Starting phenix.real_space_refine on Fri Dec 15 09:15:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jcv_9798/12_2023/6jcv_9798.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jcv_9798/12_2023/6jcv_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_9798/12_2023/6jcv_9798.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jcv_9798/12_2023/6jcv_9798.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jcv_9798/12_2023/6jcv_9798.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jcv_9798/12_2023/6jcv_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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 16.74, per 1000 atoms: 0.54 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: 13.33 Conformation dependent library (CDL) restraints added in 6.2 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: 3.32 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: 10.58 Time building geometry restraints manager: 14.09 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: 1.650 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: 9.160 Check model and map are aligned: 0.490 Set scattering table: 0.300 Process input model: 82.740 Find NCS groups from input model: 2.420 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.780 ------------------------------------------------------------------------------- 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 : 2.865 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 outliers start: 0 outliers final: 0 residues processed: 515 average time/residue: 1.1806 time to fit residues: 701.2884 Evaluate side-chains 362 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 362 time to evaluate : 2.360 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1030 ------------------------------------------------------------------------------- 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: 3.9990 overall best weight: 1.4598 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31392 Z= 0.198 Angle : 0.615 8.680 42396 Z= 0.325 Chirality : 0.045 0.164 4644 Planarity : 0.005 0.044 5388 Dihedral : 4.649 15.411 4260 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.20 % Allowed : 15.13 % Favored : 82.67 % 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: -3.53 (0.11), residues: 3888 helix: -2.44 (0.09), residues: 1980 sheet: -1.44 (0.23), residues: 540 loop : -2.24 (0.13), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 198 HIS 0.002 0.000 HIS L 252 PHE 0.011 0.001 PHE J 184 TYR 0.014 0.001 TYR F 268 ARG 0.005 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 507 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 437 time to evaluate : 3.765 Fit side-chains revert: symmetry clash outliers start: 70 outliers final: 13 residues processed: 458 average time/residue: 1.5069 time to fit residues: 809.0684 Evaluate side-chains 353 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 340 time to evaluate : 3.773 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.4142 time to fit residues: 13.5052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 290 optimal weight: 10.0000 chunk 237 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 349 optimal weight: 0.9990 chunk 377 optimal weight: 4.9990 chunk 311 optimal weight: 8.9990 chunk 346 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 280 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 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 K 253 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: 0.8622 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 31392 Z= 0.447 Angle : 0.735 7.945 42396 Z= 0.386 Chirality : 0.051 0.160 4644 Planarity : 0.004 0.041 5388 Dihedral : 4.517 16.401 4260 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.65 % Allowed : 18.24 % Favored : 78.11 % 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: -2.43 (0.12), residues: 3888 helix: -1.22 (0.10), residues: 2136 sheet: -1.45 (0.23), residues: 564 loop : -2.07 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 198 HIS 0.003 0.001 HIS H 140 PHE 0.010 0.002 PHE L 113 TYR 0.014 0.002 TYR C 217 ARG 0.007 0.001 ARG F 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 470 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 354 time to evaluate : 4.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 116 outliers final: 27 residues processed: 389 average time/residue: 1.4780 time to fit residues: 675.3815 Evaluate side-chains 332 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 305 time to evaluate : 3.958 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 7 residues processed: 26 average time/residue: 0.7993 time to fit residues: 31.7819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 0.9980 chunk 262 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 166 optimal weight: 4.9990 chunk 234 optimal weight: 3.9990 chunk 350 optimal weight: 0.9990 chunk 371 optimal weight: 4.9990 chunk 183 optimal weight: 8.9990 chunk 332 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN B 278 ASN C 278 ASN D 278 ASN E 278 ASN F 37 ASN F 278 ASN G 278 ASN H 278 ASN I 278 ASN J 278 ASN ** K 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 278 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31392 Z= 0.266 Angle : 0.633 8.271 42396 Z= 0.323 Chirality : 0.047 0.155 4644 Planarity : 0.004 0.031 5388 Dihedral : 4.253 16.913 4260 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.99 % Allowed : 19.34 % Favored : 76.67 % 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: -1.77 (0.13), residues: 3888 helix: -0.58 (0.11), residues: 2136 sheet: -1.33 (0.23), residues: 564 loop : -1.92 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 198 HIS 0.003 0.001 HIS L 196 PHE 0.012 0.001 PHE D 247 TYR 0.010 0.001 TYR A 217 ARG 0.004 0.000 ARG F 274 *********************** 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 477 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 350 time to evaluate : 3.680 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 127 outliers final: 16 residues processed: 385 average time/residue: 1.4093 time to fit residues: 644.2093 Evaluate side-chains 337 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 321 time to evaluate : 3.708 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.6675 time to fit residues: 19.5812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 5.9990 chunk 210 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 276 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 chunk 316 optimal weight: 4.9990 chunk 256 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 1.9990 chunk 333 optimal weight: 6.9990 chunk 93 optimal weight: 0.0370 overall best weight: 3.0066 ------------------------------------------------------------------------------- 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 278 ASN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 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 H 278 ASN ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 278 ASN ** J 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 278 ASN ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 31392 Z= 0.266 Angle : 0.659 9.487 42396 Z= 0.330 Chirality : 0.047 0.151 4644 Planarity : 0.003 0.030 5388 Dihedral : 4.118 16.864 4260 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.61 % Allowed : 21.95 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.43 (0.13), residues: 3888 helix: -0.27 (0.11), residues: 2208 sheet: -1.02 (0.23), residues: 564 loop : -2.03 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 198 HIS 0.003 0.001 HIS E 196 PHE 0.017 0.001 PHE L 266 TYR 0.011 0.001 TYR C 217 ARG 0.004 0.000 ARG C 274 *********************** 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 445 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 362 time to evaluate : 3.689 Fit side-chains outliers start: 83 outliers final: 39 residues processed: 389 average time/residue: 1.3714 time to fit residues: 634.8283 Evaluate side-chains 360 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 321 time to evaluate : 3.659 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 10 residues processed: 30 average time/residue: 0.6854 time to fit residues: 32.8470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.2980 chunk 73 optimal weight: 3.9990 chunk 217 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 371 optimal weight: 4.9990 chunk 308 optimal weight: 1.9990 chunk 172 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 195 optimal weight: 8.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 278 ASN D 278 ASN ** E 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 ASN F 278 ASN G 278 ASN H 278 ASN ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 278 ASN J 278 ASN ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31392 Z= 0.172 Angle : 0.630 9.857 42396 Z= 0.310 Chirality : 0.045 0.168 4644 Planarity : 0.003 0.030 5388 Dihedral : 3.964 17.288 4260 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.77 % Allowed : 23.43 % Favored : 73.81 % 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: -1.16 (0.13), residues: 3888 helix: -0.01 (0.11), residues: 2136 sheet: -0.87 (0.22), residues: 564 loop : -1.94 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 198 HIS 0.003 0.001 HIS G 196 PHE 0.015 0.001 PHE L 266 TYR 0.008 0.001 TYR L 51 ARG 0.006 0.000 ARG L 130 *********************** 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 479 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 391 time to evaluate : 3.821 Fit side-chains revert: symmetry clash outliers start: 88 outliers final: 39 residues processed: 429 average time/residue: 1.3400 time to fit residues: 686.0152 Evaluate side-chains 354 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 315 time to evaluate : 3.922 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 20 residues processed: 25 average time/residue: 0.6342 time to fit residues: 26.9740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 312 optimal weight: 10.0000 chunk 207 optimal weight: 4.9990 chunk 370 optimal weight: 4.9990 chunk 231 optimal weight: 8.9990 chunk 225 optimal weight: 1.9990 chunk 170 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN C 278 ASN D 278 ASN ** E 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 278 ASN J 278 ASN ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 31392 Z= 0.243 Angle : 0.673 10.873 42396 Z= 0.334 Chirality : 0.047 0.144 4644 Planarity : 0.003 0.029 5388 Dihedral : 3.923 16.831 4260 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.96 % Allowed : 25.50 % Favored : 71.54 % 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: -0.92 (0.13), residues: 3888 helix: 0.16 (0.11), residues: 2196 sheet: -0.81 (0.22), residues: 564 loop : -1.85 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 198 HIS 0.003 0.001 HIS L 196 PHE 0.018 0.002 PHE E 266 TYR 0.012 0.001 TYR H 217 ARG 0.005 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 416 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 322 time to evaluate : 3.848 Fit side-chains revert: symmetry clash outliers start: 94 outliers final: 38 residues processed: 372 average time/residue: 1.3531 time to fit residues: 604.0089 Evaluate side-chains 333 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 295 time to evaluate : 3.560 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 31 residues processed: 22 average time/residue: 0.8402 time to fit residues: 29.3884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.8005 > 50: distance: 43 - 69: 33.093 distance: 52 - 83: 34.243 distance: 56 - 89: 34.370 distance: 62 - 69: 34.711 distance: 63 - 97: 30.648 distance: 69 - 70: 33.169 distance: 70 - 71: 51.978 distance: 70 - 73: 5.712 distance: 71 - 72: 8.297 distance: 73 - 74: 39.750 distance: 76 - 78: 7.912 distance: 76 - 79: 39.465 distance: 77 - 78: 6.354 distance: 78 - 80: 34.340 distance: 79 - 81: 19.637 distance: 80 - 82: 29.235 distance: 81 - 82: 6.815 distance: 83 - 84: 25.541 distance: 84 - 85: 24.757 distance: 84 - 87: 42.706 distance: 87 - 88: 9.443 distance: 90 - 91: 40.145 distance: 91 - 97: 5.270 distance: 92 - 124: 41.436 distance: 97 - 98: 13.313 distance: 98 - 99: 14.601 distance: 98 - 101: 23.682 distance: 99 - 100: 48.789 distance: 99 - 106: 16.208 distance: 100 - 129: 3.016 distance: 106 - 107: 19.948 distance: 107 - 108: 39.054 distance: 107 - 110: 28.400 distance: 108 - 115: 40.823 distance: 110 - 111: 14.533 distance: 111 - 112: 32.395 distance: 112 - 113: 5.688 distance: 115 - 116: 38.773 distance: 116 - 117: 7.797 distance: 117 - 118: 4.298 distance: 117 - 124: 39.595 distance: 119 - 120: 40.759 distance: 120 - 121: 39.373 distance: 121 - 122: 39.704 distance: 125 - 128: 46.800 distance: 126 - 127: 13.201 distance: 126 - 129: 40.178 distance: 129 - 130: 39.668 distance: 130 - 131: 10.817 distance: 131 - 132: 8.819 distance: 131 - 133: 49.919 distance: 133 - 134: 6.429 distance: 134 - 135: 4.015 distance: 134 - 137: 35.291 distance: 135 - 136: 57.399 distance: 135 - 145: 32.875 distance: 138 - 139: 28.126 distance: 141 - 143: 25.812 distance: 145 - 146: 31.702 distance: 145 - 151: 34.025 distance: 147 - 148: 40.406 distance: 147 - 152: 34.982 distance: 148 - 172: 35.561