Starting phenix.real_space_refine on Tue Sep 24 01:41:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh3_11212/09_2024/6zh3_11212.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh3_11212/09_2024/6zh3_11212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh3_11212/09_2024/6zh3_11212.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh3_11212/09_2024/6zh3_11212.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh3_11212/09_2024/6zh3_11212.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh3_11212/09_2024/6zh3_11212.cif" } resolution = 3.2 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= 0.002 sd= 0.015 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 396 5.16 5 C 30564 2.51 5 N 9072 2.21 5 O 9684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 360 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 49716 Number of models: 1 Model: "" Number of chains: 36 Chain: "B" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "A" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "C" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "D" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "E" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "F" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "G" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "H" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "I" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "J" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "K" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "L" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "M" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "N" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "O" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "P" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "Q" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "R" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "S" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "T" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "U" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "V" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "W" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "X" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "Y" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "Z" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "0" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "1" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "2" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "3" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "4" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "5" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "6" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "7" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "8" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "9" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Time building chain proxies: 22.08, per 1000 atoms: 0.44 Number of scatterers: 49716 At special positions: 0 Unit cell: (172.64, 171.6, 307.84, 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 396 16.00 O 9684 8.00 N 9072 7.00 C 30564 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: 9.20 Conformation dependent library (CDL) restraints added in 4.9 seconds 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11808 Finding SS restraints... Secondary structure from input PDB file: 297 helices and 0 sheets defined 87.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.25 Creating SS restraints... Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 12 through 56 removed outlier: 3.709A pdb=" N ARG B 18 " --> pdb=" O LYS B 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG B 25 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU B 32 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU B 38 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU B 41 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS B 54 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 98 removed outlier: 4.757A pdb=" N LEU B 63 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS B 66 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN B 70 " --> pdb=" O LYS B 66 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN B 74 " --> pdb=" O GLN B 70 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG B 77 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B 83 " --> pdb=" O TYR B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 120 removed outlier: 3.723A pdb=" N LEU B 111 " --> pdb=" O ASP B 107 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 124 through 135 removed outlier: 3.783A pdb=" N GLU B 130 " --> pdb=" O ASN B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 145 Processing helix chain 'B' and resid 162 through 170 Processing helix chain 'A' and resid 2 through 10 removed outlier: 3.816A pdb=" N LYS A 6 " --> pdb=" O ASP A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 56 removed outlier: 3.785A pdb=" N ARG A 18 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 32 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 50 " --> pdb=" O GLN A 46 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS A 54 " --> pdb=" O LYS A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 98 removed outlier: 4.036A pdb=" N LEU A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS A 66 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A 83 " --> pdb=" O TYR A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 119 removed outlier: 3.535A pdb=" N GLY A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 124 through 135 removed outlier: 3.681A pdb=" N GLU A 130 " --> pdb=" O ASN A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 146 removed outlier: 3.605A pdb=" N ASP A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 170 removed outlier: 4.006A pdb=" N VAL A 167 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 10 removed outlier: 3.676A pdb=" N LYS C 6 " --> pdb=" O ASP C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 56 removed outlier: 3.576A pdb=" N ARG C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY C 28 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU C 32 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU C 41 " --> pdb=" O GLU C 37 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS C 54 " --> pdb=" O LYS C 50 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 98 removed outlier: 4.484A pdb=" N LEU C 63 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG C 77 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 83 " --> pdb=" O TYR C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 120 removed outlier: 3.536A pdb=" N ARG C 113 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU C 114 " --> pdb=" O GLY C 110 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU C 118 " --> pdb=" O GLU C 114 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 123 No H-bonds generated for 'chain 'C' and resid 121 through 123' Processing helix chain 'C' and resid 124 through 133 removed outlier: 3.633A pdb=" N GLU C 130 " --> pdb=" O ASN C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 145 Processing helix chain 'C' and resid 146 through 150 removed outlier: 3.723A pdb=" N MET C 149 " --> pdb=" O ASP C 146 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU C 150 " --> pdb=" O ASP C 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 146 through 150' Processing helix chain 'C' and resid 162 through 170 Processing helix chain 'D' and resid 2 through 10 Processing helix chain 'D' and resid 12 through 56 removed outlier: 3.646A pdb=" N ARG D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG D 25 " --> pdb=" O ARG D 21 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY D 28 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU D 32 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL D 40 " --> pdb=" O ARG D 36 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN D 47 " --> pdb=" O ASN D 43 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS D 50 " --> pdb=" O GLN D 46 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 98 removed outlier: 4.253A pdb=" N LEU D 63 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS D 66 " --> pdb=" O ARG D 62 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG D 77 " --> pdb=" O LYS D 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA D 83 " --> pdb=" O TYR D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 120 removed outlier: 3.535A pdb=" N SER D 108 " --> pdb=" O GLN D 104 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG D 113 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU D 114 " --> pdb=" O GLY D 110 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 118 " --> pdb=" O GLU D 114 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 124 through 135 removed outlier: 3.713A pdb=" N GLU D 130 " --> pdb=" O ASN D 126 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 145 Processing helix chain 'D' and resid 162 through 170 removed outlier: 3.616A pdb=" N VAL D 167 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 10 Processing helix chain 'E' and resid 12 through 56 removed outlier: 3.709A pdb=" N ARG E 18 " --> pdb=" O LYS E 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG E 25 " --> pdb=" O ARG E 21 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY E 28 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU E 32 " --> pdb=" O GLY E 28 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU E 38 " --> pdb=" O SER E 34 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL E 40 " --> pdb=" O ARG E 36 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU E 41 " --> pdb=" O GLU E 37 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN E 47 " --> pdb=" O ASN E 43 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS E 54 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 98 removed outlier: 4.757A pdb=" N LEU E 63 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS E 66 " --> pdb=" O ARG E 62 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN E 70 " --> pdb=" O LYS E 66 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN E 74 " --> pdb=" O GLN E 70 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG E 77 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA E 83 " --> pdb=" O TYR E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 120 removed outlier: 3.722A pdb=" N LEU E 111 " --> pdb=" O ASP E 107 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU E 114 " --> pdb=" O GLY E 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU E 118 " --> pdb=" O GLU E 114 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 123 No H-bonds generated for 'chain 'E' and resid 121 through 123' Processing helix chain 'E' and resid 124 through 135 removed outlier: 3.783A pdb=" N GLU E 130 " --> pdb=" O ASN E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 145 Processing helix chain 'E' and resid 162 through 170 Processing helix chain 'F' and resid 2 through 10 removed outlier: 3.816A pdb=" N LYS F 6 " --> pdb=" O ASP F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 56 removed outlier: 3.785A pdb=" N ARG F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER F 22 " --> pdb=" O ARG F 18 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG F 25 " --> pdb=" O ARG F 21 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY F 28 " --> pdb=" O LEU F 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU F 32 " --> pdb=" O GLY F 28 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU F 38 " --> pdb=" O SER F 34 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL F 40 " --> pdb=" O ARG F 36 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU F 41 " --> pdb=" O GLU F 37 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS F 50 " --> pdb=" O GLN F 46 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS F 54 " --> pdb=" O LYS F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 98 removed outlier: 4.036A pdb=" N LEU F 63 " --> pdb=" O ARG F 59 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS F 66 " --> pdb=" O ARG F 62 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG F 77 " --> pdb=" O LYS F 73 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR F 80 " --> pdb=" O ASP F 76 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA F 83 " --> pdb=" O TYR F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 119 removed outlier: 3.536A pdb=" N GLY F 110 " --> pdb=" O ALA F 106 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU F 111 " --> pdb=" O ASP F 107 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU F 114 " --> pdb=" O GLY F 110 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU F 118 " --> pdb=" O GLU F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'F' and resid 124 through 135 removed outlier: 3.681A pdb=" N GLU F 130 " --> pdb=" O ASN F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 146 removed outlier: 3.605A pdb=" N ASP F 146 " --> pdb=" O SER F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 170 removed outlier: 4.006A pdb=" N VAL F 167 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN F 168 " --> pdb=" O ASP F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 10 removed outlier: 3.676A pdb=" N LYS G 6 " --> pdb=" O ASP G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 56 removed outlier: 3.576A pdb=" N ARG G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG G 25 " --> pdb=" O ARG G 21 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY G 28 " --> pdb=" O LEU G 24 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU G 32 " --> pdb=" O GLY G 28 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU G 38 " --> pdb=" O SER G 34 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL G 40 " --> pdb=" O ARG G 36 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU G 41 " --> pdb=" O GLU G 37 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS G 54 " --> pdb=" O LYS G 50 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS G 55 " --> pdb=" O LYS G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 98 removed outlier: 4.483A pdb=" N LEU G 63 " --> pdb=" O ARG G 59 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU G 67 " --> pdb=" O LEU G 63 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN G 70 " --> pdb=" O LYS G 66 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG G 77 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA G 83 " --> pdb=" O TYR G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 120 removed outlier: 3.537A pdb=" N ARG G 113 " --> pdb=" O ALA G 109 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU G 114 " --> pdb=" O GLY G 110 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU G 118 " --> pdb=" O GLU G 114 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG G 120 " --> pdb=" O ASN G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 123 No H-bonds generated for 'chain 'G' and resid 121 through 123' Processing helix chain 'G' and resid 124 through 133 removed outlier: 3.632A pdb=" N GLU G 130 " --> pdb=" O ASN G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 145 Processing helix chain 'G' and resid 146 through 150 removed outlier: 3.723A pdb=" N MET G 149 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU G 150 " --> pdb=" O ASP G 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 146 through 150' Processing helix chain 'G' and resid 162 through 170 Processing helix chain 'H' and resid 2 through 10 Processing helix chain 'H' and resid 12 through 56 removed outlier: 3.647A pdb=" N ARG H 18 " --> pdb=" O LYS H 14 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL H 23 " --> pdb=" O ARG H 19 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG H 25 " --> pdb=" O ARG H 21 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY H 28 " --> pdb=" O LEU H 24 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU H 32 " --> pdb=" O GLY H 28 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU H 38 " --> pdb=" O SER H 34 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL H 40 " --> pdb=" O ARG H 36 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU H 41 " --> pdb=" O GLU H 37 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN H 47 " --> pdb=" O ASN H 43 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS H 50 " --> pdb=" O GLN H 46 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS H 54 " --> pdb=" O LYS H 50 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS H 55 " --> pdb=" O LYS H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 98 removed outlier: 4.253A pdb=" N LEU H 63 " --> pdb=" O ARG H 59 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS H 66 " --> pdb=" O ARG H 62 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU H 67 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN H 70 " --> pdb=" O LYS H 66 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG H 77 " --> pdb=" O LYS H 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA H 83 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 120 removed outlier: 3.535A pdb=" N SER H 108 " --> pdb=" O GLN H 104 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG H 113 " --> pdb=" O ALA H 109 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU H 114 " --> pdb=" O GLY H 110 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU H 118 " --> pdb=" O GLU H 114 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG H 120 " --> pdb=" O ASN H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 123 No H-bonds generated for 'chain 'H' and resid 121 through 123' Processing helix chain 'H' and resid 124 through 135 removed outlier: 3.713A pdb=" N GLU H 130 " --> pdb=" O ASN H 126 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU H 134 " --> pdb=" O GLU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 145 Processing helix chain 'H' and resid 162 through 170 removed outlier: 3.616A pdb=" N VAL H 167 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS H 169 " --> pdb=" O GLU H 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 10 Processing helix chain 'I' and resid 12 through 56 removed outlier: 3.709A pdb=" N ARG I 18 " --> pdb=" O LYS I 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL I 23 " --> pdb=" O ARG I 19 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG I 25 " --> pdb=" O ARG I 21 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY I 28 " --> pdb=" O LEU I 24 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU I 32 " --> pdb=" O GLY I 28 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU I 38 " --> pdb=" O SER I 34 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL I 40 " --> pdb=" O ARG I 36 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU I 41 " --> pdb=" O GLU I 37 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN I 47 " --> pdb=" O ASN I 43 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS I 54 " --> pdb=" O LYS I 50 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS I 55 " --> pdb=" O LYS I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 98 removed outlier: 4.757A pdb=" N LEU I 63 " --> pdb=" O ARG I 59 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS I 66 " --> pdb=" O ARG I 62 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU I 67 " --> pdb=" O LEU I 63 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR I 69 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN I 70 " --> pdb=" O LYS I 66 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN I 74 " --> pdb=" O GLN I 70 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG I 77 " --> pdb=" O LYS I 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA I 83 " --> pdb=" O TYR I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 120 removed outlier: 3.722A pdb=" N LEU I 111 " --> pdb=" O ASP I 107 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU I 114 " --> pdb=" O GLY I 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU I 118 " --> pdb=" O GLU I 114 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG I 120 " --> pdb=" O ASN I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 123 No H-bonds generated for 'chain 'I' and resid 121 through 123' Processing helix chain 'I' and resid 124 through 135 removed outlier: 3.783A pdb=" N GLU I 130 " --> pdb=" O ASN I 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 145 Processing helix chain 'I' and resid 162 through 170 Processing helix chain 'J' and resid 2 through 10 removed outlier: 3.816A pdb=" N LYS J 6 " --> pdb=" O ASP J 2 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 56 removed outlier: 3.784A pdb=" N ARG J 18 " --> pdb=" O LYS J 14 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER J 22 " --> pdb=" O ARG J 18 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL J 23 " --> pdb=" O ARG J 19 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG J 25 " --> pdb=" O ARG J 21 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY J 28 " --> pdb=" O LEU J 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU J 32 " --> pdb=" O GLY J 28 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU J 38 " --> pdb=" O SER J 34 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL J 40 " --> pdb=" O ARG J 36 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU J 41 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS J 50 " --> pdb=" O GLN J 46 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER J 52 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS J 54 " --> pdb=" O LYS J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 98 removed outlier: 4.035A pdb=" N LEU J 63 " --> pdb=" O ARG J 59 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS J 66 " --> pdb=" O ARG J 62 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU J 67 " --> pdb=" O LEU J 63 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR J 69 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG J 77 " --> pdb=" O LYS J 73 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR J 80 " --> pdb=" O ASP J 76 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA J 83 " --> pdb=" O TYR J 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 119 removed outlier: 3.535A pdb=" N GLY J 110 " --> pdb=" O ALA J 106 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU J 111 " --> pdb=" O ASP J 107 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU J 114 " --> pdb=" O GLY J 110 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU J 118 " --> pdb=" O GLU J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 123 No H-bonds generated for 'chain 'J' and resid 121 through 123' Processing helix chain 'J' and resid 124 through 135 removed outlier: 3.682A pdb=" N GLU J 130 " --> pdb=" O ASN J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 146 removed outlier: 3.605A pdb=" N ASP J 146 " --> pdb=" O SER J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 162 through 170 removed outlier: 4.006A pdb=" N VAL J 167 " --> pdb=" O VAL J 163 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN J 168 " --> pdb=" O ASP J 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 10 removed outlier: 3.675A pdb=" N LYS K 6 " --> pdb=" O ASP K 2 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 56 removed outlier: 3.576A pdb=" N ARG K 18 " --> pdb=" O LYS K 14 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG K 25 " --> pdb=" O ARG K 21 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY K 28 " --> pdb=" O LEU K 24 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU K 32 " --> pdb=" O GLY K 28 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU K 38 " --> pdb=" O SER K 34 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL K 40 " --> pdb=" O ARG K 36 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU K 41 " --> pdb=" O GLU K 37 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS K 54 " --> pdb=" O LYS K 50 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS K 55 " --> pdb=" O LYS K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 98 removed outlier: 4.483A pdb=" N LEU K 63 " --> pdb=" O ARG K 59 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR K 69 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN K 70 " --> pdb=" O LYS K 66 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG K 77 " --> pdb=" O LYS K 73 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA K 83 " --> pdb=" O TYR K 79 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 120 removed outlier: 3.536A pdb=" N ARG K 113 " --> pdb=" O ALA K 109 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU K 114 " --> pdb=" O GLY K 110 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU K 118 " --> pdb=" O GLU K 114 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG K 120 " --> pdb=" O ASN K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 123 No H-bonds generated for 'chain 'K' and resid 121 through 123' Processing helix chain 'K' and resid 124 through 133 removed outlier: 3.633A pdb=" N GLU K 130 " --> pdb=" O ASN K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 145 Processing helix chain 'K' and resid 146 through 150 removed outlier: 3.722A pdb=" N MET K 149 " --> pdb=" O ASP K 146 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU K 150 " --> pdb=" O ASP K 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 146 through 150' Processing helix chain 'K' and resid 162 through 170 Processing helix chain 'L' and resid 2 through 10 Processing helix chain 'L' and resid 12 through 56 removed outlier: 3.645A pdb=" N ARG L 18 " --> pdb=" O LYS L 14 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL L 23 " --> pdb=" O ARG L 19 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG L 25 " --> pdb=" O ARG L 21 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY L 28 " --> pdb=" O LEU L 24 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU L 32 " --> pdb=" O GLY L 28 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU L 38 " --> pdb=" O SER L 34 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL L 40 " --> pdb=" O ARG L 36 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU L 41 " --> pdb=" O GLU L 37 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN L 47 " --> pdb=" O ASN L 43 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS L 50 " --> pdb=" O GLN L 46 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS L 54 " --> pdb=" O LYS L 50 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS L 55 " --> pdb=" O LYS L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 98 removed outlier: 4.254A pdb=" N LEU L 63 " --> pdb=" O ARG L 59 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS L 66 " --> pdb=" O ARG L 62 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU L 67 " --> pdb=" O LEU L 63 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN L 70 " --> pdb=" O LYS L 66 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG L 77 " --> pdb=" O LYS L 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA L 83 " --> pdb=" O TYR L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 120 removed outlier: 3.536A pdb=" N SER L 108 " --> pdb=" O GLN L 104 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG L 113 " --> pdb=" O ALA L 109 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU L 114 " --> pdb=" O GLY L 110 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU L 118 " --> pdb=" O GLU L 114 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG L 120 " --> pdb=" O ASN L 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 123 No H-bonds generated for 'chain 'L' and resid 121 through 123' Processing helix chain 'L' and resid 124 through 135 removed outlier: 3.714A pdb=" N GLU L 130 " --> pdb=" O ASN L 126 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU L 134 " --> pdb=" O GLU L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 145 Processing helix chain 'L' and resid 162 through 170 removed outlier: 3.616A pdb=" N VAL L 167 " --> pdb=" O VAL L 163 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS L 169 " --> pdb=" O GLU L 165 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 10 Processing helix chain 'M' and resid 12 through 56 removed outlier: 3.709A pdb=" N ARG M 18 " --> pdb=" O LYS M 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL M 23 " --> pdb=" O ARG M 19 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG M 25 " --> pdb=" O ARG M 21 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY M 28 " --> pdb=" O LEU M 24 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU M 32 " --> pdb=" O GLY M 28 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU M 38 " --> pdb=" O SER M 34 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL M 40 " --> pdb=" O ARG M 36 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU M 41 " --> pdb=" O GLU M 37 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN M 47 " --> pdb=" O ASN M 43 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS M 54 " --> pdb=" O LYS M 50 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS M 55 " --> pdb=" O LYS M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 98 removed outlier: 4.756A pdb=" N LEU M 63 " --> pdb=" O ARG M 59 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS M 66 " --> pdb=" O ARG M 62 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU M 67 " --> pdb=" O LEU M 63 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR M 69 " --> pdb=" O ALA M 65 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN M 70 " --> pdb=" O LYS M 66 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN M 74 " --> pdb=" O GLN M 70 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG M 77 " --> pdb=" O LYS M 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA M 83 " --> pdb=" O TYR M 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 120 removed outlier: 3.723A pdb=" N LEU M 111 " --> pdb=" O ASP M 107 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU M 114 " --> pdb=" O GLY M 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU M 118 " --> pdb=" O GLU M 114 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG M 120 " --> pdb=" O ASN M 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 123 No H-bonds generated for 'chain 'M' and resid 121 through 123' Processing helix chain 'M' and resid 124 through 135 removed outlier: 3.783A pdb=" N GLU M 130 " --> pdb=" O ASN M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 139 through 145 Processing helix chain 'M' and resid 162 through 170 Processing helix chain 'N' and resid 2 through 10 removed outlier: 3.817A pdb=" N LYS N 6 " --> pdb=" O ASP N 2 " (cutoff:3.500A) Processing helix chain 'N' and resid 12 through 56 removed outlier: 3.784A pdb=" N ARG N 18 " --> pdb=" O LYS N 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER N 22 " --> pdb=" O ARG N 18 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL N 23 " --> pdb=" O ARG N 19 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG N 25 " --> pdb=" O ARG N 21 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY N 28 " --> pdb=" O LEU N 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU N 32 " --> pdb=" O GLY N 28 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU N 38 " --> pdb=" O SER N 34 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL N 40 " --> pdb=" O ARG N 36 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU N 41 " --> pdb=" O GLU N 37 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS N 50 " --> pdb=" O GLN N 46 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER N 52 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS N 54 " --> pdb=" O LYS N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 98 removed outlier: 4.036A pdb=" N LEU N 63 " --> pdb=" O ARG N 59 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS N 66 " --> pdb=" O ARG N 62 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU N 67 " --> pdb=" O LEU N 63 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR N 69 " --> pdb=" O ALA N 65 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG N 77 " --> pdb=" O LYS N 73 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR N 80 " --> pdb=" O ASP N 76 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA N 83 " --> pdb=" O TYR N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 119 removed outlier: 3.535A pdb=" N GLY N 110 " --> pdb=" O ALA N 106 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU N 111 " --> pdb=" O ASP N 107 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU N 114 " --> pdb=" O GLY N 110 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU N 118 " --> pdb=" O GLU N 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 123 No H-bonds generated for 'chain 'N' and resid 121 through 123' Processing helix chain 'N' and resid 124 through 135 removed outlier: 3.682A pdb=" N GLU N 130 " --> pdb=" O ASN N 126 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 146 removed outlier: 3.605A pdb=" N ASP N 146 " --> pdb=" O SER N 142 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 170 removed outlier: 4.006A pdb=" N VAL N 167 " --> pdb=" O VAL N 163 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN N 168 " --> pdb=" O ASP N 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 10 removed outlier: 3.676A pdb=" N LYS O 6 " --> pdb=" O ASP O 2 " (cutoff:3.500A) Processing helix chain 'O' and resid 12 through 56 removed outlier: 3.576A pdb=" N ARG O 18 " --> pdb=" O LYS O 14 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG O 25 " --> pdb=" O ARG O 21 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY O 28 " --> pdb=" O LEU O 24 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU O 32 " --> pdb=" O GLY O 28 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU O 38 " --> pdb=" O SER O 34 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL O 40 " --> pdb=" O ARG O 36 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU O 41 " --> pdb=" O GLU O 37 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS O 54 " --> pdb=" O LYS O 50 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS O 55 " --> pdb=" O LYS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 57 through 98 removed outlier: 4.484A pdb=" N LEU O 63 " --> pdb=" O ARG O 59 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU O 67 " --> pdb=" O LEU O 63 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN O 70 " --> pdb=" O LYS O 66 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG O 77 " --> pdb=" O LYS O 73 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA O 83 " --> pdb=" O TYR O 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 120 removed outlier: 3.536A pdb=" N ARG O 113 " --> pdb=" O ALA O 109 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU O 114 " --> pdb=" O GLY O 110 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU O 118 " --> pdb=" O GLU O 114 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG O 120 " --> pdb=" O ASN O 116 " (cutoff:3.500A) Processing helix chain 'O' and resid 121 through 123 No H-bonds generated for 'chain 'O' and resid 121 through 123' Processing helix chain 'O' and resid 124 through 133 removed outlier: 3.633A pdb=" N GLU O 130 " --> pdb=" O ASN O 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 139 through 145 Processing helix chain 'O' and resid 146 through 150 removed outlier: 3.722A pdb=" N MET O 149 " --> pdb=" O ASP O 146 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU O 150 " --> pdb=" O ASP O 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 146 through 150' Processing helix chain 'O' and resid 162 through 170 Processing helix chain 'P' and resid 2 through 10 Processing helix chain 'P' and resid 12 through 56 removed outlier: 3.646A pdb=" N ARG P 18 " --> pdb=" O LYS P 14 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL P 23 " --> pdb=" O ARG P 19 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG P 25 " --> pdb=" O ARG P 21 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY P 28 " --> pdb=" O LEU P 24 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU P 32 " --> pdb=" O GLY P 28 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU P 38 " --> pdb=" O SER P 34 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL P 40 " --> pdb=" O ARG P 36 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU P 41 " --> pdb=" O GLU P 37 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN P 47 " --> pdb=" O ASN P 43 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS P 50 " --> pdb=" O GLN P 46 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS P 54 " --> pdb=" O LYS P 50 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS P 55 " --> pdb=" O LYS P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 98 removed outlier: 4.253A pdb=" N LEU P 63 " --> pdb=" O ARG P 59 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS P 66 " --> pdb=" O ARG P 62 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU P 67 " --> pdb=" O LEU P 63 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN P 70 " --> pdb=" O LYS P 66 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG P 77 " --> pdb=" O LYS P 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA P 83 " --> pdb=" O TYR P 79 " (cutoff:3.500A) Processing helix chain 'P' and resid 100 through 120 removed outlier: 3.535A pdb=" N SER P 108 " --> pdb=" O GLN P 104 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG P 113 " --> pdb=" O ALA P 109 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU P 114 " --> pdb=" O GLY P 110 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU P 118 " --> pdb=" O GLU P 114 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG P 120 " --> pdb=" O ASN P 116 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 123 No H-bonds generated for 'chain 'P' and resid 121 through 123' Processing helix chain 'P' and resid 124 through 135 removed outlier: 3.714A pdb=" N GLU P 130 " --> pdb=" O ASN P 126 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU P 134 " --> pdb=" O GLU P 130 " (cutoff:3.500A) Processing helix chain 'P' and resid 139 through 145 Processing helix chain 'P' and resid 162 through 170 removed outlier: 3.616A pdb=" N VAL P 167 " --> pdb=" O VAL P 163 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS P 169 " --> pdb=" O GLU P 165 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 10 Processing helix chain 'Q' and resid 12 through 56 removed outlier: 3.710A pdb=" N ARG Q 18 " --> pdb=" O LYS Q 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL Q 23 " --> pdb=" O ARG Q 19 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG Q 25 " --> pdb=" O ARG Q 21 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY Q 28 " --> pdb=" O LEU Q 24 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU Q 32 " --> pdb=" O GLY Q 28 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU Q 38 " --> pdb=" O SER Q 34 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL Q 40 " --> pdb=" O ARG Q 36 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU Q 41 " --> pdb=" O GLU Q 37 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN Q 47 " --> pdb=" O ASN Q 43 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS Q 54 " --> pdb=" O LYS Q 50 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS Q 55 " --> pdb=" O LYS Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 57 through 98 removed outlier: 4.757A pdb=" N LEU Q 63 " --> pdb=" O ARG Q 59 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS Q 66 " --> pdb=" O ARG Q 62 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU Q 67 " --> pdb=" O LEU Q 63 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR Q 69 " --> pdb=" O ALA Q 65 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN Q 70 " --> pdb=" O LYS Q 66 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN Q 74 " --> pdb=" O GLN Q 70 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG Q 77 " --> pdb=" O LYS Q 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA Q 83 " --> pdb=" O TYR Q 79 " (cutoff:3.500A) Processing helix chain 'Q' and resid 100 through 120 removed outlier: 3.723A pdb=" N LEU Q 111 " --> pdb=" O ASP Q 107 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU Q 114 " --> pdb=" O GLY Q 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU Q 118 " --> pdb=" O GLU Q 114 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG Q 120 " --> pdb=" O ASN Q 116 " (cutoff:3.500A) Processing helix chain 'Q' and resid 121 through 123 No H-bonds generated for 'chain 'Q' and resid 121 through 123' Processing helix chain 'Q' and resid 124 through 135 removed outlier: 3.782A pdb=" N GLU Q 130 " --> pdb=" O ASN Q 126 " (cutoff:3.500A) Processing helix chain 'Q' and resid 139 through 145 Processing helix chain 'Q' and resid 162 through 170 Processing helix chain 'R' and resid 2 through 10 removed outlier: 3.816A pdb=" N LYS R 6 " --> pdb=" O ASP R 2 " (cutoff:3.500A) Processing helix chain 'R' and resid 12 through 56 removed outlier: 3.785A pdb=" N ARG R 18 " --> pdb=" O LYS R 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER R 22 " --> pdb=" O ARG R 18 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL R 23 " --> pdb=" O ARG R 19 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG R 25 " --> pdb=" O ARG R 21 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY R 28 " --> pdb=" O LEU R 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU R 32 " --> pdb=" O GLY R 28 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU R 38 " --> pdb=" O SER R 34 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL R 40 " --> pdb=" O ARG R 36 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU R 41 " --> pdb=" O GLU R 37 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS R 50 " --> pdb=" O GLN R 46 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER R 52 " --> pdb=" O LEU R 48 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS R 54 " --> pdb=" O LYS R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 57 through 98 removed outlier: 4.035A pdb=" N LEU R 63 " --> pdb=" O ARG R 59 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS R 66 " --> pdb=" O ARG R 62 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU R 67 " --> pdb=" O LEU R 63 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR R 69 " --> pdb=" O ALA R 65 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG R 77 " --> pdb=" O LYS R 73 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR R 80 " --> pdb=" O ASP R 76 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA R 83 " --> pdb=" O TYR R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 119 removed outlier: 3.535A pdb=" N GLY R 110 " --> pdb=" O ALA R 106 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU R 111 " --> pdb=" O ASP R 107 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU R 114 " --> pdb=" O GLY R 110 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU R 118 " --> pdb=" O GLU R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 123 No H-bonds generated for 'chain 'R' and resid 121 through 123' Processing helix chain 'R' and resid 124 through 135 removed outlier: 3.681A pdb=" N GLU R 130 " --> pdb=" O ASN R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 146 removed outlier: 3.604A pdb=" N ASP R 146 " --> pdb=" O SER R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 162 through 170 removed outlier: 4.006A pdb=" N VAL R 167 " --> pdb=" O VAL R 163 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN R 168 " --> pdb=" O ASP R 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 10 removed outlier: 3.676A pdb=" N LYS S 6 " --> pdb=" O ASP S 2 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 56 removed outlier: 3.576A pdb=" N ARG S 18 " --> pdb=" O LYS S 14 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG S 25 " --> pdb=" O ARG S 21 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY S 28 " --> pdb=" O LEU S 24 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU S 32 " --> pdb=" O GLY S 28 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU S 38 " --> pdb=" O SER S 34 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL S 40 " --> pdb=" O ARG S 36 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU S 41 " --> pdb=" O GLU S 37 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS S 54 " --> pdb=" O LYS S 50 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS S 55 " --> pdb=" O LYS S 51 " (cutoff:3.500A) Processing helix chain 'S' and resid 57 through 98 removed outlier: 4.483A pdb=" N LEU S 63 " --> pdb=" O ARG S 59 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU S 67 " --> pdb=" O LEU S 63 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR S 69 " --> pdb=" O ALA S 65 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN S 70 " --> pdb=" O LYS S 66 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG S 77 " --> pdb=" O LYS S 73 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA S 83 " --> pdb=" O TYR S 79 " (cutoff:3.500A) Processing helix chain 'S' and resid 100 through 120 removed outlier: 3.537A pdb=" N ARG S 113 " --> pdb=" O ALA S 109 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU S 114 " --> pdb=" O GLY S 110 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU S 118 " --> pdb=" O GLU S 114 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG S 120 " --> pdb=" O ASN S 116 " (cutoff:3.500A) Processing helix chain 'S' and resid 121 through 123 No H-bonds generated for 'chain 'S' and resid 121 through 123' Processing helix chain 'S' and resid 124 through 133 removed outlier: 3.633A pdb=" N GLU S 130 " --> pdb=" O ASN S 126 " (cutoff:3.500A) Processing helix chain 'S' and resid 139 through 145 Processing helix chain 'S' and resid 146 through 150 removed outlier: 3.722A pdb=" N MET S 149 " --> pdb=" O ASP S 146 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU S 150 " --> pdb=" O ASP S 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 146 through 150' Processing helix chain 'S' and resid 162 through 170 Processing helix chain 'T' and resid 2 through 10 Processing helix chain 'T' and resid 12 through 56 removed outlier: 3.646A pdb=" N ARG T 18 " --> pdb=" O LYS T 14 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL T 23 " --> pdb=" O ARG T 19 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG T 25 " --> pdb=" O ARG T 21 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY T 28 " --> pdb=" O LEU T 24 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU T 32 " --> pdb=" O GLY T 28 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU T 38 " --> pdb=" O SER T 34 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL T 40 " --> pdb=" O ARG T 36 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU T 41 " --> pdb=" O GLU T 37 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN T 47 " --> pdb=" O ASN T 43 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS T 50 " --> pdb=" O GLN T 46 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS T 54 " --> pdb=" O LYS T 50 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS T 55 " --> pdb=" O LYS T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 98 removed outlier: 4.253A pdb=" N LEU T 63 " --> pdb=" O ARG T 59 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS T 66 " --> pdb=" O ARG T 62 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU T 67 " --> pdb=" O LEU T 63 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN T 70 " --> pdb=" O LYS T 66 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG T 77 " --> pdb=" O LYS T 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA T 83 " --> pdb=" O TYR T 79 " (cutoff:3.500A) Processing helix chain 'T' and resid 100 through 120 removed outlier: 3.535A pdb=" N SER T 108 " --> pdb=" O GLN T 104 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG T 113 " --> pdb=" O ALA T 109 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU T 114 " --> pdb=" O GLY T 110 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU T 118 " --> pdb=" O GLU T 114 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG T 120 " --> pdb=" O ASN T 116 " (cutoff:3.500A) Processing helix chain 'T' and resid 121 through 123 No H-bonds generated for 'chain 'T' and resid 121 through 123' Processing helix chain 'T' and resid 124 through 135 removed outlier: 3.713A pdb=" N GLU T 130 " --> pdb=" O ASN T 126 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU T 134 " --> pdb=" O GLU T 130 " (cutoff:3.500A) Processing helix chain 'T' and resid 139 through 145 Processing helix chain 'T' and resid 162 through 170 removed outlier: 3.616A pdb=" N VAL T 167 " --> pdb=" O VAL T 163 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS T 169 " --> pdb=" O GLU T 165 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 10 Processing helix chain 'U' and resid 12 through 56 removed outlier: 3.709A pdb=" N ARG U 18 " --> pdb=" O LYS U 14 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL U 23 " --> pdb=" O ARG U 19 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG U 25 " --> pdb=" O ARG U 21 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY U 28 " --> pdb=" O LEU U 24 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU U 32 " --> pdb=" O GLY U 28 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU U 38 " --> pdb=" O SER U 34 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL U 40 " --> pdb=" O ARG U 36 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU U 41 " --> pdb=" O GLU U 37 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN U 47 " --> pdb=" O ASN U 43 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS U 54 " --> pdb=" O LYS U 50 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS U 55 " --> pdb=" O LYS U 51 " (cutoff:3.500A) Processing helix chain 'U' and resid 57 through 98 removed outlier: 4.757A pdb=" N LEU U 63 " --> pdb=" O ARG U 59 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS U 66 " --> pdb=" O ARG U 62 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU U 67 " --> pdb=" O LEU U 63 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR U 69 " --> pdb=" O ALA U 65 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN U 70 " --> pdb=" O LYS U 66 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN U 74 " --> pdb=" O GLN U 70 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG U 77 " --> pdb=" O LYS U 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA U 83 " --> pdb=" O TYR U 79 " (cutoff:3.500A) Processing helix chain 'U' and resid 100 through 120 removed outlier: 3.723A pdb=" N LEU U 111 " --> pdb=" O ASP U 107 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU U 114 " --> pdb=" O GLY U 110 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU U 118 " --> pdb=" O GLU U 114 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG U 120 " --> pdb=" O ASN U 116 " (cutoff:3.500A) Processing helix chain 'U' and resid 121 through 123 No H-bonds generated for 'chain 'U' and resid 121 through 123' Processing helix chain 'U' and resid 124 through 135 removed outlier: 3.782A pdb=" N GLU U 130 " --> pdb=" O ASN U 126 " (cutoff:3.500A) Processing helix chain 'U' and resid 139 through 145 Processing helix chain 'U' and resid 162 through 170 Processing helix chain 'V' and resid 2 through 10 removed outlier: 3.816A pdb=" N LYS V 6 " --> pdb=" O ASP V 2 " (cutoff:3.500A) Processing helix chain 'V' and resid 12 through 56 removed outlier: 3.785A pdb=" N ARG V 18 " --> pdb=" O LYS V 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER V 22 " --> pdb=" O ARG V 18 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL V 23 " --> pdb=" O ARG V 19 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG V 25 " --> pdb=" O ARG V 21 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY V 28 " --> pdb=" O LEU V 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU V 32 " --> pdb=" O GLY V 28 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU V 38 " --> pdb=" O SER V 34 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL V 40 " --> pdb=" O ARG V 36 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU V 41 " --> pdb=" O GLU V 37 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS V 50 " --> pdb=" O GLN V 46 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER V 52 " --> pdb=" O LEU V 48 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS V 54 " --> pdb=" O LYS V 50 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 98 removed outlier: 4.036A pdb=" N LEU V 63 " --> pdb=" O ARG V 59 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS V 66 " --> pdb=" O ARG V 62 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU V 67 " --> pdb=" O LEU V 63 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR V 69 " --> pdb=" O ALA V 65 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG V 77 " --> pdb=" O LYS V 73 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR V 80 " --> pdb=" O ASP V 76 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA V 83 " --> pdb=" O TYR V 79 " (cutoff:3.500A) Processing helix chain 'V' and resid 100 through 119 removed outlier: 3.535A pdb=" N GLY V 110 " --> pdb=" O ALA V 106 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU V 111 " --> pdb=" O ASP V 107 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU V 114 " --> pdb=" O GLY V 110 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU V 118 " --> pdb=" O GLU V 114 " (cutoff:3.500A) Processing helix chain 'V' and resid 121 through 123 No H-bonds generated for 'chain 'V' and resid 121 through 123' Processing helix chain 'V' and resid 124 through 135 removed outlier: 3.680A pdb=" N GLU V 130 " --> pdb=" O ASN V 126 " (cutoff:3.500A) Processing helix chain 'V' and resid 139 through 146 removed outlier: 3.605A pdb=" N ASP V 146 " --> pdb=" O SER V 142 " (cutoff:3.500A) Processing helix chain 'V' and resid 162 through 170 removed outlier: 4.005A pdb=" N VAL V 167 " --> pdb=" O VAL V 163 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN V 168 " --> pdb=" O ASP V 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 10 removed outlier: 3.676A pdb=" N LYS W 6 " --> pdb=" O ASP W 2 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 56 removed outlier: 3.577A pdb=" N ARG W 18 " --> pdb=" O LYS W 14 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG W 25 " --> pdb=" O ARG W 21 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY W 28 " --> pdb=" O LEU W 24 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU W 32 " --> pdb=" O GLY W 28 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU W 38 " --> pdb=" O SER W 34 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL W 40 " --> pdb=" O ARG W 36 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU W 41 " --> pdb=" O GLU W 37 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS W 54 " --> pdb=" O LYS W 50 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS W 55 " --> pdb=" O LYS W 51 " (cutoff:3.500A) Processing helix chain 'W' and resid 57 through 98 removed outlier: 4.484A pdb=" N LEU W 63 " --> pdb=" O ARG W 59 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU W 67 " --> pdb=" O LEU W 63 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR W 69 " --> pdb=" O ALA W 65 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN W 70 " --> pdb=" O LYS W 66 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG W 77 " --> pdb=" O LYS W 73 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA W 83 " --> pdb=" O TYR W 79 " (cutoff:3.500A) Processing helix chain 'W' and resid 100 through 120 removed outlier: 3.537A pdb=" N ARG W 113 " --> pdb=" O ALA W 109 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU W 114 " --> pdb=" O GLY W 110 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU W 118 " --> pdb=" O GLU W 114 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG W 120 " --> pdb=" O ASN W 116 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 123 No H-bonds generated for 'chain 'W' and resid 121 through 123' Processing helix chain 'W' and resid 124 through 133 removed outlier: 3.634A pdb=" N GLU W 130 " --> pdb=" O ASN W 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 139 through 145 Processing helix chain 'W' and resid 146 through 150 removed outlier: 3.723A pdb=" N MET W 149 " --> pdb=" O ASP W 146 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU W 150 " --> pdb=" O ASP W 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 146 through 150' Processing helix chain 'W' and resid 162 through 170 Processing helix chain 'X' and resid 2 through 10 Processing helix chain 'X' and resid 12 through 56 removed outlier: 3.647A pdb=" N ARG X 18 " --> pdb=" O LYS X 14 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL X 23 " --> pdb=" O ARG X 19 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG X 25 " --> pdb=" O ARG X 21 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY X 28 " --> pdb=" O LEU X 24 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU X 32 " --> pdb=" O GLY X 28 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU X 38 " --> pdb=" O SER X 34 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL X 40 " --> pdb=" O ARG X 36 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU X 41 " --> pdb=" O GLU X 37 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN X 47 " --> pdb=" O ASN X 43 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS X 50 " --> pdb=" O GLN X 46 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS X 54 " --> pdb=" O LYS X 50 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS X 55 " --> pdb=" O LYS X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 57 through 98 removed outlier: 4.253A pdb=" N LEU X 63 " --> pdb=" O ARG X 59 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS X 66 " --> pdb=" O ARG X 62 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU X 67 " --> pdb=" O LEU X 63 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN X 70 " --> pdb=" O LYS X 66 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG X 77 " --> pdb=" O LYS X 73 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA X 83 " --> pdb=" O TYR X 79 " (cutoff:3.500A) Processing helix chain 'X' and resid 100 through 120 removed outlier: 3.535A pdb=" N SER X 108 " --> pdb=" O GLN X 104 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG X 113 " --> pdb=" O ALA X 109 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU X 114 " --> pdb=" O GLY X 110 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU X 118 " --> pdb=" O GLU X 114 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG X 120 " --> pdb=" O ASN X 116 " (cutoff:3.500A) Processing helix chain 'X' and resid 121 through 123 No H-bonds generated for 'chain 'X' and resid 121 through 123' Processing helix chain 'X' and resid 124 through 135 removed outlier: 3.713A pdb=" N GLU X 130 " --> pdb=" O ASN X 126 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU X 134 " --> pdb=" O GLU X 130 " (cutoff:3.500A) Processing helix chain 'X' and resid 139 through 145 Processing helix chain 'X' and resid 162 through 170 removed outlier: 3.616A pdb=" N VAL X 167 " --> pdb=" O VAL X 163 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS X 169 " --> pdb=" O GLU X 165 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 10 Processing helix chain 'Y' and resid 12 through 56 removed outlier: 3.709A pdb=" N ARG Y 18 " --> pdb=" O LYS Y 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL Y 23 " --> pdb=" O ARG Y 19 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG Y 25 " --> pdb=" O ARG Y 21 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY Y 28 " --> pdb=" O LEU Y 24 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU Y 32 " --> pdb=" O GLY Y 28 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU Y 38 " --> pdb=" O SER Y 34 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL Y 40 " --> pdb=" O ARG Y 36 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU Y 41 " --> pdb=" O GLU Y 37 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN Y 47 " --> pdb=" O ASN Y 43 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS Y 54 " --> pdb=" O LYS Y 50 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS Y 55 " --> pdb=" O LYS Y 51 " (cutoff:3.500A) Processing helix chain 'Y' and resid 57 through 98 removed outlier: 4.757A pdb=" N LEU Y 63 " --> pdb=" O ARG Y 59 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS Y 66 " --> pdb=" O ARG Y 62 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU Y 67 " --> pdb=" O LEU Y 63 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR Y 69 " --> pdb=" O ALA Y 65 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN Y 70 " --> pdb=" O LYS Y 66 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN Y 74 " --> pdb=" O GLN Y 70 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG Y 77 " --> pdb=" O LYS Y 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA Y 83 " --> pdb=" O TYR Y 79 " (cutoff:3.500A) Processing helix chain 'Y' and resid 100 through 120 removed outlier: 3.723A pdb=" N LEU Y 111 " --> pdb=" O ASP Y 107 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU Y 114 " --> pdb=" O GLY Y 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU Y 118 " --> pdb=" O GLU Y 114 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG Y 120 " --> pdb=" O ASN Y 116 " (cutoff:3.500A) Processing helix chain 'Y' and resid 121 through 123 No H-bonds generated for 'chain 'Y' and resid 121 through 123' Processing helix chain 'Y' and resid 124 through 135 removed outlier: 3.782A pdb=" N GLU Y 130 " --> pdb=" O ASN Y 126 " (cutoff:3.500A) Processing helix chain 'Y' and resid 139 through 145 Processing helix chain 'Y' and resid 162 through 170 Processing helix chain 'Z' and resid 2 through 10 removed outlier: 3.816A pdb=" N LYS Z 6 " --> pdb=" O ASP Z 2 " (cutoff:3.500A) Processing helix chain 'Z' and resid 12 through 56 removed outlier: 3.785A pdb=" N ARG Z 18 " --> pdb=" O LYS Z 14 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER Z 22 " --> pdb=" O ARG Z 18 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL Z 23 " --> pdb=" O ARG Z 19 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG Z 25 " --> pdb=" O ARG Z 21 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY Z 28 " --> pdb=" O LEU Z 24 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU Z 32 " --> pdb=" O GLY Z 28 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU Z 38 " --> pdb=" O SER Z 34 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL Z 40 " --> pdb=" O ARG Z 36 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU Z 41 " --> pdb=" O GLU Z 37 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS Z 50 " --> pdb=" O GLN Z 46 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER Z 52 " --> pdb=" O LEU Z 48 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS Z 54 " --> pdb=" O LYS Z 50 " (cutoff:3.500A) Processing helix chain 'Z' and resid 57 through 98 removed outlier: 4.035A pdb=" N LEU Z 63 " --> pdb=" O ARG Z 59 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS Z 66 " --> pdb=" O ARG Z 62 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU Z 67 " --> pdb=" O LEU Z 63 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR Z 69 " --> pdb=" O ALA Z 65 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG Z 77 " --> pdb=" O LYS Z 73 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR Z 80 " --> pdb=" O ASP Z 76 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA Z 83 " --> pdb=" O TYR Z 79 " (cutoff:3.500A) Processing helix chain 'Z' and resid 100 through 119 removed outlier: 3.535A pdb=" N GLY Z 110 " --> pdb=" O ALA Z 106 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU Z 111 " --> pdb=" O ASP Z 107 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU Z 114 " --> pdb=" O GLY Z 110 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU Z 118 " --> pdb=" O GLU Z 114 " (cutoff:3.500A) Processing helix chain 'Z' and resid 121 through 123 No H-bonds generated for 'chain 'Z' and resid 121 through 123' Processing helix chain 'Z' and resid 124 through 135 removed outlier: 3.681A pdb=" N GLU Z 130 " --> pdb=" O ASN Z 126 " (cutoff:3.500A) Processing helix chain 'Z' and resid 139 through 146 removed outlier: 3.605A pdb=" N ASP Z 146 " --> pdb=" O SER Z 142 " (cutoff:3.500A) Processing helix chain 'Z' and resid 162 through 170 removed outlier: 4.006A pdb=" N VAL Z 167 " --> pdb=" O VAL Z 163 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN Z 168 " --> pdb=" O ASP Z 164 " (cutoff:3.500A) Processing helix chain '0' and resid 2 through 10 removed outlier: 3.676A pdb=" N LYS 0 6 " --> pdb=" O ASP 0 2 " (cutoff:3.500A) Processing helix chain '0' and resid 12 through 56 removed outlier: 3.576A pdb=" N ARG 0 18 " --> pdb=" O LYS 0 14 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG 0 25 " --> pdb=" O ARG 0 21 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY 0 28 " --> pdb=" O LEU 0 24 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU 0 32 " --> pdb=" O GLY 0 28 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU 0 38 " --> pdb=" O SER 0 34 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL 0 40 " --> pdb=" O ARG 0 36 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU 0 41 " --> pdb=" O GLU 0 37 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS 0 54 " --> pdb=" O LYS 0 50 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS 0 55 " --> pdb=" O LYS 0 51 " (cutoff:3.500A) Processing helix chain '0' and resid 57 through 98 removed outlier: 4.484A pdb=" N LEU 0 63 " --> pdb=" O ARG 0 59 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU 0 67 " --> pdb=" O LEU 0 63 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR 0 69 " --> pdb=" O ALA 0 65 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN 0 70 " --> pdb=" O LYS 0 66 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG 0 77 " --> pdb=" O LYS 0 73 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA 0 83 " --> pdb=" O TYR 0 79 " (cutoff:3.500A) Processing helix chain '0' and resid 100 through 120 removed outlier: 3.536A pdb=" N ARG 0 113 " --> pdb=" O ALA 0 109 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU 0 114 " --> pdb=" O GLY 0 110 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU 0 118 " --> pdb=" O GLU 0 114 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG 0 120 " --> pdb=" O ASN 0 116 " (cutoff:3.500A) Processing helix chain '0' and resid 121 through 123 No H-bonds generated for 'chain '0' and resid 121 through 123' Processing helix chain '0' and resid 124 through 133 removed outlier: 3.634A pdb=" N GLU 0 130 " --> pdb=" O ASN 0 126 " (cutoff:3.500A) Processing helix chain '0' and resid 139 through 145 Processing helix chain '0' and resid 146 through 150 removed outlier: 3.722A pdb=" N MET 0 149 " --> pdb=" O ASP 0 146 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU 0 150 " --> pdb=" O ASP 0 147 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 146 through 150' Processing helix chain '0' and resid 162 through 170 Processing helix chain '1' and resid 2 through 10 Processing helix chain '1' and resid 12 through 56 removed outlier: 3.646A pdb=" N ARG 1 18 " --> pdb=" O LYS 1 14 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL 1 23 " --> pdb=" O ARG 1 19 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG 1 25 " --> pdb=" O ARG 1 21 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY 1 28 " --> pdb=" O LEU 1 24 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU 1 32 " --> pdb=" O GLY 1 28 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU 1 38 " --> pdb=" O SER 1 34 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL 1 40 " --> pdb=" O ARG 1 36 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU 1 41 " --> pdb=" O GLU 1 37 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN 1 47 " --> pdb=" O ASN 1 43 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS 1 50 " --> pdb=" O GLN 1 46 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS 1 54 " --> pdb=" O LYS 1 50 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS 1 55 " --> pdb=" O LYS 1 51 " (cutoff:3.500A) Processing helix chain '1' and resid 57 through 98 removed outlier: 4.254A pdb=" N LEU 1 63 " --> pdb=" O ARG 1 59 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS 1 66 " --> pdb=" O ARG 1 62 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU 1 67 " --> pdb=" O LEU 1 63 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN 1 70 " --> pdb=" O LYS 1 66 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG 1 77 " --> pdb=" O LYS 1 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA 1 83 " --> pdb=" O TYR 1 79 " (cutoff:3.500A) Processing helix chain '1' and resid 100 through 120 removed outlier: 3.536A pdb=" N SER 1 108 " --> pdb=" O GLN 1 104 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG 1 113 " --> pdb=" O ALA 1 109 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU 1 114 " --> pdb=" O GLY 1 110 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU 1 118 " --> pdb=" O GLU 1 114 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG 1 120 " --> pdb=" O ASN 1 116 " (cutoff:3.500A) Processing helix chain '1' and resid 121 through 123 No H-bonds generated for 'chain '1' and resid 121 through 123' Processing helix chain '1' and resid 124 through 135 removed outlier: 3.713A pdb=" N GLU 1 130 " --> pdb=" O ASN 1 126 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU 1 134 " --> pdb=" O GLU 1 130 " (cutoff:3.500A) Processing helix chain '1' and resid 139 through 145 Processing helix chain '1' and resid 162 through 170 removed outlier: 3.616A pdb=" N VAL 1 167 " --> pdb=" O VAL 1 163 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 10 Processing helix chain '2' and resid 12 through 56 removed outlier: 3.709A pdb=" N ARG 2 18 " --> pdb=" O LYS 2 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL 2 23 " --> pdb=" O ARG 2 19 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG 2 25 " --> pdb=" O ARG 2 21 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY 2 28 " --> pdb=" O LEU 2 24 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU 2 32 " --> pdb=" O GLY 2 28 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU 2 38 " --> pdb=" O SER 2 34 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL 2 40 " --> pdb=" O ARG 2 36 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU 2 41 " --> pdb=" O GLU 2 37 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN 2 47 " --> pdb=" O ASN 2 43 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS 2 54 " --> pdb=" O LYS 2 50 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS 2 55 " --> pdb=" O LYS 2 51 " (cutoff:3.500A) Processing helix chain '2' and resid 57 through 98 removed outlier: 4.757A pdb=" N LEU 2 63 " --> pdb=" O ARG 2 59 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS 2 66 " --> pdb=" O ARG 2 62 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU 2 67 " --> pdb=" O LEU 2 63 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR 2 69 " --> pdb=" O ALA 2 65 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN 2 70 " --> pdb=" O LYS 2 66 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN 2 74 " --> pdb=" O GLN 2 70 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG 2 77 " --> pdb=" O LYS 2 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA 2 83 " --> pdb=" O TYR 2 79 " (cutoff:3.500A) Processing helix chain '2' and resid 100 through 120 removed outlier: 3.722A pdb=" N LEU 2 111 " --> pdb=" O ASP 2 107 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU 2 114 " --> pdb=" O GLY 2 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU 2 118 " --> pdb=" O GLU 2 114 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG 2 120 " --> pdb=" O ASN 2 116 " (cutoff:3.500A) Processing helix chain '2' and resid 121 through 123 No H-bonds generated for 'chain '2' and resid 121 through 123' Processing helix chain '2' and resid 124 through 135 removed outlier: 3.782A pdb=" N GLU 2 130 " --> pdb=" O ASN 2 126 " (cutoff:3.500A) Processing helix chain '2' and resid 139 through 145 Processing helix chain '2' and resid 162 through 170 Processing helix chain '3' and resid 2 through 10 removed outlier: 3.816A pdb=" N LYS 3 6 " --> pdb=" O ASP 3 2 " (cutoff:3.500A) Processing helix chain '3' and resid 12 through 56 removed outlier: 3.784A pdb=" N ARG 3 18 " --> pdb=" O LYS 3 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER 3 22 " --> pdb=" O ARG 3 18 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL 3 23 " --> pdb=" O ARG 3 19 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG 3 25 " --> pdb=" O ARG 3 21 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY 3 28 " --> pdb=" O LEU 3 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU 3 32 " --> pdb=" O GLY 3 28 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU 3 38 " --> pdb=" O SER 3 34 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL 3 40 " --> pdb=" O ARG 3 36 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU 3 41 " --> pdb=" O GLU 3 37 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS 3 50 " --> pdb=" O GLN 3 46 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER 3 52 " --> pdb=" O LEU 3 48 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS 3 54 " --> pdb=" O LYS 3 50 " (cutoff:3.500A) Processing helix chain '3' and resid 57 through 98 removed outlier: 4.036A pdb=" N LEU 3 63 " --> pdb=" O ARG 3 59 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS 3 66 " --> pdb=" O ARG 3 62 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU 3 67 " --> pdb=" O LEU 3 63 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR 3 69 " --> pdb=" O ALA 3 65 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG 3 77 " --> pdb=" O LYS 3 73 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR 3 80 " --> pdb=" O ASP 3 76 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA 3 83 " --> pdb=" O TYR 3 79 " (cutoff:3.500A) Processing helix chain '3' and resid 100 through 119 removed outlier: 3.535A pdb=" N GLY 3 110 " --> pdb=" O ALA 3 106 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU 3 111 " --> pdb=" O ASP 3 107 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU 3 114 " --> pdb=" O GLY 3 110 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU 3 118 " --> pdb=" O GLU 3 114 " (cutoff:3.500A) Processing helix chain '3' and resid 121 through 123 No H-bonds generated for 'chain '3' and resid 121 through 123' Processing helix chain '3' and resid 124 through 135 removed outlier: 3.681A pdb=" N GLU 3 130 " --> pdb=" O ASN 3 126 " (cutoff:3.500A) Processing helix chain '3' and resid 139 through 146 removed outlier: 3.605A pdb=" N ASP 3 146 " --> pdb=" O SER 3 142 " (cutoff:3.500A) Processing helix chain '3' and resid 162 through 170 removed outlier: 4.006A pdb=" N VAL 3 167 " --> pdb=" O VAL 3 163 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN 3 168 " --> pdb=" O ASP 3 164 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 10 removed outlier: 3.676A pdb=" N LYS 4 6 " --> pdb=" O ASP 4 2 " (cutoff:3.500A) Processing helix chain '4' and resid 12 through 56 removed outlier: 3.576A pdb=" N ARG 4 18 " --> pdb=" O LYS 4 14 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG 4 25 " --> pdb=" O ARG 4 21 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY 4 28 " --> pdb=" O LEU 4 24 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU 4 32 " --> pdb=" O GLY 4 28 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU 4 38 " --> pdb=" O SER 4 34 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL 4 40 " --> pdb=" O ARG 4 36 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU 4 41 " --> pdb=" O GLU 4 37 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS 4 54 " --> pdb=" O LYS 4 50 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS 4 55 " --> pdb=" O LYS 4 51 " (cutoff:3.500A) Processing helix chain '4' and resid 57 through 98 removed outlier: 4.484A pdb=" N LEU 4 63 " --> pdb=" O ARG 4 59 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU 4 67 " --> pdb=" O LEU 4 63 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR 4 69 " --> pdb=" O ALA 4 65 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN 4 70 " --> pdb=" O LYS 4 66 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG 4 77 " --> pdb=" O LYS 4 73 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA 4 83 " --> pdb=" O TYR 4 79 " (cutoff:3.500A) Processing helix chain '4' and resid 100 through 120 removed outlier: 3.537A pdb=" N ARG 4 113 " --> pdb=" O ALA 4 109 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU 4 114 " --> pdb=" O GLY 4 110 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU 4 118 " --> pdb=" O GLU 4 114 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG 4 120 " --> pdb=" O ASN 4 116 " (cutoff:3.500A) Processing helix chain '4' and resid 121 through 123 No H-bonds generated for 'chain '4' and resid 121 through 123' Processing helix chain '4' and resid 124 through 133 removed outlier: 3.634A pdb=" N GLU 4 130 " --> pdb=" O ASN 4 126 " (cutoff:3.500A) Processing helix chain '4' and resid 139 through 145 Processing helix chain '4' and resid 146 through 150 removed outlier: 3.723A pdb=" N MET 4 149 " --> pdb=" O ASP 4 146 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU 4 150 " --> pdb=" O ASP 4 147 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 146 through 150' Processing helix chain '4' and resid 162 through 170 Processing helix chain '5' and resid 2 through 10 Processing helix chain '5' and resid 12 through 56 removed outlier: 3.646A pdb=" N ARG 5 18 " --> pdb=" O LYS 5 14 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL 5 23 " --> pdb=" O ARG 5 19 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG 5 25 " --> pdb=" O ARG 5 21 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY 5 28 " --> pdb=" O LEU 5 24 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU 5 32 " --> pdb=" O GLY 5 28 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU 5 38 " --> pdb=" O SER 5 34 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL 5 40 " --> pdb=" O ARG 5 36 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN 5 47 " --> pdb=" O ASN 5 43 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS 5 50 " --> pdb=" O GLN 5 46 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS 5 54 " --> pdb=" O LYS 5 50 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS 5 55 " --> pdb=" O LYS 5 51 " (cutoff:3.500A) Processing helix chain '5' and resid 57 through 98 removed outlier: 4.253A pdb=" N LEU 5 63 " --> pdb=" O ARG 5 59 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS 5 66 " --> pdb=" O ARG 5 62 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU 5 67 " --> pdb=" O LEU 5 63 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN 5 70 " --> pdb=" O LYS 5 66 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG 5 77 " --> pdb=" O LYS 5 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA 5 83 " --> pdb=" O TYR 5 79 " (cutoff:3.500A) Processing helix chain '5' and resid 100 through 120 removed outlier: 3.535A pdb=" N SER 5 108 " --> pdb=" O GLN 5 104 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG 5 113 " --> pdb=" O ALA 5 109 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU 5 114 " --> pdb=" O GLY 5 110 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU 5 118 " --> pdb=" O GLU 5 114 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG 5 120 " --> pdb=" O ASN 5 116 " (cutoff:3.500A) Processing helix chain '5' and resid 121 through 123 No H-bonds generated for 'chain '5' and resid 121 through 123' Processing helix chain '5' and resid 124 through 135 removed outlier: 3.713A pdb=" N GLU 5 130 " --> pdb=" O ASN 5 126 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU 5 134 " --> pdb=" O GLU 5 130 " (cutoff:3.500A) Processing helix chain '5' and resid 139 through 145 Processing helix chain '5' and resid 162 through 170 removed outlier: 3.616A pdb=" N VAL 5 167 " --> pdb=" O VAL 5 163 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS 5 169 " --> pdb=" O GLU 5 165 " (cutoff:3.500A) Processing helix chain '6' and resid 2 through 10 Processing helix chain '6' and resid 12 through 56 removed outlier: 3.709A pdb=" N ARG 6 18 " --> pdb=" O LYS 6 14 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL 6 23 " --> pdb=" O ARG 6 19 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG 6 25 " --> pdb=" O ARG 6 21 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY 6 28 " --> pdb=" O LEU 6 24 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU 6 32 " --> pdb=" O GLY 6 28 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU 6 38 " --> pdb=" O SER 6 34 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL 6 40 " --> pdb=" O ARG 6 36 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU 6 41 " --> pdb=" O GLU 6 37 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN 6 47 " --> pdb=" O ASN 6 43 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS 6 54 " --> pdb=" O LYS 6 50 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS 6 55 " --> pdb=" O LYS 6 51 " (cutoff:3.500A) Processing helix chain '6' and resid 57 through 98 removed outlier: 4.757A pdb=" N LEU 6 63 " --> pdb=" O ARG 6 59 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS 6 66 " --> pdb=" O ARG 6 62 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU 6 67 " --> pdb=" O LEU 6 63 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR 6 69 " --> pdb=" O ALA 6 65 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN 6 70 " --> pdb=" O LYS 6 66 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN 6 74 " --> pdb=" O GLN 6 70 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG 6 77 " --> pdb=" O LYS 6 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA 6 83 " --> pdb=" O TYR 6 79 " (cutoff:3.500A) Processing helix chain '6' and resid 100 through 120 removed outlier: 3.723A pdb=" N LEU 6 111 " --> pdb=" O ASP 6 107 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU 6 114 " --> pdb=" O GLY 6 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU 6 118 " --> pdb=" O GLU 6 114 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG 6 120 " --> pdb=" O ASN 6 116 " (cutoff:3.500A) Processing helix chain '6' and resid 121 through 123 No H-bonds generated for 'chain '6' and resid 121 through 123' Processing helix chain '6' and resid 124 through 135 removed outlier: 3.782A pdb=" N GLU 6 130 " --> pdb=" O ASN 6 126 " (cutoff:3.500A) Processing helix chain '6' and resid 139 through 145 Processing helix chain '6' and resid 162 through 170 Processing helix chain '7' and resid 2 through 10 removed outlier: 3.816A pdb=" N LYS 7 6 " --> pdb=" O ASP 7 2 " (cutoff:3.500A) Processing helix chain '7' and resid 12 through 56 removed outlier: 3.785A pdb=" N ARG 7 18 " --> pdb=" O LYS 7 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER 7 22 " --> pdb=" O ARG 7 18 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL 7 23 " --> pdb=" O ARG 7 19 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG 7 25 " --> pdb=" O ARG 7 21 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY 7 28 " --> pdb=" O LEU 7 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU 7 32 " --> pdb=" O GLY 7 28 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU 7 38 " --> pdb=" O SER 7 34 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL 7 40 " --> pdb=" O ARG 7 36 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU 7 41 " --> pdb=" O GLU 7 37 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS 7 50 " --> pdb=" O GLN 7 46 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER 7 52 " --> pdb=" O LEU 7 48 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS 7 54 " --> pdb=" O LYS 7 50 " (cutoff:3.500A) Processing helix chain '7' and resid 57 through 98 removed outlier: 4.037A pdb=" N LEU 7 63 " --> pdb=" O ARG 7 59 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS 7 66 " --> pdb=" O ARG 7 62 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU 7 67 " --> pdb=" O LEU 7 63 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR 7 69 " --> pdb=" O ALA 7 65 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG 7 77 " --> pdb=" O LYS 7 73 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR 7 80 " --> pdb=" O ASP 7 76 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA 7 83 " --> pdb=" O TYR 7 79 " (cutoff:3.500A) Processing helix chain '7' and resid 100 through 119 removed outlier: 3.535A pdb=" N GLY 7 110 " --> pdb=" O ALA 7 106 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU 7 111 " --> pdb=" O ASP 7 107 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU 7 114 " --> pdb=" O GLY 7 110 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU 7 118 " --> pdb=" O GLU 7 114 " (cutoff:3.500A) Processing helix chain '7' and resid 121 through 123 No H-bonds generated for 'chain '7' and resid 121 through 123' Processing helix chain '7' and resid 124 through 135 removed outlier: 3.681A pdb=" N GLU 7 130 " --> pdb=" O ASN 7 126 " (cutoff:3.500A) Processing helix chain '7' and resid 139 through 146 removed outlier: 3.605A pdb=" N ASP 7 146 " --> pdb=" O SER 7 142 " (cutoff:3.500A) Processing helix chain '7' and resid 162 through 170 removed outlier: 4.006A pdb=" N VAL 7 167 " --> pdb=" O VAL 7 163 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN 7 168 " --> pdb=" O ASP 7 164 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 10 removed outlier: 3.676A pdb=" N LYS 8 6 " --> pdb=" O ASP 8 2 " (cutoff:3.500A) Processing helix chain '8' and resid 12 through 56 removed outlier: 3.576A pdb=" N ARG 8 18 " --> pdb=" O LYS 8 14 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG 8 25 " --> pdb=" O ARG 8 21 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY 8 28 " --> pdb=" O LEU 8 24 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU 8 32 " --> pdb=" O GLY 8 28 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU 8 38 " --> pdb=" O SER 8 34 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL 8 40 " --> pdb=" O ARG 8 36 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU 8 41 " --> pdb=" O GLU 8 37 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS 8 54 " --> pdb=" O LYS 8 50 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS 8 55 " --> pdb=" O LYS 8 51 " (cutoff:3.500A) Processing helix chain '8' and resid 57 through 98 removed outlier: 4.483A pdb=" N LEU 8 63 " --> pdb=" O ARG 8 59 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU 8 67 " --> pdb=" O LEU 8 63 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR 8 69 " --> pdb=" O ALA 8 65 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN 8 70 " --> pdb=" O LYS 8 66 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG 8 77 " --> pdb=" O LYS 8 73 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA 8 83 " --> pdb=" O TYR 8 79 " (cutoff:3.500A) Processing helix chain '8' and resid 100 through 120 removed outlier: 3.536A pdb=" N ARG 8 113 " --> pdb=" O ALA 8 109 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU 8 114 " --> pdb=" O GLY 8 110 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU 8 118 " --> pdb=" O GLU 8 114 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG 8 120 " --> pdb=" O ASN 8 116 " (cutoff:3.500A) Processing helix chain '8' and resid 121 through 123 No H-bonds generated for 'chain '8' and resid 121 through 123' Processing helix chain '8' and resid 124 through 133 removed outlier: 3.633A pdb=" N GLU 8 130 " --> pdb=" O ASN 8 126 " (cutoff:3.500A) Processing helix chain '8' and resid 139 through 145 Processing helix chain '8' and resid 146 through 150 removed outlier: 3.723A pdb=" N MET 8 149 " --> pdb=" O ASP 8 146 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU 8 150 " --> pdb=" O ASP 8 147 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 146 through 150' Processing helix chain '8' and resid 162 through 170 Processing helix chain '9' and resid 2 through 10 Processing helix chain '9' and resid 12 through 56 removed outlier: 3.646A pdb=" N ARG 9 18 " --> pdb=" O LYS 9 14 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL 9 23 " --> pdb=" O ARG 9 19 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG 9 25 " --> pdb=" O ARG 9 21 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY 9 28 " --> pdb=" O LEU 9 24 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU 9 32 " --> pdb=" O GLY 9 28 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU 9 38 " --> pdb=" O SER 9 34 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL 9 40 " --> pdb=" O ARG 9 36 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU 9 41 " --> pdb=" O GLU 9 37 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN 9 47 " --> pdb=" O ASN 9 43 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS 9 50 " --> pdb=" O GLN 9 46 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS 9 54 " --> pdb=" O LYS 9 50 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS 9 55 " --> pdb=" O LYS 9 51 " (cutoff:3.500A) Processing helix chain '9' and resid 57 through 98 removed outlier: 4.254A pdb=" N LEU 9 63 " --> pdb=" O ARG 9 59 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS 9 66 " --> pdb=" O ARG 9 62 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU 9 67 " --> pdb=" O LEU 9 63 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN 9 70 " --> pdb=" O LYS 9 66 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG 9 77 " --> pdb=" O LYS 9 73 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA 9 83 " --> pdb=" O TYR 9 79 " (cutoff:3.500A) Processing helix chain '9' and resid 100 through 120 removed outlier: 3.535A pdb=" N SER 9 108 " --> pdb=" O GLN 9 104 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG 9 113 " --> pdb=" O ALA 9 109 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU 9 114 " --> pdb=" O GLY 9 110 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU 9 118 " --> pdb=" O GLU 9 114 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG 9 120 " --> pdb=" O ASN 9 116 " (cutoff:3.500A) Processing helix chain '9' and resid 121 through 123 No H-bonds generated for 'chain '9' and resid 121 through 123' Processing helix chain '9' and resid 124 through 135 removed outlier: 3.713A pdb=" N GLU 9 130 " --> pdb=" O ASN 9 126 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU 9 134 " --> pdb=" O GLU 9 130 " (cutoff:3.500A) Processing helix chain '9' and resid 139 through 145 Processing helix chain '9' and resid 162 through 170 removed outlier: 3.616A pdb=" N VAL 9 167 " --> pdb=" O VAL 9 163 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS 9 169 " --> pdb=" O GLU 9 165 " (cutoff:3.500A) 3294 hydrogen bonds defined for protein. 9882 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: 14.71 Time building geometry restraints manager: 11.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 12269 1.33 - 1.45: 7526 1.45 - 1.57: 29453 1.57 - 1.69: 0 1.69 - 1.80: 792 Bond restraints: 50040 Sorted by residual: bond pdb=" CG1 ILE O 140 " pdb=" CD1 ILE O 140 " ideal model delta sigma weight residual 1.513 1.418 0.095 3.90e-02 6.57e+02 5.94e+00 bond pdb=" CG1 ILE 4 140 " pdb=" CD1 ILE 4 140 " ideal model delta sigma weight residual 1.513 1.418 0.095 3.90e-02 6.57e+02 5.93e+00 bond pdb=" CG1 ILE K 140 " pdb=" CD1 ILE K 140 " ideal model delta sigma weight residual 1.513 1.418 0.095 3.90e-02 6.57e+02 5.92e+00 bond pdb=" CG1 ILE I 140 " pdb=" CD1 ILE I 140 " ideal model delta sigma weight residual 1.513 1.418 0.095 3.90e-02 6.57e+02 5.90e+00 bond pdb=" CG1 ILE 8 140 " pdb=" CD1 ILE 8 140 " ideal model delta sigma weight residual 1.513 1.418 0.095 3.90e-02 6.57e+02 5.90e+00 ... (remaining 50035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 62183 1.75 - 3.50: 4047 3.50 - 5.25: 419 5.25 - 7.00: 86 7.00 - 8.75: 117 Bond angle restraints: 66852 Sorted by residual: angle pdb=" C ARG 1 97 " pdb=" N MET 1 98 " pdb=" CA MET 1 98 " ideal model delta sigma weight residual 121.54 129.45 -7.91 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C ARG T 97 " pdb=" N MET T 98 " pdb=" CA MET T 98 " ideal model delta sigma weight residual 121.54 129.44 -7.90 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C ARG H 97 " pdb=" N MET H 98 " pdb=" CA MET H 98 " ideal model delta sigma weight residual 121.54 129.43 -7.89 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C ARG D 97 " pdb=" N MET D 98 " pdb=" CA MET D 98 " ideal model delta sigma weight residual 121.54 129.42 -7.88 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C ARG P 97 " pdb=" N MET P 98 " pdb=" CA MET P 98 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 ... (remaining 66847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.10: 29034 15.10 - 30.21: 2151 30.21 - 45.31: 981 45.31 - 60.41: 90 60.41 - 75.52: 180 Dihedral angle restraints: 32436 sinusoidal: 14364 harmonic: 18072 Sorted by residual: dihedral pdb=" CA ARG 3 21 " pdb=" C ARG 3 21 " pdb=" N SER 3 22 " pdb=" CA SER 3 22 " ideal model delta harmonic sigma weight residual 180.00 159.12 20.88 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ARG J 21 " pdb=" C ARG J 21 " pdb=" N SER J 22 " pdb=" CA SER J 22 " ideal model delta harmonic sigma weight residual 180.00 159.14 20.86 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ARG N 21 " pdb=" C ARG N 21 " pdb=" N SER N 22 " pdb=" CA SER N 22 " ideal model delta harmonic sigma weight residual 180.00 159.15 20.85 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 32433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 4701 0.050 - 0.100: 2443 0.100 - 0.150: 350 0.150 - 0.200: 39 0.200 - 0.250: 27 Chirality restraints: 7560 Sorted by residual: chirality pdb=" CG LEU I 135 " pdb=" CB LEU I 135 " pdb=" CD1 LEU I 135 " pdb=" CD2 LEU I 135 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CG LEU Q 135 " pdb=" CB LEU Q 135 " pdb=" CD1 LEU Q 135 " pdb=" CD2 LEU Q 135 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CG LEU Y 135 " pdb=" CB LEU Y 135 " pdb=" CD1 LEU Y 135 " pdb=" CD2 LEU Y 135 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 7557 not shown) Planarity restraints: 8676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET T 98 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.12e+00 pdb=" C MET T 98 " 0.046 2.00e-02 2.50e+03 pdb=" O MET T 98 " -0.017 2.00e-02 2.50e+03 pdb=" N ASN T 99 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET 9 98 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.10e+00 pdb=" C MET 9 98 " 0.046 2.00e-02 2.50e+03 pdb=" O MET 9 98 " -0.017 2.00e-02 2.50e+03 pdb=" N ASN 9 99 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 98 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.09e+00 pdb=" C MET D 98 " 0.046 2.00e-02 2.50e+03 pdb=" O MET D 98 " -0.017 2.00e-02 2.50e+03 pdb=" N ASN D 99 " -0.016 2.00e-02 2.50e+03 ... (remaining 8673 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 14773 2.83 - 3.34: 48001 3.34 - 3.86: 77444 3.86 - 4.38: 93135 4.38 - 4.90: 155092 Nonbonded interactions: 388445 Sorted by model distance: nonbonded pdb=" O LEU Q 35 " pdb=" OG1 THR Q 39 " model vdw 2.307 3.040 nonbonded pdb=" O LEU 6 35 " pdb=" OG1 THR 6 39 " model vdw 2.307 3.040 nonbonded pdb=" O LEU M 35 " pdb=" OG1 THR M 39 " model vdw 2.307 3.040 nonbonded pdb=" O LEU 2 35 " pdb=" OG1 THR 2 39 " model vdw 2.307 3.040 nonbonded pdb=" O LEU E 35 " pdb=" OG1 THR E 39 " model vdw 2.307 3.040 ... (remaining 388440 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 '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = 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 'Q' 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' } 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.690 Check model and map are aligned: 0.300 Set scattering table: 0.380 Process input model: 81.930 Find NCS groups from input model: 1.530 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: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 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 0.095 50040 Z= 0.492 Angle : 0.979 8.751 66852 Z= 0.537 Chirality : 0.055 0.250 7560 Planarity : 0.004 0.027 8676 Dihedral : 14.139 75.518 20628 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 1.19 % Allowed : 2.38 % Favored : 96.43 % Rotamer: Outliers : 0.64 % Allowed : 4.81 % Favored : 94.55 % 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: -6.47 (0.06), residues: 6048 helix: -4.27 (0.04), residues: 5076 sheet: None (None), residues: 0 loop : -2.20 (0.16), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP W 9 TYR 0.020 0.002 TYR L 64 ARG 0.010 0.001 ARG X 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1721 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1685 time to evaluate : 4.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 LYS cc_start: 0.9131 (mmmt) cc_final: 0.8892 (mmmm) REVERT: B 36 ARG cc_start: 0.7845 (ttm110) cc_final: 0.7455 (mtm110) REVERT: B 114 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7891 (mt-10) REVERT: B 147 ASP cc_start: 0.8501 (t70) cc_final: 0.8044 (t70) REVERT: A 112 MET cc_start: 0.8700 (mmp) cc_final: 0.8356 (mmp) REVERT: A 147 ASP cc_start: 0.7729 (t70) cc_final: 0.7477 (m-30) REVERT: C 5 LYS cc_start: 0.8889 (ttmp) cc_final: 0.8637 (ttpt) REVERT: C 36 ARG cc_start: 0.8508 (ttm110) cc_final: 0.8225 (mtm110) REVERT: C 37 GLU cc_start: 0.8119 (pp20) cc_final: 0.7902 (pp20) REVERT: C 69 TYR cc_start: 0.7945 (t80) cc_final: 0.7270 (t80) REVERT: C 70 GLN cc_start: 0.8453 (mm110) cc_final: 0.8209 (mm110) REVERT: C 72 ASN cc_start: 0.8043 (m110) cc_final: 0.7837 (m-40) REVERT: C 73 LYS cc_start: 0.8571 (tttt) cc_final: 0.8215 (tptt) REVERT: C 98 MET cc_start: 0.8125 (tpp) cc_final: 0.7919 (tpt) REVERT: D 1 MET cc_start: 0.5701 (tpp) cc_final: 0.5231 (tpt) REVERT: D 67 GLU cc_start: 0.6239 (pp20) cc_final: 0.5300 (mp0) REVERT: D 123 GLN cc_start: 0.8311 (mm-40) cc_final: 0.7937 (mp10) REVERT: D 144 MET cc_start: 0.8891 (mtt) cc_final: 0.8659 (mtm) REVERT: D 147 ASP cc_start: 0.8486 (t70) cc_final: 0.8169 (t70) REVERT: E 14 LYS cc_start: 0.9056 (mmmt) cc_final: 0.8762 (mmmm) REVERT: E 33 LYS cc_start: 0.7996 (tmmm) cc_final: 0.7522 (tptt) REVERT: E 36 ARG cc_start: 0.7956 (ttm110) cc_final: 0.7707 (mtm110) REVERT: F 124 LEU cc_start: 0.8484 (pp) cc_final: 0.8058 (pp) REVERT: G 5 LYS cc_start: 0.8828 (ttmp) cc_final: 0.8477 (ttpt) REVERT: G 6 LYS cc_start: 0.9129 (mttt) cc_final: 0.7553 (tttm) REVERT: G 36 ARG cc_start: 0.8593 (ttm110) cc_final: 0.8370 (mtm110) REVERT: G 124 LEU cc_start: 0.8632 (pp) cc_final: 0.8394 (pt) REVERT: G 125 ARG cc_start: 0.8122 (ttt-90) cc_final: 0.7830 (ttt-90) REVERT: G 146 ASP cc_start: 0.7629 (p0) cc_final: 0.7370 (p0) REVERT: H 1 MET cc_start: 0.5390 (tpp) cc_final: 0.4705 (tpt) REVERT: H 32 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8006 (mm-30) REVERT: H 76 ASP cc_start: 0.8038 (m-30) cc_final: 0.7797 (m-30) REVERT: H 82 ARG cc_start: 0.8854 (tmm-80) cc_final: 0.8515 (ttp80) REVERT: I 1 MET cc_start: 0.5956 (tpp) cc_final: 0.5639 (tpt) REVERT: I 30 ASN cc_start: 0.8546 (m-40) cc_final: 0.8331 (m-40) REVERT: I 33 LYS cc_start: 0.8025 (tmmm) cc_final: 0.7746 (tptt) REVERT: I 36 ARG cc_start: 0.8018 (ttm110) cc_final: 0.7801 (mtm-85) REVERT: I 87 SER cc_start: 0.9053 (t) cc_final: 0.8624 (p) REVERT: I 134 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7863 (mm-30) REVERT: I 147 ASP cc_start: 0.8288 (t70) cc_final: 0.7757 (t70) REVERT: K 5 LYS cc_start: 0.8916 (ttmp) cc_final: 0.8683 (ttpt) REVERT: K 36 ARG cc_start: 0.8557 (ttm110) cc_final: 0.8272 (mtm110) REVERT: K 37 GLU cc_start: 0.8285 (pp20) cc_final: 0.8016 (pp20) REVERT: K 70 GLN cc_start: 0.8561 (mm110) cc_final: 0.8080 (mm110) REVERT: L 123 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8202 (mm-40) REVERT: L 124 LEU cc_start: 0.9034 (pp) cc_final: 0.8765 (pp) REVERT: M 1 MET cc_start: 0.6082 (tpp) cc_final: 0.5751 (tpp) REVERT: M 14 LYS cc_start: 0.9115 (mmmt) cc_final: 0.8829 (mmmm) REVERT: M 27 ASN cc_start: 0.8648 (m110) cc_final: 0.8345 (m110) REVERT: M 36 ARG cc_start: 0.7890 (ttm110) cc_final: 0.7484 (mtm110) REVERT: M 37 GLU cc_start: 0.8379 (pp20) cc_final: 0.8177 (pp20) REVERT: M 87 SER cc_start: 0.9025 (t) cc_final: 0.8719 (p) REVERT: N 86 ASP cc_start: 0.7977 (m-30) cc_final: 0.7478 (m-30) REVERT: N 146 ASP cc_start: 0.7661 (p0) cc_final: 0.7439 (p0) REVERT: N 147 ASP cc_start: 0.7795 (t70) cc_final: 0.7548 (t70) REVERT: O 37 GLU cc_start: 0.8267 (pp20) cc_final: 0.7964 (pp20) REVERT: O 70 GLN cc_start: 0.8504 (mm110) cc_final: 0.8044 (mm110) REVERT: O 79 TYR cc_start: 0.8981 (t80) cc_final: 0.8773 (t80) REVERT: P 107 ASP cc_start: 0.8075 (m-30) cc_final: 0.7812 (m-30) REVERT: Q 36 ARG cc_start: 0.7971 (ttm110) cc_final: 0.7598 (mtm110) REVERT: Q 87 SER cc_start: 0.9010 (t) cc_final: 0.8496 (p) REVERT: Q 147 ASP cc_start: 0.8372 (t70) cc_final: 0.7728 (t70) REVERT: R 80 THR cc_start: 0.9034 (m) cc_final: 0.8816 (p) REVERT: R 124 LEU cc_start: 0.8537 (pp) cc_final: 0.8239 (pp) REVERT: S 36 ARG cc_start: 0.8488 (ttm110) cc_final: 0.8077 (ttm110) REVERT: S 37 GLU cc_start: 0.8226 (pp20) cc_final: 0.7925 (pp20) REVERT: S 69 TYR cc_start: 0.8246 (t80) cc_final: 0.7654 (t80) REVERT: S 70 GLN cc_start: 0.8523 (mm110) cc_final: 0.8124 (mm110) REVERT: S 73 LYS cc_start: 0.8731 (tttt) cc_final: 0.8341 (tptt) REVERT: S 124 LEU cc_start: 0.8597 (pp) cc_final: 0.8396 (pt) REVERT: T 1 MET cc_start: 0.5469 (tpp) cc_final: 0.4998 (tpt) REVERT: T 98 MET cc_start: 0.8454 (tpp) cc_final: 0.8003 (tpp) REVERT: T 123 GLN cc_start: 0.8416 (mm-40) cc_final: 0.8121 (mp10) REVERT: T 124 LEU cc_start: 0.8971 (pp) cc_final: 0.8686 (pp) REVERT: T 136 MET cc_start: 0.8634 (mtp) cc_final: 0.8403 (mtp) REVERT: T 147 ASP cc_start: 0.8429 (t70) cc_final: 0.7672 (t0) REVERT: U 36 ARG cc_start: 0.7976 (ttm110) cc_final: 0.7504 (mtm110) REVERT: U 37 GLU cc_start: 0.8324 (pp20) cc_final: 0.8099 (pp20) REVERT: U 87 SER cc_start: 0.8952 (t) cc_final: 0.8518 (p) REVERT: U 98 MET cc_start: 0.8436 (tpp) cc_final: 0.8039 (tpt) REVERT: U 147 ASP cc_start: 0.8438 (t70) cc_final: 0.7653 (t70) REVERT: W 36 ARG cc_start: 0.8392 (ttm110) cc_final: 0.8147 (mtm110) REVERT: W 37 GLU cc_start: 0.8162 (pp20) cc_final: 0.7907 (pp20) REVERT: W 70 GLN cc_start: 0.8440 (mm110) cc_final: 0.8203 (mm110) REVERT: X 79 TYR cc_start: 0.8776 (t80) cc_final: 0.8546 (t80) REVERT: X 123 GLN cc_start: 0.8353 (mm-40) cc_final: 0.8044 (mp10) REVERT: X 136 MET cc_start: 0.8635 (mtp) cc_final: 0.8283 (mtp) REVERT: Y 1 MET cc_start: 0.5934 (tpp) cc_final: 0.5501 (tpt) REVERT: Y 87 SER cc_start: 0.8988 (t) cc_final: 0.8559 (p) REVERT: Y 136 MET cc_start: 0.8627 (mtp) cc_final: 0.8273 (mtp) REVERT: Z 82 ARG cc_start: 0.8042 (tmm-80) cc_final: 0.7705 (ttp-110) REVERT: Z 86 ASP cc_start: 0.7877 (m-30) cc_final: 0.7491 (m-30) REVERT: Z 124 LEU cc_start: 0.8488 (pp) cc_final: 0.8030 (pp) REVERT: 0 5 LYS cc_start: 0.8894 (ttmp) cc_final: 0.8511 (tttt) REVERT: 0 36 ARG cc_start: 0.8553 (ttm110) cc_final: 0.8348 (mtm110) REVERT: 0 37 GLU cc_start: 0.8273 (pp20) cc_final: 0.7993 (pp20) REVERT: 0 69 TYR cc_start: 0.8040 (t80) cc_final: 0.7675 (t80) REVERT: 0 73 LYS cc_start: 0.8639 (tttt) cc_final: 0.8331 (ptmt) REVERT: 1 107 ASP cc_start: 0.8111 (m-30) cc_final: 0.7788 (m-30) REVERT: 2 27 ASN cc_start: 0.8727 (m110) cc_final: 0.8520 (m110) REVERT: 2 30 ASN cc_start: 0.8491 (m-40) cc_final: 0.8154 (m-40) REVERT: 2 33 LYS cc_start: 0.7939 (tmmm) cc_final: 0.7627 (tptt) REVERT: 2 36 ARG cc_start: 0.7927 (ttm110) cc_final: 0.7579 (mtm110) REVERT: 2 76 ASP cc_start: 0.8236 (m-30) cc_final: 0.7885 (m-30) REVERT: 2 87 SER cc_start: 0.8956 (t) cc_final: 0.8436 (p) REVERT: 2 129 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.9124 (mp) REVERT: 4 15 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7998 (tm-30) REVERT: 4 37 GLU cc_start: 0.8267 (pp20) cc_final: 0.8006 (pp20) REVERT: 4 69 TYR cc_start: 0.8181 (t80) cc_final: 0.7226 (t80) REVERT: 4 70 GLN cc_start: 0.8463 (mm110) cc_final: 0.8152 (mm110) REVERT: 4 73 LYS cc_start: 0.8886 (tttt) cc_final: 0.8264 (tptt) REVERT: 4 136 MET cc_start: 0.8934 (mtp) cc_final: 0.8655 (mtp) REVERT: 5 1 MET cc_start: 0.5531 (tpp) cc_final: 0.5165 (tpt) REVERT: 5 98 MET cc_start: 0.8298 (tpp) cc_final: 0.7651 (tpp) REVERT: 5 123 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8166 (mp10) REVERT: 6 14 LYS cc_start: 0.9101 (mmmt) cc_final: 0.8899 (mmmm) REVERT: 6 27 ASN cc_start: 0.8745 (m110) cc_final: 0.8139 (m-40) REVERT: 6 36 ARG cc_start: 0.8068 (ttm110) cc_final: 0.7722 (mtm110) REVERT: 6 37 GLU cc_start: 0.8305 (pp20) cc_final: 0.7902 (mt-10) REVERT: 6 87 SER cc_start: 0.8876 (t) cc_final: 0.8399 (p) REVERT: 6 129 ILE cc_start: 0.9304 (OUTLIER) cc_final: 0.9077 (mp) REVERT: 7 15 GLU cc_start: 0.8223 (tm-30) cc_final: 0.8016 (tp30) REVERT: 7 37 GLU cc_start: 0.7841 (pp20) cc_final: 0.7628 (pp20) REVERT: 7 132 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8409 (tm-30) REVERT: 8 15 GLU cc_start: 0.8325 (tm-30) cc_final: 0.8028 (tm-30) REVERT: 8 32 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8205 (mm-30) REVERT: 8 36 ARG cc_start: 0.8684 (ttm110) cc_final: 0.8456 (mtm110) REVERT: 8 38 LEU cc_start: 0.8225 (tt) cc_final: 0.7756 (mp) REVERT: 8 41 LEU cc_start: 0.7200 (mp) cc_final: 0.6933 (tt) REVERT: 8 70 GLN cc_start: 0.8591 (mm110) cc_final: 0.8168 (mm110) REVERT: 9 1 MET cc_start: 0.5792 (tpp) cc_final: 0.5314 (tpt) REVERT: 9 98 MET cc_start: 0.8352 (tpp) cc_final: 0.8134 (tpp) REVERT: 9 123 GLN cc_start: 0.8324 (mm-40) cc_final: 0.7964 (mp10) outliers start: 36 outliers final: 2 residues processed: 1700 average time/residue: 0.6023 time to fit residues: 1616.4344 Evaluate side-chains 1120 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1116 time to evaluate : 4.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain 2 residue 129 ILE Chi-restraints excluded: chain 6 residue 129 ILE Chi-restraints excluded: chain 8 residue 129 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 516 optimal weight: 9.9990 chunk 463 optimal weight: 8.9990 chunk 257 optimal weight: 0.9980 chunk 158 optimal weight: 20.0000 chunk 312 optimal weight: 6.9990 chunk 247 optimal weight: 2.9990 chunk 479 optimal weight: 10.0000 chunk 185 optimal weight: 7.9990 chunk 291 optimal weight: 3.9990 chunk 357 optimal weight: 0.9990 chunk 555 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN B 99 ASN C 27 ASN C 42 GLN C 72 ASN C 99 ASN D 42 GLN D 72 ASN E 103 ASN ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 ASN G 74 GLN G 99 ASN H 42 GLN I 27 ASN J 30 ASN J 99 ASN K 27 ASN K 42 GLN L 42 GLN L 43 ASN L 72 ASN L 74 GLN L 126 ASN M 42 GLN N 99 ASN O 27 ASN O 42 GLN O 99 ASN P 27 ASN P 42 GLN P 43 ASN P 72 ASN P 123 GLN Q 42 GLN Q 99 ASN S 27 ASN S 42 GLN S 99 ASN T 27 ASN T 42 GLN T 72 ASN T 103 ASN V 30 ASN W 27 ASN W 42 GLN W 99 ASN X 27 ASN X 42 GLN X 43 ASN X 126 ASN Y 42 GLN Z 99 ASN 0 27 ASN 0 42 GLN 0 99 ASN 1 42 GLN 1 84 GLN 2 42 GLN ** 3 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 99 ASN ** 4 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 99 ASN 5 42 GLN 5 72 ASN 6 72 ASN 8 27 ASN 8 99 ASN 9 42 GLN 9 72 ASN 9 126 ASN Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 50040 Z= 0.270 Angle : 0.692 8.366 66852 Z= 0.373 Chirality : 0.044 0.156 7560 Planarity : 0.005 0.050 8676 Dihedral : 5.450 57.029 6812 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 1.19 % Allowed : 2.22 % Favored : 96.59 % Rotamer: Outliers : 2.21 % Allowed : 13.68 % Favored : 84.12 % 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: -3.48 (0.09), residues: 6048 helix: -2.10 (0.06), residues: 5184 sheet: None (None), residues: 0 loop : -1.88 (0.18), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 9 TYR 0.017 0.002 TYR W 79 ARG 0.008 0.001 ARG N 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1374 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1250 time to evaluate : 4.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 ARG cc_start: 0.7879 (ttm110) cc_final: 0.7584 (mtm110) REVERT: B 72 ASN cc_start: 0.8198 (m-40) cc_final: 0.7780 (t0) REVERT: B 78 MET cc_start: 0.8026 (tpp) cc_final: 0.7784 (tpp) REVERT: B 114 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7915 (mt-10) REVERT: A 71 ILE cc_start: 0.7684 (mt) cc_final: 0.7358 (tt) REVERT: A 78 MET cc_start: 0.8022 (tpp) cc_final: 0.7519 (mmt) REVERT: C 36 ARG cc_start: 0.8576 (ttm110) cc_final: 0.8360 (mtm110) REVERT: C 73 LYS cc_start: 0.8676 (tttt) cc_final: 0.8298 (tptt) REVERT: C 86 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7722 (t70) REVERT: D 1 MET cc_start: 0.5786 (tpp) cc_final: 0.5292 (tpt) REVERT: D 76 ASP cc_start: 0.8214 (m-30) cc_final: 0.7989 (m-30) REVERT: D 98 MET cc_start: 0.8182 (tpp) cc_final: 0.7831 (tpp) REVERT: D 123 GLN cc_start: 0.8310 (mm-40) cc_final: 0.7952 (mm-40) REVERT: E 14 LYS cc_start: 0.9011 (mmmt) cc_final: 0.8750 (mmmm) REVERT: E 36 ARG cc_start: 0.7986 (ttm110) cc_final: 0.7762 (mtm110) REVERT: E 89 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7887 (ttp-170) REVERT: G 5 LYS cc_start: 0.8794 (ttmp) cc_final: 0.8477 (ttpp) REVERT: G 6 LYS cc_start: 0.9209 (mttt) cc_final: 0.7571 (tttm) REVERT: G 26 LYS cc_start: 0.8664 (ttpp) cc_final: 0.8456 (ttpp) REVERT: G 147 ASP cc_start: 0.8764 (t70) cc_final: 0.8459 (t0) REVERT: H 1 MET cc_start: 0.5638 (tpp) cc_final: 0.4978 (tpt) REVERT: H 36 ARG cc_start: 0.7731 (mmp80) cc_final: 0.7209 (mtm110) REVERT: H 72 ASN cc_start: 0.8712 (m-40) cc_final: 0.8476 (m110) REVERT: H 76 ASP cc_start: 0.8310 (m-30) cc_final: 0.8018 (m-30) REVERT: I 1 MET cc_start: 0.6196 (tpp) cc_final: 0.5841 (tpt) REVERT: I 26 LYS cc_start: 0.8087 (mmtp) cc_final: 0.7876 (mptt) REVERT: I 33 LYS cc_start: 0.8116 (tmmm) cc_final: 0.7727 (tptt) REVERT: I 36 ARG cc_start: 0.8051 (ttm110) cc_final: 0.7850 (mtm-85) REVERT: I 147 ASP cc_start: 0.8578 (t70) cc_final: 0.7914 (t70) REVERT: I 149 MET cc_start: 0.8194 (mmp) cc_final: 0.7947 (mmp) REVERT: J 1 MET cc_start: 0.4089 (OUTLIER) cc_final: 0.3799 (tmm) REVERT: J 86 ASP cc_start: 0.7908 (m-30) cc_final: 0.7315 (m-30) REVERT: J 123 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8282 (mm-40) REVERT: K 5 LYS cc_start: 0.8952 (ttmp) cc_final: 0.8684 (ttpt) REVERT: K 73 LYS cc_start: 0.8774 (tttt) cc_final: 0.8281 (tptt) REVERT: K 112 MET cc_start: 0.8946 (mmp) cc_final: 0.8705 (mmp) REVERT: L 36 ARG cc_start: 0.7914 (mmp80) cc_final: 0.7665 (mtm110) REVERT: L 84 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7987 (mm-40) REVERT: L 124 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8438 (pp) REVERT: L 136 MET cc_start: 0.8356 (mtp) cc_final: 0.7871 (mtp) REVERT: M 1 MET cc_start: 0.5995 (tpp) cc_final: 0.5741 (tpp) REVERT: M 26 LYS cc_start: 0.8080 (mmtp) cc_final: 0.7690 (mmmm) REVERT: M 36 ARG cc_start: 0.7925 (ttm110) cc_final: 0.7596 (mtm110) REVERT: M 71 ILE cc_start: 0.8109 (mt) cc_final: 0.7905 (tt) REVERT: M 87 SER cc_start: 0.9198 (t) cc_final: 0.8746 (p) REVERT: N 71 ILE cc_start: 0.7950 (mt) cc_final: 0.7566 (tt) REVERT: N 86 ASP cc_start: 0.7765 (m-30) cc_final: 0.7333 (m-30) REVERT: N 87 SER cc_start: 0.8990 (m) cc_final: 0.8619 (p) REVERT: O 78 MET cc_start: 0.8499 (mmm) cc_final: 0.7907 (mmm) REVERT: O 79 TYR cc_start: 0.8927 (t80) cc_final: 0.8651 (t80) REVERT: P 36 ARG cc_start: 0.7745 (mmp80) cc_final: 0.7365 (mtm110) REVERT: P 42 GLN cc_start: 0.7188 (mm110) cc_final: 0.6612 (mt0) REVERT: P 78 MET cc_start: 0.8257 (tpp) cc_final: 0.7968 (mmt) REVERT: P 123 GLN cc_start: 0.8656 (mm110) cc_final: 0.8364 (mm-40) REVERT: Q 26 LYS cc_start: 0.8001 (mmtp) cc_final: 0.7747 (mmtt) REVERT: Q 36 ARG cc_start: 0.7950 (ttm110) cc_final: 0.7648 (mtm110) REVERT: Q 76 ASP cc_start: 0.8358 (m-30) cc_final: 0.8094 (m-30) REVERT: Q 87 SER cc_start: 0.9212 (t) cc_final: 0.8739 (p) REVERT: R 71 ILE cc_start: 0.7801 (mt) cc_final: 0.7477 (tt) REVERT: R 124 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7602 (pp) REVERT: S 70 GLN cc_start: 0.8566 (mm110) cc_final: 0.8305 (mm110) REVERT: S 124 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7916 (pp) REVERT: S 149 MET cc_start: 0.7945 (mmt) cc_final: 0.7730 (mmt) REVERT: S 150 GLU cc_start: 0.7564 (pp20) cc_final: 0.7117 (pm20) REVERT: T 1 MET cc_start: 0.5315 (tpp) cc_final: 0.4700 (tpt) REVERT: T 36 ARG cc_start: 0.7701 (mmp80) cc_final: 0.7213 (mtm110) REVERT: T 78 MET cc_start: 0.8320 (tpp) cc_final: 0.8025 (tpp) REVERT: T 98 MET cc_start: 0.8169 (tpp) cc_final: 0.7655 (tpp) REVERT: T 123 GLN cc_start: 0.8450 (mm-40) cc_final: 0.7987 (mm-40) REVERT: U 78 MET cc_start: 0.8033 (tpp) cc_final: 0.7774 (tpp) REVERT: V 71 ILE cc_start: 0.7665 (mt) cc_final: 0.7460 (tt) REVERT: W 36 ARG cc_start: 0.8540 (ttm110) cc_final: 0.8339 (mtm110) REVERT: W 73 LYS cc_start: 0.8599 (tttt) cc_final: 0.8164 (tptt) REVERT: W 78 MET cc_start: 0.8237 (mmm) cc_final: 0.7996 (mmm) REVERT: W 84 GLN cc_start: 0.8396 (mm-40) cc_final: 0.8109 (mm110) REVERT: W 87 SER cc_start: 0.8835 (m) cc_final: 0.8630 (p) REVERT: W 150 GLU cc_start: 0.7750 (pp20) cc_final: 0.7525 (pm20) REVERT: X 36 ARG cc_start: 0.7880 (mmp80) cc_final: 0.7599 (mtm110) REVERT: X 78 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.8051 (tpp) REVERT: X 104 GLN cc_start: 0.8837 (tt0) cc_final: 0.8586 (tt0) REVERT: X 136 MET cc_start: 0.8176 (mtp) cc_final: 0.7946 (mtm) REVERT: Y 37 GLU cc_start: 0.8411 (pp20) cc_final: 0.8185 (pp20) REVERT: Y 87 SER cc_start: 0.9137 (t) cc_final: 0.8804 (p) REVERT: Y 128 MET cc_start: 0.8225 (mmt) cc_final: 0.7574 (mmp) REVERT: Z 36 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7790 (ptp90) REVERT: Z 68 LEU cc_start: 0.8377 (tp) cc_final: 0.8154 (mt) REVERT: Z 86 ASP cc_start: 0.7829 (m-30) cc_final: 0.7080 (m-30) REVERT: 0 5 LYS cc_start: 0.8925 (ttmp) cc_final: 0.8509 (tttt) REVERT: 0 123 GLN cc_start: 0.8065 (mp10) cc_final: 0.7841 (mp10) REVERT: 2 26 LYS cc_start: 0.8035 (mmtp) cc_final: 0.7458 (mptt) REVERT: 2 36 ARG cc_start: 0.8042 (ttm110) cc_final: 0.7722 (mtm110) REVERT: 2 87 SER cc_start: 0.9227 (t) cc_final: 0.8592 (p) REVERT: 3 71 ILE cc_start: 0.7790 (mt) cc_final: 0.7422 (tt) REVERT: 3 78 MET cc_start: 0.8086 (tpp) cc_final: 0.7640 (mmt) REVERT: 4 78 MET cc_start: 0.8456 (tpp) cc_final: 0.8067 (mmm) REVERT: 4 136 MET cc_start: 0.8879 (mtp) cc_final: 0.8586 (mtp) REVERT: 4 147 ASP cc_start: 0.8660 (t70) cc_final: 0.8457 (t70) REVERT: 5 1 MET cc_start: 0.5681 (tpp) cc_final: 0.5378 (tpt) REVERT: 5 98 MET cc_start: 0.7926 (tpp) cc_final: 0.7219 (tpp) REVERT: 5 123 GLN cc_start: 0.8504 (mm-40) cc_final: 0.8102 (mp10) REVERT: 5 143 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7798 (tt0) REVERT: 6 36 ARG cc_start: 0.8001 (ttm110) cc_final: 0.7715 (mtm110) REVERT: 6 37 GLU cc_start: 0.8338 (pp20) cc_final: 0.7891 (mt-10) REVERT: 6 87 SER cc_start: 0.9161 (t) cc_final: 0.8560 (p) REVERT: 7 71 ILE cc_start: 0.7992 (mt) cc_final: 0.7640 (tt) REVERT: 7 132 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8484 (tm-30) REVERT: 8 15 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7538 (tm-30) REVERT: 8 73 LYS cc_start: 0.8773 (tttt) cc_final: 0.8471 (tptt) REVERT: 8 78 MET cc_start: 0.8119 (mmm) cc_final: 0.7916 (mtt) REVERT: 9 107 ASP cc_start: 0.8065 (m-30) cc_final: 0.7787 (m-30) REVERT: 9 125 ARG cc_start: 0.8655 (ttt90) cc_final: 0.8328 (tpp80) outliers start: 124 outliers final: 73 residues processed: 1320 average time/residue: 0.5411 time to fit residues: 1194.8937 Evaluate side-chains 1137 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1055 time to evaluate : 4.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 2 ASP Chi-restraints excluded: chain J residue 99 ASN Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain M residue 81 SER Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain N residue 124 LEU Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 99 ASN Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 99 ASN Chi-restraints excluded: chain Q residue 117 SER Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain S residue 22 SER Chi-restraints excluded: chain S residue 124 LEU Chi-restraints excluded: chain T residue 92 ILE Chi-restraints excluded: chain T residue 126 ASN Chi-restraints excluded: chain U residue 81 SER Chi-restraints excluded: chain U residue 105 MET Chi-restraints excluded: chain U residue 117 SER Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain V residue 117 SER Chi-restraints excluded: chain X residue 70 GLN Chi-restraints excluded: chain X residue 78 MET Chi-restraints excluded: chain X residue 80 THR Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Y residue 105 MET Chi-restraints excluded: chain Y residue 117 SER Chi-restraints excluded: chain Y residue 124 LEU Chi-restraints excluded: chain Z residue 2 ASP Chi-restraints excluded: chain Z residue 36 ARG Chi-restraints excluded: chain Z residue 99 ASN Chi-restraints excluded: chain Z residue 117 SER Chi-restraints excluded: chain 0 residue 22 SER Chi-restraints excluded: chain 0 residue 99 ASN Chi-restraints excluded: chain 1 residue 77 ARG Chi-restraints excluded: chain 1 residue 80 THR Chi-restraints excluded: chain 2 residue 40 VAL Chi-restraints excluded: chain 2 residue 81 SER Chi-restraints excluded: chain 2 residue 117 SER Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 3 residue 99 ASN Chi-restraints excluded: chain 3 residue 124 LEU Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 22 SER Chi-restraints excluded: chain 4 residue 99 ASN Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 143 GLU Chi-restraints excluded: chain 6 residue 81 SER Chi-restraints excluded: chain 6 residue 117 SER Chi-restraints excluded: chain 7 residue 2 ASP Chi-restraints excluded: chain 7 residue 117 SER Chi-restraints excluded: chain 7 residue 124 LEU Chi-restraints excluded: chain 8 residue 129 ILE Chi-restraints excluded: chain 9 residue 117 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 308 optimal weight: 0.8980 chunk 172 optimal weight: 5.9990 chunk 462 optimal weight: 2.9990 chunk 378 optimal weight: 8.9990 chunk 153 optimal weight: 0.6980 chunk 556 optimal weight: 7.9990 chunk 601 optimal weight: 50.0000 chunk 495 optimal weight: 3.9990 chunk 552 optimal weight: 7.9990 chunk 189 optimal weight: 4.9990 chunk 446 optimal weight: 8.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN D 43 ASN E 27 ASN ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN G 72 ASN H 27 ASN H 42 GLN H 43 ASN I 42 GLN K 27 ASN K 42 GLN L 27 ASN L 123 GLN M 27 ASN N 27 ASN N 99 ASN O 99 ASN O 126 ASN Q 27 ASN Q 99 ASN T 42 GLN T 43 ASN U 27 ASN U 30 ASN U 42 GLN V 27 ASN W 27 ASN W 42 GLN ** W 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 GLN Y 27 ASN 0 27 ASN 0 42 GLN 1 27 ASN 1 43 ASN 1 72 ASN 1 123 GLN 2 27 ASN 3 27 ASN 3 72 ASN 3 99 ASN 4 27 ASN 4 42 GLN 4 99 ASN ** 5 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 43 ASN 6 27 ASN 8 27 ASN 9 43 ASN 9 123 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 50040 Z= 0.272 Angle : 0.622 7.650 66852 Z= 0.332 Chirality : 0.043 0.152 7560 Planarity : 0.004 0.033 8676 Dihedral : 4.890 43.792 6808 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 1.19 % Allowed : 2.27 % Favored : 96.54 % Rotamer: Outliers : 3.45 % Allowed : 17.25 % Favored : 79.29 % 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: -1.96 (0.10), residues: 6048 helix: -1.03 (0.07), residues: 5112 sheet: None (None), residues: 0 loop : -1.69 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP 0 9 TYR 0.017 0.001 TYR M 64 ARG 0.009 0.001 ARG 3 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1304 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1110 time to evaluate : 4.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ASN cc_start: 0.7993 (m-40) cc_final: 0.7749 (m-40) REVERT: B 36 ARG cc_start: 0.7993 (ttm110) cc_final: 0.7670 (mtm110) REVERT: B 72 ASN cc_start: 0.8338 (m-40) cc_final: 0.7940 (t0) REVERT: B 78 MET cc_start: 0.8046 (tpp) cc_final: 0.7840 (tpp) REVERT: B 114 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8013 (mt-10) REVERT: A 71 ILE cc_start: 0.7627 (mt) cc_final: 0.7296 (tt) REVERT: A 78 MET cc_start: 0.8084 (tpp) cc_final: 0.7584 (mmt) REVERT: C 72 ASN cc_start: 0.8636 (m-40) cc_final: 0.8321 (m110) REVERT: C 73 LYS cc_start: 0.8731 (tttt) cc_final: 0.8344 (tptt) REVERT: C 87 SER cc_start: 0.8837 (m) cc_final: 0.8621 (p) REVERT: D 1 MET cc_start: 0.5761 (tpp) cc_final: 0.5346 (tpt) REVERT: D 36 ARG cc_start: 0.7785 (mmp80) cc_final: 0.7326 (mtm110) REVERT: D 76 ASP cc_start: 0.8248 (m-30) cc_final: 0.7956 (m-30) REVERT: D 98 MET cc_start: 0.8062 (tpp) cc_final: 0.7636 (tpp) REVERT: D 123 GLN cc_start: 0.8405 (mm-40) cc_final: 0.7988 (mm-40) REVERT: E 2 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7523 (m-30) REVERT: E 14 LYS cc_start: 0.9024 (mmmt) cc_final: 0.8814 (mmmm) REVERT: E 35 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7763 (mp) REVERT: E 36 ARG cc_start: 0.8045 (ttm110) cc_final: 0.7805 (mtm110) REVERT: E 72 ASN cc_start: 0.8579 (OUTLIER) cc_final: 0.8140 (t0) REVERT: E 80 THR cc_start: 0.9234 (OUTLIER) cc_final: 0.8892 (t) REVERT: G 5 LYS cc_start: 0.8804 (ttmp) cc_final: 0.8576 (ttpp) REVERT: G 6 LYS cc_start: 0.9198 (mttt) cc_final: 0.7516 (tttm) REVERT: G 26 LYS cc_start: 0.8661 (ttpp) cc_final: 0.8411 (ttmt) REVERT: G 112 MET cc_start: 0.9022 (mmp) cc_final: 0.8808 (mmp) REVERT: H 1 MET cc_start: 0.5637 (tpp) cc_final: 0.4931 (tpt) REVERT: H 76 ASP cc_start: 0.8245 (m-30) cc_final: 0.8002 (m-30) REVERT: I 1 MET cc_start: 0.6432 (tpp) cc_final: 0.6027 (tpt) REVERT: I 33 LYS cc_start: 0.8122 (tmmm) cc_final: 0.7661 (tptt) REVERT: I 36 ARG cc_start: 0.8090 (ttm110) cc_final: 0.7878 (mtm-85) REVERT: I 147 ASP cc_start: 0.8625 (t70) cc_final: 0.7913 (t0) REVERT: J 86 ASP cc_start: 0.7859 (m-30) cc_final: 0.7356 (m-30) REVERT: K 73 LYS cc_start: 0.8879 (tttt) cc_final: 0.8434 (tptt) REVERT: K 112 MET cc_start: 0.8918 (mmp) cc_final: 0.8644 (mmp) REVERT: K 128 MET cc_start: 0.8948 (mmt) cc_final: 0.8699 (mmt) REVERT: L 124 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8388 (pp) REVERT: M 1 MET cc_start: 0.6076 (tpp) cc_final: 0.5828 (tpp) REVERT: M 36 ARG cc_start: 0.8014 (ttm110) cc_final: 0.7613 (mtm110) REVERT: M 72 ASN cc_start: 0.8380 (m-40) cc_final: 0.8155 (t0) REVERT: M 87 SER cc_start: 0.9229 (t) cc_final: 0.8822 (p) REVERT: N 71 ILE cc_start: 0.7815 (mt) cc_final: 0.7396 (tt) REVERT: N 86 ASP cc_start: 0.7694 (m-30) cc_final: 0.7381 (m-30) REVERT: O 73 LYS cc_start: 0.8892 (tttt) cc_final: 0.8504 (tptt) REVERT: O 78 MET cc_start: 0.8537 (mmm) cc_final: 0.7879 (mmm) REVERT: O 79 TYR cc_start: 0.8989 (t80) cc_final: 0.8646 (t80) REVERT: P 42 GLN cc_start: 0.7333 (mm110) cc_final: 0.7069 (mt0) REVERT: P 72 ASN cc_start: 0.8651 (m-40) cc_final: 0.8381 (m-40) REVERT: P 123 GLN cc_start: 0.8550 (mm110) cc_final: 0.8348 (mm-40) REVERT: P 144 MET cc_start: 0.9003 (mtm) cc_final: 0.8761 (mtm) REVERT: Q 36 ARG cc_start: 0.8019 (ttm110) cc_final: 0.7743 (mtm110) REVERT: Q 87 SER cc_start: 0.9176 (t) cc_final: 0.8721 (p) REVERT: R 71 ILE cc_start: 0.7819 (mt) cc_final: 0.7456 (tt) REVERT: R 87 SER cc_start: 0.9092 (t) cc_final: 0.8865 (t) REVERT: R 124 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7740 (pp) REVERT: S 124 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8024 (pp) REVERT: T 1 MET cc_start: 0.5401 (tpp) cc_final: 0.4774 (tpt) REVERT: T 36 ARG cc_start: 0.7756 (mmp80) cc_final: 0.7299 (mtm110) REVERT: T 78 MET cc_start: 0.8262 (tpp) cc_final: 0.8043 (tpp) REVERT: T 98 MET cc_start: 0.8112 (tpp) cc_final: 0.7589 (tpp) REVERT: T 123 GLN cc_start: 0.8482 (mm-40) cc_final: 0.7958 (mm-40) REVERT: T 124 LEU cc_start: 0.8715 (pp) cc_final: 0.8512 (pp) REVERT: V 27 ASN cc_start: 0.8861 (m110) cc_final: 0.8637 (m-40) REVERT: W 36 ARG cc_start: 0.8510 (ttm110) cc_final: 0.8303 (mtm110) REVERT: W 72 ASN cc_start: 0.8617 (m-40) cc_final: 0.8157 (m-40) REVERT: W 73 LYS cc_start: 0.8665 (tttt) cc_final: 0.8258 (tptt) REVERT: W 150 GLU cc_start: 0.7789 (pp20) cc_final: 0.7347 (pm20) REVERT: X 36 ARG cc_start: 0.7883 (mmp80) cc_final: 0.7592 (mtm110) REVERT: X 104 GLN cc_start: 0.8865 (tt0) cc_final: 0.8567 (tt0) REVERT: X 136 MET cc_start: 0.8076 (mtp) cc_final: 0.7850 (mtm) REVERT: Y 1 MET cc_start: 0.6220 (tpp) cc_final: 0.5724 (tpp) REVERT: Y 26 LYS cc_start: 0.8145 (mptt) cc_final: 0.7859 (mmtt) REVERT: Y 87 SER cc_start: 0.9161 (t) cc_final: 0.8804 (p) REVERT: Y 128 MET cc_start: 0.8208 (mmt) cc_final: 0.7873 (mmt) REVERT: 1 36 ARG cc_start: 0.7890 (mmp80) cc_final: 0.7404 (mtm110) REVERT: 2 26 LYS cc_start: 0.7901 (mmtp) cc_final: 0.7448 (mptt) REVERT: 2 36 ARG cc_start: 0.8124 (ttm110) cc_final: 0.7780 (mtm110) REVERT: 2 72 ASN cc_start: 0.8461 (m-40) cc_final: 0.8184 (t0) REVERT: 2 87 SER cc_start: 0.9245 (t) cc_final: 0.8619 (p) REVERT: 3 71 ILE cc_start: 0.7726 (mt) cc_final: 0.7502 (tt) REVERT: 5 1 MET cc_start: 0.5632 (tpp) cc_final: 0.5321 (tpt) REVERT: 5 36 ARG cc_start: 0.7741 (mmp80) cc_final: 0.7438 (mtm110) REVERT: 5 42 GLN cc_start: 0.7122 (mm-40) cc_final: 0.6810 (mt0) REVERT: 5 72 ASN cc_start: 0.8365 (m-40) cc_final: 0.8114 (m-40) REVERT: 5 98 MET cc_start: 0.7913 (tpp) cc_final: 0.7383 (tpt) REVERT: 6 2 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7402 (m-30) REVERT: 6 36 ARG cc_start: 0.8163 (ttm110) cc_final: 0.7853 (mtm110) REVERT: 6 37 GLU cc_start: 0.8365 (pp20) cc_final: 0.8104 (mt-10) REVERT: 6 87 SER cc_start: 0.9181 (t) cc_final: 0.8624 (p) REVERT: 7 132 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8556 (tm-30) REVERT: 8 15 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7732 (tm-30) REVERT: 8 73 LYS cc_start: 0.8938 (tttt) cc_final: 0.8622 (tptt) outliers start: 194 outliers final: 115 residues processed: 1225 average time/residue: 0.4573 time to fit residues: 940.7723 Evaluate side-chains 1138 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1015 time to evaluate : 4.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain H residue 27 ASN Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain I residue 2 ASP Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain J residue 2 ASP Chi-restraints excluded: chain J residue 92 ILE Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 92 ILE Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain M residue 81 SER Chi-restraints excluded: chain M residue 92 ILE Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain N residue 124 LEU Chi-restraints excluded: chain N residue 130 GLU Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain P residue 92 ILE Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 99 ASN Chi-restraints excluded: chain Q residue 117 SER Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain R residue 2 ASP Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 22 SER Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 124 LEU Chi-restraints excluded: chain T residue 92 ILE Chi-restraints excluded: chain T residue 126 ASN Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 81 SER Chi-restraints excluded: chain U residue 87 SER Chi-restraints excluded: chain U residue 117 SER Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain V residue 92 ILE Chi-restraints excluded: chain V residue 117 SER Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 130 GLU Chi-restraints excluded: chain W residue 20 ILE Chi-restraints excluded: chain X residue 70 GLN Chi-restraints excluded: chain X residue 80 THR Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain X residue 123 GLN Chi-restraints excluded: chain X residue 124 LEU Chi-restraints excluded: chain Y residue 92 ILE Chi-restraints excluded: chain Y residue 99 ASN Chi-restraints excluded: chain Y residue 117 SER Chi-restraints excluded: chain Y residue 124 LEU Chi-restraints excluded: chain Z residue 2 ASP Chi-restraints excluded: chain Z residue 92 ILE Chi-restraints excluded: chain Z residue 117 SER Chi-restraints excluded: chain Z residue 152 VAL Chi-restraints excluded: chain 0 residue 20 ILE Chi-restraints excluded: chain 0 residue 22 SER Chi-restraints excluded: chain 1 residue 70 GLN Chi-restraints excluded: chain 1 residue 80 THR Chi-restraints excluded: chain 1 residue 81 SER Chi-restraints excluded: chain 1 residue 123 GLN Chi-restraints excluded: chain 1 residue 124 LEU Chi-restraints excluded: chain 1 residue 136 MET Chi-restraints excluded: chain 2 residue 81 SER Chi-restraints excluded: chain 2 residue 92 ILE Chi-restraints excluded: chain 2 residue 117 SER Chi-restraints excluded: chain 2 residue 124 LEU Chi-restraints excluded: chain 3 residue 2 ASP Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 3 residue 99 ASN Chi-restraints excluded: chain 3 residue 111 LEU Chi-restraints excluded: chain 3 residue 124 LEU Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 22 SER Chi-restraints excluded: chain 5 residue 81 SER Chi-restraints excluded: chain 6 residue 2 ASP Chi-restraints excluded: chain 6 residue 81 SER Chi-restraints excluded: chain 6 residue 92 ILE Chi-restraints excluded: chain 6 residue 117 SER Chi-restraints excluded: chain 6 residue 124 LEU Chi-restraints excluded: chain 6 residue 170 ILE Chi-restraints excluded: chain 7 residue 2 ASP Chi-restraints excluded: chain 7 residue 92 ILE Chi-restraints excluded: chain 7 residue 117 SER Chi-restraints excluded: chain 7 residue 124 LEU Chi-restraints excluded: chain 8 residue 20 ILE Chi-restraints excluded: chain 8 residue 129 ILE Chi-restraints excluded: chain 9 residue 123 GLN Chi-restraints excluded: chain 9 residue 124 LEU Chi-restraints excluded: chain 9 residue 126 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 550 optimal weight: 40.0000 chunk 418 optimal weight: 2.9990 chunk 288 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 265 optimal weight: 0.9990 chunk 373 optimal weight: 20.0000 chunk 558 optimal weight: 2.9990 chunk 591 optimal weight: 30.0000 chunk 291 optimal weight: 2.9990 chunk 529 optimal weight: 1.9990 chunk 159 optimal weight: 20.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN B 99 ASN ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN F 72 ASN F 99 ASN G 126 ASN H 27 ASN L 27 ASN L 123 GLN N 27 ASN N 99 ASN O 27 ASN Q 99 ASN S 27 ASN T 103 ASN V 42 GLN V 72 ASN ** W 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 27 ASN X 72 ASN X 123 GLN Y 27 ASN Y 84 GLN Z 42 GLN Z 99 ASN 0 27 ASN 1 72 ASN 1 84 GLN 1 123 GLN ** 5 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 84 GLN 6 27 ASN 7 72 ASN 9 123 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 50040 Z= 0.191 Angle : 0.572 8.766 66852 Z= 0.305 Chirality : 0.041 0.171 7560 Planarity : 0.003 0.035 8676 Dihedral : 4.576 42.808 6806 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 1.19 % Allowed : 2.40 % Favored : 96.41 % Rotamer: Outliers : 3.56 % Allowed : 18.84 % Favored : 77.60 % 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: 6048 helix: -0.50 (0.07), residues: 5112 sheet: None (None), residues: 0 loop : -1.54 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 9 TYR 0.016 0.001 TYR 0 79 ARG 0.008 0.000 ARG W 29 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1290 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 1090 time to evaluate : 4.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ASN cc_start: 0.8054 (m-40) cc_final: 0.7737 (m-40) REVERT: B 34 SER cc_start: 0.8532 (m) cc_final: 0.7883 (t) REVERT: B 36 ARG cc_start: 0.8002 (ttm110) cc_final: 0.7668 (mtm110) REVERT: B 72 ASN cc_start: 0.8396 (m-40) cc_final: 0.8017 (t0) REVERT: B 78 MET cc_start: 0.7938 (tpp) cc_final: 0.7612 (tpp) REVERT: B 114 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8030 (mt-10) REVERT: A 2 ASP cc_start: 0.6082 (OUTLIER) cc_final: 0.5834 (t70) REVERT: A 71 ILE cc_start: 0.7630 (mt) cc_final: 0.7338 (tt) REVERT: C 72 ASN cc_start: 0.8683 (m-40) cc_final: 0.8398 (m110) REVERT: C 73 LYS cc_start: 0.8661 (tttt) cc_final: 0.8367 (tptt) REVERT: C 86 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7817 (t0) REVERT: D 1 MET cc_start: 0.5753 (tpp) cc_final: 0.5366 (tpt) REVERT: D 76 ASP cc_start: 0.8249 (m-30) cc_final: 0.7884 (m-30) REVERT: D 123 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8002 (mm-40) REVERT: E 34 SER cc_start: 0.8776 (m) cc_final: 0.8274 (t) REVERT: E 35 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7779 (mp) REVERT: E 36 ARG cc_start: 0.8012 (ttm110) cc_final: 0.7739 (mtm110) REVERT: E 72 ASN cc_start: 0.8511 (OUTLIER) cc_final: 0.8045 (t0) REVERT: E 80 THR cc_start: 0.9237 (OUTLIER) cc_final: 0.8793 (p) REVERT: G 5 LYS cc_start: 0.8792 (ttmp) cc_final: 0.8573 (ttpp) REVERT: G 6 LYS cc_start: 0.9214 (mttt) cc_final: 0.7477 (tttm) REVERT: G 26 LYS cc_start: 0.8695 (ttpp) cc_final: 0.8467 (ttmt) REVERT: H 1 MET cc_start: 0.5638 (tpp) cc_final: 0.4960 (tpt) REVERT: H 36 ARG cc_start: 0.7771 (mmp80) cc_final: 0.7382 (mtm110) REVERT: H 76 ASP cc_start: 0.8214 (m-30) cc_final: 0.7981 (m-30) REVERT: H 129 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7836 (mp) REVERT: I 1 MET cc_start: 0.6332 (tpp) cc_final: 0.5936 (tpt) REVERT: I 20 ILE cc_start: 0.8603 (mt) cc_final: 0.8384 (tt) REVERT: I 33 LYS cc_start: 0.8121 (tmmm) cc_final: 0.7675 (tptt) REVERT: I 36 ARG cc_start: 0.8122 (ttm110) cc_final: 0.7906 (mtm-85) REVERT: I 80 THR cc_start: 0.9190 (OUTLIER) cc_final: 0.8883 (p) REVERT: I 147 ASP cc_start: 0.8561 (t70) cc_final: 0.7825 (t0) REVERT: J 86 ASP cc_start: 0.7850 (m-30) cc_final: 0.7512 (m-30) REVERT: J 123 GLN cc_start: 0.8476 (mm-40) cc_final: 0.8236 (mm-40) REVERT: K 72 ASN cc_start: 0.8510 (m-40) cc_final: 0.8162 (m-40) REVERT: K 73 LYS cc_start: 0.8937 (tttt) cc_final: 0.8501 (tptt) REVERT: K 112 MET cc_start: 0.8913 (mmp) cc_final: 0.8615 (mmp) REVERT: L 36 ARG cc_start: 0.7865 (mmp80) cc_final: 0.7549 (mtm110) REVERT: L 124 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8323 (pp) REVERT: M 36 ARG cc_start: 0.8007 (ttm110) cc_final: 0.7601 (mtm110) REVERT: M 72 ASN cc_start: 0.8373 (m-40) cc_final: 0.8149 (t0) REVERT: M 87 SER cc_start: 0.9207 (t) cc_final: 0.8844 (p) REVERT: N 71 ILE cc_start: 0.7734 (mt) cc_final: 0.7502 (tt) REVERT: N 86 ASP cc_start: 0.7787 (m-30) cc_final: 0.7454 (m-30) REVERT: O 37 GLU cc_start: 0.8374 (pp20) cc_final: 0.8140 (tm-30) REVERT: O 73 LYS cc_start: 0.8917 (tttt) cc_final: 0.8560 (tptt) REVERT: O 78 MET cc_start: 0.8548 (mmm) cc_final: 0.8176 (mmm) REVERT: P 36 ARG cc_start: 0.7687 (mmp80) cc_final: 0.7365 (mtm110) REVERT: P 42 GLN cc_start: 0.7398 (mm110) cc_final: 0.7094 (mt0) REVERT: P 72 ASN cc_start: 0.8594 (m-40) cc_final: 0.8317 (m-40) REVERT: P 144 MET cc_start: 0.9004 (mtm) cc_final: 0.8778 (mtm) REVERT: P 147 ASP cc_start: 0.8495 (t70) cc_final: 0.7828 (t0) REVERT: Q 36 ARG cc_start: 0.8029 (ttm110) cc_final: 0.7805 (mtm110) REVERT: Q 87 SER cc_start: 0.9161 (t) cc_final: 0.8682 (p) REVERT: R 87 SER cc_start: 0.9065 (t) cc_final: 0.8855 (t) REVERT: R 124 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7682 (pp) REVERT: S 72 ASN cc_start: 0.8624 (m-40) cc_final: 0.8423 (m-40) REVERT: S 73 LYS cc_start: 0.8933 (tttt) cc_final: 0.8624 (tptt) REVERT: S 90 MET cc_start: 0.7913 (mmm) cc_final: 0.7693 (mmm) REVERT: S 124 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7912 (pp) REVERT: T 1 MET cc_start: 0.5315 (tpp) cc_final: 0.4686 (tpt) REVERT: T 36 ARG cc_start: 0.7771 (mmp80) cc_final: 0.7333 (mtm110) REVERT: T 78 MET cc_start: 0.8214 (tpp) cc_final: 0.7969 (tpp) REVERT: T 98 MET cc_start: 0.7976 (tpp) cc_final: 0.7671 (tpt) REVERT: T 123 GLN cc_start: 0.8555 (mm-40) cc_final: 0.7957 (mm-40) REVERT: T 125 ARG cc_start: 0.8529 (ttm-80) cc_final: 0.8320 (tpp80) REVERT: U 26 LYS cc_start: 0.8072 (mptt) cc_final: 0.7753 (mttp) REVERT: U 147 ASP cc_start: 0.8518 (t70) cc_final: 0.7775 (t0) REVERT: V 136 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7699 (mtp) REVERT: W 72 ASN cc_start: 0.8715 (m-40) cc_final: 0.8213 (m-40) REVERT: W 73 LYS cc_start: 0.8732 (tttt) cc_final: 0.8351 (tptt) REVERT: W 128 MET cc_start: 0.8958 (mmt) cc_final: 0.8643 (mmp) REVERT: W 150 GLU cc_start: 0.7810 (pp20) cc_final: 0.7332 (pm20) REVERT: X 27 ASN cc_start: 0.8643 (OUTLIER) cc_final: 0.8396 (m-40) REVERT: X 67 GLU cc_start: 0.6736 (pp20) cc_final: 0.6019 (mp0) REVERT: X 86 ASP cc_start: 0.7833 (m-30) cc_final: 0.7612 (t0) REVERT: Y 1 MET cc_start: 0.6207 (tpp) cc_final: 0.5720 (tpp) REVERT: Y 26 LYS cc_start: 0.8191 (mptt) cc_final: 0.7900 (mmtt) REVERT: Y 87 SER cc_start: 0.9156 (t) cc_final: 0.8804 (p) REVERT: Y 128 MET cc_start: 0.8172 (mmt) cc_final: 0.7802 (mmt) REVERT: Z 98 MET cc_start: 0.7787 (tpp) cc_final: 0.7391 (tmm) REVERT: 0 70 GLN cc_start: 0.8042 (mm110) cc_final: 0.7746 (mm-40) REVERT: 0 74 GLN cc_start: 0.8205 (mm110) cc_final: 0.7938 (mm110) REVERT: 1 36 ARG cc_start: 0.7988 (mmp80) cc_final: 0.7524 (mtm110) REVERT: 2 36 ARG cc_start: 0.8122 (ttm110) cc_final: 0.7789 (mtm110) REVERT: 2 87 SER cc_start: 0.9271 (t) cc_final: 0.8677 (p) REVERT: 3 68 LEU cc_start: 0.8488 (tp) cc_final: 0.8187 (mt) REVERT: 3 71 ILE cc_start: 0.7871 (mt) cc_final: 0.7521 (tt) REVERT: 5 1 MET cc_start: 0.5559 (tpp) cc_final: 0.5277 (tpt) REVERT: 5 42 GLN cc_start: 0.7118 (mm-40) cc_final: 0.6749 (mt0) REVERT: 5 72 ASN cc_start: 0.8358 (m-40) cc_final: 0.8112 (m-40) REVERT: 5 98 MET cc_start: 0.7786 (tpp) cc_final: 0.7025 (tpp) REVERT: 5 147 ASP cc_start: 0.8424 (t70) cc_final: 0.8045 (t0) REVERT: 6 2 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7405 (m-30) REVERT: 6 36 ARG cc_start: 0.8141 (ttm110) cc_final: 0.7828 (mtm110) REVERT: 6 37 GLU cc_start: 0.8365 (pp20) cc_final: 0.8131 (mt-10) REVERT: 8 15 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7635 (tm-30) REVERT: 8 73 LYS cc_start: 0.8957 (tttt) cc_final: 0.8499 (ttmt) outliers start: 200 outliers final: 113 residues processed: 1205 average time/residue: 0.4620 time to fit residues: 938.7791 Evaluate side-chains 1140 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1014 time to evaluate : 4.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 99 ASN Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain I residue 2 ASP Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 136 MET Chi-restraints excluded: chain J residue 2 ASP Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain M residue 81 SER Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain N residue 2 ASP Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 124 LEU Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain P residue 92 ILE Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 92 ILE Chi-restraints excluded: chain Q residue 99 ASN Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 117 SER Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain R residue 2 ASP Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 22 SER Chi-restraints excluded: chain S residue 86 ASP Chi-restraints excluded: chain S residue 124 LEU Chi-restraints excluded: chain T residue 27 ASN Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain T residue 126 ASN Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 81 SER Chi-restraints excluded: chain U residue 117 SER Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain V residue 63 LEU Chi-restraints excluded: chain V residue 117 SER Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 136 MET Chi-restraints excluded: chain V residue 152 VAL Chi-restraints excluded: chain W residue 92 ILE Chi-restraints excluded: chain X residue 27 ASN Chi-restraints excluded: chain X residue 70 GLN Chi-restraints excluded: chain X residue 80 THR Chi-restraints excluded: chain X residue 126 ASN Chi-restraints excluded: chain Y residue 99 ASN Chi-restraints excluded: chain Y residue 117 SER Chi-restraints excluded: chain Y residue 124 LEU Chi-restraints excluded: chain Z residue 2 ASP Chi-restraints excluded: chain Z residue 99 ASN Chi-restraints excluded: chain 0 residue 22 SER Chi-restraints excluded: chain 1 residue 136 MET Chi-restraints excluded: chain 2 residue 81 SER Chi-restraints excluded: chain 2 residue 99 ASN Chi-restraints excluded: chain 2 residue 117 SER Chi-restraints excluded: chain 2 residue 124 LEU Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 2 ASP Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 3 residue 38 LEU Chi-restraints excluded: chain 3 residue 111 LEU Chi-restraints excluded: chain 3 residue 124 LEU Chi-restraints excluded: chain 3 residue 130 GLU Chi-restraints excluded: chain 3 residue 140 ILE Chi-restraints excluded: chain 4 residue 22 SER Chi-restraints excluded: chain 5 residue 81 SER Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 6 residue 2 ASP Chi-restraints excluded: chain 6 residue 81 SER Chi-restraints excluded: chain 6 residue 117 SER Chi-restraints excluded: chain 6 residue 124 LEU Chi-restraints excluded: chain 6 residue 170 ILE Chi-restraints excluded: chain 7 residue 2 ASP Chi-restraints excluded: chain 7 residue 117 SER Chi-restraints excluded: chain 7 residue 124 LEU Chi-restraints excluded: chain 7 residue 130 GLU Chi-restraints excluded: chain 7 residue 136 MET Chi-restraints excluded: chain 8 residue 20 ILE Chi-restraints excluded: chain 8 residue 35 LEU Chi-restraints excluded: chain 8 residue 76 ASP Chi-restraints excluded: chain 8 residue 129 ILE Chi-restraints excluded: chain 9 residue 97 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 492 optimal weight: 10.0000 chunk 335 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 440 optimal weight: 0.6980 chunk 244 optimal weight: 5.9990 chunk 504 optimal weight: 6.9990 chunk 408 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 302 optimal weight: 2.9990 chunk 530 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 ASN G 74 GLN G 126 ASN H 27 ASN H 42 GLN J 99 ASN ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 ASN L 123 GLN N 27 ASN N 99 ASN Q 99 ASN R 42 GLN S 27 ASN ** T 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 27 ASN X 27 ASN X 72 ASN X 104 GLN X 123 GLN 0 42 GLN 0 72 ASN 1 72 ASN 1 123 GLN 3 99 ASN ** 5 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 123 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 50040 Z= 0.208 Angle : 0.567 8.973 66852 Z= 0.300 Chirality : 0.042 0.201 7560 Planarity : 0.003 0.023 8676 Dihedral : 4.416 38.719 6806 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 1.19 % Allowed : 2.53 % Favored : 96.28 % Rotamer: Outliers : 3.70 % Allowed : 19.62 % Favored : 76.67 % 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: -0.67 (0.10), residues: 6048 helix: -0.12 (0.07), residues: 5112 sheet: None (None), residues: 0 loop : -1.49 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 9 TYR 0.014 0.001 TYR 3 79 ARG 0.006 0.000 ARG W 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1281 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1073 time to evaluate : 4.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 ASN cc_start: 0.8061 (m-40) cc_final: 0.7709 (m-40) REVERT: B 34 SER cc_start: 0.8467 (m) cc_final: 0.7782 (t) REVERT: B 36 ARG cc_start: 0.8009 (ttm110) cc_final: 0.7672 (mtm110) REVERT: B 72 ASN cc_start: 0.8476 (m-40) cc_final: 0.8043 (t0) REVERT: B 78 MET cc_start: 0.7956 (tpp) cc_final: 0.7673 (tpp) REVERT: B 87 SER cc_start: 0.9276 (OUTLIER) cc_final: 0.8654 (p) REVERT: B 114 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8061 (mt-10) REVERT: A 2 ASP cc_start: 0.6067 (OUTLIER) cc_final: 0.5811 (t70) REVERT: A 71 ILE cc_start: 0.7645 (mt) cc_final: 0.7321 (tt) REVERT: C 72 ASN cc_start: 0.8725 (m-40) cc_final: 0.8411 (m110) REVERT: C 73 LYS cc_start: 0.8709 (tttt) cc_final: 0.8439 (tptt) REVERT: C 78 MET cc_start: 0.8263 (mmm) cc_final: 0.7704 (mtt) REVERT: C 86 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7834 (t0) REVERT: D 1 MET cc_start: 0.5738 (tpp) cc_final: 0.5390 (tpt) REVERT: D 36 ARG cc_start: 0.7807 (mmp80) cc_final: 0.7412 (mtm110) REVERT: D 72 ASN cc_start: 0.8391 (m-40) cc_final: 0.8113 (m110) REVERT: D 76 ASP cc_start: 0.8245 (m-30) cc_final: 0.7888 (m-30) REVERT: D 84 GLN cc_start: 0.8405 (mm-40) cc_final: 0.7963 (mt0) REVERT: D 123 GLN cc_start: 0.8455 (mm-40) cc_final: 0.7987 (mm-40) REVERT: E 34 SER cc_start: 0.8698 (m) cc_final: 0.8254 (t) REVERT: E 35 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7783 (mp) REVERT: E 36 ARG cc_start: 0.7998 (ttm110) cc_final: 0.7735 (mtm110) REVERT: E 72 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8043 (t0) REVERT: E 80 THR cc_start: 0.9249 (OUTLIER) cc_final: 0.8854 (p) REVERT: F 132 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8640 (tm-30) REVERT: G 5 LYS cc_start: 0.8797 (ttmp) cc_final: 0.8592 (ttpp) REVERT: G 6 LYS cc_start: 0.9189 (mttt) cc_final: 0.7423 (tttm) REVERT: G 26 LYS cc_start: 0.8623 (ttpp) cc_final: 0.8413 (ttmt) REVERT: H 1 MET cc_start: 0.5675 (tpp) cc_final: 0.4942 (tpt) REVERT: H 27 ASN cc_start: 0.8570 (OUTLIER) cc_final: 0.8334 (t0) REVERT: H 36 ARG cc_start: 0.7851 (mmp80) cc_final: 0.7643 (mmp80) REVERT: H 76 ASP cc_start: 0.8199 (m-30) cc_final: 0.7977 (m-30) REVERT: H 129 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7804 (mp) REVERT: I 1 MET cc_start: 0.6405 (tpp) cc_final: 0.6142 (tpt) REVERT: I 20 ILE cc_start: 0.8608 (mt) cc_final: 0.8385 (tt) REVERT: I 33 LYS cc_start: 0.8082 (tmmm) cc_final: 0.7636 (tptt) REVERT: I 36 ARG cc_start: 0.8149 (ttm110) cc_final: 0.7919 (mtm-85) REVERT: I 147 ASP cc_start: 0.8579 (t70) cc_final: 0.7847 (t0) REVERT: K 73 LYS cc_start: 0.8964 (tttt) cc_final: 0.8519 (tptt) REVERT: K 112 MET cc_start: 0.8903 (mmp) cc_final: 0.8587 (mmp) REVERT: L 67 GLU cc_start: 0.6567 (pp20) cc_final: 0.5766 (mp0) REVERT: L 78 MET cc_start: 0.8506 (tpp) cc_final: 0.8304 (tpt) REVERT: L 84 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7830 (mt0) REVERT: L 124 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8328 (pp) REVERT: M 36 ARG cc_start: 0.8021 (ttm110) cc_final: 0.7653 (mtm110) REVERT: M 39 THR cc_start: 0.8034 (m) cc_final: 0.7680 (t) REVERT: M 72 ASN cc_start: 0.8390 (m-40) cc_final: 0.8170 (t0) REVERT: M 87 SER cc_start: 0.9232 (t) cc_final: 0.8861 (p) REVERT: N 71 ILE cc_start: 0.7840 (mt) cc_final: 0.7452 (tt) REVERT: N 86 ASP cc_start: 0.7780 (m-30) cc_final: 0.7357 (m-30) REVERT: O 78 MET cc_start: 0.8587 (mmm) cc_final: 0.8107 (mmm) REVERT: P 42 GLN cc_start: 0.7441 (mm110) cc_final: 0.7147 (mt0) REVERT: P 72 ASN cc_start: 0.8567 (m-40) cc_final: 0.8279 (m-40) REVERT: P 144 MET cc_start: 0.9010 (mtm) cc_final: 0.8786 (mtm) REVERT: P 147 ASP cc_start: 0.8518 (t70) cc_final: 0.7773 (t0) REVERT: Q 36 ARG cc_start: 0.8052 (ttm110) cc_final: 0.7803 (mtm110) REVERT: Q 87 SER cc_start: 0.9093 (t) cc_final: 0.8623 (p) REVERT: R 124 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7717 (pp) REVERT: S 90 MET cc_start: 0.7867 (mmm) cc_final: 0.7637 (mmm) REVERT: S 124 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7882 (pp) REVERT: T 1 MET cc_start: 0.5380 (tpp) cc_final: 0.4721 (tpt) REVERT: T 78 MET cc_start: 0.8232 (tpp) cc_final: 0.7988 (tpp) REVERT: T 98 MET cc_start: 0.7969 (tpp) cc_final: 0.7675 (tpt) REVERT: T 125 ARG cc_start: 0.8551 (ttm-80) cc_final: 0.8326 (tpp80) REVERT: U 26 LYS cc_start: 0.8069 (mptt) cc_final: 0.7773 (mttp) REVERT: U 147 ASP cc_start: 0.8526 (t70) cc_final: 0.7779 (t0) REVERT: V 27 ASN cc_start: 0.8814 (m110) cc_final: 0.8546 (m-40) REVERT: W 72 ASN cc_start: 0.8695 (m-40) cc_final: 0.8219 (m-40) REVERT: W 73 LYS cc_start: 0.8788 (tttt) cc_final: 0.8396 (tptt) REVERT: W 150 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7367 (pm20) REVERT: X 67 GLU cc_start: 0.6622 (pp20) cc_final: 0.5845 (mp0) REVERT: Y 1 MET cc_start: 0.6278 (tpp) cc_final: 0.5767 (tpp) REVERT: Y 26 LYS cc_start: 0.8190 (mptt) cc_final: 0.7930 (mttt) REVERT: Y 35 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8054 (mp) REVERT: Y 87 SER cc_start: 0.9164 (t) cc_final: 0.8819 (p) REVERT: Y 128 MET cc_start: 0.8191 (mmt) cc_final: 0.7896 (mmt) REVERT: 1 45 THR cc_start: 0.5491 (m) cc_final: 0.5168 (m) REVERT: 1 67 GLU cc_start: 0.6744 (pp20) cc_final: 0.6064 (mp0) REVERT: 1 78 MET cc_start: 0.8382 (tpp) cc_final: 0.8119 (tpp) REVERT: 2 36 ARG cc_start: 0.8154 (ttm110) cc_final: 0.7751 (mtm110) REVERT: 2 72 ASN cc_start: 0.8368 (m-40) cc_final: 0.8068 (t0) REVERT: 2 87 SER cc_start: 0.9288 (t) cc_final: 0.8688 (p) REVERT: 3 71 ILE cc_start: 0.7879 (mt) cc_final: 0.7507 (tt) REVERT: 3 107 ASP cc_start: 0.7680 (m-30) cc_final: 0.7418 (m-30) REVERT: 5 1 MET cc_start: 0.5590 (tpp) cc_final: 0.5281 (tpt) REVERT: 5 36 ARG cc_start: 0.7764 (mmp80) cc_final: 0.7499 (mtm110) REVERT: 5 42 GLN cc_start: 0.7165 (mm-40) cc_final: 0.6835 (mt0) REVERT: 5 72 ASN cc_start: 0.8408 (m-40) cc_final: 0.8155 (m-40) REVERT: 5 98 MET cc_start: 0.7700 (tpp) cc_final: 0.7232 (tpt) REVERT: 5 123 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8164 (mm-40) REVERT: 5 147 ASP cc_start: 0.8473 (t70) cc_final: 0.8071 (t0) REVERT: 6 2 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7393 (m-30) REVERT: 6 34 SER cc_start: 0.8672 (m) cc_final: 0.8227 (t) REVERT: 6 36 ARG cc_start: 0.8183 (ttm110) cc_final: 0.7854 (mtm110) REVERT: 6 37 GLU cc_start: 0.8390 (pp20) cc_final: 0.8131 (pp20) REVERT: 7 112 MET cc_start: 0.8630 (mmp) cc_final: 0.8149 (mmp) REVERT: 8 15 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7434 (tm-30) REVERT: 8 73 LYS cc_start: 0.8973 (tttt) cc_final: 0.8643 (tptt) REVERT: 8 84 GLN cc_start: 0.8603 (mm110) cc_final: 0.8376 (mm-40) outliers start: 208 outliers final: 142 residues processed: 1212 average time/residue: 0.4514 time to fit residues: 929.8894 Evaluate side-chains 1175 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1019 time to evaluate : 4.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain H residue 27 ASN Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 136 MET Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain J residue 2 ASP Chi-restraints excluded: chain J residue 99 ASN Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain M residue 81 SER Chi-restraints excluded: chain M residue 92 ILE Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain N residue 2 ASP Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain N residue 124 LEU Chi-restraints excluded: chain N residue 140 ILE Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 86 ASP Chi-restraints excluded: chain O residue 99 ASN Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain P residue 92 ILE Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 99 ASN Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 117 SER Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain Q residue 136 MET Chi-restraints excluded: chain R residue 2 ASP Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 22 SER Chi-restraints excluded: chain S residue 86 ASP Chi-restraints excluded: chain S residue 124 LEU Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain T residue 100 THR Chi-restraints excluded: chain T residue 126 ASN Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 81 SER Chi-restraints excluded: chain U residue 117 SER Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain V residue 63 LEU Chi-restraints excluded: chain V residue 117 SER Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 152 VAL Chi-restraints excluded: chain W residue 92 ILE Chi-restraints excluded: chain W residue 150 GLU Chi-restraints excluded: chain X residue 70 GLN Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain X residue 125 ARG Chi-restraints excluded: chain X residue 126 ASN Chi-restraints excluded: chain Y residue 35 LEU Chi-restraints excluded: chain Y residue 92 ILE Chi-restraints excluded: chain Y residue 99 ASN Chi-restraints excluded: chain Y residue 117 SER Chi-restraints excluded: chain Y residue 124 LEU Chi-restraints excluded: chain Z residue 2 ASP Chi-restraints excluded: chain Z residue 124 LEU Chi-restraints excluded: chain Z residue 152 VAL Chi-restraints excluded: chain 0 residue 22 SER Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 123 GLN Chi-restraints excluded: chain 1 residue 124 LEU Chi-restraints excluded: chain 2 residue 41 LEU Chi-restraints excluded: chain 2 residue 81 SER Chi-restraints excluded: chain 2 residue 92 ILE Chi-restraints excluded: chain 2 residue 96 ILE Chi-restraints excluded: chain 2 residue 99 ASN Chi-restraints excluded: chain 2 residue 117 SER Chi-restraints excluded: chain 2 residue 124 LEU Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 2 ASP Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 3 residue 63 LEU Chi-restraints excluded: chain 3 residue 111 LEU Chi-restraints excluded: chain 3 residue 124 LEU Chi-restraints excluded: chain 3 residue 152 VAL Chi-restraints excluded: chain 4 residue 22 SER Chi-restraints excluded: chain 5 residue 81 SER Chi-restraints excluded: chain 5 residue 100 THR Chi-restraints excluded: chain 5 residue 117 SER Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 6 residue 2 ASP Chi-restraints excluded: chain 6 residue 81 SER Chi-restraints excluded: chain 6 residue 92 ILE Chi-restraints excluded: chain 6 residue 117 SER Chi-restraints excluded: chain 6 residue 124 LEU Chi-restraints excluded: chain 6 residue 136 MET Chi-restraints excluded: chain 7 residue 2 ASP Chi-restraints excluded: chain 7 residue 117 SER Chi-restraints excluded: chain 7 residue 124 LEU Chi-restraints excluded: chain 7 residue 136 MET Chi-restraints excluded: chain 8 residue 20 ILE Chi-restraints excluded: chain 8 residue 35 LEU Chi-restraints excluded: chain 8 residue 129 ILE Chi-restraints excluded: chain 9 residue 97 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 199 optimal weight: 7.9990 chunk 532 optimal weight: 50.0000 chunk 116 optimal weight: 0.5980 chunk 347 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 592 optimal weight: 7.9990 chunk 491 optimal weight: 0.6980 chunk 274 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 195 optimal weight: 0.9990 chunk 310 optimal weight: 30.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN C 27 ASN G 27 ASN G 126 ASN H 27 ASN H 104 GLN K 27 ASN L 27 ASN L 72 ASN L 123 GLN N 27 ASN Q 99 ASN Q 103 ASN ** T 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 123 GLN X 72 ASN Y 27 ASN 0 27 ASN 1 72 ASN 1 123 GLN ** 5 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 50040 Z= 0.203 Angle : 0.565 9.298 66852 Z= 0.298 Chirality : 0.041 0.214 7560 Planarity : 0.003 0.027 8676 Dihedral : 4.314 35.316 6806 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 1.17 % Allowed : 2.46 % Favored : 96.36 % Rotamer: Outliers : 3.76 % Allowed : 19.94 % Favored : 76.30 % 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: -0.25 (0.10), residues: 6048 helix: 0.18 (0.07), residues: 5112 sheet: None (None), residues: 0 loop : -1.47 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 9 TYR 0.016 0.001 TYR K 79 ARG 0.005 0.000 ARG J 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1277 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 1066 time to evaluate : 4.774 Fit side-chains revert: symmetry clash REVERT: B 30 ASN cc_start: 0.8063 (m-40) cc_final: 0.7704 (m-40) REVERT: B 34 SER cc_start: 0.8362 (m) cc_final: 0.7710 (t) REVERT: B 36 ARG cc_start: 0.8020 (ttm110) cc_final: 0.7676 (mtm110) REVERT: B 72 ASN cc_start: 0.8478 (m-40) cc_final: 0.8153 (t0) REVERT: B 78 MET cc_start: 0.7907 (tpp) cc_final: 0.7639 (tpp) REVERT: B 114 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8102 (mt-10) REVERT: A 2 ASP cc_start: 0.6055 (OUTLIER) cc_final: 0.5780 (t70) REVERT: A 71 ILE cc_start: 0.7642 (mt) cc_final: 0.7289 (tt) REVERT: A 78 MET cc_start: 0.8168 (tpp) cc_final: 0.7786 (mmt) REVERT: C 72 ASN cc_start: 0.8745 (m-40) cc_final: 0.8413 (m110) REVERT: C 73 LYS cc_start: 0.8730 (tttt) cc_final: 0.8453 (tptt) REVERT: C 86 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7835 (t0) REVERT: C 123 GLN cc_start: 0.8281 (mp10) cc_final: 0.7854 (mp10) REVERT: D 1 MET cc_start: 0.5760 (tpp) cc_final: 0.5436 (tpt) REVERT: D 36 ARG cc_start: 0.7841 (mmp80) cc_final: 0.7448 (mtm110) REVERT: D 67 GLU cc_start: 0.6258 (pp20) cc_final: 0.5705 (mp0) REVERT: D 123 GLN cc_start: 0.8478 (mm-40) cc_final: 0.7987 (mm-40) REVERT: E 34 SER cc_start: 0.8614 (m) cc_final: 0.8214 (t) REVERT: E 35 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7738 (mp) REVERT: E 36 ARG cc_start: 0.7992 (ttm110) cc_final: 0.7727 (mtm110) REVERT: E 72 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.8032 (t0) REVERT: E 80 THR cc_start: 0.9222 (OUTLIER) cc_final: 0.8878 (p) REVERT: F 130 GLU cc_start: 0.7751 (tt0) cc_final: 0.7538 (pt0) REVERT: F 132 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8625 (tm-30) REVERT: G 6 LYS cc_start: 0.9184 (mttt) cc_final: 0.7484 (tttm) REVERT: G 26 LYS cc_start: 0.8590 (ttpp) cc_final: 0.8384 (ttmt) REVERT: H 1 MET cc_start: 0.5674 (tpp) cc_final: 0.4926 (tpt) REVERT: H 76 ASP cc_start: 0.8204 (m-30) cc_final: 0.7982 (m-30) REVERT: H 129 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7758 (mp) REVERT: I 1 MET cc_start: 0.6547 (tpp) cc_final: 0.6108 (tpt) REVERT: I 20 ILE cc_start: 0.8611 (mt) cc_final: 0.8406 (tt) REVERT: I 33 LYS cc_start: 0.8056 (tmmm) cc_final: 0.7609 (tptt) REVERT: I 36 ARG cc_start: 0.8177 (ttm110) cc_final: 0.7941 (mtm-85) REVERT: I 147 ASP cc_start: 0.8660 (t70) cc_final: 0.8017 (t0) REVERT: J 123 GLN cc_start: 0.8481 (mm-40) cc_final: 0.8279 (mm-40) REVERT: K 73 LYS cc_start: 0.8970 (tttt) cc_final: 0.8518 (tptt) REVERT: K 112 MET cc_start: 0.8901 (mmp) cc_final: 0.8555 (mmp) REVERT: K 123 GLN cc_start: 0.8373 (mp10) cc_final: 0.8098 (mp10) REVERT: L 36 ARG cc_start: 0.7892 (mmp80) cc_final: 0.7583 (mtm110) REVERT: L 67 GLU cc_start: 0.6446 (pp20) cc_final: 0.5713 (mp0) REVERT: L 124 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8344 (pp) REVERT: M 36 ARG cc_start: 0.8048 (ttm110) cc_final: 0.7662 (mtm110) REVERT: M 39 THR cc_start: 0.8076 (m) cc_final: 0.7709 (t) REVERT: M 72 ASN cc_start: 0.8407 (m-40) cc_final: 0.8206 (t0) REVERT: M 87 SER cc_start: 0.9232 (t) cc_final: 0.8868 (p) REVERT: N 30 ASN cc_start: 0.8415 (m-40) cc_final: 0.8155 (t0) REVERT: N 71 ILE cc_start: 0.7840 (mt) cc_final: 0.7441 (tt) REVERT: O 78 MET cc_start: 0.8588 (mmm) cc_final: 0.8051 (mmm) REVERT: P 36 ARG cc_start: 0.7791 (mmp80) cc_final: 0.7437 (mtm110) REVERT: P 42 GLN cc_start: 0.7450 (mm110) cc_final: 0.7117 (mt0) REVERT: P 72 ASN cc_start: 0.8560 (m-40) cc_final: 0.8281 (m-40) REVERT: P 144 MET cc_start: 0.9030 (mtm) cc_final: 0.8803 (mtm) REVERT: P 147 ASP cc_start: 0.8522 (t70) cc_final: 0.7760 (t0) REVERT: P 159 MET cc_start: 0.4476 (mmm) cc_final: 0.4079 (mmm) REVERT: Q 36 ARG cc_start: 0.8067 (ttm110) cc_final: 0.7749 (mtm110) REVERT: Q 87 SER cc_start: 0.9092 (t) cc_final: 0.8627 (p) REVERT: R 124 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7744 (pp) REVERT: S 124 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7846 (pp) REVERT: T 1 MET cc_start: 0.5419 (tpp) cc_final: 0.4765 (tpt) REVERT: T 36 ARG cc_start: 0.7870 (mmp80) cc_final: 0.7419 (mtm110) REVERT: T 78 MET cc_start: 0.8263 (tpp) cc_final: 0.7995 (tpp) REVERT: T 98 MET cc_start: 0.7958 (tpp) cc_final: 0.7666 (tpt) REVERT: T 147 ASP cc_start: 0.8680 (t70) cc_final: 0.7921 (t0) REVERT: U 87 SER cc_start: 0.9160 (OUTLIER) cc_final: 0.8542 (p) REVERT: U 124 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8298 (pp) REVERT: U 147 ASP cc_start: 0.8541 (t70) cc_final: 0.7788 (t0) REVERT: V 27 ASN cc_start: 0.8750 (m110) cc_final: 0.8550 (m-40) REVERT: W 72 ASN cc_start: 0.8718 (m-40) cc_final: 0.8256 (m-40) REVERT: W 73 LYS cc_start: 0.8820 (tttt) cc_final: 0.8457 (tptt) REVERT: W 150 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7339 (pm20) REVERT: X 36 ARG cc_start: 0.7914 (mmp80) cc_final: 0.7558 (mtm110) REVERT: X 67 GLU cc_start: 0.6711 (pp20) cc_final: 0.5942 (mp0) REVERT: X 72 ASN cc_start: 0.8903 (m-40) cc_final: 0.8661 (m110) REVERT: X 132 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8669 (tm-30) REVERT: Y 1 MET cc_start: 0.6293 (tpp) cc_final: 0.5779 (tpp) REVERT: Y 26 LYS cc_start: 0.8177 (mptt) cc_final: 0.7918 (mttp) REVERT: Y 34 SER cc_start: 0.8577 (m) cc_final: 0.8301 (t) REVERT: Y 87 SER cc_start: 0.9162 (t) cc_final: 0.8807 (p) REVERT: Y 128 MET cc_start: 0.8239 (mmt) cc_final: 0.7960 (mmt) REVERT: 1 36 ARG cc_start: 0.8009 (mmp80) cc_final: 0.7444 (mtm110) REVERT: 1 45 THR cc_start: 0.5579 (m) cc_final: 0.5330 (m) REVERT: 1 67 GLU cc_start: 0.6917 (pp20) cc_final: 0.6246 (mp0) REVERT: 1 78 MET cc_start: 0.8386 (tpp) cc_final: 0.8132 (tpp) REVERT: 2 36 ARG cc_start: 0.8137 (ttm110) cc_final: 0.7784 (mtm110) REVERT: 2 72 ASN cc_start: 0.8398 (m-40) cc_final: 0.8110 (t0) REVERT: 2 87 SER cc_start: 0.9255 (t) cc_final: 0.8657 (p) REVERT: 3 71 ILE cc_start: 0.7926 (mt) cc_final: 0.7525 (tt) REVERT: 3 107 ASP cc_start: 0.7663 (m-30) cc_final: 0.7402 (m-30) REVERT: 5 1 MET cc_start: 0.5536 (tpp) cc_final: 0.5199 (tpt) REVERT: 5 26 LYS cc_start: 0.8574 (mmtp) cc_final: 0.8287 (mttm) REVERT: 5 42 GLN cc_start: 0.7183 (mm-40) cc_final: 0.6828 (mt0) REVERT: 5 72 ASN cc_start: 0.8418 (m-40) cc_final: 0.8157 (m-40) REVERT: 5 98 MET cc_start: 0.7671 (tpp) cc_final: 0.7189 (tpt) REVERT: 5 147 ASP cc_start: 0.8464 (t70) cc_final: 0.8025 (t0) REVERT: 6 2 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7363 (m-30) REVERT: 6 34 SER cc_start: 0.8674 (m) cc_final: 0.8288 (t) REVERT: 6 36 ARG cc_start: 0.8144 (ttm110) cc_final: 0.7798 (mtm110) REVERT: 6 37 GLU cc_start: 0.8392 (pp20) cc_final: 0.8136 (pp20) REVERT: 7 112 MET cc_start: 0.8633 (mmp) cc_final: 0.8176 (mmp) REVERT: 8 15 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7418 (tm-30) REVERT: 8 73 LYS cc_start: 0.9024 (tttt) cc_final: 0.8590 (ttmt) REVERT: 8 76 ASP cc_start: 0.9060 (OUTLIER) cc_final: 0.8810 (t0) REVERT: 8 84 GLN cc_start: 0.8592 (mm110) cc_final: 0.8376 (mm-40) outliers start: 211 outliers final: 151 residues processed: 1208 average time/residue: 0.4463 time to fit residues: 919.5704 Evaluate side-chains 1193 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1028 time to evaluate : 4.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 136 MET Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain J residue 2 ASP Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 123 GLN Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 126 ASN Chi-restraints excluded: chain M residue 81 SER Chi-restraints excluded: chain M residue 92 ILE Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain N residue 2 ASP Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain N residue 124 LEU Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 99 ASN Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 92 ILE Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 117 SER Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain Q residue 136 MET Chi-restraints excluded: chain R residue 2 ASP Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 22 SER Chi-restraints excluded: chain S residue 86 ASP Chi-restraints excluded: chain S residue 124 LEU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain T residue 100 THR Chi-restraints excluded: chain T residue 126 ASN Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 81 SER Chi-restraints excluded: chain U residue 87 SER Chi-restraints excluded: chain U residue 117 SER Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain V residue 2 ASP Chi-restraints excluded: chain V residue 99 ASN Chi-restraints excluded: chain V residue 117 SER Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 152 VAL Chi-restraints excluded: chain W residue 150 GLU Chi-restraints excluded: chain X residue 70 GLN Chi-restraints excluded: chain X residue 80 THR Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain X residue 123 GLN Chi-restraints excluded: chain X residue 125 ARG Chi-restraints excluded: chain X residue 126 ASN Chi-restraints excluded: chain Y residue 92 ILE Chi-restraints excluded: chain Y residue 117 SER Chi-restraints excluded: chain Y residue 124 LEU Chi-restraints excluded: chain Z residue 2 ASP Chi-restraints excluded: chain Z residue 124 LEU Chi-restraints excluded: chain Z residue 152 VAL Chi-restraints excluded: chain 0 residue 22 SER Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 80 THR Chi-restraints excluded: chain 1 residue 123 GLN Chi-restraints excluded: chain 1 residue 124 LEU Chi-restraints excluded: chain 2 residue 41 LEU Chi-restraints excluded: chain 2 residue 81 SER Chi-restraints excluded: chain 2 residue 92 ILE Chi-restraints excluded: chain 2 residue 96 ILE Chi-restraints excluded: chain 2 residue 99 ASN Chi-restraints excluded: chain 2 residue 117 SER Chi-restraints excluded: chain 2 residue 124 LEU Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 2 ASP Chi-restraints excluded: chain 3 residue 29 ARG Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 3 residue 63 LEU Chi-restraints excluded: chain 3 residue 99 ASN Chi-restraints excluded: chain 3 residue 124 LEU Chi-restraints excluded: chain 3 residue 130 GLU Chi-restraints excluded: chain 3 residue 140 ILE Chi-restraints excluded: chain 3 residue 152 VAL Chi-restraints excluded: chain 4 residue 22 SER Chi-restraints excluded: chain 5 residue 81 SER Chi-restraints excluded: chain 5 residue 100 THR Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 6 residue 2 ASP Chi-restraints excluded: chain 6 residue 81 SER Chi-restraints excluded: chain 6 residue 92 ILE Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 117 SER Chi-restraints excluded: chain 6 residue 124 LEU Chi-restraints excluded: chain 6 residue 136 MET Chi-restraints excluded: chain 7 residue 2 ASP Chi-restraints excluded: chain 7 residue 117 SER Chi-restraints excluded: chain 7 residue 124 LEU Chi-restraints excluded: chain 7 residue 136 MET Chi-restraints excluded: chain 8 residue 20 ILE Chi-restraints excluded: chain 8 residue 35 LEU Chi-restraints excluded: chain 8 residue 76 ASP Chi-restraints excluded: chain 8 residue 129 ILE Chi-restraints excluded: chain 8 residue 167 VAL Chi-restraints excluded: chain 9 residue 97 ARG Chi-restraints excluded: chain 9 residue 100 THR Chi-restraints excluded: chain 9 residue 126 ASN Chi-restraints excluded: chain 9 residue 135 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 570 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 337 optimal weight: 3.9990 chunk 432 optimal weight: 9.9990 chunk 335 optimal weight: 3.9990 chunk 498 optimal weight: 2.9990 chunk 330 optimal weight: 8.9990 chunk 589 optimal weight: 0.8980 chunk 369 optimal weight: 10.0000 chunk 359 optimal weight: 4.9990 chunk 272 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 72 ASN L 27 ASN L 72 ASN L 123 GLN M 103 ASN O 42 GLN ** P 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 GLN ** T 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 123 GLN W 27 ASN Y 27 ASN 1 72 ASN 1 123 GLN 3 72 ASN ** 5 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 50040 Z= 0.279 Angle : 0.601 9.453 66852 Z= 0.314 Chirality : 0.043 0.255 7560 Planarity : 0.003 0.030 8676 Dihedral : 4.326 36.399 6806 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 1.17 % Allowed : 2.55 % Favored : 96.28 % Rotamer: Outliers : 4.04 % Allowed : 19.85 % Favored : 76.10 % 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: 0.04 (0.10), residues: 6048 helix: 0.39 (0.07), residues: 5112 sheet: None (None), residues: 0 loop : -1.45 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP 1 9 TYR 0.016 0.001 TYR 3 79 ARG 0.006 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1257 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 1030 time to evaluate : 4.720 Fit side-chains revert: symmetry clash REVERT: B 34 SER cc_start: 0.8314 (m) cc_final: 0.7705 (t) REVERT: B 36 ARG cc_start: 0.8082 (ttm110) cc_final: 0.7722 (mtm110) REVERT: B 72 ASN cc_start: 0.8393 (m-40) cc_final: 0.7983 (t0) REVERT: B 78 MET cc_start: 0.8006 (tpp) cc_final: 0.7717 (tpp) REVERT: A 2 ASP cc_start: 0.6097 (OUTLIER) cc_final: 0.5826 (t70) REVERT: A 71 ILE cc_start: 0.7669 (mt) cc_final: 0.7274 (tt) REVERT: C 72 ASN cc_start: 0.8755 (m-40) cc_final: 0.8406 (m110) REVERT: C 73 LYS cc_start: 0.8731 (tttt) cc_final: 0.8464 (tptt) REVERT: C 78 MET cc_start: 0.8153 (mmm) cc_final: 0.7891 (mtt) REVERT: C 86 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7935 (t0) REVERT: D 1 MET cc_start: 0.5818 (tpp) cc_final: 0.5569 (tpt) REVERT: D 2 ASP cc_start: 0.7442 (OUTLIER) cc_final: 0.7086 (p0) REVERT: D 67 GLU cc_start: 0.6419 (pp20) cc_final: 0.5801 (mp0) REVERT: D 123 GLN cc_start: 0.8520 (mm-40) cc_final: 0.7991 (mm-40) REVERT: E 34 SER cc_start: 0.8527 (m) cc_final: 0.8172 (t) REVERT: E 35 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7689 (mp) REVERT: E 36 ARG cc_start: 0.8021 (ttm110) cc_final: 0.7736 (mtm110) REVERT: E 72 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.8036 (t0) REVERT: E 80 THR cc_start: 0.9229 (OUTLIER) cc_final: 0.8904 (p) REVERT: F 130 GLU cc_start: 0.7813 (tt0) cc_final: 0.7587 (pt0) REVERT: G 6 LYS cc_start: 0.9173 (mttt) cc_final: 0.7438 (tttm) REVERT: G 84 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8158 (mt0) REVERT: G 86 ASP cc_start: 0.8229 (t0) cc_final: 0.7875 (t70) REVERT: H 1 MET cc_start: 0.5680 (tpp) cc_final: 0.4872 (tpt) REVERT: H 36 ARG cc_start: 0.7819 (mmp80) cc_final: 0.7475 (mmp80) REVERT: H 76 ASP cc_start: 0.8189 (m-30) cc_final: 0.7955 (m-30) REVERT: H 129 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7756 (mp) REVERT: I 1 MET cc_start: 0.6512 (tpp) cc_final: 0.6081 (tpt) REVERT: I 20 ILE cc_start: 0.8655 (mt) cc_final: 0.8423 (tt) REVERT: I 33 LYS cc_start: 0.8036 (tmmm) cc_final: 0.7426 (tptt) REVERT: I 36 ARG cc_start: 0.8170 (ttm110) cc_final: 0.7932 (mtm-85) REVERT: I 147 ASP cc_start: 0.8673 (t70) cc_final: 0.8049 (t0) REVERT: J 1 MET cc_start: 0.4253 (OUTLIER) cc_final: 0.3584 (tmm) REVERT: J 78 MET cc_start: 0.7805 (mmm) cc_final: 0.7593 (ttp) REVERT: J 123 GLN cc_start: 0.8501 (mm-40) cc_final: 0.8286 (mm-40) REVERT: K 72 ASN cc_start: 0.8655 (m-40) cc_final: 0.8391 (m110) REVERT: K 73 LYS cc_start: 0.8965 (tttt) cc_final: 0.8523 (tptt) REVERT: L 36 ARG cc_start: 0.7906 (mmp80) cc_final: 0.7555 (mtm110) REVERT: L 67 GLU cc_start: 0.6448 (pp20) cc_final: 0.5698 (mp0) REVERT: L 84 GLN cc_start: 0.8388 (mm-40) cc_final: 0.8096 (mt0) REVERT: L 124 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8384 (pp) REVERT: L 125 ARG cc_start: 0.8586 (ttm-80) cc_final: 0.8202 (tpp80) REVERT: M 34 SER cc_start: 0.8358 (m) cc_final: 0.8031 (t) REVERT: M 36 ARG cc_start: 0.8055 (ttm110) cc_final: 0.7663 (mtm110) REVERT: M 39 THR cc_start: 0.8094 (m) cc_final: 0.7713 (t) REVERT: M 87 SER cc_start: 0.9227 (t) cc_final: 0.8890 (p) REVERT: N 30 ASN cc_start: 0.8405 (m-40) cc_final: 0.8195 (t0) REVERT: N 71 ILE cc_start: 0.7863 (mt) cc_final: 0.7462 (tt) REVERT: O 78 MET cc_start: 0.8557 (mmm) cc_final: 0.8051 (mmm) REVERT: O 123 GLN cc_start: 0.8313 (mp10) cc_final: 0.8047 (mp10) REVERT: P 36 ARG cc_start: 0.7825 (mmp80) cc_final: 0.7612 (mmp80) REVERT: P 42 GLN cc_start: 0.7442 (mm110) cc_final: 0.7097 (mt0) REVERT: P 72 ASN cc_start: 0.8624 (m-40) cc_final: 0.8285 (m-40) REVERT: P 147 ASP cc_start: 0.8573 (t70) cc_final: 0.7805 (t0) REVERT: Q 36 ARG cc_start: 0.8113 (ttm110) cc_final: 0.7783 (mtm110) REVERT: Q 87 SER cc_start: 0.9112 (t) cc_final: 0.8656 (p) REVERT: S 72 ASN cc_start: 0.8804 (m-40) cc_final: 0.8570 (m-40) REVERT: S 124 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8013 (pp) REVERT: T 1 MET cc_start: 0.5454 (tpp) cc_final: 0.4783 (tpt) REVERT: T 36 ARG cc_start: 0.7911 (mmp80) cc_final: 0.7442 (mtm110) REVERT: T 78 MET cc_start: 0.8336 (tpp) cc_final: 0.8054 (tpp) REVERT: T 98 MET cc_start: 0.8046 (tpp) cc_final: 0.7510 (tpp) REVERT: T 147 ASP cc_start: 0.8691 (t70) cc_final: 0.8011 (t0) REVERT: U 34 SER cc_start: 0.8338 (m) cc_final: 0.8111 (t) REVERT: U 87 SER cc_start: 0.9176 (OUTLIER) cc_final: 0.8560 (p) REVERT: U 124 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8135 (pp) REVERT: V 136 MET cc_start: 0.7971 (mtp) cc_final: 0.7754 (mtp) REVERT: W 72 ASN cc_start: 0.8782 (m-40) cc_final: 0.8294 (m-40) REVERT: W 73 LYS cc_start: 0.8840 (tttt) cc_final: 0.8490 (tptt) REVERT: W 150 GLU cc_start: 0.7986 (pp20) cc_final: 0.7698 (pm20) REVERT: X 36 ARG cc_start: 0.7948 (mmp80) cc_final: 0.7552 (mtm110) REVERT: X 67 GLU cc_start: 0.6679 (pp20) cc_final: 0.6072 (mp0) REVERT: X 72 ASN cc_start: 0.8960 (m-40) cc_final: 0.8713 (m110) REVERT: X 147 ASP cc_start: 0.8836 (t70) cc_final: 0.8605 (t0) REVERT: Y 1 MET cc_start: 0.6345 (tpp) cc_final: 0.5796 (tpp) REVERT: Y 26 LYS cc_start: 0.8155 (mptt) cc_final: 0.7884 (mttt) REVERT: Y 87 SER cc_start: 0.9191 (t) cc_final: 0.8838 (p) REVERT: Y 128 MET cc_start: 0.8230 (mmt) cc_final: 0.7956 (mmt) REVERT: 1 36 ARG cc_start: 0.8085 (mmp80) cc_final: 0.7485 (mtm110) REVERT: 1 67 GLU cc_start: 0.7014 (pp20) cc_final: 0.6336 (mp0) REVERT: 1 78 MET cc_start: 0.8431 (tpp) cc_final: 0.8169 (tpp) REVERT: 1 84 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7873 (mt0) REVERT: 1 159 MET cc_start: 0.4382 (mmm) cc_final: 0.4074 (mmm) REVERT: 2 36 ARG cc_start: 0.8178 (ttm110) cc_final: 0.7806 (mtm110) REVERT: 2 72 ASN cc_start: 0.8440 (m-40) cc_final: 0.8180 (t0) REVERT: 2 87 SER cc_start: 0.9278 (t) cc_final: 0.8688 (p) REVERT: 2 98 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7507 (tpp) REVERT: 3 30 ASN cc_start: 0.8352 (m-40) cc_final: 0.8117 (t0) REVERT: 3 71 ILE cc_start: 0.7934 (mt) cc_final: 0.7535 (tt) REVERT: 5 1 MET cc_start: 0.5600 (tpp) cc_final: 0.5228 (tpt) REVERT: 5 26 LYS cc_start: 0.8564 (mmtp) cc_final: 0.8314 (mttm) REVERT: 5 36 ARG cc_start: 0.7771 (mmp80) cc_final: 0.7490 (mtm110) REVERT: 5 72 ASN cc_start: 0.8386 (m-40) cc_final: 0.8132 (m-40) REVERT: 5 78 MET cc_start: 0.8390 (tpp) cc_final: 0.8141 (tpp) REVERT: 5 98 MET cc_start: 0.7857 (tpp) cc_final: 0.7050 (tpp) REVERT: 5 123 GLN cc_start: 0.8414 (mm-40) cc_final: 0.8011 (mm-40) REVERT: 5 147 ASP cc_start: 0.8544 (t70) cc_final: 0.8066 (t0) REVERT: 6 2 ASP cc_start: 0.7602 (OUTLIER) cc_final: 0.7378 (m-30) REVERT: 6 34 SER cc_start: 0.8579 (m) cc_final: 0.8225 (t) REVERT: 6 37 GLU cc_start: 0.8449 (pp20) cc_final: 0.8199 (pp20) REVERT: 7 112 MET cc_start: 0.8661 (mmp) cc_final: 0.8233 (mmp) REVERT: 8 73 LYS cc_start: 0.9019 (tttt) cc_final: 0.8679 (mmtp) REVERT: 8 84 GLN cc_start: 0.8612 (mm110) cc_final: 0.8351 (mm-40) REVERT: 9 2 ASP cc_start: 0.6824 (t0) cc_final: 0.6586 (t0) REVERT: 9 92 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8099 (tt) REVERT: 9 98 MET cc_start: 0.7855 (tpp) cc_final: 0.7629 (tpp) outliers start: 227 outliers final: 163 residues processed: 1188 average time/residue: 0.4456 time to fit residues: 908.0973 Evaluate side-chains 1183 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1005 time to evaluate : 4.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain D residue 2 ASP Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 99 ASN Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 136 MET Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 2 ASP Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 126 ASN Chi-restraints excluded: chain M residue 81 SER Chi-restraints excluded: chain M residue 92 ILE Chi-restraints excluded: chain M residue 99 ASN Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain N residue 2 ASP Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain N residue 124 LEU Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 99 ASN Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 92 ILE Chi-restraints excluded: chain Q residue 117 SER Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain Q residue 136 MET Chi-restraints excluded: chain R residue 2 ASP Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 136 MET Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 22 SER Chi-restraints excluded: chain S residue 124 LEU Chi-restraints excluded: chain S residue 140 ILE Chi-restraints excluded: chain T residue 27 ASN Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain T residue 100 THR Chi-restraints excluded: chain T residue 126 ASN Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 81 SER Chi-restraints excluded: chain U residue 87 SER Chi-restraints excluded: chain U residue 117 SER Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain V residue 2 ASP Chi-restraints excluded: chain V residue 117 SER Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 140 ILE Chi-restraints excluded: chain V residue 152 VAL Chi-restraints excluded: chain W residue 27 ASN Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain X residue 70 GLN Chi-restraints excluded: chain X residue 80 THR Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain X residue 123 GLN Chi-restraints excluded: chain X residue 125 ARG Chi-restraints excluded: chain X residue 126 ASN Chi-restraints excluded: chain Y residue 92 ILE Chi-restraints excluded: chain Y residue 99 ASN Chi-restraints excluded: chain Y residue 100 THR Chi-restraints excluded: chain Y residue 117 SER Chi-restraints excluded: chain Y residue 124 LEU Chi-restraints excluded: chain Z residue 2 ASP Chi-restraints excluded: chain Z residue 105 MET Chi-restraints excluded: chain Z residue 117 SER Chi-restraints excluded: chain Z residue 124 LEU Chi-restraints excluded: chain Z residue 152 VAL Chi-restraints excluded: chain Z residue 159 MET Chi-restraints excluded: chain 0 residue 22 SER Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 80 THR Chi-restraints excluded: chain 1 residue 124 LEU Chi-restraints excluded: chain 2 residue 22 SER Chi-restraints excluded: chain 2 residue 41 LEU Chi-restraints excluded: chain 2 residue 81 SER Chi-restraints excluded: chain 2 residue 92 ILE Chi-restraints excluded: chain 2 residue 96 ILE Chi-restraints excluded: chain 2 residue 98 MET Chi-restraints excluded: chain 2 residue 117 SER Chi-restraints excluded: chain 2 residue 124 LEU Chi-restraints excluded: chain 3 residue 2 ASP Chi-restraints excluded: chain 3 residue 29 ARG Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 3 residue 63 LEU Chi-restraints excluded: chain 3 residue 124 LEU Chi-restraints excluded: chain 3 residue 140 ILE Chi-restraints excluded: chain 3 residue 152 VAL Chi-restraints excluded: chain 3 residue 163 VAL Chi-restraints excluded: chain 4 residue 22 SER Chi-restraints excluded: chain 5 residue 27 ASN Chi-restraints excluded: chain 5 residue 81 SER Chi-restraints excluded: chain 5 residue 100 THR Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 135 LEU Chi-restraints excluded: chain 6 residue 2 ASP Chi-restraints excluded: chain 6 residue 81 SER Chi-restraints excluded: chain 6 residue 92 ILE Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 117 SER Chi-restraints excluded: chain 6 residue 124 LEU Chi-restraints excluded: chain 6 residue 136 MET Chi-restraints excluded: chain 7 residue 2 ASP Chi-restraints excluded: chain 7 residue 117 SER Chi-restraints excluded: chain 7 residue 124 LEU Chi-restraints excluded: chain 8 residue 20 ILE Chi-restraints excluded: chain 8 residue 35 LEU Chi-restraints excluded: chain 8 residue 129 ILE Chi-restraints excluded: chain 8 residue 167 VAL Chi-restraints excluded: chain 9 residue 92 ILE Chi-restraints excluded: chain 9 residue 100 THR Chi-restraints excluded: chain 9 residue 126 ASN Chi-restraints excluded: chain 9 residue 135 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 364 optimal weight: 9.9990 chunk 235 optimal weight: 4.9990 chunk 352 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 375 optimal weight: 0.9980 chunk 401 optimal weight: 0.6980 chunk 291 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 463 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 ASN I 43 ASN K 42 GLN L 27 ASN L 42 GLN L 72 ASN L 123 GLN M 27 ASN O 42 GLN S 42 GLN T 123 GLN V 27 ASN W 27 ASN ** 0 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 72 ASN 1 123 GLN 5 42 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 50040 Z= 0.195 Angle : 0.573 10.371 66852 Z= 0.299 Chirality : 0.041 0.156 7560 Planarity : 0.002 0.032 8676 Dihedral : 4.192 36.260 6806 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 1.16 % Allowed : 2.43 % Favored : 96.41 % Rotamer: Outliers : 3.40 % Allowed : 20.83 % Favored : 75.77 % 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: 0.43 (0.11), residues: 6048 helix: 0.67 (0.07), residues: 5112 sheet: None (None), residues: 0 loop : -1.38 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 9 TYR 0.019 0.001 TYR 3 79 ARG 0.008 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1251 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1060 time to evaluate : 4.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 ASN cc_start: 0.8048 (m-40) cc_final: 0.7671 (m-40) REVERT: B 34 SER cc_start: 0.8195 (m) cc_final: 0.7609 (t) REVERT: B 36 ARG cc_start: 0.8088 (ttm110) cc_final: 0.7726 (mtm110) REVERT: B 72 ASN cc_start: 0.8285 (m-40) cc_final: 0.7982 (t0) REVERT: B 78 MET cc_start: 0.7918 (tpp) cc_final: 0.7654 (tpp) REVERT: A 2 ASP cc_start: 0.5938 (OUTLIER) cc_final: 0.5653 (t70) REVERT: A 71 ILE cc_start: 0.7636 (mt) cc_final: 0.7257 (tt) REVERT: C 72 ASN cc_start: 0.8765 (m-40) cc_final: 0.8322 (m110) REVERT: C 73 LYS cc_start: 0.8760 (tttt) cc_final: 0.8550 (tptt) REVERT: C 78 MET cc_start: 0.8179 (mmm) cc_final: 0.7934 (mtt) REVERT: C 86 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7912 (t0) REVERT: D 1 MET cc_start: 0.5719 (tpp) cc_final: 0.5512 (tpt) REVERT: D 36 ARG cc_start: 0.7867 (mmp80) cc_final: 0.7486 (mtm110) REVERT: D 67 GLU cc_start: 0.6394 (pp20) cc_final: 0.5808 (mp0) REVERT: D 123 GLN cc_start: 0.8561 (mm-40) cc_final: 0.7962 (mm-40) REVERT: E 34 SER cc_start: 0.8407 (m) cc_final: 0.8105 (t) REVERT: E 35 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7717 (mp) REVERT: E 36 ARG cc_start: 0.8013 (ttm110) cc_final: 0.7732 (mtm110) REVERT: E 72 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.8016 (t0) REVERT: E 80 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8900 (p) REVERT: G 6 LYS cc_start: 0.9147 (mttt) cc_final: 0.7477 (tttm) REVERT: G 84 GLN cc_start: 0.8466 (mm-40) cc_final: 0.8097 (mt0) REVERT: G 86 ASP cc_start: 0.8200 (t0) cc_final: 0.7869 (t70) REVERT: H 1 MET cc_start: 0.5671 (tpp) cc_final: 0.4929 (tpt) REVERT: H 72 ASN cc_start: 0.8531 (m-40) cc_final: 0.8255 (m110) REVERT: H 76 ASP cc_start: 0.8171 (m-30) cc_final: 0.7916 (m-30) REVERT: H 84 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8328 (mt0) REVERT: H 129 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7733 (mp) REVERT: I 1 MET cc_start: 0.6475 (tpp) cc_final: 0.6022 (tpt) REVERT: I 26 LYS cc_start: 0.7994 (mttm) cc_final: 0.7709 (mtpp) REVERT: I 36 ARG cc_start: 0.8172 (ttm110) cc_final: 0.7913 (mtm-85) REVERT: I 78 MET cc_start: 0.7995 (tpp) cc_final: 0.7711 (tpt) REVERT: I 80 THR cc_start: 0.9214 (OUTLIER) cc_final: 0.8902 (p) REVERT: I 147 ASP cc_start: 0.8665 (t70) cc_final: 0.8072 (t0) REVERT: K 72 ASN cc_start: 0.8700 (m-40) cc_final: 0.8366 (m-40) REVERT: L 67 GLU cc_start: 0.6526 (pp20) cc_final: 0.5832 (mp0) REVERT: L 84 GLN cc_start: 0.8294 (mm-40) cc_final: 0.7999 (mt0) REVERT: L 123 GLN cc_start: 0.8443 (mm110) cc_final: 0.7902 (mm-40) REVERT: L 124 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8303 (pp) REVERT: M 1 MET cc_start: 0.6162 (tpp) cc_final: 0.5956 (tpp) REVERT: M 34 SER cc_start: 0.8230 (m) cc_final: 0.7960 (t) REVERT: M 36 ARG cc_start: 0.7985 (ttm110) cc_final: 0.7601 (mtm110) REVERT: M 39 THR cc_start: 0.8087 (m) cc_final: 0.7721 (t) REVERT: M 87 SER cc_start: 0.9223 (t) cc_final: 0.8875 (p) REVERT: N 71 ILE cc_start: 0.7850 (mt) cc_final: 0.7454 (tt) REVERT: O 78 MET cc_start: 0.8601 (mmm) cc_final: 0.8035 (mmm) REVERT: O 112 MET cc_start: 0.8734 (mmp) cc_final: 0.8406 (mmp) REVERT: O 123 GLN cc_start: 0.8320 (mp10) cc_final: 0.8117 (mp10) REVERT: P 42 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.7056 (mt0) REVERT: P 72 ASN cc_start: 0.8624 (m-40) cc_final: 0.8364 (m-40) REVERT: P 147 ASP cc_start: 0.8507 (t70) cc_final: 0.7739 (t0) REVERT: Q 36 ARG cc_start: 0.7988 (ttm110) cc_final: 0.7657 (mtm110) REVERT: Q 87 SER cc_start: 0.9055 (t) cc_final: 0.8581 (p) REVERT: S 124 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7809 (pp) REVERT: T 1 MET cc_start: 0.5410 (tpp) cc_final: 0.4731 (tpt) REVERT: T 36 ARG cc_start: 0.7891 (mmp80) cc_final: 0.7342 (mtm110) REVERT: T 78 MET cc_start: 0.8288 (tpp) cc_final: 0.7999 (tpp) REVERT: T 84 GLN cc_start: 0.8344 (mm-40) cc_final: 0.7807 (mt0) REVERT: T 98 MET cc_start: 0.7934 (tpp) cc_final: 0.7651 (tpt) REVERT: T 147 ASP cc_start: 0.8635 (t70) cc_final: 0.7950 (t0) REVERT: U 87 SER cc_start: 0.9172 (OUTLIER) cc_final: 0.8569 (p) REVERT: U 124 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8176 (pp) REVERT: U 133 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8421 (ttpt) REVERT: U 147 ASP cc_start: 0.8371 (t70) cc_final: 0.8097 (t0) REVERT: V 30 ASN cc_start: 0.8238 (m-40) cc_final: 0.7885 (t0) REVERT: V 136 MET cc_start: 0.7864 (mtp) cc_final: 0.7644 (mtp) REVERT: W 72 ASN cc_start: 0.8775 (m-40) cc_final: 0.8287 (m-40) REVERT: W 73 LYS cc_start: 0.8908 (tttt) cc_final: 0.8549 (tptt) REVERT: X 36 ARG cc_start: 0.7950 (mmp80) cc_final: 0.7549 (mtm110) REVERT: X 72 ASN cc_start: 0.8950 (m-40) cc_final: 0.8712 (m110) REVERT: X 132 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8641 (tm-30) REVERT: X 147 ASP cc_start: 0.8825 (t70) cc_final: 0.8588 (t0) REVERT: Y 1 MET cc_start: 0.6229 (tpp) cc_final: 0.5683 (tpp) REVERT: Y 26 LYS cc_start: 0.8186 (mptt) cc_final: 0.7943 (mttp) REVERT: Y 87 SER cc_start: 0.9176 (t) cc_final: 0.8817 (p) REVERT: Y 128 MET cc_start: 0.8212 (mmt) cc_final: 0.7928 (mmt) REVERT: Z 78 MET cc_start: 0.7873 (mmm) cc_final: 0.7142 (ttp) REVERT: Z 128 MET cc_start: 0.8794 (mmt) cc_final: 0.8213 (mmt) REVERT: 1 36 ARG cc_start: 0.8067 (mmp80) cc_final: 0.7455 (mtm110) REVERT: 1 78 MET cc_start: 0.8377 (tpp) cc_final: 0.8130 (tpp) REVERT: 1 84 GLN cc_start: 0.8241 (mm-40) cc_final: 0.7994 (mt0) REVERT: 1 159 MET cc_start: 0.4335 (mmm) cc_final: 0.4125 (mmm) REVERT: 2 34 SER cc_start: 0.8483 (m) cc_final: 0.7979 (t) REVERT: 2 36 ARG cc_start: 0.8120 (ttm110) cc_final: 0.7780 (mtm110) REVERT: 2 72 ASN cc_start: 0.8365 (m-40) cc_final: 0.8158 (t0) REVERT: 2 87 SER cc_start: 0.9257 (t) cc_final: 0.8648 (p) REVERT: 3 71 ILE cc_start: 0.7936 (mt) cc_final: 0.7524 (tt) REVERT: 5 1 MET cc_start: 0.5525 (tpp) cc_final: 0.5196 (tpt) REVERT: 5 26 LYS cc_start: 0.8554 (mmtp) cc_final: 0.8309 (mttm) REVERT: 5 36 ARG cc_start: 0.7760 (mmp80) cc_final: 0.7380 (mtm110) REVERT: 5 72 ASN cc_start: 0.8370 (m-40) cc_final: 0.8081 (m-40) REVERT: 5 98 MET cc_start: 0.7692 (tpp) cc_final: 0.7196 (tpt) REVERT: 5 123 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7864 (mm-40) REVERT: 5 147 ASP cc_start: 0.8539 (t70) cc_final: 0.7993 (t0) REVERT: 6 34 SER cc_start: 0.8464 (m) cc_final: 0.8126 (t) REVERT: 6 37 GLU cc_start: 0.8479 (pp20) cc_final: 0.8210 (pp20) REVERT: 7 112 MET cc_start: 0.8624 (mmp) cc_final: 0.8222 (mmp) REVERT: 8 15 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7579 (tm-30) REVERT: 8 76 ASP cc_start: 0.9035 (OUTLIER) cc_final: 0.8775 (t0) REVERT: 8 84 GLN cc_start: 0.8586 (mm110) cc_final: 0.8317 (mm-40) REVERT: 9 2 ASP cc_start: 0.6922 (t0) cc_final: 0.6718 (t0) REVERT: 9 92 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.8058 (tt) outliers start: 191 outliers final: 141 residues processed: 1179 average time/residue: 0.4468 time to fit residues: 900.9080 Evaluate side-chains 1184 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1028 time to evaluate : 4.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 136 MET Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain J residue 2 ASP Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 126 ASN Chi-restraints excluded: chain M residue 81 SER Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain N residue 2 ASP Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 124 LEU Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 99 ASN Chi-restraints excluded: chain P residue 42 GLN Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 92 ILE Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 117 SER Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain Q residue 136 MET Chi-restraints excluded: chain R residue 2 ASP Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 136 MET Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 22 SER Chi-restraints excluded: chain S residue 124 LEU Chi-restraints excluded: chain S residue 140 ILE Chi-restraints excluded: chain T residue 27 ASN Chi-restraints excluded: chain T residue 100 THR Chi-restraints excluded: chain T residue 126 ASN Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 81 SER Chi-restraints excluded: chain U residue 87 SER Chi-restraints excluded: chain U residue 117 SER Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain U residue 133 LYS Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 152 VAL Chi-restraints excluded: chain W residue 27 ASN Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 70 GLN Chi-restraints excluded: chain X residue 80 THR Chi-restraints excluded: chain X residue 123 GLN Chi-restraints excluded: chain X residue 125 ARG Chi-restraints excluded: chain X residue 126 ASN Chi-restraints excluded: chain Y residue 92 ILE Chi-restraints excluded: chain Y residue 100 THR Chi-restraints excluded: chain Z residue 2 ASP Chi-restraints excluded: chain Z residue 117 SER Chi-restraints excluded: chain Z residue 124 LEU Chi-restraints excluded: chain Z residue 152 VAL Chi-restraints excluded: chain Z residue 159 MET Chi-restraints excluded: chain 0 residue 22 SER Chi-restraints excluded: chain 1 residue 27 ASN Chi-restraints excluded: chain 1 residue 124 LEU Chi-restraints excluded: chain 1 residue 136 MET Chi-restraints excluded: chain 2 residue 22 SER Chi-restraints excluded: chain 2 residue 41 LEU Chi-restraints excluded: chain 2 residue 81 SER Chi-restraints excluded: chain 2 residue 92 ILE Chi-restraints excluded: chain 2 residue 117 SER Chi-restraints excluded: chain 2 residue 124 LEU Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 2 ASP Chi-restraints excluded: chain 3 residue 29 ARG Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 3 residue 63 LEU Chi-restraints excluded: chain 3 residue 92 ILE Chi-restraints excluded: chain 3 residue 124 LEU Chi-restraints excluded: chain 3 residue 140 ILE Chi-restraints excluded: chain 3 residue 152 VAL Chi-restraints excluded: chain 3 residue 163 VAL Chi-restraints excluded: chain 4 residue 22 SER Chi-restraints excluded: chain 4 residue 136 MET Chi-restraints excluded: chain 5 residue 27 ASN Chi-restraints excluded: chain 5 residue 81 SER Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 135 LEU Chi-restraints excluded: chain 6 residue 81 SER Chi-restraints excluded: chain 6 residue 92 ILE Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 117 SER Chi-restraints excluded: chain 6 residue 124 LEU Chi-restraints excluded: chain 6 residue 136 MET Chi-restraints excluded: chain 7 residue 2 ASP Chi-restraints excluded: chain 7 residue 124 LEU Chi-restraints excluded: chain 8 residue 20 ILE Chi-restraints excluded: chain 8 residue 35 LEU Chi-restraints excluded: chain 8 residue 76 ASP Chi-restraints excluded: chain 8 residue 167 VAL Chi-restraints excluded: chain 9 residue 92 ILE Chi-restraints excluded: chain 9 residue 100 THR Chi-restraints excluded: chain 9 residue 126 ASN Chi-restraints excluded: chain 9 residue 135 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 536 optimal weight: 1.9990 chunk 565 optimal weight: 8.9990 chunk 515 optimal weight: 20.0000 chunk 549 optimal weight: 9.9990 chunk 564 optimal weight: 0.2980 chunk 330 optimal weight: 7.9990 chunk 239 optimal weight: 0.9980 chunk 431 optimal weight: 0.9990 chunk 168 optimal weight: 0.0270 chunk 496 optimal weight: 8.9990 chunk 519 optimal weight: 2.9990 overall best weight: 0.8642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 ASN D 123 GLN I 103 ASN L 27 ASN L 72 ASN O 27 ASN ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 GLN W 27 ASN 0 42 GLN 1 72 ASN 4 27 ASN 5 42 GLN 6 27 ASN 6 43 ASN 9 123 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 50040 Z= 0.158 Angle : 0.563 10.981 66852 Z= 0.294 Chirality : 0.041 0.276 7560 Planarity : 0.002 0.027 8676 Dihedral : 4.049 14.735 6804 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 1.09 % Allowed : 2.58 % Favored : 96.33 % Rotamer: Outliers : 2.78 % Allowed : 21.51 % Favored : 75.71 % 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: 0.85 (0.11), residues: 6048 helix: 0.97 (0.07), residues: 5076 sheet: None (None), residues: 0 loop : -1.25 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP 4 9 TYR 0.020 0.001 TYR 3 79 ARG 0.007 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1254 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1098 time to evaluate : 4.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 34 SER cc_start: 0.8187 (m) cc_final: 0.7651 (t) REVERT: B 36 ARG cc_start: 0.8086 (ttm110) cc_final: 0.7670 (mtm110) REVERT: B 72 ASN cc_start: 0.8350 (m-40) cc_final: 0.7914 (t0) REVERT: B 78 MET cc_start: 0.7906 (tpp) cc_final: 0.7658 (tpp) REVERT: B 114 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8064 (mt-10) REVERT: A 2 ASP cc_start: 0.5953 (t0) cc_final: 0.5673 (t70) REVERT: A 30 ASN cc_start: 0.8333 (m-40) cc_final: 0.8023 (t0) REVERT: A 71 ILE cc_start: 0.7643 (mt) cc_final: 0.7285 (tt) REVERT: C 73 LYS cc_start: 0.8844 (tttt) cc_final: 0.8601 (tptt) REVERT: C 86 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7958 (t0) REVERT: D 1 MET cc_start: 0.5675 (tpp) cc_final: 0.5444 (tpt) REVERT: D 27 ASN cc_start: 0.8569 (OUTLIER) cc_final: 0.8184 (m-40) REVERT: D 36 ARG cc_start: 0.7923 (mmp80) cc_final: 0.7464 (mtm110) REVERT: D 67 GLU cc_start: 0.6457 (pp20) cc_final: 0.5990 (mp0) REVERT: D 98 MET cc_start: 0.7834 (tpp) cc_final: 0.7537 (tpp) REVERT: D 123 GLN cc_start: 0.8587 (mm110) cc_final: 0.7877 (mm-40) REVERT: E 34 SER cc_start: 0.8327 (m) cc_final: 0.8099 (t) REVERT: E 35 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7718 (mp) REVERT: E 36 ARG cc_start: 0.7991 (ttm110) cc_final: 0.7678 (mtm110) REVERT: E 72 ASN cc_start: 0.8465 (m-40) cc_final: 0.7995 (t0) REVERT: E 80 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8889 (p) REVERT: G 6 LYS cc_start: 0.9121 (mttt) cc_final: 0.7463 (tttm) REVERT: G 86 ASP cc_start: 0.8167 (t0) cc_final: 0.7840 (t70) REVERT: H 1 MET cc_start: 0.5562 (tpp) cc_final: 0.4879 (tpt) REVERT: H 72 ASN cc_start: 0.8567 (m-40) cc_final: 0.8293 (m110) REVERT: H 76 ASP cc_start: 0.8179 (m-30) cc_final: 0.7937 (m-30) REVERT: H 84 GLN cc_start: 0.8612 (mm-40) cc_final: 0.8330 (mt0) REVERT: H 86 ASP cc_start: 0.8102 (t0) cc_final: 0.7793 (t0) REVERT: H 129 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7604 (mp) REVERT: I 1 MET cc_start: 0.6414 (tpp) cc_final: 0.6081 (tpt) REVERT: I 36 ARG cc_start: 0.8189 (ttm110) cc_final: 0.7937 (mtm-85) REVERT: I 78 MET cc_start: 0.8003 (tpp) cc_final: 0.7717 (tpt) REVERT: I 80 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.8934 (p) REVERT: I 147 ASP cc_start: 0.8626 (t70) cc_final: 0.8057 (t0) REVERT: J 123 GLN cc_start: 0.8453 (mm-40) cc_final: 0.8220 (mm-40) REVERT: K 72 ASN cc_start: 0.8642 (m-40) cc_final: 0.8372 (m110) REVERT: K 84 GLN cc_start: 0.8483 (mm110) cc_final: 0.8102 (mt0) REVERT: L 36 ARG cc_start: 0.7930 (mmp80) cc_final: 0.7595 (mtm110) REVERT: L 67 GLU cc_start: 0.6625 (pp20) cc_final: 0.6003 (mp0) REVERT: L 84 GLN cc_start: 0.8295 (mm-40) cc_final: 0.8038 (mt0) REVERT: L 123 GLN cc_start: 0.8401 (mm110) cc_final: 0.8091 (mm-40) REVERT: L 124 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8307 (pp) REVERT: M 1 MET cc_start: 0.6249 (tpp) cc_final: 0.6041 (tpp) REVERT: M 36 ARG cc_start: 0.7969 (ttm110) cc_final: 0.7636 (mtm110) REVERT: M 78 MET cc_start: 0.7805 (tpp) cc_final: 0.7605 (tpp) REVERT: M 87 SER cc_start: 0.9226 (t) cc_final: 0.8873 (p) REVERT: N 71 ILE cc_start: 0.7849 (mt) cc_final: 0.7447 (tt) REVERT: O 78 MET cc_start: 0.8610 (mmm) cc_final: 0.8048 (mmm) REVERT: O 84 GLN cc_start: 0.8530 (mm110) cc_final: 0.8286 (mm-40) REVERT: P 36 ARG cc_start: 0.7801 (mmp80) cc_final: 0.7428 (mtm110) REVERT: P 42 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.7089 (mt0) REVERT: P 67 GLU cc_start: 0.6179 (pp20) cc_final: 0.5435 (mp0) REVERT: P 143 GLU cc_start: 0.7758 (tt0) cc_final: 0.7499 (tt0) REVERT: P 147 ASP cc_start: 0.8511 (t70) cc_final: 0.7721 (t0) REVERT: Q 36 ARG cc_start: 0.7906 (ttm110) cc_final: 0.7594 (mtm110) REVERT: Q 87 SER cc_start: 0.9039 (t) cc_final: 0.8571 (p) REVERT: Q 98 MET cc_start: 0.8105 (tpp) cc_final: 0.7879 (tpp) REVERT: S 124 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7539 (pp) REVERT: T 1 MET cc_start: 0.5573 (tpp) cc_final: 0.4933 (tpt) REVERT: T 36 ARG cc_start: 0.7896 (mmp80) cc_final: 0.7334 (mtm110) REVERT: T 78 MET cc_start: 0.8202 (tpp) cc_final: 0.7955 (tpp) REVERT: T 84 GLN cc_start: 0.8334 (mm-40) cc_final: 0.7862 (mt0) REVERT: T 98 MET cc_start: 0.7827 (tpp) cc_final: 0.7513 (tpp) REVERT: T 147 ASP cc_start: 0.8610 (t70) cc_final: 0.7866 (t0) REVERT: U 124 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8214 (pp) REVERT: U 133 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8424 (ttpt) REVERT: V 30 ASN cc_start: 0.8188 (m-40) cc_final: 0.7874 (t0) REVERT: V 136 MET cc_start: 0.7785 (mtp) cc_final: 0.7577 (mtp) REVERT: W 72 ASN cc_start: 0.8768 (m-40) cc_final: 0.8293 (m-40) REVERT: X 36 ARG cc_start: 0.7966 (mmp80) cc_final: 0.7537 (mtm110) REVERT: X 72 ASN cc_start: 0.8935 (m-40) cc_final: 0.8689 (m110) REVERT: X 132 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8668 (tm-30) REVERT: X 147 ASP cc_start: 0.8790 (t70) cc_final: 0.8534 (t0) REVERT: Y 1 MET cc_start: 0.6218 (tpp) cc_final: 0.5898 (tpt) REVERT: Y 87 SER cc_start: 0.9180 (t) cc_final: 0.8833 (p) REVERT: Y 128 MET cc_start: 0.8201 (mmt) cc_final: 0.7871 (mmp) REVERT: Z 78 MET cc_start: 0.7860 (mmm) cc_final: 0.7191 (ttp) REVERT: Z 128 MET cc_start: 0.8766 (mmt) cc_final: 0.8436 (mmt) REVERT: 0 123 GLN cc_start: 0.8448 (mp10) cc_final: 0.8094 (mp10) REVERT: 1 78 MET cc_start: 0.8323 (tpp) cc_final: 0.8058 (tpp) REVERT: 1 84 GLN cc_start: 0.8151 (mm-40) cc_final: 0.7833 (mt0) REVERT: 1 128 MET cc_start: 0.8516 (mmm) cc_final: 0.8218 (mmm) REVERT: 1 159 MET cc_start: 0.4485 (mmm) cc_final: 0.4238 (mmm) REVERT: 2 34 SER cc_start: 0.8395 (m) cc_final: 0.7922 (t) REVERT: 2 36 ARG cc_start: 0.8019 (ttm110) cc_final: 0.7688 (mtm110) REVERT: 2 72 ASN cc_start: 0.8342 (m-40) cc_final: 0.8062 (t0) REVERT: 2 87 SER cc_start: 0.9259 (t) cc_final: 0.8611 (p) REVERT: 3 71 ILE cc_start: 0.7897 (mt) cc_final: 0.7510 (tt) REVERT: 3 107 ASP cc_start: 0.7642 (m-30) cc_final: 0.7354 (m-30) REVERT: 5 1 MET cc_start: 0.5482 (tpp) cc_final: 0.5145 (tpt) REVERT: 5 26 LYS cc_start: 0.8553 (mmtp) cc_final: 0.8329 (mttm) REVERT: 5 72 ASN cc_start: 0.8315 (m-40) cc_final: 0.7958 (m-40) REVERT: 5 84 GLN cc_start: 0.8417 (mm-40) cc_final: 0.7874 (mt0) REVERT: 5 98 MET cc_start: 0.7552 (tpp) cc_final: 0.7053 (tpt) REVERT: 5 123 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7788 (mm-40) REVERT: 5 147 ASP cc_start: 0.8536 (t70) cc_final: 0.8015 (t0) REVERT: 6 34 SER cc_start: 0.8414 (m) cc_final: 0.8121 (t) REVERT: 6 37 GLU cc_start: 0.8461 (pp20) cc_final: 0.8181 (pp20) REVERT: 7 112 MET cc_start: 0.8636 (mmp) cc_final: 0.8210 (mmp) REVERT: 9 2 ASP cc_start: 0.6870 (t0) cc_final: 0.6658 (t0) REVERT: 9 92 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7993 (tt) outliers start: 156 outliers final: 122 residues processed: 1193 average time/residue: 0.4435 time to fit residues: 902.3774 Evaluate side-chains 1177 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1043 time to evaluate : 4.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 136 MET Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain J residue 2 ASP Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 126 ASN Chi-restraints excluded: chain M residue 92 ILE Chi-restraints excluded: chain M residue 99 ASN Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain N residue 2 ASP Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 124 LEU Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 136 MET Chi-restraints excluded: chain P residue 42 GLN Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain Q residue 81 SER Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain R residue 2 ASP Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 136 MET Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 22 SER Chi-restraints excluded: chain S residue 124 LEU Chi-restraints excluded: chain S residue 140 ILE Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain T residue 100 THR Chi-restraints excluded: chain T residue 126 ASN Chi-restraints excluded: chain U residue 81 SER Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain U residue 133 LYS Chi-restraints excluded: chain U residue 140 ILE Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 140 ILE Chi-restraints excluded: chain V residue 152 VAL Chi-restraints excluded: chain V residue 159 MET Chi-restraints excluded: chain W residue 27 ASN Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 70 GLN Chi-restraints excluded: chain X residue 80 THR Chi-restraints excluded: chain X residue 123 GLN Chi-restraints excluded: chain X residue 126 ASN Chi-restraints excluded: chain Y residue 92 ILE Chi-restraints excluded: chain Y residue 100 THR Chi-restraints excluded: chain Y residue 124 LEU Chi-restraints excluded: chain Z residue 117 SER Chi-restraints excluded: chain Z residue 124 LEU Chi-restraints excluded: chain Z residue 152 VAL Chi-restraints excluded: chain Z residue 159 MET Chi-restraints excluded: chain 0 residue 22 SER Chi-restraints excluded: chain 1 residue 27 ASN Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 124 LEU Chi-restraints excluded: chain 1 residue 136 MET Chi-restraints excluded: chain 2 residue 92 ILE Chi-restraints excluded: chain 2 residue 96 ILE Chi-restraints excluded: chain 2 residue 124 LEU Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 2 ASP Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 3 residue 63 LEU Chi-restraints excluded: chain 3 residue 99 ASN Chi-restraints excluded: chain 3 residue 124 LEU Chi-restraints excluded: chain 3 residue 140 ILE Chi-restraints excluded: chain 3 residue 152 VAL Chi-restraints excluded: chain 3 residue 163 VAL Chi-restraints excluded: chain 4 residue 22 SER Chi-restraints excluded: chain 4 residue 136 MET Chi-restraints excluded: chain 5 residue 27 ASN Chi-restraints excluded: chain 5 residue 100 THR Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 5 residue 135 LEU Chi-restraints excluded: chain 6 residue 92 ILE Chi-restraints excluded: chain 6 residue 100 THR Chi-restraints excluded: chain 6 residue 124 LEU Chi-restraints excluded: chain 7 residue 2 ASP Chi-restraints excluded: chain 7 residue 124 LEU Chi-restraints excluded: chain 8 residue 20 ILE Chi-restraints excluded: chain 8 residue 167 VAL Chi-restraints excluded: chain 9 residue 92 ILE Chi-restraints excluded: chain 9 residue 100 THR Chi-restraints excluded: chain 9 residue 126 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 547 optimal weight: 9.9990 chunk 360 optimal weight: 7.9990 chunk 581 optimal weight: 8.9990 chunk 354 optimal weight: 0.9990 chunk 275 optimal weight: 4.9990 chunk 404 optimal weight: 6.9990 chunk 609 optimal weight: 0.9980 chunk 561 optimal weight: 1.9990 chunk 485 optimal weight: 2.9990 chunk 50 optimal weight: 0.0020 chunk 375 optimal weight: 0.9980 overall best weight: 0.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 ASN ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN E 42 GLN G 27 ASN J 99 ASN K 42 GLN L 72 ASN M 43 ASN N 42 GLN O 27 ASN S 16 GLN S 42 GLN T 123 GLN W 27 ASN Y 103 ASN ** 0 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 72 ASN 2 103 ASN 4 27 ASN 5 42 GLN 6 27 ASN 6 103 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 50040 Z= 0.165 Angle : 0.581 11.639 66852 Z= 0.301 Chirality : 0.041 0.205 7560 Planarity : 0.002 0.034 8676 Dihedral : 4.026 15.818 6804 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 1.04 % Allowed : 2.55 % Favored : 96.41 % Rotamer: Outliers : 2.53 % Allowed : 21.90 % Favored : 75.57 % 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: 1.06 (0.11), residues: 6048 helix: 1.12 (0.07), residues: 5076 sheet: None (None), residues: 0 loop : -1.23 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 9 TYR 0.021 0.001 TYR 3 79 ARG 0.009 0.000 ARG 3 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1203 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1061 time to evaluate : 4.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 SER cc_start: 0.8184 (m) cc_final: 0.7927 (t) REVERT: B 36 ARG cc_start: 0.8053 (ttm110) cc_final: 0.7627 (mtm110) REVERT: B 72 ASN cc_start: 0.8227 (m-40) cc_final: 0.7794 (t0) REVERT: A 2 ASP cc_start: 0.5945 (t0) cc_final: 0.5645 (t70) REVERT: A 30 ASN cc_start: 0.8333 (m-40) cc_final: 0.8010 (t0) REVERT: A 71 ILE cc_start: 0.7719 (mt) cc_final: 0.7347 (tt) REVERT: D 1 MET cc_start: 0.5696 (tpp) cc_final: 0.5390 (tpt) REVERT: D 2 ASP cc_start: 0.7355 (OUTLIER) cc_final: 0.7048 (p0) REVERT: D 36 ARG cc_start: 0.7880 (mmp80) cc_final: 0.7389 (mtm110) REVERT: D 67 GLU cc_start: 0.6492 (pp20) cc_final: 0.6018 (mp0) REVERT: D 123 GLN cc_start: 0.8443 (mm110) cc_final: 0.7832 (mm-40) REVERT: E 35 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7740 (mp) REVERT: E 36 ARG cc_start: 0.7931 (ttm110) cc_final: 0.7629 (mtm110) REVERT: E 72 ASN cc_start: 0.8460 (m-40) cc_final: 0.7964 (t0) REVERT: E 80 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8900 (p) REVERT: G 6 LYS cc_start: 0.9094 (mttt) cc_final: 0.7432 (tttm) REVERT: G 86 ASP cc_start: 0.8193 (t0) cc_final: 0.7884 (t70) REVERT: H 1 MET cc_start: 0.5460 (tpp) cc_final: 0.4762 (tpt) REVERT: H 36 ARG cc_start: 0.7885 (mmp80) cc_final: 0.7342 (mmp80) REVERT: H 72 ASN cc_start: 0.8585 (m-40) cc_final: 0.8304 (m110) REVERT: H 76 ASP cc_start: 0.8153 (m-30) cc_final: 0.7900 (m-30) REVERT: H 84 GLN cc_start: 0.8625 (mm-40) cc_final: 0.8345 (mt0) REVERT: H 86 ASP cc_start: 0.8116 (t0) cc_final: 0.7813 (t0) REVERT: H 128 MET cc_start: 0.8160 (mmt) cc_final: 0.7936 (mmm) REVERT: H 129 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7696 (mp) REVERT: I 1 MET cc_start: 0.6516 (tpp) cc_final: 0.6081 (tpt) REVERT: I 36 ARG cc_start: 0.8187 (ttm110) cc_final: 0.7799 (mtm110) REVERT: I 80 THR cc_start: 0.9246 (OUTLIER) cc_final: 0.8951 (p) REVERT: I 147 ASP cc_start: 0.8635 (t70) cc_final: 0.8072 (t0) REVERT: K 72 ASN cc_start: 0.8609 (m-40) cc_final: 0.8226 (m-40) REVERT: K 84 GLN cc_start: 0.8526 (mm110) cc_final: 0.8204 (mt0) REVERT: L 36 ARG cc_start: 0.7841 (mmp80) cc_final: 0.7469 (mmp80) REVERT: L 67 GLU cc_start: 0.6740 (pp20) cc_final: 0.6100 (mp0) REVERT: L 68 LEU cc_start: 0.7392 (tt) cc_final: 0.6814 (tt) REVERT: L 78 MET cc_start: 0.8567 (tpp) cc_final: 0.8344 (tpt) REVERT: L 84 GLN cc_start: 0.8286 (mm-40) cc_final: 0.8045 (mt0) REVERT: L 123 GLN cc_start: 0.8327 (mm110) cc_final: 0.8026 (mm-40) REVERT: L 124 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8265 (pp) REVERT: M 34 SER cc_start: 0.8262 (m) cc_final: 0.7960 (t) REVERT: M 36 ARG cc_start: 0.7996 (ttm110) cc_final: 0.7612 (mtm110) REVERT: M 87 SER cc_start: 0.9228 (t) cc_final: 0.8878 (p) REVERT: N 71 ILE cc_start: 0.7887 (mt) cc_final: 0.7460 (tt) REVERT: O 78 MET cc_start: 0.8590 (mmm) cc_final: 0.8094 (mmm) REVERT: O 84 GLN cc_start: 0.8507 (mm110) cc_final: 0.8302 (mm-40) REVERT: P 67 GLU cc_start: 0.6203 (pp20) cc_final: 0.5480 (mp0) REVERT: P 147 ASP cc_start: 0.8556 (t70) cc_final: 0.7839 (t0) REVERT: Q 36 ARG cc_start: 0.7883 (ttm110) cc_final: 0.7511 (mtm110) REVERT: Q 87 SER cc_start: 0.9034 (t) cc_final: 0.8572 (p) REVERT: Q 98 MET cc_start: 0.8089 (tpp) cc_final: 0.7880 (tpp) REVERT: S 124 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7751 (pp) REVERT: T 1 MET cc_start: 0.5351 (tpp) cc_final: 0.4674 (tpt) REVERT: T 36 ARG cc_start: 0.7914 (mmp80) cc_final: 0.7322 (mtm110) REVERT: T 67 GLU cc_start: 0.6000 (pp20) cc_final: 0.5239 (mp0) REVERT: T 78 MET cc_start: 0.8168 (tpp) cc_final: 0.7965 (tpp) REVERT: T 84 GLN cc_start: 0.8336 (mm-40) cc_final: 0.7897 (mt0) REVERT: T 98 MET cc_start: 0.7724 (tpp) cc_final: 0.7395 (tpp) REVERT: T 147 ASP cc_start: 0.8555 (t70) cc_final: 0.7840 (t0) REVERT: U 124 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8196 (pp) REVERT: U 133 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8462 (ttpt) REVERT: V 30 ASN cc_start: 0.8215 (m-40) cc_final: 0.7914 (t0) REVERT: W 72 ASN cc_start: 0.8747 (m-40) cc_final: 0.8306 (m-40) REVERT: X 72 ASN cc_start: 0.8921 (m-40) cc_final: 0.8679 (m110) REVERT: X 132 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8665 (tm-30) REVERT: X 147 ASP cc_start: 0.8805 (t70) cc_final: 0.8548 (t0) REVERT: Y 1 MET cc_start: 0.6301 (tpp) cc_final: 0.5993 (tpt) REVERT: Y 84 GLN cc_start: 0.8427 (mm-40) cc_final: 0.7771 (mt0) REVERT: Y 128 MET cc_start: 0.8217 (mmt) cc_final: 0.7919 (mmt) REVERT: Z 78 MET cc_start: 0.7857 (mmm) cc_final: 0.7421 (ttm) REVERT: Z 128 MET cc_start: 0.8756 (mmt) cc_final: 0.8419 (mmt) REVERT: 0 84 GLN cc_start: 0.8592 (mm110) cc_final: 0.7951 (mt0) REVERT: 1 68 LEU cc_start: 0.7546 (tp) cc_final: 0.7316 (mp) REVERT: 1 78 MET cc_start: 0.8269 (tpp) cc_final: 0.8003 (tpp) REVERT: 1 84 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7864 (mt0) REVERT: 1 159 MET cc_start: 0.4468 (mmm) cc_final: 0.4236 (mmm) REVERT: 2 34 SER cc_start: 0.8409 (m) cc_final: 0.7924 (t) REVERT: 2 36 ARG cc_start: 0.7998 (ttm110) cc_final: 0.7640 (mtm110) REVERT: 2 87 SER cc_start: 0.9246 (t) cc_final: 0.8588 (p) REVERT: 3 71 ILE cc_start: 0.7897 (mt) cc_final: 0.7508 (tt) REVERT: 3 107 ASP cc_start: 0.7618 (m-30) cc_final: 0.7319 (m-30) REVERT: 5 1 MET cc_start: 0.5475 (tpp) cc_final: 0.5132 (tpt) REVERT: 5 26 LYS cc_start: 0.8555 (mmtp) cc_final: 0.8344 (mttm) REVERT: 5 36 ARG cc_start: 0.7664 (mmp80) cc_final: 0.7274 (mtm110) REVERT: 5 72 ASN cc_start: 0.8392 (m-40) cc_final: 0.8146 (m-40) REVERT: 5 84 GLN cc_start: 0.8413 (mm-40) cc_final: 0.7888 (mt0) REVERT: 5 98 MET cc_start: 0.7537 (tpp) cc_final: 0.7011 (tpt) REVERT: 5 123 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7730 (mm-40) REVERT: 5 147 ASP cc_start: 0.8552 (t70) cc_final: 0.8023 (t0) REVERT: 6 26 LYS cc_start: 0.8064 (mttm) cc_final: 0.7856 (mtpt) REVERT: 6 34 SER cc_start: 0.8403 (m) cc_final: 0.8135 (t) REVERT: 6 37 GLU cc_start: 0.8470 (pp20) cc_final: 0.8187 (pp20) REVERT: 9 2 ASP cc_start: 0.6769 (t0) cc_final: 0.6529 (t0) REVERT: 9 92 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7963 (tt) outliers start: 142 outliers final: 120 residues processed: 1152 average time/residue: 0.4427 time to fit residues: 872.5755 Evaluate side-chains 1158 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1028 time to evaluate : 4.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain D residue 2 ASP Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 2 ASP Chi-restraints excluded: chain J residue 99 ASN Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 81 SER Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain M residue 92 ILE Chi-restraints excluded: chain M residue 99 ASN Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain N residue 2 ASP Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 124 LEU Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 22 SER Chi-restraints excluded: chain O residue 136 MET Chi-restraints excluded: chain P residue 42 GLN Chi-restraints excluded: chain P residue 81 SER Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 124 LEU Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain R residue 2 ASP Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain S residue 16 GLN Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 22 SER Chi-restraints excluded: chain S residue 124 LEU Chi-restraints excluded: chain S residue 140 ILE Chi-restraints excluded: chain T residue 81 SER Chi-restraints excluded: chain T residue 100 THR Chi-restraints excluded: chain T residue 126 ASN Chi-restraints excluded: chain U residue 81 SER Chi-restraints excluded: chain U residue 124 LEU Chi-restraints excluded: chain U residue 133 LYS Chi-restraints excluded: chain U residue 140 ILE Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 140 ILE Chi-restraints excluded: chain V residue 152 VAL Chi-restraints excluded: chain V residue 159 MET Chi-restraints excluded: chain W residue 27 ASN Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 70 GLN Chi-restraints excluded: chain X residue 80 THR Chi-restraints excluded: chain X residue 123 GLN Chi-restraints excluded: chain X residue 126 ASN Chi-restraints excluded: chain Y residue 92 ILE Chi-restraints excluded: chain Y residue 117 SER Chi-restraints excluded: chain Y residue 124 LEU Chi-restraints excluded: chain Z residue 117 SER Chi-restraints excluded: chain Z residue 124 LEU Chi-restraints excluded: chain Z residue 152 VAL Chi-restraints excluded: chain 0 residue 22 SER Chi-restraints excluded: chain 1 residue 27 ASN Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 1 residue 124 LEU Chi-restraints excluded: chain 1 residue 136 MET Chi-restraints excluded: chain 2 residue 92 ILE Chi-restraints excluded: chain 2 residue 96 ILE Chi-restraints excluded: chain 2 residue 124 LEU Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 2 ASP Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 3 residue 63 LEU Chi-restraints excluded: chain 3 residue 99 ASN Chi-restraints excluded: chain 3 residue 111 LEU Chi-restraints excluded: chain 3 residue 140 ILE Chi-restraints excluded: chain 3 residue 152 VAL Chi-restraints excluded: chain 3 residue 163 VAL Chi-restraints excluded: chain 4 residue 22 SER Chi-restraints excluded: chain 4 residue 136 MET Chi-restraints excluded: chain 5 residue 27 ASN Chi-restraints excluded: chain 5 residue 100 THR Chi-restraints excluded: chain 5 residue 126 ASN Chi-restraints excluded: chain 6 residue 92 ILE Chi-restraints excluded: chain 6 residue 124 LEU Chi-restraints excluded: chain 7 residue 2 ASP Chi-restraints excluded: chain 7 residue 124 LEU Chi-restraints excluded: chain 7 residue 136 MET Chi-restraints excluded: chain 8 residue 35 LEU Chi-restraints excluded: chain 8 residue 124 LEU Chi-restraints excluded: chain 8 residue 167 VAL Chi-restraints excluded: chain 9 residue 92 ILE Chi-restraints excluded: chain 9 residue 100 THR Chi-restraints excluded: chain 9 residue 126 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 297 optimal weight: 5.9990 chunk 385 optimal weight: 0.6980 chunk 517 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 447 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 486 optimal weight: 8.9990 chunk 203 optimal weight: 8.9990 chunk 499 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN D 72 ASN J 99 ASN L 72 ASN N 70 GLN O 42 GLN S 42 GLN V 27 ASN W 27 ASN ** 0 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 72 ASN 4 42 GLN 5 42 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.186026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3577 r_free = 0.3577 target = 0.129279 restraints weight = 68850.818| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.93 r_work: 0.3226 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 50040 Z= 0.266 Angle : 0.611 12.381 66852 Z= 0.316 Chirality : 0.043 0.251 7560 Planarity : 0.003 0.032 8676 Dihedral : 4.075 17.748 6804 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 1.16 % Allowed : 2.53 % Favored : 96.31 % Rotamer: Outliers : 2.87 % Allowed : 21.92 % Favored : 75.21 % 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: 1.06 (0.11), residues: 6048 helix: 1.11 (0.07), residues: 5076 sheet: None (None), residues: 0 loop : -1.21 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 9 TYR 0.022 0.001 TYR 3 79 ARG 0.008 0.000 ARG 3 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15734.11 seconds wall clock time: 270 minutes 45.08 seconds (16245.08 seconds total)