Starting phenix.real_space_refine on Fri Mar 6 11:57:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jcv_9798/03_2026/6jcv_9798.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jcv_9798/03_2026/6jcv_9798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6jcv_9798/03_2026/6jcv_9798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jcv_9798/03_2026/6jcv_9798.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6jcv_9798/03_2026/6jcv_9798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jcv_9798/03_2026/6jcv_9798.map" } resolution = 2.92 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= 0.004 sd= 0.438 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: 5 Type Number sf(0) Gaussians Mg 24 5.21 5 S 120 5.16 5 C 19884 2.51 5 N 5040 2.21 5 O 5808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.03s 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: 30876 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "B" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "C" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "D" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "E" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "F" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "G" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "H" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "I" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "J" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "K" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "L" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "F" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "H" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "I" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "J" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "L" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Time building chain proxies: 6.36, per 1000 atoms: 0.21 Number of scatterers: 30876 At special positions: 0 Unit cell: (143.55, 143.55, 143.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 Mg 24 11.99 O 5808 8.00 N 5040 7.00 C 19884 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.3 seconds 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7128 Finding SS restraints... Secondary structure from input PDB file: 225 helices and 12 sheets defined 60.0% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 26 through 37 removed outlier: 3.655A pdb=" N ALA A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N THR A 32 " --> pdb=" O ARG A 28 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 57 removed outlier: 3.921A pdb=" N GLU A 52 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 54 " --> pdb=" O TYR A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.855A pdb=" N VAL A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 90 Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.558A pdb=" N LYS A 98 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 113 removed outlier: 3.868A pdb=" N PHE A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 143 Processing helix chain 'A' and resid 159 through 165 removed outlier: 3.544A pdb=" N LYS A 165 " --> pdb=" O TRP A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 171 Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.737A pdb=" N GLU A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 214 removed outlier: 3.647A pdb=" N ILE A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 229 removed outlier: 4.130A pdb=" N LEU A 225 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 removed outlier: 3.653A pdb=" N ARG A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU A 240 " --> pdb=" O GLU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 253 removed outlier: 3.535A pdb=" N HIS A 253 " --> pdb=" O MET A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.698A pdb=" N ARG A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 285 removed outlier: 3.869A pdb=" N ARG A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 299 removed outlier: 3.557A pdb=" N LYS A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 296 " --> pdb=" O TRP A 292 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 312 removed outlier: 3.599A pdb=" N TRP A 307 " --> pdb=" O PHE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 324 removed outlier: 4.035A pdb=" N LYS A 320 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU A 321 " --> pdb=" O LYS A 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 37 removed outlier: 3.653A pdb=" N ALA B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N THR B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE B 33 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 57 removed outlier: 3.920A pdb=" N GLU B 52 " --> pdb=" O ASP B 48 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA B 54 " --> pdb=" O TYR B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 68 removed outlier: 3.856A pdb=" N VAL B 68 " --> pdb=" O ILE B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 90 Processing helix chain 'B' and resid 94 through 98 removed outlier: 3.554A pdb=" N LYS B 98 " --> pdb=" O LEU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.867A pdb=" N PHE B 113 " --> pdb=" O TYR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 143 Processing helix chain 'B' and resid 159 through 165 removed outlier: 3.546A pdb=" N LYS B 165 " --> pdb=" O TRP B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 171 Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.735A pdb=" N GLU B 187 " --> pdb=" O SER B 183 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 214 removed outlier: 3.648A pdb=" N ILE B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 229 removed outlier: 4.131A pdb=" N LEU B 225 " --> pdb=" O PRO B 221 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 240 removed outlier: 3.652A pdb=" N ARG B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 253 removed outlier: 3.534A pdb=" N HIS B 253 " --> pdb=" O MET B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 266 removed outlier: 3.699A pdb=" N ARG B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 285 removed outlier: 3.872A pdb=" N ARG B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR B 282 " --> pdb=" O ASN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 299 removed outlier: 3.557A pdb=" N LYS B 290 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN B 296 " --> pdb=" O TRP B 292 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN B 297 " --> pdb=" O SER B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 312 removed outlier: 3.598A pdb=" N TRP B 307 " --> pdb=" O PHE B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 324 removed outlier: 4.033A pdb=" N LYS B 320 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU B 321 " --> pdb=" O LYS B 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.654A pdb=" N ALA C 31 " --> pdb=" O GLY C 27 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N THR C 32 " --> pdb=" O ARG C 28 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE C 33 " --> pdb=" O VAL C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.920A pdb=" N GLU C 52 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 68 removed outlier: 3.856A pdb=" N VAL C 68 " --> pdb=" O ILE C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 90 Processing helix chain 'C' and resid 94 through 98 removed outlier: 3.554A pdb=" N LYS C 98 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 113 removed outlier: 3.866A pdb=" N PHE C 113 " --> pdb=" O TYR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 143 Processing helix chain 'C' and resid 159 through 165 removed outlier: 3.545A pdb=" N LYS C 165 " --> pdb=" O TRP C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 171 Processing helix chain 'C' and resid 183 through 197 removed outlier: 3.734A pdb=" N GLU C 187 " --> pdb=" O SER C 183 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU C 195 " --> pdb=" O ASP C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 214 removed outlier: 3.647A pdb=" N ILE C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 229 removed outlier: 4.132A pdb=" N LEU C 225 " --> pdb=" O PRO C 221 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU C 226 " --> pdb=" O GLU C 222 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU C 227 " --> pdb=" O ALA C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 240 removed outlier: 3.652A pdb=" N ARG C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU C 240 " --> pdb=" O GLU C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 253 removed outlier: 3.533A pdb=" N HIS C 253 " --> pdb=" O MET C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 266 removed outlier: 3.698A pdb=" N ARG C 264 " --> pdb=" O GLY C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 285 removed outlier: 3.872A pdb=" N ARG C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE C 275 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS C 281 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR C 282 " --> pdb=" O ASN C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 removed outlier: 3.558A pdb=" N LYS C 290 " --> pdb=" O GLY C 286 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN C 296 " --> pdb=" O TRP C 292 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN C 297 " --> pdb=" O SER C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 312 removed outlier: 3.598A pdb=" N TRP C 307 " --> pdb=" O PHE C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 324 removed outlier: 4.036A pdb=" N LYS C 320 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU C 321 " --> pdb=" O LYS C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 37 removed outlier: 3.653A pdb=" N ALA D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N THR D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE D 33 " --> pdb=" O VAL D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 57 removed outlier: 3.920A pdb=" N GLU D 52 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU D 53 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA D 54 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 68 removed outlier: 3.854A pdb=" N VAL D 68 " --> pdb=" O ILE D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 90 Processing helix chain 'D' and resid 94 through 98 removed outlier: 3.555A pdb=" N LYS D 98 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 113 removed outlier: 3.867A pdb=" N PHE D 113 " --> pdb=" O TYR D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 143 Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.545A pdb=" N LYS D 165 " --> pdb=" O TRP D 161 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA D 166 " --> pdb=" O ASP D 162 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 197 removed outlier: 3.734A pdb=" N GLU D 187 " --> pdb=" O SER D 183 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU D 195 " --> pdb=" O ASP D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 214 removed outlier: 3.646A pdb=" N ILE D 201 " --> pdb=" O THR D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 229 removed outlier: 4.130A pdb=" N LEU D 225 " --> pdb=" O PRO D 221 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU D 226 " --> pdb=" O GLU D 222 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU D 227 " --> pdb=" O ALA D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 240 removed outlier: 3.652A pdb=" N ARG D 239 " --> pdb=" O ALA D 235 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU D 240 " --> pdb=" O GLU D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 253 removed outlier: 3.533A pdb=" N HIS D 253 " --> pdb=" O MET D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 266 removed outlier: 3.698A pdb=" N ARG D 264 " --> pdb=" O GLY D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 285 removed outlier: 3.872A pdb=" N ARG D 274 " --> pdb=" O ASP D 270 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE D 275 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS D 281 " --> pdb=" O GLU D 277 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR D 282 " --> pdb=" O ASN D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 299 removed outlier: 3.557A pdb=" N LYS D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN D 296 " --> pdb=" O TRP D 292 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN D 297 " --> pdb=" O SER D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 312 removed outlier: 3.599A pdb=" N TRP D 307 " --> pdb=" O PHE D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 324 removed outlier: 4.034A pdb=" N LYS D 320 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU D 321 " --> pdb=" O LYS D 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 37 removed outlier: 3.654A pdb=" N ALA E 31 " --> pdb=" O GLY E 27 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N THR E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE E 33 " --> pdb=" O VAL E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 57 removed outlier: 3.922A pdb=" N GLU E 52 " --> pdb=" O ASP E 48 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU E 53 " --> pdb=" O LYS E 49 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA E 54 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 68 removed outlier: 3.855A pdb=" N VAL E 68 " --> pdb=" O ILE E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 90 Processing helix chain 'E' and resid 94 through 98 removed outlier: 3.555A pdb=" N LYS E 98 " --> pdb=" O LEU E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 113 removed outlier: 3.865A pdb=" N PHE E 113 " --> pdb=" O TYR E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 143 Processing helix chain 'E' and resid 159 through 165 removed outlier: 3.546A pdb=" N LYS E 165 " --> pdb=" O TRP E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 171 Processing helix chain 'E' and resid 183 through 197 removed outlier: 3.734A pdb=" N GLU E 187 " --> pdb=" O SER E 183 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER E 194 " --> pdb=" O LEU E 190 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU E 195 " --> pdb=" O ASP E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 214 removed outlier: 3.648A pdb=" N ILE E 201 " --> pdb=" O THR E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 229 removed outlier: 4.130A pdb=" N LEU E 225 " --> pdb=" O PRO E 221 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU E 226 " --> pdb=" O GLU E 222 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 240 removed outlier: 3.650A pdb=" N ARG E 239 " --> pdb=" O ALA E 235 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU E 240 " --> pdb=" O GLU E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 253 removed outlier: 3.534A pdb=" N HIS E 253 " --> pdb=" O MET E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 266 removed outlier: 3.698A pdb=" N ARG E 264 " --> pdb=" O GLY E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 285 removed outlier: 3.872A pdb=" N ARG E 274 " --> pdb=" O ASP E 270 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE E 275 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS E 281 " --> pdb=" O GLU E 277 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR E 282 " --> pdb=" O ASN E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 299 removed outlier: 3.558A pdb=" N LYS E 290 " --> pdb=" O GLY E 286 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN E 296 " --> pdb=" O TRP E 292 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN E 297 " --> pdb=" O SER E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 312 removed outlier: 3.599A pdb=" N TRP E 307 " --> pdb=" O PHE E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 324 removed outlier: 4.034A pdb=" N LYS E 320 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU E 321 " --> pdb=" O LYS E 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 37 removed outlier: 3.655A pdb=" N ALA F 31 " --> pdb=" O GLY F 27 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N THR F 32 " --> pdb=" O ARG F 28 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE F 33 " --> pdb=" O VAL F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 57 removed outlier: 3.922A pdb=" N GLU F 52 " --> pdb=" O ASP F 48 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU F 53 " --> pdb=" O LYS F 49 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA F 54 " --> pdb=" O TYR F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 68 removed outlier: 3.855A pdb=" N VAL F 68 " --> pdb=" O ILE F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 90 Processing helix chain 'F' and resid 94 through 98 removed outlier: 3.555A pdb=" N LYS F 98 " --> pdb=" O LEU F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 113 removed outlier: 3.868A pdb=" N PHE F 113 " --> pdb=" O TYR F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 143 Processing helix chain 'F' and resid 159 through 165 removed outlier: 3.544A pdb=" N LYS F 165 " --> pdb=" O TRP F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 171 Processing helix chain 'F' and resid 183 through 197 removed outlier: 3.735A pdb=" N GLU F 187 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER F 194 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 214 removed outlier: 3.646A pdb=" N ILE F 201 " --> pdb=" O THR F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 229 removed outlier: 4.133A pdb=" N LEU F 225 " --> pdb=" O PRO F 221 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU F 226 " --> pdb=" O GLU F 222 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU F 227 " --> pdb=" O ALA F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 240 removed outlier: 3.651A pdb=" N ARG F 239 " --> pdb=" O ALA F 235 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU F 240 " --> pdb=" O GLU F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 253 removed outlier: 3.531A pdb=" N HIS F 253 " --> pdb=" O MET F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 266 removed outlier: 3.696A pdb=" N ARG F 264 " --> pdb=" O GLY F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 285 removed outlier: 3.873A pdb=" N ARG F 274 " --> pdb=" O ASP F 270 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE F 275 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS F 281 " --> pdb=" O GLU F 277 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR F 282 " --> pdb=" O ASN F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 299 removed outlier: 3.555A pdb=" N LYS F 290 " --> pdb=" O GLY F 286 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN F 296 " --> pdb=" O TRP F 292 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN F 297 " --> pdb=" O SER F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 312 removed outlier: 3.598A pdb=" N TRP F 307 " --> pdb=" O PHE F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 324 removed outlier: 4.033A pdb=" N LYS F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU F 321 " --> pdb=" O LYS F 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.653A pdb=" N ALA G 31 " --> pdb=" O GLY G 27 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N THR G 32 " --> pdb=" O ARG G 28 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE G 33 " --> pdb=" O VAL G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 57 removed outlier: 3.919A pdb=" N GLU G 52 " --> pdb=" O ASP G 48 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU G 53 " --> pdb=" O LYS G 49 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 68 removed outlier: 3.854A pdb=" N VAL G 68 " --> pdb=" O ILE G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 90 Processing helix chain 'G' and resid 94 through 98 removed outlier: 3.556A pdb=" N LYS G 98 " --> pdb=" O LEU G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 113 removed outlier: 3.868A pdb=" N PHE G 113 " --> pdb=" O TYR G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 143 Processing helix chain 'G' and resid 159 through 165 removed outlier: 3.546A pdb=" N LYS G 165 " --> pdb=" O TRP G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 171 Processing helix chain 'G' and resid 183 through 197 removed outlier: 3.736A pdb=" N GLU G 187 " --> pdb=" O SER G 183 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER G 194 " --> pdb=" O LEU G 190 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU G 195 " --> pdb=" O ASP G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 214 removed outlier: 3.645A pdb=" N ILE G 201 " --> pdb=" O THR G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 229 removed outlier: 4.133A pdb=" N LEU G 225 " --> pdb=" O PRO G 221 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU G 226 " --> pdb=" O GLU G 222 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU G 227 " --> pdb=" O ALA G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 240 removed outlier: 3.653A pdb=" N ARG G 239 " --> pdb=" O ALA G 235 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU G 240 " --> pdb=" O GLU G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 253 removed outlier: 3.534A pdb=" N HIS G 253 " --> pdb=" O MET G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 266 removed outlier: 3.699A pdb=" N ARG G 264 " --> pdb=" O GLY G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 285 removed outlier: 3.871A pdb=" N ARG G 274 " --> pdb=" O ASP G 270 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE G 275 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS G 281 " --> pdb=" O GLU G 277 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR G 282 " --> pdb=" O ASN G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 299 removed outlier: 3.556A pdb=" N LYS G 290 " --> pdb=" O GLY G 286 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN G 296 " --> pdb=" O TRP G 292 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN G 297 " --> pdb=" O SER G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 312 removed outlier: 3.598A pdb=" N TRP G 307 " --> pdb=" O PHE G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 324 removed outlier: 4.034A pdb=" N LYS G 320 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU G 321 " --> pdb=" O LYS G 317 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 37 removed outlier: 3.656A pdb=" N ALA H 31 " --> pdb=" O GLY H 27 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N THR H 32 " --> pdb=" O ARG H 28 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE H 33 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 57 removed outlier: 3.922A pdb=" N GLU H 52 " --> pdb=" O ASP H 48 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU H 53 " --> pdb=" O LYS H 49 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA H 54 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 68 removed outlier: 3.854A pdb=" N VAL H 68 " --> pdb=" O ILE H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 90 Processing helix chain 'H' and resid 94 through 98 removed outlier: 3.558A pdb=" N LYS H 98 " --> pdb=" O LEU H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 113 removed outlier: 3.869A pdb=" N PHE H 113 " --> pdb=" O TYR H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 143 Processing helix chain 'H' and resid 159 through 171 removed outlier: 3.546A pdb=" N LYS H 165 " --> pdb=" O TRP H 161 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA H 166 " --> pdb=" O ASP H 162 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA H 168 " --> pdb=" O ALA H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 197 removed outlier: 3.735A pdb=" N GLU H 187 " --> pdb=" O SER H 183 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER H 194 " --> pdb=" O LEU H 190 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU H 195 " --> pdb=" O ASP H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 214 removed outlier: 3.647A pdb=" N ILE H 201 " --> pdb=" O THR H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 229 removed outlier: 4.130A pdb=" N LEU H 225 " --> pdb=" O PRO H 221 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU H 226 " --> pdb=" O GLU H 222 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU H 227 " --> pdb=" O ALA H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 240 removed outlier: 3.651A pdb=" N ARG H 239 " --> pdb=" O ALA H 235 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU H 240 " --> pdb=" O GLU H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 253 removed outlier: 3.534A pdb=" N HIS H 253 " --> pdb=" O MET H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 266 removed outlier: 3.699A pdb=" N ARG H 264 " --> pdb=" O GLY H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 285 removed outlier: 3.873A pdb=" N ARG H 274 " --> pdb=" O ASP H 270 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE H 275 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS H 281 " --> pdb=" O GLU H 277 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR H 282 " --> pdb=" O ASN H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 299 removed outlier: 3.557A pdb=" N LYS H 290 " --> pdb=" O GLY H 286 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN H 296 " --> pdb=" O TRP H 292 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN H 297 " --> pdb=" O SER H 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 312 removed outlier: 3.598A pdb=" N TRP H 307 " --> pdb=" O PHE H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 324 removed outlier: 4.035A pdb=" N LYS H 320 " --> pdb=" O ALA H 316 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU H 321 " --> pdb=" O LYS H 317 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 37 removed outlier: 3.654A pdb=" N ALA I 31 " --> pdb=" O GLY I 27 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N THR I 32 " --> pdb=" O ARG I 28 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE I 33 " --> pdb=" O VAL I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 removed outlier: 3.920A pdb=" N GLU I 52 " --> pdb=" O ASP I 48 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU I 53 " --> pdb=" O LYS I 49 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA I 54 " --> pdb=" O TYR I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 68 removed outlier: 3.854A pdb=" N VAL I 68 " --> pdb=" O ILE I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 90 Processing helix chain 'I' and resid 94 through 98 removed outlier: 3.555A pdb=" N LYS I 98 " --> pdb=" O LEU I 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 113 removed outlier: 3.869A pdb=" N PHE I 113 " --> pdb=" O TYR I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 143 Processing helix chain 'I' and resid 159 through 171 removed outlier: 3.545A pdb=" N LYS I 165 " --> pdb=" O TRP I 161 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA I 166 " --> pdb=" O ASP I 162 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA I 168 " --> pdb=" O ALA I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 197 removed outlier: 3.734A pdb=" N GLU I 187 " --> pdb=" O SER I 183 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER I 194 " --> pdb=" O LEU I 190 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU I 195 " --> pdb=" O ASP I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 214 removed outlier: 3.647A pdb=" N ILE I 201 " --> pdb=" O THR I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 220 through 229 removed outlier: 4.131A pdb=" N LEU I 225 " --> pdb=" O PRO I 221 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU I 226 " --> pdb=" O GLU I 222 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU I 227 " --> pdb=" O ALA I 223 " (cutoff:3.500A) Processing helix chain 'I' and resid 233 through 240 removed outlier: 3.652A pdb=" N ARG I 239 " --> pdb=" O ALA I 235 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU I 240 " --> pdb=" O GLU I 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 253 removed outlier: 3.534A pdb=" N HIS I 253 " --> pdb=" O MET I 250 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 266 removed outlier: 3.698A pdb=" N ARG I 264 " --> pdb=" O GLY I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 268 through 285 removed outlier: 3.873A pdb=" N ARG I 274 " --> pdb=" O ASP I 270 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE I 275 " --> pdb=" O VAL I 271 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS I 281 " --> pdb=" O GLU I 277 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR I 282 " --> pdb=" O ASN I 278 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 299 removed outlier: 3.557A pdb=" N LYS I 290 " --> pdb=" O GLY I 286 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN I 296 " --> pdb=" O TRP I 292 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN I 297 " --> pdb=" O SER I 293 " (cutoff:3.500A) Processing helix chain 'I' and resid 301 through 312 removed outlier: 3.599A pdb=" N TRP I 307 " --> pdb=" O PHE I 303 " (cutoff:3.500A) Processing helix chain 'I' and resid 313 through 324 removed outlier: 4.035A pdb=" N LYS I 320 " --> pdb=" O ALA I 316 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU I 321 " --> pdb=" O LYS I 317 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 37 removed outlier: 3.654A pdb=" N ALA J 31 " --> pdb=" O GLY J 27 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N THR J 32 " --> pdb=" O ARG J 28 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE J 33 " --> pdb=" O VAL J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 57 removed outlier: 3.919A pdb=" N GLU J 52 " --> pdb=" O ASP J 48 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU J 53 " --> pdb=" O LYS J 49 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA J 54 " --> pdb=" O TYR J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 68 removed outlier: 3.855A pdb=" N VAL J 68 " --> pdb=" O ILE J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 90 Processing helix chain 'J' and resid 94 through 98 removed outlier: 3.555A pdb=" N LYS J 98 " --> pdb=" O LEU J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 113 removed outlier: 3.868A pdb=" N PHE J 113 " --> pdb=" O TYR J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 143 Processing helix chain 'J' and resid 159 through 165 removed outlier: 3.545A pdb=" N LYS J 165 " --> pdb=" O TRP J 161 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 171 Processing helix chain 'J' and resid 183 through 197 removed outlier: 3.736A pdb=" N GLU J 187 " --> pdb=" O SER J 183 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER J 194 " --> pdb=" O LEU J 190 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU J 195 " --> pdb=" O ASP J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 214 removed outlier: 3.646A pdb=" N ILE J 201 " --> pdb=" O THR J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 220 through 229 removed outlier: 4.133A pdb=" N LEU J 225 " --> pdb=" O PRO J 221 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU J 226 " --> pdb=" O GLU J 222 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU J 227 " --> pdb=" O ALA J 223 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 240 removed outlier: 3.652A pdb=" N ARG J 239 " --> pdb=" O ALA J 235 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU J 240 " --> pdb=" O GLU J 236 " (cutoff:3.500A) Processing helix chain 'J' and resid 249 through 253 removed outlier: 3.533A pdb=" N HIS J 253 " --> pdb=" O MET J 250 " (cutoff:3.500A) Processing helix chain 'J' and resid 254 through 266 removed outlier: 3.696A pdb=" N ARG J 264 " --> pdb=" O GLY J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 285 removed outlier: 3.872A pdb=" N ARG J 274 " --> pdb=" O ASP J 270 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE J 275 " --> pdb=" O VAL J 271 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS J 281 " --> pdb=" O GLU J 277 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR J 282 " --> pdb=" O ASN J 278 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 299 removed outlier: 3.556A pdb=" N LYS J 290 " --> pdb=" O GLY J 286 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN J 296 " --> pdb=" O TRP J 292 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN J 297 " --> pdb=" O SER J 293 " (cutoff:3.500A) Processing helix chain 'J' and resid 301 through 312 removed outlier: 3.598A pdb=" N TRP J 307 " --> pdb=" O PHE J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 313 through 324 removed outlier: 4.034A pdb=" N LYS J 320 " --> pdb=" O ALA J 316 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU J 321 " --> pdb=" O LYS J 317 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 37 removed outlier: 3.654A pdb=" N ALA K 31 " --> pdb=" O GLY K 27 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N THR K 32 " --> pdb=" O ARG K 28 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE K 33 " --> pdb=" O VAL K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 57 removed outlier: 3.922A pdb=" N GLU K 52 " --> pdb=" O ASP K 48 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU K 53 " --> pdb=" O LYS K 49 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA K 54 " --> pdb=" O TYR K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 68 removed outlier: 3.855A pdb=" N VAL K 68 " --> pdb=" O ILE K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 90 Processing helix chain 'K' and resid 94 through 98 removed outlier: 3.555A pdb=" N LYS K 98 " --> pdb=" O LEU K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 113 removed outlier: 3.867A pdb=" N PHE K 113 " --> pdb=" O TYR K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 143 Processing helix chain 'K' and resid 159 through 165 removed outlier: 3.546A pdb=" N LYS K 165 " --> pdb=" O TRP K 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 165 through 171 Processing helix chain 'K' and resid 183 through 197 removed outlier: 3.735A pdb=" N GLU K 187 " --> pdb=" O SER K 183 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER K 194 " --> pdb=" O LEU K 190 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU K 195 " --> pdb=" O ASP K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 214 removed outlier: 3.647A pdb=" N ILE K 201 " --> pdb=" O THR K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 220 through 229 removed outlier: 4.132A pdb=" N LEU K 225 " --> pdb=" O PRO K 221 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU K 226 " --> pdb=" O GLU K 222 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU K 227 " --> pdb=" O ALA K 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 233 through 240 removed outlier: 3.651A pdb=" N ARG K 239 " --> pdb=" O ALA K 235 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU K 240 " --> pdb=" O GLU K 236 " (cutoff:3.500A) Processing helix chain 'K' and resid 249 through 253 removed outlier: 3.532A pdb=" N HIS K 253 " --> pdb=" O MET K 250 " (cutoff:3.500A) Processing helix chain 'K' and resid 254 through 266 removed outlier: 3.697A pdb=" N ARG K 264 " --> pdb=" O GLY K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 268 through 285 removed outlier: 3.870A pdb=" N ARG K 274 " --> pdb=" O ASP K 270 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE K 275 " --> pdb=" O VAL K 271 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS K 281 " --> pdb=" O GLU K 277 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR K 282 " --> pdb=" O ASN K 278 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 299 removed outlier: 3.556A pdb=" N LYS K 290 " --> pdb=" O GLY K 286 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN K 296 " --> pdb=" O TRP K 292 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN K 297 " --> pdb=" O SER K 293 " (cutoff:3.500A) Processing helix chain 'K' and resid 301 through 312 removed outlier: 3.599A pdb=" N TRP K 307 " --> pdb=" O PHE K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 313 through 324 removed outlier: 4.035A pdb=" N LYS K 320 " --> pdb=" O ALA K 316 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU K 321 " --> pdb=" O LYS K 317 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 37 removed outlier: 3.654A pdb=" N ALA L 31 " --> pdb=" O GLY L 27 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N THR L 32 " --> pdb=" O ARG L 28 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE L 33 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 57 removed outlier: 3.921A pdb=" N GLU L 52 " --> pdb=" O ASP L 48 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU L 53 " --> pdb=" O LYS L 49 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA L 54 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 68 removed outlier: 3.854A pdb=" N VAL L 68 " --> pdb=" O ILE L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 90 Processing helix chain 'L' and resid 94 through 98 removed outlier: 3.555A pdb=" N LYS L 98 " --> pdb=" O LEU L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 113 removed outlier: 3.868A pdb=" N PHE L 113 " --> pdb=" O TYR L 109 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 143 Processing helix chain 'L' and resid 159 through 165 removed outlier: 3.542A pdb=" N LYS L 165 " --> pdb=" O TRP L 161 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 171 Processing helix chain 'L' and resid 183 through 197 removed outlier: 3.736A pdb=" N GLU L 187 " --> pdb=" O SER L 183 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER L 194 " --> pdb=" O LEU L 190 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU L 195 " --> pdb=" O ASP L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 214 removed outlier: 3.647A pdb=" N ILE L 201 " --> pdb=" O THR L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 220 through 229 removed outlier: 4.132A pdb=" N LEU L 225 " --> pdb=" O PRO L 221 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU L 226 " --> pdb=" O GLU L 222 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU L 227 " --> pdb=" O ALA L 223 " (cutoff:3.500A) Processing helix chain 'L' and resid 233 through 240 removed outlier: 3.651A pdb=" N ARG L 239 " --> pdb=" O ALA L 235 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU L 240 " --> pdb=" O GLU L 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 249 through 253 removed outlier: 3.532A pdb=" N HIS L 253 " --> pdb=" O MET L 250 " (cutoff:3.500A) Processing helix chain 'L' and resid 254 through 266 removed outlier: 3.698A pdb=" N ARG L 264 " --> pdb=" O GLY L 260 " (cutoff:3.500A) Processing helix chain 'L' and resid 268 through 285 removed outlier: 3.872A pdb=" N ARG L 274 " --> pdb=" O ASP L 270 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE L 275 " --> pdb=" O VAL L 271 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS L 281 " --> pdb=" O GLU L 277 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR L 282 " --> pdb=" O ASN L 278 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 299 removed outlier: 3.558A pdb=" N LYS L 290 " --> pdb=" O GLY L 286 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN L 296 " --> pdb=" O TRP L 292 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN L 297 " --> pdb=" O SER L 293 " (cutoff:3.500A) Processing helix chain 'L' and resid 301 through 312 removed outlier: 3.599A pdb=" N TRP L 307 " --> pdb=" O PHE L 303 " (cutoff:3.500A) Processing helix chain 'L' and resid 313 through 324 removed outlier: 4.034A pdb=" N LYS L 320 " --> pdb=" O ALA L 316 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU L 321 " --> pdb=" O LYS L 317 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 removed outlier: 8.888A pdb=" N TYR A 62 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL A 43 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE A 18 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N GLY A 44 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL A 20 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL A 73 " --> pdb=" O THR A 17 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE A 101 " --> pdb=" O ASP A 123 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE A 125 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU A 103 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL A 127 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE A 105 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL A 152 " --> pdb=" O SER A 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 61 through 62 removed outlier: 8.890A pdb=" N TYR B 62 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL B 43 " --> pdb=" O TYR B 62 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE B 18 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY B 44 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL B 20 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL B 73 " --> pdb=" O THR B 17 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N PHE B 101 " --> pdb=" O ASP B 123 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE B 125 " --> pdb=" O PHE B 101 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU B 103 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL B 127 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE B 105 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL B 152 " --> pdb=" O SER B 182 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 61 through 62 removed outlier: 8.890A pdb=" N TYR C 62 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C 43 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE C 18 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N GLY C 44 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL C 20 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL C 73 " --> pdb=" O THR C 17 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE C 101 " --> pdb=" O ASP C 123 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE C 125 " --> pdb=" O PHE C 101 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU C 103 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL C 127 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N PHE C 105 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL C 152 " --> pdb=" O SER C 182 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 61 through 62 removed outlier: 8.889A pdb=" N TYR D 62 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL D 43 " --> pdb=" O TYR D 62 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE D 18 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N GLY D 44 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL D 20 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL D 73 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE D 101 " --> pdb=" O ASP D 123 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ILE D 125 " --> pdb=" O PHE D 101 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU D 103 " --> pdb=" O ILE D 125 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL D 127 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE D 105 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL D 152 " --> pdb=" O SER D 182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 61 through 62 removed outlier: 8.891A pdb=" N TYR E 62 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL E 43 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ILE E 18 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N GLY E 44 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL E 20 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL E 73 " --> pdb=" O THR E 17 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE E 101 " --> pdb=" O ASP E 123 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE E 125 " --> pdb=" O PHE E 101 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU E 103 " --> pdb=" O ILE E 125 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL E 127 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N PHE E 105 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL E 152 " --> pdb=" O SER E 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 61 through 62 removed outlier: 8.889A pdb=" N TYR F 62 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL F 43 " --> pdb=" O TYR F 62 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE F 18 " --> pdb=" O ILE F 42 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N GLY F 44 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL F 20 " --> pdb=" O GLY F 44 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL F 73 " --> pdb=" O THR F 17 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE F 101 " --> pdb=" O ASP F 123 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ILE F 125 " --> pdb=" O PHE F 101 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU F 103 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL F 127 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N PHE F 105 " --> pdb=" O VAL F 127 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL F 152 " --> pdb=" O SER F 182 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 61 through 62 removed outlier: 8.891A pdb=" N TYR G 62 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL G 43 " --> pdb=" O TYR G 62 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE G 18 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N GLY G 44 " --> pdb=" O ILE G 18 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL G 20 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL G 73 " --> pdb=" O THR G 17 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N PHE G 101 " --> pdb=" O ASP G 123 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE G 125 " --> pdb=" O PHE G 101 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU G 103 " --> pdb=" O ILE G 125 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL G 127 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N PHE G 105 " --> pdb=" O VAL G 127 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL G 152 " --> pdb=" O SER G 182 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 61 through 62 removed outlier: 8.889A pdb=" N TYR H 62 " --> pdb=" O VAL H 41 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL H 43 " --> pdb=" O TYR H 62 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE H 18 " --> pdb=" O ILE H 42 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N GLY H 44 " --> pdb=" O ILE H 18 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL H 20 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL H 73 " --> pdb=" O THR H 17 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE H 101 " --> pdb=" O ASP H 123 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE H 125 " --> pdb=" O PHE H 101 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU H 103 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL H 127 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N PHE H 105 " --> pdb=" O VAL H 127 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL H 152 " --> pdb=" O SER H 182 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 61 through 62 removed outlier: 8.890A pdb=" N TYR I 62 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL I 43 " --> pdb=" O TYR I 62 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE I 18 " --> pdb=" O ILE I 42 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N GLY I 44 " --> pdb=" O ILE I 18 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL I 20 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL I 73 " --> pdb=" O THR I 17 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE I 101 " --> pdb=" O ASP I 123 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE I 125 " --> pdb=" O PHE I 101 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU I 103 " --> pdb=" O ILE I 125 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL I 127 " --> pdb=" O LEU I 103 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N PHE I 105 " --> pdb=" O VAL I 127 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL I 152 " --> pdb=" O SER I 182 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 61 through 62 removed outlier: 8.889A pdb=" N TYR J 62 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL J 43 " --> pdb=" O TYR J 62 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE J 18 " --> pdb=" O ILE J 42 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N GLY J 44 " --> pdb=" O ILE J 18 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL J 20 " --> pdb=" O GLY J 44 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL J 73 " --> pdb=" O THR J 17 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE J 101 " --> pdb=" O ASP J 123 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ILE J 125 " --> pdb=" O PHE J 101 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU J 103 " --> pdb=" O ILE J 125 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL J 127 " --> pdb=" O LEU J 103 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N PHE J 105 " --> pdb=" O VAL J 127 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL J 152 " --> pdb=" O SER J 182 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 61 through 62 removed outlier: 8.890A pdb=" N TYR K 62 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL K 43 " --> pdb=" O TYR K 62 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE K 18 " --> pdb=" O ILE K 42 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N GLY K 44 " --> pdb=" O ILE K 18 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL K 20 " --> pdb=" O GLY K 44 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL K 73 " --> pdb=" O THR K 17 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N PHE K 101 " --> pdb=" O ASP K 123 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE K 125 " --> pdb=" O PHE K 101 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU K 103 " --> pdb=" O ILE K 125 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL K 127 " --> pdb=" O LEU K 103 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N PHE K 105 " --> pdb=" O VAL K 127 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL K 152 " --> pdb=" O SER K 182 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 61 through 62 removed outlier: 8.890A pdb=" N TYR L 62 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL L 43 " --> pdb=" O TYR L 62 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE L 18 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N GLY L 44 " --> pdb=" O ILE L 18 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL L 20 " --> pdb=" O GLY L 44 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL L 73 " --> pdb=" O THR L 17 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE L 101 " --> pdb=" O ASP L 123 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ILE L 125 " --> pdb=" O PHE L 101 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU L 103 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL L 127 " --> pdb=" O LEU L 103 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N PHE L 105 " --> pdb=" O VAL L 127 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL L 152 " --> pdb=" O SER L 182 " (cutoff:3.500A) 1251 hydrogen bonds defined for protein. 3681 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: 5.38 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9785 1.34 - 1.46: 6362 1.46 - 1.57: 15005 1.57 - 1.69: 12 1.69 - 1.81: 228 Bond restraints: 31392 Sorted by residual: bond pdb=" N ILE K 237 " pdb=" CA ILE K 237 " ideal model delta sigma weight residual 1.462 1.494 -0.032 1.17e-02 7.31e+03 7.68e+00 bond pdb=" N ILE B 237 " pdb=" CA ILE B 237 " ideal model delta sigma weight residual 1.462 1.493 -0.031 1.17e-02 7.31e+03 7.15e+00 bond pdb=" N ILE F 237 " pdb=" CA ILE F 237 " ideal model delta sigma weight residual 1.462 1.493 -0.031 1.17e-02 7.31e+03 7.13e+00 bond pdb=" N LEU G 234 " pdb=" CA LEU G 234 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.19e-02 7.06e+03 7.06e+00 bond pdb=" N ILE A 237 " pdb=" CA ILE A 237 " ideal model delta sigma weight residual 1.462 1.493 -0.031 1.17e-02 7.31e+03 7.03e+00 ... (remaining 31387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 41978 3.27 - 6.55: 358 6.55 - 9.82: 47 9.82 - 13.10: 1 13.10 - 16.37: 12 Bond angle restraints: 42396 Sorted by residual: angle pdb=" CA GLU B 233 " pdb=" CB GLU B 233 " pdb=" CG GLU B 233 " ideal model delta sigma weight residual 114.10 130.47 -16.37 2.00e+00 2.50e-01 6.70e+01 angle pdb=" CA GLU G 233 " pdb=" CB GLU G 233 " pdb=" CG GLU G 233 " ideal model delta sigma weight residual 114.10 130.46 -16.36 2.00e+00 2.50e-01 6.69e+01 angle pdb=" CA GLU I 233 " pdb=" CB GLU I 233 " pdb=" CG GLU I 233 " ideal model delta sigma weight residual 114.10 130.44 -16.34 2.00e+00 2.50e-01 6.68e+01 angle pdb=" CA GLU E 233 " pdb=" CB GLU E 233 " pdb=" CG GLU E 233 " ideal model delta sigma weight residual 114.10 130.44 -16.34 2.00e+00 2.50e-01 6.68e+01 angle pdb=" CA GLU F 233 " pdb=" CB GLU F 233 " pdb=" CG GLU F 233 " ideal model delta sigma weight residual 114.10 130.44 -16.34 2.00e+00 2.50e-01 6.67e+01 ... (remaining 42391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.51: 16333 14.51 - 29.02: 1751 29.02 - 43.52: 541 43.52 - 58.03: 95 58.03 - 72.54: 48 Dihedral angle restraints: 18768 sinusoidal: 7524 harmonic: 11244 Sorted by residual: dihedral pdb=" CA GLY H 232 " pdb=" C GLY H 232 " pdb=" N GLU H 233 " pdb=" CA GLU H 233 " ideal model delta harmonic sigma weight residual 180.00 162.14 17.86 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA GLY I 232 " pdb=" C GLY I 232 " pdb=" N GLU I 233 " pdb=" CA GLU I 233 " ideal model delta harmonic sigma weight residual 180.00 162.14 17.86 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA GLY F 232 " pdb=" C GLY F 232 " pdb=" N GLU F 233 " pdb=" CA GLU F 233 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 18765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2652 0.042 - 0.083: 1379 0.083 - 0.125: 441 0.125 - 0.166: 107 0.166 - 0.208: 65 Chirality restraints: 4644 Sorted by residual: chirality pdb=" CA LEU K 234 " pdb=" N LEU K 234 " pdb=" C LEU K 234 " pdb=" CB LEU K 234 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA LEU B 234 " pdb=" N LEU B 234 " pdb=" C LEU B 234 " pdb=" CB LEU B 234 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA LEU G 234 " pdb=" N LEU G 234 " pdb=" C LEU G 234 " pdb=" CB LEU G 234 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 4641 not shown) Planarity restraints: 5388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 92 " -0.042 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO C 93 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 93 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 93 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 92 " -0.042 5.00e-02 4.00e+02 6.29e-02 6.32e+00 pdb=" N PRO B 93 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 93 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 93 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 92 " -0.042 5.00e-02 4.00e+02 6.27e-02 6.29e+00 pdb=" N PRO D 93 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 93 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 93 " -0.036 5.00e-02 4.00e+02 ... (remaining 5385 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 10549 2.85 - 3.36: 27583 3.36 - 3.88: 49531 3.88 - 4.39: 59868 4.39 - 4.90: 100315 Nonbonded interactions: 247846 Sorted by model distance: nonbonded pdb=" OG1 THR K 4 " pdb=" O ALA K 179 " model vdw 2.341 3.040 nonbonded pdb=" OG1 THR I 4 " pdb=" O ALA I 179 " model vdw 2.341 3.040 nonbonded pdb=" OG1 THR A 4 " pdb=" O ALA A 179 " model vdw 2.341 3.040 nonbonded pdb=" OG1 THR C 4 " pdb=" O ALA C 179 " model vdw 2.342 3.040 nonbonded pdb=" OG1 THR B 4 " pdb=" O ALA B 179 " model vdw 2.342 3.040 ... (remaining 247841 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 3 through 328) selection = chain 'B' selection = (chain 'C' and resid 3 through 328) selection = chain 'D' selection = (chain 'E' and resid 3 through 328) selection = chain 'F' selection = (chain 'G' and resid 3 through 328) selection = chain 'H' selection = (chain 'I' and resid 3 through 328) selection = (chain 'J' and resid 3 through 328) selection = (chain 'K' and resid 3 through 328) selection = chain 'L' } 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: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 25.170 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 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 0.071 31392 Z= 0.342 Angle : 0.900 16.370 42396 Z= 0.503 Chirality : 0.057 0.208 4644 Planarity : 0.006 0.063 5388 Dihedral : 13.944 72.541 11640 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % 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: -5.68 (0.09), residues: 3888 helix: -4.62 (0.04), residues: 1956 sheet: -2.25 (0.20), residues: 564 loop : -2.64 (0.13), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG J 328 TYR 0.014 0.002 TYR D 282 PHE 0.012 0.002 PHE K 288 TRP 0.017 0.002 TRP G 198 HIS 0.003 0.001 HIS E 140 Details of bonding type rmsd covalent geometry : bond 0.00748 (31392) covalent geometry : angle 0.90000 (42396) hydrogen bonds : bond 0.31093 ( 1251) hydrogen bonds : angle 9.83349 ( 3681) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 515 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8306 (t0) cc_final: 0.7619 (m-30) REVERT: A 281 LYS cc_start: 0.8555 (ptpp) cc_final: 0.8265 (ptpp) REVERT: B 281 LYS cc_start: 0.8550 (ptpp) cc_final: 0.8279 (ptpp) REVERT: B 285 ASP cc_start: 0.8096 (m-30) cc_final: 0.7877 (m-30) REVERT: C 281 LYS cc_start: 0.8536 (ptpp) cc_final: 0.8271 (ptpp) REVERT: C 285 ASP cc_start: 0.8082 (m-30) cc_final: 0.7871 (m-30) REVERT: D 281 LYS cc_start: 0.8543 (ptpp) cc_final: 0.8268 (ptpp) REVERT: D 285 ASP cc_start: 0.8114 (m-30) cc_final: 0.7899 (m-30) REVERT: E 211 ASP cc_start: 0.8228 (m-30) cc_final: 0.7928 (m-30) REVERT: E 281 LYS cc_start: 0.8547 (ptpp) cc_final: 0.8244 (ptpp) REVERT: F 211 ASP cc_start: 0.8266 (m-30) cc_final: 0.7962 (m-30) REVERT: F 281 LYS cc_start: 0.8554 (ptpp) cc_final: 0.8013 (ptpp) REVERT: F 285 ASP cc_start: 0.8158 (m-30) cc_final: 0.7952 (m-30) REVERT: G 281 LYS cc_start: 0.8555 (ptpp) cc_final: 0.8283 (ptpp) REVERT: G 285 ASP cc_start: 0.8094 (m-30) cc_final: 0.7877 (m-30) REVERT: H 281 LYS cc_start: 0.8554 (ptpp) cc_final: 0.8283 (ptpp) REVERT: H 285 ASP cc_start: 0.8112 (m-30) cc_final: 0.7898 (m-30) REVERT: I 281 LYS cc_start: 0.8547 (ptpp) cc_final: 0.8266 (ptpp) REVERT: I 285 ASP cc_start: 0.8123 (m-30) cc_final: 0.7907 (m-30) REVERT: J 281 LYS cc_start: 0.8556 (ptpp) cc_final: 0.8280 (ptpp) REVERT: J 285 ASP cc_start: 0.8098 (m-30) cc_final: 0.7878 (m-30) REVERT: K 211 ASP cc_start: 0.8249 (m-30) cc_final: 0.7913 (m-30) REVERT: K 281 LYS cc_start: 0.8547 (ptpp) cc_final: 0.8252 (ptpp) REVERT: K 285 ASP cc_start: 0.8126 (m-30) cc_final: 0.7895 (m-30) REVERT: L 281 LYS cc_start: 0.8550 (ptpp) cc_final: 0.8216 (ptpp) REVERT: L 285 ASP cc_start: 0.8123 (m-30) cc_final: 0.7902 (m-30) outliers start: 0 outliers final: 0 residues processed: 515 average time/residue: 0.7949 time to fit residues: 470.0657 Evaluate side-chains 370 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 196 HIS A 253 HIS A 278 ASN B 253 HIS B 278 ASN C 253 HIS C 278 ASN D 196 HIS D 278 ASN E 278 ASN F 110 ASN F 253 HIS G 253 HIS G 278 ASN H 278 ASN I 278 ASN J 253 HIS J 278 ASN K 196 HIS K 253 HIS K 278 ASN L 110 ASN L 253 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.071520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.056769 restraints weight = 95529.309| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 4.15 r_work: 0.2918 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31392 Z= 0.133 Angle : 0.620 8.890 42396 Z= 0.325 Chirality : 0.045 0.167 4644 Planarity : 0.005 0.046 5388 Dihedral : 4.629 16.014 4260 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.64 % Allowed : 15.09 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % 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: -3.53 (0.11), residues: 3888 helix: -2.49 (0.09), residues: 1992 sheet: -1.40 (0.23), residues: 540 loop : -2.14 (0.14), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 274 TYR 0.013 0.001 TYR F 268 PHE 0.010 0.001 PHE A 184 TRP 0.018 0.001 TRP E 198 HIS 0.001 0.001 HIS G 252 Details of bonding type rmsd covalent geometry : bond 0.00305 (31392) covalent geometry : angle 0.62013 (42396) hydrogen bonds : bond 0.05132 ( 1251) hydrogen bonds : angle 4.95467 ( 3681) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 440 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8863 (t0) cc_final: 0.8604 (t0) REVERT: A 186 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8796 (pt0) REVERT: A 211 ASP cc_start: 0.9105 (m-30) cc_final: 0.8686 (m-30) REVERT: A 277 GLU cc_start: 0.9096 (pt0) cc_final: 0.8766 (pp20) REVERT: B 104 ASP cc_start: 0.8871 (t0) cc_final: 0.8606 (t0) REVERT: B 186 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8797 (pt0) REVERT: B 277 GLU cc_start: 0.9101 (pt0) cc_final: 0.8666 (pp20) REVERT: C 104 ASP cc_start: 0.8884 (t0) cc_final: 0.8611 (t0) REVERT: C 130 ARG cc_start: 0.8495 (mmp80) cc_final: 0.8286 (mmp80) REVERT: C 186 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8805 (pt0) REVERT: C 277 GLU cc_start: 0.9112 (pt0) cc_final: 0.8789 (tp30) REVERT: C 281 LYS cc_start: 0.9142 (ptpp) cc_final: 0.8936 (ptpp) REVERT: D 104 ASP cc_start: 0.8875 (t0) cc_final: 0.8614 (t0) REVERT: D 186 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8804 (pt0) REVERT: D 277 GLU cc_start: 0.9096 (pt0) cc_final: 0.8600 (tp30) REVERT: E 104 ASP cc_start: 0.8875 (t0) cc_final: 0.8627 (t0) REVERT: E 186 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8776 (pt0) REVERT: E 211 ASP cc_start: 0.8996 (m-30) cc_final: 0.8465 (m-30) REVERT: E 277 GLU cc_start: 0.9093 (pt0) cc_final: 0.8777 (pp20) REVERT: F 104 ASP cc_start: 0.8898 (t0) cc_final: 0.8612 (t0) REVERT: F 186 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8805 (pt0) REVERT: F 201 ILE cc_start: 0.9462 (tt) cc_final: 0.9260 (pp) REVERT: F 211 ASP cc_start: 0.8949 (m-30) cc_final: 0.8467 (m-30) REVERT: F 285 ASP cc_start: 0.9234 (m-30) cc_final: 0.9016 (p0) REVERT: F 291 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8396 (pp20) REVERT: G 76 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9119 (tp) REVERT: G 104 ASP cc_start: 0.8884 (t0) cc_final: 0.8608 (t0) REVERT: G 130 ARG cc_start: 0.8474 (mmp80) cc_final: 0.8258 (mmp80) REVERT: G 186 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8768 (pt0) REVERT: G 211 ASP cc_start: 0.9116 (m-30) cc_final: 0.8741 (m-30) REVERT: G 277 GLU cc_start: 0.9101 (pt0) cc_final: 0.8653 (pp20) REVERT: H 104 ASP cc_start: 0.8866 (t0) cc_final: 0.8608 (t0) REVERT: H 130 ARG cc_start: 0.8511 (mmp80) cc_final: 0.8298 (mmp80) REVERT: H 186 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8767 (pt0) REVERT: H 211 ASP cc_start: 0.9132 (m-30) cc_final: 0.8715 (m-30) REVERT: H 277 GLU cc_start: 0.9107 (pt0) cc_final: 0.8657 (pp20) REVERT: I 104 ASP cc_start: 0.8857 (t0) cc_final: 0.8612 (t0) REVERT: I 186 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8796 (pt0) REVERT: I 277 GLU cc_start: 0.9091 (pt0) cc_final: 0.8791 (tp30) REVERT: I 281 LYS cc_start: 0.9149 (ptpp) cc_final: 0.8942 (ptpp) REVERT: J 104 ASP cc_start: 0.8876 (t0) cc_final: 0.8599 (t0) REVERT: J 186 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8773 (pt0) REVERT: J 277 GLU cc_start: 0.9093 (pt0) cc_final: 0.8591 (tp30) REVERT: K 104 ASP cc_start: 0.8869 (t0) cc_final: 0.8612 (t0) REVERT: K 186 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8772 (pt0) REVERT: K 211 ASP cc_start: 0.9015 (m-30) cc_final: 0.8494 (m-30) REVERT: K 277 GLU cc_start: 0.9066 (pt0) cc_final: 0.8767 (pp20) REVERT: L 104 ASP cc_start: 0.8878 (t0) cc_final: 0.8627 (t0) REVERT: L 130 ARG cc_start: 0.8526 (mmp80) cc_final: 0.8288 (mmp80) REVERT: L 186 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8772 (pt0) REVERT: L 211 ASP cc_start: 0.9130 (m-30) cc_final: 0.8716 (m-30) outliers start: 52 outliers final: 10 residues processed: 462 average time/residue: 0.7202 time to fit residues: 388.4075 Evaluate side-chains 346 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 334 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain F residue 270 ASP Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 270 ASP Chi-restraints excluded: chain H residue 270 ASP Chi-restraints excluded: chain I residue 270 ASP Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 270 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 380 optimal weight: 3.9990 chunk 339 optimal weight: 0.0970 chunk 22 optimal weight: 9.9990 chunk 371 optimal weight: 0.9980 chunk 170 optimal weight: 7.9990 chunk 259 optimal weight: 7.9990 chunk 135 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 322 optimal weight: 0.4980 chunk 297 optimal weight: 1.9990 chunk 272 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN C 258 GLN C 278 ASN D 258 GLN D 278 ASN E 258 GLN F 110 ASN G 258 GLN ** H 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 253 HIS H 258 GLN I 253 HIS I 258 GLN I 278 ASN J 258 GLN J 278 ASN K 258 GLN L 110 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.070870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.056615 restraints weight = 97019.137| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 4.01 r_work: 0.2940 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31392 Z= 0.118 Angle : 0.593 8.339 42396 Z= 0.297 Chirality : 0.045 0.167 4644 Planarity : 0.004 0.036 5388 Dihedral : 4.144 13.651 4260 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.08 % Allowed : 17.99 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % 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: -2.27 (0.12), residues: 3888 helix: -1.19 (0.11), residues: 2028 sheet: -1.13 (0.22), residues: 540 loop : -1.91 (0.14), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 273 TYR 0.009 0.001 TYR G 217 PHE 0.008 0.001 PHE L 184 TRP 0.012 0.001 TRP K 198 HIS 0.002 0.000 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00273 (31392) covalent geometry : angle 0.59278 (42396) hydrogen bonds : bond 0.03976 ( 1251) hydrogen bonds : angle 4.37249 ( 3681) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 411 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9164 (tt) REVERT: A 104 ASP cc_start: 0.8856 (t0) cc_final: 0.8466 (m-30) REVERT: A 126 MET cc_start: 0.9375 (ttt) cc_final: 0.9154 (ttm) REVERT: A 277 GLU cc_start: 0.9144 (pt0) cc_final: 0.8759 (pp20) REVERT: A 281 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.8948 (ptpp) REVERT: B 130 ARG cc_start: 0.8559 (mmp80) cc_final: 0.8083 (mmp80) REVERT: B 131 MET cc_start: 0.8428 (tpp) cc_final: 0.8066 (tpt) REVERT: B 211 ASP cc_start: 0.9104 (t0) cc_final: 0.8868 (t0) REVERT: B 246 ILE cc_start: 0.9559 (OUTLIER) cc_final: 0.9318 (mm) REVERT: B 277 GLU cc_start: 0.9119 (pt0) cc_final: 0.8816 (pp20) REVERT: B 281 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8998 (pmtt) REVERT: C 83 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.8890 (ttm) REVERT: C 277 GLU cc_start: 0.9108 (pt0) cc_final: 0.8797 (pp20) REVERT: C 291 GLU cc_start: 0.8698 (pp20) cc_final: 0.8456 (pp20) REVERT: D 131 MET cc_start: 0.8319 (tpp) cc_final: 0.8040 (tpt) REVERT: D 186 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8845 (pt0) REVERT: D 211 ASP cc_start: 0.9182 (m-30) cc_final: 0.8954 (t0) REVERT: D 277 GLU cc_start: 0.9116 (pt0) cc_final: 0.8802 (pp20) REVERT: E 130 ARG cc_start: 0.8571 (mmp80) cc_final: 0.8094 (mmp80) REVERT: E 131 MET cc_start: 0.8510 (tpp) cc_final: 0.8193 (tpt) REVERT: E 186 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8857 (pt0) REVERT: E 274 ARG cc_start: 0.8910 (tpp80) cc_final: 0.8529 (tpp80) REVERT: E 277 GLU cc_start: 0.9118 (pt0) cc_final: 0.8755 (pp20) REVERT: E 281 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.8970 (ptpp) REVERT: F 201 ILE cc_start: 0.9481 (tt) cc_final: 0.9229 (pp) REVERT: F 270 ASP cc_start: 0.9356 (m-30) cc_final: 0.8864 (t70) REVERT: G 76 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9132 (tp) REVERT: G 104 ASP cc_start: 0.8850 (t0) cc_final: 0.8466 (m-30) REVERT: G 126 MET cc_start: 0.9342 (ttt) cc_final: 0.9089 (ttm) REVERT: G 277 GLU cc_start: 0.9108 (pt0) cc_final: 0.8704 (pp20) REVERT: G 281 LYS cc_start: 0.9263 (ptpp) cc_final: 0.9009 (ptpp) REVERT: H 104 ASP cc_start: 0.8863 (t0) cc_final: 0.8488 (m-30) REVERT: H 126 MET cc_start: 0.9354 (ttt) cc_final: 0.9100 (ttm) REVERT: H 131 MET cc_start: 0.8447 (tpp) cc_final: 0.8185 (tpt) REVERT: H 246 ILE cc_start: 0.9488 (OUTLIER) cc_final: 0.9239 (mm) REVERT: H 277 GLU cc_start: 0.9108 (pt0) cc_final: 0.8782 (pp20) REVERT: I 130 ARG cc_start: 0.8596 (mmp80) cc_final: 0.8113 (mmp80) REVERT: I 131 MET cc_start: 0.8439 (tpp) cc_final: 0.8110 (tpt) REVERT: I 186 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8854 (pt0) REVERT: I 277 GLU cc_start: 0.9088 (pt0) cc_final: 0.8777 (pp20) REVERT: J 277 GLU cc_start: 0.9110 (pt0) cc_final: 0.8775 (pp20) REVERT: K 130 ARG cc_start: 0.8591 (mmp80) cc_final: 0.8131 (mmp80) REVERT: K 131 MET cc_start: 0.8423 (tpp) cc_final: 0.8168 (tpt) REVERT: K 186 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8871 (pt0) REVERT: K 277 GLU cc_start: 0.9106 (pt0) cc_final: 0.8828 (pp20) REVERT: K 281 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8974 (pmtt) REVERT: L 83 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8970 (ttm) REVERT: L 104 ASP cc_start: 0.8848 (t0) cc_final: 0.8455 (m-30) REVERT: L 126 MET cc_start: 0.9368 (ttt) cc_final: 0.9144 (ttm) REVERT: L 265 MET cc_start: 0.9498 (ttp) cc_final: 0.9283 (ttp) outliers start: 66 outliers final: 19 residues processed: 429 average time/residue: 0.7006 time to fit residues: 353.8838 Evaluate side-chains 372 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 343 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 246 ILE Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 281 LYS Chi-restraints excluded: chain L residue 83 MET Chi-restraints excluded: chain L residue 124 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 2 optimal weight: 10.0000 chunk 247 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 182 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 228 optimal weight: 0.0980 chunk 211 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 297 optimal weight: 9.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 HIS C 196 HIS ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS ** E 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 HIS E 253 HIS F 196 HIS F 258 GLN F 278 ASN ** G 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 HIS ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 196 HIS ** J 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 196 HIS ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 196 HIS L 258 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.067957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.053575 restraints weight = 99453.642| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 4.06 r_work: 0.2859 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 31392 Z= 0.237 Angle : 0.685 9.381 42396 Z= 0.343 Chirality : 0.048 0.158 4644 Planarity : 0.004 0.037 5388 Dihedral : 4.168 14.514 4260 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.24 % Allowed : 19.03 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % 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: -1.48 (0.13), residues: 3888 helix: -0.36 (0.11), residues: 2016 sheet: -1.16 (0.22), residues: 564 loop : -1.66 (0.15), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 130 TYR 0.013 0.001 TYR K 217 PHE 0.019 0.001 PHE K 266 TRP 0.012 0.001 TRP H 198 HIS 0.003 0.001 HIS K 196 Details of bonding type rmsd covalent geometry : bond 0.00528 (31392) covalent geometry : angle 0.68529 (42396) hydrogen bonds : bond 0.04263 ( 1251) hydrogen bonds : angle 4.42247 ( 3681) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 376 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9131 (tt) REVERT: A 186 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8848 (pt0) REVERT: A 246 ILE cc_start: 0.9616 (OUTLIER) cc_final: 0.9253 (mm) REVERT: A 277 GLU cc_start: 0.9179 (pt0) cc_final: 0.8831 (pp20) REVERT: A 278 ASN cc_start: 0.9302 (m-40) cc_final: 0.8595 (m110) REVERT: A 281 LYS cc_start: 0.9339 (ptpp) cc_final: 0.8978 (ptpp) REVERT: B 104 ASP cc_start: 0.9015 (t0) cc_final: 0.8672 (t70) REVERT: B 186 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8801 (mm-30) REVERT: B 211 ASP cc_start: 0.9251 (t0) cc_final: 0.9005 (t0) REVERT: B 246 ILE cc_start: 0.9664 (OUTLIER) cc_final: 0.9279 (mm) REVERT: B 265 MET cc_start: 0.9586 (OUTLIER) cc_final: 0.9374 (ttp) REVERT: B 277 GLU cc_start: 0.9159 (pt0) cc_final: 0.8920 (pp20) REVERT: B 278 ASN cc_start: 0.9318 (m-40) cc_final: 0.8709 (m110) REVERT: C 104 ASP cc_start: 0.9022 (t0) cc_final: 0.8709 (t70) REVERT: C 186 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8753 (mm-30) REVERT: C 246 ILE cc_start: 0.9564 (OUTLIER) cc_final: 0.9277 (mm) REVERT: C 277 GLU cc_start: 0.9120 (pt0) cc_final: 0.8824 (pp20) REVERT: C 278 ASN cc_start: 0.9285 (m-40) cc_final: 0.8500 (m110) REVERT: C 281 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.9033 (ptpp) REVERT: D 104 ASP cc_start: 0.9020 (t0) cc_final: 0.8712 (t70) REVERT: D 186 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8951 (mm-30) REVERT: D 246 ILE cc_start: 0.9577 (OUTLIER) cc_final: 0.9258 (mm) REVERT: D 277 GLU cc_start: 0.9132 (pt0) cc_final: 0.8825 (pp20) REVERT: D 278 ASN cc_start: 0.9307 (m-40) cc_final: 0.8543 (m110) REVERT: D 281 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.9029 (ptpp) REVERT: E 104 ASP cc_start: 0.8976 (t0) cc_final: 0.8677 (t70) REVERT: E 186 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8976 (mm-30) REVERT: E 246 ILE cc_start: 0.9628 (OUTLIER) cc_final: 0.9246 (mm) REVERT: E 274 ARG cc_start: 0.9111 (tpp80) cc_final: 0.8565 (tpp80) REVERT: E 277 GLU cc_start: 0.9148 (pt0) cc_final: 0.8815 (pp20) REVERT: E 278 ASN cc_start: 0.9309 (m-40) cc_final: 0.8577 (m110) REVERT: E 281 LYS cc_start: 0.9364 (ptpp) cc_final: 0.9041 (ptpp) REVERT: F 104 ASP cc_start: 0.9008 (t0) cc_final: 0.8685 (t70) REVERT: F 186 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8845 (pt0) REVERT: F 277 GLU cc_start: 0.8610 (pp20) cc_final: 0.8367 (pp20) REVERT: G 76 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9333 (tp) REVERT: G 110 ASN cc_start: 0.8728 (p0) cc_final: 0.8502 (p0) REVERT: G 277 GLU cc_start: 0.9138 (pt0) cc_final: 0.8848 (pp20) REVERT: G 278 ASN cc_start: 0.9238 (m-40) cc_final: 0.8459 (m110) REVERT: H 246 ILE cc_start: 0.9578 (OUTLIER) cc_final: 0.9268 (mm) REVERT: H 277 GLU cc_start: 0.9130 (pt0) cc_final: 0.8883 (pp20) REVERT: H 278 ASN cc_start: 0.9236 (m-40) cc_final: 0.8686 (m110) REVERT: H 281 LYS cc_start: 0.9348 (ptpp) cc_final: 0.9135 (pmtt) REVERT: I 104 ASP cc_start: 0.9007 (t0) cc_final: 0.8692 (t70) REVERT: I 186 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8980 (mm-30) REVERT: I 246 ILE cc_start: 0.9556 (OUTLIER) cc_final: 0.9278 (mm) REVERT: I 277 GLU cc_start: 0.9116 (pt0) cc_final: 0.8826 (pp20) REVERT: I 278 ASN cc_start: 0.9291 (m-40) cc_final: 0.8516 (m110) REVERT: I 281 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.9047 (ptpp) REVERT: J 104 ASP cc_start: 0.9013 (t0) cc_final: 0.8686 (t70) REVERT: J 186 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8731 (mm-30) REVERT: J 211 ASP cc_start: 0.9368 (t0) cc_final: 0.9166 (t0) REVERT: J 246 ILE cc_start: 0.9607 (OUTLIER) cc_final: 0.9308 (mm) REVERT: J 265 MET cc_start: 0.9572 (OUTLIER) cc_final: 0.9358 (ttp) REVERT: J 277 GLU cc_start: 0.9123 (pt0) cc_final: 0.8871 (pp20) REVERT: J 278 ASN cc_start: 0.9268 (m-40) cc_final: 0.8689 (m110) REVERT: K 104 ASP cc_start: 0.8993 (t0) cc_final: 0.8676 (t70) REVERT: K 186 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8965 (mm-30) REVERT: K 246 ILE cc_start: 0.9566 (OUTLIER) cc_final: 0.9241 (mm) REVERT: K 277 GLU cc_start: 0.9174 (pt0) cc_final: 0.8856 (pp20) REVERT: K 278 ASN cc_start: 0.9322 (m-40) cc_final: 0.8626 (m110) REVERT: K 281 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.9052 (ptpp) REVERT: L 76 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.8857 (tt) REVERT: L 186 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8733 (mt-10) REVERT: L 274 ARG cc_start: 0.8819 (tpp80) cc_final: 0.8363 (tpp80) REVERT: L 277 GLU cc_start: 0.8512 (pp20) cc_final: 0.8267 (pp20) outliers start: 103 outliers final: 11 residues processed: 396 average time/residue: 0.7374 time to fit residues: 341.7536 Evaluate side-chains 382 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 353 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain F residue 270 ASP Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 270 ASP Chi-restraints excluded: chain H residue 246 ILE Chi-restraints excluded: chain H residue 270 ASP Chi-restraints excluded: chain I residue 246 ILE Chi-restraints excluded: chain I residue 270 ASP Chi-restraints excluded: chain I residue 281 LYS Chi-restraints excluded: chain J residue 246 ILE Chi-restraints excluded: chain J residue 265 MET Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 246 ILE Chi-restraints excluded: chain K residue 281 LYS Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 270 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 129 optimal weight: 8.9990 chunk 9 optimal weight: 0.0010 chunk 365 optimal weight: 6.9990 chunk 213 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 296 optimal weight: 5.9990 chunk 252 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 330 optimal weight: 0.7980 chunk 287 optimal weight: 5.9990 overall best weight: 2.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.068690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.054280 restraints weight = 98453.049| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 4.05 r_work: 0.2882 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31392 Z= 0.148 Angle : 0.632 9.297 42396 Z= 0.309 Chirality : 0.046 0.155 4644 Planarity : 0.003 0.031 5388 Dihedral : 3.985 14.857 4260 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.55 % Allowed : 20.44 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % 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: -1.07 (0.13), residues: 3888 helix: -0.00 (0.11), residues: 2064 sheet: -0.86 (0.22), residues: 564 loop : -1.63 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 130 TYR 0.010 0.001 TYR L 217 PHE 0.011 0.001 PHE K 266 TRP 0.014 0.001 TRP F 198 HIS 0.002 0.001 HIS B 196 Details of bonding type rmsd covalent geometry : bond 0.00343 (31392) covalent geometry : angle 0.63191 (42396) hydrogen bonds : bond 0.03702 ( 1251) hydrogen bonds : angle 4.23964 ( 3681) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 381 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9250 (tp) REVERT: A 130 ARG cc_start: 0.8696 (mmp80) cc_final: 0.7857 (mmp80) REVERT: A 186 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8757 (mt-10) REVERT: A 246 ILE cc_start: 0.9629 (OUTLIER) cc_final: 0.9268 (mm) REVERT: A 277 GLU cc_start: 0.9156 (pt0) cc_final: 0.8757 (pp20) REVERT: A 278 ASN cc_start: 0.9302 (m-40) cc_final: 0.8611 (m110) REVERT: A 281 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.8987 (ptpp) REVERT: B 104 ASP cc_start: 0.9022 (t0) cc_final: 0.8690 (t70) REVERT: B 131 MET cc_start: 0.8378 (tpp) cc_final: 0.7975 (tpt) REVERT: B 186 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8752 (mt-10) REVERT: B 211 ASP cc_start: 0.9243 (t0) cc_final: 0.8957 (t0) REVERT: B 227 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8917 (mm-30) REVERT: B 246 ILE cc_start: 0.9654 (OUTLIER) cc_final: 0.9317 (mm) REVERT: B 265 MET cc_start: 0.9558 (OUTLIER) cc_final: 0.9336 (ttp) REVERT: B 277 GLU cc_start: 0.9144 (pt0) cc_final: 0.8893 (pp20) REVERT: B 278 ASN cc_start: 0.9289 (m-40) cc_final: 0.8606 (m110) REVERT: C 104 ASP cc_start: 0.8998 (t0) cc_final: 0.8676 (t70) REVERT: C 130 ARG cc_start: 0.8690 (mmp80) cc_final: 0.8006 (mmp80) REVERT: C 131 MET cc_start: 0.8363 (tpp) cc_final: 0.7969 (tpt) REVERT: C 186 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8717 (mt-10) REVERT: C 246 ILE cc_start: 0.9608 (OUTLIER) cc_final: 0.9324 (mm) REVERT: C 277 GLU cc_start: 0.9101 (pt0) cc_final: 0.8814 (pp20) REVERT: C 278 ASN cc_start: 0.9261 (m-40) cc_final: 0.8534 (m110) REVERT: C 281 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.9005 (ptpp) REVERT: D 104 ASP cc_start: 0.9020 (t0) cc_final: 0.8698 (t70) REVERT: D 131 MET cc_start: 0.8294 (tpp) cc_final: 0.8026 (OUTLIER) REVERT: D 186 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8909 (mm-30) REVERT: D 246 ILE cc_start: 0.9621 (OUTLIER) cc_final: 0.9319 (mm) REVERT: D 277 GLU cc_start: 0.9118 (pt0) cc_final: 0.8777 (pp20) REVERT: D 278 ASN cc_start: 0.9297 (m-40) cc_final: 0.8598 (m110) REVERT: D 281 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8975 (ptpp) REVERT: E 104 ASP cc_start: 0.9037 (t0) cc_final: 0.8688 (t70) REVERT: E 131 MET cc_start: 0.8338 (tpp) cc_final: 0.7959 (tpt) REVERT: E 186 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8955 (mm-30) REVERT: E 246 ILE cc_start: 0.9613 (OUTLIER) cc_final: 0.9204 (mm) REVERT: E 274 ARG cc_start: 0.9059 (tpp80) cc_final: 0.8519 (tpp80) REVERT: E 277 GLU cc_start: 0.9143 (pt0) cc_final: 0.8757 (pp20) REVERT: E 278 ASN cc_start: 0.9299 (m-40) cc_final: 0.8584 (m110) REVERT: E 281 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.8980 (ptpp) REVERT: F 83 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8951 (tmm) REVERT: F 104 ASP cc_start: 0.9001 (t0) cc_final: 0.8664 (t0) REVERT: F 131 MET cc_start: 0.8380 (tpp) cc_final: 0.8083 (tpt) REVERT: F 186 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8724 (mt-10) REVERT: F 246 ILE cc_start: 0.9640 (OUTLIER) cc_final: 0.9266 (mm) REVERT: G 76 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9287 (tp) REVERT: G 130 ARG cc_start: 0.8676 (mmp80) cc_final: 0.8001 (mmp80) REVERT: G 131 MET cc_start: 0.8334 (tpp) cc_final: 0.7962 (tpt) REVERT: G 186 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8683 (mt-10) REVERT: G 277 GLU cc_start: 0.9151 (pt0) cc_final: 0.8857 (pp20) REVERT: G 278 ASN cc_start: 0.9212 (m-40) cc_final: 0.8398 (m110) REVERT: H 131 MET cc_start: 0.8435 (tpp) cc_final: 0.8097 (tpt) REVERT: H 186 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8677 (mt-10) REVERT: H 246 ILE cc_start: 0.9604 (OUTLIER) cc_final: 0.9306 (mm) REVERT: H 277 GLU cc_start: 0.9130 (pt0) cc_final: 0.8798 (pp20) REVERT: H 278 ASN cc_start: 0.9226 (m-40) cc_final: 0.8544 (m110) REVERT: H 281 LYS cc_start: 0.9319 (ptpp) cc_final: 0.9028 (ptpp) REVERT: I 104 ASP cc_start: 0.9017 (t0) cc_final: 0.8686 (t70) REVERT: I 131 MET cc_start: 0.8392 (tpp) cc_final: 0.8008 (tpt) REVERT: I 186 GLU cc_start: 0.9180 (mm-30) cc_final: 0.8928 (mm-30) REVERT: I 246 ILE cc_start: 0.9599 (OUTLIER) cc_final: 0.9305 (mm) REVERT: I 277 GLU cc_start: 0.9106 (pt0) cc_final: 0.8798 (pp20) REVERT: I 278 ASN cc_start: 0.9291 (m-40) cc_final: 0.8561 (m110) REVERT: I 281 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.9028 (ptpp) REVERT: J 104 ASP cc_start: 0.9013 (t0) cc_final: 0.8673 (t70) REVERT: J 131 MET cc_start: 0.8365 (tpp) cc_final: 0.8033 (tpt) REVERT: J 186 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8738 (mt-10) REVERT: J 211 ASP cc_start: 0.9347 (t0) cc_final: 0.9067 (t0) REVERT: J 246 ILE cc_start: 0.9647 (OUTLIER) cc_final: 0.9320 (mm) REVERT: J 265 MET cc_start: 0.9536 (OUTLIER) cc_final: 0.9309 (ttp) REVERT: J 277 GLU cc_start: 0.9076 (pt0) cc_final: 0.8827 (pp20) REVERT: J 278 ASN cc_start: 0.9226 (m-40) cc_final: 0.8475 (m110) REVERT: K 104 ASP cc_start: 0.8989 (t0) cc_final: 0.8655 (t70) REVERT: K 131 MET cc_start: 0.8468 (tpp) cc_final: 0.8104 (tpt) REVERT: K 186 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8909 (mm-30) REVERT: K 246 ILE cc_start: 0.9599 (OUTLIER) cc_final: 0.9247 (mm) REVERT: K 277 GLU cc_start: 0.9138 (pt0) cc_final: 0.8788 (pp20) REVERT: K 278 ASN cc_start: 0.9298 (m-40) cc_final: 0.8527 (m110) REVERT: K 281 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.9049 (ptpp) REVERT: L 76 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.8816 (tt) REVERT: L 131 MET cc_start: 0.8354 (tpp) cc_final: 0.8094 (tpt) REVERT: L 186 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8720 (mt-10) REVERT: L 274 ARG cc_start: 0.8715 (tpp80) cc_final: 0.8453 (tpp80) outliers start: 81 outliers final: 15 residues processed: 408 average time/residue: 0.7202 time to fit residues: 344.6917 Evaluate side-chains 377 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 341 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 270 ASP Chi-restraints excluded: chain G residue 281 LYS Chi-restraints excluded: chain H residue 246 ILE Chi-restraints excluded: chain I residue 246 ILE Chi-restraints excluded: chain I residue 281 LYS Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain J residue 246 ILE Chi-restraints excluded: chain J residue 265 MET Chi-restraints excluded: chain K residue 246 ILE Chi-restraints excluded: chain K residue 281 LYS Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 270 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 311 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 331 optimal weight: 0.5980 chunk 273 optimal weight: 9.9990 chunk 167 optimal weight: 9.9990 chunk 363 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 296 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 302 optimal weight: 7.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 278 ASN ** G 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 278 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.068969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.054450 restraints weight = 99089.185| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 4.11 r_work: 0.2886 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31392 Z= 0.146 Angle : 0.639 10.768 42396 Z= 0.311 Chirality : 0.046 0.195 4644 Planarity : 0.003 0.029 5388 Dihedral : 3.886 13.701 4260 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.64 % Allowed : 20.53 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % 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: -0.78 (0.13), residues: 3888 helix: 0.25 (0.11), residues: 2064 sheet: -0.72 (0.22), residues: 564 loop : -1.55 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 130 TYR 0.010 0.001 TYR L 217 PHE 0.017 0.001 PHE E 266 TRP 0.014 0.001 TRP F 198 HIS 0.003 0.001 HIS H 196 Details of bonding type rmsd covalent geometry : bond 0.00338 (31392) covalent geometry : angle 0.63894 (42396) hydrogen bonds : bond 0.03557 ( 1251) hydrogen bonds : angle 4.13920 ( 3681) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 397 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.8356 (tpp) cc_final: 0.8088 (tpt) REVERT: A 186 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8777 (mt-10) REVERT: A 246 ILE cc_start: 0.9645 (OUTLIER) cc_final: 0.9274 (mm) REVERT: A 277 GLU cc_start: 0.9154 (pt0) cc_final: 0.8788 (pp20) REVERT: A 278 ASN cc_start: 0.9319 (m-40) cc_final: 0.8619 (m110) REVERT: A 281 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.8962 (ptpp) REVERT: B 104 ASP cc_start: 0.9004 (t0) cc_final: 0.8708 (t70) REVERT: B 131 MET cc_start: 0.8526 (tpp) cc_final: 0.8215 (tpt) REVERT: B 186 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8804 (mt-10) REVERT: B 211 ASP cc_start: 0.9289 (t0) cc_final: 0.9002 (t0) REVERT: B 227 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8922 (mm-30) REVERT: B 246 ILE cc_start: 0.9680 (OUTLIER) cc_final: 0.9325 (mm) REVERT: B 277 GLU cc_start: 0.9144 (pt0) cc_final: 0.8934 (pp20) REVERT: B 278 ASN cc_start: 0.9297 (m-40) cc_final: 0.8862 (m110) REVERT: B 281 LYS cc_start: 0.9239 (pmtt) cc_final: 0.9028 (pmtt) REVERT: C 76 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9159 (tp) REVERT: C 104 ASP cc_start: 0.8957 (t0) cc_final: 0.8662 (t70) REVERT: C 131 MET cc_start: 0.8524 (tpp) cc_final: 0.8301 (tpt) REVERT: C 186 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8776 (mt-10) REVERT: C 246 ILE cc_start: 0.9657 (OUTLIER) cc_final: 0.9287 (mm) REVERT: C 277 GLU cc_start: 0.9126 (pt0) cc_final: 0.8863 (pp20) REVERT: C 278 ASN cc_start: 0.9275 (m-40) cc_final: 0.8716 (m110) REVERT: C 281 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.9008 (pmtt) REVERT: D 104 ASP cc_start: 0.8976 (t0) cc_final: 0.8658 (t70) REVERT: D 130 ARG cc_start: 0.8819 (mmp80) cc_final: 0.8607 (mmp80) REVERT: D 131 MET cc_start: 0.8520 (tpp) cc_final: 0.8162 (tpt) REVERT: D 186 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8962 (mm-30) REVERT: D 246 ILE cc_start: 0.9666 (OUTLIER) cc_final: 0.9236 (mm) REVERT: D 277 GLU cc_start: 0.9130 (pt0) cc_final: 0.8769 (pp20) REVERT: D 278 ASN cc_start: 0.9279 (m-40) cc_final: 0.8618 (m110) REVERT: D 281 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.8957 (ptpp) REVERT: E 83 MET cc_start: 0.9394 (OUTLIER) cc_final: 0.9161 (ttp) REVERT: E 104 ASP cc_start: 0.8990 (t0) cc_final: 0.8644 (t70) REVERT: E 131 MET cc_start: 0.8503 (tpp) cc_final: 0.8112 (tpt) REVERT: E 186 GLU cc_start: 0.9216 (mm-30) cc_final: 0.9008 (mm-30) REVERT: E 246 ILE cc_start: 0.9621 (OUTLIER) cc_final: 0.9219 (mm) REVERT: E 274 ARG cc_start: 0.9066 (tpp80) cc_final: 0.8524 (tpp80) REVERT: E 277 GLU cc_start: 0.9146 (pt0) cc_final: 0.8802 (pp20) REVERT: E 278 ASN cc_start: 0.9303 (m-40) cc_final: 0.8579 (m110) REVERT: E 281 LYS cc_start: 0.9365 (OUTLIER) cc_final: 0.9013 (ptpp) REVERT: F 104 ASP cc_start: 0.9013 (t0) cc_final: 0.8688 (t0) REVERT: F 131 MET cc_start: 0.8539 (tpp) cc_final: 0.8238 (tpt) REVERT: F 186 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8744 (mt-10) REVERT: F 246 ILE cc_start: 0.9666 (OUTLIER) cc_final: 0.9275 (mm) REVERT: F 274 ARG cc_start: 0.8839 (tpp80) cc_final: 0.8411 (tpp80) REVERT: F 277 GLU cc_start: 0.8594 (pp20) cc_final: 0.8244 (pp20) REVERT: G 83 MET cc_start: 0.9381 (ttp) cc_final: 0.9093 (tmm) REVERT: G 131 MET cc_start: 0.8530 (tpp) cc_final: 0.8267 (tpt) REVERT: G 186 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8717 (mt-10) REVERT: G 277 GLU cc_start: 0.9150 (pt0) cc_final: 0.8875 (pp20) REVERT: G 278 ASN cc_start: 0.9232 (m-40) cc_final: 0.8477 (m110) REVERT: H 131 MET cc_start: 0.8606 (tpp) cc_final: 0.8253 (tpt) REVERT: H 186 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8729 (mt-10) REVERT: H 246 ILE cc_start: 0.9653 (OUTLIER) cc_final: 0.9295 (mm) REVERT: H 277 GLU cc_start: 0.9144 (pt0) cc_final: 0.8817 (pp20) REVERT: H 278 ASN cc_start: 0.9230 (m-40) cc_final: 0.8505 (m110) REVERT: H 281 LYS cc_start: 0.9328 (ptpp) cc_final: 0.9036 (ptpp) REVERT: I 104 ASP cc_start: 0.8985 (t0) cc_final: 0.8700 (t70) REVERT: I 131 MET cc_start: 0.8516 (tpp) cc_final: 0.8173 (tpt) REVERT: I 186 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8991 (mm-30) REVERT: I 246 ILE cc_start: 0.9650 (OUTLIER) cc_final: 0.9285 (mm) REVERT: I 277 GLU cc_start: 0.9130 (pt0) cc_final: 0.8760 (pp20) REVERT: I 278 ASN cc_start: 0.9277 (m-40) cc_final: 0.8631 (m110) REVERT: I 281 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.8968 (ptpp) REVERT: J 104 ASP cc_start: 0.8966 (t0) cc_final: 0.8685 (t70) REVERT: J 131 MET cc_start: 0.8510 (tpp) cc_final: 0.8187 (tpt) REVERT: J 186 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8761 (mt-10) REVERT: J 211 ASP cc_start: 0.9387 (t0) cc_final: 0.9083 (t0) REVERT: J 246 ILE cc_start: 0.9690 (OUTLIER) cc_final: 0.9329 (mm) REVERT: J 277 GLU cc_start: 0.9099 (pt0) cc_final: 0.8899 (pp20) REVERT: J 278 ASN cc_start: 0.9220 (m-40) cc_final: 0.8670 (m110) REVERT: K 104 ASP cc_start: 0.8954 (t0) cc_final: 0.8679 (t70) REVERT: K 131 MET cc_start: 0.8625 (tpp) cc_final: 0.8278 (tpt) REVERT: K 186 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8980 (mm-30) REVERT: K 246 ILE cc_start: 0.9650 (OUTLIER) cc_final: 0.9236 (mm) REVERT: K 277 GLU cc_start: 0.9148 (pt0) cc_final: 0.8872 (pp20) REVERT: K 278 ASN cc_start: 0.9308 (m-40) cc_final: 0.8754 (m110) REVERT: K 281 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.9032 (pmtt) REVERT: L 76 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.8998 (tt) REVERT: L 131 MET cc_start: 0.8612 (tpp) cc_final: 0.8271 (tpt) REVERT: L 186 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8761 (mt-10) REVERT: L 201 ILE cc_start: 0.9403 (tp) cc_final: 0.9191 (pp) REVERT: L 274 ARG cc_start: 0.8810 (tpp80) cc_final: 0.8411 (tpp80) REVERT: L 277 GLU cc_start: 0.8587 (pp20) cc_final: 0.8271 (pp20) outliers start: 84 outliers final: 4 residues processed: 449 average time/residue: 0.6546 time to fit residues: 348.3786 Evaluate side-chains 358 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 335 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain G residue 281 LYS Chi-restraints excluded: chain H residue 246 ILE Chi-restraints excluded: chain I residue 246 ILE Chi-restraints excluded: chain I residue 281 LYS Chi-restraints excluded: chain J residue 246 ILE Chi-restraints excluded: chain K residue 246 ILE Chi-restraints excluded: chain K residue 281 LYS Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 78 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 127 optimal weight: 0.8980 chunk 17 optimal weight: 0.3980 chunk 210 optimal weight: 2.9990 chunk 145 optimal weight: 0.0770 chunk 78 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 382 optimal weight: 0.9980 chunk 360 optimal weight: 0.9980 chunk 159 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 342 optimal weight: 5.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 ASN ** G 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 ASN I 37 ASN ** I 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 ASN ** J 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 ASN L 110 ASN ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.069783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.055416 restraints weight = 98551.400| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 4.09 r_work: 0.2918 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31392 Z= 0.110 Angle : 0.646 12.166 42396 Z= 0.310 Chirality : 0.045 0.170 4644 Planarity : 0.003 0.038 5388 Dihedral : 3.825 17.102 4260 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.60 % Allowed : 22.08 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % 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 (0.13), residues: 3888 helix: 0.49 (0.11), residues: 2028 sheet: -0.42 (0.23), residues: 552 loop : -1.56 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 130 TYR 0.008 0.001 TYR H 51 PHE 0.016 0.001 PHE G 247 TRP 0.013 0.001 TRP F 198 HIS 0.002 0.000 HIS F 196 Details of bonding type rmsd covalent geometry : bond 0.00260 (31392) covalent geometry : angle 0.64584 (42396) hydrogen bonds : bond 0.03204 ( 1251) hydrogen bonds : angle 3.97542 ( 3681) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 379 time to evaluate : 1.139 Fit side-chains revert: symmetry clash REVERT: A 131 MET cc_start: 0.8593 (tpp) cc_final: 0.8206 (tpt) REVERT: A 186 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8767 (mt-10) REVERT: A 246 ILE cc_start: 0.9657 (OUTLIER) cc_final: 0.9233 (mm) REVERT: A 277 GLU cc_start: 0.9143 (pt0) cc_final: 0.8804 (pp20) REVERT: A 278 ASN cc_start: 0.9249 (m-40) cc_final: 0.8498 (m110) REVERT: A 281 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.8978 (ptpp) REVERT: B 104 ASP cc_start: 0.9025 (t0) cc_final: 0.8664 (t0) REVERT: B 131 MET cc_start: 0.8672 (tpp) cc_final: 0.8356 (tpt) REVERT: B 186 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8762 (mt-10) REVERT: B 211 ASP cc_start: 0.9277 (t0) cc_final: 0.8969 (t0) REVERT: B 246 ILE cc_start: 0.9668 (OUTLIER) cc_final: 0.9301 (mm) REVERT: B 277 GLU cc_start: 0.9134 (pt0) cc_final: 0.8898 (pp20) REVERT: B 278 ASN cc_start: 0.9280 (m-40) cc_final: 0.8706 (m110) REVERT: C 104 ASP cc_start: 0.8983 (t0) cc_final: 0.8683 (t0) REVERT: C 186 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8741 (mt-10) REVERT: C 265 MET cc_start: 0.9509 (OUTLIER) cc_final: 0.9305 (ttp) REVERT: C 277 GLU cc_start: 0.9089 (pt0) cc_final: 0.8712 (pp20) REVERT: C 278 ASN cc_start: 0.9245 (m-40) cc_final: 0.8517 (m110) REVERT: C 281 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8917 (ptpp) REVERT: D 104 ASP cc_start: 0.8989 (t0) cc_final: 0.8690 (t0) REVERT: D 131 MET cc_start: 0.8587 (tpp) cc_final: 0.8298 (tpt) REVERT: D 265 MET cc_start: 0.9484 (OUTLIER) cc_final: 0.9237 (ttp) REVERT: D 277 GLU cc_start: 0.9125 (pt0) cc_final: 0.8881 (pp20) REVERT: D 278 ASN cc_start: 0.9266 (m-40) cc_final: 0.8747 (m110) REVERT: D 281 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.9009 (pmtt) REVERT: E 104 ASP cc_start: 0.9040 (t0) cc_final: 0.8671 (t0) REVERT: E 131 MET cc_start: 0.8617 (tpp) cc_final: 0.8326 (tpt) REVERT: E 246 ILE cc_start: 0.9663 (OUTLIER) cc_final: 0.9261 (mm) REVERT: E 274 ARG cc_start: 0.9040 (tpp80) cc_final: 0.8486 (tpp80) REVERT: E 277 GLU cc_start: 0.9114 (pt0) cc_final: 0.8772 (pp20) REVERT: E 278 ASN cc_start: 0.9278 (m-40) cc_final: 0.8507 (m110) REVERT: E 281 LYS cc_start: 0.9344 (OUTLIER) cc_final: 0.8980 (ptpp) REVERT: F 104 ASP cc_start: 0.9078 (t0) cc_final: 0.8713 (t0) REVERT: F 186 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8745 (mt-10) REVERT: F 246 ILE cc_start: 0.9674 (OUTLIER) cc_final: 0.9232 (mm) REVERT: F 274 ARG cc_start: 0.8823 (tpp80) cc_final: 0.8429 (tpp80) REVERT: F 277 GLU cc_start: 0.8532 (pp20) cc_final: 0.8208 (pp20) REVERT: G 83 MET cc_start: 0.9371 (ttp) cc_final: 0.9113 (ttm) REVERT: G 104 ASP cc_start: 0.9068 (t0) cc_final: 0.8714 (m-30) REVERT: G 131 MET cc_start: 0.8664 (tpp) cc_final: 0.8354 (tpt) REVERT: G 186 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8724 (mt-10) REVERT: G 277 GLU cc_start: 0.9152 (pt0) cc_final: 0.8868 (pp20) REVERT: G 278 ASN cc_start: 0.9231 (m-40) cc_final: 0.8750 (m110) REVERT: G 281 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.9050 (pmtt) REVERT: H 95 LEU cc_start: 0.9371 (pp) cc_final: 0.9152 (pp) REVERT: H 104 ASP cc_start: 0.9055 (t0) cc_final: 0.8658 (t0) REVERT: H 131 MET cc_start: 0.8732 (tpp) cc_final: 0.8478 (tpt) REVERT: H 186 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8733 (mt-10) REVERT: H 246 ILE cc_start: 0.9682 (OUTLIER) cc_final: 0.9289 (mm) REVERT: H 277 GLU cc_start: 0.9138 (pt0) cc_final: 0.8849 (pp20) REVERT: H 278 ASN cc_start: 0.9210 (m-40) cc_final: 0.8616 (m110) REVERT: H 281 LYS cc_start: 0.9313 (ptpp) cc_final: 0.9012 (pmtt) REVERT: I 104 ASP cc_start: 0.9040 (t0) cc_final: 0.8698 (t0) REVERT: I 131 MET cc_start: 0.8673 (tpp) cc_final: 0.8344 (tpt) REVERT: I 277 GLU cc_start: 0.9116 (pt0) cc_final: 0.8722 (pp20) REVERT: I 278 ASN cc_start: 0.9258 (m-40) cc_final: 0.8562 (m110) REVERT: I 281 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.8943 (ptpp) REVERT: J 104 ASP cc_start: 0.9038 (t0) cc_final: 0.8692 (t0) REVERT: J 186 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8750 (mt-10) REVERT: J 211 ASP cc_start: 0.9352 (t0) cc_final: 0.9017 (t0) REVERT: J 246 ILE cc_start: 0.9681 (OUTLIER) cc_final: 0.9289 (mt) REVERT: J 277 GLU cc_start: 0.9109 (pt0) cc_final: 0.8891 (pp20) REVERT: J 278 ASN cc_start: 0.9187 (m-40) cc_final: 0.8602 (m110) REVERT: K 104 ASP cc_start: 0.9019 (t0) cc_final: 0.8669 (t0) REVERT: K 131 MET cc_start: 0.8724 (tpp) cc_final: 0.8367 (tpt) REVERT: K 186 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8892 (mm-30) REVERT: K 277 GLU cc_start: 0.9123 (pt0) cc_final: 0.8695 (pp20) REVERT: K 278 ASN cc_start: 0.9263 (m-40) cc_final: 0.8519 (m110) REVERT: K 281 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.8982 (ptpp) REVERT: L 76 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9002 (tt) REVERT: L 131 MET cc_start: 0.8649 (tpp) cc_final: 0.8360 (tpt) REVERT: L 186 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8716 (mt-10) REVERT: L 274 ARG cc_start: 0.8811 (tpp80) cc_final: 0.8516 (tpp80) REVERT: L 277 GLU cc_start: 0.8619 (pp20) cc_final: 0.8348 (pp20) outliers start: 51 outliers final: 3 residues processed: 403 average time/residue: 0.6543 time to fit residues: 311.7539 Evaluate side-chains 361 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 342 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain G residue 281 LYS Chi-restraints excluded: chain H residue 246 ILE Chi-restraints excluded: chain I residue 281 LYS Chi-restraints excluded: chain J residue 246 ILE Chi-restraints excluded: chain K residue 281 LYS Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 78 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 141 optimal weight: 6.9990 chunk 278 optimal weight: 6.9990 chunk 206 optimal weight: 10.0000 chunk 231 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 293 optimal weight: 10.0000 chunk 243 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 369 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 ASN ** I 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 110 ASN ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 278 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.066503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.052317 restraints weight = 100970.100| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 4.07 r_work: 0.2833 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 31392 Z= 0.294 Angle : 0.757 11.400 42396 Z= 0.379 Chirality : 0.050 0.158 4644 Planarity : 0.004 0.052 5388 Dihedral : 4.023 17.023 4260 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.54 % Allowed : 23.02 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % 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: -0.38 (0.13), residues: 3888 helix: 0.60 (0.11), residues: 2064 sheet: -0.46 (0.23), residues: 564 loop : -1.46 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 130 TYR 0.016 0.002 TYR J 217 PHE 0.019 0.002 PHE H 266 TRP 0.011 0.001 TRP K 198 HIS 0.005 0.001 HIS H 196 Details of bonding type rmsd covalent geometry : bond 0.00643 (31392) covalent geometry : angle 0.75702 (42396) hydrogen bonds : bond 0.03946 ( 1251) hydrogen bonds : angle 4.39270 ( 3681) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 348 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.9283 (ttp) cc_final: 0.8851 (ttp) REVERT: A 186 GLU cc_start: 0.9222 (mm-30) cc_final: 0.9009 (mm-30) REVERT: A 246 ILE cc_start: 0.9686 (OUTLIER) cc_final: 0.9308 (mm) REVERT: A 274 ARG cc_start: 0.9138 (tpp80) cc_final: 0.8621 (tpp80) REVERT: A 277 GLU cc_start: 0.9134 (pt0) cc_final: 0.8806 (pp20) REVERT: A 278 ASN cc_start: 0.9269 (m-40) cc_final: 0.8496 (m110) REVERT: A 281 LYS cc_start: 0.9380 (OUTLIER) cc_final: 0.9142 (ptpp) REVERT: B 104 ASP cc_start: 0.9029 (t0) cc_final: 0.8749 (t0) REVERT: B 131 MET cc_start: 0.8646 (tpp) cc_final: 0.8358 (tpt) REVERT: B 186 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8962 (mm-30) REVERT: B 211 ASP cc_start: 0.9342 (t0) cc_final: 0.9056 (t0) REVERT: B 274 ARG cc_start: 0.9200 (tpp80) cc_final: 0.8885 (tpp80) REVERT: B 277 GLU cc_start: 0.9145 (pt0) cc_final: 0.8933 (pp20) REVERT: B 278 ASN cc_start: 0.9308 (m-40) cc_final: 0.8738 (m110) REVERT: C 104 ASP cc_start: 0.9016 (t0) cc_final: 0.8726 (t0) REVERT: C 126 MET cc_start: 0.9384 (ttt) cc_final: 0.9131 (ptm) REVERT: C 131 MET cc_start: 0.8350 (tpp) cc_final: 0.8074 (tpt) REVERT: C 186 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8923 (mm-30) REVERT: C 246 ILE cc_start: 0.9687 (OUTLIER) cc_final: 0.9332 (mm) REVERT: C 274 ARG cc_start: 0.9142 (tpp80) cc_final: 0.8713 (tpp80) REVERT: C 277 GLU cc_start: 0.9113 (pt0) cc_final: 0.8863 (pp20) REVERT: C 278 ASN cc_start: 0.9275 (m-40) cc_final: 0.8711 (m110) REVERT: C 281 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.9001 (pmtt) REVERT: D 104 ASP cc_start: 0.9020 (t0) cc_final: 0.8753 (t0) REVERT: D 131 MET cc_start: 0.8590 (tpp) cc_final: 0.8307 (tpt) REVERT: D 274 ARG cc_start: 0.9121 (tpp80) cc_final: 0.8658 (tpp80) REVERT: D 277 GLU cc_start: 0.9146 (pt0) cc_final: 0.8765 (pp20) REVERT: D 278 ASN cc_start: 0.9310 (m-40) cc_final: 0.8709 (m110) REVERT: D 281 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.8979 (ptpp) REVERT: E 104 ASP cc_start: 0.9022 (t0) cc_final: 0.8722 (t0) REVERT: E 246 ILE cc_start: 0.9682 (OUTLIER) cc_final: 0.9254 (mm) REVERT: E 274 ARG cc_start: 0.9121 (tpp80) cc_final: 0.8696 (tpp80) REVERT: E 277 GLU cc_start: 0.9148 (pt0) cc_final: 0.8776 (pp20) REVERT: E 278 ASN cc_start: 0.9309 (m-40) cc_final: 0.8620 (m110) REVERT: E 281 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.8939 (ptpp) REVERT: F 104 ASP cc_start: 0.9100 (t0) cc_final: 0.8747 (t0) REVERT: F 131 MET cc_start: 0.8386 (tpp) cc_final: 0.7986 (tpt) REVERT: F 186 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8999 (mm-30) REVERT: F 274 ARG cc_start: 0.8914 (tpp80) cc_final: 0.8647 (tpp80) REVERT: G 131 MET cc_start: 0.8673 (tpp) cc_final: 0.8417 (tpt) REVERT: G 186 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8881 (mm-30) REVERT: G 274 ARG cc_start: 0.9115 (tpp80) cc_final: 0.8702 (tpp80) REVERT: G 277 GLU cc_start: 0.9153 (pt0) cc_final: 0.8881 (pp20) REVERT: G 278 ASN cc_start: 0.9272 (m-40) cc_final: 0.8573 (m110) REVERT: H 104 ASP cc_start: 0.9036 (t0) cc_final: 0.8718 (t0) REVERT: H 131 MET cc_start: 0.8763 (tpp) cc_final: 0.8388 (tpt) REVERT: H 186 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8835 (mm-30) REVERT: H 274 ARG cc_start: 0.9130 (tpp80) cc_final: 0.8626 (tpp80) REVERT: H 277 GLU cc_start: 0.9144 (pt0) cc_final: 0.8755 (pp20) REVERT: H 278 ASN cc_start: 0.9270 (m-40) cc_final: 0.8614 (m110) REVERT: H 281 LYS cc_start: 0.9335 (ptpp) cc_final: 0.9004 (ptpp) REVERT: I 104 ASP cc_start: 0.9062 (t0) cc_final: 0.8738 (t0) REVERT: I 246 ILE cc_start: 0.9681 (OUTLIER) cc_final: 0.9331 (mm) REVERT: I 274 ARG cc_start: 0.9131 (tpp80) cc_final: 0.8607 (tpp80) REVERT: I 277 GLU cc_start: 0.9142 (pt0) cc_final: 0.8748 (pp20) REVERT: I 278 ASN cc_start: 0.9298 (m-40) cc_final: 0.8638 (m110) REVERT: I 281 LYS cc_start: 0.9351 (OUTLIER) cc_final: 0.9001 (ptpp) REVERT: J 104 ASP cc_start: 0.9054 (t0) cc_final: 0.8727 (t0) REVERT: J 131 MET cc_start: 0.8333 (tpp) cc_final: 0.8019 (tpt) REVERT: J 186 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8932 (mm-30) REVERT: J 211 ASP cc_start: 0.9406 (t0) cc_final: 0.9079 (t0) REVERT: J 274 ARG cc_start: 0.9169 (tpp80) cc_final: 0.8797 (tpp80) REVERT: J 278 ASN cc_start: 0.9254 (m-40) cc_final: 0.8754 (m110) REVERT: K 104 ASP cc_start: 0.9036 (t0) cc_final: 0.8753 (t0) REVERT: K 126 MET cc_start: 0.9375 (ttt) cc_final: 0.9157 (ppp) REVERT: K 131 MET cc_start: 0.8765 (tpp) cc_final: 0.8432 (tpt) REVERT: K 265 MET cc_start: 0.9601 (OUTLIER) cc_final: 0.9282 (ttm) REVERT: K 274 ARG cc_start: 0.9214 (tpp80) cc_final: 0.8754 (tpp80) REVERT: K 277 GLU cc_start: 0.9151 (pt0) cc_final: 0.8762 (pp20) REVERT: K 278 ASN cc_start: 0.9284 (m-40) cc_final: 0.8576 (m110) REVERT: K 281 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.9013 (ptpp) REVERT: L 76 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9063 (tt) REVERT: L 131 MET cc_start: 0.8668 (tpp) cc_final: 0.8345 (tpt) REVERT: L 186 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8955 (mm-30) REVERT: L 265 MET cc_start: 0.9636 (OUTLIER) cc_final: 0.9304 (ttm) REVERT: L 274 ARG cc_start: 0.8935 (tpp80) cc_final: 0.8589 (tpp80) REVERT: L 277 GLU cc_start: 0.8645 (pp20) cc_final: 0.8332 (pp20) outliers start: 49 outliers final: 7 residues processed: 374 average time/residue: 0.7132 time to fit residues: 311.9158 Evaluate side-chains 350 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 330 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain G residue 281 LYS Chi-restraints excluded: chain H residue 246 ILE Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 246 ILE Chi-restraints excluded: chain I residue 281 LYS Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain K residue 246 ILE Chi-restraints excluded: chain K residue 265 MET Chi-restraints excluded: chain K residue 281 LYS Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 265 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 10 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 258 optimal weight: 9.9990 chunk 146 optimal weight: 8.9990 chunk 29 optimal weight: 0.7980 chunk 113 optimal weight: 0.0070 chunk 136 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 281 optimal weight: 2.9990 chunk 240 optimal weight: 0.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN ** G 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 ASN ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 110 ASN ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.068747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.054457 restraints weight = 98883.282| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 4.09 r_work: 0.2891 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 31392 Z= 0.124 Angle : 0.707 12.205 42396 Z= 0.337 Chirality : 0.046 0.155 4644 Planarity : 0.003 0.041 5388 Dihedral : 3.878 18.114 4260 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.88 % Allowed : 23.77 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.13), residues: 3888 helix: 0.81 (0.11), residues: 2112 sheet: -0.42 (0.23), residues: 552 loop : -1.65 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 130 TYR 0.008 0.001 TYR K 51 PHE 0.018 0.001 PHE F 247 TRP 0.016 0.001 TRP L 198 HIS 0.006 0.001 HIS E 196 Details of bonding type rmsd covalent geometry : bond 0.00297 (31392) covalent geometry : angle 0.70706 (42396) hydrogen bonds : bond 0.03364 ( 1251) hydrogen bonds : angle 4.07042 ( 3681) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 363 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 ASN cc_start: 0.9059 (p0) cc_final: 0.8707 (p0) REVERT: A 131 MET cc_start: 0.8216 (tpp) cc_final: 0.7943 (tpt) REVERT: A 186 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8900 (mm-30) REVERT: A 246 ILE cc_start: 0.9665 (OUTLIER) cc_final: 0.9278 (mm) REVERT: A 274 ARG cc_start: 0.9067 (tpp80) cc_final: 0.8516 (tpp80) REVERT: A 277 GLU cc_start: 0.9126 (pt0) cc_final: 0.8784 (pp20) REVERT: A 278 ASN cc_start: 0.9266 (m-40) cc_final: 0.8545 (m110) REVERT: A 281 LYS cc_start: 0.9354 (OUTLIER) cc_final: 0.8962 (ptpp) REVERT: B 104 ASP cc_start: 0.9057 (t0) cc_final: 0.8707 (t0) REVERT: B 126 MET cc_start: 0.9345 (ttt) cc_final: 0.9086 (ptm) REVERT: B 130 ARG cc_start: 0.8888 (mmp80) cc_final: 0.8593 (mmp80) REVERT: B 131 MET cc_start: 0.8676 (tpp) cc_final: 0.8327 (tpt) REVERT: B 186 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8779 (mt-10) REVERT: B 211 ASP cc_start: 0.9294 (t0) cc_final: 0.8981 (t0) REVERT: B 274 ARG cc_start: 0.9112 (tpp80) cc_final: 0.8678 (tpp80) REVERT: B 277 GLU cc_start: 0.9123 (pt0) cc_final: 0.8898 (pp20) REVERT: B 278 ASN cc_start: 0.9251 (m-40) cc_final: 0.8735 (m110) REVERT: C 104 ASP cc_start: 0.9040 (t0) cc_final: 0.8678 (t0) REVERT: C 126 MET cc_start: 0.9343 (ttt) cc_final: 0.9104 (ptm) REVERT: C 131 MET cc_start: 0.8412 (tpp) cc_final: 0.8006 (tpt) REVERT: C 186 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8740 (mt-10) REVERT: C 246 ILE cc_start: 0.9672 (OUTLIER) cc_final: 0.9296 (mm) REVERT: C 274 ARG cc_start: 0.9042 (tpp80) cc_final: 0.8558 (tpp80) REVERT: C 277 GLU cc_start: 0.9082 (pt0) cc_final: 0.8684 (pp20) REVERT: C 278 ASN cc_start: 0.9260 (m-40) cc_final: 0.8563 (m110) REVERT: C 281 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8891 (ptpp) REVERT: D 104 ASP cc_start: 0.9067 (t0) cc_final: 0.8691 (t0) REVERT: D 246 ILE cc_start: 0.9682 (OUTLIER) cc_final: 0.9287 (mm) REVERT: D 274 ARG cc_start: 0.9034 (tpp80) cc_final: 0.8585 (tpp80) REVERT: D 277 GLU cc_start: 0.9095 (pt0) cc_final: 0.8885 (pp20) REVERT: D 278 ASN cc_start: 0.9290 (m-40) cc_final: 0.8828 (m110) REVERT: D 281 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.9008 (pmtt) REVERT: E 104 ASP cc_start: 0.9010 (t0) cc_final: 0.8668 (t0) REVERT: E 130 ARG cc_start: 0.8868 (mmp80) cc_final: 0.8334 (mmp80) REVERT: E 131 MET cc_start: 0.8329 (tpp) cc_final: 0.8029 (tpt) REVERT: E 246 ILE cc_start: 0.9670 (OUTLIER) cc_final: 0.9281 (mm) REVERT: E 274 ARG cc_start: 0.9055 (tpp80) cc_final: 0.8503 (tpp80) REVERT: E 277 GLU cc_start: 0.9112 (pt0) cc_final: 0.8786 (pp20) REVERT: E 278 ASN cc_start: 0.9271 (m-40) cc_final: 0.8520 (m110) REVERT: E 281 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.8968 (ptpp) REVERT: F 104 ASP cc_start: 0.9114 (t0) cc_final: 0.8673 (t0) REVERT: F 131 MET cc_start: 0.8500 (tpp) cc_final: 0.8126 (tpt) REVERT: F 186 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8939 (mm-30) REVERT: F 274 ARG cc_start: 0.8797 (tpp80) cc_final: 0.8407 (tpp80) REVERT: F 277 GLU cc_start: 0.8481 (pp20) cc_final: 0.8164 (pp20) REVERT: G 186 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8745 (mt-10) REVERT: G 264 ARG cc_start: 0.9499 (OUTLIER) cc_final: 0.9123 (mmt90) REVERT: G 274 ARG cc_start: 0.9051 (tpp80) cc_final: 0.8521 (tpp80) REVERT: G 277 GLU cc_start: 0.9134 (pt0) cc_final: 0.8854 (pp20) REVERT: G 278 ASN cc_start: 0.9221 (m-40) cc_final: 0.8416 (m110) REVERT: H 104 ASP cc_start: 0.9053 (t0) cc_final: 0.8692 (t0) REVERT: H 131 MET cc_start: 0.8747 (tpp) cc_final: 0.8431 (tpt) REVERT: H 186 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8802 (mm-30) REVERT: H 274 ARG cc_start: 0.9071 (tpp80) cc_final: 0.8523 (tpp80) REVERT: H 277 GLU cc_start: 0.9137 (pt0) cc_final: 0.8798 (pp20) REVERT: H 278 ASN cc_start: 0.9234 (m-40) cc_final: 0.8499 (m110) REVERT: H 281 LYS cc_start: 0.9313 (ptpp) cc_final: 0.8981 (ptpp) REVERT: I 104 ASP cc_start: 0.9071 (t0) cc_final: 0.8704 (t0) REVERT: I 126 MET cc_start: 0.9582 (ptm) cc_final: 0.9338 (ppp) REVERT: I 130 ARG cc_start: 0.8888 (mmp80) cc_final: 0.8392 (mmp80) REVERT: I 131 MET cc_start: 0.8331 (tpp) cc_final: 0.8036 (tpt) REVERT: I 246 ILE cc_start: 0.9670 (OUTLIER) cc_final: 0.9292 (mm) REVERT: I 274 ARG cc_start: 0.9052 (tpp80) cc_final: 0.8550 (tpp80) REVERT: I 277 GLU cc_start: 0.9105 (pt0) cc_final: 0.8879 (pp20) REVERT: I 278 ASN cc_start: 0.9264 (m-40) cc_final: 0.8757 (m110) REVERT: I 281 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.9027 (pmtt) REVERT: J 104 ASP cc_start: 0.9071 (t0) cc_final: 0.8684 (t0) REVERT: J 131 MET cc_start: 0.8440 (tpp) cc_final: 0.8133 (tpt) REVERT: J 186 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8780 (mt-10) REVERT: J 211 ASP cc_start: 0.9363 (t0) cc_final: 0.9016 (t0) REVERT: J 274 ARG cc_start: 0.8884 (tpp80) cc_final: 0.8372 (tpp80) REVERT: J 277 GLU cc_start: 0.8671 (pp20) cc_final: 0.8374 (pp20) REVERT: J 278 ASN cc_start: 0.8917 (m-40) cc_final: 0.8575 (m110) REVERT: K 104 ASP cc_start: 0.9042 (t0) cc_final: 0.8681 (t0) REVERT: K 131 MET cc_start: 0.8740 (tpp) cc_final: 0.8415 (tpt) REVERT: K 246 ILE cc_start: 0.9677 (OUTLIER) cc_final: 0.9259 (mm) REVERT: K 274 ARG cc_start: 0.9137 (tpp80) cc_final: 0.8617 (tpp80) REVERT: K 277 GLU cc_start: 0.9098 (pt0) cc_final: 0.8690 (pp20) REVERT: K 278 ASN cc_start: 0.9261 (m-40) cc_final: 0.8523 (m110) REVERT: K 281 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.8931 (ptpp) REVERT: L 131 MET cc_start: 0.8626 (tpp) cc_final: 0.8330 (tpt) REVERT: L 186 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8869 (mm-30) REVERT: L 265 MET cc_start: 0.9576 (OUTLIER) cc_final: 0.9214 (ttm) REVERT: L 274 ARG cc_start: 0.8837 (tpp80) cc_final: 0.8443 (tpp80) REVERT: L 277 GLU cc_start: 0.8623 (pp20) cc_final: 0.8292 (pp20) outliers start: 28 outliers final: 4 residues processed: 379 average time/residue: 0.6955 time to fit residues: 307.9086 Evaluate side-chains 348 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 330 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain G residue 264 ARG Chi-restraints excluded: chain G residue 281 LYS Chi-restraints excluded: chain H residue 246 ILE Chi-restraints excluded: chain I residue 246 ILE Chi-restraints excluded: chain I residue 281 LYS Chi-restraints excluded: chain K residue 246 ILE Chi-restraints excluded: chain K residue 281 LYS Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 265 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 206 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 359 optimal weight: 0.7980 chunk 183 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 144 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 chunk 230 optimal weight: 4.9990 chunk 335 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 364 optimal weight: 7.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.068170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.053908 restraints weight = 99593.151| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 4.09 r_work: 0.2871 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 31392 Z= 0.171 Angle : 0.721 12.775 42396 Z= 0.348 Chirality : 0.047 0.155 4644 Planarity : 0.004 0.041 5388 Dihedral : 3.879 17.969 4260 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.88 % Allowed : 24.15 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % 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: -0.12 (0.14), residues: 3888 helix: 0.94 (0.11), residues: 2112 sheet: -0.56 (0.23), residues: 576 loop : -1.59 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 130 TYR 0.011 0.001 TYR I 217 PHE 0.016 0.001 PHE C 266 TRP 0.012 0.001 TRP K 198 HIS 0.005 0.001 HIS I 196 Details of bonding type rmsd covalent geometry : bond 0.00400 (31392) covalent geometry : angle 0.72097 (42396) hydrogen bonds : bond 0.03443 ( 1251) hydrogen bonds : angle 4.10342 ( 3681) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 340 time to evaluate : 1.255 Fit side-chains revert: symmetry clash REVERT: A 83 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8918 (ppp) REVERT: A 131 MET cc_start: 0.8205 (tpp) cc_final: 0.7944 (tpt) REVERT: A 186 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8964 (mm-30) REVERT: A 246 ILE cc_start: 0.9665 (OUTLIER) cc_final: 0.9263 (mm) REVERT: A 274 ARG cc_start: 0.9084 (tpp80) cc_final: 0.8508 (tpp80) REVERT: A 277 GLU cc_start: 0.9146 (pt0) cc_final: 0.8758 (pp20) REVERT: A 278 ASN cc_start: 0.9276 (m-40) cc_final: 0.8563 (m110) REVERT: A 281 LYS cc_start: 0.9369 (OUTLIER) cc_final: 0.8977 (ptpp) REVERT: B 104 ASP cc_start: 0.9042 (t0) cc_final: 0.8700 (t0) REVERT: B 126 MET cc_start: 0.9376 (ttt) cc_final: 0.9111 (ptm) REVERT: B 131 MET cc_start: 0.8712 (tpp) cc_final: 0.8408 (tpt) REVERT: B 186 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8790 (mt-10) REVERT: B 211 ASP cc_start: 0.9325 (t0) cc_final: 0.9023 (t0) REVERT: B 274 ARG cc_start: 0.9142 (tpp80) cc_final: 0.8700 (tpp80) REVERT: B 277 GLU cc_start: 0.9132 (pt0) cc_final: 0.8893 (pp20) REVERT: B 278 ASN cc_start: 0.9258 (m-40) cc_final: 0.8608 (m110) REVERT: C 104 ASP cc_start: 0.9017 (t0) cc_final: 0.8677 (t0) REVERT: C 126 MET cc_start: 0.9334 (ttt) cc_final: 0.9072 (ptm) REVERT: C 130 ARG cc_start: 0.8853 (mmp80) cc_final: 0.8593 (mmp80) REVERT: C 131 MET cc_start: 0.8479 (tpp) cc_final: 0.8103 (tpt) REVERT: C 186 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8861 (mm-30) REVERT: C 246 ILE cc_start: 0.9672 (OUTLIER) cc_final: 0.9272 (mm) REVERT: C 274 ARG cc_start: 0.9074 (tpp80) cc_final: 0.8507 (tpp80) REVERT: C 277 GLU cc_start: 0.9104 (pt0) cc_final: 0.8679 (pp20) REVERT: C 278 ASN cc_start: 0.9258 (m-40) cc_final: 0.8542 (m110) REVERT: C 281 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.8939 (ptpp) REVERT: D 104 ASP cc_start: 0.9029 (t0) cc_final: 0.8686 (t0) REVERT: D 130 ARG cc_start: 0.8865 (mmp80) cc_final: 0.8556 (mmp80) REVERT: D 131 MET cc_start: 0.8170 (tpp) cc_final: 0.7906 (tpt) REVERT: D 246 ILE cc_start: 0.9679 (OUTLIER) cc_final: 0.9257 (mm) REVERT: D 274 ARG cc_start: 0.9052 (tpp80) cc_final: 0.8489 (tpp80) REVERT: D 277 GLU cc_start: 0.9112 (pt0) cc_final: 0.8788 (pp20) REVERT: D 278 ASN cc_start: 0.9308 (m-40) cc_final: 0.8630 (m110) REVERT: D 281 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.9021 (ptpp) REVERT: E 104 ASP cc_start: 0.9005 (t0) cc_final: 0.8670 (t0) REVERT: E 130 ARG cc_start: 0.8836 (mmp80) cc_final: 0.8290 (mmp80) REVERT: E 131 MET cc_start: 0.8308 (tpp) cc_final: 0.7986 (tpt) REVERT: E 246 ILE cc_start: 0.9668 (OUTLIER) cc_final: 0.9270 (mm) REVERT: E 274 ARG cc_start: 0.9080 (tpp80) cc_final: 0.8531 (tpp80) REVERT: E 277 GLU cc_start: 0.9131 (pt0) cc_final: 0.8756 (pp20) REVERT: E 278 ASN cc_start: 0.9288 (m-40) cc_final: 0.8576 (m110) REVERT: E 281 LYS cc_start: 0.9368 (OUTLIER) cc_final: 0.8955 (ptpp) REVERT: F 104 ASP cc_start: 0.9102 (t0) cc_final: 0.8695 (t0) REVERT: F 131 MET cc_start: 0.8532 (tpp) cc_final: 0.8146 (tpt) REVERT: F 186 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8986 (mm-30) REVERT: F 274 ARG cc_start: 0.8817 (tpp80) cc_final: 0.8450 (tpp80) REVERT: F 277 GLU cc_start: 0.8396 (pp20) cc_final: 0.8112 (pp20) REVERT: G 130 ARG cc_start: 0.8845 (mmp80) cc_final: 0.8595 (mmp80) REVERT: G 186 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8753 (mt-10) REVERT: G 264 ARG cc_start: 0.9503 (OUTLIER) cc_final: 0.9080 (mmt90) REVERT: G 274 ARG cc_start: 0.9092 (tpp80) cc_final: 0.8626 (tpp80) REVERT: G 277 GLU cc_start: 0.9147 (pt0) cc_final: 0.8886 (pp20) REVERT: G 278 ASN cc_start: 0.9240 (m-40) cc_final: 0.8733 (m110) REVERT: G 281 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.9032 (pmtt) REVERT: H 104 ASP cc_start: 0.9016 (t0) cc_final: 0.8715 (t0) REVERT: H 131 MET cc_start: 0.8778 (tpp) cc_final: 0.8492 (tpt) REVERT: H 186 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8750 (mt-10) REVERT: H 274 ARG cc_start: 0.9083 (tpp80) cc_final: 0.8521 (tpp80) REVERT: H 277 GLU cc_start: 0.9143 (pt0) cc_final: 0.8786 (pp20) REVERT: H 278 ASN cc_start: 0.9254 (m-40) cc_final: 0.8563 (m110) REVERT: H 281 LYS cc_start: 0.9334 (ptpp) cc_final: 0.9039 (ptpp) REVERT: I 104 ASP cc_start: 0.9057 (t0) cc_final: 0.8724 (t0) REVERT: I 126 MET cc_start: 0.9621 (ptm) cc_final: 0.9362 (ppp) REVERT: I 130 ARG cc_start: 0.8859 (mmp80) cc_final: 0.8560 (mmp80) REVERT: I 131 MET cc_start: 0.8333 (tpp) cc_final: 0.8004 (tpt) REVERT: I 246 ILE cc_start: 0.9667 (OUTLIER) cc_final: 0.9300 (mm) REVERT: I 274 ARG cc_start: 0.9069 (tpp80) cc_final: 0.8508 (tpp80) REVERT: I 277 GLU cc_start: 0.9115 (pt0) cc_final: 0.8735 (pp20) REVERT: I 278 ASN cc_start: 0.9284 (m-40) cc_final: 0.8635 (m110) REVERT: I 281 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.8978 (ptpp) REVERT: J 104 ASP cc_start: 0.9061 (t0) cc_final: 0.8700 (t0) REVERT: J 131 MET cc_start: 0.8527 (tpp) cc_final: 0.8232 (tpt) REVERT: J 186 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8941 (mm-30) REVERT: J 211 ASP cc_start: 0.9385 (t0) cc_final: 0.9043 (t0) REVERT: J 274 ARG cc_start: 0.8929 (tpp80) cc_final: 0.8649 (tpp80) REVERT: K 104 ASP cc_start: 0.9043 (t0) cc_final: 0.8707 (t0) REVERT: K 126 MET cc_start: 0.9572 (ptm) cc_final: 0.9360 (ppp) REVERT: K 186 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8773 (pt0) REVERT: K 274 ARG cc_start: 0.9158 (tpp80) cc_final: 0.8636 (tpp80) REVERT: K 277 GLU cc_start: 0.9119 (pt0) cc_final: 0.8716 (pp20) REVERT: K 278 ASN cc_start: 0.9274 (m-40) cc_final: 0.8533 (m110) REVERT: K 281 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.8942 (ptpp) REVERT: L 131 MET cc_start: 0.8642 (tpp) cc_final: 0.8335 (tpt) REVERT: L 186 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8895 (mm-30) REVERT: L 265 MET cc_start: 0.9591 (OUTLIER) cc_final: 0.9249 (ttm) REVERT: L 274 ARG cc_start: 0.8851 (tpp80) cc_final: 0.8436 (tpp80) REVERT: L 277 GLU cc_start: 0.8598 (pp20) cc_final: 0.8252 (pp20) outliers start: 28 outliers final: 3 residues processed: 357 average time/residue: 0.7351 time to fit residues: 304.9606 Evaluate side-chains 350 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 332 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 264 ARG Chi-restraints excluded: chain G residue 281 LYS Chi-restraints excluded: chain I residue 246 ILE Chi-restraints excluded: chain I residue 281 LYS Chi-restraints excluded: chain K residue 281 LYS Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 265 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 340 optimal weight: 1.9990 chunk 377 optimal weight: 7.9990 chunk 366 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 93 optimal weight: 0.6980 chunk 259 optimal weight: 5.9990 chunk 363 optimal weight: 0.0570 chunk 128 optimal weight: 10.0000 chunk 288 optimal weight: 4.9990 chunk 307 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 overall best weight: 1.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.068824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.054539 restraints weight = 99509.286| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 4.10 r_work: 0.2887 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 31392 Z= 0.136 Angle : 0.717 12.876 42396 Z= 0.341 Chirality : 0.046 0.153 4644 Planarity : 0.004 0.039 5388 Dihedral : 3.821 18.057 4260 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.66 % Allowed : 24.59 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.14), residues: 3888 helix: 0.81 (0.11), residues: 2184 sheet: -0.52 (0.23), residues: 552 loop : -1.60 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 130 TYR 0.009 0.001 TYR I 217 PHE 0.016 0.001 PHE C 266 TRP 0.013 0.001 TRP K 198 HIS 0.005 0.001 HIS I 196 Details of bonding type rmsd covalent geometry : bond 0.00324 (31392) covalent geometry : angle 0.71700 (42396) hydrogen bonds : bond 0.03305 ( 1251) hydrogen bonds : angle 4.00938 ( 3681) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8941.38 seconds wall clock time: 153 minutes 33.62 seconds (9213.62 seconds total)