Starting phenix.real_space_refine on Thu Mar 21 18:50:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jcv_9798/03_2024/6jcv_9798.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jcv_9798/03_2024/6jcv_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jcv_9798/03_2024/6jcv_9798.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jcv_9798/03_2024/6jcv_9798.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jcv_9798/03_2024/6jcv_9798.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jcv_9798/03_2024/6jcv_9798.pdb" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Residue "A ARG 35": "NH1" <-> "NH2" Residue "A ASP 270": "OD1" <-> "OD2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B ASP 270": "OD1" <-> "OD2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C ASP 270": "OD1" <-> "OD2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "D ARG 35": "NH1" <-> "NH2" Residue "D ASP 270": "OD1" <-> "OD2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "E ARG 35": "NH1" <-> "NH2" Residue "E ASP 270": "OD1" <-> "OD2" Residue "E ARG 273": "NH1" <-> "NH2" Residue "F ARG 35": "NH1" <-> "NH2" Residue "F ASP 270": "OD1" <-> "OD2" Residue "F ARG 273": "NH1" <-> "NH2" Residue "G ARG 35": "NH1" <-> "NH2" Residue "G ASP 270": "OD1" <-> "OD2" Residue "G ARG 273": "NH1" <-> "NH2" Residue "H ARG 35": "NH1" <-> "NH2" Residue "H ASP 270": "OD1" <-> "OD2" Residue "H ARG 273": "NH1" <-> "NH2" Residue "I ARG 35": "NH1" <-> "NH2" Residue "I ASP 270": "OD1" <-> "OD2" Residue "I ARG 273": "NH1" <-> "NH2" Residue "J ARG 35": "NH1" <-> "NH2" Residue "J ASP 270": "OD1" <-> "OD2" Residue "J ARG 273": "NH1" <-> "NH2" Residue "K ARG 35": "NH1" <-> "NH2" Residue "K ASP 270": "OD1" <-> "OD2" Residue "K ARG 273": "NH1" <-> "NH2" Residue "L ARG 35": "NH1" <-> "NH2" Residue "L ASP 270": "OD1" <-> "OD2" Residue "L ARG 273": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 14.50, per 1000 atoms: 0.47 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 - 3.50 Amino acid : False - 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: 12.08 Conformation dependent library (CDL) restraints added in 4.8 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: 3.03 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: 9.59 Time building geometry restraints manager: 12.95 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: 99.70 - 106.64: 733 106.64 - 113.58: 17119 113.58 - 120.51: 13491 120.51 - 127.45: 10733 127.45 - 134.39: 320 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 2.440 nonbonded pdb=" OG1 THR I 4 " pdb=" O ALA I 179 " model vdw 2.341 2.440 nonbonded pdb=" OG1 THR A 4 " pdb=" O ALA A 179 " model vdw 2.341 2.440 nonbonded pdb=" OG1 THR C 4 " pdb=" O ALA C 179 " model vdw 2.342 2.440 nonbonded pdb=" OG1 THR B 4 " pdb=" O ALA B 179 " model vdw 2.342 2.440 ... (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 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: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 9.240 Check model and map are aligned: 0.490 Set scattering table: 0.300 Process input model: 71.440 Find NCS groups from input model: 2.220 Set up NCS constraints: 0.190 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:13.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.150 ------------------------------------------------------------------------------- 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= 0.476 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 : 5.00 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.017 0.002 TRP G 198 HIS 0.003 0.001 HIS E 140 PHE 0.012 0.002 PHE K 288 TYR 0.014 0.002 TYR D 282 ARG 0.003 0.001 ARG J 328 *********************** 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 fitting. rotamer outliers: 0 poor density : 515 time to evaluate : 3.582 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: 0.7620 (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: 0.8095 (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: 0.8084 (m-30) cc_final: 0.7872 (m-30) REVERT: D 281 LYS cc_start: 0.8544 (ptpp) cc_final: 0.8269 (ptpp) REVERT: D 285 ASP cc_start: 0.8113 (m-30) cc_final: 0.7900 (m-30) REVERT: E 211 ASP cc_start: 0.8227 (m-30) cc_final: 0.7928 (m-30) REVERT: E 281 LYS cc_start: 0.8546 (ptpp) cc_final: 0.8244 (ptpp) REVERT: F 211 ASP cc_start: 0.8265 (m-30) cc_final: 0.7962 (m-30) REVERT: F 281 LYS cc_start: 0.8554 (ptpp) cc_final: 0.8014 (ptpp) REVERT: F 285 ASP cc_start: 0.8159 (m-30) cc_final: 0.7951 (m-30) REVERT: G 281 LYS cc_start: 0.8556 (ptpp) cc_final: 0.8283 (ptpp) REVERT: G 285 ASP cc_start: 0.8093 (m-30) cc_final: 0.7876 (m-30) REVERT: H 281 LYS cc_start: 0.8554 (ptpp) cc_final: 0.8283 (ptpp) REVERT: H 285 ASP cc_start: 0.8113 (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: 0.8124 (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: 0.8248 (m-30) cc_final: 0.7913 (m-30) REVERT: K 281 LYS cc_start: 0.8547 (ptpp) cc_final: 0.8251 (ptpp) REVERT: K 285 ASP cc_start: 0.8127 (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: 0.7903 (m-30) outliers start: 0 outliers final: 0 residues processed: 515 average time/residue: 1.6022 time to fit residues: 951.4439 Evaluate side-chains 370 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 2.9990 chunk 291 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 196 optimal weight: 0.0040 chunk 155 optimal weight: 0.9990 chunk 300 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 224 optimal weight: 0.2980 chunk 348 optimal weight: 0.9990 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN A 258 GLN A 278 ASN ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS B 278 ASN C 37 ASN C 253 HIS C 258 GLN C 278 ASN ** D 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 GLN D 278 ASN ** E 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 GLN E 278 ASN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN F 258 GLN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 253 HIS G 258 GLN G 278 ASN ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 258 GLN H 278 ASN ** I 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 258 GLN I 278 ASN ** J 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 GLN J 278 ASN ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 258 GLN K 278 ASN ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 110 ASN L 258 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31392 Z= 0.197 Angle : 0.616 8.990 42396 Z= 0.324 Chirality : 0.045 0.165 4644 Planarity : 0.005 0.045 5388 Dihedral : 4.633 15.721 4260 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.98 % Allowed : 14.78 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.11), residues: 3888 helix: -2.48 (0.09), residues: 1980 sheet: -1.41 (0.23), residues: 540 loop : -2.25 (0.13), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 198 HIS 0.001 0.000 HIS G 252 PHE 0.011 0.001 PHE H 184 TYR 0.014 0.001 TYR F 268 ARG 0.004 0.000 ARG K 274 *********************** 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 516 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 453 time to evaluate : 3.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7333 (pp20) REVERT: B 291 GLU cc_start: 0.7625 (pp20) cc_final: 0.7407 (pp20) REVERT: D 291 GLU cc_start: 0.7618 (pp20) cc_final: 0.7400 (pp20) REVERT: F 126 MET cc_start: 0.8134 (ttm) cc_final: 0.7900 (ttm) REVERT: G 76 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9161 (tp) REVERT: H 83 MET cc_start: 0.8222 (ttp) cc_final: 0.7820 (ttp) REVERT: H 291 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7326 (pp20) REVERT: I 291 GLU cc_start: 0.7633 (pp20) cc_final: 0.7421 (pp20) REVERT: K 83 MET cc_start: 0.8226 (ttp) cc_final: 0.7837 (ttp) REVERT: K 211 ASP cc_start: 0.8097 (m-30) cc_final: 0.7755 (m-30) outliers start: 63 outliers final: 13 residues processed: 475 average time/residue: 1.4478 time to fit residues: 805.6050 Evaluate side-chains 362 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 346 time to evaluate : 3.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain B 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 202 LEU 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 270 ASP Chi-restraints excluded: chain H residue 291 GLU Chi-restraints excluded: chain I residue 270 ASP Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 270 ASP Chi-restraints excluded: chain L residue 270 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 290 optimal weight: 10.0000 chunk 237 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 349 optimal weight: 0.0370 chunk 377 optimal weight: 7.9990 chunk 311 optimal weight: 9.9990 chunk 346 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 280 optimal weight: 8.9990 overall best weight: 4.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 196 HIS A 253 HIS B 37 ASN B 196 HIS B 258 GLN C 37 ASN C 196 HIS D 37 ASN D 196 HIS D 253 HIS E 37 ASN E 196 HIS E 253 HIS F 37 ASN F 110 ASN F 196 HIS F 253 HIS G 37 ASN G 196 HIS H 37 ASN H 196 HIS H 253 HIS I 37 ASN I 196 HIS I 253 HIS J 37 ASN J 196 HIS J 253 HIS K 37 ASN K 196 HIS L 37 ASN L 110 ASN L 196 HIS L 253 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 31392 Z= 0.393 Angle : 0.691 8.596 42396 Z= 0.361 Chirality : 0.050 0.162 4644 Planarity : 0.004 0.038 5388 Dihedral : 4.405 16.990 4260 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.02 % Allowed : 18.74 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.12), residues: 3888 helix: -1.21 (0.10), residues: 2064 sheet: -1.41 (0.24), residues: 564 loop : -2.01 (0.15), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 198 HIS 0.002 0.001 HIS G 140 PHE 0.009 0.001 PHE F 288 TYR 0.015 0.002 TYR C 217 ARG 0.005 0.001 ARG B 273 *********************** 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 446 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 350 time to evaluate : 3.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.8396 (ttp) cc_final: 0.7702 (ttp) REVERT: A 186 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8226 (mm-30) REVERT: A 291 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7494 (pp20) REVERT: B 76 LEU cc_start: 0.9556 (OUTLIER) cc_final: 0.9268 (tt) REVERT: B 131 MET cc_start: 0.8349 (tpp) cc_final: 0.8029 (tpt) REVERT: B 186 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8183 (mm-30) REVERT: B 281 LYS cc_start: 0.8902 (ptpp) cc_final: 0.8559 (ptpp) REVERT: C 76 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9232 (tt) REVERT: C 126 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.8027 (ttm) REVERT: C 278 ASN cc_start: 0.8433 (m-40) cc_final: 0.8119 (m110) REVERT: D 76 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9244 (tt) REVERT: D 126 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.8028 (ttm) REVERT: D 131 MET cc_start: 0.8261 (tpp) cc_final: 0.7942 (tpt) REVERT: E 76 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9171 (tt) REVERT: E 83 MET cc_start: 0.8309 (ttp) cc_final: 0.7666 (ttp) REVERT: E 131 MET cc_start: 0.8353 (tpp) cc_final: 0.8037 (tpt) REVERT: E 274 ARG cc_start: 0.8186 (tpp80) cc_final: 0.7921 (tpp80) REVERT: F 126 MET cc_start: 0.8284 (ttm) cc_final: 0.8082 (ttm) REVERT: F 211 ASP cc_start: 0.8127 (t0) cc_final: 0.7895 (t0) REVERT: G 76 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9070 (tp) REVERT: G 83 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8432 (tpp) REVERT: G 278 ASN cc_start: 0.8473 (m-40) cc_final: 0.8199 (m110) REVERT: H 126 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.8019 (ttm) REVERT: H 278 ASN cc_start: 0.8456 (m-40) cc_final: 0.8193 (m110) REVERT: H 291 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7514 (pp20) REVERT: I 76 LEU cc_start: 0.9557 (OUTLIER) cc_final: 0.9165 (tt) REVERT: I 83 MET cc_start: 0.8314 (ttp) cc_final: 0.7628 (ttp) REVERT: I 278 ASN cc_start: 0.8366 (m-40) cc_final: 0.8128 (m110) REVERT: I 281 LYS cc_start: 0.8904 (ptpp) cc_final: 0.8674 (ptpp) REVERT: J 76 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9128 (tt) REVERT: J 83 MET cc_start: 0.8303 (ttp) cc_final: 0.7641 (ttp) REVERT: J 211 ASP cc_start: 0.8025 (t0) cc_final: 0.7782 (t0) REVERT: J 278 ASN cc_start: 0.8403 (m-40) cc_final: 0.8126 (m110) REVERT: K 278 ASN cc_start: 0.8583 (m-40) cc_final: 0.8166 (m110) outliers start: 96 outliers final: 12 residues processed: 389 average time/residue: 1.3869 time to fit residues: 637.0906 Evaluate side-chains 343 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 318 time to evaluate : 3.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain E residue 76 LEU 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 83 MET Chi-restraints excluded: chain G residue 270 ASP Chi-restraints excluded: chain H residue 126 MET Chi-restraints excluded: chain H residue 270 ASP Chi-restraints excluded: chain H residue 291 GLU Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 270 ASP Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 270 ASP Chi-restraints excluded: chain L residue 270 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 0.9990 chunk 262 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 166 optimal weight: 6.9990 chunk 234 optimal weight: 5.9990 chunk 350 optimal weight: 3.9990 chunk 371 optimal weight: 0.9980 chunk 183 optimal weight: 10.0000 chunk 332 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN B 278 ASN C 37 ASN D 278 ASN E 278 ASN F 278 ASN K 253 HIS L 278 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 31392 Z= 0.300 Angle : 0.650 8.947 42396 Z= 0.329 Chirality : 0.048 0.156 4644 Planarity : 0.004 0.031 5388 Dihedral : 4.229 14.795 4260 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.87 % Allowed : 19.53 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.13), residues: 3888 helix: -0.53 (0.11), residues: 2136 sheet: -1.23 (0.22), residues: 564 loop : -2.06 (0.15), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 198 HIS 0.003 0.001 HIS H 196 PHE 0.010 0.001 PHE I 247 TYR 0.010 0.001 TYR C 217 ARG 0.005 0.001 ARG H 130 *********************** 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 480 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 357 time to evaluate : 3.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ASN cc_start: 0.8625 (p0) cc_final: 0.8359 (p0) REVERT: A 131 MET cc_start: 0.8389 (tpp) cc_final: 0.8067 (tpt) REVERT: A 186 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8265 (mm-30) REVERT: A 274 ARG cc_start: 0.8201 (tpp80) cc_final: 0.7862 (tpp80) REVERT: A 278 ASN cc_start: 0.8470 (m-40) cc_final: 0.8234 (m110) REVERT: B 76 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9251 (tt) REVERT: B 104 ASP cc_start: 0.8361 (t0) cc_final: 0.7935 (m-30) REVERT: B 126 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7995 (ttm) REVERT: B 131 MET cc_start: 0.8460 (tpp) cc_final: 0.8247 (OUTLIER) REVERT: B 186 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8264 (mm-30) REVERT: B 274 ARG cc_start: 0.8176 (tpp80) cc_final: 0.7787 (tpp80) REVERT: C 76 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9292 (tt) REVERT: C 126 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7763 (ttm) REVERT: C 130 ARG cc_start: 0.8358 (mmp80) cc_final: 0.8050 (mmp80) REVERT: C 131 MET cc_start: 0.8366 (tpp) cc_final: 0.8044 (OUTLIER) REVERT: C 246 ILE cc_start: 0.9446 (OUTLIER) cc_final: 0.9213 (mm) REVERT: D 76 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.9305 (tt) REVERT: D 126 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7755 (ttm) REVERT: D 246 ILE cc_start: 0.9448 (OUTLIER) cc_final: 0.9223 (mm) REVERT: D 274 ARG cc_start: 0.8193 (tpp80) cc_final: 0.7865 (tpp80) REVERT: E 76 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9162 (tt) REVERT: E 126 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.8018 (ttm) REVERT: E 274 ARG cc_start: 0.8095 (tpp80) cc_final: 0.7774 (tpp80) REVERT: E 278 ASN cc_start: 0.8498 (m-40) cc_final: 0.8257 (m110) REVERT: F 126 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7928 (ttm) REVERT: F 131 MET cc_start: 0.8359 (tpp) cc_final: 0.8045 (tpt) REVERT: F 211 ASP cc_start: 0.8276 (t0) cc_final: 0.7987 (t0) REVERT: F 274 ARG cc_start: 0.8176 (tpp80) cc_final: 0.7973 (tpp80) REVERT: G 110 ASN cc_start: 0.8496 (p0) cc_final: 0.7963 (p0) REVERT: G 126 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.8027 (ttm) REVERT: G 130 ARG cc_start: 0.8352 (mmp80) cc_final: 0.8053 (mmp80) REVERT: G 131 MET cc_start: 0.8375 (tpp) cc_final: 0.8056 (OUTLIER) REVERT: G 274 ARG cc_start: 0.8221 (tpp80) cc_final: 0.7883 (tpp80) REVERT: H 126 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7738 (ttm) REVERT: H 131 MET cc_start: 0.8374 (tpp) cc_final: 0.8088 (OUTLIER) REVERT: I 76 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9144 (tt) REVERT: I 126 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.8019 (ttm) REVERT: I 130 ARG cc_start: 0.8513 (mmp80) cc_final: 0.8040 (mmp80) REVERT: I 131 MET cc_start: 0.8347 (tpp) cc_final: 0.8023 (OUTLIER) REVERT: I 274 ARG cc_start: 0.8201 (tpp80) cc_final: 0.7835 (tpp80) REVERT: I 278 ASN cc_start: 0.8417 (m-40) cc_final: 0.8213 (m110) REVERT: J 76 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9172 (tt) REVERT: J 131 MET cc_start: 0.8359 (tpp) cc_final: 0.8051 (OUTLIER) REVERT: J 211 ASP cc_start: 0.8202 (t0) cc_final: 0.7911 (t0) REVERT: J 274 ARG cc_start: 0.8199 (tpp80) cc_final: 0.7859 (tpp80) REVERT: K 83 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8475 (ttp) REVERT: K 126 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.8027 (ttm) REVERT: K 131 MET cc_start: 0.8355 (tpp) cc_final: 0.8021 (OUTLIER) REVERT: L 131 MET cc_start: 0.8376 (tpp) cc_final: 0.8068 (OUTLIER) outliers start: 123 outliers final: 31 residues processed: 399 average time/residue: 1.3859 time to fit residues: 653.2435 Evaluate side-chains 379 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 338 time to evaluate : 3.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 78 ILE 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 D residue 40 ASN Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain F residue 270 ASP Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain G residue 270 ASP Chi-restraints excluded: chain H residue 126 MET Chi-restraints excluded: chain H residue 270 ASP Chi-restraints excluded: chain I residue 40 ASN Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 126 MET Chi-restraints excluded: chain I residue 270 ASP Chi-restraints excluded: chain J residue 76 LEU Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 110 ASN Chi-restraints excluded: chain K residue 126 MET Chi-restraints excluded: chain K residue 270 ASP Chi-restraints excluded: chain L residue 126 MET 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 309 optimal weight: 0.9990 chunk 210 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 276 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 316 optimal weight: 3.9990 chunk 256 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 189 optimal weight: 1.9990 chunk 333 optimal weight: 0.1980 chunk 93 optimal weight: 0.0980 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 278 ASN C 37 ASN C 278 ASN D 278 ASN ** F 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 278 ASN H 278 ASN J 278 ASN K 278 ASN L 278 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 31392 Z= 0.173 Angle : 0.611 12.096 42396 Z= 0.303 Chirality : 0.046 0.150 4644 Planarity : 0.003 0.032 5388 Dihedral : 3.970 16.704 4260 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.18 % Allowed : 21.76 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.13), residues: 3888 helix: -0.19 (0.11), residues: 2136 sheet: -0.86 (0.23), residues: 540 loop : -1.97 (0.15), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 198 HIS 0.003 0.001 HIS K 196 PHE 0.013 0.001 PHE F 266 TYR 0.008 0.001 TYR B 268 ARG 0.005 0.000 ARG F 273 *********************** 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 517 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 416 time to evaluate : 3.632 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8194 (mm-30) REVERT: B 104 ASP cc_start: 0.8335 (t0) cc_final: 0.7921 (m-30) REVERT: B 126 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7875 (ttm) REVERT: B 186 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8180 (mm-30) REVERT: B 274 ARG cc_start: 0.8144 (tpp80) cc_final: 0.7732 (tpp80) REVERT: C 131 MET cc_start: 0.8437 (tpp) cc_final: 0.8212 (tpt) REVERT: D 76 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9038 (tt) REVERT: D 131 MET cc_start: 0.8240 (tpp) cc_final: 0.7946 (tpt) REVERT: D 246 ILE cc_start: 0.9460 (OUTLIER) cc_final: 0.9252 (mt) REVERT: D 274 ARG cc_start: 0.8184 (tpp80) cc_final: 0.7942 (tpp80) REVERT: E 274 ARG cc_start: 0.8047 (tpp80) cc_final: 0.7633 (tpp80) REVERT: E 277 GLU cc_start: 0.7636 (pp20) cc_final: 0.7398 (pp20) REVERT: F 211 ASP cc_start: 0.8281 (t0) cc_final: 0.7967 (t0) REVERT: F 274 ARG cc_start: 0.8193 (tpp80) cc_final: 0.7968 (tpp80) REVERT: G 83 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8247 (ttm) REVERT: G 131 MET cc_start: 0.8471 (tpp) cc_final: 0.8253 (tpt) REVERT: H 131 MET cc_start: 0.8459 (tpp) cc_final: 0.8228 (OUTLIER) REVERT: H 278 ASN cc_start: 0.8610 (m-40) cc_final: 0.8333 (m110) REVERT: I 83 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8158 (ttp) REVERT: I 131 MET cc_start: 0.8461 (tpp) cc_final: 0.8240 (tpt) REVERT: I 274 ARG cc_start: 0.8113 (tpp80) cc_final: 0.7688 (tpp80) REVERT: J 131 MET cc_start: 0.8463 (tpp) cc_final: 0.8238 (tpt) REVERT: J 211 ASP cc_start: 0.8185 (t0) cc_final: 0.7858 (t0) REVERT: J 274 ARG cc_start: 0.8164 (tpp80) cc_final: 0.7923 (tpp80) REVERT: K 40 ASN cc_start: 0.8401 (OUTLIER) cc_final: 0.8107 (p0) REVERT: K 83 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8385 (ttp) REVERT: K 131 MET cc_start: 0.8473 (tpp) cc_final: 0.8232 (tpt) REVERT: L 131 MET cc_start: 0.8481 (tpp) cc_final: 0.8253 (tpt) outliers start: 101 outliers final: 24 residues processed: 461 average time/residue: 1.3683 time to fit residues: 746.7518 Evaluate side-chains 348 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 318 time to evaluate : 3.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain F residue 40 ASN Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 270 ASP Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 270 ASP Chi-restraints excluded: chain H residue 270 ASP Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain I residue 270 ASP Chi-restraints excluded: chain J residue 40 ASN Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 40 ASN Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 110 ASN Chi-restraints excluded: chain K residue 270 ASP 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 124 optimal weight: 0.8980 chunk 334 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 217 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 371 optimal weight: 3.9990 chunk 308 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 195 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 ASN C 278 ASN D 278 ASN ** E 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 278 ASN I 278 ASN ** J 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 31392 Z= 0.218 Angle : 0.651 9.851 42396 Z= 0.321 Chirality : 0.046 0.169 4644 Planarity : 0.003 0.034 5388 Dihedral : 3.908 16.722 4260 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.30 % Allowed : 22.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.13), residues: 3888 helix: 0.08 (0.11), residues: 2124 sheet: -0.75 (0.22), residues: 540 loop : -1.75 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 198 HIS 0.003 0.001 HIS H 196 PHE 0.017 0.002 PHE E 266 TYR 0.010 0.001 TYR H 217 ARG 0.005 0.000 ARG H 274 *********************** 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 429 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 356 time to evaluate : 3.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.8317 (tpp) cc_final: 0.7985 (tpt) REVERT: A 186 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8236 (mm-30) REVERT: B 40 ASN cc_start: 0.8323 (OUTLIER) cc_final: 0.8025 (p0) REVERT: B 104 ASP cc_start: 0.8365 (t0) cc_final: 0.7973 (m-30) REVERT: B 126 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7838 (ttm) REVERT: B 131 MET cc_start: 0.8275 (tpp) cc_final: 0.7938 (OUTLIER) REVERT: B 186 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8247 (mm-30) REVERT: C 278 ASN cc_start: 0.8598 (m-40) cc_final: 0.8308 (m110) REVERT: D 40 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.8048 (p0) REVERT: D 110 ASN cc_start: 0.8932 (OUTLIER) cc_final: 0.8365 (p0) REVERT: D 246 ILE cc_start: 0.9496 (OUTLIER) cc_final: 0.9266 (mt) REVERT: D 274 ARG cc_start: 0.8273 (tpp80) cc_final: 0.7986 (tpp80) REVERT: E 83 MET cc_start: 0.8501 (ttp) cc_final: 0.8212 (tmm) REVERT: E 130 ARG cc_start: 0.8589 (mmp80) cc_final: 0.8305 (mmp80) REVERT: E 131 MET cc_start: 0.8295 (tpp) cc_final: 0.7901 (tpt) REVERT: F 131 MET cc_start: 0.8354 (tpp) cc_final: 0.8044 (tpt) REVERT: F 211 ASP cc_start: 0.8391 (t0) cc_final: 0.8073 (t0) REVERT: F 227 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8505 (mm-30) REVERT: F 274 ARG cc_start: 0.8232 (tpp80) cc_final: 0.7915 (tpp80) REVERT: G 40 ASN cc_start: 0.8298 (OUTLIER) cc_final: 0.7978 (p0) REVERT: G 83 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8329 (ttm) REVERT: G 110 ASN cc_start: 0.8374 (p0) cc_final: 0.8045 (p0) REVERT: G 274 ARG cc_start: 0.8321 (tpp80) cc_final: 0.8047 (tpp80) REVERT: H 40 ASN cc_start: 0.8294 (OUTLIER) cc_final: 0.7980 (p0) REVERT: H 277 GLU cc_start: 0.7773 (pp20) cc_final: 0.7545 (pp20) REVERT: I 40 ASN cc_start: 0.8334 (OUTLIER) cc_final: 0.8030 (p0) REVERT: I 83 MET cc_start: 0.8560 (tmm) cc_final: 0.8105 (ttp) REVERT: J 40 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.8025 (p0) REVERT: J 211 ASP cc_start: 0.8304 (t0) cc_final: 0.7960 (t0) REVERT: J 274 ARG cc_start: 0.8272 (tpp80) cc_final: 0.8019 (tpp80) REVERT: K 40 ASN cc_start: 0.8402 (OUTLIER) cc_final: 0.8100 (p0) REVERT: K 83 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8411 (ttp) outliers start: 73 outliers final: 22 residues processed: 380 average time/residue: 1.4287 time to fit residues: 639.1120 Evaluate side-chains 344 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 311 time to evaluate : 3.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain F residue 40 ASN Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 270 ASP Chi-restraints excluded: chain G residue 40 ASN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 270 ASP Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 270 ASP Chi-restraints excluded: chain I residue 40 ASN Chi-restraints excluded: chain I residue 270 ASP Chi-restraints excluded: chain J residue 40 ASN Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 40 ASN Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 110 ASN Chi-restraints excluded: chain K residue 270 ASP Chi-restraints excluded: chain L residue 40 ASN Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 270 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 211 optimal weight: 0.6980 chunk 271 optimal weight: 9.9990 chunk 210 optimal weight: 4.9990 chunk 312 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 370 optimal weight: 2.9990 chunk 231 optimal weight: 9.9990 chunk 225 optimal weight: 3.9990 chunk 170 optimal weight: 8.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 278 ASN K 278 ASN L 278 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 31392 Z= 0.265 Angle : 0.692 10.973 42396 Z= 0.342 Chirality : 0.047 0.173 4644 Planarity : 0.003 0.032 5388 Dihedral : 3.903 16.777 4260 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.83 % Allowed : 24.59 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.13), residues: 3888 helix: 0.29 (0.11), residues: 2196 sheet: -0.79 (0.22), residues: 564 loop : -1.79 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 198 HIS 0.003 0.001 HIS B 196 PHE 0.018 0.001 PHE E 266 TYR 0.014 0.001 TYR L 217 ARG 0.006 0.000 ARG E 274 *********************** 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 412 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 322 time to evaluate : 3.337 Fit side-chains REVERT: A 40 ASN cc_start: 0.8410 (OUTLIER) cc_final: 0.8106 (p0) REVERT: A 131 MET cc_start: 0.8449 (tpp) cc_final: 0.8202 (tpt) REVERT: B 40 ASN cc_start: 0.8342 (OUTLIER) cc_final: 0.8023 (p0) REVERT: B 104 ASP cc_start: 0.8356 (t0) cc_final: 0.7970 (m-30) REVERT: B 126 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7846 (ttm) REVERT: B 131 MET cc_start: 0.8388 (tpp) cc_final: 0.8060 (OUTLIER) REVERT: C 40 ASN cc_start: 0.8289 (OUTLIER) cc_final: 0.8051 (p0) REVERT: C 131 MET cc_start: 0.8221 (tpp) cc_final: 0.7923 (tpt) REVERT: C 277 GLU cc_start: 0.7818 (pp20) cc_final: 0.7575 (pp20) REVERT: D 40 ASN cc_start: 0.8357 (OUTLIER) cc_final: 0.8063 (p0) REVERT: D 83 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8328 (ttp) REVERT: D 110 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.7883 (p0) REVERT: D 274 ARG cc_start: 0.8267 (tpp80) cc_final: 0.7911 (tpp80) REVERT: D 277 GLU cc_start: 0.7728 (pp20) cc_final: 0.7509 (pp20) REVERT: E 83 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8170 (tmm) REVERT: E 131 MET cc_start: 0.8428 (tpp) cc_final: 0.8114 (tpt) REVERT: E 265 MET cc_start: 0.8794 (ttp) cc_final: 0.8522 (ttp) REVERT: F 40 ASN cc_start: 0.8410 (OUTLIER) cc_final: 0.8096 (p0) REVERT: F 83 MET cc_start: 0.8543 (ttp) cc_final: 0.8207 (ttp) REVERT: F 126 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7827 (ttm) REVERT: F 131 MET cc_start: 0.8494 (tpp) cc_final: 0.8212 (tpt) REVERT: F 211 ASP cc_start: 0.8466 (t0) cc_final: 0.8140 (t0) REVERT: F 274 ARG cc_start: 0.8245 (tpp80) cc_final: 0.8023 (tpp80) REVERT: G 40 ASN cc_start: 0.8347 (OUTLIER) cc_final: 0.8020 (p0) REVERT: G 83 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8396 (ttm) REVERT: G 110 ASN cc_start: 0.8474 (p0) cc_final: 0.8142 (p0) REVERT: G 131 MET cc_start: 0.8225 (tpp) cc_final: 0.7936 (tpt) REVERT: H 40 ASN cc_start: 0.8347 (OUTLIER) cc_final: 0.8024 (p0) REVERT: H 131 MET cc_start: 0.8233 (tpp) cc_final: 0.7974 (tpt) REVERT: H 277 GLU cc_start: 0.7805 (pp20) cc_final: 0.7564 (pp20) REVERT: I 40 ASN cc_start: 0.8349 (OUTLIER) cc_final: 0.8047 (p0) REVERT: I 131 MET cc_start: 0.8200 (tpp) cc_final: 0.7882 (tpt) REVERT: J 40 ASN cc_start: 0.8364 (OUTLIER) cc_final: 0.8014 (p0) REVERT: J 131 MET cc_start: 0.8317 (tpp) cc_final: 0.8059 (tpt) REVERT: J 211 ASP cc_start: 0.8398 (t0) cc_final: 0.8063 (t0) REVERT: J 274 ARG cc_start: 0.8293 (tpp80) cc_final: 0.7969 (tpp80) REVERT: K 40 ASN cc_start: 0.8399 (OUTLIER) cc_final: 0.8115 (p0) REVERT: K 83 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8402 (ttp) REVERT: K 131 MET cc_start: 0.8271 (tpp) cc_final: 0.7941 (OUTLIER) REVERT: L 40 ASN cc_start: 0.8418 (OUTLIER) cc_final: 0.8085 (p0) REVERT: L 83 MET cc_start: 0.8550 (ttp) cc_final: 0.8188 (ttp) REVERT: L 131 MET cc_start: 0.8281 (tpp) cc_final: 0.8013 (tpt) REVERT: L 265 MET cc_start: 0.8815 (ttp) cc_final: 0.8604 (ttp) outliers start: 90 outliers final: 38 residues processed: 355 average time/residue: 1.3429 time to fit residues: 566.1774 Evaluate side-chains 349 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 295 time to evaluate : 3.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain F residue 40 ASN Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain F residue 270 ASP Chi-restraints excluded: chain G residue 40 ASN Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 270 ASP Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 126 MET Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain H residue 270 ASP Chi-restraints excluded: chain I residue 40 ASN Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 270 ASP Chi-restraints excluded: chain J residue 40 ASN Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 40 ASN Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 270 ASP Chi-restraints excluded: chain L residue 40 ASN Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 201 ILE Chi-restraints excluded: chain L residue 270 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 0.0770 chunk 147 optimal weight: 1.9990 chunk 221 optimal weight: 6.9990 chunk 111 optimal weight: 0.0570 chunk 72 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 235 optimal weight: 0.3980 chunk 252 optimal weight: 4.9990 chunk 182 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 290 optimal weight: 9.9990 overall best weight: 1.5060 ------------------------------------------------------------------------------- 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 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 ASN ** E 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 278 ASN ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31392 Z= 0.196 Angle : 0.665 11.358 42396 Z= 0.326 Chirality : 0.046 0.152 4644 Planarity : 0.003 0.034 5388 Dihedral : 3.852 18.376 4260 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.26 % Allowed : 25.06 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.13), residues: 3888 helix: 0.42 (0.11), residues: 2196 sheet: -0.88 (0.21), residues: 576 loop : -1.59 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 198 HIS 0.003 0.001 HIS D 196 PHE 0.026 0.001 PHE A 105 TYR 0.008 0.001 TYR A 51 ARG 0.006 0.000 ARG G 274 *********************** 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 386 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 314 time to evaluate : 3.230 Fit side-chains REVERT: A 40 ASN cc_start: 0.8411 (OUTLIER) cc_final: 0.8069 (p0) REVERT: B 40 ASN cc_start: 0.8343 (m110) cc_final: 0.8032 (p0) REVERT: B 104 ASP cc_start: 0.8309 (t0) cc_final: 0.7918 (m-30) REVERT: B 126 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7747 (ttm) REVERT: B 131 MET cc_start: 0.8499 (tpp) cc_final: 0.8222 (OUTLIER) REVERT: C 40 ASN cc_start: 0.8277 (m-40) cc_final: 0.8059 (p0) REVERT: C 131 MET cc_start: 0.8341 (tpp) cc_final: 0.7999 (OUTLIER) REVERT: D 40 ASN cc_start: 0.8346 (OUTLIER) cc_final: 0.8069 (p0) REVERT: D 83 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8349 (ttp) REVERT: D 110 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.7907 (p0) REVERT: D 131 MET cc_start: 0.8033 (tpp) cc_final: 0.7768 (tpt) REVERT: D 274 ARG cc_start: 0.8187 (tpp80) cc_final: 0.7848 (tpp80) REVERT: E 40 ASN cc_start: 0.8400 (m-40) cc_final: 0.8075 (p0) REVERT: E 83 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8264 (ttp) REVERT: E 131 MET cc_start: 0.8392 (tpp) cc_final: 0.8190 (tpt) REVERT: E 265 MET cc_start: 0.8754 (ttp) cc_final: 0.8513 (ttp) REVERT: F 40 ASN cc_start: 0.8381 (OUTLIER) cc_final: 0.8084 (p0) REVERT: F 104 ASP cc_start: 0.8418 (t0) cc_final: 0.8095 (t0) REVERT: F 126 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7657 (ttm) REVERT: F 131 MET cc_start: 0.8522 (tpp) cc_final: 0.8204 (tpt) REVERT: F 211 ASP cc_start: 0.8494 (t0) cc_final: 0.8132 (t0) REVERT: G 40 ASN cc_start: 0.8349 (m110) cc_final: 0.8031 (p0) REVERT: G 110 ASN cc_start: 0.8444 (p0) cc_final: 0.8012 (p0) REVERT: G 131 MET cc_start: 0.8347 (tpp) cc_final: 0.8002 (OUTLIER) REVERT: H 40 ASN cc_start: 0.8368 (m110) cc_final: 0.8055 (p0) REVERT: H 110 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8401 (p0) REVERT: H 131 MET cc_start: 0.8336 (tpp) cc_final: 0.7987 (OUTLIER) REVERT: I 40 ASN cc_start: 0.8339 (OUTLIER) cc_final: 0.8050 (p0) REVERT: I 83 MET cc_start: 0.8498 (ttp) cc_final: 0.8132 (tmm) REVERT: I 131 MET cc_start: 0.8320 (tpp) cc_final: 0.7973 (OUTLIER) REVERT: J 40 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.8037 (p0) REVERT: J 131 MET cc_start: 0.8363 (tpp) cc_final: 0.8036 (OUTLIER) REVERT: J 211 ASP cc_start: 0.8401 (t0) cc_final: 0.8053 (t0) REVERT: J 274 ARG cc_start: 0.8247 (tpp80) cc_final: 0.8029 (tpp80) REVERT: K 40 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.8111 (p0) REVERT: K 83 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8363 (ttp) REVERT: K 131 MET cc_start: 0.8310 (tpp) cc_final: 0.8049 (tpt) REVERT: L 40 ASN cc_start: 0.8408 (m-40) cc_final: 0.8076 (p0) REVERT: L 131 MET cc_start: 0.8363 (tpp) cc_final: 0.8018 (OUTLIER) outliers start: 72 outliers final: 44 residues processed: 347 average time/residue: 1.3062 time to fit residues: 539.5215 Evaluate side-chains 350 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 300 time to evaluate : 3.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain F residue 40 ASN Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain F residue 270 ASP Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 270 ASP Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 110 ASN Chi-restraints excluded: chain H residue 126 MET Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain H residue 270 ASP Chi-restraints excluded: chain I residue 40 ASN Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 270 ASP Chi-restraints excluded: chain J residue 40 ASN Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 104 ASP Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 40 ASN Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 270 ASP Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 270 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 4.9990 chunk 354 optimal weight: 10.0000 chunk 323 optimal weight: 10.0000 chunk 344 optimal weight: 8.9990 chunk 207 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 270 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 311 optimal weight: 5.9990 chunk 326 optimal weight: 9.9990 chunk 343 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN ** E 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 278 ASN ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 31392 Z= 0.350 Angle : 0.745 12.097 42396 Z= 0.371 Chirality : 0.049 0.160 4644 Planarity : 0.004 0.038 5388 Dihedral : 4.003 19.590 4260 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.26 % Allowed : 25.22 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.13), residues: 3888 helix: 0.60 (0.11), residues: 2208 sheet: -0.73 (0.22), residues: 564 loop : -1.71 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 198 HIS 0.005 0.001 HIS D 196 PHE 0.043 0.002 PHE J 105 TYR 0.015 0.001 TYR L 217 ARG 0.007 0.000 ARG F 274 *********************** 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 379 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 307 time to evaluate : 3.488 Fit side-chains revert: symmetry clash REVERT: A 40 ASN cc_start: 0.8462 (OUTLIER) cc_final: 0.8154 (p0) REVERT: A 131 MET cc_start: 0.8202 (tpp) cc_final: 0.7866 (tpt) REVERT: B 40 ASN cc_start: 0.8403 (OUTLIER) cc_final: 0.7969 (p0) REVERT: B 104 ASP cc_start: 0.8370 (t0) cc_final: 0.7998 (m-30) REVERT: B 126 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7895 (ttm) REVERT: B 131 MET cc_start: 0.8546 (tpp) cc_final: 0.8258 (OUTLIER) REVERT: C 40 ASN cc_start: 0.8322 (OUTLIER) cc_final: 0.8107 (p0) REVERT: C 131 MET cc_start: 0.8472 (tpp) cc_final: 0.8172 (tpt) REVERT: D 40 ASN cc_start: 0.8389 (OUTLIER) cc_final: 0.7981 (p0) REVERT: D 131 MET cc_start: 0.8129 (tpp) cc_final: 0.7756 (tpt) REVERT: E 40 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.8131 (p0) REVERT: E 265 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8450 (ttm) REVERT: F 40 ASN cc_start: 0.8445 (OUTLIER) cc_final: 0.8102 (p0) REVERT: F 126 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7771 (ttm) REVERT: F 131 MET cc_start: 0.8614 (tpp) cc_final: 0.8372 (tpt) REVERT: F 211 ASP cc_start: 0.8617 (t0) cc_final: 0.8275 (t0) REVERT: G 40 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.8036 (p0) REVERT: G 131 MET cc_start: 0.8501 (tpp) cc_final: 0.8220 (tpt) REVERT: H 40 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.8052 (p0) REVERT: H 131 MET cc_start: 0.8490 (tpp) cc_final: 0.8203 (tpt) REVERT: I 40 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.8020 (p0) REVERT: I 83 MET cc_start: 0.8603 (ttp) cc_final: 0.8324 (ttp) REVERT: I 131 MET cc_start: 0.8476 (tpp) cc_final: 0.8180 (OUTLIER) REVERT: J 40 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.7971 (p0) REVERT: J 131 MET cc_start: 0.8498 (tpp) cc_final: 0.8194 (tpt) REVERT: J 211 ASP cc_start: 0.8559 (t0) cc_final: 0.8229 (t0) REVERT: K 40 ASN cc_start: 0.8363 (OUTLIER) cc_final: 0.8080 (p0) REVERT: K 83 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8439 (ttp) REVERT: K 131 MET cc_start: 0.8426 (tpp) cc_final: 0.8081 (OUTLIER) REVERT: L 40 ASN cc_start: 0.8417 (OUTLIER) cc_final: 0.8088 (p0) REVERT: L 131 MET cc_start: 0.8499 (tpp) cc_final: 0.8167 (tpt) outliers start: 72 outliers final: 41 residues processed: 329 average time/residue: 1.3723 time to fit residues: 533.6855 Evaluate side-chains 349 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 295 time to evaluate : 3.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain F residue 40 ASN Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain F residue 270 ASP Chi-restraints excluded: chain G residue 40 ASN Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 270 ASP Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain H residue 270 ASP Chi-restraints excluded: chain I residue 40 ASN Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 270 ASP Chi-restraints excluded: chain J residue 40 ASN Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 40 ASN Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 270 ASP Chi-restraints excluded: chain L residue 40 ASN Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 270 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 8.9990 chunk 364 optimal weight: 10.0000 chunk 222 optimal weight: 0.8980 chunk 173 optimal weight: 9.9990 chunk 253 optimal weight: 0.8980 chunk 382 optimal weight: 0.0370 chunk 352 optimal weight: 6.9990 chunk 304 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 235 optimal weight: 2.9990 chunk 186 optimal weight: 0.7980 overall best weight: 1.1260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31392 Z= 0.187 Angle : 0.715 12.503 42396 Z= 0.347 Chirality : 0.046 0.154 4644 Planarity : 0.004 0.036 5388 Dihedral : 3.880 16.339 4260 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.60 % Allowed : 26.13 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 3888 helix: 0.72 (0.11), residues: 2172 sheet: -0.65 (0.22), residues: 564 loop : -1.64 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 198 HIS 0.006 0.001 HIS D 196 PHE 0.030 0.002 PHE H 105 TYR 0.008 0.001 TYR K 51 ARG 0.008 0.001 ARG L 130 ********************** 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 363 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 312 time to evaluate : 3.561 Fit side-chains REVERT: A 40 ASN cc_start: 0.8452 (m-40) cc_final: 0.8072 (p0) REVERT: A 131 MET cc_start: 0.8266 (tpp) cc_final: 0.7937 (tpt) REVERT: B 40 ASN cc_start: 0.8394 (m110) cc_final: 0.7946 (p0) REVERT: B 104 ASP cc_start: 0.8344 (t0) cc_final: 0.7960 (m-30) REVERT: B 126 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7742 (ttm) REVERT: B 130 ARG cc_start: 0.8584 (mmp80) cc_final: 0.8364 (mmp80) REVERT: B 131 MET cc_start: 0.8573 (tpp) cc_final: 0.8324 (tpt) REVERT: B 186 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7990 (mm-30) REVERT: C 40 ASN cc_start: 0.8300 (OUTLIER) cc_final: 0.8048 (p0) REVERT: C 130 ARG cc_start: 0.8514 (mmp80) cc_final: 0.8286 (mmp80) REVERT: C 131 MET cc_start: 0.8495 (tpp) cc_final: 0.8154 (OUTLIER) REVERT: D 40 ASN cc_start: 0.8364 (OUTLIER) cc_final: 0.7963 (p0) REVERT: D 110 ASN cc_start: 0.8602 (OUTLIER) cc_final: 0.8362 (p0) REVERT: D 131 MET cc_start: 0.8245 (tpp) cc_final: 0.8000 (tpt) REVERT: E 40 ASN cc_start: 0.8412 (OUTLIER) cc_final: 0.8111 (p0) REVERT: E 265 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8474 (ttp) REVERT: F 40 ASN cc_start: 0.8431 (m110) cc_final: 0.8018 (p0) REVERT: F 131 MET cc_start: 0.8656 (tpp) cc_final: 0.8384 (tpt) REVERT: F 211 ASP cc_start: 0.8543 (t0) cc_final: 0.8201 (t0) REVERT: G 40 ASN cc_start: 0.8397 (m110) cc_final: 0.7938 (p0) REVERT: G 130 ARG cc_start: 0.8518 (mmp80) cc_final: 0.8301 (mmp80) REVERT: G 131 MET cc_start: 0.8481 (tpp) cc_final: 0.8167 (OUTLIER) REVERT: H 40 ASN cc_start: 0.8401 (m110) cc_final: 0.7950 (p0) REVERT: H 131 MET cc_start: 0.8501 (tpp) cc_final: 0.8193 (OUTLIER) REVERT: I 40 ASN cc_start: 0.8365 (OUTLIER) cc_final: 0.7955 (p0) REVERT: I 83 MET cc_start: 0.8469 (ttp) cc_final: 0.8108 (tmm) REVERT: I 130 ARG cc_start: 0.8468 (mmp80) cc_final: 0.8237 (mmp80) REVERT: I 131 MET cc_start: 0.8474 (tpp) cc_final: 0.8143 (OUTLIER) REVERT: J 40 ASN cc_start: 0.8363 (OUTLIER) cc_final: 0.7959 (p0) REVERT: J 131 MET cc_start: 0.8533 (tpp) cc_final: 0.8258 (OUTLIER) REVERT: J 211 ASP cc_start: 0.8467 (t0) cc_final: 0.8129 (t0) REVERT: K 40 ASN cc_start: 0.8349 (OUTLIER) cc_final: 0.8033 (p0) REVERT: K 83 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8324 (ttp) REVERT: K 131 MET cc_start: 0.8491 (tpp) cc_final: 0.8178 (OUTLIER) REVERT: L 40 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.8107 (p0) REVERT: L 131 MET cc_start: 0.8513 (tpp) cc_final: 0.8234 (OUTLIER) outliers start: 51 outliers final: 34 residues processed: 332 average time/residue: 1.3713 time to fit residues: 538.9903 Evaluate side-chains 326 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 288 time to evaluate : 3.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 270 ASP Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 270 ASP Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 270 ASP Chi-restraints excluded: chain I residue 40 ASN Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 270 ASP Chi-restraints excluded: chain J residue 40 ASN Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 40 ASN Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 270 ASP Chi-restraints excluded: chain L residue 40 ASN Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 104 ASP Chi-restraints excluded: chain L residue 270 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 1.9990 chunk 324 optimal weight: 0.0170 chunk 93 optimal weight: 4.9990 chunk 280 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 305 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 313 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 overall best weight: 1.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 ASN ** 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 = 0.3352 r_free = 0.3352 target = 0.068260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.054172 restraints weight = 100008.830| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 4.05 r_work: 0.2890 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31392 Z= 0.223 Angle : 0.741 14.061 42396 Z= 0.364 Chirality : 0.046 0.154 4644 Planarity : 0.004 0.039 5388 Dihedral : 3.888 17.081 4260 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.79 % Allowed : 26.29 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.14), residues: 3888 helix: 0.73 (0.11), residues: 2172 sheet: -0.73 (0.22), residues: 576 loop : -1.51 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 198 HIS 0.005 0.001 HIS D 196 PHE 0.026 0.002 PHE L 105 TYR 0.011 0.001 TYR G 217 ARG 0.006 0.000 ARG F 274 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9791.01 seconds wall clock time: 175 minutes 32.47 seconds (10532.47 seconds total)