-30) REVERT: A 227 MET cc_start: 0.8734 (mmm) cc_final: 0.8250 (ttt) REVERT: A 294 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.7812 (mpt) REVERT: B 21 ARG cc_start: 0.8609 (ttm110) cc_final: 0.8250 (ttp80) REVERT: B 63 ASP cc_start: 0.8780 (t70) cc_final: 0.8530 (t0) REVERT: B 279 LYS cc_start: 0.8367 (mttt) cc_final: 0.7681 (mmpt) REVERT: C 171 ASP cc_start: 0.7465 (m-30) cc_final: 0.7084 (t0) REVERT: D 266 MET cc_start: 0.8894 (mmm) cc_final: 0.8499 (mmm) REVERT: D 294 TYR cc_start: 0.8847 (t80) cc_final: 0.8577 (t80) REVERT: E 70 MET cc_start: 0.9019 (mmm) cc_final: 0.8648 (mmt) REVERT: E 189 GLU cc_start: 0.8784 (pt0) cc_final: 0.8472 (pt0) REVERT: E 239 GLN cc_start: 0.9002 (tt0) cc_final: 0.8595 (tt0) REVERT: J 46 GLU cc_start: 0.8687 (tt0) cc_final: 0.8407 (mt-10) REVERT: J 73 ASP cc_start: 0.8476 (t70) cc_final: 0.7993 (t0) REVERT: L 9 LYS cc_start: 0.8411 (tptt) cc_final: 0.7797 (tptp) REVERT: L 45 LYS cc_start: 0.8901 (mmmm) cc_final: 0.8557 (mppt) REVERT: L 56 THR cc_start: 0.9059 (m) cc_final: 0.8769 (p) REVERT: K 73 ASP cc_start: 0.8237 (t70) cc_final: 0.7746 (t0) REVERT: K 96 CYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7249 (p) outliers start: 31 outliers final: 21 residues processed: 206 average time/residue: 1.3763 time to fit residues: 319.5054 Evaluate side-chains 209 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain K residue 10 GLU Chi-restraints excluded: chain K residue 55 ASN Chi-restraints excluded: chain K residue 77 ASN Chi-restraints excluded: chain K residue 96 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 158 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 134 optimal weight: 0.3980 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 HIS K 3 GLN K 5 GLN K 110 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.087987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.060513 restraints weight = 96591.451| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.33 r_work: 0.2725 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18233 Z= 0.187 Angle : 0.553 6.815 24763 Z= 0.282 Chirality : 0.042 0.224 2821 Planarity : 0.004 0.073 3002 Dihedral : 9.830 162.296 3179 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.96 % Allowed : 15.35 % Favored : 82.69 % 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: 0.39 (0.19), residues: 2103 helix: 2.77 (0.21), residues: 588 sheet: -0.70 (0.20), residues: 645 loop : -0.68 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 312 TYR 0.014 0.001 TYR E 172 PHE 0.011 0.001 PHE E 113 TRP 0.010 0.001 TRP C 237 HIS 0.009 0.001 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00428 (18202) covalent geometry : angle 0.54589 (24679) SS BOND : bond 0.00576 ( 9) SS BOND : angle 1.20915 ( 18) hydrogen bonds : bond 0.03601 ( 770) hydrogen bonds : angle 4.37742 ( 2493) link_ALPHA1-2 : bond 0.00109 ( 3) link_ALPHA1-2 : angle 1.79473 ( 9) link_ALPHA1-3 : bond 0.00734 ( 2) link_ALPHA1-3 : angle 1.15550 ( 6) link_ALPHA1-6 : bond 0.00111 ( 2) link_ALPHA1-6 : angle 2.05008 ( 6) link_BETA1-4 : bond 0.00262 ( 9) link_BETA1-4 : angle 1.79420 ( 27) link_NAG-ASN : bond 0.00169 ( 6) link_NAG-ASN : angle 1.72811 ( 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 231 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 194 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLN cc_start: 0.8441 (tp40) cc_final: 0.7947 (tm-30) REVERT: A 227 MET cc_start: 0.8729 (mmm) cc_final: 0.8231 (ttt) REVERT: A 294 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.7810 (mpt) REVERT: B 21 ARG cc_start: 0.8606 (ttm110) cc_final: 0.8222 (ttp80) REVERT: B 63 ASP cc_start: 0.8813 (t70) cc_final: 0.8547 (t0) REVERT: B 232 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8240 (mp) REVERT: B 279 LYS cc_start: 0.8378 (mttt) cc_final: 0.7673 (mmpt) REVERT: D 63 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.8059 (t70) REVERT: D 266 MET cc_start: 0.8913 (mmm) cc_final: 0.8652 (tpp) REVERT: D 294 TYR cc_start: 0.8821 (t80) cc_final: 0.8600 (t80) REVERT: E 70 MET cc_start: 0.9015 (mmm) cc_final: 0.8624 (mmt) REVERT: E 189 GLU cc_start: 0.8805 (pt0) cc_final: 0.8489 (pt0) REVERT: E 239 GLN cc_start: 0.9015 (tt0) cc_final: 0.8594 (tt0) REVERT: J 46 GLU cc_start: 0.8693 (tt0) cc_final: 0.8423 (mt-10) REVERT: J 73 ASP cc_start: 0.8517 (t70) cc_final: 0.8029 (t0) REVERT: L 9 LYS cc_start: 0.8384 (tptt) cc_final: 0.7781 (tptp) REVERT: L 45 LYS cc_start: 0.8878 (mmmm) cc_final: 0.8508 (mppt) REVERT: L 56 THR cc_start: 0.9062 (m) cc_final: 0.8786 (p) REVERT: K 5 GLN cc_start: 0.8782 (tp-100) cc_final: 0.8428 (mp10) REVERT: K 73 ASP cc_start: 0.8104 (t70) cc_final: 0.7619 (t0) REVERT: K 96 CYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7299 (p) outliers start: 37 outliers final: 24 residues processed: 217 average time/residue: 1.3138 time to fit residues: 322.4738 Evaluate side-chains 218 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain K residue 55 ASN Chi-restraints excluded: chain K residue 77 ASN Chi-restraints excluded: chain K residue 96 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 46 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 170 optimal weight: 0.0020 chunk 27 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 chunk 187 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN B 56 HIS K 110 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.089241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.061895 restraints weight = 96748.867| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.36 r_work: 0.2746 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.206 18233 Z= 0.115 Angle : 0.631 39.337 24763 Z= 0.294 Chirality : 0.045 0.868 2821 Planarity : 0.004 0.062 3002 Dihedral : 9.516 161.400 3179 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.33 % Allowed : 16.25 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.19), residues: 2103 helix: 2.96 (0.21), residues: 584 sheet: -0.66 (0.20), residues: 640 loop : -0.63 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 312 TYR 0.016 0.001 TYR E 314 PHE 0.009 0.001 PHE E 77 TRP 0.011 0.001 TRP C 237 HIS 0.003 0.001 HIS D 110 Details of bonding type rmsd covalent geometry : bond 0.00284 (18202) covalent geometry : angle 0.62680 (24679) SS BOND : bond 0.00443 ( 9) SS BOND : angle 0.81557 ( 18) hydrogen bonds : bond 0.03296 ( 770) hydrogen bonds : angle 4.20973 ( 2493) link_ALPHA1-2 : bond 0.00237 ( 3) link_ALPHA1-2 : angle 1.65606 ( 9) link_ALPHA1-3 : bond 0.00891 ( 2) link_ALPHA1-3 : angle 1.16226 ( 6) link_ALPHA1-6 : bond 0.00220 ( 2) link_ALPHA1-6 : angle 1.84614 ( 6) link_BETA1-4 : bond 0.00292 ( 9) link_BETA1-4 : angle 1.60281 ( 27) link_NAG-ASN : bond 0.00086 ( 6) link_NAG-ASN : angle 1.50347 ( 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 218 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLN cc_start: 0.8429 (tp40) cc_final: 0.7953 (tm-30) REVERT: A 227 MET cc_start: 0.8717 (mmm) cc_final: 0.8218 (ttt) REVERT: A 294 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.7791 (mpt) REVERT: B 63 ASP cc_start: 0.8808 (t70) cc_final: 0.8553 (t0) REVERT: B 232 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8284 (mp) REVERT: B 279 LYS cc_start: 0.8348 (mttt) cc_final: 0.7788 (mptp) REVERT: C 138 MET cc_start: 0.9345 (mtt) cc_final: 0.8969 (mtt) REVERT: C 329 SER cc_start: 0.8543 (t) cc_final: 0.8336 (p) REVERT: D 63 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.8031 (t0) REVERT: D 266 MET cc_start: 0.8891 (mmm) cc_final: 0.8633 (tpp) REVERT: E 70 MET cc_start: 0.9021 (mmm) cc_final: 0.8636 (mmt) REVERT: E 189 GLU cc_start: 0.8777 (pt0) cc_final: 0.8454 (pt0) REVERT: E 239 GLN cc_start: 0.9025 (tt0) cc_final: 0.8622 (tt0) REVERT: E 276 MET cc_start: 0.9455 (tpt) cc_final: 0.9173 (tpt) REVERT: J 46 GLU cc_start: 0.8692 (tt0) cc_final: 0.8440 (mt-10) REVERT: J 73 ASP cc_start: 0.8535 (t70) cc_final: 0.8033 (t0) REVERT: L 9 LYS cc_start: 0.8278 (tptt) cc_final: 0.7677 (tptp) REVERT: L 45 LYS cc_start: 0.8858 (mmmm) cc_final: 0.8493 (mppt) REVERT: L 56 THR cc_start: 0.9027 (m) cc_final: 0.8755 (p) REVERT: K 5 GLN cc_start: 0.8635 (tp-100) cc_final: 0.8386 (mp10) REVERT: K 73 ASP cc_start: 0.8112 (t70) cc_final: 0.7654 (t0) REVERT: K 96 CYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7202 (p) outliers start: 25 outliers final: 16 residues processed: 207 average time/residue: 1.3974 time to fit residues: 327.5000 Evaluate side-chains 208 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain K residue 55 ASN Chi-restraints excluded: chain K residue 77 ASN Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 96 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 60 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 HIS K 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.087818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.060375 restraints weight = 96949.010| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.35 r_work: 0.2716 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 18233 Z= 0.217 Angle : 0.571 8.287 24763 Z= 0.291 Chirality : 0.043 0.220 2821 Planarity : 0.004 0.058 3002 Dihedral : 9.668 160.269 3179 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.43 % Allowed : 16.30 % Favored : 82.26 % 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: 0.50 (0.19), residues: 2103 helix: 2.83 (0.21), residues: 588 sheet: -0.60 (0.20), residues: 636 loop : -0.62 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 312 TYR 0.015 0.001 TYR A 299 PHE 0.013 0.001 PHE E 113 TRP 0.012 0.001 TRP C 237 HIS 0.008 0.001 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00500 (18202) covalent geometry : angle 0.56242 (24679) SS BOND : bond 0.00578 ( 9) SS BOND : angle 1.35846 ( 18) hydrogen bonds : bond 0.03619 ( 770) hydrogen bonds : angle 4.37416 ( 2493) link_ALPHA1-2 : bond 0.00187 ( 3) link_ALPHA1-2 : angle 1.96296 ( 9) link_ALPHA1-3 : bond 0.00695 ( 2) link_ALPHA1-3 : angle 1.26122 ( 6) link_ALPHA1-6 : bond 0.00268 ( 2) link_ALPHA1-6 : angle 2.18529 ( 6) link_BETA1-4 : bond 0.00297 ( 9) link_BETA1-4 : angle 1.87667 ( 27) link_NAG-ASN : bond 0.00252 ( 6) link_NAG-ASN : angle 1.84072 ( 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 216 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLN cc_start: 0.8470 (tp40) cc_final: 0.7984 (tm-30) REVERT: A 227 MET cc_start: 0.8708 (mmm) cc_final: 0.8252 (ttt) REVERT: A 294 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.7867 (mpt) REVERT: B 63 ASP cc_start: 0.8800 (t70) cc_final: 0.8552 (t0) REVERT: B 232 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8304 (mp) REVERT: B 279 LYS cc_start: 0.8476 (mttt) cc_final: 0.7734 (mmpt) REVERT: D 63 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.8117 (t70) REVERT: D 266 MET cc_start: 0.8922 (mmm) cc_final: 0.8716 (tpp) REVERT: E 70 MET cc_start: 0.9042 (mmm) cc_final: 0.8622 (mmt) REVERT: E 189 GLU cc_start: 0.8775 (pt0) cc_final: 0.8468 (pt0) REVERT: E 239 GLN cc_start: 0.9029 (tt0) cc_final: 0.8624 (tt0) REVERT: J 46 GLU cc_start: 0.8722 (tt0) cc_final: 0.8467 (mt-10) REVERT: J 73 ASP cc_start: 0.8595 (t70) cc_final: 0.8117 (t0) REVERT: L 9 LYS cc_start: 0.8354 (tptt) cc_final: 0.7749 (tptp) REVERT: L 45 LYS cc_start: 0.8879 (mmmm) cc_final: 0.8531 (mppt) REVERT: L 56 THR cc_start: 0.9093 (m) cc_final: 0.8813 (p) REVERT: K 3 GLN cc_start: 0.8490 (tp-100) cc_final: 0.7730 (tm-30) REVERT: K 73 ASP cc_start: 0.8052 (t70) cc_final: 0.7567 (t0) REVERT: K 96 CYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7359 (p) outliers start: 27 outliers final: 18 residues processed: 205 average time/residue: 1.2994 time to fit residues: 301.8339 Evaluate side-chains 209 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain K residue 55 ASN Chi-restraints excluded: chain K residue 77 ASN Chi-restraints excluded: chain K residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 92 optimal weight: 0.0970 chunk 1 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.087940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.060605 restraints weight = 97087.431| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.33 r_work: 0.2714 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.5012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18233 Z= 0.189 Angle : 0.557 6.507 24763 Z= 0.284 Chirality : 0.043 0.223 2821 Planarity : 0.004 0.055 3002 Dihedral : 9.619 158.044 3179 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.43 % Allowed : 16.36 % Favored : 82.21 % 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: 2.89 (0.21), residues: 586 sheet: -0.57 (0.20), residues: 636 loop : -0.63 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 312 TYR 0.014 0.001 TYR A 299 PHE 0.010 0.001 PHE E 113 TRP 0.015 0.001 TRP C 237 HIS 0.007 0.001 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00433 (18202) covalent geometry : angle 0.54990 (24679) SS BOND : bond 0.00539 ( 9) SS BOND : angle 1.16614 ( 18) hydrogen bonds : bond 0.03588 ( 770) hydrogen bonds : angle 4.35626 ( 2493) link_ALPHA1-2 : bond 0.00171 ( 3) link_ALPHA1-2 : angle 1.84189 ( 9) link_ALPHA1-3 : bond 0.00736 ( 2) link_ALPHA1-3 : angle 1.19072 ( 6) link_ALPHA1-6 : bond 0.00065 ( 2) link_ALPHA1-6 : angle 2.05291 ( 6) link_BETA1-4 : bond 0.00251 ( 9) link_BETA1-4 : angle 1.82699 ( 27) link_NAG-ASN : bond 0.00140 ( 6) link_NAG-ASN : angle 1.71257 ( 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 218 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLN cc_start: 0.8465 (tp40) cc_final: 0.7972 (tm-30) REVERT: A 227 MET cc_start: 0.8717 (mmm) cc_final: 0.8236 (ttt) REVERT: A 294 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.7810 (mpt) REVERT: B 63 ASP cc_start: 0.8810 (t70) cc_final: 0.8546 (t0) REVERT: B 232 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8295 (mp) REVERT: B 279 LYS cc_start: 0.8433 (mttt) cc_final: 0.7719 (mmpt) REVERT: E 70 MET cc_start: 0.9043 (mmm) cc_final: 0.8593 (mmt) REVERT: E 189 GLU cc_start: 0.8762 (pt0) cc_final: 0.8470 (pt0) REVERT: E 239 GLN cc_start: 0.9043 (tt0) cc_final: 0.8638 (tt0) REVERT: J 46 GLU cc_start: 0.8711 (tt0) cc_final: 0.8431 (mt-10) REVERT: J 73 ASP cc_start: 0.8515 (t70) cc_final: 0.8032 (t0) REVERT: L 9 LYS cc_start: 0.8355 (tptt) cc_final: 0.7751 (tptp) REVERT: L 45 LYS cc_start: 0.8919 (mmmm) cc_final: 0.8564 (mppt) REVERT: L 56 THR cc_start: 0.9104 (m) cc_final: 0.8822 (p) REVERT: K 5 GLN cc_start: 0.8831 (tp40) cc_final: 0.8628 (tp40) REVERT: K 73 ASP cc_start: 0.8018 (t70) cc_final: 0.7535 (t0) REVERT: K 96 CYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7322 (p) outliers start: 27 outliers final: 17 residues processed: 209 average time/residue: 1.0954 time to fit residues: 260.4045 Evaluate side-chains 209 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain K residue 55 ASN Chi-restraints excluded: chain K residue 77 ASN Chi-restraints excluded: chain K residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 147 optimal weight: 1.9990 chunk 109 optimal weight: 0.0770 chunk 146 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 206 optimal weight: 0.3980 chunk 130 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 overall best weight: 1.0944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.088701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.061385 restraints weight = 96657.726| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.36 r_work: 0.2736 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18233 Z= 0.130 Angle : 0.531 6.728 24763 Z= 0.270 Chirality : 0.042 0.208 2821 Planarity : 0.004 0.054 3002 Dihedral : 9.320 155.988 3179 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.22 % Allowed : 16.68 % Favored : 82.10 % 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: 0.64 (0.19), residues: 2103 helix: 2.98 (0.21), residues: 586 sheet: -0.54 (0.20), residues: 641 loop : -0.54 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 312 TYR 0.015 0.001 TYR E 314 PHE 0.018 0.001 PHE A 306 TRP 0.018 0.001 TRP C 237 HIS 0.004 0.001 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00299 (18202) covalent geometry : angle 0.52495 (24679) SS BOND : bond 0.00482 ( 9) SS BOND : angle 0.93604 ( 18) hydrogen bonds : bond 0.03342 ( 770) hydrogen bonds : angle 4.21743 ( 2493) link_ALPHA1-2 : bond 0.00176 ( 3) link_ALPHA1-2 : angle 1.67507 ( 9) link_ALPHA1-3 : bond 0.00869 ( 2) link_ALPHA1-3 : angle 1.18538 ( 6) link_ALPHA1-6 : bond 0.00160 ( 2) link_ALPHA1-6 : angle 1.92301 ( 6) link_BETA1-4 : bond 0.00265 ( 9) link_BETA1-4 : angle 1.67978 ( 27) link_NAG-ASN : bond 0.00057 ( 6) link_NAG-ASN : angle 1.52595 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10963.31 seconds wall clock time: 186 minutes 4.89 seconds (11164.89 seconds total)