Starting phenix.real_space_refine on Thu Sep 26 22:45:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd3_10147/09_2024/6sd3_10147.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd3_10147/09_2024/6sd3_10147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd3_10147/09_2024/6sd3_10147.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd3_10147/09_2024/6sd3_10147.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd3_10147/09_2024/6sd3_10147.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd3_10147/09_2024/6sd3_10147.cif" } resolution = 3.3 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= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 134 5.16 5 C 38604 2.51 5 N 11658 2.21 5 O 12748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 382 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 63144 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "B" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "C" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "D" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "E" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "F" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "G" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "H" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "I" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "J" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "K" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "L" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "M" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "N" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "O" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "P" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "Q" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1220 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 2 Chain: "R" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "S" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "T" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "U" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "V" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "W" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "X" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "Y" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "Z" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "a" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "b" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "c" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 4 Chain: "d" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "e" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "f" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "g" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "h" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1220 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 5, 'TRANS': 148} Chain breaks: 2 Time building chain proxies: 26.63, per 1000 atoms: 0.42 Number of scatterers: 63144 At special positions: 0 Unit cell: (249.066, 247.422, 123.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 134 16.00 O 12748 8.00 N 11658 7.00 C 38604 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.91 Conformation dependent library (CDL) restraints added in 5.9 seconds 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15504 Finding SS restraints... Secondary structure from input PDB file: 220 helices and 164 sheets defined 35.1% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.27 Creating SS restraints... Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER A 192 " --> pdb=" O GLU A 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 194 " --> pdb=" O GLN A 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 198 " --> pdb=" O VAL A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 226 Processing helix chain 'A' and resid 230 through 258 removed outlier: 3.585A pdb=" N GLU A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 249 " --> pdb=" O ILE A 245 " (cutoff:3.500A) Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 405 through 421 removed outlier: 3.814A pdb=" N GLY A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 427 Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR B 146 " --> pdb=" O ARG B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER B 192 " --> pdb=" O GLU B 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 194 " --> pdb=" O GLN B 190 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 258 removed outlier: 3.679A pdb=" N ALA B 238 " --> pdb=" O GLN B 234 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 245 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 287 through 291 Processing helix chain 'B' and resid 405 through 421 removed outlier: 3.508A pdb=" N THR B 416 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY B 421 " --> pdb=" O ARG B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 427 Processing helix chain 'C' and resid 127 through 132 Processing helix chain 'C' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER C 192 " --> pdb=" O GLU C 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA C 193 " --> pdb=" O GLY C 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C 194 " --> pdb=" O GLN C 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL C 198 " --> pdb=" O VAL C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 258 Proline residue: C 255 - end of helix Processing helix chain 'C' and resid 287 through 291 Processing helix chain 'C' and resid 405 through 421 removed outlier: 3.923A pdb=" N GLY C 421 " --> pdb=" O ARG C 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 132 Processing helix chain 'D' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR D 146 " --> pdb=" O ARG D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER D 192 " --> pdb=" O GLU D 188 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA D 193 " --> pdb=" O GLY D 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL D 194 " --> pdb=" O GLN D 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL D 198 " --> pdb=" O VAL D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 258 removed outlier: 3.568A pdb=" N ALA D 238 " --> pdb=" O GLN D 234 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE D 245 " --> pdb=" O VAL D 241 " (cutoff:3.500A) Proline residue: D 255 - end of helix Processing helix chain 'D' and resid 287 through 291 Processing helix chain 'D' and resid 405 through 421 removed outlier: 3.507A pdb=" N MET D 409 " --> pdb=" O THR D 405 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY D 421 " --> pdb=" O ARG D 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 132 Processing helix chain 'E' and resid 132 through 146 removed outlier: 3.634A pdb=" N THR E 146 " --> pdb=" O ARG E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER E 192 " --> pdb=" O GLU E 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA E 193 " --> pdb=" O GLY E 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL E 194 " --> pdb=" O GLN E 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL E 198 " --> pdb=" O VAL E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 258 removed outlier: 3.644A pdb=" N ALA E 233 " --> pdb=" O ASP E 229 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN E 234 " --> pdb=" O LEU E 230 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA E 238 " --> pdb=" O GLN E 234 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU E 242 " --> pdb=" O ALA E 238 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE E 245 " --> pdb=" O VAL E 241 " (cutoff:3.500A) Proline residue: E 255 - end of helix Processing helix chain 'E' and resid 287 through 291 Processing helix chain 'E' and resid 405 through 421 removed outlier: 3.635A pdb=" N ASP E 414 " --> pdb=" O LYS E 410 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR E 416 " --> pdb=" O ILE E 412 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY E 421 " --> pdb=" O ARG E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 427 Processing helix chain 'F' and resid 127 through 132 Processing helix chain 'F' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR F 146 " --> pdb=" O ARG F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER F 192 " --> pdb=" O GLU F 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA F 193 " --> pdb=" O GLY F 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL F 194 " --> pdb=" O GLN F 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL F 198 " --> pdb=" O VAL F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 258 removed outlier: 3.623A pdb=" N ASP F 240 " --> pdb=" O LYS F 236 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE F 245 " --> pdb=" O VAL F 241 " (cutoff:3.500A) Proline residue: F 255 - end of helix Processing helix chain 'F' and resid 287 through 291 Processing helix chain 'F' and resid 405 through 421 removed outlier: 3.741A pdb=" N ILE F 412 " --> pdb=" O GLN F 408 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY F 421 " --> pdb=" O ARG F 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 132 Processing helix chain 'G' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR G 146 " --> pdb=" O ARG G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 200 removed outlier: 4.400A pdb=" N SER G 192 " --> pdb=" O GLU G 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA G 193 " --> pdb=" O GLY G 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL G 194 " --> pdb=" O GLN G 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL G 198 " --> pdb=" O VAL G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 258 removed outlier: 3.555A pdb=" N LEU G 235 " --> pdb=" O ASN G 231 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS G 236 " --> pdb=" O ASP G 232 " (cutoff:3.500A) Proline residue: G 255 - end of helix Processing helix chain 'G' and resid 287 through 291 Processing helix chain 'G' and resid 405 through 421 removed outlier: 3.670A pdb=" N GLY G 421 " --> pdb=" O ARG G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 423 through 427 Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR H 146 " --> pdb=" O ARG H 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER H 192 " --> pdb=" O GLU H 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA H 193 " --> pdb=" O GLY H 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL H 194 " --> pdb=" O GLN H 190 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL H 198 " --> pdb=" O VAL H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 258 removed outlier: 3.603A pdb=" N ILE H 245 " --> pdb=" O VAL H 241 " (cutoff:3.500A) Proline residue: H 255 - end of helix Processing helix chain 'H' and resid 287 through 291 Processing helix chain 'H' and resid 405 through 420 removed outlier: 3.717A pdb=" N ILE H 412 " --> pdb=" O GLN H 408 " (cutoff:3.500A) Processing helix chain 'H' and resid 423 through 427 Processing helix chain 'I' and resid 127 through 132 Processing helix chain 'I' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR I 146 " --> pdb=" O ARG I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER I 192 " --> pdb=" O GLU I 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA I 193 " --> pdb=" O GLY I 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL I 194 " --> pdb=" O GLN I 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL I 198 " --> pdb=" O VAL I 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 232 through 258 removed outlier: 3.609A pdb=" N ALA I 238 " --> pdb=" O GLN I 234 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE I 245 " --> pdb=" O VAL I 241 " (cutoff:3.500A) Proline residue: I 255 - end of helix Processing helix chain 'I' and resid 287 through 291 Processing helix chain 'I' and resid 405 through 421 removed outlier: 3.728A pdb=" N ILE I 412 " --> pdb=" O GLN I 408 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY I 421 " --> pdb=" O ARG I 417 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 132 Processing helix chain 'J' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR J 146 " --> pdb=" O ARG J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER J 192 " --> pdb=" O GLU J 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA J 193 " --> pdb=" O GLY J 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL J 194 " --> pdb=" O GLN J 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL J 198 " --> pdb=" O VAL J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 230 through 258 removed outlier: 3.998A pdb=" N LYS J 236 " --> pdb=" O ASP J 232 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP J 240 " --> pdb=" O LYS J 236 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE J 245 " --> pdb=" O VAL J 241 " (cutoff:3.500A) Proline residue: J 255 - end of helix Processing helix chain 'J' and resid 405 through 421 removed outlier: 3.765A pdb=" N GLY J 421 " --> pdb=" O ARG J 417 " (cutoff:3.500A) Processing helix chain 'J' and resid 423 through 427 Processing helix chain 'K' and resid 127 through 132 Processing helix chain 'K' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR K 146 " --> pdb=" O ARG K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER K 192 " --> pdb=" O GLU K 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA K 193 " --> pdb=" O GLY K 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL K 194 " --> pdb=" O GLN K 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL K 198 " --> pdb=" O VAL K 194 " (cutoff:3.500A) Processing helix chain 'K' and resid 229 through 258 removed outlier: 3.609A pdb=" N LEU K 235 " --> pdb=" O ASN K 231 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE K 245 " --> pdb=" O VAL K 241 " (cutoff:3.500A) Proline residue: K 255 - end of helix Processing helix chain 'K' and resid 287 through 291 removed outlier: 3.557A pdb=" N LYS K 290 " --> pdb=" O ASP K 287 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 421 removed outlier: 3.686A pdb=" N GLY K 421 " --> pdb=" O ARG K 417 " (cutoff:3.500A) Processing helix chain 'K' and resid 423 through 427 Processing helix chain 'L' and resid 127 through 132 Processing helix chain 'L' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR L 146 " --> pdb=" O ARG L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER L 192 " --> pdb=" O GLU L 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA L 193 " --> pdb=" O GLY L 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL L 194 " --> pdb=" O GLN L 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL L 198 " --> pdb=" O VAL L 194 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 258 removed outlier: 3.522A pdb=" N ILE L 245 " --> pdb=" O VAL L 241 " (cutoff:3.500A) Proline residue: L 255 - end of helix Processing helix chain 'L' and resid 287 through 291 Processing helix chain 'L' and resid 405 through 420 removed outlier: 3.758A pdb=" N LYS L 410 " --> pdb=" O ALA L 406 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR L 416 " --> pdb=" O ILE L 412 " (cutoff:3.500A) Processing helix chain 'L' and resid 423 through 427 Processing helix chain 'M' and resid 127 through 132 Processing helix chain 'M' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR M 146 " --> pdb=" O ARG M 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER M 192 " --> pdb=" O GLU M 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA M 193 " --> pdb=" O GLY M 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL M 194 " --> pdb=" O GLN M 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL M 198 " --> pdb=" O VAL M 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 232 through 258 removed outlier: 3.651A pdb=" N ALA M 238 " --> pdb=" O GLN M 234 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE M 245 " --> pdb=" O VAL M 241 " (cutoff:3.500A) Proline residue: M 255 - end of helix Processing helix chain 'M' and resid 287 through 291 Processing helix chain 'M' and resid 405 through 411 Processing helix chain 'M' and resid 411 through 420 Processing helix chain 'M' and resid 423 through 427 Processing helix chain 'N' and resid 127 through 132 Processing helix chain 'N' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR N 146 " --> pdb=" O ARG N 142 " (cutoff:3.500A) Processing helix chain 'N' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER N 192 " --> pdb=" O GLU N 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA N 193 " --> pdb=" O GLY N 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL N 194 " --> pdb=" O GLN N 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL N 198 " --> pdb=" O VAL N 194 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 258 Proline residue: N 255 - end of helix Processing helix chain 'N' and resid 287 through 291 Processing helix chain 'N' and resid 405 through 421 removed outlier: 3.520A pdb=" N LYS N 410 " --> pdb=" O ALA N 406 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY N 421 " --> pdb=" O ARG N 417 " (cutoff:3.500A) Processing helix chain 'O' and resid 127 through 132 Processing helix chain 'O' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR O 146 " --> pdb=" O ARG O 142 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER O 192 " --> pdb=" O GLU O 188 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA O 193 " --> pdb=" O GLY O 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL O 194 " --> pdb=" O GLN O 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL O 198 " --> pdb=" O VAL O 194 " (cutoff:3.500A) Processing helix chain 'O' and resid 229 through 258 removed outlier: 3.639A pdb=" N LEU O 235 " --> pdb=" O ASN O 231 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU O 242 " --> pdb=" O ALA O 238 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE O 245 " --> pdb=" O VAL O 241 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER O 254 " --> pdb=" O GLU O 250 " (cutoff:3.500A) Proline residue: O 255 - end of helix Processing helix chain 'O' and resid 287 through 291 Processing helix chain 'O' and resid 405 through 421 removed outlier: 4.007A pdb=" N ILE O 412 " --> pdb=" O GLN O 408 " (cutoff:3.500A) Processing helix chain 'P' and resid 127 through 132 Processing helix chain 'P' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR P 146 " --> pdb=" O ARG P 142 " (cutoff:3.500A) Processing helix chain 'P' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER P 192 " --> pdb=" O GLU P 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA P 193 " --> pdb=" O GLY P 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL P 194 " --> pdb=" O GLN P 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL P 198 " --> pdb=" O VAL P 194 " (cutoff:3.500A) Processing helix chain 'P' and resid 228 through 258 removed outlier: 3.637A pdb=" N ALA P 233 " --> pdb=" O ASP P 229 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU P 235 " --> pdb=" O ASN P 231 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU P 242 " --> pdb=" O ALA P 238 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE P 245 " --> pdb=" O VAL P 241 " (cutoff:3.500A) Proline residue: P 255 - end of helix Processing helix chain 'P' and resid 287 through 291 Processing helix chain 'P' and resid 405 through 421 removed outlier: 3.793A pdb=" N ILE P 412 " --> pdb=" O GLN P 408 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY P 421 " --> pdb=" O ARG P 417 " (cutoff:3.500A) Processing helix chain 'P' and resid 423 through 427 Processing helix chain 'Q' and resid 232 through 258 removed outlier: 3.701A pdb=" N LYS Q 236 " --> pdb=" O ASP Q 232 " (cutoff:3.500A) Proline residue: Q 255 - end of helix Processing helix chain 'Q' and resid 287 through 291 Processing helix chain 'Q' and resid 405 through 420 removed outlier: 3.692A pdb=" N ILE Q 412 " --> pdb=" O GLN Q 408 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU Q 415 " --> pdb=" O GLN Q 411 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 132 Processing helix chain 'R' and resid 132 through 146 removed outlier: 3.634A pdb=" N THR R 146 " --> pdb=" O ARG R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER R 192 " --> pdb=" O GLU R 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA R 193 " --> pdb=" O GLY R 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL R 194 " --> pdb=" O GLN R 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL R 198 " --> pdb=" O VAL R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 230 through 258 removed outlier: 3.621A pdb=" N GLU R 242 " --> pdb=" O ALA R 238 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE R 245 " --> pdb=" O VAL R 241 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE R 249 " --> pdb=" O ILE R 245 " (cutoff:3.500A) Proline residue: R 255 - end of helix Processing helix chain 'R' and resid 287 through 291 Processing helix chain 'R' and resid 405 through 421 removed outlier: 3.807A pdb=" N GLY R 421 " --> pdb=" O ARG R 417 " (cutoff:3.500A) Processing helix chain 'R' and resid 423 through 427 Processing helix chain 'S' and resid 127 through 132 Processing helix chain 'S' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR S 146 " --> pdb=" O ARG S 142 " (cutoff:3.500A) Processing helix chain 'S' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER S 192 " --> pdb=" O GLU S 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA S 193 " --> pdb=" O GLY S 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL S 194 " --> pdb=" O GLN S 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL S 198 " --> pdb=" O VAL S 194 " (cutoff:3.500A) Processing helix chain 'S' and resid 232 through 258 removed outlier: 3.699A pdb=" N ALA S 238 " --> pdb=" O GLN S 234 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU S 242 " --> pdb=" O ALA S 238 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE S 245 " --> pdb=" O VAL S 241 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER S 254 " --> pdb=" O GLU S 250 " (cutoff:3.500A) Proline residue: S 255 - end of helix Processing helix chain 'S' and resid 287 through 291 Processing helix chain 'S' and resid 405 through 421 removed outlier: 3.506A pdb=" N THR S 416 " --> pdb=" O ILE S 412 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY S 421 " --> pdb=" O ARG S 417 " (cutoff:3.500A) Processing helix chain 'S' and resid 423 through 427 Processing helix chain 'T' and resid 127 through 132 Processing helix chain 'T' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR T 146 " --> pdb=" O ARG T 142 " (cutoff:3.500A) Processing helix chain 'T' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER T 192 " --> pdb=" O GLU T 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA T 193 " --> pdb=" O GLY T 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL T 194 " --> pdb=" O GLN T 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL T 198 " --> pdb=" O VAL T 194 " (cutoff:3.500A) Processing helix chain 'T' and resid 232 through 258 removed outlier: 3.512A pdb=" N ILE T 245 " --> pdb=" O VAL T 241 " (cutoff:3.500A) Proline residue: T 255 - end of helix Processing helix chain 'T' and resid 287 through 291 Processing helix chain 'T' and resid 405 through 421 removed outlier: 3.924A pdb=" N GLY T 421 " --> pdb=" O ARG T 417 " (cutoff:3.500A) Processing helix chain 'U' and resid 127 through 132 Processing helix chain 'U' and resid 132 through 146 removed outlier: 3.634A pdb=" N THR U 146 " --> pdb=" O ARG U 142 " (cutoff:3.500A) Processing helix chain 'U' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER U 192 " --> pdb=" O GLU U 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA U 193 " --> pdb=" O GLY U 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL U 194 " --> pdb=" O GLN U 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL U 198 " --> pdb=" O VAL U 194 " (cutoff:3.500A) Processing helix chain 'U' and resid 232 through 258 removed outlier: 3.502A pdb=" N ALA U 238 " --> pdb=" O GLN U 234 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE U 245 " --> pdb=" O VAL U 241 " (cutoff:3.500A) Proline residue: U 255 - end of helix Processing helix chain 'U' and resid 287 through 291 Processing helix chain 'U' and resid 405 through 421 removed outlier: 3.540A pdb=" N MET U 409 " --> pdb=" O THR U 405 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS U 410 " --> pdb=" O ALA U 406 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY U 421 " --> pdb=" O ARG U 417 " (cutoff:3.500A) Processing helix chain 'V' and resid 127 through 132 Processing helix chain 'V' and resid 132 through 146 removed outlier: 3.634A pdb=" N THR V 146 " --> pdb=" O ARG V 142 " (cutoff:3.500A) Processing helix chain 'V' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER V 192 " --> pdb=" O GLU V 188 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA V 193 " --> pdb=" O GLY V 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL V 194 " --> pdb=" O GLN V 190 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL V 198 " --> pdb=" O VAL V 194 " (cutoff:3.500A) Processing helix chain 'V' and resid 229 through 258 removed outlier: 3.533A pdb=" N ALA V 233 " --> pdb=" O ASP V 229 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN V 234 " --> pdb=" O LEU V 230 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA V 238 " --> pdb=" O GLN V 234 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU V 242 " --> pdb=" O ALA V 238 " (cutoff:3.500A) Proline residue: V 255 - end of helix Processing helix chain 'V' and resid 287 through 291 Processing helix chain 'V' and resid 405 through 421 removed outlier: 3.749A pdb=" N ASP V 414 " --> pdb=" O LYS V 410 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR V 416 " --> pdb=" O ILE V 412 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY V 421 " --> pdb=" O ARG V 417 " (cutoff:3.500A) Processing helix chain 'V' and resid 423 through 427 Processing helix chain 'W' and resid 127 through 132 Processing helix chain 'W' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR W 146 " --> pdb=" O ARG W 142 " (cutoff:3.500A) Processing helix chain 'W' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER W 192 " --> pdb=" O GLU W 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA W 193 " --> pdb=" O GLY W 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL W 194 " --> pdb=" O GLN W 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL W 198 " --> pdb=" O VAL W 194 " (cutoff:3.500A) Processing helix chain 'W' and resid 230 through 258 removed outlier: 3.605A pdb=" N ASP W 240 " --> pdb=" O LYS W 236 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE W 245 " --> pdb=" O VAL W 241 " (cutoff:3.500A) Proline residue: W 255 - end of helix Processing helix chain 'W' and resid 287 through 291 Processing helix chain 'W' and resid 405 through 421 removed outlier: 3.543A pdb=" N ILE W 412 " --> pdb=" O GLN W 408 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY W 421 " --> pdb=" O ARG W 417 " (cutoff:3.500A) Processing helix chain 'X' and resid 127 through 132 Processing helix chain 'X' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR X 146 " --> pdb=" O ARG X 142 " (cutoff:3.500A) Processing helix chain 'X' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER X 192 " --> pdb=" O GLU X 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA X 193 " --> pdb=" O GLY X 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL X 194 " --> pdb=" O GLN X 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL X 198 " --> pdb=" O VAL X 194 " (cutoff:3.500A) Processing helix chain 'X' and resid 230 through 258 removed outlier: 4.000A pdb=" N LEU X 235 " --> pdb=" O ASN X 231 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS X 236 " --> pdb=" O ASP X 232 " (cutoff:3.500A) Proline residue: X 255 - end of helix Processing helix chain 'X' and resid 287 through 291 Processing helix chain 'X' and resid 405 through 421 removed outlier: 3.552A pdb=" N GLU X 418 " --> pdb=" O ASP X 414 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY X 421 " --> pdb=" O ARG X 417 " (cutoff:3.500A) Processing helix chain 'X' and resid 423 through 427 Processing helix chain 'Y' and resid 127 through 132 Processing helix chain 'Y' and resid 132 through 146 removed outlier: 3.634A pdb=" N THR Y 146 " --> pdb=" O ARG Y 142 " (cutoff:3.500A) Processing helix chain 'Y' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER Y 192 " --> pdb=" O GLU Y 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA Y 193 " --> pdb=" O GLY Y 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL Y 194 " --> pdb=" O GLN Y 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL Y 198 " --> pdb=" O VAL Y 194 " (cutoff:3.500A) Processing helix chain 'Y' and resid 232 through 258 removed outlier: 3.547A pdb=" N GLU Y 242 " --> pdb=" O ALA Y 238 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE Y 245 " --> pdb=" O VAL Y 241 " (cutoff:3.500A) Proline residue: Y 255 - end of helix Processing helix chain 'Y' and resid 287 through 291 Processing helix chain 'Y' and resid 405 through 420 removed outlier: 3.722A pdb=" N ILE Y 412 " --> pdb=" O GLN Y 408 " (cutoff:3.500A) Processing helix chain 'Y' and resid 423 through 427 Processing helix chain 'Z' and resid 127 through 132 Processing helix chain 'Z' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR Z 146 " --> pdb=" O ARG Z 142 " (cutoff:3.500A) Processing helix chain 'Z' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER Z 192 " --> pdb=" O GLU Z 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA Z 193 " --> pdb=" O GLY Z 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL Z 194 " --> pdb=" O GLN Z 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL Z 198 " --> pdb=" O VAL Z 194 " (cutoff:3.500A) Processing helix chain 'Z' and resid 230 through 258 removed outlier: 3.591A pdb=" N GLN Z 234 " --> pdb=" O LEU Z 230 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE Z 245 " --> pdb=" O VAL Z 241 " (cutoff:3.500A) Proline residue: Z 255 - end of helix Processing helix chain 'Z' and resid 287 through 291 Processing helix chain 'Z' and resid 405 through 421 removed outlier: 3.726A pdb=" N ILE Z 412 " --> pdb=" O GLN Z 408 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY Z 421 " --> pdb=" O ARG Z 417 " (cutoff:3.500A) Processing helix chain 'a' and resid 127 through 132 Processing helix chain 'a' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR a 146 " --> pdb=" O ARG a 142 " (cutoff:3.500A) Processing helix chain 'a' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER a 192 " --> pdb=" O GLU a 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA a 193 " --> pdb=" O GLY a 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL a 194 " --> pdb=" O GLN a 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL a 198 " --> pdb=" O VAL a 194 " (cutoff:3.500A) Processing helix chain 'a' and resid 232 through 258 removed outlier: 3.771A pdb=" N ASP a 240 " --> pdb=" O LYS a 236 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE a 245 " --> pdb=" O VAL a 241 " (cutoff:3.500A) Proline residue: a 255 - end of helix Processing helix chain 'a' and resid 405 through 421 removed outlier: 3.756A pdb=" N GLY a 421 " --> pdb=" O ARG a 417 " (cutoff:3.500A) Processing helix chain 'a' and resid 423 through 427 Processing helix chain 'b' and resid 127 through 132 Processing helix chain 'b' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR b 146 " --> pdb=" O ARG b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER b 192 " --> pdb=" O GLU b 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA b 193 " --> pdb=" O GLY b 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL b 194 " --> pdb=" O GLN b 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL b 198 " --> pdb=" O VAL b 194 " (cutoff:3.500A) Processing helix chain 'b' and resid 232 through 258 removed outlier: 3.616A pdb=" N ILE b 245 " --> pdb=" O VAL b 241 " (cutoff:3.500A) Proline residue: b 255 - end of helix Processing helix chain 'b' and resid 287 through 291 removed outlier: 3.554A pdb=" N LYS b 290 " --> pdb=" O ASP b 287 " (cutoff:3.500A) Processing helix chain 'b' and resid 405 through 421 removed outlier: 3.684A pdb=" N GLY b 421 " --> pdb=" O ARG b 417 " (cutoff:3.500A) Processing helix chain 'b' and resid 423 through 427 Processing helix chain 'c' and resid 127 through 132 Processing helix chain 'c' and resid 132 through 146 removed outlier: 3.632A pdb=" N THR c 146 " --> pdb=" O ARG c 142 " (cutoff:3.500A) Processing helix chain 'c' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER c 192 " --> pdb=" O GLU c 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA c 193 " --> pdb=" O GLY c 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL c 194 " --> pdb=" O GLN c 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL c 198 " --> pdb=" O VAL c 194 " (cutoff:3.500A) Processing helix chain 'c' and resid 232 through 258 removed outlier: 3.537A pdb=" N ILE c 245 " --> pdb=" O VAL c 241 " (cutoff:3.500A) Proline residue: c 255 - end of helix Processing helix chain 'c' and resid 287 through 291 Processing helix chain 'c' and resid 405 through 420 removed outlier: 3.761A pdb=" N LYS c 410 " --> pdb=" O ALA c 406 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR c 416 " --> pdb=" O ILE c 412 " (cutoff:3.500A) Processing helix chain 'c' and resid 423 through 427 Processing helix chain 'd' and resid 127 through 132 Processing helix chain 'd' and resid 132 through 146 removed outlier: 3.634A pdb=" N THR d 146 " --> pdb=" O ARG d 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER d 192 " --> pdb=" O GLU d 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA d 193 " --> pdb=" O GLY d 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL d 194 " --> pdb=" O GLN d 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL d 198 " --> pdb=" O VAL d 194 " (cutoff:3.500A) Processing helix chain 'd' and resid 229 through 231 No H-bonds generated for 'chain 'd' and resid 229 through 231' Processing helix chain 'd' and resid 232 through 258 removed outlier: 3.715A pdb=" N ALA d 238 " --> pdb=" O GLN d 234 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE d 245 " --> pdb=" O VAL d 241 " (cutoff:3.500A) Proline residue: d 255 - end of helix Processing helix chain 'd' and resid 287 through 291 Processing helix chain 'd' and resid 405 through 411 Processing helix chain 'd' and resid 411 through 420 Processing helix chain 'd' and resid 423 through 427 Processing helix chain 'e' and resid 127 through 132 Processing helix chain 'e' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR e 146 " --> pdb=" O ARG e 142 " (cutoff:3.500A) Processing helix chain 'e' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER e 192 " --> pdb=" O GLU e 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA e 193 " --> pdb=" O GLY e 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL e 194 " --> pdb=" O GLN e 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL e 198 " --> pdb=" O VAL e 194 " (cutoff:3.500A) Processing helix chain 'e' and resid 232 through 258 Proline residue: e 255 - end of helix Processing helix chain 'e' and resid 287 through 291 Processing helix chain 'e' and resid 405 through 421 removed outlier: 3.521A pdb=" N LYS e 410 " --> pdb=" O ALA e 406 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY e 421 " --> pdb=" O ARG e 417 " (cutoff:3.500A) Processing helix chain 'f' and resid 127 through 132 Processing helix chain 'f' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR f 146 " --> pdb=" O ARG f 142 " (cutoff:3.500A) Processing helix chain 'f' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER f 192 " --> pdb=" O GLU f 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA f 193 " --> pdb=" O GLY f 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL f 194 " --> pdb=" O GLN f 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL f 198 " --> pdb=" O VAL f 194 " (cutoff:3.500A) Processing helix chain 'f' and resid 232 through 258 removed outlier: 3.665A pdb=" N GLU f 242 " --> pdb=" O ALA f 238 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE f 245 " --> pdb=" O VAL f 241 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER f 254 " --> pdb=" O GLU f 250 " (cutoff:3.500A) Proline residue: f 255 - end of helix Processing helix chain 'f' and resid 287 through 291 Processing helix chain 'f' and resid 405 through 421 removed outlier: 4.012A pdb=" N ILE f 412 " --> pdb=" O GLN f 408 " (cutoff:3.500A) Processing helix chain 'g' and resid 127 through 132 Processing helix chain 'g' and resid 132 through 146 removed outlier: 3.634A pdb=" N THR g 146 " --> pdb=" O ARG g 142 " (cutoff:3.500A) Processing helix chain 'g' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER g 192 " --> pdb=" O GLU g 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA g 193 " --> pdb=" O GLY g 189 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL g 194 " --> pdb=" O GLN g 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL g 198 " --> pdb=" O VAL g 194 " (cutoff:3.500A) Processing helix chain 'g' and resid 232 through 258 removed outlier: 3.700A pdb=" N GLU g 242 " --> pdb=" O ALA g 238 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE g 245 " --> pdb=" O VAL g 241 " (cutoff:3.500A) Proline residue: g 255 - end of helix Processing helix chain 'g' and resid 287 through 291 Processing helix chain 'g' and resid 405 through 421 removed outlier: 3.799A pdb=" N ILE g 412 " --> pdb=" O GLN g 408 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY g 421 " --> pdb=" O ARG g 417 " (cutoff:3.500A) Processing helix chain 'g' and resid 423 through 427 Processing helix chain 'h' and resid 232 through 258 removed outlier: 3.577A pdb=" N LYS h 236 " --> pdb=" O ASP h 232 " (cutoff:3.500A) Proline residue: h 255 - end of helix Processing helix chain 'h' and resid 287 through 291 Processing helix chain 'h' and resid 405 through 420 removed outlier: 3.691A pdb=" N ILE h 412 " --> pdb=" O GLN h 408 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU h 415 " --> pdb=" O GLN h 411 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR A 179 " --> pdb=" O LYS A 151 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS A 156 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 262 through 270 removed outlier: 3.505A pdb=" N ARG A 384 " --> pdb=" O GLN A 269 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N THR A 429 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU A 385 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ASN A 431 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL A 387 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL A 433 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL A 389 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 292 through 295 removed outlier: 4.312A pdb=" N THR A 292 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN A 365 " --> pdb=" O ARG A 294 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 298 through 299 Processing sheet with id=AA6, first strand: chain 'A' and resid 374 through 376 removed outlier: 3.666A pdb=" N HIS A 374 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.693A pdb=" N THR B 179 " --> pdb=" O LYS B 151 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 156 through 157 removed outlier: 3.544A pdb=" N HIS B 156 " --> pdb=" O SER B 175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 262 through 270 Processing sheet with id=AB1, first strand: chain 'B' and resid 281 through 282 Processing sheet with id=AB2, first strand: chain 'B' and resid 363 through 366 removed outlier: 6.321A pdb=" N THR B 363 " --> pdb=" O ARG B 296 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ARG B 296 " --> pdb=" O THR B 363 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASN B 365 " --> pdb=" O ARG B 294 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ARG B 294 " --> pdb=" O TYR C 366 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG B 296 " --> pdb=" O SER C 364 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR C 363 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ARG C 296 " --> pdb=" O THR C 363 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN C 365 " --> pdb=" O ARG C 294 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ARG C 294 " --> pdb=" O TYR D 366 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR D 363 " --> pdb=" O ARG D 296 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ARG D 296 " --> pdb=" O THR D 363 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN D 365 " --> pdb=" O ARG D 294 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 359 through 360 removed outlier: 3.942A pdb=" N GLN B 359 " --> pdb=" O SER B 301 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR C 179 " --> pdb=" O LYS C 151 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS C 156 " --> pdb=" O SER C 175 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 262 through 271 removed outlier: 3.518A pdb=" N ARG C 384 " --> pdb=" O GLN C 269 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASP C 271 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE C 382 " --> pdb=" O ASP C 271 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N THR C 429 " --> pdb=" O GLU C 383 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU C 385 " --> pdb=" O THR C 429 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ASN C 431 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL C 387 " --> pdb=" O ASN C 431 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N VAL C 433 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL C 389 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 281 through 282 Processing sheet with id=AB8, first strand: chain 'C' and resid 300 through 301 Processing sheet with id=AB9, first strand: chain 'C' and resid 374 through 376 Processing sheet with id=AC1, first strand: chain 'D' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR D 179 " --> pdb=" O LYS D 151 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS D 156 " --> pdb=" O SER D 175 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 262 through 270 removed outlier: 6.628A pdb=" N HIS D 263 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL D 389 " --> pdb=" O HIS D 263 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLN D 265 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL D 387 " --> pdb=" O GLN D 265 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR D 267 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU D 385 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLN D 269 " --> pdb=" O GLU D 383 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N THR D 429 " --> pdb=" O GLU D 383 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU D 385 " --> pdb=" O THR D 429 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N ASN D 431 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL D 387 " --> pdb=" O ASN D 431 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N VAL D 433 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL D 389 " --> pdb=" O VAL D 433 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 281 through 282 Processing sheet with id=AC5, first strand: chain 'D' and resid 298 through 299 removed outlier: 6.399A pdb=" N ASN E 361 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU E 298 " --> pdb=" O ASN E 361 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR E 363 " --> pdb=" O ARG E 296 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ARG E 296 " --> pdb=" O THR E 363 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN E 365 " --> pdb=" O ARG E 294 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ARG E 294 " --> pdb=" O TYR F 366 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR F 363 " --> pdb=" O ARG F 296 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ARG F 296 " --> pdb=" O THR F 363 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN F 365 " --> pdb=" O ARG F 294 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR E 179 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS E 156 " --> pdb=" O SER E 175 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 262 through 270 removed outlier: 6.557A pdb=" N HIS E 263 " --> pdb=" O VAL E 389 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL E 389 " --> pdb=" O HIS E 263 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLN E 265 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL E 387 " --> pdb=" O GLN E 265 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR E 267 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU E 385 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN E 269 " --> pdb=" O GLU E 383 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N THR E 429 " --> pdb=" O GLU E 383 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU E 385 " --> pdb=" O THR E 429 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ASN E 431 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL E 387 " --> pdb=" O ASN E 431 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N VAL E 433 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL E 389 " --> pdb=" O VAL E 433 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR F 179 " --> pdb=" O LYS F 151 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS F 156 " --> pdb=" O SER F 175 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 262 through 271 removed outlier: 6.617A pdb=" N HIS F 263 " --> pdb=" O VAL F 389 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL F 389 " --> pdb=" O HIS F 263 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLN F 265 " --> pdb=" O VAL F 387 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL F 387 " --> pdb=" O GLN F 265 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR F 267 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LEU F 385 " --> pdb=" O THR F 267 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLN F 269 " --> pdb=" O GLU F 383 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP F 381 " --> pdb=" O ASP F 271 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N THR F 429 " --> pdb=" O GLU F 383 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU F 385 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N ASN F 431 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL F 387 " --> pdb=" O ASN F 431 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N VAL F 433 " --> pdb=" O VAL F 387 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL F 389 " --> pdb=" O VAL F 433 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 300 through 301 removed outlier: 3.819A pdb=" N GLN G 359 " --> pdb=" O SER G 301 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 374 through 376 removed outlier: 3.522A pdb=" N HIS F 374 " --> pdb=" O GLU G 276 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR G 179 " --> pdb=" O LYS G 151 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS G 156 " --> pdb=" O SER G 175 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 262 through 271 removed outlier: 6.565A pdb=" N HIS G 263 " --> pdb=" O VAL G 389 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL G 389 " --> pdb=" O HIS G 263 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN G 265 " --> pdb=" O VAL G 387 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL G 387 " --> pdb=" O GLN G 265 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR G 267 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU G 385 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN G 269 " --> pdb=" O GLU G 383 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP G 381 " --> pdb=" O ASP G 271 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N THR G 429 " --> pdb=" O GLU G 383 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU G 385 " --> pdb=" O THR G 429 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ASN G 431 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL G 387 " --> pdb=" O ASN G 431 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N VAL G 433 " --> pdb=" O VAL G 387 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL G 389 " --> pdb=" O VAL G 433 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 281 through 282 Processing sheet with id=AD9, first strand: chain 'G' and resid 363 through 366 removed outlier: 6.354A pdb=" N THR G 363 " --> pdb=" O ARG G 296 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ARG G 296 " --> pdb=" O THR G 363 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN G 365 " --> pdb=" O ARG G 294 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ARG G 294 " --> pdb=" O TYR H 366 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG G 296 " --> pdb=" O SER H 364 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASN H 361 " --> pdb=" O LEU H 298 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU H 298 " --> pdb=" O ASN H 361 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N THR H 363 " --> pdb=" O ARG H 296 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ARG H 296 " --> pdb=" O THR H 363 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN H 365 " --> pdb=" O ARG H 294 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ARG H 294 " --> pdb=" O TYR I 366 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR I 363 " --> pdb=" O ARG I 296 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ARG I 296 " --> pdb=" O THR I 363 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN I 365 " --> pdb=" O ARG I 294 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 363 through 366 removed outlier: 6.354A pdb=" N THR G 363 " --> pdb=" O ARG G 296 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ARG G 296 " --> pdb=" O THR G 363 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN G 365 " --> pdb=" O ARG G 294 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ARG G 294 " --> pdb=" O TYR H 366 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG G 296 " --> pdb=" O SER H 364 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASN H 361 " --> pdb=" O LEU H 298 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU H 298 " --> pdb=" O ASN H 361 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N THR H 363 " --> pdb=" O ARG H 296 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ARG H 296 " --> pdb=" O THR H 363 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN H 365 " --> pdb=" O ARG H 294 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR H 179 " --> pdb=" O LYS H 151 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS H 156 " --> pdb=" O SER H 175 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 262 through 271 removed outlier: 6.576A pdb=" N HIS H 263 " --> pdb=" O VAL H 389 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL H 389 " --> pdb=" O HIS H 263 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLN H 265 " --> pdb=" O VAL H 387 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL H 387 " --> pdb=" O GLN H 265 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR H 267 " --> pdb=" O LEU H 385 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU H 385 " --> pdb=" O THR H 267 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLN H 269 " --> pdb=" O GLU H 383 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP H 381 " --> pdb=" O ASP H 271 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N THR H 429 " --> pdb=" O GLU H 383 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU H 385 " --> pdb=" O THR H 429 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ASN H 431 " --> pdb=" O LEU H 385 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL H 387 " --> pdb=" O ASN H 431 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N VAL H 433 " --> pdb=" O VAL H 387 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL H 389 " --> pdb=" O VAL H 433 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR I 179 " --> pdb=" O LYS I 151 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS I 156 " --> pdb=" O SER I 175 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 262 through 271 removed outlier: 6.556A pdb=" N HIS I 263 " --> pdb=" O VAL I 389 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL I 389 " --> pdb=" O HIS I 263 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLN I 265 " --> pdb=" O VAL I 387 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL I 387 " --> pdb=" O GLN I 265 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR I 267 " --> pdb=" O LEU I 385 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU I 385 " --> pdb=" O THR I 267 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLN I 269 " --> pdb=" O GLU I 383 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP I 381 " --> pdb=" O ASP I 271 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N THR I 429 " --> pdb=" O GLU I 383 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU I 385 " --> pdb=" O THR I 429 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASN I 431 " --> pdb=" O LEU I 385 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL I 387 " --> pdb=" O ASN I 431 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL I 433 " --> pdb=" O VAL I 387 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL I 389 " --> pdb=" O VAL I 433 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 281 through 282 Processing sheet with id=AE9, first strand: chain 'I' and resid 300 through 301 Processing sheet with id=AF1, first strand: chain 'J' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR J 179 " --> pdb=" O LYS J 151 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 156 through 157 removed outlier: 3.544A pdb=" N HIS J 156 " --> pdb=" O SER J 175 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 262 through 271 removed outlier: 6.056A pdb=" N ASP J 271 " --> pdb=" O ILE J 382 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE J 382 " --> pdb=" O ASP J 271 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N THR J 429 " --> pdb=" O GLU J 383 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU J 385 " --> pdb=" O THR J 429 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N ASN J 431 " --> pdb=" O LEU J 385 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL J 387 " --> pdb=" O ASN J 431 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL J 433 " --> pdb=" O VAL J 387 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL J 389 " --> pdb=" O VAL J 433 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 281 through 282 Processing sheet with id=AF5, first strand: chain 'J' and resid 363 through 366 removed outlier: 6.598A pdb=" N THR J 363 " --> pdb=" O ARG J 296 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ARG J 296 " --> pdb=" O THR J 363 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASN J 365 " --> pdb=" O ARG J 294 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ARG J 294 " --> pdb=" O TYR K 366 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASN K 365 " --> pdb=" O ARG K 294 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR K 179 " --> pdb=" O LYS K 151 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS K 156 " --> pdb=" O SER K 175 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 262 through 271 removed outlier: 3.539A pdb=" N ARG K 384 " --> pdb=" O GLN K 269 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ASP K 271 " --> pdb=" O ILE K 382 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE K 382 " --> pdb=" O ASP K 271 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N THR K 429 " --> pdb=" O GLU K 383 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU K 385 " --> pdb=" O THR K 429 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ASN K 431 " --> pdb=" O LEU K 385 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL K 387 " --> pdb=" O ASN K 431 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N VAL K 433 " --> pdb=" O VAL K 387 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL K 389 " --> pdb=" O VAL K 433 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 281 through 282 Processing sheet with id=AG1, first strand: chain 'K' and resid 300 through 301 Processing sheet with id=AG2, first strand: chain 'K' and resid 374 through 376 removed outlier: 3.671A pdb=" N HIS K 374 " --> pdb=" O GLU L 276 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR L 179 " --> pdb=" O LYS L 151 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 156 through 157 removed outlier: 3.546A pdb=" N HIS L 156 " --> pdb=" O SER L 175 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 262 through 271 removed outlier: 6.518A pdb=" N HIS L 263 " --> pdb=" O VAL L 389 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL L 389 " --> pdb=" O HIS L 263 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLN L 265 " --> pdb=" O VAL L 387 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL L 387 " --> pdb=" O GLN L 265 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR L 267 " --> pdb=" O LEU L 385 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU L 385 " --> pdb=" O THR L 267 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLN L 269 " --> pdb=" O GLU L 383 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP L 381 " --> pdb=" O ASP L 271 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N THR L 429 " --> pdb=" O GLU L 383 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU L 385 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ASN L 431 " --> pdb=" O LEU L 385 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL L 387 " --> pdb=" O ASN L 431 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N VAL L 433 " --> pdb=" O VAL L 387 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL L 389 " --> pdb=" O VAL L 433 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 281 through 282 Processing sheet with id=AG7, first strand: chain 'L' and resid 364 through 366 removed outlier: 6.535A pdb=" N ASN L 365 " --> pdb=" O ARG L 294 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ARG L 294 " --> pdb=" O TYR M 366 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN M 297 " --> pdb=" O THR M 363 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN M 365 " --> pdb=" O SER M 295 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ARG M 294 " --> pdb=" O TYR N 366 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG M 296 " --> pdb=" O SER N 364 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU N 362 " --> pdb=" O LEU M 298 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ASN N 365 " --> pdb=" O ARG N 294 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 364 through 366 removed outlier: 6.535A pdb=" N ASN L 365 " --> pdb=" O ARG L 294 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ARG L 294 " --> pdb=" O TYR M 366 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN M 297 " --> pdb=" O THR M 363 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN M 365 " --> pdb=" O SER M 295 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ARG M 294 " --> pdb=" O TYR N 366 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG M 296 " --> pdb=" O SER N 364 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU N 362 " --> pdb=" O LEU M 298 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 374 through 376 Processing sheet with id=AH1, first strand: chain 'M' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR M 179 " --> pdb=" O LYS M 151 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'M' and resid 156 through 157 removed outlier: 3.544A pdb=" N HIS M 156 " --> pdb=" O SER M 175 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'M' and resid 262 through 271 removed outlier: 6.385A pdb=" N ASP M 271 " --> pdb=" O ILE M 382 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE M 382 " --> pdb=" O ASP M 271 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N THR M 429 " --> pdb=" O GLU M 383 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU M 385 " --> pdb=" O THR M 429 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N ASN M 431 " --> pdb=" O LEU M 385 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL M 387 " --> pdb=" O ASN M 431 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL M 433 " --> pdb=" O VAL M 387 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL M 389 " --> pdb=" O VAL M 433 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'M' and resid 374 through 376 Processing sheet with id=AH5, first strand: chain 'N' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR N 179 " --> pdb=" O LYS N 151 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'N' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS N 156 " --> pdb=" O SER N 175 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'N' and resid 262 through 271 removed outlier: 6.726A pdb=" N HIS N 263 " --> pdb=" O VAL N 389 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL N 389 " --> pdb=" O HIS N 263 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN N 265 " --> pdb=" O VAL N 387 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL N 387 " --> pdb=" O GLN N 265 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR N 267 " --> pdb=" O LEU N 385 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU N 385 " --> pdb=" O THR N 267 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLN N 269 " --> pdb=" O GLU N 383 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP N 381 " --> pdb=" O ASP N 271 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N THR N 429 " --> pdb=" O GLU N 383 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU N 385 " --> pdb=" O THR N 429 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ASN N 431 " --> pdb=" O LEU N 385 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL N 387 " --> pdb=" O ASN N 431 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL N 433 " --> pdb=" O VAL N 387 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL N 389 " --> pdb=" O VAL N 433 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'N' and resid 281 through 282 Processing sheet with id=AH9, first strand: chain 'O' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR O 179 " --> pdb=" O LYS O 151 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'O' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS O 156 " --> pdb=" O SER O 175 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'O' and resid 262 through 271 removed outlier: 3.500A pdb=" N ARG O 384 " --> pdb=" O GLN O 269 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASP O 271 " --> pdb=" O ILE O 382 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ILE O 382 " --> pdb=" O ASP O 271 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N THR O 429 " --> pdb=" O GLU O 383 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU O 385 " --> pdb=" O THR O 429 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N ASN O 431 " --> pdb=" O LEU O 385 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL O 387 " --> pdb=" O ASN O 431 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL O 433 " --> pdb=" O VAL O 387 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL O 389 " --> pdb=" O VAL O 433 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'O' and resid 281 through 282 Processing sheet with id=AI4, first strand: chain 'O' and resid 363 through 366 removed outlier: 6.286A pdb=" N THR O 363 " --> pdb=" O ARG O 296 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ARG O 296 " --> pdb=" O THR O 363 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN O 365 " --> pdb=" O ARG O 294 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ARG O 294 " --> pdb=" O TYR P 366 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR P 363 " --> pdb=" O ARG P 296 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ARG P 296 " --> pdb=" O THR P 363 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASN P 365 " --> pdb=" O ARG P 294 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG P 294 " --> pdb=" O TYR Q 366 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR Q 363 " --> pdb=" O ARG Q 296 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ARG Q 296 " --> pdb=" O THR Q 363 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ASN Q 365 " --> pdb=" O ARG Q 294 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'O' and resid 300 through 301 removed outlier: 4.051A pdb=" N GLN P 359 " --> pdb=" O SER P 301 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'O' and resid 374 through 376 Processing sheet with id=AI7, first strand: chain 'P' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR P 179 " --> pdb=" O LYS P 151 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'P' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS P 156 " --> pdb=" O SER P 175 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'P' and resid 262 through 271 removed outlier: 6.161A pdb=" N ASP P 271 " --> pdb=" O ILE P 382 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ILE P 382 " --> pdb=" O ASP P 271 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N THR P 429 " --> pdb=" O GLU P 383 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU P 385 " --> pdb=" O THR P 429 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N ASN P 431 " --> pdb=" O LEU P 385 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL P 387 " --> pdb=" O ASN P 431 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL P 433 " --> pdb=" O VAL P 387 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL P 389 " --> pdb=" O VAL P 433 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'P' and resid 374 through 376 Processing sheet with id=AJ2, first strand: chain 'Q' and resid 262 through 271 removed outlier: 6.131A pdb=" N ASP Q 271 " --> pdb=" O ILE Q 382 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE Q 382 " --> pdb=" O ASP Q 271 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'R' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR R 179 " --> pdb=" O LYS R 151 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'R' and resid 156 through 157 removed outlier: 3.544A pdb=" N HIS R 156 " --> pdb=" O SER R 175 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'R' and resid 262 through 270 removed outlier: 8.783A pdb=" N THR R 429 " --> pdb=" O GLU R 383 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU R 385 " --> pdb=" O THR R 429 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N ASN R 431 " --> pdb=" O LEU R 385 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL R 387 " --> pdb=" O ASN R 431 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N VAL R 433 " --> pdb=" O VAL R 387 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL R 389 " --> pdb=" O VAL R 433 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'R' and resid 292 through 295 removed outlier: 4.316A pdb=" N THR R 292 " --> pdb=" O GLU R 367 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASN R 365 " --> pdb=" O ARG R 294 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'R' and resid 298 through 299 Processing sheet with id=AJ8, first strand: chain 'S' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR S 179 " --> pdb=" O LYS S 151 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'S' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS S 156 " --> pdb=" O SER S 175 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'S' and resid 262 through 270 Processing sheet with id=AK2, first strand: chain 'S' and resid 281 through 282 Processing sheet with id=AK3, first strand: chain 'S' and resid 359 through 360 removed outlier: 3.937A pdb=" N GLN S 359 " --> pdb=" O SER S 301 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG S 296 " --> pdb=" O SER T 364 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ARG S 294 " --> pdb=" O TYR T 366 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASN S 365 " --> pdb=" O ARG S 294 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ARG S 296 " --> pdb=" O THR S 363 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR S 363 " --> pdb=" O ARG S 296 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'S' and resid 359 through 360 removed outlier: 3.937A pdb=" N GLN S 359 " --> pdb=" O SER S 301 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN T 361 " --> pdb=" O LEU T 298 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU T 298 " --> pdb=" O ASN T 361 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR T 363 " --> pdb=" O ARG T 296 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG T 296 " --> pdb=" O THR T 363 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASN T 365 " --> pdb=" O ARG T 294 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ARG T 294 " --> pdb=" O TYR U 366 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR U 363 " --> pdb=" O ARG U 296 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ARG U 296 " --> pdb=" O THR U 363 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN U 365 " --> pdb=" O ARG U 294 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'T' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR T 179 " --> pdb=" O LYS T 151 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'T' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS T 156 " --> pdb=" O SER T 175 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'T' and resid 262 through 271 removed outlier: 6.269A pdb=" N ASP T 271 " --> pdb=" O ILE T 382 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE T 382 " --> pdb=" O ASP T 271 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N THR T 429 " --> pdb=" O GLU T 383 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU T 385 " --> pdb=" O THR T 429 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N ASN T 431 " --> pdb=" O LEU T 385 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL T 387 " --> pdb=" O ASN T 431 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N VAL T 433 " --> pdb=" O VAL T 387 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL T 389 " --> pdb=" O VAL T 433 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'T' and resid 281 through 282 Processing sheet with id=AK9, first strand: chain 'T' and resid 374 through 376 Processing sheet with id=AL1, first strand: chain 'U' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR U 179 " --> pdb=" O LYS U 151 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'U' and resid 156 through 157 removed outlier: 3.544A pdb=" N HIS U 156 " --> pdb=" O SER U 175 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'U' and resid 262 through 270 removed outlier: 6.642A pdb=" N HIS U 263 " --> pdb=" O VAL U 389 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL U 389 " --> pdb=" O HIS U 263 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLN U 265 " --> pdb=" O VAL U 387 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL U 387 " --> pdb=" O GLN U 265 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR U 267 " --> pdb=" O LEU U 385 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU U 385 " --> pdb=" O THR U 267 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLN U 269 " --> pdb=" O GLU U 383 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N THR U 429 " --> pdb=" O GLU U 383 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU U 385 " --> pdb=" O THR U 429 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ASN U 431 " --> pdb=" O LEU U 385 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL U 387 " --> pdb=" O ASN U 431 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N VAL U 433 " --> pdb=" O VAL U 387 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL U 389 " --> pdb=" O VAL U 433 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'U' and resid 281 through 282 Processing sheet with id=AL5, first strand: chain 'V' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR V 179 " --> pdb=" O LYS V 151 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'V' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS V 156 " --> pdb=" O SER V 175 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'V' and resid 262 through 270 removed outlier: 6.554A pdb=" N HIS V 263 " --> pdb=" O VAL V 389 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL V 389 " --> pdb=" O HIS V 263 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLN V 265 " --> pdb=" O VAL V 387 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL V 387 " --> pdb=" O GLN V 265 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR V 267 " --> pdb=" O LEU V 385 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU V 385 " --> pdb=" O THR V 267 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLN V 269 " --> pdb=" O GLU V 383 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'V' and resid 361 through 366 removed outlier: 6.374A pdb=" N ASN V 361 " --> pdb=" O LEU V 298 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU V 298 " --> pdb=" O ASN V 361 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR V 363 " --> pdb=" O ARG V 296 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ARG V 296 " --> pdb=" O THR V 363 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN V 365 " --> pdb=" O ARG V 294 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ARG V 294 " --> pdb=" O TYR W 366 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR W 363 " --> pdb=" O ARG W 296 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ARG W 296 " --> pdb=" O THR W 363 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN W 365 " --> pdb=" O ARG W 294 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'W' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR W 179 " --> pdb=" O LYS W 151 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'W' and resid 156 through 157 removed outlier: 3.544A pdb=" N HIS W 156 " --> pdb=" O SER W 175 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'W' and resid 262 through 271 removed outlier: 6.619A pdb=" N HIS W 263 " --> pdb=" O VAL W 389 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL W 389 " --> pdb=" O HIS W 263 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLN W 265 " --> pdb=" O VAL W 387 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL W 387 " --> pdb=" O GLN W 265 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR W 267 " --> pdb=" O LEU W 385 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LEU W 385 " --> pdb=" O THR W 267 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLN W 269 " --> pdb=" O GLU W 383 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP W 381 " --> pdb=" O ASP W 271 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N THR W 429 " --> pdb=" O GLU W 383 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU W 385 " --> pdb=" O THR W 429 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N ASN W 431 " --> pdb=" O LEU W 385 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL W 387 " --> pdb=" O ASN W 431 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N VAL W 433 " --> pdb=" O VAL W 387 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL W 389 " --> pdb=" O VAL W 433 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'W' and resid 300 through 301 removed outlier: 3.827A pdb=" N GLN X 359 " --> pdb=" O SER X 301 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'W' and resid 374 through 376 removed outlier: 3.530A pdb=" N HIS W 374 " --> pdb=" O GLU X 276 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'X' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR X 179 " --> pdb=" O LYS X 151 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'X' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS X 156 " --> pdb=" O SER X 175 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'X' and resid 262 through 271 removed outlier: 6.587A pdb=" N HIS X 263 " --> pdb=" O VAL X 389 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL X 389 " --> pdb=" O HIS X 263 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLN X 265 " --> pdb=" O VAL X 387 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL X 387 " --> pdb=" O GLN X 265 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR X 267 " --> pdb=" O LEU X 385 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU X 385 " --> pdb=" O THR X 267 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLN X 269 " --> pdb=" O GLU X 383 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP X 381 " --> pdb=" O ASP X 271 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N THR X 429 " --> pdb=" O GLU X 383 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU X 385 " --> pdb=" O THR X 429 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ASN X 431 " --> pdb=" O LEU X 385 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL X 387 " --> pdb=" O ASN X 431 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N VAL X 433 " --> pdb=" O VAL X 387 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL X 389 " --> pdb=" O VAL X 433 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'X' and resid 281 through 282 Processing sheet with id=AM9, first strand: chain 'X' and resid 363 through 366 removed outlier: 6.374A pdb=" N THR X 363 " --> pdb=" O ARG X 296 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ARG X 296 " --> pdb=" O THR X 363 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN X 365 " --> pdb=" O ARG X 294 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ARG X 294 " --> pdb=" O TYR Y 366 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG X 296 " --> pdb=" O SER Y 364 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASN Y 361 " --> pdb=" O LEU Y 298 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU Y 298 " --> pdb=" O ASN Y 361 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N THR Y 363 " --> pdb=" O ARG Y 296 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ARG Y 296 " --> pdb=" O THR Y 363 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN Y 365 " --> pdb=" O ARG Y 294 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ARG Y 294 " --> pdb=" O TYR Z 366 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR Z 363 " --> pdb=" O ARG Z 296 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ARG Z 296 " --> pdb=" O THR Z 363 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASN Z 365 " --> pdb=" O ARG Z 294 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'X' and resid 363 through 366 removed outlier: 6.374A pdb=" N THR X 363 " --> pdb=" O ARG X 296 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ARG X 296 " --> pdb=" O THR X 363 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN X 365 " --> pdb=" O ARG X 294 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ARG X 294 " --> pdb=" O TYR Y 366 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG X 296 " --> pdb=" O SER Y 364 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASN Y 361 " --> pdb=" O LEU Y 298 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU Y 298 " --> pdb=" O ASN Y 361 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N THR Y 363 " --> pdb=" O ARG Y 296 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ARG Y 296 " --> pdb=" O THR Y 363 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN Y 365 " --> pdb=" O ARG Y 294 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'Y' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR Y 179 " --> pdb=" O LYS Y 151 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'Y' and resid 156 through 157 removed outlier: 3.544A pdb=" N HIS Y 156 " --> pdb=" O SER Y 175 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'Y' and resid 262 through 271 removed outlier: 6.572A pdb=" N HIS Y 263 " --> pdb=" O VAL Y 389 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL Y 389 " --> pdb=" O HIS Y 263 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN Y 265 " --> pdb=" O VAL Y 387 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL Y 387 " --> pdb=" O GLN Y 265 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR Y 267 " --> pdb=" O LEU Y 385 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU Y 385 " --> pdb=" O THR Y 267 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN Y 269 " --> pdb=" O GLU Y 383 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP Y 381 " --> pdb=" O ASP Y 271 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N THR Y 429 " --> pdb=" O GLU Y 383 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU Y 385 " --> pdb=" O THR Y 429 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N ASN Y 431 " --> pdb=" O LEU Y 385 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL Y 387 " --> pdb=" O ASN Y 431 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N VAL Y 433 " --> pdb=" O VAL Y 387 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL Y 389 " --> pdb=" O VAL Y 433 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'Z' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR Z 179 " --> pdb=" O LYS Z 151 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'Z' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS Z 156 " --> pdb=" O SER Z 175 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'Z' and resid 262 through 271 removed outlier: 6.557A pdb=" N HIS Z 263 " --> pdb=" O VAL Z 389 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL Z 389 " --> pdb=" O HIS Z 263 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN Z 265 " --> pdb=" O VAL Z 387 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL Z 387 " --> pdb=" O GLN Z 265 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR Z 267 " --> pdb=" O LEU Z 385 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU Z 385 " --> pdb=" O THR Z 267 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLN Z 269 " --> pdb=" O GLU Z 383 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP Z 381 " --> pdb=" O ASP Z 271 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N THR Z 429 " --> pdb=" O GLU Z 383 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU Z 385 " --> pdb=" O THR Z 429 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N ASN Z 431 " --> pdb=" O LEU Z 385 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL Z 387 " --> pdb=" O ASN Z 431 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N VAL Z 433 " --> pdb=" O VAL Z 387 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL Z 389 " --> pdb=" O VAL Z 433 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'Z' and resid 281 through 282 Processing sheet with id=AN9, first strand: chain 'Z' and resid 300 through 301 Processing sheet with id=AO1, first strand: chain 'a' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR a 179 " --> pdb=" O LYS a 151 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'a' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS a 156 " --> pdb=" O SER a 175 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'a' and resid 262 through 271 removed outlier: 6.063A pdb=" N ASP a 271 " --> pdb=" O ILE a 382 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE a 382 " --> pdb=" O ASP a 271 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N THR a 429 " --> pdb=" O GLU a 383 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU a 385 " --> pdb=" O THR a 429 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N ASN a 431 " --> pdb=" O LEU a 385 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL a 387 " --> pdb=" O ASN a 431 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL a 433 " --> pdb=" O VAL a 387 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL a 389 " --> pdb=" O VAL a 433 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'a' and resid 281 through 282 Processing sheet with id=AO5, first strand: chain 'a' and resid 363 through 366 removed outlier: 6.598A pdb=" N THR a 363 " --> pdb=" O ARG a 296 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ARG a 296 " --> pdb=" O THR a 363 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN a 365 " --> pdb=" O ARG a 294 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ARG a 294 " --> pdb=" O TYR b 366 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASN b 365 " --> pdb=" O ARG b 294 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'b' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR b 179 " --> pdb=" O LYS b 151 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'b' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS b 156 " --> pdb=" O SER b 175 " (cutoff:3.500A) Processing sheet with id=AO8, first strand: chain 'b' and resid 262 through 271 removed outlier: 3.536A pdb=" N ARG b 384 " --> pdb=" O GLN b 269 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ASP b 271 " --> pdb=" O ILE b 382 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE b 382 " --> pdb=" O ASP b 271 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N THR b 429 " --> pdb=" O GLU b 383 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU b 385 " --> pdb=" O THR b 429 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ASN b 431 " --> pdb=" O LEU b 385 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL b 387 " --> pdb=" O ASN b 431 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N VAL b 433 " --> pdb=" O VAL b 387 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL b 389 " --> pdb=" O VAL b 433 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'b' and resid 281 through 282 Processing sheet with id=AP1, first strand: chain 'b' and resid 300 through 301 Processing sheet with id=AP2, first strand: chain 'c' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR c 179 " --> pdb=" O LYS c 151 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'c' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS c 156 " --> pdb=" O SER c 175 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'c' and resid 262 through 271 removed outlier: 6.525A pdb=" N HIS c 263 " --> pdb=" O VAL c 389 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL c 389 " --> pdb=" O HIS c 263 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLN c 265 " --> pdb=" O VAL c 387 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL c 387 " --> pdb=" O GLN c 265 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR c 267 " --> pdb=" O LEU c 385 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU c 385 " --> pdb=" O THR c 267 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN c 269 " --> pdb=" O GLU c 383 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP c 381 " --> pdb=" O ASP c 271 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N THR c 429 " --> pdb=" O GLU c 383 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU c 385 " --> pdb=" O THR c 429 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ASN c 431 " --> pdb=" O LEU c 385 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL c 387 " --> pdb=" O ASN c 431 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N VAL c 433 " --> pdb=" O VAL c 387 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL c 389 " --> pdb=" O VAL c 433 " (cutoff:3.500A) Processing sheet with id=AP5, first strand: chain 'c' and resid 281 through 282 Processing sheet with id=AP6, first strand: chain 'c' and resid 364 through 366 removed outlier: 6.549A pdb=" N ASN c 365 " --> pdb=" O ARG c 294 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ARG c 294 " --> pdb=" O TYR d 366 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN d 297 " --> pdb=" O THR d 363 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN d 365 " --> pdb=" O SER d 295 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ARG d 294 " --> pdb=" O TYR e 366 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG d 296 " --> pdb=" O SER e 364 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU e 362 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN e 365 " --> pdb=" O ARG e 294 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'c' and resid 364 through 366 removed outlier: 6.549A pdb=" N ASN c 365 " --> pdb=" O ARG c 294 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ARG c 294 " --> pdb=" O TYR d 366 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN d 297 " --> pdb=" O THR d 363 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN d 365 " --> pdb=" O SER d 295 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ARG d 294 " --> pdb=" O TYR e 366 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG d 296 " --> pdb=" O SER e 364 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU e 362 " --> pdb=" O LEU d 298 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'c' and resid 374 through 376 Processing sheet with id=AP9, first strand: chain 'd' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR d 179 " --> pdb=" O LYS d 151 " (cutoff:3.500A) Processing sheet with id=AQ1, first strand: chain 'd' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS d 156 " --> pdb=" O SER d 175 " (cutoff:3.500A) Processing sheet with id=AQ2, first strand: chain 'd' and resid 262 through 271 removed outlier: 6.381A pdb=" N ASP d 271 " --> pdb=" O ILE d 382 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE d 382 " --> pdb=" O ASP d 271 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N THR d 429 " --> pdb=" O GLU d 383 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU d 385 " --> pdb=" O THR d 429 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ASN d 431 " --> pdb=" O LEU d 385 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL d 387 " --> pdb=" O ASN d 431 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL d 433 " --> pdb=" O VAL d 387 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL d 389 " --> pdb=" O VAL d 433 " (cutoff:3.500A) Processing sheet with id=AQ3, first strand: chain 'd' and resid 374 through 376 removed outlier: 3.504A pdb=" N HIS d 374 " --> pdb=" O GLU e 276 " (cutoff:3.500A) Processing sheet with id=AQ4, first strand: chain 'e' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR e 179 " --> pdb=" O LYS e 151 " (cutoff:3.500A) Processing sheet with id=AQ5, first strand: chain 'e' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS e 156 " --> pdb=" O SER e 175 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'e' and resid 262 through 271 removed outlier: 6.765A pdb=" N HIS e 263 " --> pdb=" O VAL e 389 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL e 389 " --> pdb=" O HIS e 263 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLN e 265 " --> pdb=" O VAL e 387 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL e 387 " --> pdb=" O GLN e 265 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR e 267 " --> pdb=" O LEU e 385 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU e 385 " --> pdb=" O THR e 267 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN e 269 " --> pdb=" O GLU e 383 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP e 381 " --> pdb=" O ASP e 271 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N THR e 429 " --> pdb=" O GLU e 383 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU e 385 " --> pdb=" O THR e 429 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ASN e 431 " --> pdb=" O LEU e 385 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL e 387 " --> pdb=" O ASN e 431 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N VAL e 433 " --> pdb=" O VAL e 387 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL e 389 " --> pdb=" O VAL e 433 " (cutoff:3.500A) Processing sheet with id=AQ7, first strand: chain 'e' and resid 281 through 282 Processing sheet with id=AQ8, first strand: chain 'f' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR f 179 " --> pdb=" O LYS f 151 " (cutoff:3.500A) Processing sheet with id=AQ9, first strand: chain 'f' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS f 156 " --> pdb=" O SER f 175 " (cutoff:3.500A) Processing sheet with id=AR1, first strand: chain 'f' and resid 262 through 271 removed outlier: 6.480A pdb=" N ASP f 271 " --> pdb=" O ILE f 382 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE f 382 " --> pdb=" O ASP f 271 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N THR f 429 " --> pdb=" O GLU f 383 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU f 385 " --> pdb=" O THR f 429 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N ASN f 431 " --> pdb=" O LEU f 385 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL f 387 " --> pdb=" O ASN f 431 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL f 433 " --> pdb=" O VAL f 387 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL f 389 " --> pdb=" O VAL f 433 " (cutoff:3.500A) Processing sheet with id=AR2, first strand: chain 'f' and resid 281 through 282 Processing sheet with id=AR3, first strand: chain 'f' and resid 363 through 366 removed outlier: 6.283A pdb=" N THR f 363 " --> pdb=" O ARG f 296 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ARG f 296 " --> pdb=" O THR f 363 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASN f 365 " --> pdb=" O ARG f 294 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ARG f 294 " --> pdb=" O TYR g 366 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR g 363 " --> pdb=" O ARG g 296 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ARG g 296 " --> pdb=" O THR g 363 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASN g 365 " --> pdb=" O ARG g 294 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ARG g 294 " --> pdb=" O TYR h 366 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR h 363 " --> pdb=" O ARG h 296 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ARG h 296 " --> pdb=" O THR h 363 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ASN h 365 " --> pdb=" O ARG h 294 " (cutoff:3.500A) Processing sheet with id=AR4, first strand: chain 'f' and resid 300 through 301 removed outlier: 4.047A pdb=" N GLN g 359 " --> pdb=" O SER g 301 " (cutoff:3.500A) Processing sheet with id=AR5, first strand: chain 'f' and resid 374 through 376 Processing sheet with id=AR6, first strand: chain 'g' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR g 179 " --> pdb=" O LYS g 151 " (cutoff:3.500A) Processing sheet with id=AR7, first strand: chain 'g' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS g 156 " --> pdb=" O SER g 175 " (cutoff:3.500A) Processing sheet with id=AR8, first strand: chain 'g' and resid 262 through 271 removed outlier: 6.648A pdb=" N HIS g 263 " --> pdb=" O VAL g 389 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL g 389 " --> pdb=" O HIS g 263 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLN g 265 " --> pdb=" O VAL g 387 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL g 387 " --> pdb=" O GLN g 265 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR g 267 " --> pdb=" O LEU g 385 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU g 385 " --> pdb=" O THR g 267 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLN g 269 " --> pdb=" O GLU g 383 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP g 381 " --> pdb=" O ASP g 271 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N THR g 429 " --> pdb=" O GLU g 383 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU g 385 " --> pdb=" O THR g 429 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN g 431 " --> pdb=" O LEU g 385 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL g 387 " --> pdb=" O ASN g 431 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL g 433 " --> pdb=" O VAL g 387 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL g 389 " --> pdb=" O VAL g 433 " (cutoff:3.500A) Processing sheet with id=AR9, first strand: chain 'g' and resid 281 through 282 Processing sheet with id=AS1, first strand: chain 'g' and resid 374 through 376 Processing sheet with id=AS2, first strand: chain 'h' and resid 262 through 271 removed outlier: 6.151A pdb=" N ASP h 271 " --> pdb=" O ILE h 382 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE h 382 " --> pdb=" O ASP h 271 " (cutoff:3.500A) 2256 hydrogen bonds defined for protein. 6252 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: 23.44 Time building geometry restraints manager: 13.16 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: 22239 1.34 - 1.45: 8556 1.45 - 1.57: 32800 1.57 - 1.69: 8 1.69 - 1.81: 268 Bond restraints: 63871 Sorted by residual: bond pdb=" N PRO a 160 " pdb=" CA PRO a 160 " ideal model delta sigma weight residual 1.466 1.576 -0.110 1.50e-02 4.44e+03 5.39e+01 bond pdb=" N SER a 171 " pdb=" CA SER a 171 " ideal model delta sigma weight residual 1.458 1.569 -0.111 1.90e-02 2.77e+03 3.43e+01 bond pdb=" N PRO f 160 " pdb=" CA PRO f 160 " ideal model delta sigma weight residual 1.466 1.545 -0.079 1.50e-02 4.44e+03 2.78e+01 bond pdb=" N SER d 171 " pdb=" CA SER d 171 " ideal model delta sigma weight residual 1.458 1.551 -0.093 1.90e-02 2.77e+03 2.42e+01 bond pdb=" N SER O 171 " pdb=" CA SER O 171 " ideal model delta sigma weight residual 1.458 1.549 -0.091 1.90e-02 2.77e+03 2.27e+01 ... (remaining 63866 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.81: 86022 3.81 - 7.62: 377 7.62 - 11.43: 29 11.43 - 15.25: 19 15.25 - 19.06: 6 Bond angle restraints: 86453 Sorted by residual: angle pdb=" C ASN I 224 " pdb=" N THR I 225 " pdb=" CA THR I 225 " ideal model delta sigma weight residual 122.84 107.67 15.17 1.30e+00 5.92e-01 1.36e+02 angle pdb=" CA GLN G 222 " pdb=" C GLN G 222 " pdb=" N SER G 223 " ideal model delta sigma weight residual 116.84 98.91 17.93 1.71e+00 3.42e-01 1.10e+02 angle pdb=" C SER G 223 " pdb=" N ASN G 224 " pdb=" CA ASN G 224 " ideal model delta sigma weight residual 120.68 103.38 17.30 1.70e+00 3.46e-01 1.04e+02 angle pdb=" N PRO a 160 " pdb=" CA PRO a 160 " pdb=" CB PRO a 160 " ideal model delta sigma weight residual 103.00 92.08 10.92 1.10e+00 8.26e-01 9.85e+01 angle pdb=" O GLN G 222 " pdb=" C GLN G 222 " pdb=" N SER G 223 " ideal model delta sigma weight residual 122.59 134.17 -11.58 1.33e+00 5.65e-01 7.58e+01 ... (remaining 86448 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 35733 17.76 - 35.53: 3245 35.53 - 53.29: 519 53.29 - 71.05: 78 71.05 - 88.82: 46 Dihedral angle restraints: 39621 sinusoidal: 15906 harmonic: 23715 Sorted by residual: dihedral pdb=" C PRO a 160 " pdb=" N PRO a 160 " pdb=" CA PRO a 160 " pdb=" CB PRO a 160 " ideal model delta harmonic sigma weight residual -120.70 -105.73 -14.97 0 2.50e+00 1.60e-01 3.59e+01 dihedral pdb=" N SER J 171 " pdb=" C SER J 171 " pdb=" CA SER J 171 " pdb=" CB SER J 171 " ideal model delta harmonic sigma weight residual 122.80 137.51 -14.71 0 2.50e+00 1.60e-01 3.46e+01 dihedral pdb=" N PRO a 160 " pdb=" C PRO a 160 " pdb=" CA PRO a 160 " pdb=" CB PRO a 160 " ideal model delta harmonic sigma weight residual 115.10 101.26 13.84 0 2.50e+00 1.60e-01 3.06e+01 ... (remaining 39618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 9996 0.107 - 0.213: 146 0.213 - 0.320: 26 0.320 - 0.426: 1 0.426 - 0.533: 3 Chirality restraints: 10172 Sorted by residual: chirality pdb=" CA SER J 171 " pdb=" N SER J 171 " pdb=" C SER J 171 " pdb=" CB SER J 171 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.10e+00 chirality pdb=" CA SER U 171 " pdb=" N SER U 171 " pdb=" C SER U 171 " pdb=" CB SER U 171 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.56e+00 chirality pdb=" CA SER F 171 " pdb=" N SER F 171 " pdb=" C SER F 171 " pdb=" CB SER F 171 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.97e+00 ... (remaining 10169 not shown) Planarity restraints: 11549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN G 222 " -0.033 2.00e-02 2.50e+03 7.98e-02 6.37e+01 pdb=" C GLN G 222 " 0.137 2.00e-02 2.50e+03 pdb=" O GLN G 222 " -0.059 2.00e-02 2.50e+03 pdb=" N SER G 223 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 228 " -0.630 9.50e-02 1.11e+02 2.82e-01 4.86e+01 pdb=" NE ARG L 228 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG L 228 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG L 228 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG L 228 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY L 227 " 0.031 2.00e-02 2.50e+03 6.36e-02 4.04e+01 pdb=" C GLY L 227 " -0.110 2.00e-02 2.50e+03 pdb=" O GLY L 227 " 0.042 2.00e-02 2.50e+03 pdb=" N ARG L 228 " 0.037 2.00e-02 2.50e+03 ... (remaining 11546 not shown) Histogram of nonbonded interaction distances: 0.39 - 1.29: 29 1.29 - 2.19: 135 2.19 - 3.10: 48559 3.10 - 4.00: 154538 4.00 - 4.90: 315018 Warning: very small nonbonded interaction distances. Nonbonded interactions: 518279 Sorted by model distance: nonbonded pdb=" OD1 ASP R 187 " pdb=" CB PRO S 206 " model vdw 0.390 3.440 nonbonded pdb=" OD1 ASP A 187 " pdb=" CB PRO B 206 " model vdw 0.466 3.440 nonbonded pdb=" OD2 ASP M 187 " pdb=" CD PRO N 207 " model vdw 0.561 3.440 nonbonded pdb=" OD2 ASP d 187 " pdb=" CD PRO e 207 " model vdw 0.592 3.440 nonbonded pdb=" OD2 ASP G 187 " pdb=" CD PRO H 207 " model vdw 0.709 3.440 ... (remaining 518274 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'Q' selection = chain 'h' } 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: 4.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 1.870 Check model and map are aligned: 0.350 Set scattering table: 0.440 Process input model: 106.990 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.470 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: 0.020 Load rotamer database and sin/cos tables:2.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 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 : 0.008 0.111 63871 Z= 0.530 Angle : 0.837 19.058 86453 Z= 0.497 Chirality : 0.045 0.533 10172 Planarity : 0.006 0.282 11549 Dihedral : 13.902 88.818 24117 Min Nonbonded Distance : 0.390 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.73 % Allowed : 10.80 % Favored : 88.47 % Rotamer: Outliers : 1.24 % Allowed : 7.90 % Favored : 90.86 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % 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: -5.37 (0.08), residues: 7942 helix: -4.10 (0.06), residues: 2432 sheet: -3.02 (0.09), residues: 3108 loop : -3.04 (0.11), residues: 2402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS K 281 PHE 0.015 0.002 PHE H 422 TYR 0.023 0.002 TYR V 393 ARG 0.009 0.000 ARG E 370 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 786 time to evaluate : 5.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLN cc_start: 0.8949 (tt0) cc_final: 0.8739 (pp30) REVERT: A 196 HIS cc_start: 0.8952 (m-70) cc_final: 0.8733 (m90) REVERT: A 236 LYS cc_start: 0.9048 (mtmt) cc_final: 0.8621 (mttp) REVERT: A 376 LYS cc_start: 0.8649 (tttt) cc_final: 0.8385 (ttpt) REVERT: A 425 LYS cc_start: 0.9112 (ptpt) cc_final: 0.8809 (ptpp) REVERT: C 126 PHE cc_start: 0.6884 (t80) cc_final: 0.6579 (t80) REVERT: D 151 LYS cc_start: 0.8528 (ttmt) cc_final: 0.8259 (tptp) REVERT: D 196 HIS cc_start: 0.8841 (m-70) cc_final: 0.8390 (m-70) REVERT: E 377 MET cc_start: 0.8610 (mmt) cc_final: 0.8212 (mpp) REVERT: F 218 HIS cc_start: 0.8144 (m-70) cc_final: 0.7847 (m-70) REVERT: G 180 LEU cc_start: 0.8881 (mt) cc_final: 0.8590 (mt) REVERT: G 196 HIS cc_start: 0.9097 (m-70) cc_final: 0.8484 (m90) REVERT: H 140 LEU cc_start: 0.8443 (mt) cc_final: 0.8208 (mp) REVERT: H 214 ASP cc_start: 0.5527 (OUTLIER) cc_final: 0.4901 (p0) REVERT: H 252 ILE cc_start: 0.9546 (tp) cc_final: 0.9324 (tp) REVERT: H 377 MET cc_start: 0.8359 (mmt) cc_final: 0.8006 (mpp) REVERT: I 144 ILE cc_start: 0.9390 (mt) cc_final: 0.9182 (mm) REVERT: I 197 LEU cc_start: 0.9117 (tp) cc_final: 0.8698 (tp) REVERT: I 252 ILE cc_start: 0.9473 (tp) cc_final: 0.9256 (tp) REVERT: I 376 LYS cc_start: 0.8772 (tttt) cc_final: 0.8527 (tttm) REVERT: J 132 TYR cc_start: 0.9047 (t80) cc_final: 0.8580 (t80) REVERT: K 376 LYS cc_start: 0.8742 (tttt) cc_final: 0.8501 (tttp) REVERT: L 126 PHE cc_start: 0.8420 (t80) cc_final: 0.8181 (t80) REVERT: L 151 LYS cc_start: 0.7406 (ttmt) cc_final: 0.6978 (ttmp) REVERT: L 172 PRO cc_start: 0.4111 (OUTLIER) cc_final: 0.3869 (Cg_endo) REVERT: L 236 LYS cc_start: 0.8931 (mtmt) cc_final: 0.8533 (mtpp) REVERT: M 132 TYR cc_start: 0.9119 (t80) cc_final: 0.8841 (t80) REVERT: M 196 HIS cc_start: 0.8741 (m-70) cc_final: 0.8499 (m-70) REVERT: M 197 LEU cc_start: 0.9108 (tp) cc_final: 0.8784 (tp) REVERT: M 236 LYS cc_start: 0.8671 (mtmt) cc_final: 0.8464 (mtpp) REVERT: M 250 GLU cc_start: 0.7831 (pp20) cc_final: 0.7606 (pp20) REVERT: M 376 LYS cc_start: 0.8636 (tttt) cc_final: 0.8331 (ttpp) REVERT: N 156 HIS cc_start: 0.8015 (m-70) cc_final: 0.7097 (t70) REVERT: O 151 LYS cc_start: 0.8849 (ttmt) cc_final: 0.8648 (ptpt) REVERT: O 376 LYS cc_start: 0.8520 (tttt) cc_final: 0.8311 (ttpt) REVERT: P 136 LEU cc_start: 0.9093 (tp) cc_final: 0.8777 (tt) REVERT: P 222 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7414 (pm20) REVERT: R 376 LYS cc_start: 0.8618 (tttt) cc_final: 0.8418 (ttpt) REVERT: R 425 LYS cc_start: 0.9151 (ptpt) cc_final: 0.8832 (ptpp) REVERT: S 409 MET cc_start: 0.9013 (mmm) cc_final: 0.8625 (tpt) REVERT: T 126 PHE cc_start: 0.6668 (t80) cc_final: 0.6227 (t80) REVERT: T 132 TYR cc_start: 0.8861 (t80) cc_final: 0.8523 (t80) REVERT: U 151 LYS cc_start: 0.8394 (ttmt) cc_final: 0.8174 (tptp) REVERT: U 196 HIS cc_start: 0.9238 (m-70) cc_final: 0.8730 (m-70) REVERT: V 377 MET cc_start: 0.8623 (mmt) cc_final: 0.8219 (mpp) REVERT: W 409 MET cc_start: 0.8768 (mmm) cc_final: 0.8388 (tpp) REVERT: X 180 LEU cc_start: 0.8805 (mt) cc_final: 0.8409 (mt) REVERT: X 196 HIS cc_start: 0.9146 (m-70) cc_final: 0.8637 (m90) REVERT: X 230 LEU cc_start: 0.8206 (tt) cc_final: 0.7909 (mp) REVERT: Y 214 ASP cc_start: 0.5423 (OUTLIER) cc_final: 0.4984 (p0) REVERT: Y 252 ILE cc_start: 0.9543 (tp) cc_final: 0.9323 (tp) REVERT: Y 377 MET cc_start: 0.8362 (mmt) cc_final: 0.7972 (mpp) REVERT: Z 144 ILE cc_start: 0.9383 (mt) cc_final: 0.9140 (mm) REVERT: Z 197 LEU cc_start: 0.9101 (tp) cc_final: 0.8653 (tp) REVERT: Z 252 ILE cc_start: 0.9478 (tp) cc_final: 0.9262 (tp) REVERT: Z 376 LYS cc_start: 0.8795 (tttt) cc_final: 0.8538 (tttm) REVERT: a 132 TYR cc_start: 0.9046 (t80) cc_final: 0.8579 (t80) REVERT: a 223 SER cc_start: 0.4946 (OUTLIER) cc_final: 0.4680 (p) REVERT: c 126 PHE cc_start: 0.8355 (t80) cc_final: 0.7995 (t80) REVERT: c 132 TYR cc_start: 0.8783 (t80) cc_final: 0.8441 (t80) REVERT: c 151 LYS cc_start: 0.7596 (ttmt) cc_final: 0.7203 (ttmp) REVERT: c 160 PRO cc_start: 0.4865 (OUTLIER) cc_final: 0.4323 (Cg_exo) REVERT: c 236 LYS cc_start: 0.8910 (mtmt) cc_final: 0.8464 (mtpp) REVERT: d 132 TYR cc_start: 0.9001 (t80) cc_final: 0.8684 (t80) REVERT: d 140 LEU cc_start: 0.9505 (mt) cc_final: 0.9285 (mm) REVERT: d 197 LEU cc_start: 0.9135 (tp) cc_final: 0.8817 (tp) REVERT: d 376 LYS cc_start: 0.8546 (tttt) cc_final: 0.8330 (ttpt) REVERT: e 156 HIS cc_start: 0.7911 (m-70) cc_final: 0.6974 (t70) REVERT: f 130 VAL cc_start: 0.8791 (t) cc_final: 0.8360 (m) REVERT: f 160 PRO cc_start: 0.4534 (OUTLIER) cc_final: 0.4158 (Cg_endo) REVERT: f 376 LYS cc_start: 0.8522 (tttt) cc_final: 0.8308 (ttpt) REVERT: g 136 LEU cc_start: 0.8906 (tp) cc_final: 0.8688 (tt) outliers start: 88 outliers final: 23 residues processed: 872 average time/residue: 0.6292 time to fit residues: 911.9256 Evaluate side-chains 547 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 517 time to evaluate : 5.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain G residue 172 PRO Chi-restraints excluded: chain H residue 214 ASP Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain L residue 172 PRO Chi-restraints excluded: chain L residue 228 ARG Chi-restraints excluded: chain L residue 299 ASN Chi-restraints excluded: chain M residue 172 PRO Chi-restraints excluded: chain N residue 214 ASP Chi-restraints excluded: chain O residue 160 PRO Chi-restraints excluded: chain O residue 223 SER Chi-restraints excluded: chain P residue 222 GLN Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain R residue 223 SER Chi-restraints excluded: chain T residue 222 GLN Chi-restraints excluded: chain U residue 223 SER Chi-restraints excluded: chain X residue 160 PRO Chi-restraints excluded: chain Y residue 214 ASP Chi-restraints excluded: chain a residue 223 SER Chi-restraints excluded: chain b residue 224 ASN Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain c residue 160 PRO Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain e residue 214 ASP Chi-restraints excluded: chain f residue 160 PRO Chi-restraints excluded: chain g residue 369 ASP Chi-restraints excluded: chain h residue 369 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 673 optimal weight: 2.9990 chunk 604 optimal weight: 7.9990 chunk 335 optimal weight: 7.9990 chunk 206 optimal weight: 3.9990 chunk 407 optimal weight: 40.0000 chunk 323 optimal weight: 5.9990 chunk 625 optimal weight: 0.9990 chunk 242 optimal weight: 1.9990 chunk 380 optimal weight: 2.9990 chunk 465 optimal weight: 3.9990 chunk 724 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN A 263 HIS A 274 ASN A 361 ASN A 434 ASN B 263 HIS B 274 ASN B 361 ASN B 434 ASN ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN C 261 ASN C 263 HIS C 361 ASN C 431 ASN ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 HIS D 274 ASN D 299 ASN D 434 ASN E 434 ASN F 263 HIS F 274 ASN ** F 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 431 ASN F 434 ASN ** G 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 231 ASN ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 263 HIS G 361 ASN G 434 ASN H 196 HIS H 299 ASN H 434 ASN I 218 HIS I 434 ASN ** J 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 218 HIS J 263 HIS J 359 GLN J 365 ASN J 434 ASN K 263 HIS K 269 GLN K 281 HIS K 299 ASN K 365 ASN K 434 ASN L 263 HIS ** L 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 GLN M 231 ASN M 263 HIS M 431 ASN N 263 HIS N 299 ASN N 431 ASN N 434 ASN ** O 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 218 HIS O 263 HIS O 434 ASN ** P 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 218 HIS P 224 ASN P 231 ASN P 263 HIS P 274 ASN P 365 ASN Q 263 HIS Q 431 ASN Q 434 ASN R 231 ASN R 263 HIS R 274 ASN R 361 ASN R 434 ASN S 231 ASN S 263 HIS S 274 ASN S 361 ASN S 434 ASN T 222 GLN T 231 ASN T 261 ASN T 263 HIS T 361 ASN T 431 ASN ** T 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 218 HIS U 231 ASN U 274 ASN U 299 ASN ** U 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 434 ASN ** W 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 222 GLN W 263 HIS W 274 ASN ** W 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 431 ASN W 434 ASN ** X 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 263 HIS X 361 ASN X 434 ASN Y 299 ASN Y 434 ASN Z 218 HIS ** a 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 218 HIS a 231 ASN a 263 HIS a 359 GLN a 365 ASN a 434 ASN b 263 HIS b 269 GLN b 281 HIS b 299 ASN b 365 ASN b 434 ASN c 263 HIS c 274 ASN c 299 ASN c 365 ASN ** c 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 133 GLN ** d 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 231 ASN d 263 HIS d 431 ASN d 434 ASN e 299 ASN e 431 ASN e 434 ASN ** f 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 218 HIS f 263 HIS f 434 ASN g 196 HIS g 218 HIS g 224 ASN g 263 HIS g 274 ASN g 365 ASN h 263 HIS h 431 ASN h 434 ASN Total number of N/Q/H flips: 132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 63871 Z= 0.221 Angle : 0.621 11.950 86453 Z= 0.316 Chirality : 0.041 0.168 10172 Planarity : 0.004 0.064 11549 Dihedral : 5.364 55.530 8846 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.05 % Favored : 95.86 % Rotamer: Outliers : 1.52 % Allowed : 11.97 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.29 (0.09), residues: 7942 helix: -1.51 (0.09), residues: 2450 sheet: -2.23 (0.10), residues: 2986 loop : -2.38 (0.11), residues: 2506 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS f 196 PHE 0.021 0.001 PHE d 126 TYR 0.018 0.001 TYR P 132 ARG 0.006 0.000 ARG b 228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 595 time to evaluate : 5.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.9079 (mtmt) cc_final: 0.8624 (mttp) REVERT: A 376 LYS cc_start: 0.8174 (tttt) cc_final: 0.7948 (ttpt) REVERT: A 425 LYS cc_start: 0.9098 (ptpt) cc_final: 0.8774 (ptpp) REVERT: C 126 PHE cc_start: 0.6976 (t80) cc_final: 0.6539 (t80) REVERT: C 186 LEU cc_start: 0.8625 (mt) cc_final: 0.8393 (tp) REVERT: D 126 PHE cc_start: 0.7586 (t80) cc_final: 0.7193 (t80) REVERT: D 151 LYS cc_start: 0.8413 (ttmt) cc_final: 0.8086 (tptp) REVERT: D 196 HIS cc_start: 0.9282 (m-70) cc_final: 0.8950 (m-70) REVERT: D 242 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7600 (pt0) REVERT: E 377 MET cc_start: 0.8581 (mmt) cc_final: 0.8167 (mpp) REVERT: F 218 HIS cc_start: 0.8474 (m-70) cc_final: 0.7837 (m-70) REVERT: F 409 MET cc_start: 0.8698 (tpp) cc_final: 0.8468 (tpp) REVERT: G 196 HIS cc_start: 0.9064 (m-70) cc_final: 0.8622 (m90) REVERT: H 377 MET cc_start: 0.8316 (mmt) cc_final: 0.7986 (mpp) REVERT: I 144 ILE cc_start: 0.9537 (mt) cc_final: 0.9232 (mm) REVERT: I 147 LEU cc_start: 0.9270 (tp) cc_final: 0.9061 (mt) REVERT: I 197 LEU cc_start: 0.9013 (tp) cc_final: 0.8492 (tp) REVERT: I 218 HIS cc_start: 0.6915 (m90) cc_final: 0.6633 (m90) REVERT: I 376 LYS cc_start: 0.8578 (tttt) cc_final: 0.8353 (tttm) REVERT: J 218 HIS cc_start: 0.6596 (m-70) cc_final: 0.6311 (m170) REVERT: K 236 LYS cc_start: 0.8568 (mtpt) cc_final: 0.7991 (mtmm) REVERT: K 376 LYS cc_start: 0.8138 (tttt) cc_final: 0.7932 (tttp) REVERT: L 126 PHE cc_start: 0.8331 (t80) cc_final: 0.7860 (t80) REVERT: L 151 LYS cc_start: 0.7469 (ttmt) cc_final: 0.7166 (ttmm) REVERT: L 236 LYS cc_start: 0.8758 (mtmt) cc_final: 0.8454 (mtpp) REVERT: M 126 PHE cc_start: 0.7874 (t80) cc_final: 0.7537 (t80) REVERT: M 196 HIS cc_start: 0.8746 (m-70) cc_final: 0.8525 (m-70) REVERT: M 197 LEU cc_start: 0.9104 (tp) cc_final: 0.8754 (tp) REVERT: M 376 LYS cc_start: 0.8192 (tttt) cc_final: 0.7886 (ttpp) REVERT: M 409 MET cc_start: 0.8639 (tpp) cc_final: 0.8409 (tpp) REVERT: N 155 VAL cc_start: 0.8003 (OUTLIER) cc_final: 0.7247 (t) REVERT: N 156 HIS cc_start: 0.7893 (m-70) cc_final: 0.6959 (t70) REVERT: N 409 MET cc_start: 0.8575 (mmm) cc_final: 0.8345 (tpp) REVERT: P 136 LEU cc_start: 0.9072 (tp) cc_final: 0.8860 (tt) REVERT: P 222 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7349 (pm20) REVERT: Q 409 MET cc_start: 0.8861 (tpt) cc_final: 0.8465 (tpt) REVERT: R 376 LYS cc_start: 0.8550 (tttt) cc_final: 0.8333 (ttpt) REVERT: R 425 LYS cc_start: 0.9137 (ptpt) cc_final: 0.8804 (ptpp) REVERT: T 126 PHE cc_start: 0.6737 (t80) cc_final: 0.6351 (t80) REVERT: T 132 TYR cc_start: 0.8916 (t80) cc_final: 0.8491 (t80) REVERT: U 151 LYS cc_start: 0.8349 (ttmt) cc_final: 0.7969 (tptp) REVERT: U 196 HIS cc_start: 0.9264 (m-70) cc_final: 0.8778 (m-70) REVERT: U 242 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7620 (pt0) REVERT: V 377 MET cc_start: 0.8583 (mmt) cc_final: 0.8192 (mpp) REVERT: W 218 HIS cc_start: 0.7889 (m-70) cc_final: 0.7611 (m-70) REVERT: W 409 MET cc_start: 0.8727 (mmm) cc_final: 0.8258 (tpp) REVERT: X 180 LEU cc_start: 0.8737 (mt) cc_final: 0.8354 (pp) REVERT: X 196 HIS cc_start: 0.9218 (m-70) cc_final: 0.8743 (m90) REVERT: X 197 LEU cc_start: 0.9324 (tp) cc_final: 0.9097 (tt) REVERT: Y 159 MET cc_start: 0.5599 (mpp) cc_final: 0.5245 (ttm) REVERT: Y 377 MET cc_start: 0.8317 (mmt) cc_final: 0.7985 (mpp) REVERT: Z 144 ILE cc_start: 0.9513 (mt) cc_final: 0.9199 (mm) REVERT: Z 157 LEU cc_start: 0.9247 (mp) cc_final: 0.8569 (tt) REVERT: Z 197 LEU cc_start: 0.9012 (tp) cc_final: 0.8488 (tp) REVERT: Z 218 HIS cc_start: 0.7013 (m90) cc_final: 0.6733 (m90) REVERT: Z 376 LYS cc_start: 0.8596 (tttt) cc_final: 0.8363 (tttm) REVERT: a 218 HIS cc_start: 0.6417 (m-70) cc_final: 0.6127 (m170) REVERT: a 223 SER cc_start: 0.5235 (OUTLIER) cc_final: 0.4965 (p) REVERT: b 236 LYS cc_start: 0.8351 (mtpt) cc_final: 0.7803 (mtmm) REVERT: c 151 LYS cc_start: 0.7513 (ttmt) cc_final: 0.7073 (ttmm) REVERT: c 197 LEU cc_start: 0.9147 (tp) cc_final: 0.8672 (tt) REVERT: c 236 LYS cc_start: 0.8803 (mtmt) cc_final: 0.8470 (mtpp) REVERT: d 151 LYS cc_start: 0.8342 (ptmt) cc_final: 0.8044 (ptpp) REVERT: d 197 LEU cc_start: 0.9156 (tp) cc_final: 0.8822 (tp) REVERT: d 376 LYS cc_start: 0.8152 (tttt) cc_final: 0.7875 (ttpp) REVERT: d 409 MET cc_start: 0.8647 (tpp) cc_final: 0.8414 (tpp) REVERT: e 155 VAL cc_start: 0.8017 (OUTLIER) cc_final: 0.7230 (t) REVERT: e 156 HIS cc_start: 0.7804 (m-70) cc_final: 0.6922 (t70) REVERT: e 409 MET cc_start: 0.8569 (mmm) cc_final: 0.8341 (tpp) REVERT: g 136 LEU cc_start: 0.9008 (tp) cc_final: 0.8740 (tt) REVERT: h 409 MET cc_start: 0.8854 (tpt) cc_final: 0.8460 (tpt) outliers start: 108 outliers final: 60 residues processed: 680 average time/residue: 0.6290 time to fit residues: 714.9035 Evaluate side-chains 566 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 502 time to evaluate : 5.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain H residue 236 LYS Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 379 VAL Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 196 HIS Chi-restraints excluded: chain N residue 236 LYS Chi-restraints excluded: chain N residue 410 LYS Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 156 HIS Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 222 GLN Chi-restraints excluded: chain Q residue 266 VAL Chi-restraints excluded: chain R residue 151 LYS Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain T residue 194 VAL Chi-restraints excluded: chain T residue 231 ASN Chi-restraints excluded: chain U residue 155 VAL Chi-restraints excluded: chain U residue 194 VAL Chi-restraints excluded: chain U residue 375 THR Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 223 SER Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 212 LEU Chi-restraints excluded: chain Z residue 225 THR Chi-restraints excluded: chain Z residue 267 THR Chi-restraints excluded: chain a residue 155 VAL Chi-restraints excluded: chain a residue 223 SER Chi-restraints excluded: chain a residue 379 VAL Chi-restraints excluded: chain b residue 155 VAL Chi-restraints excluded: chain c residue 136 LEU Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain c residue 256 ILE Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain e residue 155 VAL Chi-restraints excluded: chain e residue 196 HIS Chi-restraints excluded: chain e residue 410 LYS Chi-restraints excluded: chain f residue 155 VAL Chi-restraints excluded: chain f residue 156 HIS Chi-restraints excluded: chain f residue 157 LEU Chi-restraints excluded: chain f residue 230 LEU Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 178 VAL Chi-restraints excluded: chain h residue 266 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 402 optimal weight: 9.9990 chunk 224 optimal weight: 30.0000 chunk 603 optimal weight: 9.9990 chunk 493 optimal weight: 4.9990 chunk 199 optimal weight: 40.0000 chunk 725 optimal weight: 3.9990 chunk 784 optimal weight: 0.9990 chunk 646 optimal weight: 30.0000 chunk 719 optimal weight: 2.9990 chunk 247 optimal weight: 30.0000 chunk 582 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 434 ASN C 231 ASN ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 HIS ** F 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 196 HIS ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 359 GLN J 361 ASN K 196 HIS ** L 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 365 ASN T 222 GLN ** T 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 361 ASN W 218 HIS ** W 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 196 HIS Z 222 GLN a 359 GLN a 361 ASN ** c 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 218 HIS h 365 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 63871 Z= 0.224 Angle : 0.565 12.054 86453 Z= 0.284 Chirality : 0.040 0.169 10172 Planarity : 0.003 0.040 11549 Dihedral : 4.804 48.444 8787 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.32 % Favored : 95.62 % Rotamer: Outliers : 2.02 % Allowed : 13.03 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.19 (0.10), residues: 7942 helix: 0.07 (0.11), residues: 2492 sheet: -2.02 (0.10), residues: 3084 loop : -1.93 (0.12), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.001 HIS g 196 PHE 0.011 0.001 PHE H 422 TYR 0.023 0.001 TYR M 132 ARG 0.011 0.000 ARG L 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 531 time to evaluate : 5.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LYS cc_start: 0.9028 (mtmt) cc_final: 0.8597 (mttp) REVERT: A 376 LYS cc_start: 0.8150 (tttt) cc_final: 0.7922 (ttpt) REVERT: A 425 LYS cc_start: 0.9101 (ptpt) cc_final: 0.8782 (ptpp) REVERT: B 267 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8873 (p) REVERT: C 126 PHE cc_start: 0.7068 (t80) cc_final: 0.6606 (t80) REVERT: D 126 PHE cc_start: 0.7660 (t80) cc_final: 0.7265 (t80) REVERT: D 151 LYS cc_start: 0.8394 (ttmt) cc_final: 0.8051 (tptp) REVERT: D 196 HIS cc_start: 0.9225 (m-70) cc_final: 0.8895 (m-70) REVERT: D 242 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7655 (pt0) REVERT: E 377 MET cc_start: 0.8567 (mmt) cc_final: 0.8176 (mpp) REVERT: F 218 HIS cc_start: 0.8660 (m-70) cc_final: 0.8016 (m-70) REVERT: G 187 ASP cc_start: 0.5907 (OUTLIER) cc_final: 0.4788 (m-30) REVERT: H 377 MET cc_start: 0.8305 (mmt) cc_final: 0.7971 (mpp) REVERT: I 144 ILE cc_start: 0.9568 (mt) cc_final: 0.9247 (mm) REVERT: I 147 LEU cc_start: 0.9317 (tp) cc_final: 0.9080 (mt) REVERT: I 157 LEU cc_start: 0.9133 (mp) cc_final: 0.8519 (tp) REVERT: I 197 LEU cc_start: 0.9036 (tp) cc_final: 0.8545 (tp) REVERT: I 218 HIS cc_start: 0.7135 (m90) cc_final: 0.6862 (m90) REVERT: J 126 PHE cc_start: 0.8190 (t80) cc_final: 0.7803 (t80) REVERT: J 159 MET cc_start: 0.7639 (tmm) cc_final: 0.7108 (tmm) REVERT: J 218 HIS cc_start: 0.6765 (m-70) cc_final: 0.6388 (m170) REVERT: K 236 LYS cc_start: 0.8545 (mtpt) cc_final: 0.8016 (mtmm) REVERT: K 376 LYS cc_start: 0.8114 (tttt) cc_final: 0.7795 (ttmt) REVERT: L 151 LYS cc_start: 0.7430 (ttmt) cc_final: 0.6944 (ttmm) REVERT: L 236 LYS cc_start: 0.8788 (mtmt) cc_final: 0.8454 (mtpp) REVERT: M 126 PHE cc_start: 0.7990 (t80) cc_final: 0.7664 (t80) REVERT: M 132 TYR cc_start: 0.8918 (t80) cc_final: 0.8699 (t80) REVERT: M 196 HIS cc_start: 0.8746 (m-70) cc_final: 0.8507 (m-70) REVERT: M 197 LEU cc_start: 0.9131 (tp) cc_final: 0.8813 (tp) REVERT: M 376 LYS cc_start: 0.8152 (tttt) cc_final: 0.7858 (ttpp) REVERT: M 409 MET cc_start: 0.8476 (tpp) cc_final: 0.8253 (tpp) REVERT: N 155 VAL cc_start: 0.7984 (OUTLIER) cc_final: 0.7202 (t) REVERT: N 156 HIS cc_start: 0.7793 (m-70) cc_final: 0.6804 (t70) REVERT: P 136 LEU cc_start: 0.9128 (tp) cc_final: 0.8900 (tt) REVERT: P 222 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7457 (pm20) REVERT: Q 409 MET cc_start: 0.8890 (tpt) cc_final: 0.8483 (tpt) REVERT: R 376 LYS cc_start: 0.8581 (tttt) cc_final: 0.8340 (ttpt) REVERT: R 425 LYS cc_start: 0.9129 (ptpt) cc_final: 0.8786 (ptpp) REVERT: T 126 PHE cc_start: 0.6941 (t80) cc_final: 0.6539 (t80) REVERT: T 132 TYR cc_start: 0.8912 (t80) cc_final: 0.8618 (t80) REVERT: U 151 LYS cc_start: 0.8365 (ttmt) cc_final: 0.7967 (tptp) REVERT: U 196 HIS cc_start: 0.9302 (m-70) cc_final: 0.8876 (m-70) REVERT: U 242 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7626 (pt0) REVERT: U 267 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8619 (p) REVERT: V 377 MET cc_start: 0.8571 (mmt) cc_final: 0.8169 (mpp) REVERT: W 409 MET cc_start: 0.8733 (mmm) cc_final: 0.8277 (tpp) REVERT: X 159 MET cc_start: 0.7784 (tmm) cc_final: 0.7500 (tmm) REVERT: X 187 ASP cc_start: 0.5903 (OUTLIER) cc_final: 0.5009 (m-30) REVERT: X 196 HIS cc_start: 0.9263 (m-70) cc_final: 0.8987 (m-70) REVERT: Y 159 MET cc_start: 0.5667 (OUTLIER) cc_final: 0.5080 (ttm) REVERT: Y 377 MET cc_start: 0.8323 (mmt) cc_final: 0.7994 (mpp) REVERT: Z 157 LEU cc_start: 0.9167 (mp) cc_final: 0.8651 (tp) REVERT: Z 197 LEU cc_start: 0.9035 (tp) cc_final: 0.8498 (tp) REVERT: Z 218 HIS cc_start: 0.7133 (m90) cc_final: 0.6885 (m90) REVERT: a 218 HIS cc_start: 0.6806 (m-70) cc_final: 0.6412 (m170) REVERT: b 236 LYS cc_start: 0.8365 (mtpt) cc_final: 0.7868 (mtmm) REVERT: c 151 LYS cc_start: 0.7465 (ttmt) cc_final: 0.7007 (ttmm) REVERT: c 197 LEU cc_start: 0.9144 (tp) cc_final: 0.8634 (tt) REVERT: d 151 LYS cc_start: 0.8325 (ptmt) cc_final: 0.8059 (ptpp) REVERT: d 197 LEU cc_start: 0.9160 (tp) cc_final: 0.8864 (tp) REVERT: d 376 LYS cc_start: 0.8123 (tttt) cc_final: 0.7860 (ttpp) REVERT: d 409 MET cc_start: 0.8485 (tpp) cc_final: 0.8257 (tpp) REVERT: e 155 VAL cc_start: 0.8001 (OUTLIER) cc_final: 0.7269 (t) REVERT: e 156 HIS cc_start: 0.7642 (m-70) cc_final: 0.6651 (t70) REVERT: g 180 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8216 (tp) REVERT: h 409 MET cc_start: 0.8857 (tpt) cc_final: 0.8472 (tpt) outliers start: 143 outliers final: 84 residues processed: 641 average time/residue: 0.6072 time to fit residues: 655.4274 Evaluate side-chains 572 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 479 time to evaluate : 5.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain E residue 196 HIS Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain G residue 132 TYR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain H residue 236 LYS Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 379 VAL Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 199 SER Chi-restraints excluded: chain L residue 132 TYR Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 196 HIS Chi-restraints excluded: chain N residue 236 LYS Chi-restraints excluded: chain N residue 410 LYS Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 156 HIS Chi-restraints excluded: chain O residue 416 THR Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 222 GLN Chi-restraints excluded: chain P residue 425 LYS Chi-restraints excluded: chain Q residue 266 VAL Chi-restraints excluded: chain Q residue 416 THR Chi-restraints excluded: chain R residue 151 LYS Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 375 THR Chi-restraints excluded: chain T residue 194 VAL Chi-restraints excluded: chain U residue 132 TYR Chi-restraints excluded: chain U residue 155 VAL Chi-restraints excluded: chain U residue 194 VAL Chi-restraints excluded: chain U residue 267 THR Chi-restraints excluded: chain U residue 375 THR Chi-restraints excluded: chain V residue 196 HIS Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 198 VAL Chi-restraints excluded: chain X residue 132 TYR Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 157 LEU Chi-restraints excluded: chain X residue 187 ASP Chi-restraints excluded: chain X residue 230 LEU Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 159 MET Chi-restraints excluded: chain Y residue 223 SER Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 212 LEU Chi-restraints excluded: chain Z residue 225 THR Chi-restraints excluded: chain Z residue 267 THR Chi-restraints excluded: chain a residue 155 VAL Chi-restraints excluded: chain a residue 223 SER Chi-restraints excluded: chain a residue 379 VAL Chi-restraints excluded: chain b residue 155 VAL Chi-restraints excluded: chain b residue 199 SER Chi-restraints excluded: chain c residue 136 LEU Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain c residue 256 ILE Chi-restraints excluded: chain d residue 187 ASP Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain e residue 155 VAL Chi-restraints excluded: chain e residue 196 HIS Chi-restraints excluded: chain e residue 410 LYS Chi-restraints excluded: chain f residue 155 VAL Chi-restraints excluded: chain f residue 156 HIS Chi-restraints excluded: chain f residue 157 LEU Chi-restraints excluded: chain f residue 230 LEU Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain f residue 416 THR Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 176 VAL Chi-restraints excluded: chain g residue 180 LEU Chi-restraints excluded: chain g residue 425 LYS Chi-restraints excluded: chain h residue 266 VAL Chi-restraints excluded: chain h residue 416 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 717 optimal weight: 10.0000 chunk 545 optimal weight: 20.0000 chunk 376 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 346 optimal weight: 4.9990 chunk 487 optimal weight: 8.9990 chunk 728 optimal weight: 8.9990 chunk 771 optimal weight: 4.9990 chunk 380 optimal weight: 8.9990 chunk 690 optimal weight: 6.9990 chunk 207 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 HIS B 156 HIS B 434 ASN C 222 GLN C 231 ASN C 281 HIS ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 269 GLN E 361 ASN ** F 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 222 GLN J 131 ASN K 196 HIS K 285 ASN L 222 GLN L 434 ASN M 196 HIS M 434 ASN N 224 ASN ** O 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 434 ASN Q 411 GLN ** R 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 231 ASN T 274 ASN T 281 HIS ** T 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 269 GLN W 222 GLN ** W 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 196 HIS a 131 ASN a 434 ASN b 285 ASN c 434 ASN ** d 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 196 HIS g 434 ASN h 411 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 63871 Z= 0.452 Angle : 0.662 13.855 86453 Z= 0.335 Chirality : 0.041 0.164 10172 Planarity : 0.004 0.066 11549 Dihedral : 5.004 49.864 8787 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.77 % Favored : 93.16 % Rotamer: Outliers : 2.44 % Allowed : 14.05 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.00 (0.10), residues: 7942 helix: 0.47 (0.11), residues: 2492 sheet: -2.08 (0.10), residues: 3098 loop : -1.86 (0.12), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS W 196 PHE 0.022 0.002 PHE d 126 TYR 0.015 0.002 TYR d 282 ARG 0.009 0.000 ARG b 228 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 499 time to evaluate : 5.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLN cc_start: 0.9189 (tt0) cc_final: 0.8967 (tp40) REVERT: A 159 MET cc_start: 0.7489 (tmm) cc_final: 0.7206 (tmm) REVERT: A 236 LYS cc_start: 0.9101 (mtmt) cc_final: 0.8778 (mttm) REVERT: A 376 LYS cc_start: 0.8271 (tttt) cc_final: 0.8008 (ttpt) REVERT: A 425 LYS cc_start: 0.9091 (ptpt) cc_final: 0.8791 (ptpp) REVERT: C 126 PHE cc_start: 0.7040 (t80) cc_final: 0.6574 (t80) REVERT: C 180 LEU cc_start: 0.8230 (tp) cc_final: 0.8029 (tp) REVERT: D 196 HIS cc_start: 0.9245 (m-70) cc_final: 0.8924 (m-70) REVERT: D 242 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7547 (mt-10) REVERT: D 425 LYS cc_start: 0.8724 (pttt) cc_final: 0.8507 (pttt) REVERT: E 377 MET cc_start: 0.8569 (mmt) cc_final: 0.8159 (mpp) REVERT: F 190 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7916 (mt0) REVERT: F 218 HIS cc_start: 0.8665 (m-70) cc_final: 0.8016 (m-70) REVERT: F 377 MET cc_start: 0.8191 (mpp) cc_final: 0.7908 (mpt) REVERT: G 187 ASP cc_start: 0.5938 (OUTLIER) cc_final: 0.4797 (m-30) REVERT: G 197 LEU cc_start: 0.9382 (tp) cc_final: 0.9163 (tp) REVERT: I 144 ILE cc_start: 0.9602 (mt) cc_final: 0.9333 (mm) REVERT: I 147 LEU cc_start: 0.9347 (tp) cc_final: 0.9098 (mt) REVERT: I 157 LEU cc_start: 0.9213 (mp) cc_final: 0.8595 (tp) REVERT: I 197 LEU cc_start: 0.9110 (tp) cc_final: 0.8730 (tp) REVERT: I 218 HIS cc_start: 0.7206 (m90) cc_final: 0.6937 (m90) REVERT: J 218 HIS cc_start: 0.6857 (m-70) cc_final: 0.6479 (m170) REVERT: K 236 LYS cc_start: 0.8487 (mtpt) cc_final: 0.7986 (mtmm) REVERT: K 376 LYS cc_start: 0.8307 (tttt) cc_final: 0.8088 (tttp) REVERT: L 126 PHE cc_start: 0.8520 (t80) cc_final: 0.8089 (t80) REVERT: L 151 LYS cc_start: 0.7547 (ttmt) cc_final: 0.7099 (ttmm) REVERT: L 420 MET cc_start: 0.8954 (ptm) cc_final: 0.8697 (ptt) REVERT: M 126 PHE cc_start: 0.8097 (t80) cc_final: 0.7821 (t80) REVERT: M 196 HIS cc_start: 0.8779 (m90) cc_final: 0.8573 (m-70) REVERT: M 197 LEU cc_start: 0.9123 (tp) cc_final: 0.8895 (tp) REVERT: M 376 LYS cc_start: 0.8205 (tttt) cc_final: 0.7907 (ttpp) REVERT: N 156 HIS cc_start: 0.7488 (m-70) cc_final: 0.6449 (t70) REVERT: Q 409 MET cc_start: 0.8899 (tpt) cc_final: 0.8461 (tpt) REVERT: R 376 LYS cc_start: 0.8707 (tttt) cc_final: 0.8506 (ttpt) REVERT: R 425 LYS cc_start: 0.9134 (ptpt) cc_final: 0.8822 (ptpp) REVERT: T 126 PHE cc_start: 0.6987 (t80) cc_final: 0.6560 (t80) REVERT: T 132 TYR cc_start: 0.9010 (t80) cc_final: 0.8692 (t80) REVERT: U 196 HIS cc_start: 0.9302 (m-70) cc_final: 0.8885 (m-70) REVERT: U 242 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7572 (mt-10) REVERT: U 267 THR cc_start: 0.9182 (OUTLIER) cc_final: 0.8534 (p) REVERT: U 425 LYS cc_start: 0.8705 (pttt) cc_final: 0.8490 (pttt) REVERT: V 377 MET cc_start: 0.8574 (mmt) cc_final: 0.8148 (mpp) REVERT: W 377 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7992 (mpt) REVERT: W 409 MET cc_start: 0.8765 (mmm) cc_final: 0.8314 (tpp) REVERT: X 187 ASP cc_start: 0.5924 (OUTLIER) cc_final: 0.4814 (m-30) REVERT: X 196 HIS cc_start: 0.9303 (m-70) cc_final: 0.9026 (m-70) REVERT: Y 159 MET cc_start: 0.5402 (OUTLIER) cc_final: 0.4696 (ttm) REVERT: Z 197 LEU cc_start: 0.9127 (tp) cc_final: 0.8842 (tp) REVERT: Z 218 HIS cc_start: 0.7283 (m90) cc_final: 0.6839 (m90) REVERT: a 218 HIS cc_start: 0.6837 (m-70) cc_final: 0.6471 (m170) REVERT: b 236 LYS cc_start: 0.8386 (mtpt) cc_final: 0.7917 (mtmm) REVERT: c 126 PHE cc_start: 0.8571 (t80) cc_final: 0.8320 (t80) REVERT: c 151 LYS cc_start: 0.7609 (ttmt) cc_final: 0.7114 (ttmm) REVERT: c 197 LEU cc_start: 0.9217 (tp) cc_final: 0.8684 (tt) REVERT: d 151 LYS cc_start: 0.8355 (ptmt) cc_final: 0.8115 (ptpp) REVERT: d 197 LEU cc_start: 0.9152 (tp) cc_final: 0.8913 (tp) REVERT: d 376 LYS cc_start: 0.8167 (tttt) cc_final: 0.7885 (ttpp) REVERT: e 155 VAL cc_start: 0.8212 (OUTLIER) cc_final: 0.7394 (t) REVERT: e 156 HIS cc_start: 0.7291 (m-70) cc_final: 0.6204 (t70) REVERT: g 186 LEU cc_start: 0.7818 (tp) cc_final: 0.7446 (tp) REVERT: h 409 MET cc_start: 0.8898 (tpt) cc_final: 0.8441 (tpt) outliers start: 173 outliers final: 109 residues processed: 635 average time/residue: 0.6172 time to fit residues: 661.6267 Evaluate side-chains 586 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 470 time to evaluate : 5.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain E residue 196 HIS Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 190 GLN Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain G residue 132 TYR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 159 MET Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain H residue 236 LYS Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 267 THR Chi-restraints excluded: chain J residue 379 VAL Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain L residue 132 TYR Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain M residue 377 MET Chi-restraints excluded: chain N residue 196 HIS Chi-restraints excluded: chain N residue 205 LEU Chi-restraints excluded: chain N residue 224 ASN Chi-restraints excluded: chain N residue 236 LYS Chi-restraints excluded: chain N residue 410 LYS Chi-restraints excluded: chain O residue 132 TYR Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 156 HIS Chi-restraints excluded: chain O residue 194 VAL Chi-restraints excluded: chain O residue 416 THR Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 375 THR Chi-restraints excluded: chain Q residue 252 ILE Chi-restraints excluded: chain Q residue 266 VAL Chi-restraints excluded: chain Q residue 416 THR Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 151 LYS Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 375 THR Chi-restraints excluded: chain T residue 194 VAL Chi-restraints excluded: chain U residue 132 TYR Chi-restraints excluded: chain U residue 267 THR Chi-restraints excluded: chain U residue 375 THR Chi-restraints excluded: chain V residue 196 HIS Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 198 VAL Chi-restraints excluded: chain W residue 377 MET Chi-restraints excluded: chain X residue 132 TYR Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 157 LEU Chi-restraints excluded: chain X residue 187 ASP Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 230 LEU Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 159 MET Chi-restraints excluded: chain Y residue 223 SER Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain Z residue 212 LEU Chi-restraints excluded: chain Z residue 225 THR Chi-restraints excluded: chain Z residue 267 THR Chi-restraints excluded: chain Z residue 416 THR Chi-restraints excluded: chain a residue 155 VAL Chi-restraints excluded: chain a residue 267 THR Chi-restraints excluded: chain a residue 379 VAL Chi-restraints excluded: chain b residue 155 VAL Chi-restraints excluded: chain b residue 199 SER Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain c residue 132 TYR Chi-restraints excluded: chain c residue 136 LEU Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain c residue 256 ILE Chi-restraints excluded: chain c residue 416 THR Chi-restraints excluded: chain d residue 187 ASP Chi-restraints excluded: chain d residue 228 ARG Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain e residue 155 VAL Chi-restraints excluded: chain e residue 196 HIS Chi-restraints excluded: chain e residue 410 LYS Chi-restraints excluded: chain f residue 155 VAL Chi-restraints excluded: chain f residue 156 HIS Chi-restraints excluded: chain f residue 157 LEU Chi-restraints excluded: chain f residue 230 LEU Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain f residue 416 THR Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 176 VAL Chi-restraints excluded: chain g residue 180 LEU Chi-restraints excluded: chain g residue 369 ASP Chi-restraints excluded: chain h residue 266 VAL Chi-restraints excluded: chain h residue 358 THR Chi-restraints excluded: chain h residue 416 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 642 optimal weight: 6.9990 chunk 437 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 574 optimal weight: 40.0000 chunk 318 optimal weight: 6.9990 chunk 658 optimal weight: 6.9990 chunk 533 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 393 optimal weight: 7.9990 chunk 692 optimal weight: 50.0000 chunk 194 optimal weight: 0.0370 overall best weight: 3.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 196 HIS ** M 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 224 ASN ** O 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 218 HIS ** R 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 196 HIS a 434 ASN ** d 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 129 GLN ** e 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 196 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 63871 Z= 0.254 Angle : 0.560 12.227 86453 Z= 0.280 Chirality : 0.040 0.166 10172 Planarity : 0.003 0.040 11549 Dihedral : 4.650 38.913 8783 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.19 % Favored : 95.76 % Rotamer: Outliers : 2.28 % Allowed : 15.11 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.50 (0.10), residues: 7942 helix: 1.04 (0.11), residues: 2480 sheet: -1.88 (0.10), residues: 3106 loop : -1.64 (0.12), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS W 196 PHE 0.012 0.001 PHE d 422 TYR 0.022 0.001 TYR K 132 ARG 0.004 0.000 ARG b 228 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 501 time to evaluate : 5.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLN cc_start: 0.9196 (tt0) cc_final: 0.8965 (tp40) REVERT: A 159 MET cc_start: 0.7487 (tmm) cc_final: 0.7238 (tmm) REVERT: A 236 LYS cc_start: 0.9090 (mtmt) cc_final: 0.8702 (mttp) REVERT: A 376 LYS cc_start: 0.8162 (tttt) cc_final: 0.7927 (ttpt) REVERT: A 425 LYS cc_start: 0.9090 (ptpt) cc_final: 0.8789 (ptpp) REVERT: B 267 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8838 (p) REVERT: C 126 PHE cc_start: 0.7044 (t80) cc_final: 0.6586 (t80) REVERT: C 180 LEU cc_start: 0.8236 (tp) cc_final: 0.8011 (tp) REVERT: D 126 PHE cc_start: 0.7917 (t80) cc_final: 0.7571 (t80) REVERT: D 196 HIS cc_start: 0.9244 (m-70) cc_final: 0.8925 (m-70) REVERT: D 425 LYS cc_start: 0.8678 (pttt) cc_final: 0.8424 (pttt) REVERT: E 377 MET cc_start: 0.8562 (mmt) cc_final: 0.8137 (mpp) REVERT: E 409 MET cc_start: 0.8615 (tpp) cc_final: 0.8305 (tpp) REVERT: F 159 MET cc_start: 0.6292 (tpt) cc_final: 0.5533 (ppp) REVERT: F 218 HIS cc_start: 0.8702 (m-70) cc_final: 0.8080 (m-70) REVERT: F 377 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7955 (mpt) REVERT: G 187 ASP cc_start: 0.6027 (OUTLIER) cc_final: 0.4832 (m-30) REVERT: H 250 GLU cc_start: 0.7832 (pp20) cc_final: 0.7536 (pp20) REVERT: H 377 MET cc_start: 0.8338 (mmt) cc_final: 0.7907 (mpp) REVERT: I 144 ILE cc_start: 0.9614 (mt) cc_final: 0.9347 (mm) REVERT: I 147 LEU cc_start: 0.9362 (tp) cc_final: 0.9118 (mt) REVERT: I 157 LEU cc_start: 0.9228 (mp) cc_final: 0.8620 (tp) REVERT: I 197 LEU cc_start: 0.9118 (tp) cc_final: 0.8767 (tp) REVERT: I 218 HIS cc_start: 0.7296 (m90) cc_final: 0.6875 (m90) REVERT: J 218 HIS cc_start: 0.6971 (m-70) cc_final: 0.6561 (m170) REVERT: K 236 LYS cc_start: 0.8477 (mtpt) cc_final: 0.7981 (mtmm) REVERT: K 376 LYS cc_start: 0.8230 (tttt) cc_final: 0.8016 (tttp) REVERT: L 151 LYS cc_start: 0.7567 (ttmt) cc_final: 0.7126 (ttmm) REVERT: L 197 LEU cc_start: 0.9312 (tp) cc_final: 0.8824 (tt) REVERT: L 420 MET cc_start: 0.8921 (ptm) cc_final: 0.8678 (ptt) REVERT: M 126 PHE cc_start: 0.8095 (t80) cc_final: 0.7832 (t80) REVERT: M 196 HIS cc_start: 0.8784 (m90) cc_final: 0.8571 (m-70) REVERT: M 376 LYS cc_start: 0.8145 (tttt) cc_final: 0.7824 (ttpp) REVERT: N 156 HIS cc_start: 0.7215 (m-70) cc_final: 0.6141 (t70) REVERT: N 410 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.9134 (ptmm) REVERT: O 236 LYS cc_start: 0.8850 (mmtm) cc_final: 0.8576 (mmtm) REVERT: P 218 HIS cc_start: 0.7451 (m90) cc_final: 0.7218 (m-70) REVERT: Q 409 MET cc_start: 0.8899 (tpt) cc_final: 0.8520 (tpt) REVERT: R 218 HIS cc_start: 0.8212 (t-90) cc_final: 0.8012 (t-90) REVERT: R 376 LYS cc_start: 0.8645 (tttt) cc_final: 0.8444 (ttpt) REVERT: R 425 LYS cc_start: 0.9140 (ptpt) cc_final: 0.8821 (ptpp) REVERT: S 176 VAL cc_start: 0.7866 (OUTLIER) cc_final: 0.7653 (t) REVERT: T 126 PHE cc_start: 0.6989 (t80) cc_final: 0.6573 (t80) REVERT: T 132 TYR cc_start: 0.8991 (t80) cc_final: 0.8608 (t80) REVERT: U 196 HIS cc_start: 0.9297 (m-70) cc_final: 0.8890 (m-70) REVERT: U 267 THR cc_start: 0.9155 (OUTLIER) cc_final: 0.8667 (p) REVERT: U 425 LYS cc_start: 0.8693 (pttt) cc_final: 0.8432 (pttt) REVERT: V 377 MET cc_start: 0.8560 (mmt) cc_final: 0.8046 (mpp) REVERT: W 190 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8326 (mt0) REVERT: W 218 HIS cc_start: 0.8261 (m-70) cc_final: 0.7645 (m-70) REVERT: W 377 MET cc_start: 0.8214 (mpp) cc_final: 0.8009 (mpt) REVERT: W 409 MET cc_start: 0.8770 (mmm) cc_final: 0.8389 (tpp) REVERT: X 196 HIS cc_start: 0.9281 (m-70) cc_final: 0.9001 (m-70) REVERT: Y 159 MET cc_start: 0.5507 (OUTLIER) cc_final: 0.4742 (ttm) REVERT: Y 250 GLU cc_start: 0.7830 (pp20) cc_final: 0.7531 (pp20) REVERT: Y 377 MET cc_start: 0.8324 (mmt) cc_final: 0.7913 (mpp) REVERT: Z 197 LEU cc_start: 0.9107 (tp) cc_final: 0.8848 (tp) REVERT: Z 218 HIS cc_start: 0.7330 (m90) cc_final: 0.6880 (m90) REVERT: Z 232 ASP cc_start: 0.7772 (p0) cc_final: 0.7053 (t0) REVERT: a 218 HIS cc_start: 0.7049 (m-70) cc_final: 0.6633 (m170) REVERT: b 236 LYS cc_start: 0.8365 (mtpt) cc_final: 0.7888 (mttm) REVERT: c 126 PHE cc_start: 0.8606 (t80) cc_final: 0.8357 (t80) REVERT: c 151 LYS cc_start: 0.7576 (ttmt) cc_final: 0.7072 (ttmm) REVERT: c 197 LEU cc_start: 0.9292 (tp) cc_final: 0.8889 (tt) REVERT: d 151 LYS cc_start: 0.8407 (ptmt) cc_final: 0.8097 (ptpp) REVERT: d 197 LEU cc_start: 0.9144 (tp) cc_final: 0.8937 (tp) REVERT: d 376 LYS cc_start: 0.8129 (tttt) cc_final: 0.7865 (ttpp) REVERT: e 155 VAL cc_start: 0.8239 (OUTLIER) cc_final: 0.7453 (t) REVERT: e 156 HIS cc_start: 0.7119 (m-70) cc_final: 0.5966 (t70) REVERT: e 410 LYS cc_start: 0.9344 (OUTLIER) cc_final: 0.9134 (ptmm) REVERT: h 409 MET cc_start: 0.8883 (tpt) cc_final: 0.8516 (tpt) outliers start: 162 outliers final: 105 residues processed: 629 average time/residue: 0.5986 time to fit residues: 636.2518 Evaluate side-chains 585 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 470 time to evaluate : 5.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain E residue 196 HIS Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain G residue 132 TYR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain H residue 236 LYS Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 267 THR Chi-restraints excluded: chain J residue 379 VAL Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain L residue 132 TYR Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 196 HIS Chi-restraints excluded: chain N residue 236 LYS Chi-restraints excluded: chain N residue 410 LYS Chi-restraints excluded: chain O residue 132 TYR Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 156 HIS Chi-restraints excluded: chain O residue 416 THR Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain Q residue 252 ILE Chi-restraints excluded: chain Q residue 266 VAL Chi-restraints excluded: chain Q residue 358 THR Chi-restraints excluded: chain Q residue 375 THR Chi-restraints excluded: chain Q residue 416 THR Chi-restraints excluded: chain R residue 151 LYS Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 375 THR Chi-restraints excluded: chain S residue 176 VAL Chi-restraints excluded: chain S residue 196 HIS Chi-restraints excluded: chain T residue 194 VAL Chi-restraints excluded: chain U residue 132 TYR Chi-restraints excluded: chain U residue 187 ASP Chi-restraints excluded: chain U residue 194 VAL Chi-restraints excluded: chain U residue 267 THR Chi-restraints excluded: chain U residue 375 THR Chi-restraints excluded: chain V residue 196 HIS Chi-restraints excluded: chain V residue 256 ILE Chi-restraints excluded: chain V residue 267 THR Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 190 GLN Chi-restraints excluded: chain W residue 198 VAL Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 157 LEU Chi-restraints excluded: chain X residue 230 LEU Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 159 MET Chi-restraints excluded: chain Y residue 223 SER Chi-restraints excluded: chain Y residue 405 THR Chi-restraints excluded: chain Y residue 430 LEU Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 212 LEU Chi-restraints excluded: chain Z residue 225 THR Chi-restraints excluded: chain Z residue 267 THR Chi-restraints excluded: chain a residue 155 VAL Chi-restraints excluded: chain a residue 176 VAL Chi-restraints excluded: chain a residue 267 THR Chi-restraints excluded: chain a residue 379 VAL Chi-restraints excluded: chain b residue 155 VAL Chi-restraints excluded: chain b residue 176 VAL Chi-restraints excluded: chain b residue 199 SER Chi-restraints excluded: chain b residue 223 SER Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain c residue 132 TYR Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain c residue 256 ILE Chi-restraints excluded: chain d residue 187 ASP Chi-restraints excluded: chain d residue 221 THR Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain e residue 155 VAL Chi-restraints excluded: chain e residue 176 VAL Chi-restraints excluded: chain e residue 196 HIS Chi-restraints excluded: chain e residue 410 LYS Chi-restraints excluded: chain f residue 155 VAL Chi-restraints excluded: chain f residue 156 HIS Chi-restraints excluded: chain f residue 157 LEU Chi-restraints excluded: chain f residue 230 LEU Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain f residue 416 THR Chi-restraints excluded: chain g residue 147 LEU Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 176 VAL Chi-restraints excluded: chain g residue 180 LEU Chi-restraints excluded: chain h residue 266 VAL Chi-restraints excluded: chain h residue 375 THR Chi-restraints excluded: chain h residue 416 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 259 optimal weight: 0.3980 chunk 694 optimal weight: 50.0000 chunk 152 optimal weight: 0.0030 chunk 452 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 772 optimal weight: 3.9990 chunk 640 optimal weight: 9.9990 chunk 357 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 255 optimal weight: 8.9990 chunk 405 optimal weight: 40.0000 overall best weight: 2.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 HIS B 434 ASN C 231 ASN ** F 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 434 ASN K 196 HIS ** M 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 224 ASN ** O 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 224 ASN T 196 HIS ** U 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 196 HIS a 434 ASN ** d 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 222 GLN ** f 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 222 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 63871 Z= 0.209 Angle : 0.542 12.611 86453 Z= 0.269 Chirality : 0.039 0.215 10172 Planarity : 0.003 0.037 11549 Dihedral : 4.462 50.068 8783 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.88 % Favored : 96.07 % Rotamer: Outliers : 2.20 % Allowed : 15.47 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.20 (0.10), residues: 7942 helix: 1.31 (0.11), residues: 2488 sheet: -1.67 (0.10), residues: 3072 loop : -1.58 (0.12), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS W 196 PHE 0.021 0.001 PHE L 126 TYR 0.022 0.001 TYR F 132 ARG 0.014 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 495 time to evaluate : 5.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLN cc_start: 0.9192 (tt0) cc_final: 0.8980 (tp40) REVERT: A 159 MET cc_start: 0.7466 (tmm) cc_final: 0.7052 (tmm) REVERT: A 236 LYS cc_start: 0.9088 (mtmt) cc_final: 0.8771 (mttp) REVERT: A 376 LYS cc_start: 0.8146 (tttt) cc_final: 0.7866 (ttpt) REVERT: A 425 LYS cc_start: 0.9104 (ptpt) cc_final: 0.8801 (ptpp) REVERT: B 267 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8801 (p) REVERT: C 126 PHE cc_start: 0.7011 (t80) cc_final: 0.6566 (t80) REVERT: D 126 PHE cc_start: 0.7969 (t80) cc_final: 0.7631 (t80) REVERT: D 196 HIS cc_start: 0.9261 (m-70) cc_final: 0.8950 (m-70) REVERT: D 425 LYS cc_start: 0.8719 (pttt) cc_final: 0.8494 (pttt) REVERT: E 377 MET cc_start: 0.8535 (mmt) cc_final: 0.8031 (mpp) REVERT: E 409 MET cc_start: 0.8585 (tpp) cc_final: 0.8297 (tpp) REVERT: F 159 MET cc_start: 0.6424 (tpt) cc_final: 0.5675 (ppp) REVERT: F 218 HIS cc_start: 0.8730 (m-70) cc_final: 0.8433 (m-70) REVERT: F 377 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7924 (mpt) REVERT: G 187 ASP cc_start: 0.6157 (OUTLIER) cc_final: 0.4974 (m-30) REVERT: G 197 LEU cc_start: 0.9396 (tp) cc_final: 0.9104 (pp) REVERT: H 250 GLU cc_start: 0.7833 (pp20) cc_final: 0.7543 (pp20) REVERT: H 377 MET cc_start: 0.8281 (mmt) cc_final: 0.7876 (mpp) REVERT: I 144 ILE cc_start: 0.9609 (mt) cc_final: 0.9351 (mm) REVERT: I 147 LEU cc_start: 0.9371 (tp) cc_final: 0.9128 (mt) REVERT: I 157 LEU cc_start: 0.9215 (mp) cc_final: 0.8617 (tp) REVERT: I 197 LEU cc_start: 0.9132 (tp) cc_final: 0.8802 (tp) REVERT: I 218 HIS cc_start: 0.7318 (m90) cc_final: 0.7074 (m90) REVERT: I 405 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8712 (p) REVERT: J 218 HIS cc_start: 0.7188 (m-70) cc_final: 0.6787 (m170) REVERT: K 236 LYS cc_start: 0.8459 (mtpt) cc_final: 0.7974 (mtmm) REVERT: K 376 LYS cc_start: 0.8171 (tttt) cc_final: 0.7966 (tttp) REVERT: L 126 PHE cc_start: 0.8527 (t80) cc_final: 0.8104 (t80) REVERT: L 151 LYS cc_start: 0.7565 (ttmt) cc_final: 0.7121 (ttmm) REVERT: L 420 MET cc_start: 0.8898 (ptm) cc_final: 0.8681 (ptt) REVERT: M 126 PHE cc_start: 0.8053 (t80) cc_final: 0.7808 (t80) REVERT: M 196 HIS cc_start: 0.8789 (m90) cc_final: 0.8540 (m-70) REVERT: M 376 LYS cc_start: 0.8094 (tttt) cc_final: 0.7868 (ttpt) REVERT: N 156 HIS cc_start: 0.7136 (m-70) cc_final: 0.6024 (t70) REVERT: N 410 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.9148 (ptmm) REVERT: O 236 LYS cc_start: 0.8858 (mmtm) cc_final: 0.8612 (mmtm) REVERT: P 180 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7739 (pp) REVERT: P 218 HIS cc_start: 0.7508 (m90) cc_final: 0.7248 (m-70) REVERT: Q 409 MET cc_start: 0.8894 (tpt) cc_final: 0.8514 (tpt) REVERT: R 425 LYS cc_start: 0.9143 (ptpt) cc_final: 0.8833 (ptpp) REVERT: S 159 MET cc_start: 0.4716 (pmm) cc_final: 0.4283 (mmm) REVERT: T 126 PHE cc_start: 0.7006 (t80) cc_final: 0.6585 (t80) REVERT: T 132 TYR cc_start: 0.8992 (t80) cc_final: 0.8598 (t80) REVERT: U 196 HIS cc_start: 0.9312 (m-70) cc_final: 0.8947 (m-70) REVERT: U 267 THR cc_start: 0.8990 (OUTLIER) cc_final: 0.8634 (p) REVERT: U 425 LYS cc_start: 0.8716 (pttt) cc_final: 0.8324 (pttm) REVERT: V 205 LEU cc_start: 0.7904 (mp) cc_final: 0.7520 (tp) REVERT: V 377 MET cc_start: 0.8540 (mmt) cc_final: 0.8021 (mpp) REVERT: V 409 MET cc_start: 0.8680 (tpp) cc_final: 0.8454 (tpp) REVERT: W 190 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8321 (mt0) REVERT: W 218 HIS cc_start: 0.8250 (m-70) cc_final: 0.7633 (m-70) REVERT: W 377 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.8033 (mpt) REVERT: W 409 MET cc_start: 0.8780 (mmm) cc_final: 0.8430 (tpp) REVERT: X 187 ASP cc_start: 0.6106 (OUTLIER) cc_final: 0.5070 (m-30) REVERT: X 196 HIS cc_start: 0.9322 (m-70) cc_final: 0.9046 (m-70) REVERT: Y 159 MET cc_start: 0.5481 (OUTLIER) cc_final: 0.4591 (ttm) REVERT: Y 250 GLU cc_start: 0.7835 (pp20) cc_final: 0.7539 (pp20) REVERT: Y 377 MET cc_start: 0.8272 (mmt) cc_final: 0.7848 (mpp) REVERT: Z 197 LEU cc_start: 0.9101 (tp) cc_final: 0.8853 (tp) REVERT: Z 232 ASP cc_start: 0.7718 (p0) cc_final: 0.7090 (t0) REVERT: a 218 HIS cc_start: 0.7074 (m-70) cc_final: 0.6645 (m170) REVERT: c 126 PHE cc_start: 0.8582 (t80) cc_final: 0.8338 (t80) REVERT: c 151 LYS cc_start: 0.7562 (ttmt) cc_final: 0.7059 (ttmm) REVERT: d 151 LYS cc_start: 0.8398 (ptmt) cc_final: 0.8103 (ptpp) REVERT: d 376 LYS cc_start: 0.8088 (tttt) cc_final: 0.7843 (ttpp) REVERT: e 155 VAL cc_start: 0.8289 (OUTLIER) cc_final: 0.7419 (t) REVERT: e 156 HIS cc_start: 0.7108 (m-70) cc_final: 0.5937 (t70) REVERT: e 222 GLN cc_start: 0.3695 (OUTLIER) cc_final: 0.2787 (pt0) REVERT: e 410 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.9149 (ptmm) REVERT: h 409 MET cc_start: 0.8877 (tpt) cc_final: 0.8506 (tpt) outliers start: 156 outliers final: 110 residues processed: 621 average time/residue: 0.6392 time to fit residues: 675.9690 Evaluate side-chains 593 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 469 time to evaluate : 5.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain G residue 132 TYR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain H residue 236 LYS Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 267 THR Chi-restraints excluded: chain J residue 379 VAL Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain L residue 132 TYR Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 196 HIS Chi-restraints excluded: chain N residue 224 ASN Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain N residue 236 LYS Chi-restraints excluded: chain N residue 410 LYS Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 156 HIS Chi-restraints excluded: chain O residue 416 THR Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain Q residue 252 ILE Chi-restraints excluded: chain Q residue 266 VAL Chi-restraints excluded: chain Q residue 358 THR Chi-restraints excluded: chain Q residue 375 THR Chi-restraints excluded: chain Q residue 416 THR Chi-restraints excluded: chain R residue 151 LYS Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 375 THR Chi-restraints excluded: chain R residue 391 VAL Chi-restraints excluded: chain S residue 196 HIS Chi-restraints excluded: chain T residue 194 VAL Chi-restraints excluded: chain T residue 375 THR Chi-restraints excluded: chain U residue 132 TYR Chi-restraints excluded: chain U residue 187 ASP Chi-restraints excluded: chain U residue 267 THR Chi-restraints excluded: chain U residue 375 THR Chi-restraints excluded: chain V residue 196 HIS Chi-restraints excluded: chain V residue 256 ILE Chi-restraints excluded: chain V residue 267 THR Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 190 GLN Chi-restraints excluded: chain W residue 198 VAL Chi-restraints excluded: chain W residue 267 THR Chi-restraints excluded: chain W residue 369 ASP Chi-restraints excluded: chain W residue 377 MET Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 157 LEU Chi-restraints excluded: chain X residue 187 ASP Chi-restraints excluded: chain X residue 230 LEU Chi-restraints excluded: chain X residue 254 SER Chi-restraints excluded: chain X residue 409 MET Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 159 MET Chi-restraints excluded: chain Y residue 220 LEU Chi-restraints excluded: chain Y residue 223 SER Chi-restraints excluded: chain Y residue 405 THR Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 212 LEU Chi-restraints excluded: chain Z residue 225 THR Chi-restraints excluded: chain Z residue 267 THR Chi-restraints excluded: chain Z residue 416 THR Chi-restraints excluded: chain a residue 155 VAL Chi-restraints excluded: chain a residue 176 VAL Chi-restraints excluded: chain a residue 187 ASP Chi-restraints excluded: chain a residue 267 THR Chi-restraints excluded: chain a residue 379 VAL Chi-restraints excluded: chain b residue 176 VAL Chi-restraints excluded: chain b residue 197 LEU Chi-restraints excluded: chain b residue 223 SER Chi-restraints excluded: chain c residue 132 TYR Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain c residue 256 ILE Chi-restraints excluded: chain d residue 221 THR Chi-restraints excluded: chain d residue 228 ARG Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain e residue 155 VAL Chi-restraints excluded: chain e residue 176 VAL Chi-restraints excluded: chain e residue 196 HIS Chi-restraints excluded: chain e residue 222 GLN Chi-restraints excluded: chain e residue 410 LYS Chi-restraints excluded: chain f residue 155 VAL Chi-restraints excluded: chain f residue 156 HIS Chi-restraints excluded: chain f residue 230 LEU Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain f residue 416 THR Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 176 VAL Chi-restraints excluded: chain g residue 178 VAL Chi-restraints excluded: chain g residue 180 LEU Chi-restraints excluded: chain h residue 266 VAL Chi-restraints excluded: chain h residue 416 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 744 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 439 optimal weight: 9.9990 chunk 563 optimal weight: 9.9990 chunk 436 optimal weight: 10.0000 chunk 649 optimal weight: 0.9980 chunk 431 optimal weight: 20.0000 chunk 769 optimal weight: 1.9990 chunk 481 optimal weight: 0.9990 chunk 468 optimal weight: 9.9990 chunk 355 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN ** F 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 196 HIS M 190 GLN M 434 ASN N 224 ASN ** O 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 224 ASN ** U 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 196 HIS Y 431 ASN ** d 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 222 GLN ** f 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 63871 Z= 0.183 Angle : 0.530 12.683 86453 Z= 0.261 Chirality : 0.039 0.176 10172 Planarity : 0.003 0.037 11549 Dihedral : 4.355 59.934 8783 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.24 % Favored : 96.73 % Rotamer: Outliers : 2.20 % Allowed : 15.56 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.96 (0.10), residues: 7942 helix: 1.51 (0.11), residues: 2488 sheet: -1.54 (0.10), residues: 3068 loop : -1.45 (0.12), residues: 2386 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS W 196 PHE 0.017 0.001 PHE L 126 TYR 0.025 0.001 TYR b 132 ARG 0.010 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 502 time to evaluate : 5.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLN cc_start: 0.9219 (tt0) cc_final: 0.9014 (tp40) REVERT: A 159 MET cc_start: 0.7518 (tmm) cc_final: 0.7096 (tmm) REVERT: A 236 LYS cc_start: 0.9032 (mtmt) cc_final: 0.8732 (mttp) REVERT: A 376 LYS cc_start: 0.8148 (tttt) cc_final: 0.7861 (ttpt) REVERT: A 425 LYS cc_start: 0.9135 (ptpt) cc_final: 0.8817 (ptpp) REVERT: B 267 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8778 (p) REVERT: C 126 PHE cc_start: 0.6977 (t80) cc_final: 0.6526 (t80) REVERT: D 126 PHE cc_start: 0.8083 (t80) cc_final: 0.7744 (t80) REVERT: D 196 HIS cc_start: 0.9272 (m-70) cc_final: 0.8969 (m-70) REVERT: D 425 LYS cc_start: 0.8729 (pttt) cc_final: 0.8484 (pttt) REVERT: E 377 MET cc_start: 0.8531 (mmt) cc_final: 0.8065 (mpp) REVERT: E 409 MET cc_start: 0.8590 (tpp) cc_final: 0.8329 (tpp) REVERT: F 159 MET cc_start: 0.6452 (tpt) cc_final: 0.5701 (ppp) REVERT: F 218 HIS cc_start: 0.8719 (m-70) cc_final: 0.8058 (m-70) REVERT: F 377 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7945 (mpt) REVERT: G 187 ASP cc_start: 0.6191 (OUTLIER) cc_final: 0.5043 (m-30) REVERT: H 250 GLU cc_start: 0.7864 (pp20) cc_final: 0.7562 (pp20) REVERT: H 377 MET cc_start: 0.8268 (mmt) cc_final: 0.7930 (mpp) REVERT: I 144 ILE cc_start: 0.9616 (mt) cc_final: 0.9363 (mm) REVERT: I 147 LEU cc_start: 0.9372 (tp) cc_final: 0.9132 (mt) REVERT: I 157 LEU cc_start: 0.9181 (mp) cc_final: 0.8620 (tp) REVERT: I 197 LEU cc_start: 0.9132 (tp) cc_final: 0.8802 (tp) REVERT: I 218 HIS cc_start: 0.7341 (m90) cc_final: 0.7073 (m90) REVERT: I 405 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8712 (p) REVERT: J 218 HIS cc_start: 0.7244 (m-70) cc_final: 0.6908 (m-70) REVERT: K 236 LYS cc_start: 0.8452 (mtpt) cc_final: 0.7961 (mtmm) REVERT: K 376 LYS cc_start: 0.8194 (tttt) cc_final: 0.7988 (tttp) REVERT: L 126 PHE cc_start: 0.8572 (t80) cc_final: 0.8168 (t80) REVERT: L 151 LYS cc_start: 0.7582 (ttmt) cc_final: 0.7128 (ttmm) REVERT: L 197 LEU cc_start: 0.9413 (tp) cc_final: 0.9198 (tt) REVERT: L 236 LYS cc_start: 0.8791 (mtpt) cc_final: 0.8467 (mtpp) REVERT: M 126 PHE cc_start: 0.8103 (t80) cc_final: 0.7857 (t80) REVERT: M 196 HIS cc_start: 0.8812 (m90) cc_final: 0.8538 (m-70) REVERT: M 376 LYS cc_start: 0.8059 (tttt) cc_final: 0.7853 (ttpt) REVERT: N 156 HIS cc_start: 0.7093 (m-70) cc_final: 0.5960 (t70) REVERT: O 236 LYS cc_start: 0.8869 (mmtm) cc_final: 0.8621 (mmtm) REVERT: P 180 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7713 (pp) REVERT: P 218 HIS cc_start: 0.7604 (m90) cc_final: 0.7334 (m-70) REVERT: Q 409 MET cc_start: 0.8900 (tpt) cc_final: 0.8527 (tpt) REVERT: R 425 LYS cc_start: 0.9137 (ptpt) cc_final: 0.8828 (ptpp) REVERT: S 159 MET cc_start: 0.4627 (pmm) cc_final: 0.4270 (mmm) REVERT: T 126 PHE cc_start: 0.6971 (t80) cc_final: 0.6551 (t80) REVERT: T 132 TYR cc_start: 0.8984 (t80) cc_final: 0.8591 (t80) REVERT: U 196 HIS cc_start: 0.9311 (m-70) cc_final: 0.8961 (m-70) REVERT: U 267 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8600 (p) REVERT: U 425 LYS cc_start: 0.8723 (pttt) cc_final: 0.8485 (pttt) REVERT: V 205 LEU cc_start: 0.7915 (mp) cc_final: 0.7568 (tp) REVERT: V 377 MET cc_start: 0.8526 (mmt) cc_final: 0.8049 (mpp) REVERT: V 409 MET cc_start: 0.8666 (tpp) cc_final: 0.8202 (tpp) REVERT: W 190 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8291 (mt0) REVERT: W 218 HIS cc_start: 0.8198 (m-70) cc_final: 0.7606 (m-70) REVERT: W 377 MET cc_start: 0.8287 (mpp) cc_final: 0.8056 (mpt) REVERT: W 409 MET cc_start: 0.8782 (mmm) cc_final: 0.8429 (tpp) REVERT: X 187 ASP cc_start: 0.6049 (OUTLIER) cc_final: 0.5034 (m-30) REVERT: X 196 HIS cc_start: 0.9315 (m-70) cc_final: 0.9048 (m-70) REVERT: Y 159 MET cc_start: 0.5435 (OUTLIER) cc_final: 0.4451 (ttm) REVERT: Y 250 GLU cc_start: 0.7835 (pp20) cc_final: 0.7532 (pp20) REVERT: Y 377 MET cc_start: 0.8255 (mmt) cc_final: 0.7937 (mpp) REVERT: Z 197 LEU cc_start: 0.9103 (tp) cc_final: 0.8886 (tp) REVERT: Z 232 ASP cc_start: 0.7680 (p0) cc_final: 0.7242 (t70) REVERT: a 218 HIS cc_start: 0.7234 (m-70) cc_final: 0.6821 (m170) REVERT: c 126 PHE cc_start: 0.8576 (t80) cc_final: 0.8336 (t80) REVERT: c 151 LYS cc_start: 0.7582 (ttmt) cc_final: 0.7145 (ttmm) REVERT: d 151 LYS cc_start: 0.8393 (ptmt) cc_final: 0.8096 (ptpp) REVERT: d 376 LYS cc_start: 0.8061 (tttt) cc_final: 0.7844 (ttpt) REVERT: e 155 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.7531 (t) REVERT: e 156 HIS cc_start: 0.7081 (m-70) cc_final: 0.5891 (t70) REVERT: h 409 MET cc_start: 0.8874 (tpt) cc_final: 0.8508 (tpt) outliers start: 156 outliers final: 114 residues processed: 632 average time/residue: 0.5808 time to fit residues: 624.8488 Evaluate side-chains 604 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 480 time to evaluate : 5.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain E residue 196 HIS Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 267 THR Chi-restraints excluded: chain J residue 379 VAL Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain L residue 132 TYR Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 196 HIS Chi-restraints excluded: chain N residue 224 ASN Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain N residue 236 LYS Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain Q residue 252 ILE Chi-restraints excluded: chain Q residue 266 VAL Chi-restraints excluded: chain Q residue 358 THR Chi-restraints excluded: chain Q residue 416 THR Chi-restraints excluded: chain R residue 151 LYS Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 375 THR Chi-restraints excluded: chain R residue 391 VAL Chi-restraints excluded: chain S residue 196 HIS Chi-restraints excluded: chain T residue 375 THR Chi-restraints excluded: chain U residue 132 TYR Chi-restraints excluded: chain U residue 155 VAL Chi-restraints excluded: chain U residue 187 ASP Chi-restraints excluded: chain U residue 267 THR Chi-restraints excluded: chain U residue 375 THR Chi-restraints excluded: chain V residue 196 HIS Chi-restraints excluded: chain V residue 256 ILE Chi-restraints excluded: chain V residue 267 THR Chi-restraints excluded: chain V residue 304 VAL Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 190 GLN Chi-restraints excluded: chain W residue 198 VAL Chi-restraints excluded: chain W residue 369 ASP Chi-restraints excluded: chain X residue 132 TYR Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 157 LEU Chi-restraints excluded: chain X residue 187 ASP Chi-restraints excluded: chain X residue 230 LEU Chi-restraints excluded: chain X residue 254 SER Chi-restraints excluded: chain X residue 409 MET Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 159 MET Chi-restraints excluded: chain Y residue 220 LEU Chi-restraints excluded: chain Y residue 223 SER Chi-restraints excluded: chain Y residue 405 THR Chi-restraints excluded: chain Y residue 430 LEU Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 225 THR Chi-restraints excluded: chain Z residue 267 THR Chi-restraints excluded: chain Z residue 416 THR Chi-restraints excluded: chain a residue 155 VAL Chi-restraints excluded: chain a residue 176 VAL Chi-restraints excluded: chain a residue 187 ASP Chi-restraints excluded: chain a residue 267 THR Chi-restraints excluded: chain a residue 379 VAL Chi-restraints excluded: chain b residue 176 VAL Chi-restraints excluded: chain b residue 197 LEU Chi-restraints excluded: chain b residue 223 SER Chi-restraints excluded: chain c residue 132 TYR Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain c residue 256 ILE Chi-restraints excluded: chain c residue 416 THR Chi-restraints excluded: chain d residue 187 ASP Chi-restraints excluded: chain d residue 221 THR Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain e residue 155 VAL Chi-restraints excluded: chain e residue 176 VAL Chi-restraints excluded: chain e residue 196 HIS Chi-restraints excluded: chain f residue 155 VAL Chi-restraints excluded: chain f residue 230 LEU Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 176 VAL Chi-restraints excluded: chain g residue 178 VAL Chi-restraints excluded: chain g residue 180 LEU Chi-restraints excluded: chain h residue 266 VAL Chi-restraints excluded: chain h residue 358 THR Chi-restraints excluded: chain h residue 416 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 475 optimal weight: 9.9990 chunk 307 optimal weight: 10.0000 chunk 459 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 chunk 488 optimal weight: 9.9990 chunk 524 optimal weight: 9.9990 chunk 380 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 604 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 ASN C 231 ASN ** F 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 GLN J 434 ASN K 196 HIS L 222 GLN M 434 ASN ** O 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 224 ASN ** U 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 196 HIS a 434 ASN ** f 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 63871 Z= 0.298 Angle : 0.578 13.883 86453 Z= 0.286 Chirality : 0.040 0.159 10172 Planarity : 0.003 0.047 11549 Dihedral : 4.457 52.777 8783 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.51 % Favored : 94.45 % Rotamer: Outliers : 2.24 % Allowed : 15.77 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.02 (0.10), residues: 7942 helix: 1.48 (0.11), residues: 2482 sheet: -1.59 (0.10), residues: 3094 loop : -1.47 (0.12), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS b 196 PHE 0.015 0.001 PHE L 126 TYR 0.021 0.001 TYR W 132 ARG 0.016 0.000 ARG G 142 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 484 time to evaluate : 5.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 LYS cc_start: 0.8369 (ptmt) cc_final: 0.8122 (ptmm) REVERT: A 159 MET cc_start: 0.7548 (tmm) cc_final: 0.7137 (tmm) REVERT: A 236 LYS cc_start: 0.9084 (mtmt) cc_final: 0.8781 (mttp) REVERT: A 376 LYS cc_start: 0.8200 (tttt) cc_final: 0.7891 (ttmt) REVERT: A 425 LYS cc_start: 0.9100 (ptpt) cc_final: 0.8800 (ptpp) REVERT: C 126 PHE cc_start: 0.7011 (t80) cc_final: 0.6547 (t80) REVERT: D 126 PHE cc_start: 0.8164 (t80) cc_final: 0.7831 (t80) REVERT: D 196 HIS cc_start: 0.9285 (m-70) cc_final: 0.8986 (m-70) REVERT: D 377 MET cc_start: 0.8283 (mpp) cc_final: 0.7680 (mpp) REVERT: D 425 LYS cc_start: 0.8746 (pttt) cc_final: 0.8519 (pttt) REVERT: E 409 MET cc_start: 0.8610 (tpp) cc_final: 0.8364 (tpp) REVERT: F 159 MET cc_start: 0.6541 (tpt) cc_final: 0.5718 (ppp) REVERT: F 218 HIS cc_start: 0.8761 (m-70) cc_final: 0.8457 (m-70) REVERT: F 377 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7937 (mpt) REVERT: G 187 ASP cc_start: 0.6200 (OUTLIER) cc_final: 0.5156 (m-30) REVERT: H 250 GLU cc_start: 0.7868 (pp20) cc_final: 0.7576 (pp20) REVERT: H 377 MET cc_start: 0.8286 (mmt) cc_final: 0.7946 (mpp) REVERT: I 144 ILE cc_start: 0.9615 (mt) cc_final: 0.9374 (mm) REVERT: I 147 LEU cc_start: 0.9382 (tp) cc_final: 0.9127 (mt) REVERT: I 157 LEU cc_start: 0.9064 (mp) cc_final: 0.8549 (tp) REVERT: I 197 LEU cc_start: 0.9119 (tp) cc_final: 0.8845 (tp) REVERT: I 218 HIS cc_start: 0.7398 (m90) cc_final: 0.7112 (m90) REVERT: I 405 THR cc_start: 0.9082 (OUTLIER) cc_final: 0.8767 (p) REVERT: J 218 HIS cc_start: 0.7268 (m-70) cc_final: 0.6852 (m170) REVERT: K 236 LYS cc_start: 0.8533 (mtpt) cc_final: 0.8046 (mtmm) REVERT: K 376 LYS cc_start: 0.8256 (tttt) cc_final: 0.8050 (tttp) REVERT: L 126 PHE cc_start: 0.8595 (t80) cc_final: 0.8352 (t80) REVERT: L 151 LYS cc_start: 0.7624 (ttmt) cc_final: 0.7221 (ttmm) REVERT: L 197 LEU cc_start: 0.9422 (tp) cc_final: 0.9206 (tt) REVERT: L 420 MET cc_start: 0.8797 (ptm) cc_final: 0.8481 (ptt) REVERT: M 126 PHE cc_start: 0.8122 (t80) cc_final: 0.7877 (t80) REVERT: M 196 HIS cc_start: 0.8861 (m90) cc_final: 0.8578 (m-70) REVERT: M 376 LYS cc_start: 0.8110 (tttt) cc_final: 0.7904 (ttpt) REVERT: N 156 HIS cc_start: 0.6981 (m-70) cc_final: 0.5826 (t70) REVERT: O 236 LYS cc_start: 0.8864 (mmtm) cc_final: 0.8586 (mmtm) REVERT: P 180 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7689 (pp) REVERT: Q 409 MET cc_start: 0.8920 (tpt) cc_final: 0.8531 (tpt) REVERT: R 425 LYS cc_start: 0.9134 (ptpt) cc_final: 0.8820 (ptpp) REVERT: S 159 MET cc_start: 0.4746 (pmm) cc_final: 0.4348 (mmm) REVERT: T 126 PHE cc_start: 0.6920 (t80) cc_final: 0.6507 (t80) REVERT: T 132 TYR cc_start: 0.9025 (t80) cc_final: 0.8614 (t80) REVERT: T 231 ASN cc_start: 0.7936 (OUTLIER) cc_final: 0.7646 (t0) REVERT: U 196 HIS cc_start: 0.9314 (m-70) cc_final: 0.8968 (m-70) REVERT: U 377 MET cc_start: 0.8327 (mpp) cc_final: 0.7690 (mpp) REVERT: U 425 LYS cc_start: 0.8770 (pttt) cc_final: 0.8534 (pttt) REVERT: V 205 LEU cc_start: 0.7962 (mp) cc_final: 0.7659 (tp) REVERT: V 230 LEU cc_start: 0.9121 (tt) cc_final: 0.8580 (mp) REVERT: V 409 MET cc_start: 0.8676 (tpp) cc_final: 0.8469 (tpp) REVERT: W 190 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8342 (mt0) REVERT: W 218 HIS cc_start: 0.8176 (m-70) cc_final: 0.7554 (m-70) REVERT: W 377 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.8005 (mpt) REVERT: W 409 MET cc_start: 0.8803 (mmm) cc_final: 0.8449 (tpp) REVERT: X 187 ASP cc_start: 0.6050 (OUTLIER) cc_final: 0.5011 (m-30) REVERT: X 196 HIS cc_start: 0.9343 (m-70) cc_final: 0.9065 (m-70) REVERT: Y 159 MET cc_start: 0.5272 (OUTLIER) cc_final: 0.4379 (ttm) REVERT: Y 377 MET cc_start: 0.8278 (mmt) cc_final: 0.7937 (mpp) REVERT: Z 218 HIS cc_start: 0.7303 (m90) cc_final: 0.6943 (m90) REVERT: Z 232 ASP cc_start: 0.7721 (p0) cc_final: 0.7144 (t0) REVERT: a 218 HIS cc_start: 0.7219 (m-70) cc_final: 0.6818 (m170) REVERT: a 250 GLU cc_start: 0.7899 (pt0) cc_final: 0.7691 (pp20) REVERT: c 126 PHE cc_start: 0.8614 (t80) cc_final: 0.8386 (t80) REVERT: c 151 LYS cc_start: 0.7627 (ttmt) cc_final: 0.7145 (ttmm) REVERT: d 151 LYS cc_start: 0.8370 (ptmt) cc_final: 0.8075 (ptpp) REVERT: d 376 LYS cc_start: 0.8087 (tttt) cc_final: 0.7856 (ttpt) REVERT: e 156 HIS cc_start: 0.7030 (m-70) cc_final: 0.5834 (t70) REVERT: h 409 MET cc_start: 0.8899 (tpt) cc_final: 0.8509 (tpt) outliers start: 159 outliers final: 132 residues processed: 609 average time/residue: 0.6278 time to fit residues: 651.1557 Evaluate side-chains 611 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 470 time to evaluate : 5.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain E residue 196 HIS Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain H residue 236 LYS Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 267 THR Chi-restraints excluded: chain J residue 379 VAL Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain L residue 132 TYR Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 196 HIS Chi-restraints excluded: chain N residue 205 LEU Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain N residue 236 LYS Chi-restraints excluded: chain O residue 132 TYR Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 156 HIS Chi-restraints excluded: chain O residue 198 VAL Chi-restraints excluded: chain O residue 416 THR Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 156 HIS Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain Q residue 252 ILE Chi-restraints excluded: chain Q residue 266 VAL Chi-restraints excluded: chain Q residue 358 THR Chi-restraints excluded: chain Q residue 416 THR Chi-restraints excluded: chain R residue 151 LYS Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 391 VAL Chi-restraints excluded: chain S residue 196 HIS Chi-restraints excluded: chain T residue 231 ASN Chi-restraints excluded: chain U residue 132 TYR Chi-restraints excluded: chain U residue 155 VAL Chi-restraints excluded: chain U residue 187 ASP Chi-restraints excluded: chain U residue 375 THR Chi-restraints excluded: chain V residue 196 HIS Chi-restraints excluded: chain V residue 256 ILE Chi-restraints excluded: chain V residue 267 THR Chi-restraints excluded: chain V residue 304 VAL Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 190 GLN Chi-restraints excluded: chain W residue 198 VAL Chi-restraints excluded: chain W residue 267 THR Chi-restraints excluded: chain W residue 369 ASP Chi-restraints excluded: chain W residue 377 MET Chi-restraints excluded: chain W residue 412 ILE Chi-restraints excluded: chain X residue 132 TYR Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 157 LEU Chi-restraints excluded: chain X residue 187 ASP Chi-restraints excluded: chain X residue 230 LEU Chi-restraints excluded: chain X residue 254 SER Chi-restraints excluded: chain X residue 409 MET Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 159 MET Chi-restraints excluded: chain Y residue 220 LEU Chi-restraints excluded: chain Y residue 223 SER Chi-restraints excluded: chain Y residue 405 THR Chi-restraints excluded: chain Y residue 430 LEU Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 212 LEU Chi-restraints excluded: chain Z residue 225 THR Chi-restraints excluded: chain Z residue 267 THR Chi-restraints excluded: chain Z residue 416 THR Chi-restraints excluded: chain a residue 155 VAL Chi-restraints excluded: chain a residue 176 VAL Chi-restraints excluded: chain a residue 187 ASP Chi-restraints excluded: chain a residue 267 THR Chi-restraints excluded: chain a residue 379 VAL Chi-restraints excluded: chain b residue 176 VAL Chi-restraints excluded: chain b residue 197 LEU Chi-restraints excluded: chain b residue 223 SER Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain c residue 132 TYR Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain c residue 194 VAL Chi-restraints excluded: chain c residue 249 ILE Chi-restraints excluded: chain c residue 256 ILE Chi-restraints excluded: chain c residue 416 THR Chi-restraints excluded: chain d residue 187 ASP Chi-restraints excluded: chain d residue 221 THR Chi-restraints excluded: chain d residue 228 ARG Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain e residue 155 VAL Chi-restraints excluded: chain e residue 176 VAL Chi-restraints excluded: chain e residue 196 HIS Chi-restraints excluded: chain f residue 155 VAL Chi-restraints excluded: chain f residue 230 LEU Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 176 VAL Chi-restraints excluded: chain g residue 178 VAL Chi-restraints excluded: chain g residue 180 LEU Chi-restraints excluded: chain g residue 368 VAL Chi-restraints excluded: chain g residue 369 ASP Chi-restraints excluded: chain h residue 266 VAL Chi-restraints excluded: chain h residue 358 THR Chi-restraints excluded: chain h residue 375 THR Chi-restraints excluded: chain h residue 416 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 699 optimal weight: 9.9990 chunk 736 optimal weight: 10.0000 chunk 672 optimal weight: 0.9980 chunk 716 optimal weight: 3.9990 chunk 431 optimal weight: 50.0000 chunk 312 optimal weight: 30.0000 chunk 562 optimal weight: 6.9990 chunk 219 optimal weight: 7.9990 chunk 647 optimal weight: 0.0670 chunk 677 optimal weight: 4.9990 chunk 714 optimal weight: 9.9990 overall best weight: 3.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN E 133 GLN ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 196 HIS ** M 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 224 ASN ** U 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 434 ASN ** d 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 263 HIS ** f 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 63871 Z= 0.241 Angle : 0.552 13.784 86453 Z= 0.273 Chirality : 0.039 0.152 10172 Planarity : 0.003 0.037 11549 Dihedral : 4.356 44.856 8783 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.58 % Favored : 96.40 % Rotamer: Outliers : 2.16 % Allowed : 16.01 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.84 (0.10), residues: 7942 helix: 1.63 (0.11), residues: 2482 sheet: -1.47 (0.10), residues: 3070 loop : -1.40 (0.12), residues: 2390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS K 196 PHE 0.015 0.001 PHE L 126 TYR 0.027 0.001 TYR b 132 ARG 0.010 0.000 ARG G 142 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 485 time to evaluate : 5.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 LYS cc_start: 0.8285 (ptmt) cc_final: 0.8020 (ptmm) REVERT: A 236 LYS cc_start: 0.9081 (mtmt) cc_final: 0.8782 (mttp) REVERT: A 376 LYS cc_start: 0.8162 (tttt) cc_final: 0.7854 (ttmt) REVERT: A 425 LYS cc_start: 0.9094 (ptpt) cc_final: 0.8792 (ptpp) REVERT: B 267 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8778 (p) REVERT: C 126 PHE cc_start: 0.7038 (t80) cc_final: 0.6570 (t80) REVERT: D 126 PHE cc_start: 0.8198 (t80) cc_final: 0.7874 (t80) REVERT: D 196 HIS cc_start: 0.9300 (m-70) cc_final: 0.9006 (m-70) REVERT: D 425 LYS cc_start: 0.8780 (pttt) cc_final: 0.8536 (pttt) REVERT: E 377 MET cc_start: 0.8553 (mmm) cc_final: 0.8027 (mpp) REVERT: E 409 MET cc_start: 0.8589 (tpp) cc_final: 0.8351 (tpp) REVERT: F 159 MET cc_start: 0.6464 (tpt) cc_final: 0.5718 (ppp) REVERT: F 218 HIS cc_start: 0.8820 (m-70) cc_final: 0.8496 (m-70) REVERT: F 377 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7945 (mpt) REVERT: F 393 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.8346 (m-10) REVERT: G 187 ASP cc_start: 0.6154 (OUTLIER) cc_final: 0.5144 (m-30) REVERT: H 250 GLU cc_start: 0.7869 (pp20) cc_final: 0.7580 (pp20) REVERT: H 377 MET cc_start: 0.8289 (mmt) cc_final: 0.7936 (mpp) REVERT: I 144 ILE cc_start: 0.9616 (mt) cc_final: 0.9371 (mm) REVERT: I 147 LEU cc_start: 0.9414 (tp) cc_final: 0.9136 (mt) REVERT: I 157 LEU cc_start: 0.9074 (mp) cc_final: 0.8546 (tp) REVERT: I 197 LEU cc_start: 0.9153 (tp) cc_final: 0.8898 (tp) REVERT: I 218 HIS cc_start: 0.7433 (m90) cc_final: 0.7133 (m90) REVERT: I 405 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8740 (p) REVERT: J 218 HIS cc_start: 0.7306 (m-70) cc_final: 0.6981 (m-70) REVERT: K 236 LYS cc_start: 0.8530 (mtpt) cc_final: 0.8047 (mtmm) REVERT: K 376 LYS cc_start: 0.8235 (tttt) cc_final: 0.8032 (tttp) REVERT: L 151 LYS cc_start: 0.7608 (ttmt) cc_final: 0.7234 (ttmm) REVERT: L 197 LEU cc_start: 0.9434 (tp) cc_final: 0.9217 (tt) REVERT: L 420 MET cc_start: 0.8805 (ptm) cc_final: 0.8498 (ptt) REVERT: M 126 PHE cc_start: 0.8113 (t80) cc_final: 0.7870 (t80) REVERT: M 196 HIS cc_start: 0.8886 (m90) cc_final: 0.8601 (m-70) REVERT: M 376 LYS cc_start: 0.8098 (tttt) cc_final: 0.7890 (ttpt) REVERT: N 156 HIS cc_start: 0.6960 (m-70) cc_final: 0.5795 (t70) REVERT: O 236 LYS cc_start: 0.8872 (mmtm) cc_final: 0.8597 (mmtm) REVERT: P 180 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7712 (pp) REVERT: P 218 HIS cc_start: 0.7510 (m-70) cc_final: 0.7144 (m90) REVERT: Q 409 MET cc_start: 0.8922 (tpt) cc_final: 0.8553 (tpt) REVERT: R 425 LYS cc_start: 0.9131 (ptpt) cc_final: 0.8815 (ptpp) REVERT: S 159 MET cc_start: 0.4723 (pmm) cc_final: 0.4390 (mmm) REVERT: T 126 PHE cc_start: 0.6923 (t80) cc_final: 0.6503 (t80) REVERT: T 132 TYR cc_start: 0.9024 (t80) cc_final: 0.8589 (t80) REVERT: T 231 ASN cc_start: 0.7865 (OUTLIER) cc_final: 0.7588 (t0) REVERT: U 126 PHE cc_start: 0.8222 (t80) cc_final: 0.7801 (t80) REVERT: U 196 HIS cc_start: 0.9313 (m-70) cc_final: 0.8984 (m-70) REVERT: U 425 LYS cc_start: 0.8773 (pttt) cc_final: 0.8530 (pttt) REVERT: V 205 LEU cc_start: 0.8066 (mp) cc_final: 0.7763 (tp) REVERT: V 230 LEU cc_start: 0.9088 (tt) cc_final: 0.8588 (mt) REVERT: V 409 MET cc_start: 0.8645 (tpp) cc_final: 0.8424 (tpp) REVERT: W 377 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.8009 (mpt) REVERT: W 409 MET cc_start: 0.8814 (mmm) cc_final: 0.8457 (tpp) REVERT: X 187 ASP cc_start: 0.6078 (OUTLIER) cc_final: 0.5028 (m-30) REVERT: X 196 HIS cc_start: 0.9306 (m-70) cc_final: 0.8966 (m170) REVERT: Y 159 MET cc_start: 0.5145 (OUTLIER) cc_final: 0.4213 (ttm) REVERT: Y 377 MET cc_start: 0.8286 (mmt) cc_final: 0.7954 (mpp) REVERT: Z 218 HIS cc_start: 0.7225 (m90) cc_final: 0.6872 (m90) REVERT: Z 232 ASP cc_start: 0.7701 (p0) cc_final: 0.7141 (t0) REVERT: a 218 HIS cc_start: 0.7202 (m-70) cc_final: 0.6777 (m170) REVERT: b 236 LYS cc_start: 0.8372 (mtpt) cc_final: 0.7920 (mttp) REVERT: c 126 PHE cc_start: 0.8603 (t80) cc_final: 0.8379 (t80) REVERT: c 151 LYS cc_start: 0.7619 (ttmt) cc_final: 0.7230 (ttmm) REVERT: d 151 LYS cc_start: 0.8368 (ptmt) cc_final: 0.8068 (ptpp) REVERT: d 376 LYS cc_start: 0.8095 (tttt) cc_final: 0.7850 (ttpt) REVERT: e 156 HIS cc_start: 0.6903 (m-70) cc_final: 0.5699 (t70) REVERT: g 180 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.7953 (pp) REVERT: h 409 MET cc_start: 0.8889 (tpt) cc_final: 0.8522 (tpt) outliers start: 153 outliers final: 134 residues processed: 604 average time/residue: 0.5837 time to fit residues: 599.4729 Evaluate side-chains 616 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 471 time to evaluate : 5.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain E residue 196 HIS Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain F residue 393 TYR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 194 VAL Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 267 THR Chi-restraints excluded: chain J residue 379 VAL Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain L residue 132 TYR Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 196 HIS Chi-restraints excluded: chain N residue 205 LEU Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain N residue 236 LYS Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 156 HIS Chi-restraints excluded: chain O residue 416 THR Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain Q residue 252 ILE Chi-restraints excluded: chain Q residue 266 VAL Chi-restraints excluded: chain Q residue 358 THR Chi-restraints excluded: chain Q residue 416 THR Chi-restraints excluded: chain R residue 151 LYS Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 391 VAL Chi-restraints excluded: chain S residue 196 HIS Chi-restraints excluded: chain S residue 416 THR Chi-restraints excluded: chain T residue 231 ASN Chi-restraints excluded: chain T residue 375 THR Chi-restraints excluded: chain U residue 132 TYR Chi-restraints excluded: chain U residue 155 VAL Chi-restraints excluded: chain U residue 187 ASP Chi-restraints excluded: chain U residue 375 THR Chi-restraints excluded: chain V residue 196 HIS Chi-restraints excluded: chain V residue 223 SER Chi-restraints excluded: chain V residue 256 ILE Chi-restraints excluded: chain V residue 267 THR Chi-restraints excluded: chain V residue 304 VAL Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 198 VAL Chi-restraints excluded: chain W residue 267 THR Chi-restraints excluded: chain W residue 369 ASP Chi-restraints excluded: chain W residue 377 MET Chi-restraints excluded: chain W residue 412 ILE Chi-restraints excluded: chain X residue 132 TYR Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 157 LEU Chi-restraints excluded: chain X residue 187 ASP Chi-restraints excluded: chain X residue 230 LEU Chi-restraints excluded: chain X residue 254 SER Chi-restraints excluded: chain X residue 409 MET Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 159 MET Chi-restraints excluded: chain Y residue 220 LEU Chi-restraints excluded: chain Y residue 223 SER Chi-restraints excluded: chain Y residue 405 THR Chi-restraints excluded: chain Y residue 430 LEU Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 194 VAL Chi-restraints excluded: chain Z residue 212 LEU Chi-restraints excluded: chain Z residue 225 THR Chi-restraints excluded: chain Z residue 267 THR Chi-restraints excluded: chain Z residue 416 THR Chi-restraints excluded: chain a residue 155 VAL Chi-restraints excluded: chain a residue 176 VAL Chi-restraints excluded: chain a residue 187 ASP Chi-restraints excluded: chain a residue 267 THR Chi-restraints excluded: chain a residue 379 VAL Chi-restraints excluded: chain b residue 176 VAL Chi-restraints excluded: chain b residue 197 LEU Chi-restraints excluded: chain b residue 223 SER Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain c residue 132 TYR Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain c residue 194 VAL Chi-restraints excluded: chain c residue 256 ILE Chi-restraints excluded: chain c residue 416 THR Chi-restraints excluded: chain d residue 187 ASP Chi-restraints excluded: chain d residue 221 THR Chi-restraints excluded: chain d residue 228 ARG Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain e residue 155 VAL Chi-restraints excluded: chain e residue 176 VAL Chi-restraints excluded: chain e residue 196 HIS Chi-restraints excluded: chain f residue 155 VAL Chi-restraints excluded: chain f residue 156 HIS Chi-restraints excluded: chain f residue 230 LEU Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 176 VAL Chi-restraints excluded: chain g residue 178 VAL Chi-restraints excluded: chain g residue 180 LEU Chi-restraints excluded: chain g residue 368 VAL Chi-restraints excluded: chain g residue 369 ASP Chi-restraints excluded: chain h residue 266 VAL Chi-restraints excluded: chain h residue 358 THR Chi-restraints excluded: chain h residue 375 THR Chi-restraints excluded: chain h residue 416 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 470 optimal weight: 10.0000 chunk 757 optimal weight: 1.9990 chunk 462 optimal weight: 0.9990 chunk 359 optimal weight: 5.9990 chunk 526 optimal weight: 6.9990 chunk 795 optimal weight: 0.9990 chunk 731 optimal weight: 4.9990 chunk 633 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 489 optimal weight: 1.9990 chunk 388 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 HIS B 434 ASN C 231 ASN ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 434 ASN K 196 HIS M 133 GLN M 190 GLN ** M 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 196 HIS P 218 HIS ** U 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 133 GLN ** W 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 263 HIS ** d 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 63871 Z= 0.177 Angle : 0.542 13.265 86453 Z= 0.266 Chirality : 0.039 0.171 10172 Planarity : 0.003 0.055 11549 Dihedral : 4.266 40.909 8783 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.30 % Favored : 96.69 % Rotamer: Outliers : 1.96 % Allowed : 16.32 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.58 (0.10), residues: 7942 helix: 1.87 (0.11), residues: 2440 sheet: -1.34 (0.10), residues: 3056 loop : -1.22 (0.12), residues: 2446 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS c 196 PHE 0.022 0.001 PHE L 126 TYR 0.037 0.001 TYR V 132 ARG 0.022 0.000 ARG A 142 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15884 Ramachandran restraints generated. 7942 Oldfield, 0 Emsley, 7942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 485 time to evaluate : 7.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 LYS cc_start: 0.8240 (ptmt) cc_final: 0.7970 (ptmm) REVERT: A 236 LYS cc_start: 0.9022 (mtmt) cc_final: 0.8725 (mttp) REVERT: A 376 LYS cc_start: 0.8142 (tttt) cc_final: 0.7832 (ttmt) REVERT: A 425 LYS cc_start: 0.9097 (ptpt) cc_final: 0.8790 (ptpp) REVERT: B 267 THR cc_start: 0.9036 (OUTLIER) cc_final: 0.8768 (p) REVERT: C 126 PHE cc_start: 0.7042 (t80) cc_final: 0.6573 (t80) REVERT: D 126 PHE cc_start: 0.8201 (t80) cc_final: 0.7879 (t80) REVERT: D 196 HIS cc_start: 0.9302 (m-70) cc_final: 0.9009 (m-70) REVERT: D 425 LYS cc_start: 0.8762 (pttt) cc_final: 0.8517 (pttt) REVERT: E 377 MET cc_start: 0.8541 (mmm) cc_final: 0.7980 (mpp) REVERT: E 409 MET cc_start: 0.8556 (tpp) cc_final: 0.8322 (tpp) REVERT: F 159 MET cc_start: 0.6480 (tpt) cc_final: 0.5682 (ppp) REVERT: F 218 HIS cc_start: 0.8814 (m-70) cc_final: 0.8496 (m-70) REVERT: F 377 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7916 (mpt) REVERT: H 250 GLU cc_start: 0.7879 (pp20) cc_final: 0.7587 (pp20) REVERT: H 377 MET cc_start: 0.8252 (mmt) cc_final: 0.7919 (mpp) REVERT: I 144 ILE cc_start: 0.9616 (mt) cc_final: 0.9380 (mm) REVERT: I 147 LEU cc_start: 0.9424 (tp) cc_final: 0.9148 (mt) REVERT: I 157 LEU cc_start: 0.9069 (mp) cc_final: 0.8538 (tp) REVERT: I 197 LEU cc_start: 0.9151 (tp) cc_final: 0.8919 (tp) REVERT: I 218 HIS cc_start: 0.7431 (m90) cc_final: 0.6893 (m-70) REVERT: I 405 THR cc_start: 0.9060 (OUTLIER) cc_final: 0.8759 (p) REVERT: J 218 HIS cc_start: 0.7369 (m-70) cc_final: 0.7034 (m-70) REVERT: K 236 LYS cc_start: 0.8496 (mtpt) cc_final: 0.8029 (mtmm) REVERT: K 376 LYS cc_start: 0.8224 (tttt) cc_final: 0.8005 (tttp) REVERT: L 151 LYS cc_start: 0.7598 (ttmt) cc_final: 0.7241 (ttmm) REVERT: L 197 LEU cc_start: 0.9434 (tp) cc_final: 0.9207 (tt) REVERT: L 420 MET cc_start: 0.8769 (ptm) cc_final: 0.8451 (ptt) REVERT: M 126 PHE cc_start: 0.8100 (t80) cc_final: 0.7858 (t80) REVERT: M 196 HIS cc_start: 0.8883 (m90) cc_final: 0.8606 (m-70) REVERT: M 376 LYS cc_start: 0.8065 (tttt) cc_final: 0.7864 (ttpt) REVERT: N 156 HIS cc_start: 0.6970 (m-70) cc_final: 0.5798 (t70) REVERT: O 236 LYS cc_start: 0.8872 (mmtm) cc_final: 0.8594 (mmtm) REVERT: P 180 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7716 (pp) REVERT: Q 409 MET cc_start: 0.8904 (tpt) cc_final: 0.8538 (tpt) REVERT: R 425 LYS cc_start: 0.9127 (ptpt) cc_final: 0.8809 (ptpp) REVERT: S 159 MET cc_start: 0.4763 (pmm) cc_final: 0.4440 (mmm) REVERT: T 126 PHE cc_start: 0.6925 (t80) cc_final: 0.6502 (t80) REVERT: T 132 TYR cc_start: 0.8992 (t80) cc_final: 0.8544 (t80) REVERT: T 231 ASN cc_start: 0.7915 (OUTLIER) cc_final: 0.7627 (t0) REVERT: U 126 PHE cc_start: 0.8229 (t80) cc_final: 0.7812 (t80) REVERT: U 196 HIS cc_start: 0.9315 (m-70) cc_final: 0.8996 (m-70) REVERT: U 377 MET cc_start: 0.8263 (mpp) cc_final: 0.7678 (mpp) REVERT: U 425 LYS cc_start: 0.8760 (pttt) cc_final: 0.8521 (pttt) REVERT: V 205 LEU cc_start: 0.8065 (mp) cc_final: 0.7800 (tp) REVERT: V 230 LEU cc_start: 0.9057 (tt) cc_final: 0.8591 (mt) REVERT: V 377 MET cc_start: 0.8545 (mmm) cc_final: 0.7980 (mpp) REVERT: V 409 MET cc_start: 0.8625 (tpp) cc_final: 0.8415 (tpp) REVERT: W 377 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.8036 (mpt) REVERT: W 409 MET cc_start: 0.8811 (mmm) cc_final: 0.8456 (tpp) REVERT: X 187 ASP cc_start: 0.6077 (OUTLIER) cc_final: 0.5038 (m-30) REVERT: X 196 HIS cc_start: 0.9305 (m-70) cc_final: 0.8958 (m170) REVERT: Y 159 MET cc_start: 0.5179 (OUTLIER) cc_final: 0.4190 (ttm) REVERT: Y 377 MET cc_start: 0.8258 (mmt) cc_final: 0.7933 (mpp) REVERT: Z 218 HIS cc_start: 0.7272 (m90) cc_final: 0.6900 (m90) REVERT: Z 232 ASP cc_start: 0.7705 (p0) cc_final: 0.7305 (t70) REVERT: a 218 HIS cc_start: 0.7240 (m-70) cc_final: 0.6803 (m170) REVERT: b 236 LYS cc_start: 0.8367 (mtpt) cc_final: 0.7900 (mttp) REVERT: c 126 PHE cc_start: 0.8597 (t80) cc_final: 0.8372 (t80) REVERT: c 151 LYS cc_start: 0.7618 (ttmt) cc_final: 0.7233 (ttmm) REVERT: d 151 LYS cc_start: 0.8359 (ptmt) cc_final: 0.8072 (ptpp) REVERT: d 376 LYS cc_start: 0.8070 (tttt) cc_final: 0.7832 (ttpt) REVERT: e 156 HIS cc_start: 0.6894 (m-70) cc_final: 0.5705 (t70) REVERT: g 180 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.7950 (pp) REVERT: h 409 MET cc_start: 0.8871 (tpt) cc_final: 0.8517 (tpt) outliers start: 139 outliers final: 122 residues processed: 593 average time/residue: 0.5954 time to fit residues: 598.9008 Evaluate side-chains 605 residues out of total 7090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 474 time to evaluate : 5.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 187 ASP Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain E residue 196 HIS Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 254 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain I residue 416 THR Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 267 THR Chi-restraints excluded: chain J residue 379 VAL Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain L residue 132 TYR Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 196 HIS Chi-restraints excluded: chain N residue 205 LEU Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain N residue 236 LYS Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 156 HIS Chi-restraints excluded: chain O residue 416 THR Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain Q residue 252 ILE Chi-restraints excluded: chain Q residue 266 VAL Chi-restraints excluded: chain Q residue 358 THR Chi-restraints excluded: chain Q residue 416 THR Chi-restraints excluded: chain R residue 151 LYS Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 187 ASP Chi-restraints excluded: chain R residue 391 VAL Chi-restraints excluded: chain S residue 196 HIS Chi-restraints excluded: chain T residue 231 ASN Chi-restraints excluded: chain U residue 132 TYR Chi-restraints excluded: chain U residue 155 VAL Chi-restraints excluded: chain U residue 187 ASP Chi-restraints excluded: chain U residue 375 THR Chi-restraints excluded: chain V residue 196 HIS Chi-restraints excluded: chain V residue 223 SER Chi-restraints excluded: chain V residue 256 ILE Chi-restraints excluded: chain V residue 267 THR Chi-restraints excluded: chain V residue 304 VAL Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 198 VAL Chi-restraints excluded: chain W residue 267 THR Chi-restraints excluded: chain W residue 369 ASP Chi-restraints excluded: chain W residue 377 MET Chi-restraints excluded: chain W residue 412 ILE Chi-restraints excluded: chain X residue 132 TYR Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 157 LEU Chi-restraints excluded: chain X residue 187 ASP Chi-restraints excluded: chain X residue 230 LEU Chi-restraints excluded: chain X residue 254 SER Chi-restraints excluded: chain X residue 409 MET Chi-restraints excluded: chain Y residue 155 VAL Chi-restraints excluded: chain Y residue 159 MET Chi-restraints excluded: chain Y residue 220 LEU Chi-restraints excluded: chain Y residue 223 SER Chi-restraints excluded: chain Y residue 405 THR Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 212 LEU Chi-restraints excluded: chain Z residue 225 THR Chi-restraints excluded: chain Z residue 267 THR Chi-restraints excluded: chain Z residue 416 THR Chi-restraints excluded: chain a residue 155 VAL Chi-restraints excluded: chain a residue 176 VAL Chi-restraints excluded: chain a residue 267 THR Chi-restraints excluded: chain a residue 379 VAL Chi-restraints excluded: chain b residue 176 VAL Chi-restraints excluded: chain b residue 197 LEU Chi-restraints excluded: chain b residue 223 SER Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain c residue 132 TYR Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain c residue 256 ILE Chi-restraints excluded: chain c residue 416 THR Chi-restraints excluded: chain d residue 187 ASP Chi-restraints excluded: chain d residue 221 THR Chi-restraints excluded: chain d residue 228 ARG Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain e residue 155 VAL Chi-restraints excluded: chain e residue 176 VAL Chi-restraints excluded: chain e residue 196 HIS Chi-restraints excluded: chain f residue 155 VAL Chi-restraints excluded: chain f residue 156 HIS Chi-restraints excluded: chain f residue 230 LEU Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 176 VAL Chi-restraints excluded: chain g residue 178 VAL Chi-restraints excluded: chain g residue 180 LEU Chi-restraints excluded: chain g residue 368 VAL Chi-restraints excluded: chain h residue 266 VAL Chi-restraints excluded: chain h residue 358 THR Chi-restraints excluded: chain h residue 375 THR Chi-restraints excluded: chain h residue 416 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 502 optimal weight: 2.9990 chunk 674 optimal weight: 2.9990 chunk 193 optimal weight: 20.0000 chunk 583 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 175 optimal weight: 40.0000 chunk 634 optimal weight: 10.0000 chunk 265 optimal weight: 20.0000 chunk 651 optimal weight: 0.7980 chunk 80 optimal weight: 20.0000 chunk 116 optimal weight: 30.0000 overall best weight: 4.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 ASN C 231 ASN ** F 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 218 HIS J 434 ASN K 196 HIS ** O 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 196 HIS ** U 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 434 ASN ** d 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.101616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.065336 restraints weight = 171174.228| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.20 r_work: 0.3100 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 63871 Z= 0.283 Angle : 0.574 12.722 86453 Z= 0.283 Chirality : 0.040 0.171 10172 Planarity : 0.003 0.046 11549 Dihedral : 4.355 39.230 8783 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.48 % Favored : 94.51 % Rotamer: Outliers : 2.10 % Allowed : 16.35 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.76 (0.10), residues: 7942 helix: 1.66 (0.11), residues: 2484 sheet: -1.40 (0.10), residues: 3110 loop : -1.34 (0.12), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS K 196 PHE 0.021 0.001 PHE L 126 TYR 0.027 0.001 TYR b 132 ARG 0.017 0.000 ARG G 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13356.16 seconds wall clock time: 234 minutes 31.82 seconds (14071.82 seconds total)