Starting phenix.real_space_refine on Wed Mar 4 23:45:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x3z_22037/03_2026/6x3z_22037.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x3z_22037/03_2026/6x3z_22037.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x3z_22037/03_2026/6x3z_22037.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x3z_22037/03_2026/6x3z_22037.map" model { file = "/net/cci-nas-00/data/ceres_data/6x3z_22037/03_2026/6x3z_22037.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x3z_22037/03_2026/6x3z_22037.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 97 5.16 5 C 11211 2.51 5 N 2828 2.21 5 O 3229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17365 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "B" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "C" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "D" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "E" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2729 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "I" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 802 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "J" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 907 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 914 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'ABU': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'ABU': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.29, per 1000 atoms: 0.25 Number of scatterers: 17365 At special positions: 0 Unit cell: (134.475, 146.025, 106.425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 97 16.00 O 3229 8.00 N 2828 7.00 C 11211 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.02 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 165 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN G 4 " - " MAN G 5 " " MAN G 5 " - " MAN G 6 " " MAN G 8 " - " MAN G 9 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN G 7 " - " MAN G 10 " ALPHA1-6 " BMA G 3 " - " MAN G 7 " " MAN G 7 " - " MAN G 8 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG A 404 " - " ASN A 80 " " NAG C 404 " - " ASN C 80 " " NAG D 401 " - " ASN D 111 " " NAG F 1 " - " ASN A 149 " " NAG G 1 " - " ASN B 111 " " NAG H 1 " - " ASN C 149 " " NAG M 1 " - " ASN E 208 " Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 800.4 milliseconds 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4020 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 28 sheets defined 31.2% alpha, 39.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 8 through 20 Processing helix chain 'A' and resid 84 through 90 removed outlier: 3.569A pdb=" N ASP A 89 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 removed outlier: 4.559A pdb=" N ARG A 142 " --> pdb=" O ASP A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 238 removed outlier: 4.121A pdb=" N LEU A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N MET A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Proline residue: A 228 - end of helix Processing helix chain 'A' and resid 239 through 242 Processing helix chain 'A' and resid 246 through 270 removed outlier: 3.861A pdb=" N ARG A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 305 Processing helix chain 'A' and resid 309 through 339 removed outlier: 3.989A pdb=" N ALA A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Proline residue: A 325 - end of helix Processing helix chain 'B' and resid 12 through 23 Processing helix chain 'B' and resid 73 through 76 removed outlier: 3.987A pdb=" N LYS B 76 " --> pdb=" O GLU B 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 73 through 76' Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.788A pdb=" N ILE B 94 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 223 through 230 removed outlier: 4.032A 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 274 removed outlier: 3.568A pdb=" N ARG B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 311 Processing helix chain 'B' and resid 314 through 345 removed outlier: 4.018A pdb=" N ALA B 318 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA B 319 " --> pdb=" O PRO B 315 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Proline residue: B 330 - end of helix removed outlier: 3.614A pdb=" N LEU B 345 " --> pdb=" O TRP B 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 20 removed outlier: 3.987A pdb=" N VAL C 12 " --> pdb=" O ASN C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.524A pdb=" N ASP C 89 " --> pdb=" O ARG C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 236 removed outlier: 5.042A pdb=" N MET C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Proline residue: C 228 - end of helix Processing helix chain 'C' and resid 237 through 242 removed outlier: 4.278A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 270 removed outlier: 4.238A pdb=" N ARG C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 4.111A 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: 3.938A pdb=" N ALA C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE C 322 " --> pdb=" O ARG C 318 " (cutoff:3.500A) Proline residue: C 325 - end of helix Processing helix chain 'D' and resid 12 through 23 Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 223 through 230 removed outlier: 3.789A pdb=" N ILE D 228 " --> pdb=" O GLY D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 243 Processing helix chain 'D' and resid 244 through 247 Processing helix chain 'D' and resid 251 through 275 removed outlier: 3.641A pdb=" N ARG D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 310 Processing helix chain 'D' and resid 314 through 346 removed outlier: 3.846A pdb=" N ILE D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 3.932A 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 99 through 106 removed outlier: 4.150A pdb=" N MET E 102 " --> pdb=" O ASN E 99 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY E 104 " --> pdb=" O ASN E 101 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE E 106 " --> pdb=" O VAL E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 253 removed outlier: 4.097A pdb=" N ILE E 238 " --> pdb=" O GLY E 234 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Proline residue: E 243 - end of helix removed outlier: 3.564A pdb=" N VAL E 253 " --> pdb=" O VAL E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 256 No H-bonds generated for 'chain 'E' and resid 254 through 256' Processing helix chain 'E' and resid 261 through 285 removed outlier: 3.691A pdb=" N LYS E 285 " --> pdb=" O THR E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 324 removed outlier: 4.313A pdb=" N SER E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER E 323 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 329 removed outlier: 3.539A pdb=" N ALA E 328 " --> pdb=" O GLN E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 357 removed outlier: 4.624A pdb=" N SER E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE E 337 " --> pdb=" O SER E 333 " (cutoff:3.500A) Proline residue: E 340 - end of helix removed outlier: 4.063A pdb=" N LEU E 357 " --> pdb=" O SER E 353 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.717A pdb=" N ASP J 90 " --> pdb=" O THR J 87 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR J 91 " --> pdb=" O SER J 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 87 through 91' Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.700A pdb=" N THR K 32 " --> pdb=" O ILE K 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 83 removed outlier: 4.523A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.877A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR A 131 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL A 106 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ARG A 129 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N THR A 176 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE A 42 " --> pdb=" O THR A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.752A pdb=" N CYS A 150 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE A 212 " --> pdb=" O CYS A 150 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLY A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL A 199 " --> pdb=" O GLY A 203 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N TYR A 205 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS A 197 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ARG A 207 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N THR A 195 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER A 209 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU A 193 " --> pdb=" O SER A 209 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER A 211 " --> pdb=" O TYR A 191 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TYR A 191 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LYS A 213 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 86 removed outlier: 4.176A pdb=" N LEU B 119 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 108 through 109 removed outlier: 7.383A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.075A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLY B 195 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS B 220 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N LEU B 193 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 81 through 83 removed outlier: 3.749A pdb=" N LEU C 83 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.847A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL C 106 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ARG C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N THR C 176 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE C 42 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.638A pdb=" N CYS C 150 " --> pdb=" O PHE C 212 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE C 212 " --> pdb=" O CYS C 150 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP C 190 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 83 through 86 removed outlier: 4.399A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N GLU D 59 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 108 through 109 removed outlier: 7.383A pdb=" N GLU D 59 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 99 through 101 removed outlier: 3.804A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 99 through 101 removed outlier: 3.804A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LYS D 220 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU D 193 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 95 through 98 removed outlier: 3.816A pdb=" N LEU E 131 " --> pdb=" O LEU E 98 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLU E 150 " --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N SER E 116 " --> pdb=" O GLU E 150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 95 through 98 removed outlier: 3.816A pdb=" N LEU E 131 " --> pdb=" O LEU E 98 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR E 73 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE E 62 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASP E 75 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU E 52 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N THR E 51 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N GLN E 182 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE E 53 " --> pdb=" O GLN E 182 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS E 184 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR E 55 " --> pdb=" O LYS E 184 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N SER E 186 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N MET E 57 " --> pdb=" O SER E 186 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL E 188 " --> pdb=" O MET E 57 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL E 59 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N VAL E 190 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N SER E 61 " --> pdb=" O VAL E 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 111 through 113 removed outlier: 3.678A pdb=" N PHE E 227 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.589A pdb=" N MET I 11 " --> pdb=" O GLU I 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.643A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N TYR I 49 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR I 96 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.833A pdb=" N MET J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ARG J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.902A pdb=" N TYR J 107 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.613A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.698A pdb=" N THR L 96 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.549A pdb=" N GLU K 10 " --> pdb=" O SER K 113 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N MET K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.549A pdb=" N GLU K 10 " --> pdb=" O SER K 113 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TYR K 107 " --> pdb=" O ARG K 98 " (cutoff:3.500A) 907 hydrogen bonds defined for protein. 2589 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.36 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4287 1.33 - 1.46: 4733 1.46 - 1.58: 8612 1.58 - 1.71: 0 1.71 - 1.83: 167 Bond restraints: 17799 Sorted by residual: bond pdb=" CD ABU A 405 " pdb=" OE1 ABU A 405 " ideal model delta sigma weight residual 1.247 1.336 -0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" CD ABU C 405 " pdb=" OE2 ABU C 405 " ideal model delta sigma weight residual 1.250 1.338 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" N GLN A 148 " pdb=" CA GLN A 148 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.21e-02 6.83e+03 7.78e+00 bond pdb=" N ASN E 208 " pdb=" CA ASN E 208 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.15e-02 7.56e+03 7.64e+00 bond pdb=" N SER C 211 " pdb=" CA SER C 211 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.23e-02 6.61e+03 7.15e+00 ... (remaining 17794 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.94: 23922 3.94 - 7.88: 257 7.88 - 11.81: 18 11.81 - 15.75: 6 15.75 - 19.69: 1 Bond angle restraints: 24204 Sorted by residual: angle pdb=" CA ARG C 269 " pdb=" CB ARG C 269 " pdb=" CG ARG C 269 " ideal model delta sigma weight residual 114.10 126.39 -12.29 2.00e+00 2.50e-01 3.77e+01 angle pdb=" CA LEU E 345 " pdb=" CB LEU E 345 " pdb=" CG LEU E 345 " ideal model delta sigma weight residual 116.30 135.99 -19.69 3.50e+00 8.16e-02 3.16e+01 angle pdb=" CA THR I 31 " pdb=" CB THR I 31 " pdb=" CG2 THR I 31 " ideal model delta sigma weight residual 110.50 118.08 -7.58 1.70e+00 3.46e-01 1.99e+01 angle pdb=" C CYS C 150 " pdb=" CA CYS C 150 " pdb=" CB CYS C 150 " ideal model delta sigma weight residual 109.35 117.96 -8.61 1.98e+00 2.55e-01 1.89e+01 angle pdb=" C CYS A 150 " pdb=" CA CYS A 150 " pdb=" CB CYS A 150 " ideal model delta sigma weight residual 109.70 117.49 -7.79 1.81e+00 3.05e-01 1.85e+01 ... (remaining 24199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 10079 21.85 - 43.71: 592 43.71 - 65.56: 46 65.56 - 87.41: 37 87.41 - 109.26: 14 Dihedral angle restraints: 10768 sinusoidal: 4512 harmonic: 6256 Sorted by residual: dihedral pdb=" CB CYS A 136 " pdb=" SG CYS A 136 " pdb=" SG CYS A 150 " pdb=" CB CYS A 150 " ideal model delta sinusoidal sigma weight residual -86.00 -7.40 -78.60 1 1.00e+01 1.00e-02 7.70e+01 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 -13.57 -72.43 1 1.00e+01 1.00e-02 6.70e+01 dihedral pdb=" CB CYS C 136 " pdb=" SG CYS C 136 " pdb=" SG CYS C 150 " pdb=" CB CYS C 150 " ideal model delta sinusoidal sigma weight residual -86.00 -19.82 -66.18 1 1.00e+01 1.00e-02 5.72e+01 ... (remaining 10765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.914: 2795 0.914 - 1.827: 0 1.827 - 2.741: 0 2.741 - 3.655: 0 3.655 - 4.569: 2 Chirality restraints: 2797 Sorted by residual: chirality pdb=" C1 MAN G 9 " pdb=" O2 MAN G 8 " pdb=" C2 MAN G 9 " pdb=" O5 MAN G 9 " both_signs ideal model delta sigma weight residual False 2.40 1.63 0.77 2.00e-02 2.50e+03 1.47e+03 chirality pdb=" C1 MAN G 6 " pdb=" O2 MAN G 5 " pdb=" C2 MAN G 6 " pdb=" O5 MAN G 6 " both_signs ideal model delta sigma weight residual False 2.40 1.66 0.74 2.00e-02 2.50e+03 1.37e+03 chirality pdb=" C1 MAN G 4 " pdb=" O3 BMA G 3 " pdb=" C2 MAN G 4 " pdb=" O5 MAN G 4 " both_signs ideal model delta sigma weight residual False 2.40 1.70 0.70 2.00e-02 2.50e+03 1.22e+03 ... (remaining 2794 not shown) Planarity restraints: 2988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " -0.289 2.00e-02 2.50e+03 2.43e-01 7.36e+02 pdb=" C7 NAG M 2 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " -0.185 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " 0.414 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " 0.150 2.00e-02 2.50e+03 1.26e-01 1.99e+02 pdb=" C7 NAG M 1 " -0.030 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " -0.036 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " -0.202 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " 0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " 0.146 2.00e-02 2.50e+03 1.20e-01 1.81e+02 pdb=" C7 NAG F 2 " -0.039 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " 0.108 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " -0.195 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " -0.020 2.00e-02 2.50e+03 ... (remaining 2985 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2920 2.77 - 3.30: 15374 3.30 - 3.83: 29493 3.83 - 4.37: 35165 4.37 - 4.90: 62034 Nonbonded interactions: 144986 Sorted by model distance: nonbonded pdb=" O VAL B 257 " pdb=" OG1 THR B 261 " model vdw 2.232 3.040 nonbonded pdb=" OH TYR C 226 " pdb=" OH TYR C 335 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR B 99 " pdb=" OH TYR B 169 " model vdw 2.286 3.040 nonbonded pdb=" O THR C 256 " pdb=" OG1 THR C 260 " model vdw 2.287 3.040 nonbonded pdb=" OG1 THR E 111 " pdb=" OH TYR E 181 " model vdw 2.308 3.040 ... (remaining 144981 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 10 through 347) } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'I' selection = (chain 'L' and resid 1 through 105) } ncs_group { reference = chain 'J' selection = (chain 'K' and resid 2 through 117) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.320 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: 0.030 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.560 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 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 : 0.007 0.089 17829 Z= 0.349 Angle : 1.120 20.626 24285 Z= 0.580 Chirality : 0.142 4.569 2797 Planarity : 0.009 0.243 2981 Dihedral : 14.388 109.265 6721 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.69 % Allowed : 5.63 % Favored : 93.68 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.16), residues: 2103 helix: -0.27 (0.20), residues: 564 sheet: -0.96 (0.19), residues: 632 loop : -2.37 (0.17), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 269 TYR 0.042 0.003 TYR C 157 PHE 0.045 0.004 PHE B 258 TRP 0.024 0.002 TRP A 336 HIS 0.005 0.002 HIS B 151 Details of bonding type rmsd covalent geometry : bond 0.00722 (17799) covalent geometry : angle 1.08878 (24204) SS BOND : bond 0.00492 ( 9) SS BOND : angle 3.49183 ( 18) hydrogen bonds : bond 0.13995 ( 803) hydrogen bonds : angle 6.08484 ( 2589) link_ALPHA1-2 : bond 0.02206 ( 3) link_ALPHA1-2 : angle 7.81921 ( 9) link_ALPHA1-3 : bond 0.00494 ( 2) link_ALPHA1-3 : angle 4.18411 ( 6) link_ALPHA1-6 : bond 0.00711 ( 2) link_ALPHA1-6 : angle 2.60871 ( 6) link_BETA1-4 : bond 0.01064 ( 7) link_BETA1-4 : angle 2.62237 ( 21) link_NAG-ASN : bond 0.02367 ( 7) link_NAG-ASN : angle 5.82116 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 409 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 LEU cc_start: 0.8493 (mt) cc_final: 0.8217 (mp) REVERT: A 319 TRP cc_start: 0.7432 (t60) cc_final: 0.6880 (t-100) REVERT: B 24 ASP cc_start: 0.7732 (t0) cc_final: 0.7253 (p0) REVERT: B 71 LYS cc_start: 0.8337 (tttp) cc_final: 0.8092 (tttp) REVERT: B 73 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7826 (mm-30) REVERT: B 98 ASP cc_start: 0.7600 (p0) cc_final: 0.7227 (p0) REVERT: B 335 ILE cc_start: 0.8155 (pt) cc_final: 0.7906 (mp) REVERT: C 41 ASN cc_start: 0.7848 (m110) cc_final: 0.7347 (t0) REVERT: C 54 ASN cc_start: 0.8106 (m110) cc_final: 0.7851 (m110) REVERT: C 137 MET cc_start: 0.8279 (mmm) cc_final: 0.7985 (mmm) REVERT: D 93 LYS cc_start: 0.7971 (mmmt) cc_final: 0.7734 (tptp) REVERT: E 33 ASN cc_start: 0.8174 (m-40) cc_final: 0.7907 (m-40) REVERT: I 13 MET cc_start: 0.7054 (ppp) cc_final: 0.6479 (ppp) REVERT: I 60 ASP cc_start: 0.8418 (t70) cc_final: 0.8206 (t0) REVERT: J 46 GLU cc_start: 0.8170 (tt0) cc_final: 0.7871 (tt0) REVERT: J 63 LYS cc_start: 0.8741 (mttp) cc_final: 0.8529 (ttpt) REVERT: J 65 GLN cc_start: 0.8115 (tp40) cc_final: 0.7882 (tp40) REVERT: J 80 TYR cc_start: 0.8792 (m-80) cc_final: 0.8368 (m-80) REVERT: K 73 ASP cc_start: 0.8170 (t0) cc_final: 0.7765 (t0) outliers start: 13 outliers final: 3 residues processed: 417 average time/residue: 0.1501 time to fit residues: 91.9763 Evaluate side-chains 323 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 320 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 54 ASN A 65 GLN A 185 GLN B 68 GLN B 242 GLN C 65 GLN C 303 ASN C 309 GLN D 68 GLN D 102 HIS D 116 ASN D 151 HIS D 189 ASN D 275 ASN D 308 ASN D 314 GLN D 346 ASN E 128 ASN I 1 ASN I 38 GLN J 6 GLN K 6 GLN K 110 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.151212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.115240 restraints weight = 21822.534| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.46 r_work: 0.3107 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17829 Z= 0.169 Angle : 0.696 23.588 24285 Z= 0.332 Chirality : 0.051 0.962 2797 Planarity : 0.004 0.044 2981 Dihedral : 8.557 76.793 2787 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.49 % Allowed : 11.52 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.17), residues: 2103 helix: 0.60 (0.21), residues: 558 sheet: -0.73 (0.19), residues: 640 loop : -1.77 (0.19), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 61 TYR 0.018 0.001 TYR E 314 PHE 0.027 0.002 PHE E 158 TRP 0.013 0.001 TRP A 237 HIS 0.003 0.001 HIS D 110 Details of bonding type rmsd covalent geometry : bond 0.00365 (17799) covalent geometry : angle 0.64350 (24204) SS BOND : bond 0.00217 ( 9) SS BOND : angle 2.65454 ( 18) hydrogen bonds : bond 0.03380 ( 803) hydrogen bonds : angle 4.73823 ( 2589) link_ALPHA1-2 : bond 0.00633 ( 3) link_ALPHA1-2 : angle 1.77683 ( 9) link_ALPHA1-3 : bond 0.01582 ( 2) link_ALPHA1-3 : angle 1.48217 ( 6) link_ALPHA1-6 : bond 0.00791 ( 2) link_ALPHA1-6 : angle 1.65871 ( 6) link_BETA1-4 : bond 0.00283 ( 7) link_BETA1-4 : angle 2.60911 ( 21) link_NAG-ASN : bond 0.00480 ( 7) link_NAG-ASN : angle 8.25260 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 341 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: A 86 ARG cc_start: 0.8506 (mtm-85) cc_final: 0.7949 (ptp90) REVERT: A 95 ASP cc_start: 0.8518 (p0) cc_final: 0.8315 (p0) REVERT: A 151 THR cc_start: 0.8463 (p) cc_final: 0.8202 (p) REVERT: A 304 TYR cc_start: 0.6734 (t80) cc_final: 0.6481 (t80) REVERT: A 319 TRP cc_start: 0.7626 (t60) cc_final: 0.6997 (t-100) REVERT: B 24 ASP cc_start: 0.8071 (t0) cc_final: 0.7169 (p0) REVERT: B 58 MET cc_start: 0.8775 (mtp) cc_final: 0.8219 (mmm) REVERT: B 71 LYS cc_start: 0.8879 (tttp) cc_final: 0.8614 (tptm) REVERT: B 98 ASP cc_start: 0.7983 (p0) cc_final: 0.7503 (p0) REVERT: B 246 TRP cc_start: 0.7253 (m100) cc_final: 0.6770 (m-10) REVERT: C 41 ASN cc_start: 0.8596 (m110) cc_final: 0.8083 (t0) REVERT: C 54 ASN cc_start: 0.8350 (m110) cc_final: 0.7877 (m110) REVERT: C 68 ARG cc_start: 0.8850 (ttt-90) cc_final: 0.8604 (ttt-90) REVERT: C 70 LYS cc_start: 0.8963 (mttt) cc_final: 0.8623 (mtmm) REVERT: C 323 PHE cc_start: 0.5659 (m-10) cc_final: 0.5415 (m-10) REVERT: D 58 MET cc_start: 0.8528 (mmm) cc_final: 0.8102 (mtm) REVERT: D 93 LYS cc_start: 0.8193 (mmmt) cc_final: 0.7915 (tptp) REVERT: D 112 MET cc_start: 0.8622 (tpp) cc_final: 0.7787 (tpp) REVERT: D 209 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8255 (mt-10) REVERT: D 266 MET cc_start: 0.8379 (mmt) cc_final: 0.8144 (mmt) REVERT: E 34 LEU cc_start: 0.8400 (mt) cc_final: 0.8127 (mp) REVERT: E 252 TRP cc_start: 0.8325 (m-10) cc_final: 0.8020 (m-10) REVERT: I 13 MET cc_start: 0.7359 (ppp) cc_final: 0.6469 (ppp) REVERT: I 60 ASP cc_start: 0.8646 (t70) cc_final: 0.8415 (t0) REVERT: J 63 LYS cc_start: 0.8790 (mttp) cc_final: 0.8497 (ttpt) REVERT: J 65 GLN cc_start: 0.8247 (tp40) cc_final: 0.7998 (tp40) REVERT: K 43 GLN cc_start: 0.8470 (mt0) cc_final: 0.8077 (tt0) REVERT: K 73 ASP cc_start: 0.8192 (t0) cc_final: 0.7690 (t0) outliers start: 28 outliers final: 19 residues processed: 352 average time/residue: 0.1478 time to fit residues: 78.2907 Evaluate side-chains 327 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 308 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain K residue 20 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 12 optimal weight: 4.9990 chunk 157 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 167 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 116 ASN E 69 ASN L 53 ASN K 110 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.151350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.114920 restraints weight = 21957.345| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.43 r_work: 0.3090 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17829 Z= 0.141 Angle : 0.611 11.623 24285 Z= 0.297 Chirality : 0.044 0.242 2797 Planarity : 0.004 0.047 2981 Dihedral : 6.977 67.376 2783 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.23 % Allowed : 13.54 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.17), residues: 2103 helix: 1.01 (0.21), residues: 557 sheet: -0.51 (0.20), residues: 606 loop : -1.48 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 61 TYR 0.017 0.001 TYR B 294 PHE 0.024 0.001 PHE E 158 TRP 0.011 0.001 TRP A 237 HIS 0.002 0.001 HIS D 110 Details of bonding type rmsd covalent geometry : bond 0.00303 (17799) covalent geometry : angle 0.58828 (24204) SS BOND : bond 0.00215 ( 9) SS BOND : angle 1.82421 ( 18) hydrogen bonds : bond 0.03085 ( 803) hydrogen bonds : angle 4.44910 ( 2589) link_ALPHA1-2 : bond 0.00356 ( 3) link_ALPHA1-2 : angle 1.62295 ( 9) link_ALPHA1-3 : bond 0.01249 ( 2) link_ALPHA1-3 : angle 1.22992 ( 6) link_ALPHA1-6 : bond 0.00613 ( 2) link_ALPHA1-6 : angle 1.64227 ( 6) link_BETA1-4 : bond 0.00776 ( 7) link_BETA1-4 : angle 2.95323 ( 21) link_NAG-ASN : bond 0.00707 ( 7) link_NAG-ASN : angle 4.39162 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 326 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.7217 (ttp) cc_final: 0.6323 (ttp) REVERT: A 319 TRP cc_start: 0.7634 (t60) cc_final: 0.6897 (t-100) REVERT: B 24 ASP cc_start: 0.8098 (t0) cc_final: 0.7157 (p0) REVERT: B 58 MET cc_start: 0.8804 (mtp) cc_final: 0.8135 (mmm) REVERT: B 71 LYS cc_start: 0.8901 (tttp) cc_final: 0.8623 (tptm) REVERT: B 98 ASP cc_start: 0.8060 (p0) cc_final: 0.7571 (p0) REVERT: B 294 TYR cc_start: 0.7191 (t80) cc_final: 0.6808 (t80) REVERT: C 41 ASN cc_start: 0.8557 (m110) cc_final: 0.8072 (t0) REVERT: C 54 ASN cc_start: 0.8345 (m110) cc_final: 0.7899 (m110) REVERT: C 70 LYS cc_start: 0.8982 (mttt) cc_final: 0.8748 (mtpp) REVERT: C 162 ASP cc_start: 0.8547 (p0) cc_final: 0.8340 (p0) REVERT: C 289 PHE cc_start: 0.7515 (t80) cc_final: 0.6957 (t80) REVERT: C 323 PHE cc_start: 0.5631 (m-10) cc_final: 0.5346 (m-10) REVERT: D 58 MET cc_start: 0.8471 (mmm) cc_final: 0.8076 (mtm) REVERT: D 93 LYS cc_start: 0.8260 (mmmt) cc_final: 0.7966 (tptp) REVERT: D 112 MET cc_start: 0.8798 (tpp) cc_final: 0.7812 (tpp) REVERT: D 204 GLN cc_start: 0.8403 (mm-40) cc_final: 0.8095 (mm110) REVERT: D 209 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8317 (mt-10) REVERT: D 236 MET cc_start: 0.6840 (mtt) cc_final: 0.6440 (mtp) REVERT: D 266 MET cc_start: 0.8307 (mmt) cc_final: 0.7336 (tpp) REVERT: E 252 TRP cc_start: 0.8357 (m-10) cc_final: 0.8118 (m-10) REVERT: E 338 PHE cc_start: 0.8013 (t80) cc_final: 0.7778 (t80) REVERT: I 13 MET cc_start: 0.7443 (ppp) cc_final: 0.6560 (ppp) REVERT: I 60 ASP cc_start: 0.8631 (t70) cc_final: 0.8419 (t0) REVERT: J 43 GLN cc_start: 0.8132 (mm110) cc_final: 0.7884 (mm110) REVERT: J 63 LYS cc_start: 0.8785 (mttp) cc_final: 0.8493 (ttpt) REVERT: J 65 GLN cc_start: 0.8259 (tp40) cc_final: 0.8013 (tp40) REVERT: J 80 TYR cc_start: 0.8839 (m-80) cc_final: 0.8476 (m-80) REVERT: K 73 ASP cc_start: 0.8209 (t0) cc_final: 0.7696 (t0) REVERT: K 110 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8600 (pm20) outliers start: 42 outliers final: 27 residues processed: 351 average time/residue: 0.1366 time to fit residues: 72.8217 Evaluate side-chains 328 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 300 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 110 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 102 optimal weight: 2.9990 chunk 132 optimal weight: 0.1980 chunk 201 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 0.0970 chunk 206 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 189 ASN D 216 HIS E 258 ASN L 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.149856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.113411 restraints weight = 21886.810| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.44 r_work: 0.3056 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17829 Z= 0.191 Angle : 0.616 9.685 24285 Z= 0.303 Chirality : 0.044 0.329 2797 Planarity : 0.004 0.048 2981 Dihedral : 6.342 57.361 2783 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.19 % Allowed : 14.23 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.18), residues: 2103 helix: 1.26 (0.22), residues: 559 sheet: -0.48 (0.20), residues: 607 loop : -1.21 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 61 TYR 0.025 0.001 TYR E 314 PHE 0.026 0.002 PHE E 346 TRP 0.011 0.001 TRP A 237 HIS 0.003 0.001 HIS D 110 Details of bonding type rmsd covalent geometry : bond 0.00435 (17799) covalent geometry : angle 0.59693 (24204) SS BOND : bond 0.00169 ( 9) SS BOND : angle 1.98198 ( 18) hydrogen bonds : bond 0.03039 ( 803) hydrogen bonds : angle 4.40771 ( 2589) link_ALPHA1-2 : bond 0.00263 ( 3) link_ALPHA1-2 : angle 1.82310 ( 9) link_ALPHA1-3 : bond 0.01324 ( 2) link_ALPHA1-3 : angle 1.48424 ( 6) link_ALPHA1-6 : bond 0.00401 ( 2) link_ALPHA1-6 : angle 1.80920 ( 6) link_BETA1-4 : bond 0.00637 ( 7) link_BETA1-4 : angle 2.29446 ( 21) link_NAG-ASN : bond 0.00804 ( 7) link_NAG-ASN : angle 4.06509 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 316 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8907 (mmtm) cc_final: 0.8704 (mmtm) REVERT: A 319 TRP cc_start: 0.7581 (t60) cc_final: 0.6821 (t-100) REVERT: B 24 ASP cc_start: 0.8228 (t0) cc_final: 0.7230 (p0) REVERT: B 71 LYS cc_start: 0.8973 (tttp) cc_final: 0.8742 (tptm) REVERT: B 98 ASP cc_start: 0.8188 (p0) cc_final: 0.7759 (p0) REVERT: B 294 TYR cc_start: 0.7227 (t80) cc_final: 0.6926 (t80) REVERT: C 9 MET cc_start: 0.8332 (tpp) cc_final: 0.7982 (tpp) REVERT: C 54 ASN cc_start: 0.8444 (m110) cc_final: 0.7984 (m110) REVERT: C 162 ASP cc_start: 0.8625 (p0) cc_final: 0.8400 (p0) REVERT: C 289 PHE cc_start: 0.7570 (t80) cc_final: 0.7041 (t80) REVERT: D 58 MET cc_start: 0.8488 (mmm) cc_final: 0.8129 (mtm) REVERT: D 93 LYS cc_start: 0.8398 (mmmt) cc_final: 0.8084 (tptp) REVERT: D 112 MET cc_start: 0.8860 (tpp) cc_final: 0.8018 (tpp) REVERT: E 338 PHE cc_start: 0.8129 (t80) cc_final: 0.7908 (t80) REVERT: I 13 MET cc_start: 0.7520 (ppp) cc_final: 0.6705 (ppp) REVERT: J 43 GLN cc_start: 0.8128 (mm110) cc_final: 0.7804 (mm-40) REVERT: J 63 LYS cc_start: 0.8766 (mttp) cc_final: 0.8490 (ttmt) REVERT: J 80 TYR cc_start: 0.8950 (m-80) cc_final: 0.8675 (m-80) REVERT: L 63 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.8171 (p) REVERT: K 73 ASP cc_start: 0.8213 (t0) cc_final: 0.7644 (t0) outliers start: 60 outliers final: 37 residues processed: 350 average time/residue: 0.1299 time to fit residues: 69.8424 Evaluate side-chains 346 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 308 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 157 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 192 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 180 optimal weight: 0.0000 chunk 204 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 193 optimal weight: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN B 189 ASN D 189 ASN E 80 GLN L 53 ASN K 110 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.147831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.113051 restraints weight = 21780.769| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.42 r_work: 0.3048 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17829 Z= 0.216 Angle : 0.632 10.237 24285 Z= 0.310 Chirality : 0.045 0.278 2797 Planarity : 0.004 0.041 2981 Dihedral : 6.247 58.174 2783 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.19 % Allowed : 15.03 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.18), residues: 2103 helix: 1.35 (0.22), residues: 560 sheet: -0.55 (0.20), residues: 626 loop : -1.06 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 61 TYR 0.021 0.001 TYR E 314 PHE 0.019 0.002 PHE E 158 TRP 0.012 0.001 TRP E 252 HIS 0.004 0.001 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00497 (17799) covalent geometry : angle 0.61099 (24204) SS BOND : bond 0.00602 ( 9) SS BOND : angle 2.21562 ( 18) hydrogen bonds : bond 0.03086 ( 803) hydrogen bonds : angle 4.43677 ( 2589) link_ALPHA1-2 : bond 0.00249 ( 3) link_ALPHA1-2 : angle 1.87695 ( 9) link_ALPHA1-3 : bond 0.01177 ( 2) link_ALPHA1-3 : angle 1.40057 ( 6) link_ALPHA1-6 : bond 0.00331 ( 2) link_ALPHA1-6 : angle 1.87318 ( 6) link_BETA1-4 : bond 0.00589 ( 7) link_BETA1-4 : angle 2.07145 ( 21) link_NAG-ASN : bond 0.00293 ( 7) link_NAG-ASN : angle 4.42571 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 308 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 TRP cc_start: 0.7607 (t60) cc_final: 0.6841 (t-100) REVERT: A 338 TYR cc_start: 0.7567 (t80) cc_final: 0.7280 (t80) REVERT: B 24 ASP cc_start: 0.8280 (t0) cc_final: 0.7301 (p0) REVERT: B 98 ASP cc_start: 0.8266 (p0) cc_final: 0.7833 (p0) REVERT: B 294 TYR cc_start: 0.7315 (t80) cc_final: 0.6997 (t80) REVERT: C 9 MET cc_start: 0.8327 (tpp) cc_final: 0.7971 (tpp) REVERT: C 41 ASN cc_start: 0.8657 (m110) cc_final: 0.8231 (m-40) REVERT: C 54 ASN cc_start: 0.8505 (m110) cc_final: 0.8040 (m110) REVERT: C 55 MET cc_start: 0.9100 (mmt) cc_final: 0.8809 (mmt) REVERT: C 59 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8642 (pt) REVERT: C 162 ASP cc_start: 0.8614 (p0) cc_final: 0.8370 (p0) REVERT: C 323 PHE cc_start: 0.5778 (m-10) cc_final: 0.5538 (m-10) REVERT: D 58 MET cc_start: 0.8530 (mmm) cc_final: 0.8163 (mtm) REVERT: D 93 LYS cc_start: 0.8461 (mmmt) cc_final: 0.8212 (tptp) REVERT: D 112 MET cc_start: 0.8864 (tpp) cc_final: 0.8014 (tpp) REVERT: E 338 PHE cc_start: 0.8196 (t80) cc_final: 0.7936 (t80) REVERT: I 13 MET cc_start: 0.7537 (ppp) cc_final: 0.6777 (ppp) REVERT: J 19 LYS cc_start: 0.8875 (tptt) cc_final: 0.8658 (tptp) REVERT: J 43 GLN cc_start: 0.8158 (mm110) cc_final: 0.7822 (mm-40) REVERT: J 63 LYS cc_start: 0.8728 (mttp) cc_final: 0.8479 (ttmt) REVERT: J 80 TYR cc_start: 0.8937 (m-80) cc_final: 0.8612 (m-80) REVERT: K 73 ASP cc_start: 0.8230 (t0) cc_final: 0.7632 (t0) outliers start: 60 outliers final: 50 residues processed: 345 average time/residue: 0.1274 time to fit residues: 67.5913 Evaluate side-chains 358 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 307 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 110 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 143 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 97 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 332 ASN B 151 HIS B 189 ASN K 110 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.150446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.114551 restraints weight = 21591.624| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.32 r_work: 0.3070 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17829 Z= 0.126 Angle : 0.581 9.649 24285 Z= 0.285 Chirality : 0.043 0.264 2797 Planarity : 0.004 0.043 2981 Dihedral : 6.014 59.399 2783 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.39 % Allowed : 17.15 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.18), residues: 2103 helix: 1.52 (0.22), residues: 560 sheet: -0.37 (0.21), residues: 606 loop : -0.97 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 61 TYR 0.034 0.001 TYR E 314 PHE 0.024 0.001 PHE E 346 TRP 0.010 0.001 TRP C 319 HIS 0.002 0.001 HIS L 87 Details of bonding type rmsd covalent geometry : bond 0.00275 (17799) covalent geometry : angle 0.56393 (24204) SS BOND : bond 0.00168 ( 9) SS BOND : angle 1.88897 ( 18) hydrogen bonds : bond 0.02898 ( 803) hydrogen bonds : angle 4.28021 ( 2589) link_ALPHA1-2 : bond 0.00355 ( 3) link_ALPHA1-2 : angle 1.59995 ( 9) link_ALPHA1-3 : bond 0.01381 ( 2) link_ALPHA1-3 : angle 1.17881 ( 6) link_ALPHA1-6 : bond 0.00539 ( 2) link_ALPHA1-6 : angle 1.64706 ( 6) link_BETA1-4 : bond 0.00555 ( 7) link_BETA1-4 : angle 1.83314 ( 21) link_NAG-ASN : bond 0.00372 ( 7) link_NAG-ASN : angle 3.94018 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 310 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 TRP cc_start: 0.7609 (t60) cc_final: 0.6869 (t-100) REVERT: A 338 TYR cc_start: 0.7597 (t80) cc_final: 0.7253 (t80) REVERT: B 24 ASP cc_start: 0.8223 (t0) cc_final: 0.7233 (p0) REVERT: B 71 LYS cc_start: 0.8962 (tttp) cc_final: 0.8742 (tptm) REVERT: B 98 ASP cc_start: 0.8167 (p0) cc_final: 0.7758 (p0) REVERT: B 294 TYR cc_start: 0.7337 (t80) cc_final: 0.7063 (t80) REVERT: C 9 MET cc_start: 0.8313 (tpp) cc_final: 0.7983 (tpp) REVERT: C 54 ASN cc_start: 0.8418 (m110) cc_final: 0.7961 (m-40) REVERT: C 55 MET cc_start: 0.9042 (mmt) cc_final: 0.8773 (mmt) REVERT: C 59 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8619 (pt) REVERT: C 289 PHE cc_start: 0.7497 (t80) cc_final: 0.7131 (t80) REVERT: C 323 PHE cc_start: 0.5747 (m-10) cc_final: 0.5495 (m-10) REVERT: D 93 LYS cc_start: 0.8426 (mmmt) cc_final: 0.8202 (tptp) REVERT: D 112 MET cc_start: 0.8852 (tpp) cc_final: 0.8023 (tpp) REVERT: E 338 PHE cc_start: 0.8174 (t80) cc_final: 0.7906 (t80) REVERT: I 13 MET cc_start: 0.7556 (ppp) cc_final: 0.6854 (ppp) REVERT: J 43 GLN cc_start: 0.8119 (mm110) cc_final: 0.7776 (mm-40) REVERT: J 63 LYS cc_start: 0.8737 (mttp) cc_final: 0.8471 (ttmt) REVERT: J 80 TYR cc_start: 0.8955 (m-80) cc_final: 0.8625 (m-80) REVERT: K 73 ASP cc_start: 0.8196 (t0) cc_final: 0.7633 (t0) outliers start: 45 outliers final: 36 residues processed: 337 average time/residue: 0.1252 time to fit residues: 65.2885 Evaluate side-chains 336 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 299 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain K residue 20 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 1 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 192 optimal weight: 9.9990 chunk 12 optimal weight: 0.0970 chunk 167 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 189 ASN L 53 ASN K 110 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.149248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.112909 restraints weight = 21814.016| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.40 r_work: 0.2992 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17829 Z= 0.180 Angle : 0.606 9.633 24285 Z= 0.297 Chirality : 0.044 0.272 2797 Planarity : 0.004 0.053 2981 Dihedral : 5.980 59.826 2783 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.13 % Allowed : 16.94 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.18), residues: 2103 helix: 1.51 (0.22), residues: 560 sheet: -0.47 (0.20), residues: 631 loop : -0.83 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 61 TYR 0.029 0.001 TYR E 314 PHE 0.018 0.001 PHE E 158 TRP 0.012 0.001 TRP E 252 HIS 0.003 0.001 HIS D 110 Details of bonding type rmsd covalent geometry : bond 0.00411 (17799) covalent geometry : angle 0.58801 (24204) SS BOND : bond 0.00388 ( 9) SS BOND : angle 2.30475 ( 18) hydrogen bonds : bond 0.02965 ( 803) hydrogen bonds : angle 4.33006 ( 2589) link_ALPHA1-2 : bond 0.00245 ( 3) link_ALPHA1-2 : angle 1.80259 ( 9) link_ALPHA1-3 : bond 0.01208 ( 2) link_ALPHA1-3 : angle 1.34001 ( 6) link_ALPHA1-6 : bond 0.00309 ( 2) link_ALPHA1-6 : angle 1.82227 ( 6) link_BETA1-4 : bond 0.00481 ( 7) link_BETA1-4 : angle 1.85450 ( 21) link_NAG-ASN : bond 0.00271 ( 7) link_NAG-ASN : angle 3.97228 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 308 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.8493 (mtm110) cc_final: 0.8284 (mtm-85) REVERT: A 180 LYS cc_start: 0.8958 (mmtt) cc_final: 0.8553 (mmtm) REVERT: A 226 TYR cc_start: 0.8421 (m-80) cc_final: 0.8192 (m-10) REVERT: A 319 TRP cc_start: 0.7565 (t60) cc_final: 0.6883 (t-100) REVERT: A 338 TYR cc_start: 0.7622 (t80) cc_final: 0.7354 (t80) REVERT: B 24 ASP cc_start: 0.8302 (t0) cc_final: 0.7301 (p0) REVERT: B 71 LYS cc_start: 0.9013 (tttp) cc_final: 0.8783 (tptm) REVERT: B 98 ASP cc_start: 0.8308 (p0) cc_final: 0.7881 (p0) REVERT: C 9 MET cc_start: 0.8345 (tpp) cc_final: 0.8052 (tpp) REVERT: C 41 ASN cc_start: 0.8672 (m110) cc_final: 0.8281 (m-40) REVERT: C 54 ASN cc_start: 0.8477 (m110) cc_final: 0.8010 (m-40) REVERT: C 59 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8621 (pt) REVERT: C 162 ASP cc_start: 0.8557 (p0) cc_final: 0.8158 (p0) REVERT: D 112 MET cc_start: 0.8837 (tpp) cc_final: 0.8045 (tpp) REVERT: E 306 PHE cc_start: 0.6909 (OUTLIER) cc_final: 0.6630 (m-10) REVERT: E 338 PHE cc_start: 0.8186 (t80) cc_final: 0.7903 (t80) REVERT: I 13 MET cc_start: 0.7604 (ppp) cc_final: 0.6912 (ppp) REVERT: J 43 GLN cc_start: 0.8141 (mm110) cc_final: 0.7795 (mm-40) REVERT: J 63 LYS cc_start: 0.8738 (mttp) cc_final: 0.8466 (ttmt) REVERT: J 80 TYR cc_start: 0.8921 (m-80) cc_final: 0.8583 (m-80) REVERT: K 73 ASP cc_start: 0.8217 (t0) cc_final: 0.7593 (t0) outliers start: 59 outliers final: 48 residues processed: 345 average time/residue: 0.1248 time to fit residues: 66.3616 Evaluate side-chains 353 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 303 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 110 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 138 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 30 optimal weight: 40.0000 chunk 76 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 199 optimal weight: 6.9990 chunk 180 optimal weight: 0.9990 chunk 60 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: A 113 ASN A 185 GLN B 189 ASN E 347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.146996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.110751 restraints weight = 21923.818| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.45 r_work: 0.3023 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17829 Z= 0.230 Angle : 0.643 9.681 24285 Z= 0.315 Chirality : 0.045 0.282 2797 Planarity : 0.004 0.048 2981 Dihedral : 6.073 57.806 2783 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.61 % Allowed : 16.62 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.19), residues: 2103 helix: 1.48 (0.22), residues: 560 sheet: -0.48 (0.20), residues: 631 loop : -0.82 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 61 TYR 0.027 0.002 TYR E 314 PHE 0.026 0.002 PHE E 346 TRP 0.024 0.001 TRP E 252 HIS 0.004 0.001 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00532 (17799) covalent geometry : angle 0.62481 (24204) SS BOND : bond 0.00166 ( 9) SS BOND : angle 2.43657 ( 18) hydrogen bonds : bond 0.03090 ( 803) hydrogen bonds : angle 4.46325 ( 2589) link_ALPHA1-2 : bond 0.00251 ( 3) link_ALPHA1-2 : angle 1.90832 ( 9) link_ALPHA1-3 : bond 0.01107 ( 2) link_ALPHA1-3 : angle 1.38988 ( 6) link_ALPHA1-6 : bond 0.00256 ( 2) link_ALPHA1-6 : angle 1.94035 ( 6) link_BETA1-4 : bond 0.00455 ( 7) link_BETA1-4 : angle 1.92320 ( 21) link_NAG-ASN : bond 0.00295 ( 7) link_NAG-ASN : angle 4.07994 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 307 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.8563 (mtm110) cc_final: 0.8352 (mtm-85) REVERT: A 153 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8486 (mm-30) REVERT: A 261 MET cc_start: 0.7818 (tpp) cc_final: 0.7313 (mtp) REVERT: A 294 MET cc_start: 0.7386 (mtp) cc_final: 0.7057 (ttp) REVERT: A 319 TRP cc_start: 0.7537 (t60) cc_final: 0.6879 (t-100) REVERT: A 338 TYR cc_start: 0.7704 (t80) cc_final: 0.7490 (t80) REVERT: B 24 ASP cc_start: 0.8341 (t0) cc_final: 0.7418 (p0) REVERT: B 98 ASP cc_start: 0.8315 (p0) cc_final: 0.7886 (p0) REVERT: B 144 GLU cc_start: 0.8487 (mm-30) cc_final: 0.7923 (mm-30) REVERT: C 9 MET cc_start: 0.8329 (tpp) cc_final: 0.8035 (tpp) REVERT: C 41 ASN cc_start: 0.8693 (m110) cc_final: 0.8286 (m-40) REVERT: C 54 ASN cc_start: 0.8571 (m110) cc_final: 0.8092 (m-40) REVERT: C 59 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8652 (pt) REVERT: C 162 ASP cc_start: 0.8608 (p0) cc_final: 0.8345 (p0) REVERT: C 282 ASP cc_start: 0.7834 (m-30) cc_final: 0.7553 (m-30) REVERT: D 112 MET cc_start: 0.8850 (tpp) cc_final: 0.8030 (tpp) REVERT: E 256 TRP cc_start: 0.8378 (m-90) cc_final: 0.7870 (m-10) REVERT: E 306 PHE cc_start: 0.7015 (OUTLIER) cc_final: 0.6662 (m-10) REVERT: E 338 PHE cc_start: 0.8215 (t80) cc_final: 0.7882 (t80) REVERT: I 13 MET cc_start: 0.7647 (ppp) cc_final: 0.7001 (ppp) REVERT: J 43 GLN cc_start: 0.8191 (mm110) cc_final: 0.7845 (mm-40) REVERT: J 63 LYS cc_start: 0.8716 (mttp) cc_final: 0.8472 (ttmt) REVERT: J 80 TYR cc_start: 0.8937 (m-80) cc_final: 0.8616 (m-80) REVERT: L 13 MET cc_start: 0.7086 (ppp) cc_final: 0.6778 (ppp) REVERT: K 73 ASP cc_start: 0.8295 (t0) cc_final: 0.7672 (t0) outliers start: 68 outliers final: 56 residues processed: 351 average time/residue: 0.1265 time to fit residues: 68.9447 Evaluate side-chains 362 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 304 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 69 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 118 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 199 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 189 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.149970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.113208 restraints weight = 21832.784| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.30 r_work: 0.3064 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17829 Z= 0.130 Angle : 0.595 9.966 24285 Z= 0.292 Chirality : 0.044 0.262 2797 Planarity : 0.004 0.042 2981 Dihedral : 5.865 55.924 2783 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.87 % Allowed : 17.74 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.19), residues: 2103 helix: 1.55 (0.22), residues: 561 sheet: -0.40 (0.21), residues: 629 loop : -0.71 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 61 TYR 0.025 0.001 TYR E 314 PHE 0.018 0.001 PHE E 158 TRP 0.033 0.001 TRP E 252 HIS 0.002 0.001 HIS D 110 Details of bonding type rmsd covalent geometry : bond 0.00288 (17799) covalent geometry : angle 0.57828 (24204) SS BOND : bond 0.00183 ( 9) SS BOND : angle 2.09904 ( 18) hydrogen bonds : bond 0.02939 ( 803) hydrogen bonds : angle 4.30335 ( 2589) link_ALPHA1-2 : bond 0.00339 ( 3) link_ALPHA1-2 : angle 1.62545 ( 9) link_ALPHA1-3 : bond 0.01362 ( 2) link_ALPHA1-3 : angle 1.16205 ( 6) link_ALPHA1-6 : bond 0.00428 ( 2) link_ALPHA1-6 : angle 1.66617 ( 6) link_BETA1-4 : bond 0.00530 ( 7) link_BETA1-4 : angle 1.76449 ( 21) link_NAG-ASN : bond 0.00286 ( 7) link_NAG-ASN : angle 3.77011 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 310 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8420 (mm-30) REVERT: A 180 LYS cc_start: 0.8971 (mmtt) cc_final: 0.8728 (mmtm) REVERT: A 261 MET cc_start: 0.7733 (tpp) cc_final: 0.7230 (mtp) REVERT: A 294 MET cc_start: 0.7234 (mtp) cc_final: 0.6959 (ttp) REVERT: A 319 TRP cc_start: 0.7552 (t60) cc_final: 0.6839 (t-100) REVERT: A 338 TYR cc_start: 0.7621 (t80) cc_final: 0.7348 (t80) REVERT: B 24 ASP cc_start: 0.8291 (t0) cc_final: 0.7396 (p0) REVERT: B 98 ASP cc_start: 0.8234 (p0) cc_final: 0.7828 (p0) REVERT: B 144 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7883 (mm-30) REVERT: C 9 MET cc_start: 0.8294 (tpp) cc_final: 0.8025 (tpp) REVERT: C 14 GLU cc_start: 0.8234 (tp30) cc_final: 0.7872 (tp30) REVERT: C 54 ASN cc_start: 0.8438 (m110) cc_final: 0.7987 (m-40) REVERT: C 59 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8645 (pt) REVERT: C 162 ASP cc_start: 0.8519 (p0) cc_final: 0.8136 (p0) REVERT: C 282 ASP cc_start: 0.7789 (m-30) cc_final: 0.7526 (m-30) REVERT: D 112 MET cc_start: 0.8810 (tpp) cc_final: 0.8035 (tpp) REVERT: E 252 TRP cc_start: 0.8809 (m-10) cc_final: 0.8607 (m-10) REVERT: E 306 PHE cc_start: 0.6901 (OUTLIER) cc_final: 0.6607 (m-10) REVERT: E 338 PHE cc_start: 0.8216 (t80) cc_final: 0.7877 (t80) REVERT: I 13 MET cc_start: 0.7051 (ppp) cc_final: 0.6315 (ppp) REVERT: J 43 GLN cc_start: 0.8172 (mm110) cc_final: 0.7814 (mm-40) REVERT: J 63 LYS cc_start: 0.8735 (mttp) cc_final: 0.8444 (ttmt) REVERT: J 80 TYR cc_start: 0.8889 (m-80) cc_final: 0.8622 (m-80) REVERT: L 13 MET cc_start: 0.7001 (ppp) cc_final: 0.6722 (ppp) REVERT: K 65 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7598 (mm-40) REVERT: K 73 ASP cc_start: 0.8259 (t0) cc_final: 0.7627 (t0) outliers start: 54 outliers final: 45 residues processed: 342 average time/residue: 0.1263 time to fit residues: 67.2213 Evaluate side-chains 347 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 300 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 90 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 146 optimal weight: 0.6980 chunk 179 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 163 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 189 ASN L 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.150615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.113735 restraints weight = 21722.514| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.25 r_work: 0.3036 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17829 Z= 0.125 Angle : 0.589 9.667 24285 Z= 0.290 Chirality : 0.044 0.260 2797 Planarity : 0.004 0.042 2981 Dihedral : 5.748 56.241 2783 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.60 % Allowed : 18.00 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.19), residues: 2103 helix: 1.58 (0.22), residues: 561 sheet: -0.39 (0.21), residues: 625 loop : -0.63 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 61 TYR 0.027 0.001 TYR B 294 PHE 0.026 0.001 PHE C 289 TRP 0.031 0.001 TRP E 252 HIS 0.004 0.001 HIS E 163 Details of bonding type rmsd covalent geometry : bond 0.00279 (17799) covalent geometry : angle 0.57328 (24204) SS BOND : bond 0.00181 ( 9) SS BOND : angle 1.98961 ( 18) hydrogen bonds : bond 0.02889 ( 803) hydrogen bonds : angle 4.23587 ( 2589) link_ALPHA1-2 : bond 0.00327 ( 3) link_ALPHA1-2 : angle 1.66695 ( 9) link_ALPHA1-3 : bond 0.01351 ( 2) link_ALPHA1-3 : angle 1.21007 ( 6) link_ALPHA1-6 : bond 0.00351 ( 2) link_ALPHA1-6 : angle 1.69373 ( 6) link_BETA1-4 : bond 0.00511 ( 7) link_BETA1-4 : angle 1.73240 ( 21) link_NAG-ASN : bond 0.00267 ( 7) link_NAG-ASN : angle 3.70716 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 306 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8425 (mm-30) REVERT: A 180 LYS cc_start: 0.8949 (mmtt) cc_final: 0.8701 (mmtm) REVERT: A 261 MET cc_start: 0.7703 (tpp) cc_final: 0.7212 (mtp) REVERT: A 294 MET cc_start: 0.7241 (mtp) cc_final: 0.6969 (ttp) REVERT: A 319 TRP cc_start: 0.7545 (t60) cc_final: 0.6849 (t-100) REVERT: A 338 TYR cc_start: 0.7620 (t80) cc_final: 0.7287 (t80) REVERT: B 24 ASP cc_start: 0.8251 (t0) cc_final: 0.7349 (p0) REVERT: B 71 LYS cc_start: 0.8963 (tttp) cc_final: 0.8744 (tptm) REVERT: B 98 ASP cc_start: 0.8181 (p0) cc_final: 0.7787 (p0) REVERT: B 246 TRP cc_start: 0.7154 (m100) cc_final: 0.6448 (m-10) REVERT: C 9 MET cc_start: 0.8311 (tpp) cc_final: 0.8042 (tpp) REVERT: C 14 GLU cc_start: 0.8231 (tp30) cc_final: 0.7880 (tp30) REVERT: C 41 ASN cc_start: 0.8558 (m110) cc_final: 0.8092 (m110) REVERT: C 54 ASN cc_start: 0.8417 (m110) cc_final: 0.7950 (m-40) REVERT: C 55 MET cc_start: 0.9049 (mmt) cc_final: 0.8806 (mmt) REVERT: C 261 MET cc_start: 0.7794 (tpp) cc_final: 0.7307 (mmm) REVERT: C 282 ASP cc_start: 0.7797 (m-30) cc_final: 0.7531 (m-30) REVERT: D 112 MET cc_start: 0.8817 (tpp) cc_final: 0.8016 (tpp) REVERT: E 252 TRP cc_start: 0.8830 (m-10) cc_final: 0.8625 (m-10) REVERT: E 306 PHE cc_start: 0.6869 (OUTLIER) cc_final: 0.6581 (m-10) REVERT: E 338 PHE cc_start: 0.8214 (t80) cc_final: 0.7881 (t80) REVERT: I 61 ARG cc_start: 0.7963 (ptt-90) cc_final: 0.7597 (ptp-170) REVERT: J 19 LYS cc_start: 0.8797 (tptp) cc_final: 0.8263 (tptp) REVERT: J 43 GLN cc_start: 0.8129 (mm110) cc_final: 0.7783 (mm-40) REVERT: J 63 LYS cc_start: 0.8731 (mttp) cc_final: 0.8431 (ttmt) REVERT: L 13 MET cc_start: 0.7027 (ppp) cc_final: 0.6771 (ppp) REVERT: K 65 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7625 (mm-40) REVERT: K 73 ASP cc_start: 0.8293 (t0) cc_final: 0.7656 (t0) outliers start: 49 outliers final: 43 residues processed: 334 average time/residue: 0.1266 time to fit residues: 65.8357 Evaluate side-chains 347 residues out of total 1883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 303 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 8 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 152 optimal weight: 0.4980 chunk 115 optimal weight: 0.8980 chunk 194 optimal weight: 9.9990 chunk 176 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 171 optimal weight: 0.6980 chunk 190 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN L 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.151250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.114266 restraints weight = 21838.603| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.36 r_work: 0.3096 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17829 Z= 0.127 Angle : 0.579 9.847 24285 Z= 0.285 Chirality : 0.043 0.260 2797 Planarity : 0.004 0.042 2981 Dihedral : 5.653 56.164 2783 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.50 % Allowed : 18.22 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.19), residues: 2103 helix: 1.57 (0.22), residues: 566 sheet: -0.31 (0.20), residues: 640 loop : -0.59 (0.22), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 61 TYR 0.026 0.001 TYR E 314 PHE 0.017 0.001 PHE E 158 TRP 0.030 0.001 TRP E 252 HIS 0.002 0.001 HIS D 110 Details of bonding type rmsd covalent geometry : bond 0.00284 (17799) covalent geometry : angle 0.56301 (24204) SS BOND : bond 0.00198 ( 9) SS BOND : angle 1.87819 ( 18) hydrogen bonds : bond 0.02841 ( 803) hydrogen bonds : angle 4.19661 ( 2589) link_ALPHA1-2 : bond 0.00327 ( 3) link_ALPHA1-2 : angle 1.68958 ( 9) link_ALPHA1-3 : bond 0.01284 ( 2) link_ALPHA1-3 : angle 1.20785 ( 6) link_ALPHA1-6 : bond 0.00332 ( 2) link_ALPHA1-6 : angle 1.70529 ( 6) link_BETA1-4 : bond 0.00504 ( 7) link_BETA1-4 : angle 1.71268 ( 21) link_NAG-ASN : bond 0.00270 ( 7) link_NAG-ASN : angle 3.63961 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4621.61 seconds wall clock time: 79 minutes 52.86 seconds (4792.86 seconds total)