Starting phenix.real_space_refine on Mon Dec 30 19:59:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uaf_42062/12_2024/8uaf_42062_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uaf_42062/12_2024/8uaf_42062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uaf_42062/12_2024/8uaf_42062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uaf_42062/12_2024/8uaf_42062.map" model { file = "/net/cci-nas-00/data/ceres_data/8uaf_42062/12_2024/8uaf_42062_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uaf_42062/12_2024/8uaf_42062_neut.cif" } resolution = 3.18 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= 0.003 sd= 0.042 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: 6 Type Number sf(0) Gaussians P 34 5.49 5 Mg 5 5.21 5 S 144 5.16 5 C 40882 2.51 5 N 10927 2.21 5 O 12023 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 64015 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 3181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3181 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 386} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3050 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 369} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3181 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 386} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3067 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 372} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3190 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 388} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2457 Classifications: {'peptide': 383} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PTRANS': 11, 'TRANS': 371} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 646 Unresolved non-hydrogen angles: 830 Unresolved non-hydrogen dihedrals: 550 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 6, 'TYR:plan': 12, 'ASN:plan1': 12, 'TRP:plan': 2, 'ASP:plan': 11, 'PHE:plan': 11, 'GLU:plan': 15, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 407 Chain: "G" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3115 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 379} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3067 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 372} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 3141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3141 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 3063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3063 Classifications: {'peptide': 383} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 371} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3178 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 3063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3063 Classifications: {'peptide': 383} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 371} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 4536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4536 Classifications: {'peptide': 573} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 550} Chain breaks: 2 Chain: "N" Number of atoms: 4548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4548 Classifications: {'peptide': 574} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 551} Chain breaks: 2 Chain: "O" Number of atoms: 4637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4637 Classifications: {'peptide': 585} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 561} Chain breaks: 1 Chain: "P" Number of atoms: 4346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4346 Classifications: {'peptide': 549} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 526} Chain breaks: 4 Chain: "Q" Number of atoms: 4389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4389 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 530} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "R" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4170 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 19, 'TRANS': 504} Chain breaks: 3 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 28.51, per 1000 atoms: 0.45 Number of scatterers: 64015 At special positions: 0 Unit cell: (199.8, 183.15, 214.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 144 16.00 P 34 15.00 Mg 5 11.99 O 12023 8.00 N 10927 7.00 C 40882 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.46 Conformation dependent library (CDL) restraints added in 7.4 seconds 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14852 Finding SS restraints... Secondary structure from input PDB file: 354 helices and 72 sheets defined 44.8% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.27 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 removed outlier: 3.552A pdb=" N PHE A 15 " --> pdb=" O ASN A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 38 removed outlier: 3.546A pdb=" N SER A 37 " --> pdb=" O ALA A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 59 through 65 removed outlier: 3.806A pdb=" N LEU A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP A 65 " --> pdb=" O GLY A 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 59 through 65' Processing helix chain 'A' and resid 71 through 78 Processing helix chain 'A' and resid 82 through 100 removed outlier: 4.190A pdb=" N ASP A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 122 removed outlier: 3.558A pdb=" N LYS A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 120 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 132 removed outlier: 4.256A pdb=" N GLN A 129 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ARG A 131 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 132 " --> pdb=" O GLN A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 140 removed outlier: 3.983A pdb=" N LYS A 137 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS A 138 " --> pdb=" O GLN A 135 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASP A 139 " --> pdb=" O GLY A 136 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA A 140 " --> pdb=" O LYS A 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 134 through 140' Processing helix chain 'A' and resid 141 through 154 removed outlier: 3.584A pdb=" N LYS A 145 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 147 " --> pdb=" O TYR A 143 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 148 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN A 154 " --> pdb=" O LYS A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 181 removed outlier: 3.570A pdb=" N TRP A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.635A pdb=" N ASP A 202 " --> pdb=" O GLN A 199 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 203 " --> pdb=" O ASN A 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 199 through 203' Processing helix chain 'A' and resid 244 through 252 Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 280 through 295 removed outlier: 3.978A pdb=" N TYR A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 295 " --> pdb=" O PHE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 321 removed outlier: 3.786A pdb=" N ARG A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 317 " --> pdb=" O HIS A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 324 No H-bonds generated for 'chain 'A' and resid 322 through 324' Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 349 through 360 Processing helix chain 'A' and resid 371 through 375 removed outlier: 3.627A pdb=" N ALA A 375 " --> pdb=" O GLY A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 383 removed outlier: 3.501A pdb=" N PHE A 380 " --> pdb=" O TYR A 376 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 406 removed outlier: 3.647A pdb=" N LEU A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 406 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 23 removed outlier: 3.545A pdb=" N PHE B 15 " --> pdb=" O ASN B 11 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER B 17 " --> pdb=" O ASP B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 38 removed outlier: 3.603A pdb=" N SER B 37 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 56 removed outlier: 3.881A pdb=" N VAL B 48 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TRP B 49 " --> pdb=" O MET B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 66 removed outlier: 4.163A pdb=" N LEU B 60 " --> pdb=" O TYR B 56 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY B 61 " --> pdb=" O PRO B 57 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 62 " --> pdb=" O GLU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 78 removed outlier: 3.621A pdb=" N ASP B 76 " --> pdb=" O GLN B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 99 removed outlier: 3.502A pdb=" N LEU B 85 " --> pdb=" O ASN B 81 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG B 99 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 122 removed outlier: 3.505A pdb=" N VAL B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 removed outlier: 3.827A pdb=" N PHE B 130 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ARG B 131 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU B 132 " --> pdb=" O GLN B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 127 through 132' Processing helix chain 'B' and resid 134 through 140 removed outlier: 3.689A pdb=" N LYS B 138 " --> pdb=" O GLN B 135 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ASP B 139 " --> pdb=" O GLY B 136 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA B 140 " --> pdb=" O LYS B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 154 removed outlier: 3.648A pdb=" N ASN B 154 " --> pdb=" O LYS B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 181 removed outlier: 3.523A pdb=" N LEU B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 201 removed outlier: 3.891A pdb=" N PHE B 201 " --> pdb=" O PRO B 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 201' Processing helix chain 'B' and resid 244 through 252 Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 274 through 278 removed outlier: 3.988A pdb=" N SER B 277 " --> pdb=" O ASN B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 295 removed outlier: 3.682A pdb=" N ILE B 295 " --> pdb=" O PHE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 321 removed outlier: 3.596A pdb=" N ASN B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 317 " --> pdb=" O HIS B 313 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 324 No H-bonds generated for 'chain 'B' and resid 322 through 324' Processing helix chain 'B' and resid 335 through 345 removed outlier: 4.238A pdb=" N ALA B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 360 removed outlier: 3.615A pdb=" N ALA B 354 " --> pdb=" O GLU B 350 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 removed outlier: 3.786A pdb=" N ALA B 375 " --> pdb=" O GLY B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 384 removed outlier: 3.763A pdb=" N LEU B 384 " --> pdb=" O PHE B 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 23 Processing helix chain 'C' and resid 34 through 41 removed outlier: 3.618A pdb=" N SER C 37 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY C 39 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY C 41 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 56 removed outlier: 3.577A pdb=" N TRP C 49 " --> pdb=" O MET C 45 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN C 54 " --> pdb=" O LYS C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 66 removed outlier: 4.325A pdb=" N GLY C 61 " --> pdb=" O PRO C 57 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA C 62 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 78 Processing helix chain 'C' and resid 82 through 100 Processing helix chain 'C' and resid 101 through 124 removed outlier: 3.742A pdb=" N GLU C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU C 107 " --> pdb=" O ASP C 103 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE C 108 " --> pdb=" O GLU C 104 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG C 109 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS C 110 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA C 122 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 131 removed outlier: 3.843A pdb=" N GLN C 129 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG C 131 " --> pdb=" O GLU C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 138 removed outlier: 3.621A pdb=" N LYS C 137 " --> pdb=" O ASN C 134 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS C 138 " --> pdb=" O GLN C 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 134 through 138' Processing helix chain 'C' and resid 141 through 154 removed outlier: 3.950A pdb=" N LYS C 145 " --> pdb=" O PHE C 141 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU C 146 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN C 154 " --> pdb=" O LYS C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 181 removed outlier: 3.785A pdb=" N ASP C 179 " --> pdb=" O TRP C 175 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 removed outlier: 3.862A pdb=" N PHE C 201 " --> pdb=" O PRO C 198 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C 203 " --> pdb=" O ASN C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 253 through 259 removed outlier: 3.844A pdb=" N ILE C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 295 removed outlier: 4.469A pdb=" N VAL C 283 " --> pdb=" O THR C 279 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR C 284 " --> pdb=" O ILE C 280 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE C 295 " --> pdb=" O PHE C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 322 removed outlier: 3.721A pdb=" N LEU C 322 " --> pdb=" O ILE C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 346 Processing helix chain 'C' and resid 349 through 360 removed outlier: 3.519A pdb=" N LYS C 353 " --> pdb=" O SER C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 383 removed outlier: 3.902A pdb=" N VAL C 381 " --> pdb=" O PHE C 377 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU C 382 " --> pdb=" O ASN C 378 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 407 removed outlier: 3.581A pdb=" N LEU C 399 " --> pdb=" O ILE C 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 23 removed outlier: 3.545A pdb=" N CYS D 23 " --> pdb=" O VAL D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 41 removed outlier: 3.790A pdb=" N SER D 37 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY D 39 " --> pdb=" O ALA D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 55 Processing helix chain 'D' and resid 57 through 65 removed outlier: 3.661A pdb=" N GLY D 61 " --> pdb=" O PRO D 57 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 77 Processing helix chain 'D' and resid 81 through 100 removed outlier: 3.606A pdb=" N LYS D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR D 98 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG D 99 " --> pdb=" O VAL D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 122 removed outlier: 3.839A pdb=" N GLU D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL D 119 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA D 122 " --> pdb=" O GLU D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 138 removed outlier: 3.653A pdb=" N LYS D 137 " --> pdb=" O ASN D 134 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS D 138 " --> pdb=" O GLN D 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 134 through 138' Processing helix chain 'D' and resid 141 through 154 removed outlier: 4.164A pdb=" N ASN D 154 " --> pdb=" O LYS D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 179 removed outlier: 3.659A pdb=" N ASP D 179 " --> pdb=" O TRP D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 201 No H-bonds generated for 'chain 'D' and resid 199 through 201' Processing helix chain 'D' and resid 244 through 253 removed outlier: 3.786A pdb=" N ILE D 253 " --> pdb=" O TYR D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 259 Processing helix chain 'D' and resid 282 through 295 removed outlier: 3.560A pdb=" N GLU D 286 " --> pdb=" O PHE D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 322 removed outlier: 3.930A pdb=" N GLY D 320 " --> pdb=" O ARG D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 345 removed outlier: 3.911A pdb=" N LYS D 345 " --> pdb=" O THR D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 360 removed outlier: 3.680A pdb=" N ALA D 354 " --> pdb=" O GLU D 350 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE D 355 " --> pdb=" O ALA D 351 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS D 359 " --> pdb=" O ILE D 355 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN D 360 " --> pdb=" O VAL D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 375 Processing helix chain 'D' and resid 376 through 384 removed outlier: 3.696A pdb=" N LEU D 384 " --> pdb=" O PHE D 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 23 removed outlier: 3.537A pdb=" N PHE E 15 " --> pdb=" O ASN E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 38 removed outlier: 4.026A pdb=" N SER E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL E 38 " --> pdb=" O GLY E 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 34 through 38' Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 57 through 63 removed outlier: 3.798A pdb=" N GLY E 61 " --> pdb=" O PRO E 57 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA E 62 " --> pdb=" O GLU E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 78 removed outlier: 3.935A pdb=" N SER E 75 " --> pdb=" O SER E 71 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 84 through 100 removed outlier: 4.179A pdb=" N GLU E 88 " --> pdb=" O LEU E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 122 removed outlier: 3.613A pdb=" N GLU E 105 " --> pdb=" O CYS E 101 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLU E 107 " --> pdb=" O ASP E 103 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE E 108 " --> pdb=" O GLU E 104 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU E 112 " --> pdb=" O PHE E 108 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER E 113 " --> pdb=" O ARG E 109 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER E 114 " --> pdb=" O LYS E 110 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU E 115 " --> pdb=" O ILE E 111 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS E 121 " --> pdb=" O LYS E 117 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 140 No H-bonds generated for 'chain 'E' and resid 138 through 140' Processing helix chain 'E' and resid 141 through 153 removed outlier: 3.933A pdb=" N LYS E 145 " --> pdb=" O PHE E 141 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU E 146 " --> pdb=" O LYS E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 181 removed outlier: 3.713A pdb=" N TRP E 175 " --> pdb=" O LEU E 171 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP E 179 " --> pdb=" O TRP E 175 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU E 180 " --> pdb=" O ALA E 176 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY E 181 " --> pdb=" O ALA E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 252 Processing helix chain 'E' and resid 252 through 259 Processing helix chain 'E' and resid 280 through 296 removed outlier: 4.411A pdb=" N TYR E 284 " --> pdb=" O ILE E 280 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU E 286 " --> pdb=" O PHE E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 322 Processing helix chain 'E' and resid 335 through 346 removed outlier: 3.584A pdb=" N LYS E 342 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS E 345 " --> pdb=" O THR E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 360 Processing helix chain 'E' and resid 371 through 375 Processing helix chain 'E' and resid 376 through 384 removed outlier: 4.067A pdb=" N GLU E 382 " --> pdb=" O ASN E 378 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS E 383 " --> pdb=" O SER E 379 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU E 384 " --> pdb=" O PHE E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 406 removed outlier: 3.639A pdb=" N GLU E 401 " --> pdb=" O ASP E 397 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU E 406 " --> pdb=" O ALA E 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 23 removed outlier: 3.672A pdb=" N PHE F 15 " --> pdb=" O ASN F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 41 Processing helix chain 'F' and resid 44 through 56 Processing helix chain 'F' and resid 56 through 66 removed outlier: 4.093A pdb=" N LEU F 60 " --> pdb=" O TYR F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 78 Processing helix chain 'F' and resid 81 through 99 removed outlier: 3.775A pdb=" N LEU F 85 " --> pdb=" O ASN F 81 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE F 86 " --> pdb=" O VAL F 82 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP F 87 " --> pdb=" O GLU F 83 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU F 88 " --> pdb=" O LEU F 84 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR F 98 " --> pdb=" O SER F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 121 removed outlier: 3.741A pdb=" N GLU F 107 " --> pdb=" O ASP F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 132 removed outlier: 3.950A pdb=" N GLN F 129 " --> pdb=" O THR F 126 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE F 130 " --> pdb=" O GLY F 127 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG F 131 " --> pdb=" O GLU F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 154 removed outlier: 3.763A pdb=" N GLU F 146 " --> pdb=" O LYS F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 179 removed outlier: 3.953A pdb=" N TRP F 175 " --> pdb=" O LEU F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 252 Processing helix chain 'F' and resid 252 through 258 Processing helix chain 'F' and resid 282 through 295 removed outlier: 3.603A pdb=" N ILE F 295 " --> pdb=" O PHE F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 322 removed outlier: 3.785A pdb=" N ASN F 315 " --> pdb=" O ASP F 311 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU F 319 " --> pdb=" O ASN F 315 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY F 320 " --> pdb=" O ARG F 316 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU F 322 " --> pdb=" O ILE F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 341 Processing helix chain 'F' and resid 350 through 360 removed outlier: 3.879A pdb=" N ALA F 354 " --> pdb=" O GLU F 350 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE F 355 " --> pdb=" O ALA F 351 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 384 removed outlier: 3.875A pdb=" N LEU F 384 " --> pdb=" O PHE F 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 23 removed outlier: 3.722A pdb=" N PHE G 15 " --> pdb=" O ASN G 11 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR G 20 " --> pdb=" O ARG G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 41 removed outlier: 3.604A pdb=" N ALA G 36 " --> pdb=" O GLY G 33 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL G 38 " --> pdb=" O GLY G 35 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY G 39 " --> pdb=" O ALA G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 54 Processing helix chain 'G' and resid 61 through 66 removed outlier: 4.159A pdb=" N ASP G 65 " --> pdb=" O GLY G 61 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 66' Processing helix chain 'G' and resid 71 through 78 Processing helix chain 'G' and resid 81 through 99 removed outlier: 3.814A pdb=" N LEU G 85 " --> pdb=" O ASN G 81 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE G 86 " --> pdb=" O VAL G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 108 removed outlier: 3.540A pdb=" N GLU G 107 " --> pdb=" O ASP G 103 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE G 108 " --> pdb=" O GLU G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 124 removed outlier: 3.666A pdb=" N LEU G 112 " --> pdb=" O PHE G 108 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER G 113 " --> pdb=" O ARG G 109 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER G 114 " --> pdb=" O LYS G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 130 removed outlier: 3.750A pdb=" N GLN G 129 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE G 130 " --> pdb=" O GLY G 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 126 through 130' Processing helix chain 'G' and resid 143 through 153 Processing helix chain 'G' and resid 172 through 181 removed outlier: 3.933A pdb=" N ALA G 176 " --> pdb=" O ALA G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 201 removed outlier: 4.287A pdb=" N PHE G 201 " --> pdb=" O PRO G 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 198 through 201' Processing helix chain 'G' and resid 244 through 252 Processing helix chain 'G' and resid 252 through 258 removed outlier: 3.601A pdb=" N ILE G 257 " --> pdb=" O ILE G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 277 through 296 removed outlier: 3.793A pdb=" N PHE G 282 " --> pdb=" O HIS G 278 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL G 283 " --> pdb=" O THR G 279 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N TYR G 284 " --> pdb=" O ILE G 280 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER G 296 " --> pdb=" O GLY G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 322 Processing helix chain 'G' and resid 335 through 345 removed outlier: 3.671A pdb=" N ALA G 339 " --> pdb=" O GLU G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 349 through 358 removed outlier: 3.763A pdb=" N LEU G 358 " --> pdb=" O ALA G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 361 No H-bonds generated for 'chain 'G' and resid 359 through 361' Processing helix chain 'G' and resid 377 through 384 removed outlier: 4.488A pdb=" N LEU G 384 " --> pdb=" O PHE G 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 396 through 406 removed outlier: 3.609A pdb=" N LEU G 406 " --> pdb=" O ALA G 402 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 23 Processing helix chain 'H' and resid 34 through 38 removed outlier: 3.631A pdb=" N SER H 37 " --> pdb=" O ALA H 34 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL H 38 " --> pdb=" O GLY H 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 34 through 38' Processing helix chain 'H' and resid 44 through 54 removed outlier: 3.677A pdb=" N GLN H 54 " --> pdb=" O LYS H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 65 Processing helix chain 'H' and resid 73 through 78 Processing helix chain 'H' and resid 81 through 100 Processing helix chain 'H' and resid 102 through 115 removed outlier: 3.856A pdb=" N LYS H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE H 111 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU H 115 " --> pdb=" O ILE H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 121 Processing helix chain 'H' and resid 138 through 140 No H-bonds generated for 'chain 'H' and resid 138 through 140' Processing helix chain 'H' and resid 141 through 154 removed outlier: 3.628A pdb=" N ASN H 154 " --> pdb=" O LYS H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 181 removed outlier: 4.006A pdb=" N ASP H 179 " --> pdb=" O TRP H 175 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 201 removed outlier: 4.009A pdb=" N PHE H 201 " --> pdb=" O PRO H 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 198 through 201' Processing helix chain 'H' and resid 244 through 252 Processing helix chain 'H' and resid 253 through 259 Processing helix chain 'H' and resid 282 through 295 removed outlier: 3.656A pdb=" N ARG H 290 " --> pdb=" O GLU H 286 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE H 295 " --> pdb=" O PHE H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 311 through 322 removed outlier: 3.922A pdb=" N ASN H 315 " --> pdb=" O ASP H 311 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU H 322 " --> pdb=" O ILE H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 335 through 345 removed outlier: 3.904A pdb=" N ALA H 339 " --> pdb=" O GLU H 335 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE H 340 " --> pdb=" O LEU H 336 " (cutoff:3.500A) Processing helix chain 'H' and resid 349 through 360 removed outlier: 4.068A pdb=" N ILE H 355 " --> pdb=" O ALA H 351 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN H 360 " --> pdb=" O VAL H 356 " (cutoff:3.500A) Processing helix chain 'H' and resid 372 through 375 Processing helix chain 'H' and resid 376 through 384 removed outlier: 3.536A pdb=" N HIS H 383 " --> pdb=" O SER H 379 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU H 384 " --> pdb=" O PHE H 380 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 21 removed outlier: 3.725A pdb=" N SER I 17 " --> pdb=" O ASP I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 51 Processing helix chain 'I' and resid 51 through 56 removed outlier: 4.071A pdb=" N ASN I 55 " --> pdb=" O SER I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 66 removed outlier: 4.277A pdb=" N ALA I 62 " --> pdb=" O GLU I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 78 Processing helix chain 'I' and resid 82 through 100 removed outlier: 3.537A pdb=" N SER I 94 " --> pdb=" O THR I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 123 removed outlier: 3.520A pdb=" N GLU I 105 " --> pdb=" O CYS I 101 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA I 122 " --> pdb=" O GLU I 118 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA I 123 " --> pdb=" O VAL I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 125 No H-bonds generated for 'chain 'I' and resid 124 through 125' Processing helix chain 'I' and resid 126 through 132 removed outlier: 3.702A pdb=" N GLN I 129 " --> pdb=" O THR I 126 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG I 131 " --> pdb=" O GLU I 128 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU I 132 " --> pdb=" O GLN I 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 140 No H-bonds generated for 'chain 'I' and resid 138 through 140' Processing helix chain 'I' and resid 141 through 153 removed outlier: 3.812A pdb=" N LYS I 145 " --> pdb=" O PHE I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 181 removed outlier: 3.580A pdb=" N ALA I 176 " --> pdb=" O ALA I 172 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA I 177 " --> pdb=" O LEU I 173 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP I 179 " --> pdb=" O TRP I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 244 through 252 Processing helix chain 'I' and resid 252 through 259 Processing helix chain 'I' and resid 277 through 295 removed outlier: 3.831A pdb=" N PHE I 282 " --> pdb=" O HIS I 278 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL I 283 " --> pdb=" O THR I 279 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR I 284 " --> pdb=" O ILE I 280 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU I 293 " --> pdb=" O ARG I 289 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE I 294 " --> pdb=" O ARG I 290 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE I 295 " --> pdb=" O PHE I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 311 through 320 Processing helix chain 'I' and resid 321 through 324 removed outlier: 3.618A pdb=" N ASN I 324 " --> pdb=" O ALA I 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 321 through 324' Processing helix chain 'I' and resid 335 through 346 Processing helix chain 'I' and resid 349 through 358 removed outlier: 3.609A pdb=" N LEU I 358 " --> pdb=" O ALA I 354 " (cutoff:3.500A) Processing helix chain 'I' and resid 376 through 384 removed outlier: 3.779A pdb=" N VAL I 381 " --> pdb=" O PHE I 377 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU I 382 " --> pdb=" O ASN I 378 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS I 383 " --> pdb=" O SER I 379 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU I 384 " --> pdb=" O PHE I 380 " (cutoff:3.500A) Processing helix chain 'I' and resid 396 through 406 removed outlier: 4.076A pdb=" N VAL I 400 " --> pdb=" O VAL I 396 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU I 406 " --> pdb=" O ALA I 402 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 23 removed outlier: 3.532A pdb=" N SER J 17 " --> pdb=" O ASP J 13 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS J 23 " --> pdb=" O VAL J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 41 Processing helix chain 'J' and resid 44 through 56 Processing helix chain 'J' and resid 56 through 61 removed outlier: 3.723A pdb=" N LEU J 60 " --> pdb=" O TYR J 56 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY J 61 " --> pdb=" O PRO J 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 56 through 61' Processing helix chain 'J' and resid 72 through 78 Processing helix chain 'J' and resid 81 through 100 removed outlier: 3.720A pdb=" N LEU J 85 " --> pdb=" O ASN J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 124 removed outlier: 3.716A pdb=" N GLU J 105 " --> pdb=" O CYS J 101 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS J 110 " --> pdb=" O GLU J 106 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE J 111 " --> pdb=" O GLU J 107 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR J 116 " --> pdb=" O LEU J 112 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS J 117 " --> pdb=" O SER J 113 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU J 118 " --> pdb=" O SER J 114 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS J 121 " --> pdb=" O LYS J 117 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA J 122 " --> pdb=" O GLU J 118 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA J 123 " --> pdb=" O VAL J 119 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU J 124 " --> pdb=" O THR J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 132 removed outlier: 3.990A pdb=" N GLN J 129 " --> pdb=" O THR J 126 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG J 131 " --> pdb=" O GLU J 128 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 140 removed outlier: 3.700A pdb=" N LYS J 137 " --> pdb=" O ASN J 134 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS J 138 " --> pdb=" O GLN J 135 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASP J 139 " --> pdb=" O GLY J 136 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA J 140 " --> pdb=" O LYS J 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 134 through 140' Processing helix chain 'J' and resid 141 through 154 removed outlier: 3.805A pdb=" N LYS J 145 " --> pdb=" O PHE J 141 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN J 154 " --> pdb=" O LYS J 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 181 Processing helix chain 'J' and resid 198 through 202 removed outlier: 3.796A pdb=" N PHE J 201 " --> pdb=" O PRO J 198 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP J 202 " --> pdb=" O GLN J 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 198 through 202' Processing helix chain 'J' and resid 244 through 252 removed outlier: 4.044A pdb=" N TYR J 249 " --> pdb=" O ALA J 245 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ASP J 250 " --> pdb=" O SER J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 258 Processing helix chain 'J' and resid 282 through 295 removed outlier: 4.072A pdb=" N GLU J 286 " --> pdb=" O PHE J 282 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET J 287 " --> pdb=" O VAL J 283 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE J 288 " --> pdb=" O TYR J 284 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE J 295 " --> pdb=" O PHE J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 311 through 321 removed outlier: 3.519A pdb=" N ASN J 315 " --> pdb=" O ASP J 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 346 removed outlier: 3.708A pdb=" N ALA J 339 " --> pdb=" O GLU J 335 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY J 346 " --> pdb=" O LYS J 342 " (cutoff:3.500A) Processing helix chain 'J' and resid 349 through 360 removed outlier: 3.583A pdb=" N LYS J 353 " --> pdb=" O SER J 349 " (cutoff:3.500A) Processing helix chain 'J' and resid 372 through 375 Processing helix chain 'J' and resid 376 through 384 removed outlier: 3.722A pdb=" N LEU J 384 " --> pdb=" O PHE J 380 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 23 removed outlier: 3.692A pdb=" N PHE K 15 " --> pdb=" O ASN K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 41 removed outlier: 4.506A pdb=" N GLY K 39 " --> pdb=" O ALA K 36 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY K 41 " --> pdb=" O VAL K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 56 removed outlier: 3.633A pdb=" N VAL K 48 " --> pdb=" O THR K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 66 removed outlier: 4.194A pdb=" N LEU K 63 " --> pdb=" O LEU K 59 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE K 64 " --> pdb=" O LEU K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 78 removed outlier: 3.554A pdb=" N SER K 75 " --> pdb=" O SER K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 100 removed outlier: 3.535A pdb=" N LEU K 85 " --> pdb=" O ASN K 81 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS K 91 " --> pdb=" O ASP K 87 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE K 92 " --> pdb=" O GLU K 88 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N SER K 94 " --> pdb=" O THR K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 121 removed outlier: 3.768A pdb=" N GLU K 105 " --> pdb=" O CYS K 101 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU K 106 " --> pdb=" O GLU K 102 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU K 107 " --> pdb=" O ASP K 103 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE K 108 " --> pdb=" O GLU K 104 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG K 109 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS K 110 " --> pdb=" O GLU K 106 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE K 111 " --> pdb=" O GLU K 107 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS K 121 " --> pdb=" O LYS K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 124 No H-bonds generated for 'chain 'K' and resid 122 through 124' Processing helix chain 'K' and resid 126 through 132 removed outlier: 3.652A pdb=" N GLN K 129 " --> pdb=" O THR K 126 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG K 131 " --> pdb=" O GLU K 128 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU K 132 " --> pdb=" O GLN K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 141 through 154 removed outlier: 4.043A pdb=" N LYS K 145 " --> pdb=" O PHE K 141 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU K 146 " --> pdb=" O LYS K 142 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN K 154 " --> pdb=" O LYS K 150 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 181 removed outlier: 3.596A pdb=" N ASP K 179 " --> pdb=" O TRP K 175 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU K 180 " --> pdb=" O ALA K 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 244 through 252 Processing helix chain 'K' and resid 252 through 258 Processing helix chain 'K' and resid 280 through 295 removed outlier: 3.865A pdb=" N TYR K 284 " --> pdb=" O ILE K 280 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY K 292 " --> pdb=" O PHE K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 312 through 322 removed outlier: 4.028A pdb=" N LEU K 322 " --> pdb=" O ILE K 318 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 346 removed outlier: 3.694A pdb=" N LYS K 345 " --> pdb=" O THR K 341 " (cutoff:3.500A) Processing helix chain 'K' and resid 349 through 361 Processing helix chain 'K' and resid 371 through 375 removed outlier: 3.659A pdb=" N ALA K 375 " --> pdb=" O GLY K 372 " (cutoff:3.500A) Processing helix chain 'K' and resid 376 through 383 removed outlier: 3.692A pdb=" N GLU K 382 " --> pdb=" O ASN K 378 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS K 383 " --> pdb=" O SER K 379 " (cutoff:3.500A) Processing helix chain 'K' and resid 395 through 406 Processing helix chain 'L' and resid 11 through 22 Processing helix chain 'L' and resid 37 through 41 Processing helix chain 'L' and resid 44 through 56 removed outlier: 3.621A pdb=" N VAL L 48 " --> pdb=" O THR L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 66 removed outlier: 3.644A pdb=" N LEU L 60 " --> pdb=" O TYR L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 77 removed outlier: 3.773A pdb=" N SER L 75 " --> pdb=" O SER L 71 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP L 76 " --> pdb=" O GLN L 72 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN L 77 " --> pdb=" O ILE L 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 71 through 77' Processing helix chain 'L' and resid 81 through 99 removed outlier: 3.734A pdb=" N LEU L 85 " --> pdb=" O ASN L 81 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE L 86 " --> pdb=" O VAL L 82 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP L 87 " --> pdb=" O GLU L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 122 removed outlier: 4.172A pdb=" N GLU L 107 " --> pdb=" O ASP L 103 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE L 108 " --> pdb=" O GLU L 104 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ARG L 109 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 132 removed outlier: 3.910A pdb=" N PHE L 130 " --> pdb=" O GLY L 127 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG L 131 " --> pdb=" O GLU L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 142 removed outlier: 3.576A pdb=" N PHE L 141 " --> pdb=" O LYS L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 153 Processing helix chain 'L' and resid 172 through 181 Processing helix chain 'L' and resid 198 through 202 removed outlier: 3.525A pdb=" N PHE L 201 " --> pdb=" O PRO L 198 " (cutoff:3.500A) Processing helix chain 'L' and resid 244 through 252 Processing helix chain 'L' and resid 252 through 258 Processing helix chain 'L' and resid 281 through 296 removed outlier: 4.548A pdb=" N GLY L 285 " --> pdb=" O GLY L 281 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 321 Processing helix chain 'L' and resid 322 through 324 No H-bonds generated for 'chain 'L' and resid 322 through 324' Processing helix chain 'L' and resid 335 through 345 removed outlier: 4.018A pdb=" N ALA L 339 " --> pdb=" O GLU L 335 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS L 345 " --> pdb=" O THR L 341 " (cutoff:3.500A) Processing helix chain 'L' and resid 349 through 360 removed outlier: 3.629A pdb=" N LYS L 353 " --> pdb=" O SER L 349 " (cutoff:3.500A) Processing helix chain 'L' and resid 371 through 375 Processing helix chain 'L' and resid 376 through 382 Processing helix chain 'M' and resid 129 through 137 removed outlier: 3.515A pdb=" N ILE M 135 " --> pdb=" O ASP M 131 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR M 137 " --> pdb=" O LEU M 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 165 through 169 Processing helix chain 'M' and resid 183 through 198 removed outlier: 3.781A pdb=" N VAL M 194 " --> pdb=" O LEU M 190 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER M 195 " --> pdb=" O THR M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 214 removed outlier: 3.911A pdb=" N ALA M 213 " --> pdb=" O GLY M 210 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN M 214 " --> pdb=" O GLU M 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 210 through 214' Processing helix chain 'M' and resid 259 through 261 No H-bonds generated for 'chain 'M' and resid 259 through 261' Processing helix chain 'M' and resid 262 through 271 removed outlier: 3.747A pdb=" N LEU M 266 " --> pdb=" O GLY M 262 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE M 267 " --> pdb=" O PHE M 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 276 through 287 removed outlier: 4.128A pdb=" N ALA M 280 " --> pdb=" O THR M 276 " (cutoff:3.500A) Processing helix chain 'M' and resid 321 through 330 removed outlier: 4.098A pdb=" N TRP M 325 " --> pdb=" O LYS M 321 " (cutoff:3.500A) Processing helix chain 'M' and resid 344 through 356 removed outlier: 3.725A pdb=" N THR M 348 " --> pdb=" O LYS M 344 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL M 356 " --> pdb=" O GLU M 352 " (cutoff:3.500A) Processing helix chain 'M' and resid 367 through 373 removed outlier: 3.806A pdb=" N PHE M 371 " --> pdb=" O ASP M 367 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN M 373 " --> pdb=" O PHE M 369 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 385 removed outlier: 3.619A pdb=" N VAL M 378 " --> pdb=" O VAL M 374 " (cutoff:3.500A) Processing helix chain 'M' and resid 407 through 422 removed outlier: 4.312A pdb=" N ALA M 412 " --> pdb=" O HIS M 408 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N MET M 413 " --> pdb=" O TRP M 409 " (cutoff:3.500A) Processing helix chain 'M' and resid 445 through 465 removed outlier: 3.729A pdb=" N SER M 451 " --> pdb=" O PRO M 447 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA M 452 " --> pdb=" O MET M 448 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LEU M 453 " --> pdb=" O LEU M 449 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU M 454 " --> pdb=" O LEU M 450 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU M 455 " --> pdb=" O SER M 451 " (cutoff:3.500A) Processing helix chain 'M' and resid 522 through 528 Processing helix chain 'M' and resid 543 through 550 removed outlier: 3.715A pdb=" N ARG M 547 " --> pdb=" O LEU M 543 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N MET M 550 " --> pdb=" O LEU M 546 " (cutoff:3.500A) Processing helix chain 'M' and resid 559 through 564 removed outlier: 3.981A pdb=" N SER M 562 " --> pdb=" O LYS M 559 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU M 564 " --> pdb=" O ILE M 561 " (cutoff:3.500A) Processing helix chain 'M' and resid 597 through 603 removed outlier: 3.948A pdb=" N GLU M 601 " --> pdb=" O VAL M 597 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 33 removed outlier: 4.180A pdb=" N GLY N 33 " --> pdb=" O GLY N 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 30 through 33' Processing helix chain 'N' and resid 129 through 137 removed outlier: 4.563A pdb=" N ILE N 135 " --> pdb=" O ASP N 131 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE N 136 " --> pdb=" O PHE N 132 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR N 137 " --> pdb=" O LEU N 133 " (cutoff:3.500A) Processing helix chain 'N' and resid 143 through 145 No H-bonds generated for 'chain 'N' and resid 143 through 145' Processing helix chain 'N' and resid 165 through 169 removed outlier: 3.622A pdb=" N LEU N 169 " --> pdb=" O VAL N 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 165 through 169' Processing helix chain 'N' and resid 182 through 198 removed outlier: 3.657A pdb=" N PHE N 186 " --> pdb=" O GLY N 182 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS N 197 " --> pdb=" O LYS N 193 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR N 198 " --> pdb=" O VAL N 194 " (cutoff:3.500A) Processing helix chain 'N' and resid 261 through 271 removed outlier: 3.502A pdb=" N GLY N 265 " --> pdb=" O LEU N 261 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE N 267 " --> pdb=" O PHE N 263 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU N 269 " --> pdb=" O GLY N 265 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 287 removed outlier: 3.807A pdb=" N ASN N 283 " --> pdb=" O PRO N 279 " (cutoff:3.500A) Processing helix chain 'N' and resid 288 through 291 Processing helix chain 'N' and resid 319 through 321 No H-bonds generated for 'chain 'N' and resid 319 through 321' Processing helix chain 'N' and resid 322 through 331 Processing helix chain 'N' and resid 344 through 355 removed outlier: 4.019A pdb=" N THR N 348 " --> pdb=" O LYS N 344 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA N 351 " --> pdb=" O ALA N 347 " (cutoff:3.500A) Processing helix chain 'N' and resid 368 through 372 Processing helix chain 'N' and resid 374 through 386 removed outlier: 3.562A pdb=" N VAL N 378 " --> pdb=" O VAL N 374 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU N 386 " --> pdb=" O GLN N 382 " (cutoff:3.500A) Processing helix chain 'N' and resid 387 through 392 removed outlier: 3.744A pdb=" N SER N 392 " --> pdb=" O ILE N 388 " (cutoff:3.500A) Processing helix chain 'N' and resid 407 through 422 removed outlier: 3.670A pdb=" N LYS N 411 " --> pdb=" O THR N 407 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU N 416 " --> pdb=" O ALA N 412 " (cutoff:3.500A) Processing helix chain 'N' and resid 442 through 444 No H-bonds generated for 'chain 'N' and resid 442 through 444' Processing helix chain 'N' and resid 445 through 465 Processing helix chain 'N' and resid 478 through 482 Processing helix chain 'N' and resid 498 through 503 Processing helix chain 'N' and resid 517 through 521 Processing helix chain 'N' and resid 522 through 527 Processing helix chain 'N' and resid 539 through 550 Processing helix chain 'N' and resid 557 through 564 removed outlier: 3.968A pdb=" N SER N 562 " --> pdb=" O LYS N 559 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY N 563 " --> pdb=" O GLN N 560 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU N 564 " --> pdb=" O ILE N 561 " (cutoff:3.500A) Processing helix chain 'O' and resid 129 through 137 Processing helix chain 'O' and resid 143 through 145 No H-bonds generated for 'chain 'O' and resid 143 through 145' Processing helix chain 'O' and resid 165 through 169 Processing helix chain 'O' and resid 182 through 198 Processing helix chain 'O' and resid 212 through 217 removed outlier: 3.661A pdb=" N THR O 217 " --> pdb=" O GLN O 214 " (cutoff:3.500A) Processing helix chain 'O' and resid 261 through 271 Processing helix chain 'O' and resid 276 through 287 removed outlier: 3.758A pdb=" N ALA O 280 " --> pdb=" O THR O 276 " (cutoff:3.500A) Processing helix chain 'O' and resid 322 through 332 Processing helix chain 'O' and resid 344 through 355 removed outlier: 4.089A pdb=" N THR O 348 " --> pdb=" O LYS O 344 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU O 349 " --> pdb=" O SER O 345 " (cutoff:3.500A) Processing helix chain 'O' and resid 367 through 385 removed outlier: 3.590A pdb=" N PHE O 371 " --> pdb=" O ASP O 367 " (cutoff:3.500A) Proline residue: O 376 - end of helix Processing helix chain 'O' and resid 387 through 392 removed outlier: 3.766A pdb=" N SER O 392 " --> pdb=" O ILE O 388 " (cutoff:3.500A) Processing helix chain 'O' and resid 409 through 421 removed outlier: 3.765A pdb=" N MET O 413 " --> pdb=" O TRP O 409 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE O 420 " --> pdb=" O GLU O 416 " (cutoff:3.500A) Processing helix chain 'O' and resid 445 through 465 removed outlier: 3.727A pdb=" N SER O 451 " --> pdb=" O PRO O 447 " (cutoff:3.500A) Processing helix chain 'O' and resid 495 through 507 removed outlier: 4.256A pdb=" N ARG O 499 " --> pdb=" O LYS O 495 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU O 500 " --> pdb=" O ALA O 496 " (cutoff:3.500A) Processing helix chain 'O' and resid 522 through 528 removed outlier: 3.986A pdb=" N LEU O 526 " --> pdb=" O SER O 522 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA O 527 " --> pdb=" O PRO O 523 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET O 528 " --> pdb=" O THR O 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 522 through 528' Processing helix chain 'O' and resid 539 through 550 removed outlier: 3.803A pdb=" N LEU O 543 " --> pdb=" O ASN O 539 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA O 545 " --> pdb=" O ARG O 541 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA O 549 " --> pdb=" O ALA O 545 " (cutoff:3.500A) Processing helix chain 'O' and resid 554 through 558 Processing helix chain 'O' and resid 560 through 564 Processing helix chain 'O' and resid 597 through 603 removed outlier: 3.821A pdb=" N GLU O 601 " --> pdb=" O VAL O 597 " (cutoff:3.500A) Processing helix chain 'P' and resid 129 through 138 Processing helix chain 'P' and resid 143 through 147 Processing helix chain 'P' and resid 165 through 170 removed outlier: 3.724A pdb=" N SER P 170 " --> pdb=" O ASP P 166 " (cutoff:3.500A) Processing helix chain 'P' and resid 182 through 198 removed outlier: 3.520A pdb=" N PHE P 186 " --> pdb=" O GLY P 182 " (cutoff:3.500A) Processing helix chain 'P' and resid 213 through 217 removed outlier: 3.574A pdb=" N PHE P 216 " --> pdb=" O ALA P 213 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR P 217 " --> pdb=" O GLN P 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 213 through 217' Processing helix chain 'P' and resid 264 through 269 removed outlier: 3.828A pdb=" N LEU P 269 " --> pdb=" O GLY P 265 " (cutoff:3.500A) Processing helix chain 'P' and resid 276 through 287 removed outlier: 4.286A pdb=" N ALA P 280 " --> pdb=" O THR P 276 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA P 287 " --> pdb=" O ASN P 283 " (cutoff:3.500A) Processing helix chain 'P' and resid 344 through 354 Processing helix chain 'P' and resid 375 through 387 removed outlier: 3.589A pdb=" N LYS P 379 " --> pdb=" O LEU P 375 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE P 380 " --> pdb=" O PRO P 376 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE P 381 " --> pdb=" O LEU P 377 " (cutoff:3.500A) Processing helix chain 'P' and resid 389 through 392 Processing helix chain 'P' and resid 407 through 418 removed outlier: 3.840A pdb=" N LYS P 411 " --> pdb=" O THR P 407 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP P 418 " --> pdb=" O SER P 414 " (cutoff:3.500A) Processing helix chain 'P' and resid 445 through 465 removed outlier: 3.777A pdb=" N LEU P 449 " --> pdb=" O HIS P 445 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE P 462 " --> pdb=" O ALA P 458 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG P 463 " --> pdb=" O GLU P 459 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG P 464 " --> pdb=" O ILE P 460 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY P 465 " --> pdb=" O LEU P 461 " (cutoff:3.500A) Processing helix chain 'P' and resid 497 through 504 removed outlier: 3.678A pdb=" N ALA P 501 " --> pdb=" O TYR P 497 " (cutoff:3.500A) Processing helix chain 'P' and resid 517 through 521 Processing helix chain 'P' and resid 522 through 527 removed outlier: 3.847A pdb=" N LEU P 526 " --> pdb=" O SER P 522 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA P 527 " --> pdb=" O PRO P 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 522 through 527' Processing helix chain 'P' and resid 539 through 548 Processing helix chain 'P' and resid 555 through 562 removed outlier: 3.844A pdb=" N GLN P 560 " --> pdb=" O GLN P 556 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER P 562 " --> pdb=" O LEU P 558 " (cutoff:3.500A) Processing helix chain 'P' and resid 599 through 603 removed outlier: 3.946A pdb=" N ALA P 603 " --> pdb=" O GLU P 600 " (cutoff:3.500A) Processing helix chain 'Q' and resid 129 through 138 removed outlier: 3.696A pdb=" N TYR Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER Q 138 " --> pdb=" O ASN Q 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 140 through 144 removed outlier: 3.868A pdb=" N LEU Q 144 " --> pdb=" O LYS Q 141 " (cutoff:3.500A) Processing helix chain 'Q' and resid 165 through 170 removed outlier: 3.632A pdb=" N SER Q 170 " --> pdb=" O ASP Q 166 " (cutoff:3.500A) Processing helix chain 'Q' and resid 182 through 198 removed outlier: 3.631A pdb=" N PHE Q 186 " --> pdb=" O GLY Q 182 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR Q 198 " --> pdb=" O VAL Q 194 " (cutoff:3.500A) Processing helix chain 'Q' and resid 262 through 270 Processing helix chain 'Q' and resid 277 through 286 Processing helix chain 'Q' and resid 321 through 332 Processing helix chain 'Q' and resid 343 through 354 removed outlier: 4.249A pdb=" N ALA Q 347 " --> pdb=" O PHE Q 343 " (cutoff:3.500A) Processing helix chain 'Q' and resid 367 through 372 removed outlier: 3.771A pdb=" N PHE Q 371 " --> pdb=" O ASP Q 367 " (cutoff:3.500A) Processing helix chain 'Q' and resid 374 through 385 removed outlier: 3.617A pdb=" N VAL Q 378 " --> pdb=" O VAL Q 374 " (cutoff:3.500A) Processing helix chain 'Q' and resid 387 through 392 Processing helix chain 'Q' and resid 407 through 421 removed outlier: 3.774A pdb=" N LYS Q 411 " --> pdb=" O THR Q 407 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU Q 416 " --> pdb=" O ALA Q 412 " (cutoff:3.500A) Processing helix chain 'Q' and resid 445 through 465 removed outlier: 3.553A pdb=" N LEU Q 449 " --> pdb=" O HIS Q 445 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG Q 463 " --> pdb=" O GLU Q 459 " (cutoff:3.500A) Processing helix chain 'Q' and resid 498 through 505 removed outlier: 4.557A pdb=" N LYS Q 502 " --> pdb=" O GLU Q 498 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG Q 505 " --> pdb=" O ALA Q 501 " (cutoff:3.500A) Processing helix chain 'Q' and resid 517 through 521 Processing helix chain 'Q' and resid 522 through 529 removed outlier: 3.991A pdb=" N ALA Q 527 " --> pdb=" O PRO Q 523 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS Q 529 " --> pdb=" O VAL Q 525 " (cutoff:3.500A) Processing helix chain 'Q' and resid 539 through 549 removed outlier: 3.500A pdb=" N LEU Q 546 " --> pdb=" O ASP Q 542 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR Q 548 " --> pdb=" O GLN Q 544 " (cutoff:3.500A) Processing helix chain 'Q' and resid 557 through 564 removed outlier: 3.555A pdb=" N SER Q 562 " --> pdb=" O LYS Q 559 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 137 removed outlier: 3.924A pdb=" N LEU R 133 " --> pdb=" O THR R 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 170 Processing helix chain 'R' and resid 182 through 198 removed outlier: 3.590A pdb=" N GLU R 196 " --> pdb=" O ARG R 192 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS R 197 " --> pdb=" O LYS R 193 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR R 198 " --> pdb=" O VAL R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 271 Processing helix chain 'R' and resid 276 through 287 removed outlier: 4.149A pdb=" N ALA R 280 " --> pdb=" O THR R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 321 through 332 Processing helix chain 'R' and resid 342 through 353 removed outlier: 4.150A pdb=" N LEU R 346 " --> pdb=" O PRO R 342 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA R 347 " --> pdb=" O PHE R 343 " (cutoff:3.500A) Processing helix chain 'R' and resid 367 through 386 removed outlier: 4.236A pdb=" N PHE R 371 " --> pdb=" O ASP R 367 " (cutoff:3.500A) Proline residue: R 376 - end of helix removed outlier: 3.864A pdb=" N LEU R 384 " --> pdb=" O ILE R 380 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA R 385 " --> pdb=" O ILE R 381 " (cutoff:3.500A) Processing helix chain 'R' and resid 390 through 394 removed outlier: 3.846A pdb=" N VAL R 394 " --> pdb=" O LYS R 391 " (cutoff:3.500A) Processing helix chain 'R' and resid 407 through 420 removed outlier: 3.756A pdb=" N LYS R 411 " --> pdb=" O THR R 407 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET R 413 " --> pdb=" O TRP R 409 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLU R 416 " --> pdb=" O ALA R 412 " (cutoff:3.500A) Processing helix chain 'R' and resid 445 through 465 removed outlier: 3.930A pdb=" N LEU R 454 " --> pdb=" O LEU R 450 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU R 455 " --> pdb=" O SER R 451 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET R 456 " --> pdb=" O ALA R 452 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY R 465 " --> pdb=" O LEU R 461 " (cutoff:3.500A) Processing helix chain 'R' and resid 478 through 483 removed outlier: 4.008A pdb=" N TYR R 482 " --> pdb=" O GLU R 478 " (cutoff:3.500A) Processing helix chain 'R' and resid 491 through 507 removed outlier: 3.773A pdb=" N LYS R 495 " --> pdb=" O ASP R 491 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG R 505 " --> pdb=" O ALA R 501 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS R 506 " --> pdb=" O LYS R 502 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE R 507 " --> pdb=" O GLU R 503 " (cutoff:3.500A) Processing helix chain 'R' and resid 522 through 528 removed outlier: 3.665A pdb=" N MET R 528 " --> pdb=" O THR R 524 " (cutoff:3.500A) Processing helix chain 'R' and resid 539 through 550 removed outlier: 3.823A pdb=" N LEU R 543 " --> pdb=" O ASN R 539 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR R 548 " --> pdb=" O GLN R 544 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA R 549 " --> pdb=" O ALA R 545 " (cutoff:3.500A) Processing helix chain 'R' and resid 554 through 562 removed outlier: 3.529A pdb=" N LEU R 558 " --> pdb=" O ASN R 554 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER R 562 " --> pdb=" O LEU R 558 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 10 removed outlier: 3.791A pdb=" N ASN A 8 " --> pdb=" O GLN A 5 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A 5 " --> pdb=" O ASN A 8 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ILE A 3 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 29 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 303 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 163 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE A 164 " --> pdb=" O TYR A 224 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLN A 183 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU A 223 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N PHE A 185 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LYS A 225 " --> pdb=" O PHE A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 188 through 189 removed outlier: 3.650A pdb=" N SER A 189 " --> pdb=" O GLN A 195 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN A 195 " --> pdb=" O SER A 189 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 234 Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 5 removed outlier: 3.511A pdb=" N VAL B 368 " --> pdb=" O TYR B 4 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR B 367 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL B 28 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N PHE B 165 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL B 30 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE B 164 " --> pdb=" O TYR B 224 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 183 through 185 Processing sheet with id=AA6, first strand: chain 'B' and resid 188 through 189 removed outlier: 3.597A pdb=" N SER B 189 " --> pdb=" O GLN B 195 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN B 195 " --> pdb=" O SER B 189 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AA8, first strand: chain 'B' and resid 232 through 234 Processing sheet with id=AA9, first strand: chain 'C' and resid 8 through 9 removed outlier: 3.934A pdb=" N ASN C 8 " --> pdb=" O GLN C 5 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN C 5 " --> pdb=" O ASN C 8 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR C 367 " --> pdb=" O VAL C 329 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS C 328 " --> pdb=" O THR C 300 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLY C 29 " --> pdb=" O PHE C 303 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N ASN C 305 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU C 31 " --> pdb=" O ASN C 305 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL C 30 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 223 " --> pdb=" O PHE C 185 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 188 through 189 Processing sheet with id=AB2, first strand: chain 'C' and resid 232 through 234 Processing sheet with id=AB3, first strand: chain 'D' and resid 3 through 5 removed outlier: 3.599A pdb=" N THR D 367 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR D 332 " --> pdb=" O ILE D 304 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL D 28 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N PHE D 165 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL D 30 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE D 164 " --> pdb=" O TYR D 224 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 183 through 185 Processing sheet with id=AB5, first strand: chain 'D' and resid 188 through 189 removed outlier: 3.661A pdb=" N SER D 189 " --> pdb=" O GLN D 195 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN D 195 " --> pdb=" O SER D 189 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 203 through 207 Processing sheet with id=AB7, first strand: chain 'D' and resid 232 through 234 Processing sheet with id=AB8, first strand: chain 'E' and resid 3 through 4 removed outlier: 8.488A pdb=" N VAL E 369 " --> pdb=" O VAL E 329 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE E 331 " --> pdb=" O VAL E 369 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS E 328 " --> pdb=" O THR E 300 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL E 28 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N PHE E 165 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL E 30 " --> pdb=" O PHE E 165 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE E 164 " --> pdb=" O TYR E 224 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA E 221 " --> pdb=" O GLN E 183 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 188 through 189 Processing sheet with id=AC1, first strand: chain 'E' and resid 232 through 234 Processing sheet with id=AC2, first strand: chain 'F' and resid 8 through 9 removed outlier: 3.665A pdb=" N ALA F 163 " --> pdb=" O VAL F 28 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR F 166 " --> pdb=" O TYR F 224 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA F 221 " --> pdb=" O GLN F 183 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU F 223 " --> pdb=" O PHE F 185 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 188 through 189 Processing sheet with id=AC4, first strand: chain 'F' and resid 203 through 207 Processing sheet with id=AC5, first strand: chain 'F' and resid 232 through 234 Processing sheet with id=AC6, first strand: chain 'G' and resid 4 through 5 removed outlier: 3.592A pdb=" N VAL G 330 " --> pdb=" O LEU G 302 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL G 30 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE G 164 " --> pdb=" O TYR G 224 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLN G 183 " --> pdb=" O ALA G 221 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LEU G 223 " --> pdb=" O GLN G 183 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N PHE G 185 " --> pdb=" O LEU G 223 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LYS G 225 " --> pdb=" O PHE G 185 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 188 through 189 Processing sheet with id=AC8, first strand: chain 'G' and resid 232 through 234 removed outlier: 4.040A pdb=" N TYR G 233 " --> pdb=" O ASN G 241 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 8 through 10 removed outlier: 4.423A pdb=" N ILE H 3 " --> pdb=" O LEU H 10 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N THR H 367 " --> pdb=" O PHE H 327 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL H 329 " --> pdb=" O THR H 367 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N VAL H 369 " --> pdb=" O VAL H 329 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE H 331 " --> pdb=" O VAL H 369 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS H 328 " --> pdb=" O THR H 300 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL H 28 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N PHE H 165 " --> pdb=" O VAL H 28 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL H 30 " --> pdb=" O PHE H 165 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE H 164 " --> pdb=" O TYR H 224 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA H 221 " --> pdb=" O GLN H 183 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU H 223 " --> pdb=" O PHE H 185 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 188 through 189 removed outlier: 3.605A pdb=" N SER H 189 " --> pdb=" O GLN H 195 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN H 195 " --> pdb=" O SER H 189 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'H' and resid 203 through 207 Processing sheet with id=AD3, first strand: chain 'H' and resid 233 through 234 removed outlier: 3.675A pdb=" N TYR H 233 " --> pdb=" O ASN H 241 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 8 through 9 removed outlier: 3.706A pdb=" N ASN I 8 " --> pdb=" O GLN I 5 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL I 28 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N PHE I 165 " --> pdb=" O VAL I 28 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL I 30 " --> pdb=" O PHE I 165 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE I 164 " --> pdb=" O TYR I 224 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 188 through 189 Processing sheet with id=AD6, first strand: chain 'I' and resid 232 through 233 Processing sheet with id=AD7, first strand: chain 'J' and resid 8 through 9 removed outlier: 3.640A pdb=" N ASN J 8 " --> pdb=" O GLN J 5 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR J 332 " --> pdb=" O ILE J 304 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL J 28 " --> pdb=" O ALA J 163 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N PHE J 165 " --> pdb=" O VAL J 28 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL J 30 " --> pdb=" O PHE J 165 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE J 164 " --> pdb=" O TYR J 224 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU J 223 " --> pdb=" O PHE J 185 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 188 through 189 removed outlier: 3.980A pdb=" N SER J 189 " --> pdb=" O GLN J 195 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN J 195 " --> pdb=" O SER J 189 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'J' and resid 232 through 234 removed outlier: 3.755A pdb=" N TYR J 233 " --> pdb=" O ASN J 241 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 3 through 4 removed outlier: 8.556A pdb=" N THR K 367 " --> pdb=" O PHE K 327 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL K 329 " --> pdb=" O THR K 367 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N VAL K 369 " --> pdb=" O VAL K 329 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE K 331 " --> pdb=" O VAL K 369 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL K 28 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N PHE K 165 " --> pdb=" O VAL K 28 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL K 30 " --> pdb=" O PHE K 165 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE K 164 " --> pdb=" O TYR K 224 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLN K 183 " --> pdb=" O ALA K 221 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU K 223 " --> pdb=" O GLN K 183 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N PHE K 185 " --> pdb=" O LEU K 223 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LYS K 225 " --> pdb=" O PHE K 185 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 188 through 189 Processing sheet with id=AE3, first strand: chain 'K' and resid 232 through 234 Processing sheet with id=AE4, first strand: chain 'L' and resid 8 through 9 removed outlier: 3.796A pdb=" N ASN L 8 " --> pdb=" O GLN L 5 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL L 368 " --> pdb=" O TYR L 4 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N VAL L 369 " --> pdb=" O VAL L 329 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE L 331 " --> pdb=" O VAL L 369 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN L 27 " --> pdb=" O ALA L 301 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N PHE L 303 " --> pdb=" O ASN L 27 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLY L 29 " --> pdb=" O PHE L 303 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ASN L 305 " --> pdb=" O GLY L 29 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU L 31 " --> pdb=" O ASN L 305 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL L 28 " --> pdb=" O ALA L 163 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N PHE L 165 " --> pdb=" O VAL L 28 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL L 30 " --> pdb=" O PHE L 165 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE L 164 " --> pdb=" O TYR L 224 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLN L 183 " --> pdb=" O ALA L 221 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU L 223 " --> pdb=" O GLN L 183 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N PHE L 185 " --> pdb=" O LEU L 223 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LYS L 225 " --> pdb=" O PHE L 185 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 188 through 189 removed outlier: 3.574A pdb=" N GLN L 195 " --> pdb=" O SER L 189 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 232 through 234 Processing sheet with id=AE7, first strand: chain 'M' and resid 13 through 18 removed outlier: 3.512A pdb=" N VAL M 16 " --> pdb=" O ARG M 24 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ARG M 24 " --> pdb=" O VAL M 16 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 23 through 27 current: chain 'M' and resid 59 through 70 removed outlier: 3.896A pdb=" N GLY M 100 " --> pdb=" O VAL M 62 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ARG M 64 " --> pdb=" O ALA M 98 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA M 98 " --> pdb=" O ARG M 64 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N THR M 66 " --> pdb=" O ALA M 96 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ALA M 96 " --> pdb=" O THR M 66 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N MET M 68 " --> pdb=" O ILE M 94 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ILE M 94 " --> pdb=" O MET M 68 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N PHE M 70 " --> pdb=" O ARG M 92 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ARG M 92 " --> pdb=" O PHE M 70 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE M 101 " --> pdb=" O ILE M 112 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 110 through 112 current: chain 'N' and resid 22 through 27 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 22 through 27 current: chain 'N' and resid 60 through 70 removed outlier: 6.193A pdb=" N LEU N 60 " --> pdb=" O PHE N 101 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE N 101 " --> pdb=" O LEU N 60 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL N 62 " --> pdb=" O ILE N 99 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE N 95 " --> pdb=" O THR N 66 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N MET N 68 " --> pdb=" O GLN N 93 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLN N 93 " --> pdb=" O MET N 68 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 110 through 112 current: chain 'O' and resid 22 through 26 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 22 through 26 current: chain 'O' and resid 60 through 70 removed outlier: 6.153A pdb=" N LEU O 60 " --> pdb=" O PHE O 101 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE O 101 " --> pdb=" O LEU O 60 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL O 62 " --> pdb=" O ILE O 99 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE O 95 " --> pdb=" O THR O 66 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N MET O 68 " --> pdb=" O GLN O 93 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLN O 93 " --> pdb=" O MET O 68 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS O 103 " --> pdb=" O VAL O 110 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 109 through 112 current: chain 'P' and resid 22 through 26 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 22 through 26 current: chain 'P' and resid 59 through 70 removed outlier: 6.318A pdb=" N LEU P 60 " --> pdb=" O PHE P 101 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N PHE P 101 " --> pdb=" O LEU P 60 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL P 62 " --> pdb=" O ILE P 99 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE P 95 " --> pdb=" O THR P 66 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N MET P 68 " --> pdb=" O GLN P 93 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLN P 93 " --> pdb=" O MET P 68 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 35 through 37 Processing sheet with id=AE9, first strand: chain 'M' and resid 160 through 164 removed outlier: 4.094A pdb=" N GLY M 151 " --> pdb=" O ILE M 161 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA M 163 " --> pdb=" O GLU M 149 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLU M 149 " --> pdb=" O ALA M 163 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE M 572 " --> pdb=" O TRP M 532 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA M 174 " --> pdb=" O ASN M 531 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR M 515 " --> pdb=" O VAL M 175 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER M 510 " --> pdb=" O THR M 472 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL M 204 " --> pdb=" O LEU M 475 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS M 223 " --> pdb=" O ILE M 435 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ASN M 437 " --> pdb=" O LYS M 223 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N THR M 225 " --> pdb=" O ASN M 437 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS M 254 " --> pdb=" O ILE M 226 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 256 through 257 removed outlier: 6.350A pdb=" N ILE M 256 " --> pdb=" O ASN M 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'M' and resid 292 through 294 removed outlier: 3.621A pdb=" N HIS M 292 " --> pdb=" O TYR M 299 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 357 through 358 removed outlier: 4.208A pdb=" N LYS M 365 " --> pdb=" O ALA M 357 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 35 through 37 Processing sheet with id=AF5, first strand: chain 'N' and resid 160 through 164 removed outlier: 4.137A pdb=" N GLY N 151 " --> pdb=" O ILE N 161 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA N 163 " --> pdb=" O GLU N 149 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLU N 149 " --> pdb=" O ALA N 163 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL N 152 " --> pdb=" O SER N 583 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL N 580 " --> pdb=" O ALA N 571 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL N 570 " --> pdb=" O SER N 534 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE N 572 " --> pdb=" O TRP N 532 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL N 513 " --> pdb=" O LEU N 173 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER N 510 " --> pdb=" O THR N 472 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER N 514 " --> pdb=" O LEU N 476 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL N 204 " --> pdb=" O LEU N 475 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE N 203 " --> pdb=" O HIS N 434 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N VAL N 436 " --> pdb=" O ILE N 203 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE N 205 " --> pdb=" O VAL N 436 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LYS N 223 " --> pdb=" O ILE N 435 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ASN N 437 " --> pdb=" O LYS N 223 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR N 225 " --> pdb=" O ASN N 437 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LYS N 254 " --> pdb=" O HIS N 224 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE N 226 " --> pdb=" O LYS N 254 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 256 through 257 removed outlier: 6.713A pdb=" N ILE N 256 " --> pdb=" O ASN N 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'N' and resid 292 through 293 removed outlier: 3.618A pdb=" N TYR N 299 " --> pdb=" O HIS N 292 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE N 308 " --> pdb=" O LEU N 300 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 356 through 359 removed outlier: 3.816A pdb=" N GLY N 363 " --> pdb=" O ASP N 359 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'O' and resid 36 through 37 Processing sheet with id=AG1, first strand: chain 'O' and resid 160 through 164 removed outlier: 7.166A pdb=" N ILE O 161 " --> pdb=" O LEU O 150 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL O 580 " --> pdb=" O ALA O 571 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE O 572 " --> pdb=" O TRP O 532 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 253 through 254 removed outlier: 8.290A pdb=" N LYS O 254 " --> pdb=" O HIS O 224 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE O 226 " --> pdb=" O LYS O 254 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LYS O 223 " --> pdb=" O ILE O 435 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ASN O 437 " --> pdb=" O LYS O 223 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N THR O 225 " --> pdb=" O ASN O 437 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU O 477 " --> pdb=" O PHE O 206 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU O 474 " --> pdb=" O ILE O 512 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N SER O 514 " --> pdb=" O LEU O 474 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU O 476 " --> pdb=" O SER O 514 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'O' and resid 256 through 257 removed outlier: 6.809A pdb=" N ILE O 256 " --> pdb=" O ASN O 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'O' and resid 299 through 301 removed outlier: 3.760A pdb=" N PHE O 308 " --> pdb=" O LEU O 300 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'P' and resid 160 through 161 removed outlier: 4.241A pdb=" N GLY P 151 " --> pdb=" O ILE P 161 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER P 534 " --> pdb=" O VAL P 570 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N PHE P 572 " --> pdb=" O TRP P 532 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP P 532 " --> pdb=" O PHE P 572 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'P' and resid 173 through 175 removed outlier: 6.796A pdb=" N VAL P 204 " --> pdb=" O LEU P 475 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE P 203 " --> pdb=" O HIS P 434 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL P 436 " --> pdb=" O ILE P 203 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE P 205 " --> pdb=" O VAL P 436 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LYS P 254 " --> pdb=" O HIS P 224 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE P 226 " --> pdb=" O LYS P 254 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 256 through 257 removed outlier: 6.319A pdb=" N ILE P 256 " --> pdb=" O ASN P 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'P' and resid 292 through 293 Processing sheet with id=AG9, first strand: chain 'Q' and resid 109 through 112 removed outlier: 3.908A pdb=" N VAL Q 110 " --> pdb=" O LYS Q 103 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS Q 103 " --> pdb=" O VAL Q 110 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE Q 112 " --> pdb=" O PHE Q 101 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE Q 101 " --> pdb=" O ILE Q 112 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLN Q 93 " --> pdb=" O MET Q 68 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N MET Q 68 " --> pdb=" O GLN Q 93 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE Q 95 " --> pdb=" O THR Q 66 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL Q 62 " --> pdb=" O ILE Q 99 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE Q 101 " --> pdb=" O LEU Q 60 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU Q 60 " --> pdb=" O PHE Q 101 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE Q 52 " --> pdb=" O ALA Q 63 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER Q 124 " --> pdb=" O ASP Q 55 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY Q 13 " --> pdb=" O ALA Q 125 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG Q 24 " --> pdb=" O VAL Q 16 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE Q 23 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA Q 96 " --> pdb=" O ILE Q 23 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Q' and resid 160 through 164 removed outlier: 4.074A pdb=" N GLY Q 151 " --> pdb=" O ILE Q 161 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA Q 163 " --> pdb=" O GLU Q 149 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N GLU Q 149 " --> pdb=" O ALA Q 163 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL Q 580 " --> pdb=" O ALA Q 571 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA Q 571 " --> pdb=" O VAL Q 580 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE Q 572 " --> pdb=" O TRP Q 532 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP Q 532 " --> pdb=" O PHE Q 572 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA Q 174 " --> pdb=" O PHE Q 533 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Q' and resid 222 through 226 removed outlier: 3.657A pdb=" N ILE Q 435 " --> pdb=" O LYS Q 223 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ILE Q 203 " --> pdb=" O HIS Q 434 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N VAL Q 436 " --> pdb=" O ILE Q 203 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE Q 205 " --> pdb=" O VAL Q 436 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR Q 472 " --> pdb=" O SER Q 510 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Q' and resid 300 through 301 Processing sheet with id=AH4, first strand: chain 'R' and resid 15 through 19 removed outlier: 4.543A pdb=" N GLY R 17 " --> pdb=" O ARG R 24 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'R' and resid 54 through 55 removed outlier: 4.336A pdb=" N PHE R 54 " --> pdb=" O VAL R 61 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL R 61 " --> pdb=" O PHE R 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'R' and resid 148 through 152 removed outlier: 4.167A pdb=" N LEU R 150 " --> pdb=" O ILE R 161 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ILE R 161 " --> pdb=" O LEU R 150 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'R' and resid 472 through 474 removed outlier: 3.566A pdb=" N ILE R 512 " --> pdb=" O LEU R 474 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR R 515 " --> pdb=" O VAL R 175 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA R 569 " --> pdb=" O ILE R 582 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE R 582 " --> pdb=" O ALA R 569 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ALA R 571 " --> pdb=" O VAL R 580 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL R 580 " --> pdb=" O ALA R 571 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'R' and resid 203 through 206 removed outlier: 8.105A pdb=" N ILE R 203 " --> pdb=" O HIS R 434 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N VAL R 436 " --> pdb=" O ILE R 203 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE R 205 " --> pdb=" O VAL R 436 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'R' and resid 356 through 358 removed outlier: 4.248A pdb=" N ALA R 357 " --> pdb=" O LYS R 365 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS R 365 " --> pdb=" O ALA R 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 2157 hydrogen bonds defined for protein. 6162 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: 25.64 Time building geometry restraints manager: 13.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 16970 1.33 - 1.46: 19550 1.46 - 1.59: 28615 1.59 - 1.72: 52 1.72 - 1.85: 239 Bond restraints: 65426 Sorted by residual: bond pdb=" C1D NAD F 501 " pdb=" N1N NAD F 501 " ideal model delta sigma weight residual 1.481 1.727 -0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" O5D NAD F 501 " pdb=" PN NAD F 501 " ideal model delta sigma weight residual 1.637 1.855 -0.218 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C1D NAD H 501 " pdb=" N1N NAD H 501 " ideal model delta sigma weight residual 1.481 1.697 -0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" O5D NAD E 501 " pdb=" PN NAD E 501 " ideal model delta sigma weight residual 1.637 1.837 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" O5D NAD H 501 " pdb=" PN NAD H 501 " ideal model delta sigma weight residual 1.637 1.828 -0.191 2.00e-02 2.50e+03 9.08e+01 ... (remaining 65421 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 88104 3.63 - 7.26: 383 7.26 - 10.88: 56 10.88 - 14.51: 7 14.51 - 18.14: 1 Bond angle restraints: 88551 Sorted by residual: angle pdb=" PA AR6 I 501 " pdb=" O3A AR6 I 501 " pdb=" PB AR6 I 501 " ideal model delta sigma weight residual 123.67 141.81 -18.14 3.00e+00 1.11e-01 3.66e+01 angle pdb=" CA PHE A 165 " pdb=" CB PHE A 165 " pdb=" CG PHE A 165 " ideal model delta sigma weight residual 113.80 118.35 -4.55 1.00e+00 1.00e+00 2.07e+01 angle pdb=" O3 NAD E 501 " pdb=" PN NAD E 501 " pdb=" O5D NAD E 501 " ideal model delta sigma weight residual 98.00 111.12 -13.12 3.00e+00 1.11e-01 1.91e+01 angle pdb=" C LYS K 43 " pdb=" CA LYS K 43 " pdb=" CB LYS K 43 " ideal model delta sigma weight residual 111.42 106.01 5.41 1.31e+00 5.83e-01 1.71e+01 angle pdb=" C LEU O 329 " pdb=" N ARG O 330 " pdb=" CA ARG O 330 " ideal model delta sigma weight residual 120.44 115.07 5.37 1.30e+00 5.92e-01 1.71e+01 ... (remaining 88546 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 38050 35.72 - 71.44: 835 71.44 - 107.16: 150 107.16 - 142.88: 24 142.88 - 178.61: 54 Dihedral angle restraints: 39113 sinusoidal: 15899 harmonic: 23214 Sorted by residual: dihedral pdb=" C5' ADP M 701 " pdb=" O5' ADP M 701 " pdb=" PA ADP M 701 " pdb=" O2A ADP M 701 " ideal model delta sinusoidal sigma weight residual 300.00 149.94 150.06 1 2.00e+01 2.50e-03 4.48e+01 dihedral pdb=" C5' ADP N 701 " pdb=" O5' ADP N 701 " pdb=" PA ADP N 701 " pdb=" O2A ADP N 701 " ideal model delta sinusoidal sigma weight residual -60.00 82.01 -142.01 1 2.00e+01 2.50e-03 4.29e+01 dihedral pdb=" O1B ADP M 701 " pdb=" O3A ADP M 701 " pdb=" PB ADP M 701 " pdb=" PA ADP M 701 " ideal model delta sinusoidal sigma weight residual -60.00 78.64 -138.64 1 2.00e+01 2.50e-03 4.20e+01 ... (remaining 39110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.118: 9632 1.118 - 2.235: 0 2.235 - 3.353: 0 3.353 - 4.471: 0 4.471 - 5.589: 24 Chirality restraints: 9656 Sorted by residual: chirality pdb=" C3D NAD G 501 " pdb=" C2D NAD G 501 " pdb=" C4D NAD G 501 " pdb=" O3D NAD G 501 " both_signs ideal model delta sigma weight residual False -2.73 2.86 -5.59 2.00e-01 2.50e+01 7.81e+02 chirality pdb=" C3D NAD F 501 " pdb=" C2D NAD F 501 " pdb=" C4D NAD F 501 " pdb=" O3D NAD F 501 " both_signs ideal model delta sigma weight residual False -2.73 2.86 -5.58 2.00e-01 2.50e+01 7.80e+02 chirality pdb=" C3D NAD B 501 " pdb=" C2D NAD B 501 " pdb=" C4D NAD B 501 " pdb=" O3D NAD B 501 " both_signs ideal model delta sigma weight residual False -2.73 2.86 -5.58 2.00e-01 2.50e+01 7.80e+02 ... (remaining 9653 not shown) Planarity restraints: 11363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR O 291 " 0.015 2.00e-02 2.50e+03 3.00e-02 8.99e+00 pdb=" C THR O 291 " -0.052 2.00e-02 2.50e+03 pdb=" O THR O 291 " 0.020 2.00e-02 2.50e+03 pdb=" N HIS O 292 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU N 309 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.77e+00 pdb=" C LEU N 309 " 0.042 2.00e-02 2.50e+03 pdb=" O LEU N 309 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU N 310 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 164 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C ILE A 164 " 0.040 2.00e-02 2.50e+03 pdb=" O ILE A 164 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE A 165 " -0.014 2.00e-02 2.50e+03 ... (remaining 11360 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 58 2.36 - 2.99: 30793 2.99 - 3.63: 85269 3.63 - 4.26: 124123 4.26 - 4.90: 214833 Nonbonded interactions: 455076 Sorted by model distance: nonbonded pdb=" OG SER P 184 " pdb="MG MG P 701 " model vdw 1.721 2.170 nonbonded pdb=" OG SER M 184 " pdb="MG MG M 702 " model vdw 1.816 2.170 nonbonded pdb="MG MG P 701 " pdb=" O1B ADP P 702 " model vdw 1.873 2.170 nonbonded pdb=" O ILE G 269 " pdb=" OH TYR G 284 " model vdw 2.177 3.040 nonbonded pdb=" OD1 ASN E 254 " pdb=" ND2 ASN E 258 " model vdw 2.204 3.120 ... (remaining 455071 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 83 or (resid 84 through 126 and (name N or name \ CA or name C or name O or name CB )) or resid 127 or (resid 128 through 135 and \ (name N or name CA or name C or name O or name CB )) or resid 136 or (resid 137 \ through 157 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 8 or (resid 159 through 180 and (name N or name CA or name C or name O or name C \ B )) or resid 181 or (resid 182 through 186 and (name N or name CA or name C or \ name O or name CB )) or resid 187 or (resid 188 through 189 and (name N or name \ CA or name C or name O or name CB )) or resid 190 or (resid 191 through 208 and \ (name N or name CA or name C or name O or name CB )) or (resid 218 through 227 a \ nd (name N or name CA or name C or name O or name CB )) or resid 228 or (resid 2 \ 29 through 264 and (name N or name CA or name C or name O or name CB )) or resid \ 265 or (resid 266 through 271 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 272 through 275 and (name N or name CA or name C or name O or \ name CB )) or resid 276 through 387)) selection = (chain 'B' and (resid 2 through 83 or (resid 84 through 126 and (name N or name \ CA or name C or name O or name CB )) or resid 127 or (resid 128 through 135 and \ (name N or name CA or name C or name O or name CB )) or resid 136 or (resid 137 \ through 157 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 8 or (resid 159 through 180 and (name N or name CA or name C or name O or name C \ B )) or resid 181 or (resid 182 through 186 and (name N or name CA or name C or \ name O or name CB )) or resid 187 or (resid 188 through 189 and (name N or name \ CA or name C or name O or name CB )) or resid 190 or (resid 191 through 227 and \ (name N or name CA or name C or name O or name CB )) or resid 228 or (resid 229 \ through 264 and (name N or name CA or name C or name O or name CB )) or resid 26 \ 5 or (resid 266 through 271 and (name N or name CA or name C or name O or name C \ B )) or (resid 272 through 275 and (name N or name CA or name C or name O or nam \ e CB )) or resid 276 through 387)) selection = (chain 'C' and (resid 2 through 83 or (resid 84 through 126 and (name N or name \ CA or name C or name O or name CB )) or resid 127 or (resid 128 through 135 and \ (name N or name CA or name C or name O or name CB )) or resid 136 or (resid 137 \ through 157 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 8 or (resid 159 through 180 and (name N or name CA or name C or name O or name C \ B )) or resid 181 or (resid 182 through 186 and (name N or name CA or name C or \ name O or name CB )) or resid 187 or (resid 188 through 189 and (name N or name \ CA or name C or name O or name CB )) or resid 190 or (resid 191 through 208 and \ (name N or name CA or name C or name O or name CB )) or (resid 218 through 227 a \ nd (name N or name CA or name C or name O or name CB )) or resid 228 or (resid 2 \ 29 through 264 and (name N or name CA or name C or name O or name CB )) or resid \ 265 or (resid 266 through 271 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 272 through 275 and (name N or name CA or name C or name O or \ name CB )) or resid 276 through 387)) selection = (chain 'D' and (resid 2 through 83 or (resid 84 through 126 and (name N or name \ CA or name C or name O or name CB )) or resid 127 or (resid 128 through 135 and \ (name N or name CA or name C or name O or name CB )) or resid 136 or (resid 137 \ through 157 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 8 or (resid 159 through 180 and (name N or name CA or name C or name O or name C \ B )) or resid 181 or (resid 182 through 186 and (name N or name CA or name C or \ name O or name CB )) or resid 187 or (resid 188 through 189 and (name N or name \ CA or name C or name O or name CB )) or resid 190 or (resid 191 through 208 and \ (name N or name CA or name C or name O or name CB )) or (resid 218 through 227 a \ nd (name N or name CA or name C or name O or name CB )) or resid 228 or (resid 2 \ 29 through 264 and (name N or name CA or name C or name O or name CB )) or resid \ 265 or (resid 266 through 271 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 272 through 275 and (name N or name CA or name C or name O or \ name CB )) or resid 276 through 387)) selection = (chain 'E' and (resid 2 through 83 or (resid 84 through 126 and (name N or name \ CA or name C or name O or name CB )) or resid 127 or (resid 128 through 135 and \ (name N or name CA or name C or name O or name CB )) or resid 136 or (resid 137 \ through 157 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 8 or (resid 159 through 180 and (name N or name CA or name C or name O or name C \ B )) or resid 181 or (resid 182 through 186 and (name N or name CA or name C or \ name O or name CB )) or resid 187 or (resid 188 through 189 and (name N or name \ CA or name C or name O or name CB )) or resid 190 or (resid 191 through 208 and \ (name N or name CA or name C or name O or name CB )) or (resid 218 through 227 a \ nd (name N or name CA or name C or name O or name CB )) or resid 228 or (resid 2 \ 29 through 264 and (name N or name CA or name C or name O or name CB )) or resid \ 265 or (resid 266 through 271 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 272 through 275 and (name N or name CA or name C or name O or \ name CB )) or resid 276 through 387)) selection = (chain 'F' and (resid 2 through 208 or resid 218 through 387)) selection = (chain 'G' and (resid 2 through 83 or (resid 84 through 126 and (name N or name \ CA or name C or name O or name CB )) or resid 127 or (resid 128 through 135 and \ (name N or name CA or name C or name O or name CB )) or resid 136 or (resid 137 \ through 157 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 8 or (resid 159 through 180 and (name N or name CA or name C or name O or name C \ B )) or resid 181 or (resid 182 through 186 and (name N or name CA or name C or \ name O or name CB )) or resid 187 or (resid 188 through 189 and (name N or name \ CA or name C or name O or name CB )) or resid 190 or (resid 191 through 208 and \ (name N or name CA or name C or name O or name CB )) or (resid 218 through 227 a \ nd (name N or name CA or name C or name O or name CB )) or resid 228 or (resid 2 \ 29 through 264 and (name N or name CA or name C or name O or name CB )) or resid \ 265 or (resid 266 through 271 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 272 through 275 and (name N or name CA or name C or name O or \ name CB )) or resid 276 through 387)) selection = (chain 'H' and (resid 2 through 83 or (resid 84 through 126 and (name N or name \ CA or name C or name O or name CB )) or resid 127 or (resid 128 through 135 and \ (name N or name CA or name C or name O or name CB )) or resid 136 or (resid 137 \ through 157 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 8 or (resid 159 through 180 and (name N or name CA or name C or name O or name C \ B )) or resid 181 or (resid 182 through 186 and (name N or name CA or name C or \ name O or name CB )) or resid 187 or (resid 188 through 189 and (name N or name \ CA or name C or name O or name CB )) or resid 190 or (resid 191 through 208 and \ (name N or name CA or name C or name O or name CB )) or (resid 218 through 227 a \ nd (name N or name CA or name C or name O or name CB )) or resid 228 or (resid 2 \ 29 through 264 and (name N or name CA or name C or name O or name CB )) or resid \ 265 or (resid 266 through 271 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 272 through 275 and (name N or name CA or name C or name O or \ name CB )) or resid 276 through 387)) selection = (chain 'I' and (resid 2 through 83 or (resid 84 through 126 and (name N or name \ CA or name C or name O or name CB )) or resid 127 or (resid 128 through 135 and \ (name N or name CA or name C or name O or name CB )) or resid 136 or (resid 137 \ through 157 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 8 or (resid 159 through 180 and (name N or name CA or name C or name O or name C \ B )) or resid 181 or (resid 182 through 186 and (name N or name CA or name C or \ name O or name CB )) or resid 187 or (resid 188 through 189 and (name N or name \ CA or name C or name O or name CB )) or resid 190 or (resid 191 through 208 and \ (name N or name CA or name C or name O or name CB )) or (resid 218 through 227 a \ nd (name N or name CA or name C or name O or name CB )) or resid 228 or (resid 2 \ 29 through 264 and (name N or name CA or name C or name O or name CB )) or resid \ 265 or (resid 266 through 271 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 272 through 275 and (name N or name CA or name C or name O or \ name CB )) or resid 276 through 387)) selection = (chain 'J' and (resid 2 through 83 or (resid 84 through 126 and (name N or name \ CA or name C or name O or name CB )) or resid 127 or (resid 128 through 135 and \ (name N or name CA or name C or name O or name CB )) or resid 136 or (resid 137 \ through 157 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 8 or (resid 159 through 180 and (name N or name CA or name C or name O or name C \ B )) or resid 181 or (resid 182 through 186 and (name N or name CA or name C or \ name O or name CB )) or resid 187 or (resid 188 through 189 and (name N or name \ CA or name C or name O or name CB )) or resid 190 or (resid 191 through 208 and \ (name N or name CA or name C or name O or name CB )) or (resid 218 through 227 a \ nd (name N or name CA or name C or name O or name CB )) or resid 228 or (resid 2 \ 29 through 264 and (name N or name CA or name C or name O or name CB )) or resid \ 265 or (resid 266 through 271 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 272 through 275 and (name N or name CA or name C or name O or \ name CB )) or resid 276 through 387)) selection = (chain 'K' and (resid 2 through 83 or (resid 84 through 126 and (name N or name \ CA or name C or name O or name CB )) or resid 127 or (resid 128 through 135 and \ (name N or name CA or name C or name O or name CB )) or resid 136 or (resid 137 \ through 157 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 8 or (resid 159 through 180 and (name N or name CA or name C or name O or name C \ B )) or resid 181 or (resid 182 through 186 and (name N or name CA or name C or \ name O or name CB )) or resid 187 or (resid 188 through 189 and (name N or name \ CA or name C or name O or name CB )) or resid 190 or (resid 191 through 208 and \ (name N or name CA or name C or name O or name CB )) or (resid 218 through 227 a \ nd (name N or name CA or name C or name O or name CB )) or resid 228 or (resid 2 \ 29 through 264 and (name N or name CA or name C or name O or name CB )) or resid \ 265 or (resid 266 through 271 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 272 through 275 and (name N or name CA or name C or name O or \ name CB )) or resid 276 through 387)) selection = (chain 'L' and (resid 2 through 83 or (resid 84 through 126 and (name N or name \ CA or name C or name O or name CB )) or resid 127 or (resid 128 through 135 and \ (name N or name CA or name C or name O or name CB )) or resid 136 or (resid 137 \ through 157 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 8 or (resid 159 through 180 and (name N or name CA or name C or name O or name C \ B )) or resid 181 or (resid 182 through 186 and (name N or name CA or name C or \ name O or name CB )) or resid 187 or (resid 188 through 189 and (name N or name \ CA or name C or name O or name CB )) or resid 190 or (resid 191 through 208 and \ (name N or name CA or name C or name O or name CB )) or (resid 218 through 227 a \ nd (name N or name CA or name C or name O or name CB )) or resid 228 or (resid 2 \ 29 through 264 and (name N or name CA or name C or name O or name CB )) or resid \ 265 or (resid 266 through 271 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 272 through 275 and (name N or name CA or name C or name O or \ name CB )) or resid 276 through 387)) } ncs_group { reference = (chain 'M' and (resid 10 through 28 or resid 46 through 67 or resid 93 through 2 \ 27 or resid 238 through 328 or resid 336 through 355 or resid 375 through 584)) selection = (chain 'N' and (resid 10 through 28 or resid 46 through 67 or resid 93 through 2 \ 27 or resid 238 through 328 or resid 336 through 355 or resid 375 through 484 or \ resid 498 through 584)) selection = (chain 'O' and (resid 10 through 28 or resid 46 through 67 or resid 93 through 2 \ 27 or resid 238 through 328 or resid 336 through 355 or resid 375 through 484 or \ resid 498 through 584)) selection = (chain 'P' and (resid 10 through 28 or resid 46 through 67 or resid 93 through 2 \ 27 or resid 238 through 355 or resid 375 through 484 or resid 498 through 584)) selection = (chain 'Q' and (resid 10 through 28 or resid 46 through 67 or resid 93 through 2 \ 27 or resid 238 through 328 or resid 336 through 355 or resid 375 through 484 or \ resid 498 through 584)) selection = (chain 'R' and (resid 10 through 227 or resid 238 through 328 or resid 336 throu \ gh 355 or resid 375 through 484 or resid 498 through 584)) } 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: 3.030 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: 0.050 Extract box with map and model: 1.910 Check model and map are aligned: 0.350 Set scattering table: 0.440 Process input model: 114.170 Find NCS groups from input model: 3.110 Set up NCS constraints: 0.220 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:2.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 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 : 0.005 0.246 65426 Z= 0.339 Angle : 0.643 18.142 88551 Z= 0.317 Chirality : 0.273 5.589 9656 Planarity : 0.003 0.089 11363 Dihedral : 18.112 178.605 24261 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -0.70 (0.09), residues: 7933 helix: 0.64 (0.10), residues: 2959 sheet: 0.29 (0.18), residues: 932 loop : -1.52 (0.09), residues: 4042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP P 532 HIS 0.006 0.001 HIS O 292 PHE 0.018 0.001 PHE L 288 TYR 0.017 0.001 TYR O 109 ARG 0.004 0.000 ARG Q 463 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1508 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1508 time to evaluate : 5.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 SER cc_start: 0.8288 (m) cc_final: 0.8071 (t) REVERT: A 293 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7192 (tm-30) REVERT: A 374 LYS cc_start: 0.7855 (mttt) cc_final: 0.7571 (mttt) REVERT: B 88 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6649 (mt-10) REVERT: B 97 LYS cc_start: 0.8212 (ttmm) cc_final: 0.8012 (ttmm) REVERT: B 132 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7732 (mm-30) REVERT: B 202 ASP cc_start: 0.7585 (m-30) cc_final: 0.7380 (m-30) REVERT: B 250 ASP cc_start: 0.7929 (m-30) cc_final: 0.7632 (m-30) REVERT: B 256 ILE cc_start: 0.8449 (tt) cc_final: 0.8238 (tt) REVERT: C 105 GLU cc_start: 0.7748 (tt0) cc_final: 0.7541 (mt-10) REVERT: C 106 GLU cc_start: 0.7187 (tp30) cc_final: 0.6931 (tp30) REVERT: C 142 LYS cc_start: 0.7910 (ttmt) cc_final: 0.7688 (ttmt) REVERT: C 352 GLU cc_start: 0.6586 (mp0) cc_final: 0.6077 (mp0) REVERT: D 50 LYS cc_start: 0.7891 (mmmt) cc_final: 0.7353 (mmmm) REVERT: D 66 LYS cc_start: 0.7217 (mtmm) cc_final: 0.6928 (mtmm) REVERT: D 74 ASP cc_start: 0.7422 (m-30) cc_final: 0.6996 (m-30) REVERT: D 97 LYS cc_start: 0.8516 (ttmm) cc_final: 0.8262 (ttmm) REVERT: D 107 GLU cc_start: 0.7461 (tm-30) cc_final: 0.6899 (tm-30) REVERT: D 197 TYR cc_start: 0.8181 (m-10) cc_final: 0.7641 (m-80) REVERT: D 335 GLU cc_start: 0.7434 (pm20) cc_final: 0.7230 (pm20) REVERT: D 363 PHE cc_start: 0.7756 (m-80) cc_final: 0.7432 (m-80) REVERT: E 49 TRP cc_start: 0.7331 (t-100) cc_final: 0.7127 (t-100) REVERT: E 54 GLN cc_start: 0.8410 (tm-30) cc_final: 0.7989 (tm-30) REVERT: E 250 ASP cc_start: 0.7761 (m-30) cc_final: 0.7349 (m-30) REVERT: E 342 LYS cc_start: 0.7688 (tttm) cc_final: 0.7469 (tttm) REVERT: F 4 TYR cc_start: 0.7984 (m-80) cc_final: 0.7637 (m-80) REVERT: F 21 SER cc_start: 0.8373 (t) cc_final: 0.8074 (t) REVERT: F 296 SER cc_start: 0.8976 (m) cc_final: 0.8721 (m) REVERT: F 312 TYR cc_start: 0.6276 (t80) cc_final: 0.5798 (t80) REVERT: F 315 ASN cc_start: 0.7811 (p0) cc_final: 0.7589 (p0) REVERT: G 58 GLU cc_start: 0.7365 (tm-30) cc_final: 0.6804 (tm-30) REVERT: G 110 LYS cc_start: 0.7592 (mppt) cc_final: 0.7315 (tppt) REVERT: G 142 LYS cc_start: 0.7872 (ttpp) cc_final: 0.7447 (ttpp) REVERT: G 178 GLU cc_start: 0.7049 (tt0) cc_final: 0.6716 (tt0) REVERT: G 249 TYR cc_start: 0.7873 (t80) cc_final: 0.7661 (t80) REVERT: G 250 ASP cc_start: 0.8098 (t0) cc_final: 0.7842 (t0) REVERT: G 259 LYS cc_start: 0.8031 (tptp) cc_final: 0.7181 (tptp) REVERT: G 280 ILE cc_start: 0.7595 (mt) cc_final: 0.7323 (mm) REVERT: H 110 LYS cc_start: 0.8242 (ttmm) cc_final: 0.7957 (mtpp) REVERT: H 129 GLN cc_start: 0.7593 (mt0) cc_final: 0.7378 (mt0) REVERT: H 174 GLU cc_start: 0.6238 (mp0) cc_final: 0.6011 (mp0) REVERT: H 382 GLU cc_start: 0.7652 (tp30) cc_final: 0.7287 (tp30) REVERT: I 182 ILE cc_start: 0.8051 (pt) cc_final: 0.7805 (mt) REVERT: I 323 LEU cc_start: 0.8897 (mt) cc_final: 0.8664 (mp) REVERT: I 345 LYS cc_start: 0.8436 (tttm) cc_final: 0.8205 (ttmm) REVERT: J 100 ARG cc_start: 0.6648 (mtp85) cc_final: 0.6385 (mtp85) REVERT: J 376 TYR cc_start: 0.8277 (m-10) cc_final: 0.8057 (m-80) REVERT: J 377 PHE cc_start: 0.7776 (t80) cc_final: 0.7570 (t80) REVERT: K 30 VAL cc_start: 0.8098 (m) cc_final: 0.7760 (t) REVERT: K 76 ASP cc_start: 0.7072 (m-30) cc_final: 0.6825 (m-30) REVERT: K 106 GLU cc_start: 0.7421 (pm20) cc_final: 0.7153 (pm20) REVERT: K 128 GLU cc_start: 0.7109 (tm-30) cc_final: 0.6811 (tm-30) REVERT: K 286 GLU cc_start: 0.5970 (mm-30) cc_final: 0.5414 (mm-30) REVERT: K 296 SER cc_start: 0.8833 (t) cc_final: 0.8626 (t) REVERT: L 51 SER cc_start: 0.8440 (m) cc_final: 0.8180 (m) REVERT: L 104 GLU cc_start: 0.6975 (tt0) cc_final: 0.6658 (tt0) REVERT: L 118 GLU cc_start: 0.7672 (tp30) cc_final: 0.7397 (tp30) REVERT: L 202 ASP cc_start: 0.6887 (m-30) cc_final: 0.6645 (m-30) REVERT: L 222 TYR cc_start: 0.8341 (m-10) cc_final: 0.8066 (m-80) REVERT: M 97 TYR cc_start: 0.5386 (m-80) cc_final: 0.4985 (m-80) REVERT: M 251 TYR cc_start: 0.7911 (p90) cc_final: 0.7444 (p90) REVERT: M 254 LYS cc_start: 0.7922 (tppp) cc_final: 0.7635 (tppp) REVERT: M 292 HIS cc_start: 0.7129 (m90) cc_final: 0.6687 (m90) REVERT: M 299 TYR cc_start: 0.8364 (p90) cc_final: 0.8102 (p90) REVERT: M 308 PHE cc_start: 0.7907 (t80) cc_final: 0.7535 (t80) REVERT: M 352 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7140 (mm-30) REVERT: M 390 PHE cc_start: 0.8353 (t80) cc_final: 0.8108 (t80) REVERT: M 395 ASN cc_start: 0.7138 (t0) cc_final: 0.6898 (t0) REVERT: M 456 MET cc_start: 0.7098 (ptt) cc_final: 0.6868 (ptt) REVERT: M 476 LEU cc_start: 0.6964 (mp) cc_final: 0.6612 (mp) REVERT: M 516 GLN cc_start: 0.7501 (pt0) cc_final: 0.7178 (pt0) REVERT: M 595 ASP cc_start: 0.6914 (m-30) cc_final: 0.6616 (m-30) REVERT: N 114 GLU cc_start: 0.7109 (tt0) cc_final: 0.6870 (tt0) REVERT: N 193 LYS cc_start: 0.8132 (ttmm) cc_final: 0.7828 (ttmm) REVERT: N 266 LEU cc_start: 0.8396 (mt) cc_final: 0.7994 (mt) REVERT: N 268 LYS cc_start: 0.8171 (mtpt) cc_final: 0.7915 (mtpt) REVERT: N 271 ARG cc_start: 0.7598 (mtp85) cc_final: 0.7366 (mtp85) REVERT: N 277 GLN cc_start: 0.7677 (mt0) cc_final: 0.7381 (mt0) REVERT: N 353 PHE cc_start: 0.7140 (m-80) cc_final: 0.6860 (m-80) REVERT: N 379 LYS cc_start: 0.8187 (pttp) cc_final: 0.7937 (pttm) REVERT: N 425 LYS cc_start: 0.8153 (ttpt) cc_final: 0.7907 (ttmt) REVERT: N 467 GLU cc_start: 0.8061 (tp30) cc_final: 0.7659 (tp30) REVERT: O 186 PHE cc_start: 0.8281 (t80) cc_final: 0.8008 (t80) REVERT: O 268 LYS cc_start: 0.7901 (mtmt) cc_final: 0.7597 (mtpp) REVERT: O 327 ASP cc_start: 0.7176 (t0) cc_final: 0.6730 (t0) REVERT: O 380 ILE cc_start: 0.8167 (tp) cc_final: 0.7948 (tp) REVERT: O 448 MET cc_start: 0.6551 (tpt) cc_final: 0.6266 (tpt) REVERT: O 540 GLU cc_start: 0.7235 (tp30) cc_final: 0.6764 (tp30) REVERT: P 153 ASP cc_start: 0.7245 (p0) cc_final: 0.6812 (p0) REVERT: P 183 LYS cc_start: 0.7677 (mmmm) cc_final: 0.6971 (mtpp) REVERT: P 186 PHE cc_start: 0.6355 (t80) cc_final: 0.6092 (t80) REVERT: P 246 TYR cc_start: 0.7555 (t80) cc_final: 0.7213 (t80) REVERT: P 277 GLN cc_start: 0.7561 (mt0) cc_final: 0.7260 (mp-120) REVERT: P 379 LYS cc_start: 0.7695 (ptpt) cc_final: 0.6931 (ptpt) REVERT: P 438 MET cc_start: 0.7201 (mtp) cc_final: 0.6956 (mtt) REVERT: P 459 GLU cc_start: 0.7650 (tp30) cc_final: 0.7083 (tp30) REVERT: P 508 LYS cc_start: 0.7812 (mttp) cc_final: 0.7454 (mtpp) REVERT: Q 146 LYS cc_start: 0.7836 (mppt) cc_final: 0.7477 (mppt) REVERT: Q 424 GLU cc_start: 0.6826 (tm-30) cc_final: 0.6199 (tm-30) REVERT: Q 444 ASP cc_start: 0.7665 (m-30) cc_final: 0.7299 (m-30) REVERT: Q 448 MET cc_start: 0.6418 (mmp) cc_final: 0.6216 (mmp) REVERT: Q 455 GLU cc_start: 0.7699 (pt0) cc_final: 0.6840 (pt0) REVERT: Q 459 GLU cc_start: 0.7303 (mt-10) cc_final: 0.7019 (mt-10) REVERT: Q 520 GLU cc_start: 0.6632 (mp0) cc_final: 0.5995 (mp0) REVERT: R 171 ARG cc_start: 0.6570 (tpt-90) cc_final: 0.5908 (tpt-90) REVERT: R 221 ASN cc_start: 0.7455 (t0) cc_final: 0.7130 (t0) REVERT: R 540 GLU cc_start: 0.6882 (tp30) cc_final: 0.6115 (tp30) outliers start: 0 outliers final: 0 residues processed: 1508 average time/residue: 0.6350 time to fit residues: 1574.4545 Evaluate side-chains 1342 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1342 time to evaluate : 5.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 672 optimal weight: 0.0980 chunk 603 optimal weight: 3.9990 chunk 334 optimal weight: 8.9990 chunk 206 optimal weight: 0.1980 chunk 406 optimal weight: 4.9990 chunk 322 optimal weight: 0.9990 chunk 623 optimal weight: 0.8980 chunk 241 optimal weight: 0.9990 chunk 379 optimal weight: 0.6980 chunk 464 optimal weight: 8.9990 chunk 722 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN B 72 GLN B 77 ASN C 135 GLN C 159 GLN C 227 HIS D 24 GLN D 227 HIS D 299 GLN D 360 ASN G 135 GLN G 199 GLN H 247 GLN I 227 HIS I 299 GLN I 315 ASN I 365 GLN J 24 GLN ** K 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 234 GLN K 266 GLN M 26 ASN M 214 GLN M 539 ASN N 47 GLN N 200 ASN N 585 ASN O 481 HIS ** O 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 HIS P 586 GLN Q 187 ASN Q 214 GLN Q 221 ASN R 373 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 65426 Z= 0.146 Angle : 0.558 12.498 88551 Z= 0.275 Chirality : 0.042 0.388 9656 Planarity : 0.003 0.054 11363 Dihedral : 11.612 146.084 9413 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.85 % Allowed : 7.80 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -0.57 (0.09), residues: 7933 helix: 0.73 (0.10), residues: 3073 sheet: 0.45 (0.18), residues: 914 loop : -1.52 (0.09), residues: 3946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 409 HIS 0.005 0.001 HIS Q 481 PHE 0.015 0.001 PHE N 308 TYR 0.027 0.001 TYR R 497 ARG 0.009 0.000 ARG O 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1434 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 1377 time to evaluate : 5.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 SER cc_start: 0.8398 (m) cc_final: 0.8116 (t) REVERT: A 293 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7153 (tm-30) REVERT: A 374 LYS cc_start: 0.7857 (mttt) cc_final: 0.7583 (mttt) REVERT: A 380 PHE cc_start: 0.8420 (t80) cc_final: 0.8210 (t80) REVERT: B 202 ASP cc_start: 0.7615 (m-30) cc_final: 0.7414 (m-30) REVERT: B 250 ASP cc_start: 0.7886 (m-30) cc_final: 0.7633 (m-30) REVERT: B 258 ASN cc_start: 0.7838 (m-40) cc_final: 0.7623 (m-40) REVERT: C 20 TYR cc_start: 0.7869 (t80) cc_final: 0.7654 (t80) REVERT: C 56 TYR cc_start: 0.7727 (m-80) cc_final: 0.7515 (m-80) REVERT: C 95 VAL cc_start: 0.6633 (t) cc_final: 0.6237 (t) REVERT: C 105 GLU cc_start: 0.7726 (tt0) cc_final: 0.7388 (tt0) REVERT: C 106 GLU cc_start: 0.7165 (tp30) cc_final: 0.6934 (tp30) REVERT: C 142 LYS cc_start: 0.7909 (ttmt) cc_final: 0.7697 (ttmt) REVERT: C 352 GLU cc_start: 0.6773 (mp0) cc_final: 0.6216 (mp0) REVERT: C 353 LYS cc_start: 0.7362 (mtmm) cc_final: 0.6949 (mtmm) REVERT: D 50 LYS cc_start: 0.7897 (mmmt) cc_final: 0.7593 (ttmm) REVERT: D 74 ASP cc_start: 0.7496 (m-30) cc_final: 0.7121 (m-30) REVERT: D 97 LYS cc_start: 0.8518 (ttmm) cc_final: 0.8293 (ttmm) REVERT: D 106 GLU cc_start: 0.7572 (pp20) cc_final: 0.7084 (pp20) REVERT: D 107 GLU cc_start: 0.7505 (tm-30) cc_final: 0.6810 (tm-30) REVERT: D 110 LYS cc_start: 0.8202 (mttp) cc_final: 0.7852 (mttp) REVERT: D 112 LEU cc_start: 0.7448 (mt) cc_final: 0.7211 (mt) REVERT: D 197 TYR cc_start: 0.8234 (m-10) cc_final: 0.7665 (m-80) REVERT: D 227 HIS cc_start: 0.7243 (m90) cc_final: 0.6872 (m90) REVERT: D 335 GLU cc_start: 0.7302 (pm20) cc_final: 0.6770 (pm20) REVERT: E 49 TRP cc_start: 0.7583 (t-100) cc_final: 0.7191 (t-100) REVERT: E 54 GLN cc_start: 0.8403 (tm-30) cc_final: 0.7895 (tm-30) REVERT: E 128 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7458 (tt0) REVERT: E 250 ASP cc_start: 0.7619 (m-30) cc_final: 0.7200 (m-30) REVERT: E 316 ARG cc_start: 0.7728 (tpt-90) cc_final: 0.7082 (tmm-80) REVERT: E 342 LYS cc_start: 0.7404 (tttm) cc_final: 0.7162 (tttm) REVERT: E 401 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7525 (mm-30) REVERT: F 21 SER cc_start: 0.8490 (t) cc_final: 0.8193 (t) REVERT: F 55 ASN cc_start: 0.8044 (m-40) cc_final: 0.7459 (m110) REVERT: F 296 SER cc_start: 0.8947 (m) cc_final: 0.8665 (m) REVERT: G 58 GLU cc_start: 0.7363 (tm-30) cc_final: 0.6807 (tm-30) REVERT: G 110 LYS cc_start: 0.7665 (mppt) cc_final: 0.7345 (tppt) REVERT: G 142 LYS cc_start: 0.7855 (ttpp) cc_final: 0.7406 (ttpp) REVERT: G 250 ASP cc_start: 0.8052 (t0) cc_final: 0.7803 (t0) REVERT: G 259 LYS cc_start: 0.7941 (tptp) cc_final: 0.6814 (tptp) REVERT: G 262 PHE cc_start: 0.7026 (p90) cc_final: 0.6408 (p90) REVERT: G 303 PHE cc_start: 0.6713 (m-10) cc_final: 0.6508 (m-10) REVERT: H 43 LYS cc_start: 0.6680 (OUTLIER) cc_final: 0.6438 (ptmt) REVERT: H 110 LYS cc_start: 0.8271 (ttmm) cc_final: 0.7974 (mtpp) REVERT: H 364 ASN cc_start: 0.7688 (t0) cc_final: 0.7364 (t0) REVERT: J 46 LYS cc_start: 0.8481 (mtpp) cc_final: 0.8181 (mtpp) REVERT: J 100 ARG cc_start: 0.6626 (mtp85) cc_final: 0.6386 (mtp85) REVERT: J 108 PHE cc_start: 0.8574 (m-80) cc_final: 0.8214 (m-80) REVERT: J 126 THR cc_start: 0.8840 (m) cc_final: 0.8580 (p) REVERT: J 154 ASN cc_start: 0.8349 (m-40) cc_final: 0.8133 (m110) REVERT: K 76 ASP cc_start: 0.7050 (m-30) cc_final: 0.6607 (m-30) REVERT: K 106 GLU cc_start: 0.7456 (pm20) cc_final: 0.7030 (pm20) REVERT: K 128 GLU cc_start: 0.7013 (tm-30) cc_final: 0.6750 (tm-30) REVERT: K 361 MET cc_start: 0.7555 (ptp) cc_final: 0.7336 (mtm) REVERT: L 50 LYS cc_start: 0.8206 (mttm) cc_final: 0.7981 (mttm) REVERT: L 51 SER cc_start: 0.8367 (m) cc_final: 0.8078 (m) REVERT: L 88 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6699 (mp0) REVERT: L 104 GLU cc_start: 0.6901 (tt0) cc_final: 0.6594 (tt0) REVERT: L 118 GLU cc_start: 0.7687 (tp30) cc_final: 0.7410 (tp30) REVERT: L 251 GLU cc_start: 0.7124 (tt0) cc_final: 0.6922 (tt0) REVERT: L 323 LEU cc_start: 0.7858 (mt) cc_final: 0.7475 (mt) REVERT: L 344 SER cc_start: 0.7970 (t) cc_final: 0.7527 (m) REVERT: M 97 TYR cc_start: 0.5389 (m-80) cc_final: 0.5013 (m-80) REVERT: M 183 LYS cc_start: 0.7101 (pttt) cc_final: 0.6360 (ptmt) REVERT: M 254 LYS cc_start: 0.7921 (tppp) cc_final: 0.7632 (tppp) REVERT: M 319 GLN cc_start: 0.8094 (pm20) cc_final: 0.7311 (mt0) REVERT: M 352 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7222 (mm-30) REVERT: M 390 PHE cc_start: 0.8324 (t80) cc_final: 0.8110 (t80) REVERT: M 391 LYS cc_start: 0.7696 (ptpt) cc_final: 0.7457 (ptpt) REVERT: N 114 GLU cc_start: 0.7072 (tt0) cc_final: 0.6820 (tt0) REVERT: N 193 LYS cc_start: 0.8199 (ttmm) cc_final: 0.7899 (ttmm) REVERT: N 268 LYS cc_start: 0.8142 (mtpt) cc_final: 0.7834 (mtpp) REVERT: N 277 GLN cc_start: 0.7064 (mt0) cc_final: 0.6825 (mt0) REVERT: N 340 TRP cc_start: 0.8070 (m100) cc_final: 0.7708 (m100) REVERT: N 353 PHE cc_start: 0.7019 (m-80) cc_final: 0.6779 (m-80) REVERT: N 467 GLU cc_start: 0.8114 (tp30) cc_final: 0.7805 (tp30) REVERT: O 21 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6975 (mt-10) REVERT: O 64 ARG cc_start: 0.6772 (ptp-110) cc_final: 0.5977 (ptt180) REVERT: O 186 PHE cc_start: 0.8329 (t80) cc_final: 0.8106 (t80) REVERT: O 268 LYS cc_start: 0.7904 (mtmt) cc_final: 0.7604 (mtpp) REVERT: O 327 ASP cc_start: 0.7229 (t0) cc_final: 0.6770 (t0) REVERT: O 380 ILE cc_start: 0.8092 (tp) cc_final: 0.7848 (tp) REVERT: O 416 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6769 (tm-30) REVERT: O 448 MET cc_start: 0.6810 (tpt) cc_final: 0.6514 (tpt) REVERT: P 25 ILE cc_start: 0.8065 (mt) cc_final: 0.7861 (mt) REVERT: P 183 LYS cc_start: 0.7790 (mmmm) cc_final: 0.6946 (mtpp) REVERT: P 192 ARG cc_start: 0.7655 (mtp180) cc_final: 0.7419 (mtp85) REVERT: P 246 TYR cc_start: 0.7527 (t80) cc_final: 0.7181 (t80) REVERT: P 277 GLN cc_start: 0.7417 (mt0) cc_final: 0.7159 (mp10) REVERT: P 281 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8403 (mt) REVERT: P 379 LYS cc_start: 0.7536 (ptpt) cc_final: 0.7281 (ptpp) REVERT: P 401 GLU cc_start: 0.7464 (tm-30) cc_final: 0.7146 (tm-30) REVERT: P 459 GLU cc_start: 0.7662 (tp30) cc_final: 0.7087 (tp30) REVERT: P 495 LYS cc_start: 0.7164 (OUTLIER) cc_final: 0.6827 (mtpt) REVERT: P 508 LYS cc_start: 0.7768 (mttp) cc_final: 0.7365 (mmtp) REVERT: Q 137 TYR cc_start: 0.8297 (m-80) cc_final: 0.7983 (m-80) REVERT: Q 146 LYS cc_start: 0.7810 (mppt) cc_final: 0.7509 (mppt) REVERT: Q 192 ARG cc_start: 0.6630 (ttt180) cc_final: 0.6200 (ttt90) REVERT: Q 418 ASP cc_start: 0.7766 (m-30) cc_final: 0.7524 (m-30) REVERT: Q 444 ASP cc_start: 0.7789 (m-30) cc_final: 0.7475 (m-30) REVERT: Q 448 MET cc_start: 0.6674 (mmp) cc_final: 0.6232 (mmp) REVERT: Q 451 SER cc_start: 0.7741 (m) cc_final: 0.6677 (p) REVERT: Q 455 GLU cc_start: 0.7700 (pt0) cc_final: 0.6934 (pt0) REVERT: Q 459 GLU cc_start: 0.7363 (mt-10) cc_final: 0.7089 (mt-10) REVERT: Q 516 GLN cc_start: 0.7082 (pp30) cc_final: 0.6830 (pp30) REVERT: Q 520 GLU cc_start: 0.6518 (mp0) cc_final: 0.5826 (mp0) REVERT: Q 536 ARG cc_start: 0.6294 (tpt-90) cc_final: 0.5556 (tpt-90) REVERT: Q 592 LYS cc_start: 0.7798 (mmmt) cc_final: 0.7297 (mmmt) REVERT: R 22 ARG cc_start: 0.6451 (mtt90) cc_final: 0.6010 (mtt90) REVERT: R 221 ASN cc_start: 0.7682 (t0) cc_final: 0.7457 (t0) REVERT: R 259 GLN cc_start: 0.6841 (pp30) cc_final: 0.6568 (pm20) REVERT: R 382 GLN cc_start: 0.7425 (pp30) cc_final: 0.6886 (pp30) REVERT: R 473 VAL cc_start: 0.7196 (t) cc_final: 0.6818 (p) REVERT: R 540 GLU cc_start: 0.6873 (tp30) cc_final: 0.6081 (tp30) outliers start: 57 outliers final: 33 residues processed: 1398 average time/residue: 0.6312 time to fit residues: 1446.3806 Evaluate side-chains 1372 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 1335 time to evaluate : 5.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain I residue 65 ASP Chi-restraints excluded: chain I residue 266 GLN Chi-restraints excluded: chain J residue 389 LEU Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain L residue 9 LYS Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 559 LYS Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 124 SER Chi-restraints excluded: chain N residue 203 ILE Chi-restraints excluded: chain N residue 515 THR Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 124 SER Chi-restraints excluded: chain O residue 473 VAL Chi-restraints excluded: chain P residue 281 LEU Chi-restraints excluded: chain P residue 495 LYS Chi-restraints excluded: chain P residue 574 SER Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 170 SER Chi-restraints excluded: chain Q residue 193 LYS Chi-restraints excluded: chain Q residue 425 LYS Chi-restraints excluded: chain Q residue 449 LEU Chi-restraints excluded: chain R residue 14 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 401 optimal weight: 0.3980 chunk 224 optimal weight: 5.9990 chunk 601 optimal weight: 5.9990 chunk 492 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 chunk 724 optimal weight: 0.8980 chunk 782 optimal weight: 4.9990 chunk 644 optimal weight: 2.9990 chunk 718 optimal weight: 0.4980 chunk 246 optimal weight: 2.9990 chunk 580 optimal weight: 9.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN C 24 GLN C 258 ASN D 24 GLN ** H 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 247 GLN I 365 GLN J 254 ASN K 77 ASN K 360 ASN M 214 GLN ** O 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 383 GLN ** O 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 214 GLN Q 395 ASN Q 397 ASN ** R 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 65426 Z= 0.244 Angle : 0.568 12.863 88551 Z= 0.287 Chirality : 0.043 0.170 9656 Planarity : 0.004 0.063 11363 Dihedral : 10.227 144.704 9413 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.65 % Allowed : 11.16 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -0.66 (0.09), residues: 7933 helix: 0.72 (0.10), residues: 3045 sheet: 0.34 (0.17), residues: 972 loop : -1.62 (0.09), residues: 3916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 532 HIS 0.007 0.001 HIS J 313 PHE 0.019 0.002 PHE P 101 TYR 0.029 0.002 TYR O 246 ARG 0.010 0.000 ARG N 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1478 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 1368 time to evaluate : 5.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 SER cc_start: 0.8410 (m) cc_final: 0.8133 (t) REVERT: A 293 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7234 (tm-30) REVERT: A 374 LYS cc_start: 0.7712 (mttt) cc_final: 0.7493 (mttt) REVERT: B 88 GLU cc_start: 0.6995 (mt-10) cc_final: 0.6731 (mt-10) REVERT: B 97 LYS cc_start: 0.8243 (ttmm) cc_final: 0.8029 (ttmm) REVERT: B 128 GLU cc_start: 0.7061 (tm-30) cc_final: 0.6834 (tm-30) REVERT: B 132 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8054 (mm-30) REVERT: B 179 ASP cc_start: 0.8091 (t0) cc_final: 0.7855 (t0) REVERT: B 202 ASP cc_start: 0.7639 (m-30) cc_final: 0.7431 (m-30) REVERT: B 242 GLU cc_start: 0.7907 (tt0) cc_final: 0.7368 (tt0) REVERT: B 258 ASN cc_start: 0.7907 (m-40) cc_final: 0.7674 (m-40) REVERT: C 102 GLU cc_start: 0.7301 (mp0) cc_final: 0.7039 (mp0) REVERT: C 105 GLU cc_start: 0.7779 (tt0) cc_final: 0.7567 (tt0) REVERT: C 106 GLU cc_start: 0.7372 (tp30) cc_final: 0.7128 (tp30) REVERT: C 352 GLU cc_start: 0.6800 (mp0) cc_final: 0.6209 (mp0) REVERT: D 50 LYS cc_start: 0.7954 (mmmt) cc_final: 0.7295 (mmmm) REVERT: D 74 ASP cc_start: 0.7526 (m-30) cc_final: 0.7154 (m-30) REVERT: D 97 LYS cc_start: 0.8490 (ttmm) cc_final: 0.8254 (ttmm) REVERT: D 110 LYS cc_start: 0.8252 (mttp) cc_final: 0.7932 (mttp) REVERT: D 118 GLU cc_start: 0.7851 (tp30) cc_final: 0.7455 (tp30) REVERT: D 197 TYR cc_start: 0.8248 (m-10) cc_final: 0.7705 (m-80) REVERT: E 54 GLN cc_start: 0.8434 (tm-30) cc_final: 0.7898 (tm-30) REVERT: E 66 LYS cc_start: 0.7914 (tptm) cc_final: 0.7351 (tptt) REVERT: E 128 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7499 (tt0) REVERT: E 340 ILE cc_start: 0.7767 (mt) cc_final: 0.7560 (mt) REVERT: E 342 LYS cc_start: 0.7495 (tttm) cc_final: 0.7236 (tttm) REVERT: E 401 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7536 (mm-30) REVERT: F 21 SER cc_start: 0.8481 (t) cc_final: 0.8196 (t) REVERT: F 296 SER cc_start: 0.8910 (m) cc_final: 0.8674 (m) REVERT: F 361 MET cc_start: 0.6802 (mtt) cc_final: 0.6394 (mtt) REVERT: F 389 LEU cc_start: 0.8124 (mt) cc_final: 0.7855 (mt) REVERT: G 43 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7980 (ptmt) REVERT: G 58 GLU cc_start: 0.7394 (tm-30) cc_final: 0.6863 (tm-30) REVERT: G 110 LYS cc_start: 0.7807 (mppt) cc_final: 0.7479 (tppt) REVERT: G 142 LYS cc_start: 0.7930 (ttpp) cc_final: 0.7479 (ttpp) REVERT: G 250 ASP cc_start: 0.8096 (t0) cc_final: 0.7817 (t0) REVERT: G 259 LYS cc_start: 0.7981 (tptp) cc_final: 0.6850 (tptp) REVERT: G 262 PHE cc_start: 0.6956 (p90) cc_final: 0.6541 (p90) REVERT: H 43 LYS cc_start: 0.6702 (ptmt) cc_final: 0.6475 (ptmt) REVERT: H 60 LEU cc_start: 0.8259 (tp) cc_final: 0.7939 (tp) REVERT: H 110 LYS cc_start: 0.8316 (ttmm) cc_final: 0.8010 (mtpp) REVERT: H 364 ASN cc_start: 0.7619 (t0) cc_final: 0.7200 (t0) REVERT: I 74 ASP cc_start: 0.7722 (m-30) cc_final: 0.7457 (t0) REVERT: I 288 PHE cc_start: 0.7907 (t80) cc_final: 0.7681 (t80) REVERT: I 300 THR cc_start: 0.8511 (m) cc_final: 0.8166 (p) REVERT: J 46 LYS cc_start: 0.8474 (mtpp) cc_final: 0.8238 (mtpp) REVERT: J 108 PHE cc_start: 0.8485 (m-80) cc_final: 0.8181 (m-80) REVERT: J 142 LYS cc_start: 0.7787 (tppt) cc_final: 0.7378 (ttpp) REVERT: J 189 SER cc_start: 0.8352 (p) cc_final: 0.8111 (m) REVERT: K 76 ASP cc_start: 0.7024 (m-30) cc_final: 0.6572 (m-30) REVERT: K 106 GLU cc_start: 0.7563 (pm20) cc_final: 0.7165 (pm20) REVERT: K 128 GLU cc_start: 0.7079 (tm-30) cc_final: 0.6830 (tm-30) REVERT: K 353 LYS cc_start: 0.7686 (mptt) cc_final: 0.7043 (mptt) REVERT: K 357 THR cc_start: 0.8188 (p) cc_final: 0.7764 (p) REVERT: L 51 SER cc_start: 0.8356 (m) cc_final: 0.8066 (m) REVERT: L 88 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: L 99 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.5715 (ttp-170) REVERT: L 104 GLU cc_start: 0.6892 (tt0) cc_final: 0.6559 (tt0) REVERT: L 118 GLU cc_start: 0.7715 (tp30) cc_final: 0.7407 (tp30) REVERT: L 227 HIS cc_start: 0.7106 (m90) cc_final: 0.6827 (m90) REVERT: L 323 LEU cc_start: 0.7970 (mt) cc_final: 0.7599 (mt) REVERT: M 97 TYR cc_start: 0.5520 (m-80) cc_final: 0.5037 (m-80) REVERT: M 157 LYS cc_start: 0.7664 (mttm) cc_final: 0.7377 (mmtt) REVERT: M 254 LYS cc_start: 0.8033 (tppp) cc_final: 0.7683 (tppp) REVERT: M 318 ASN cc_start: 0.8765 (t0) cc_final: 0.8520 (t0) REVERT: M 319 GLN cc_start: 0.7991 (pm20) cc_final: 0.7466 (mt0) REVERT: M 352 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7209 (mm-30) REVERT: M 413 MET cc_start: 0.4015 (ppp) cc_final: 0.3763 (ppp) REVERT: M 468 ARG cc_start: 0.7035 (ttm110) cc_final: 0.6683 (ttm110) REVERT: N 114 GLU cc_start: 0.7104 (tt0) cc_final: 0.6845 (tt0) REVERT: N 193 LYS cc_start: 0.8269 (ttmm) cc_final: 0.7931 (ttmm) REVERT: N 251 TYR cc_start: 0.8108 (p90) cc_final: 0.7830 (p90) REVERT: N 277 GLN cc_start: 0.7162 (mt0) cc_final: 0.6760 (mt0) REVERT: N 352 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7523 (mm-30) REVERT: N 353 PHE cc_start: 0.7073 (m-80) cc_final: 0.6816 (m-80) REVERT: O 268 LYS cc_start: 0.7947 (mtmt) cc_final: 0.7612 (mtpp) REVERT: O 276 THR cc_start: 0.7903 (OUTLIER) cc_final: 0.7435 (t) REVERT: O 327 ASP cc_start: 0.7169 (t0) cc_final: 0.6745 (t0) REVERT: O 416 GLU cc_start: 0.7263 (tm-30) cc_final: 0.6788 (tm-30) REVERT: O 424 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7642 (mm-30) REVERT: O 448 MET cc_start: 0.7007 (tpt) cc_final: 0.6685 (tpt) REVERT: P 19 GLU cc_start: 0.6581 (mp0) cc_final: 0.6258 (mp0) REVERT: P 47 GLN cc_start: 0.7469 (pt0) cc_final: 0.7017 (pt0) REVERT: P 50 ASP cc_start: 0.6019 (m-30) cc_final: 0.5769 (m-30) REVERT: P 183 LYS cc_start: 0.7910 (mmmm) cc_final: 0.6990 (mtpp) REVERT: P 192 ARG cc_start: 0.7666 (mtp180) cc_final: 0.7437 (mtp85) REVERT: P 246 TYR cc_start: 0.7653 (t80) cc_final: 0.7399 (t80) REVERT: P 255 LYS cc_start: 0.6132 (tptt) cc_final: 0.5921 (tptt) REVERT: P 277 GLN cc_start: 0.7454 (mt0) cc_final: 0.7119 (mp-120) REVERT: P 379 LYS cc_start: 0.7634 (ptpt) cc_final: 0.7358 (ptpp) REVERT: P 459 GLU cc_start: 0.7717 (tp30) cc_final: 0.7152 (tp30) REVERT: P 467 GLU cc_start: 0.7309 (tp30) cc_final: 0.6501 (tp30) REVERT: P 502 LYS cc_start: 0.7286 (mmtt) cc_final: 0.6751 (mmtt) REVERT: P 508 LYS cc_start: 0.7803 (mttp) cc_final: 0.7302 (mmtp) REVERT: P 524 THR cc_start: 0.7288 (t) cc_final: 0.5424 (p) REVERT: Q 68 MET cc_start: 0.7979 (tpp) cc_final: 0.7746 (tpp) REVERT: Q 137 TYR cc_start: 0.8468 (m-80) cc_final: 0.8019 (m-80) REVERT: Q 146 LYS cc_start: 0.7916 (mppt) cc_final: 0.7641 (mppt) REVERT: Q 192 ARG cc_start: 0.6653 (ttt180) cc_final: 0.6221 (ttt90) REVERT: Q 444 ASP cc_start: 0.7877 (m-30) cc_final: 0.7422 (m-30) REVERT: Q 448 MET cc_start: 0.6803 (mmp) cc_final: 0.6495 (mmp) REVERT: Q 455 GLU cc_start: 0.7708 (pt0) cc_final: 0.6913 (pt0) REVERT: Q 459 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7135 (mt-10) REVERT: Q 468 ARG cc_start: 0.7528 (ttp-110) cc_final: 0.7221 (ttm110) REVERT: Q 516 GLN cc_start: 0.7232 (pp30) cc_final: 0.6925 (pp30) REVERT: Q 520 GLU cc_start: 0.6782 (mp0) cc_final: 0.6057 (mp0) REVERT: R 22 ARG cc_start: 0.6426 (mtt90) cc_final: 0.5997 (mtt90) REVERT: R 105 GLU cc_start: 0.6511 (pm20) cc_final: 0.5294 (tp30) REVERT: R 146 LYS cc_start: 0.5493 (tptp) cc_final: 0.5179 (tptt) REVERT: R 221 ASN cc_start: 0.7597 (t0) cc_final: 0.7346 (t0) REVERT: R 382 GLN cc_start: 0.7526 (pp30) cc_final: 0.7020 (pp30) REVERT: R 473 VAL cc_start: 0.7166 (t) cc_final: 0.6838 (p) REVERT: R 499 ARG cc_start: 0.6836 (mmp-170) cc_final: 0.6422 (mmp-170) outliers start: 110 outliers final: 72 residues processed: 1403 average time/residue: 0.6461 time to fit residues: 1486.9800 Evaluate side-chains 1411 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 1335 time to evaluate : 5.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 227 HIS Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 266 GLN Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain J residue 234 GLN Chi-restraints excluded: chain J residue 358 LEU Chi-restraints excluded: chain J residue 389 LEU Chi-restraints excluded: chain K residue 243 VAL Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 342 LYS Chi-restraints excluded: chain L residue 9 LYS Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 99 ARG Chi-restraints excluded: chain L residue 293 GLU Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 203 ILE Chi-restraints excluded: chain N residue 414 SER Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain N residue 481 HIS Chi-restraints excluded: chain N residue 520 GLU Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 258 TYR Chi-restraints excluded: chain O residue 276 THR Chi-restraints excluded: chain O residue 443 GLN Chi-restraints excluded: chain O residue 472 THR Chi-restraints excluded: chain O residue 473 VAL Chi-restraints excluded: chain O residue 520 GLU Chi-restraints excluded: chain O residue 539 ASN Chi-restraints excluded: chain O residue 544 GLN Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 203 ILE Chi-restraints excluded: chain P residue 574 SER Chi-restraints excluded: chain P residue 582 ILE Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 193 LYS Chi-restraints excluded: chain Q residue 283 ASN Chi-restraints excluded: chain Q residue 395 ASN Chi-restraints excluded: chain Q residue 425 LYS Chi-restraints excluded: chain Q residue 483 LEU Chi-restraints excluded: chain Q residue 584 ILE Chi-restraints excluded: chain R residue 14 TYR Chi-restraints excluded: chain R residue 469 SER Chi-restraints excluded: chain R residue 476 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 715 optimal weight: 6.9990 chunk 544 optimal weight: 0.6980 chunk 375 optimal weight: 0.2980 chunk 80 optimal weight: 3.9990 chunk 345 optimal weight: 0.9990 chunk 486 optimal weight: 1.9990 chunk 726 optimal weight: 5.9990 chunk 769 optimal weight: 30.0000 chunk 379 optimal weight: 3.9990 chunk 688 optimal weight: 2.9990 chunk 207 optimal weight: 8.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 HIS C 8 ASN C 24 GLN D 24 GLN D 360 ASN I 247 GLN J 135 GLN J 218 HIS K 77 ASN M 214 GLN ** M 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 560 GLN ** O 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 383 GLN O 481 HIS ** O 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 427 GLN P 556 GLN P 586 GLN Q 26 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 65426 Z= 0.219 Angle : 0.549 13.845 88551 Z= 0.277 Chirality : 0.042 0.156 9656 Planarity : 0.004 0.067 11363 Dihedral : 9.457 143.652 9413 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.24 % Favored : 94.74 % Rotamer: Outliers : 1.95 % Allowed : 13.12 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -0.66 (0.09), residues: 7933 helix: 0.76 (0.10), residues: 3038 sheet: 0.31 (0.18), residues: 960 loop : -1.65 (0.09), residues: 3935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 49 HIS 0.005 0.001 HIS J 313 PHE 0.023 0.001 PHE M 457 TYR 0.022 0.001 TYR R 497 ARG 0.010 0.000 ARG P 581 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1479 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 1349 time to evaluate : 5.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 SER cc_start: 0.8414 (m) cc_final: 0.8103 (t) REVERT: A 74 ASP cc_start: 0.6794 (m-30) cc_final: 0.6582 (m-30) REVERT: A 293 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7279 (tm-30) REVERT: A 335 GLU cc_start: 0.7392 (pp20) cc_final: 0.7107 (pp20) REVERT: A 338 GLU cc_start: 0.6140 (mp0) cc_final: 0.5757 (mp0) REVERT: A 374 LYS cc_start: 0.7720 (mttt) cc_final: 0.7494 (mttt) REVERT: A 380 PHE cc_start: 0.8413 (t80) cc_final: 0.8199 (t80) REVERT: B 88 GLU cc_start: 0.7006 (mt-10) cc_final: 0.6741 (mt-10) REVERT: B 97 LYS cc_start: 0.8245 (ttmm) cc_final: 0.8029 (ttmm) REVERT: B 128 GLU cc_start: 0.7080 (tm-30) cc_final: 0.6836 (tm-30) REVERT: B 132 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8156 (mm-30) REVERT: B 242 GLU cc_start: 0.7901 (tt0) cc_final: 0.7164 (tt0) REVERT: B 258 ASN cc_start: 0.7847 (m-40) cc_final: 0.7632 (m-40) REVERT: C 56 TYR cc_start: 0.7939 (m-80) cc_final: 0.7736 (m-80) REVERT: C 106 GLU cc_start: 0.7360 (tp30) cc_final: 0.7092 (tp30) REVERT: C 352 GLU cc_start: 0.6789 (mp0) cc_final: 0.6195 (mp0) REVERT: D 50 LYS cc_start: 0.7948 (mmmt) cc_final: 0.7675 (ttmm) REVERT: D 97 LYS cc_start: 0.8533 (ttmm) cc_final: 0.8303 (ttmm) REVERT: D 107 GLU cc_start: 0.7440 (tm-30) cc_final: 0.7131 (tt0) REVERT: D 110 LYS cc_start: 0.8236 (mttp) cc_final: 0.7951 (mttp) REVERT: D 118 GLU cc_start: 0.7877 (tp30) cc_final: 0.7478 (tp30) REVERT: D 197 TYR cc_start: 0.8253 (m-10) cc_final: 0.7716 (m-80) REVERT: D 312 TYR cc_start: 0.8269 (t80) cc_final: 0.8059 (t80) REVERT: D 335 GLU cc_start: 0.7547 (pm20) cc_final: 0.7291 (pm20) REVERT: E 54 GLN cc_start: 0.8421 (tm-30) cc_final: 0.8137 (tm-30) REVERT: E 66 LYS cc_start: 0.7949 (tptm) cc_final: 0.7450 (tptt) REVERT: E 338 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7702 (tm-30) REVERT: E 342 LYS cc_start: 0.7506 (tttm) cc_final: 0.7242 (tttm) REVERT: F 296 SER cc_start: 0.8895 (m) cc_final: 0.8670 (m) REVERT: F 361 MET cc_start: 0.6892 (mtt) cc_final: 0.6445 (mtt) REVERT: F 389 LEU cc_start: 0.8127 (mt) cc_final: 0.7851 (mt) REVERT: G 43 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8026 (ptmt) REVERT: G 58 GLU cc_start: 0.7392 (tm-30) cc_final: 0.6874 (tm-30) REVERT: G 110 LYS cc_start: 0.7821 (mppt) cc_final: 0.7494 (tppt) REVERT: G 142 LYS cc_start: 0.7883 (ttpp) cc_final: 0.7424 (ttpp) REVERT: G 250 ASP cc_start: 0.8074 (t0) cc_final: 0.7795 (t0) REVERT: G 259 LYS cc_start: 0.8002 (tptp) cc_final: 0.6885 (tptp) REVERT: G 262 PHE cc_start: 0.6865 (p90) cc_final: 0.6495 (p90) REVERT: G 316 ARG cc_start: 0.7228 (mtm110) cc_final: 0.7018 (mtm110) REVERT: H 43 LYS cc_start: 0.6621 (ptmt) cc_final: 0.6402 (ptmt) REVERT: H 60 LEU cc_start: 0.8245 (tp) cc_final: 0.7930 (tp) REVERT: H 110 LYS cc_start: 0.8318 (ttmm) cc_final: 0.8014 (mtpp) REVERT: H 364 ASN cc_start: 0.7621 (t0) cc_final: 0.7132 (t0) REVERT: I 74 ASP cc_start: 0.7766 (m-30) cc_final: 0.7486 (t0) REVERT: I 300 THR cc_start: 0.8516 (m) cc_final: 0.8164 (p) REVERT: I 366 VAL cc_start: 0.9083 (OUTLIER) cc_final: 0.8880 (p) REVERT: J 46 LYS cc_start: 0.8371 (mtpp) cc_final: 0.8113 (mtpp) REVERT: J 108 PHE cc_start: 0.8464 (m-80) cc_final: 0.8203 (m-80) REVERT: J 126 THR cc_start: 0.8819 (m) cc_final: 0.8511 (p) REVERT: J 142 LYS cc_start: 0.7729 (tppt) cc_final: 0.7456 (tttp) REVERT: J 184 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6252 (pp) REVERT: J 189 SER cc_start: 0.8352 (p) cc_final: 0.8110 (m) REVERT: J 316 ARG cc_start: 0.8341 (mmm160) cc_final: 0.8058 (mmm160) REVERT: K 9 LYS cc_start: 0.8216 (tttt) cc_final: 0.7951 (mmtt) REVERT: K 76 ASP cc_start: 0.7066 (m-30) cc_final: 0.6612 (m-30) REVERT: K 106 GLU cc_start: 0.7584 (pm20) cc_final: 0.7031 (pm20) REVERT: K 128 GLU cc_start: 0.7026 (tm-30) cc_final: 0.6781 (tm-30) REVERT: K 129 GLN cc_start: 0.8338 (mm-40) cc_final: 0.8034 (mt0) REVERT: K 335 GLU cc_start: 0.7431 (mp0) cc_final: 0.7084 (mp0) REVERT: K 353 LYS cc_start: 0.7736 (mptt) cc_final: 0.7240 (mptt) REVERT: L 50 LYS cc_start: 0.8208 (mttm) cc_final: 0.7876 (mttm) REVERT: L 51 SER cc_start: 0.8360 (m) cc_final: 0.8068 (m) REVERT: L 88 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: L 99 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.5748 (ttp-170) REVERT: L 104 GLU cc_start: 0.6860 (tt0) cc_final: 0.6543 (tt0) REVERT: L 118 GLU cc_start: 0.7724 (tp30) cc_final: 0.7415 (tp30) REVERT: L 227 HIS cc_start: 0.7077 (m90) cc_final: 0.6808 (m90) REVERT: L 251 GLU cc_start: 0.7117 (tt0) cc_final: 0.6878 (tt0) REVERT: L 323 LEU cc_start: 0.7945 (mt) cc_final: 0.7597 (mt) REVERT: M 97 TYR cc_start: 0.5557 (m-80) cc_final: 0.5032 (m-80) REVERT: M 149 GLU cc_start: 0.6672 (pp20) cc_final: 0.6460 (mt-10) REVERT: M 157 LYS cc_start: 0.7671 (mttm) cc_final: 0.7372 (mmtt) REVERT: M 254 LYS cc_start: 0.8072 (tppp) cc_final: 0.7676 (tppp) REVERT: M 318 ASN cc_start: 0.8803 (t0) cc_final: 0.8584 (t0) REVERT: M 319 GLN cc_start: 0.7937 (pm20) cc_final: 0.7522 (mt0) REVERT: M 352 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7219 (mm-30) REVERT: M 468 ARG cc_start: 0.6954 (ttm110) cc_final: 0.6642 (ttm110) REVERT: M 538 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8333 (p) REVERT: N 114 GLU cc_start: 0.7106 (tt0) cc_final: 0.6819 (tt0) REVERT: N 268 LYS cc_start: 0.8251 (mtpt) cc_final: 0.7915 (mtpp) REVERT: N 310 LEU cc_start: 0.7495 (mt) cc_final: 0.7291 (mt) REVERT: N 352 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7387 (mm-30) REVERT: N 353 PHE cc_start: 0.7017 (m-80) cc_final: 0.6770 (m-80) REVERT: O 186 PHE cc_start: 0.8301 (t80) cc_final: 0.8070 (t80) REVERT: O 268 LYS cc_start: 0.7953 (mtmt) cc_final: 0.7596 (mtpp) REVERT: O 276 THR cc_start: 0.7832 (OUTLIER) cc_final: 0.7415 (t) REVERT: O 327 ASP cc_start: 0.7220 (t0) cc_final: 0.6792 (t0) REVERT: O 416 GLU cc_start: 0.7278 (tm-30) cc_final: 0.6839 (tm-30) REVERT: O 448 MET cc_start: 0.6954 (tpt) cc_final: 0.6602 (tpt) REVERT: O 601 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8068 (mm-30) REVERT: P 19 GLU cc_start: 0.6622 (mp0) cc_final: 0.6292 (mp0) REVERT: P 50 ASP cc_start: 0.5997 (m-30) cc_final: 0.5778 (m-30) REVERT: P 183 LYS cc_start: 0.7844 (mmmm) cc_final: 0.7063 (mtpp) REVERT: P 246 TYR cc_start: 0.7643 (t80) cc_final: 0.7370 (t80) REVERT: P 255 LYS cc_start: 0.6131 (tptt) cc_final: 0.5913 (tttt) REVERT: P 459 GLU cc_start: 0.7702 (tp30) cc_final: 0.7139 (tp30) REVERT: P 467 GLU cc_start: 0.7270 (tp30) cc_final: 0.6998 (tm-30) REVERT: P 502 LYS cc_start: 0.7223 (mmtt) cc_final: 0.6688 (mmtt) REVERT: P 508 LYS cc_start: 0.7779 (mttp) cc_final: 0.7365 (mmtp) REVERT: P 524 THR cc_start: 0.7293 (t) cc_final: 0.5408 (p) REVERT: Q 50 ASP cc_start: 0.7610 (t0) cc_final: 0.7129 (t0) REVERT: Q 68 MET cc_start: 0.7934 (tpp) cc_final: 0.7724 (tpp) REVERT: Q 146 LYS cc_start: 0.7913 (mppt) cc_final: 0.7657 (mppt) REVERT: Q 192 ARG cc_start: 0.6623 (ttt180) cc_final: 0.6164 (ttt90) REVERT: Q 211 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6951 (mm-30) REVERT: Q 444 ASP cc_start: 0.7889 (m-30) cc_final: 0.7432 (m-30) REVERT: Q 448 MET cc_start: 0.6700 (mmp) cc_final: 0.6432 (mmp) REVERT: Q 455 GLU cc_start: 0.7625 (pt0) cc_final: 0.6840 (pt0) REVERT: Q 459 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7218 (mt-10) REVERT: Q 516 GLN cc_start: 0.7325 (pp30) cc_final: 0.7017 (pp30) REVERT: Q 520 GLU cc_start: 0.6804 (mp0) cc_final: 0.6040 (mp0) REVERT: Q 592 LYS cc_start: 0.7687 (mmmt) cc_final: 0.7331 (mmmt) REVERT: R 22 ARG cc_start: 0.6429 (mtt90) cc_final: 0.5994 (mtt90) REVERT: R 105 GLU cc_start: 0.6396 (pm20) cc_final: 0.5400 (tp30) REVERT: R 221 ASN cc_start: 0.7725 (t0) cc_final: 0.7454 (t0) REVERT: R 259 GLN cc_start: 0.6885 (pp30) cc_final: 0.6599 (pm20) REVERT: R 382 GLN cc_start: 0.7561 (pp30) cc_final: 0.7062 (pp30) REVERT: R 473 VAL cc_start: 0.7211 (t) cc_final: 0.6900 (p) REVERT: R 499 ARG cc_start: 0.6787 (mmp-170) cc_final: 0.6348 (mmp-170) REVERT: R 540 GLU cc_start: 0.6872 (tp30) cc_final: 0.6248 (tp30) outliers start: 130 outliers final: 96 residues processed: 1397 average time/residue: 0.6411 time to fit residues: 1473.3212 Evaluate side-chains 1426 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 1323 time to evaluate : 5.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 227 HIS Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 266 GLN Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 234 GLN Chi-restraints excluded: chain J residue 389 LEU Chi-restraints excluded: chain K residue 243 VAL Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 300 THR Chi-restraints excluded: chain K residue 342 LYS Chi-restraints excluded: chain L residue 9 LYS Chi-restraints excluded: chain L residue 45 MET Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 99 ARG Chi-restraints excluded: chain L residue 293 GLU Chi-restraints excluded: chain L residue 342 LYS Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 156 THR Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 124 SER Chi-restraints excluded: chain N residue 203 ILE Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain N residue 481 HIS Chi-restraints excluded: chain N residue 520 GLU Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 258 TYR Chi-restraints excluded: chain O residue 276 THR Chi-restraints excluded: chain O residue 288 ILE Chi-restraints excluded: chain O residue 396 LEU Chi-restraints excluded: chain O residue 443 GLN Chi-restraints excluded: chain O residue 472 THR Chi-restraints excluded: chain O residue 473 VAL Chi-restraints excluded: chain O residue 544 GLN Chi-restraints excluded: chain P residue 12 ILE Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 427 GLN Chi-restraints excluded: chain P residue 556 GLN Chi-restraints excluded: chain P residue 558 LEU Chi-restraints excluded: chain P residue 574 SER Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 425 LYS Chi-restraints excluded: chain Q residue 473 VAL Chi-restraints excluded: chain Q residue 483 LEU Chi-restraints excluded: chain Q residue 558 LEU Chi-restraints excluded: chain Q residue 584 ILE Chi-restraints excluded: chain R residue 14 TYR Chi-restraints excluded: chain R residue 476 LEU Chi-restraints excluded: chain R residue 524 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 640 optimal weight: 3.9990 chunk 436 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 572 optimal weight: 2.9990 chunk 317 optimal weight: 0.0980 chunk 656 optimal weight: 8.9990 chunk 531 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 392 optimal weight: 2.9990 chunk 690 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN D 360 ASN E 199 GLN G 227 HIS G 365 GLN J 218 HIS J 378 ASN K 77 ASN ** M 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 26 ASN N 560 GLN O 224 HIS ** O 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 383 GLN ** O 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 427 GLN Q 277 GLN Q 395 ASN ** R 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 65426 Z= 0.355 Angle : 0.632 14.196 88551 Z= 0.321 Chirality : 0.045 0.239 9656 Planarity : 0.004 0.071 11363 Dihedral : 9.336 156.103 9413 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.55 % Favored : 93.43 % Rotamer: Outliers : 2.58 % Allowed : 14.30 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -0.95 (0.09), residues: 7933 helix: 0.53 (0.10), residues: 3015 sheet: 0.04 (0.17), residues: 973 loop : -1.78 (0.09), residues: 3945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 49 HIS 0.009 0.001 HIS P 224 PHE 0.022 0.002 PHE P 101 TYR 0.030 0.002 TYR E 224 ARG 0.010 0.001 ARG P 581 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1527 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 1355 time to evaluate : 6.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 SER cc_start: 0.8413 (m) cc_final: 0.8132 (t) REVERT: A 74 ASP cc_start: 0.6808 (m-30) cc_final: 0.6552 (m-30) REVERT: A 293 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7350 (tm-30) REVERT: A 335 GLU cc_start: 0.7353 (pp20) cc_final: 0.7056 (pp20) REVERT: A 338 GLU cc_start: 0.6192 (mp0) cc_final: 0.5782 (mp0) REVERT: B 72 GLN cc_start: 0.7522 (tp40) cc_final: 0.6981 (tm-30) REVERT: B 88 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6771 (mt-10) REVERT: B 97 LYS cc_start: 0.8234 (ttmm) cc_final: 0.8012 (ttmm) REVERT: B 128 GLU cc_start: 0.7160 (tm-30) cc_final: 0.6901 (tm-30) REVERT: B 242 GLU cc_start: 0.7928 (tt0) cc_final: 0.7176 (tt0) REVERT: C 102 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7058 (mp0) REVERT: C 106 GLU cc_start: 0.7562 (tp30) cc_final: 0.7241 (tp30) REVERT: C 352 GLU cc_start: 0.6922 (mp0) cc_final: 0.6347 (mp0) REVERT: D 50 LYS cc_start: 0.7970 (mmmt) cc_final: 0.7691 (ttmm) REVERT: D 97 LYS cc_start: 0.8535 (ttmm) cc_final: 0.8308 (ttmm) REVERT: D 110 LYS cc_start: 0.8266 (mttp) cc_final: 0.7976 (mttp) REVERT: D 118 GLU cc_start: 0.7878 (tp30) cc_final: 0.7480 (tp30) REVERT: D 197 TYR cc_start: 0.8269 (m-10) cc_final: 0.7723 (m-80) REVERT: D 311 ASP cc_start: 0.7557 (t0) cc_final: 0.7309 (t0) REVERT: D 363 PHE cc_start: 0.8014 (m-80) cc_final: 0.7685 (m-80) REVERT: E 54 GLN cc_start: 0.8428 (tm-30) cc_final: 0.8128 (tm-30) REVERT: E 66 LYS cc_start: 0.7973 (tptm) cc_final: 0.7449 (tptt) REVERT: E 340 ILE cc_start: 0.7793 (mt) cc_final: 0.7537 (mt) REVERT: E 342 LYS cc_start: 0.7534 (tttm) cc_final: 0.7270 (tttm) REVERT: E 382 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6817 (pm20) REVERT: F 296 SER cc_start: 0.8899 (m) cc_final: 0.8688 (m) REVERT: F 361 MET cc_start: 0.6943 (mtt) cc_final: 0.6467 (mtt) REVERT: F 389 LEU cc_start: 0.8095 (mt) cc_final: 0.7816 (mt) REVERT: G 43 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8102 (ptmt) REVERT: G 110 LYS cc_start: 0.7850 (mppt) cc_final: 0.7531 (tppt) REVERT: G 142 LYS cc_start: 0.7947 (ttpp) cc_final: 0.7514 (ttpp) REVERT: G 250 ASP cc_start: 0.8110 (t0) cc_final: 0.7798 (t0) REVERT: G 259 LYS cc_start: 0.8062 (tptp) cc_final: 0.6905 (tptp) REVERT: G 262 PHE cc_start: 0.6861 (p90) cc_final: 0.6539 (p90) REVERT: G 316 ARG cc_start: 0.7262 (mtm110) cc_final: 0.7041 (mtm110) REVERT: H 43 LYS cc_start: 0.6619 (ptmt) cc_final: 0.6400 (ptmt) REVERT: H 110 LYS cc_start: 0.8364 (ttmm) cc_final: 0.8050 (mtpp) REVERT: H 291 PHE cc_start: 0.7654 (t80) cc_final: 0.7272 (t80) REVERT: H 364 ASN cc_start: 0.7661 (t0) cc_final: 0.7134 (t0) REVERT: I 74 ASP cc_start: 0.7801 (m-30) cc_final: 0.7518 (t0) REVERT: J 46 LYS cc_start: 0.8424 (mtpp) cc_final: 0.8122 (mtpp) REVERT: J 108 PHE cc_start: 0.8460 (m-80) cc_final: 0.8256 (m-80) REVERT: J 116 TYR cc_start: 0.7009 (OUTLIER) cc_final: 0.6735 (m-80) REVERT: J 142 LYS cc_start: 0.7788 (tppt) cc_final: 0.7503 (tttp) REVERT: J 184 LEU cc_start: 0.6657 (OUTLIER) cc_final: 0.6329 (pp) REVERT: J 189 SER cc_start: 0.8343 (p) cc_final: 0.8137 (m) REVERT: J 287 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6470 (mtt) REVERT: K 76 ASP cc_start: 0.7069 (m-30) cc_final: 0.6634 (m-30) REVERT: K 106 GLU cc_start: 0.7581 (pm20) cc_final: 0.7198 (pm20) REVERT: K 128 GLU cc_start: 0.7116 (tm-30) cc_final: 0.6755 (tm-30) REVERT: K 129 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8114 (mt0) REVERT: K 286 GLU cc_start: 0.6467 (mm-30) cc_final: 0.5568 (mm-30) REVERT: K 353 LYS cc_start: 0.7801 (mptt) cc_final: 0.7399 (mptt) REVERT: L 50 LYS cc_start: 0.8254 (mttm) cc_final: 0.7909 (mttm) REVERT: L 51 SER cc_start: 0.8386 (m) cc_final: 0.8107 (m) REVERT: L 99 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.5877 (ttp-170) REVERT: L 104 GLU cc_start: 0.6866 (tt0) cc_final: 0.6541 (tt0) REVERT: L 118 GLU cc_start: 0.7729 (tp30) cc_final: 0.7416 (tp30) REVERT: L 227 HIS cc_start: 0.7046 (m90) cc_final: 0.6809 (m90) REVERT: L 323 LEU cc_start: 0.7957 (mt) cc_final: 0.7625 (mt) REVERT: M 59 ILE cc_start: 0.7322 (pt) cc_final: 0.7011 (mt) REVERT: M 149 GLU cc_start: 0.6988 (pp20) cc_final: 0.6679 (mt-10) REVERT: M 157 LYS cc_start: 0.7780 (mttm) cc_final: 0.7424 (mmtt) REVERT: M 254 LYS cc_start: 0.8154 (tppp) cc_final: 0.7719 (tppp) REVERT: M 294 LYS cc_start: 0.7887 (tmtt) cc_final: 0.7612 (tmtt) REVERT: M 319 GLN cc_start: 0.7866 (pm20) cc_final: 0.7626 (mt0) REVERT: M 352 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7264 (mm-30) REVERT: M 396 LEU cc_start: 0.5454 (OUTLIER) cc_final: 0.5251 (pp) REVERT: M 460 ILE cc_start: 0.6971 (mp) cc_final: 0.6598 (mt) REVERT: M 468 ARG cc_start: 0.7004 (ttm110) cc_final: 0.6566 (ttp-110) REVERT: N 114 GLU cc_start: 0.7150 (tt0) cc_final: 0.6839 (tt0) REVERT: N 268 LYS cc_start: 0.8346 (mtpt) cc_final: 0.8079 (mtpt) REVERT: N 277 GLN cc_start: 0.7447 (mt0) cc_final: 0.7237 (mt0) REVERT: N 352 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7423 (mm-30) REVERT: N 353 PHE cc_start: 0.7052 (m-80) cc_final: 0.6799 (m-80) REVERT: O 268 LYS cc_start: 0.8007 (mtmt) cc_final: 0.7755 (mtpp) REVERT: O 327 ASP cc_start: 0.7200 (t0) cc_final: 0.6786 (t0) REVERT: O 380 ILE cc_start: 0.8150 (tp) cc_final: 0.7926 (tp) REVERT: O 416 GLU cc_start: 0.7277 (tm-30) cc_final: 0.6866 (tm-30) REVERT: O 424 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7636 (mm-30) REVERT: O 448 MET cc_start: 0.7023 (tpt) cc_final: 0.6555 (tpt) REVERT: P 110 VAL cc_start: 0.7391 (OUTLIER) cc_final: 0.7171 (m) REVERT: P 176 LEU cc_start: 0.6289 (OUTLIER) cc_final: 0.5350 (mt) REVERT: P 183 LYS cc_start: 0.7973 (mmmm) cc_final: 0.7039 (mmmm) REVERT: P 246 TYR cc_start: 0.7660 (t80) cc_final: 0.7360 (t80) REVERT: P 277 GLN cc_start: 0.7597 (mt0) cc_final: 0.7255 (mp-120) REVERT: P 379 LYS cc_start: 0.7866 (ptpt) cc_final: 0.7383 (ptpt) REVERT: P 427 GLN cc_start: 0.6859 (OUTLIER) cc_final: 0.6603 (pt0) REVERT: P 459 GLU cc_start: 0.7734 (tp30) cc_final: 0.7163 (tp30) REVERT: P 467 GLU cc_start: 0.7495 (tp30) cc_final: 0.6785 (tp30) REVERT: P 508 LYS cc_start: 0.7873 (mttp) cc_final: 0.7385 (mmtp) REVERT: P 524 THR cc_start: 0.7366 (t) cc_final: 0.5527 (p) REVERT: Q 50 ASP cc_start: 0.7627 (t0) cc_final: 0.7126 (t0) REVERT: Q 146 LYS cc_start: 0.8035 (mppt) cc_final: 0.7737 (mppt) REVERT: Q 211 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7232 (mm-30) REVERT: Q 297 ASN cc_start: 0.4470 (OUTLIER) cc_final: 0.4116 (t0) REVERT: Q 444 ASP cc_start: 0.7839 (m-30) cc_final: 0.7573 (m-30) REVERT: Q 448 MET cc_start: 0.6828 (mmp) cc_final: 0.6515 (mmp) REVERT: Q 455 GLU cc_start: 0.7618 (pt0) cc_final: 0.6887 (pt0) REVERT: Q 459 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7351 (mt-10) REVERT: Q 516 GLN cc_start: 0.7343 (pp30) cc_final: 0.6929 (pp30) REVERT: Q 517 ARG cc_start: 0.7465 (mmm-85) cc_final: 0.6967 (mmm-85) REVERT: Q 520 GLU cc_start: 0.6920 (mp0) cc_final: 0.6417 (mp0) REVERT: Q 592 LYS cc_start: 0.7791 (mmmt) cc_final: 0.7464 (mmmt) REVERT: R 22 ARG cc_start: 0.6494 (mtt90) cc_final: 0.6031 (mtt90) REVERT: R 105 GLU cc_start: 0.6378 (pm20) cc_final: 0.5406 (tp30) REVERT: R 221 ASN cc_start: 0.7817 (t0) cc_final: 0.7526 (t0) REVERT: R 259 GLN cc_start: 0.6878 (pp30) cc_final: 0.6637 (pm20) REVERT: R 382 GLN cc_start: 0.7595 (pp30) cc_final: 0.7115 (pp30) REVERT: R 473 VAL cc_start: 0.7224 (t) cc_final: 0.6905 (p) REVERT: R 499 ARG cc_start: 0.6838 (mmp-170) cc_final: 0.6541 (mmp-170) REVERT: R 540 GLU cc_start: 0.6935 (tp30) cc_final: 0.6343 (tp30) outliers start: 172 outliers final: 122 residues processed: 1434 average time/residue: 0.6438 time to fit residues: 1527.7630 Evaluate side-chains 1447 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 1314 time to evaluate : 5.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain G residue 405 ASN Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 227 HIS Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 65 ASP Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 253 ILE Chi-restraints excluded: chain I residue 266 GLN Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain J residue 116 TYR Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 234 GLN Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 287 MET Chi-restraints excluded: chain J residue 358 LEU Chi-restraints excluded: chain J residue 389 LEU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 47 ASP Chi-restraints excluded: chain K residue 243 VAL Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 300 THR Chi-restraints excluded: chain L residue 9 LYS Chi-restraints excluded: chain L residue 45 MET Chi-restraints excluded: chain L residue 99 ARG Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain L residue 168 ASN Chi-restraints excluded: chain L residue 293 GLU Chi-restraints excluded: chain L residue 342 LYS Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 156 THR Chi-restraints excluded: chain M residue 227 LEU Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain M residue 396 LEU Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 26 ASN Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 124 SER Chi-restraints excluded: chain N residue 203 ILE Chi-restraints excluded: chain N residue 414 SER Chi-restraints excluded: chain N residue 417 VAL Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain N residue 481 HIS Chi-restraints excluded: chain N residue 520 GLU Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 258 TYR Chi-restraints excluded: chain O residue 288 ILE Chi-restraints excluded: chain O residue 317 THR Chi-restraints excluded: chain O residue 396 LEU Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 443 GLN Chi-restraints excluded: chain O residue 472 THR Chi-restraints excluded: chain O residue 473 VAL Chi-restraints excluded: chain O residue 539 ASN Chi-restraints excluded: chain P residue 110 VAL Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 176 LEU Chi-restraints excluded: chain P residue 203 ILE Chi-restraints excluded: chain P residue 267 ILE Chi-restraints excluded: chain P residue 414 SER Chi-restraints excluded: chain P residue 427 GLN Chi-restraints excluded: chain P residue 558 LEU Chi-restraints excluded: chain P residue 574 SER Chi-restraints excluded: chain P residue 597 VAL Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 283 ASN Chi-restraints excluded: chain Q residue 297 ASN Chi-restraints excluded: chain Q residue 425 LYS Chi-restraints excluded: chain Q residue 473 VAL Chi-restraints excluded: chain Q residue 483 LEU Chi-restraints excluded: chain Q residue 511 LEU Chi-restraints excluded: chain Q residue 558 LEU Chi-restraints excluded: chain Q residue 584 ILE Chi-restraints excluded: chain R residue 14 TYR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 476 LEU Chi-restraints excluded: chain R residue 524 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 258 optimal weight: 0.9980 chunk 692 optimal weight: 0.2980 chunk 152 optimal weight: 0.9980 chunk 451 optimal weight: 1.9990 chunk 189 optimal weight: 20.0000 chunk 770 optimal weight: 10.0000 chunk 639 optimal weight: 4.9990 chunk 356 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 254 optimal weight: 1.9990 chunk 404 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 8 ASN D 360 ASN G 55 ASN ** H 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 218 HIS ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 ASN K 78 ASN K 360 ASN L 360 ASN ** M 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 26 ASN ** N 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 560 GLN ** O 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 383 GLN ** O 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 ASN P 427 GLN R 319 GLN R 429 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 65426 Z= 0.183 Angle : 0.544 15.044 88551 Z= 0.275 Chirality : 0.041 0.170 9656 Planarity : 0.004 0.069 11363 Dihedral : 8.938 152.982 9413 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.04 % Favored : 94.95 % Rotamer: Outliers : 2.14 % Allowed : 16.04 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -0.74 (0.09), residues: 7933 helix: 0.75 (0.10), residues: 3024 sheet: 0.26 (0.18), residues: 944 loop : -1.73 (0.09), residues: 3965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP E 49 HIS 0.009 0.001 HIS O 480 PHE 0.025 0.001 PHE M 457 TYR 0.027 0.001 TYR F 312 ARG 0.007 0.000 ARG P 581 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1476 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 1333 time to evaluate : 5.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 SER cc_start: 0.8408 (m) cc_final: 0.8132 (t) REVERT: A 74 ASP cc_start: 0.6751 (m-30) cc_final: 0.6507 (m-30) REVERT: A 293 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7331 (tm-30) REVERT: A 335 GLU cc_start: 0.7298 (pp20) cc_final: 0.7053 (pp20) REVERT: B 72 GLN cc_start: 0.7406 (tp40) cc_final: 0.6937 (tm-30) REVERT: B 88 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6728 (mt-10) REVERT: B 97 LYS cc_start: 0.8255 (ttmm) cc_final: 0.8041 (ttmm) REVERT: B 128 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6847 (tm-30) REVERT: B 132 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8078 (mm-30) REVERT: B 242 GLU cc_start: 0.7884 (tt0) cc_final: 0.7560 (tt0) REVERT: B 250 ASP cc_start: 0.7799 (m-30) cc_final: 0.7587 (m-30) REVERT: C 106 GLU cc_start: 0.7493 (tp30) cc_final: 0.7180 (tp30) REVERT: C 353 LYS cc_start: 0.7344 (mtmm) cc_final: 0.7018 (mtmm) REVERT: D 50 LYS cc_start: 0.7947 (mmmt) cc_final: 0.7672 (ttmm) REVERT: D 97 LYS cc_start: 0.8540 (ttmm) cc_final: 0.8317 (ttmm) REVERT: D 110 LYS cc_start: 0.8258 (mttp) cc_final: 0.7950 (mttp) REVERT: D 118 GLU cc_start: 0.7882 (tp30) cc_final: 0.7508 (tp30) REVERT: D 197 TYR cc_start: 0.8313 (m-10) cc_final: 0.7748 (m-80) REVERT: D 311 ASP cc_start: 0.7600 (t0) cc_final: 0.7353 (t0) REVERT: D 335 GLU cc_start: 0.7685 (pm20) cc_final: 0.7304 (pm20) REVERT: D 363 PHE cc_start: 0.7957 (m-80) cc_final: 0.7621 (m-80) REVERT: E 54 GLN cc_start: 0.8426 (tm-30) cc_final: 0.8129 (tm-30) REVERT: E 340 ILE cc_start: 0.7691 (mt) cc_final: 0.7470 (mt) REVERT: E 342 LYS cc_start: 0.7433 (tttm) cc_final: 0.7162 (tttm) REVERT: E 382 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6753 (pm20) REVERT: F 296 SER cc_start: 0.8887 (m) cc_final: 0.8670 (m) REVERT: F 312 TYR cc_start: 0.5992 (t80) cc_final: 0.5788 (t80) REVERT: F 389 LEU cc_start: 0.8162 (mt) cc_final: 0.7878 (mt) REVERT: G 43 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8054 (ptmt) REVERT: G 55 ASN cc_start: 0.7765 (m-40) cc_final: 0.7556 (m110) REVERT: G 110 LYS cc_start: 0.7836 (mppt) cc_final: 0.7502 (tppt) REVERT: G 142 LYS cc_start: 0.7891 (ttpp) cc_final: 0.7468 (ttpp) REVERT: G 178 GLU cc_start: 0.6824 (tt0) cc_final: 0.5880 (mt-10) REVERT: G 250 ASP cc_start: 0.8043 (t0) cc_final: 0.7758 (t0) REVERT: G 259 LYS cc_start: 0.8046 (tptp) cc_final: 0.6965 (tptp) REVERT: G 262 PHE cc_start: 0.6883 (p90) cc_final: 0.6578 (p90) REVERT: G 316 ARG cc_start: 0.7236 (mtm110) cc_final: 0.7027 (mtm110) REVERT: H 43 LYS cc_start: 0.6597 (ptmt) cc_final: 0.6390 (ptmt) REVERT: H 159 GLN cc_start: 0.8592 (mt0) cc_final: 0.8330 (mt0) REVERT: H 205 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.7154 (m-80) REVERT: H 364 ASN cc_start: 0.7651 (t0) cc_final: 0.7097 (t0) REVERT: I 74 ASP cc_start: 0.7786 (m-30) cc_final: 0.7479 (t0) REVERT: I 300 THR cc_start: 0.8544 (m) cc_final: 0.8185 (p) REVERT: J 46 LYS cc_start: 0.8290 (mtpp) cc_final: 0.8033 (mtpp) REVERT: J 108 PHE cc_start: 0.8454 (m-80) cc_final: 0.8219 (m-80) REVERT: J 116 TYR cc_start: 0.6931 (OUTLIER) cc_final: 0.6643 (m-80) REVERT: J 126 THR cc_start: 0.8800 (m) cc_final: 0.8511 (p) REVERT: J 189 SER cc_start: 0.8350 (p) cc_final: 0.8091 (m) REVERT: J 316 ARG cc_start: 0.8325 (mmm160) cc_final: 0.8056 (mmm160) REVERT: K 9 LYS cc_start: 0.8207 (tttt) cc_final: 0.7971 (mmtt) REVERT: K 76 ASP cc_start: 0.7036 (m-30) cc_final: 0.6612 (m-30) REVERT: K 106 GLU cc_start: 0.7560 (pm20) cc_final: 0.7150 (pm20) REVERT: K 128 GLU cc_start: 0.7050 (tm-30) cc_final: 0.6802 (tm-30) REVERT: K 129 GLN cc_start: 0.8338 (mm-40) cc_final: 0.8101 (mt0) REVERT: K 335 GLU cc_start: 0.7409 (mp0) cc_final: 0.7199 (mp0) REVERT: K 353 LYS cc_start: 0.7795 (mptt) cc_final: 0.7485 (mptt) REVERT: L 50 LYS cc_start: 0.8234 (mttm) cc_final: 0.7876 (mttm) REVERT: L 51 SER cc_start: 0.8264 (m) cc_final: 0.8000 (m) REVERT: L 88 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6942 (mp0) REVERT: L 99 ARG cc_start: 0.6874 (OUTLIER) cc_final: 0.5740 (ttp-170) REVERT: L 104 GLU cc_start: 0.6782 (tt0) cc_final: 0.6412 (tt0) REVERT: L 118 GLU cc_start: 0.7713 (tp30) cc_final: 0.7413 (tp30) REVERT: L 227 HIS cc_start: 0.7071 (m90) cc_final: 0.6799 (m90) REVERT: L 323 LEU cc_start: 0.7874 (mt) cc_final: 0.7531 (mt) REVERT: M 59 ILE cc_start: 0.7252 (pt) cc_final: 0.6978 (mt) REVERT: M 149 GLU cc_start: 0.7028 (pp20) cc_final: 0.6689 (mt-10) REVERT: M 157 LYS cc_start: 0.7681 (mttm) cc_final: 0.7259 (mmtt) REVERT: M 254 LYS cc_start: 0.8142 (tppp) cc_final: 0.7721 (tppp) REVERT: M 294 LYS cc_start: 0.7834 (tmtt) cc_final: 0.7632 (tmtt) REVERT: M 352 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7258 (mm-30) REVERT: M 444 ASP cc_start: 0.6752 (t0) cc_final: 0.6545 (t0) REVERT: N 114 GLU cc_start: 0.7074 (tt0) cc_final: 0.6776 (tt0) REVERT: N 268 LYS cc_start: 0.8281 (mtpt) cc_final: 0.8032 (mtpt) REVERT: N 309 LEU cc_start: 0.8147 (mt) cc_final: 0.7748 (tt) REVERT: N 343 PHE cc_start: 0.7803 (t80) cc_final: 0.7523 (t80) REVERT: N 352 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7388 (mm-30) REVERT: N 353 PHE cc_start: 0.6921 (m-80) cc_final: 0.6673 (m-80) REVERT: N 506 LYS cc_start: 0.8372 (tptp) cc_final: 0.8132 (tppt) REVERT: O 268 LYS cc_start: 0.7963 (mtmt) cc_final: 0.7594 (mtpp) REVERT: O 327 ASP cc_start: 0.7241 (t0) cc_final: 0.6780 (t0) REVERT: O 380 ILE cc_start: 0.8130 (tp) cc_final: 0.7884 (tp) REVERT: O 416 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6843 (tm-30) REVERT: O 448 MET cc_start: 0.6898 (tpt) cc_final: 0.6486 (tpt) REVERT: P 183 LYS cc_start: 0.7891 (mmmm) cc_final: 0.7172 (mtpp) REVERT: P 246 TYR cc_start: 0.7639 (t80) cc_final: 0.7398 (t80) REVERT: P 379 LYS cc_start: 0.7822 (ptpt) cc_final: 0.7473 (ptpp) REVERT: P 441 LEU cc_start: 0.7896 (tp) cc_final: 0.7645 (tp) REVERT: P 459 GLU cc_start: 0.7701 (tp30) cc_final: 0.7139 (tp30) REVERT: P 508 LYS cc_start: 0.7755 (mttp) cc_final: 0.7501 (mtpp) REVERT: P 524 THR cc_start: 0.7305 (t) cc_final: 0.5410 (p) REVERT: Q 50 ASP cc_start: 0.7593 (t0) cc_final: 0.6958 (t0) REVERT: Q 64 ARG cc_start: 0.7226 (tpt-90) cc_final: 0.6896 (tpt-90) REVERT: Q 146 LYS cc_start: 0.7947 (mppt) cc_final: 0.7670 (mppt) REVERT: Q 160 LYS cc_start: 0.7041 (mmtm) cc_final: 0.6640 (mppt) REVERT: Q 332 ARG cc_start: 0.6915 (mmt180) cc_final: 0.6708 (mmt180) REVERT: Q 444 ASP cc_start: 0.7861 (m-30) cc_final: 0.7418 (m-30) REVERT: Q 448 MET cc_start: 0.6763 (mmp) cc_final: 0.6472 (mmp) REVERT: Q 455 GLU cc_start: 0.7579 (pt0) cc_final: 0.6791 (pt0) REVERT: Q 459 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7281 (mt-10) REVERT: Q 516 GLN cc_start: 0.7301 (pp30) cc_final: 0.6981 (pp30) REVERT: Q 520 GLU cc_start: 0.6867 (mp0) cc_final: 0.6114 (mp0) REVERT: Q 592 LYS cc_start: 0.7804 (mmmt) cc_final: 0.7509 (mmmt) REVERT: R 22 ARG cc_start: 0.6463 (mtt90) cc_final: 0.6019 (mtt90) REVERT: R 105 GLU cc_start: 0.6427 (pm20) cc_final: 0.5463 (tp30) REVERT: R 382 GLN cc_start: 0.7576 (pp30) cc_final: 0.7047 (pp30) REVERT: R 473 VAL cc_start: 0.7199 (t) cc_final: 0.6919 (p) REVERT: R 499 ARG cc_start: 0.6778 (mmp-170) cc_final: 0.6373 (mmp-170) REVERT: R 540 GLU cc_start: 0.6883 (tp30) cc_final: 0.6258 (tp30) outliers start: 143 outliers final: 104 residues processed: 1393 average time/residue: 0.6296 time to fit residues: 1457.3215 Evaluate side-chains 1413 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 1303 time to evaluate : 5.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 405 ASN Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 205 PHE Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 240 VAL Chi-restraints excluded: chain I residue 266 GLN Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 116 TYR Chi-restraints excluded: chain J residue 234 GLN Chi-restraints excluded: chain J residue 389 LEU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 300 THR Chi-restraints excluded: chain K residue 342 LYS Chi-restraints excluded: chain L residue 9 LYS Chi-restraints excluded: chain L residue 45 MET Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 99 ARG Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 293 GLU Chi-restraints excluded: chain L residue 335 GLU Chi-restraints excluded: chain L residue 342 LYS Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 227 LEU Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain M residue 420 PHE Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 26 ASN Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 124 SER Chi-restraints excluded: chain N residue 203 ILE Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain N residue 481 HIS Chi-restraints excluded: chain N residue 498 GLU Chi-restraints excluded: chain N residue 520 GLU Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 28 HIS Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 258 TYR Chi-restraints excluded: chain O residue 288 ILE Chi-restraints excluded: chain O residue 411 LYS Chi-restraints excluded: chain O residue 443 GLN Chi-restraints excluded: chain O residue 472 THR Chi-restraints excluded: chain O residue 473 VAL Chi-restraints excluded: chain O residue 478 GLU Chi-restraints excluded: chain O residue 544 GLN Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 414 SER Chi-restraints excluded: chain P residue 574 SER Chi-restraints excluded: chain P residue 597 VAL Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 193 LYS Chi-restraints excluded: chain Q residue 425 LYS Chi-restraints excluded: chain Q residue 473 VAL Chi-restraints excluded: chain Q residue 483 LEU Chi-restraints excluded: chain Q residue 558 LEU Chi-restraints excluded: chain Q residue 584 ILE Chi-restraints excluded: chain R residue 14 TYR Chi-restraints excluded: chain R residue 438 MET Chi-restraints excluded: chain R residue 469 SER Chi-restraints excluded: chain R residue 476 LEU Chi-restraints excluded: chain R residue 524 THR Chi-restraints excluded: chain R residue 531 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 742 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 438 optimal weight: 0.0870 chunk 562 optimal weight: 1.9990 chunk 435 optimal weight: 5.9990 chunk 648 optimal weight: 8.9990 chunk 430 optimal weight: 4.9990 chunk 767 optimal weight: 20.0000 chunk 480 optimal weight: 4.9990 chunk 467 optimal weight: 0.4980 chunk 354 optimal weight: 3.9990 overall best weight: 1.9164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 8 ASN C 24 GLN D 72 GLN J 218 HIS ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 ASN ** M 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 26 ASN ** N 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 560 GLN ** O 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 383 GLN ** O 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 221 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 65426 Z= 0.288 Angle : 0.595 15.229 88551 Z= 0.302 Chirality : 0.043 0.169 9656 Planarity : 0.004 0.070 11363 Dihedral : 9.007 156.742 9413 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.39 % Favored : 93.60 % Rotamer: Outliers : 2.50 % Allowed : 16.13 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -0.88 (0.09), residues: 7933 helix: 0.65 (0.10), residues: 3014 sheet: 0.09 (0.17), residues: 958 loop : -1.79 (0.09), residues: 3961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 49 HIS 0.008 0.001 HIS N 28 PHE 0.019 0.002 PHE P 101 TYR 0.026 0.002 TYR E 224 ARG 0.010 0.000 ARG Q 468 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1510 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 1343 time to evaluate : 5.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 SER cc_start: 0.8399 (m) cc_final: 0.8110 (t) REVERT: A 293 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7375 (tm-30) REVERT: A 335 GLU cc_start: 0.7288 (pp20) cc_final: 0.7014 (pp20) REVERT: B 72 GLN cc_start: 0.7450 (tp40) cc_final: 0.6924 (tm-30) REVERT: B 88 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6778 (mt-10) REVERT: B 97 LYS cc_start: 0.8252 (ttmm) cc_final: 0.8029 (ttmm) REVERT: B 128 GLU cc_start: 0.7168 (tm-30) cc_final: 0.6892 (tm-30) REVERT: B 132 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8175 (mm-30) REVERT: B 242 GLU cc_start: 0.7908 (tt0) cc_final: 0.7594 (tt0) REVERT: C 106 GLU cc_start: 0.7558 (tp30) cc_final: 0.7235 (tp30) REVERT: C 352 GLU cc_start: 0.6877 (mp0) cc_final: 0.6310 (mp0) REVERT: D 50 LYS cc_start: 0.7962 (mmmt) cc_final: 0.7687 (ttmm) REVERT: D 97 LYS cc_start: 0.8546 (ttmm) cc_final: 0.8317 (ttmm) REVERT: D 110 LYS cc_start: 0.8271 (mttp) cc_final: 0.7960 (mttp) REVERT: D 118 GLU cc_start: 0.7930 (tp30) cc_final: 0.7540 (tp30) REVERT: D 197 TYR cc_start: 0.8268 (m-10) cc_final: 0.7722 (m-80) REVERT: D 363 PHE cc_start: 0.7979 (m-80) cc_final: 0.7680 (m-80) REVERT: E 54 GLN cc_start: 0.8441 (tm-30) cc_final: 0.8123 (tm-30) REVERT: E 250 ASP cc_start: 0.7657 (m-30) cc_final: 0.7380 (m-30) REVERT: E 342 LYS cc_start: 0.7458 (tttm) cc_final: 0.7193 (tttm) REVERT: E 382 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6876 (pm20) REVERT: F 296 SER cc_start: 0.8889 (m) cc_final: 0.8675 (m) REVERT: F 389 LEU cc_start: 0.8058 (mt) cc_final: 0.7740 (mt) REVERT: G 43 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8049 (ptmt) REVERT: G 55 ASN cc_start: 0.7751 (m-40) cc_final: 0.7540 (m110) REVERT: G 110 LYS cc_start: 0.7676 (mppt) cc_final: 0.7359 (tppt) REVERT: G 142 LYS cc_start: 0.7923 (ttpp) cc_final: 0.7574 (ttpp) REVERT: G 173 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6608 (mt) REVERT: G 178 GLU cc_start: 0.6969 (tt0) cc_final: 0.6046 (mt-10) REVERT: G 250 ASP cc_start: 0.8087 (t0) cc_final: 0.7771 (t0) REVERT: G 259 LYS cc_start: 0.8080 (tptp) cc_final: 0.6965 (tptp) REVERT: G 262 PHE cc_start: 0.6835 (p90) cc_final: 0.6618 (p90) REVERT: G 316 ARG cc_start: 0.7274 (mtm110) cc_final: 0.7064 (mtm110) REVERT: H 43 LYS cc_start: 0.6599 (ptmt) cc_final: 0.6398 (ptmt) REVERT: H 159 GLN cc_start: 0.8598 (mt0) cc_final: 0.8304 (mt0) REVERT: H 205 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.7121 (m-80) REVERT: H 291 PHE cc_start: 0.7567 (t80) cc_final: 0.7134 (t80) REVERT: H 364 ASN cc_start: 0.7679 (t0) cc_final: 0.7111 (t0) REVERT: I 74 ASP cc_start: 0.7817 (m-30) cc_final: 0.7514 (t0) REVERT: J 46 LYS cc_start: 0.8339 (mtpp) cc_final: 0.8113 (mtpp) REVERT: J 54 GLN cc_start: 0.8163 (tt0) cc_final: 0.7957 (tt0) REVERT: J 108 PHE cc_start: 0.8444 (m-80) cc_final: 0.8239 (m-80) REVERT: J 189 SER cc_start: 0.8343 (p) cc_final: 0.8122 (m) REVERT: J 287 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.6512 (mtt) REVERT: K 76 ASP cc_start: 0.7045 (m-30) cc_final: 0.6607 (m-30) REVERT: K 106 GLU cc_start: 0.7614 (pm20) cc_final: 0.7237 (pm20) REVERT: K 128 GLU cc_start: 0.7090 (tm-30) cc_final: 0.6843 (tm-30) REVERT: K 129 GLN cc_start: 0.8400 (mm-40) cc_final: 0.8129 (mt0) REVERT: K 286 GLU cc_start: 0.6328 (mm-30) cc_final: 0.5247 (mm-30) REVERT: K 353 LYS cc_start: 0.7822 (mptt) cc_final: 0.7528 (mptt) REVERT: L 50 LYS cc_start: 0.8252 (mttm) cc_final: 0.7891 (mttm) REVERT: L 51 SER cc_start: 0.8374 (m) cc_final: 0.8094 (m) REVERT: L 88 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.6891 (mp0) REVERT: L 99 ARG cc_start: 0.6963 (OUTLIER) cc_final: 0.5818 (ttp-170) REVERT: L 104 GLU cc_start: 0.6786 (tt0) cc_final: 0.6438 (tt0) REVERT: L 118 GLU cc_start: 0.7741 (tp30) cc_final: 0.7401 (tp30) REVERT: L 227 HIS cc_start: 0.7043 (m90) cc_final: 0.6796 (m90) REVERT: L 323 LEU cc_start: 0.7893 (mt) cc_final: 0.7555 (mt) REVERT: M 59 ILE cc_start: 0.7344 (pt) cc_final: 0.7024 (mt) REVERT: M 149 GLU cc_start: 0.7090 (pp20) cc_final: 0.6720 (mt-10) REVERT: M 157 LYS cc_start: 0.7748 (mttm) cc_final: 0.7295 (mmtt) REVERT: M 202 ARG cc_start: 0.6133 (ttm170) cc_final: 0.5876 (ttm170) REVERT: M 254 LYS cc_start: 0.8170 (tppp) cc_final: 0.7729 (tppp) REVERT: M 294 LYS cc_start: 0.7892 (tmtt) cc_final: 0.7677 (tmtt) REVERT: M 352 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7331 (mm-30) REVERT: M 444 ASP cc_start: 0.6888 (t0) cc_final: 0.6658 (t0) REVERT: N 114 GLU cc_start: 0.7132 (tt0) cc_final: 0.6819 (tt0) REVERT: N 268 LYS cc_start: 0.8322 (mtpt) cc_final: 0.8065 (mtpt) REVERT: N 309 LEU cc_start: 0.8160 (mt) cc_final: 0.7752 (tt) REVERT: N 352 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7393 (mm-30) REVERT: N 353 PHE cc_start: 0.6976 (m-80) cc_final: 0.6722 (m-80) REVERT: N 380 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8122 (mp) REVERT: O 186 PHE cc_start: 0.8286 (t80) cc_final: 0.8021 (t80) REVERT: O 268 LYS cc_start: 0.7999 (mtmt) cc_final: 0.7734 (mtpp) REVERT: O 327 ASP cc_start: 0.7242 (t0) cc_final: 0.6780 (t0) REVERT: O 380 ILE cc_start: 0.8233 (tp) cc_final: 0.7996 (tp) REVERT: O 416 GLU cc_start: 0.7267 (tm-30) cc_final: 0.6856 (tm-30) REVERT: O 424 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7627 (mm-30) REVERT: O 448 MET cc_start: 0.6935 (tpt) cc_final: 0.6437 (tpt) REVERT: O 506 LYS cc_start: 0.6028 (ttmm) cc_final: 0.5811 (mtpp) REVERT: P 110 VAL cc_start: 0.7362 (OUTLIER) cc_final: 0.7159 (m) REVERT: P 176 LEU cc_start: 0.6124 (OUTLIER) cc_final: 0.5148 (mt) REVERT: P 183 LYS cc_start: 0.7951 (mmmm) cc_final: 0.7077 (mmmm) REVERT: P 211 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6914 (mm-30) REVERT: P 246 TYR cc_start: 0.7641 (t80) cc_final: 0.7336 (t80) REVERT: P 277 GLN cc_start: 0.7611 (mt0) cc_final: 0.7332 (mp-120) REVERT: P 401 GLU cc_start: 0.7409 (tm-30) cc_final: 0.7072 (tm-30) REVERT: P 459 GLU cc_start: 0.7727 (tp30) cc_final: 0.7164 (tp30) REVERT: P 508 LYS cc_start: 0.7835 (mttp) cc_final: 0.7372 (mmtp) REVERT: P 524 THR cc_start: 0.7324 (t) cc_final: 0.5353 (p) REVERT: Q 35 LEU cc_start: -0.0729 (OUTLIER) cc_final: -0.1629 (mt) REVERT: Q 50 ASP cc_start: 0.7617 (t0) cc_final: 0.7019 (t0) REVERT: Q 64 ARG cc_start: 0.7246 (tpt-90) cc_final: 0.7037 (tpt-90) REVERT: Q 146 LYS cc_start: 0.8039 (mppt) cc_final: 0.7730 (mppt) REVERT: Q 160 LYS cc_start: 0.7062 (mmtm) cc_final: 0.6645 (mppt) REVERT: Q 211 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7187 (mm-30) REVERT: Q 424 GLU cc_start: 0.6879 (tm-30) cc_final: 0.5960 (tm-30) REVERT: Q 444 ASP cc_start: 0.7825 (m-30) cc_final: 0.7474 (m-30) REVERT: Q 448 MET cc_start: 0.6972 (mmp) cc_final: 0.6629 (mmp) REVERT: Q 455 GLU cc_start: 0.7621 (pt0) cc_final: 0.6850 (pt0) REVERT: Q 459 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7336 (mt-10) REVERT: Q 467 GLU cc_start: 0.7959 (pm20) cc_final: 0.7218 (pm20) REVERT: Q 516 GLN cc_start: 0.7330 (pp30) cc_final: 0.6988 (pp30) REVERT: Q 520 GLU cc_start: 0.6916 (mp0) cc_final: 0.6172 (mp0) REVERT: Q 547 ARG cc_start: 0.7949 (ptp-170) cc_final: 0.7733 (ptm160) REVERT: R 22 ARG cc_start: 0.6494 (mtt90) cc_final: 0.6021 (mtt90) REVERT: R 105 GLU cc_start: 0.6452 (pm20) cc_final: 0.6003 (pp20) REVERT: R 382 GLN cc_start: 0.7576 (pp30) cc_final: 0.7068 (pp30) REVERT: R 473 VAL cc_start: 0.7213 (t) cc_final: 0.6936 (p) REVERT: R 499 ARG cc_start: 0.6776 (mmp-170) cc_final: 0.6506 (mmp-170) REVERT: R 540 GLU cc_start: 0.6965 (tp30) cc_final: 0.6374 (tp30) outliers start: 167 outliers final: 126 residues processed: 1424 average time/residue: 0.6379 time to fit residues: 1506.2780 Evaluate side-chains 1460 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 1323 time to evaluate : 5.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 405 ASN Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 129 GLN Chi-restraints excluded: chain H residue 205 PHE Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 240 VAL Chi-restraints excluded: chain I residue 266 GLN Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 116 TYR Chi-restraints excluded: chain J residue 234 GLN Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 287 MET Chi-restraints excluded: chain J residue 358 LEU Chi-restraints excluded: chain J residue 389 LEU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 300 THR Chi-restraints excluded: chain K residue 342 LYS Chi-restraints excluded: chain L residue 9 LYS Chi-restraints excluded: chain L residue 45 MET Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 99 ARG Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 293 GLU Chi-restraints excluded: chain L residue 335 GLU Chi-restraints excluded: chain L residue 342 LYS Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 156 THR Chi-restraints excluded: chain M residue 227 LEU Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain M residue 413 MET Chi-restraints excluded: chain M residue 420 PHE Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 26 ASN Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 124 SER Chi-restraints excluded: chain N residue 203 ILE Chi-restraints excluded: chain N residue 349 LEU Chi-restraints excluded: chain N residue 380 ILE Chi-restraints excluded: chain N residue 417 VAL Chi-restraints excluded: chain N residue 448 MET Chi-restraints excluded: chain N residue 481 HIS Chi-restraints excluded: chain N residue 520 GLU Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain N residue 580 VAL Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 28 HIS Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 258 TYR Chi-restraints excluded: chain O residue 288 ILE Chi-restraints excluded: chain O residue 317 THR Chi-restraints excluded: chain O residue 396 LEU Chi-restraints excluded: chain O residue 443 GLN Chi-restraints excluded: chain O residue 472 THR Chi-restraints excluded: chain O residue 473 VAL Chi-restraints excluded: chain O residue 478 GLU Chi-restraints excluded: chain O residue 520 GLU Chi-restraints excluded: chain O residue 539 ASN Chi-restraints excluded: chain O residue 544 GLN Chi-restraints excluded: chain P residue 12 ILE Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 110 VAL Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 176 LEU Chi-restraints excluded: chain P residue 574 SER Chi-restraints excluded: chain P residue 597 VAL Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 283 ASN Chi-restraints excluded: chain Q residue 425 LYS Chi-restraints excluded: chain Q residue 473 VAL Chi-restraints excluded: chain Q residue 483 LEU Chi-restraints excluded: chain Q residue 558 LEU Chi-restraints excluded: chain Q residue 584 ILE Chi-restraints excluded: chain R residue 14 TYR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 456 MET Chi-restraints excluded: chain R residue 469 SER Chi-restraints excluded: chain R residue 476 LEU Chi-restraints excluded: chain R residue 524 THR Chi-restraints excluded: chain R residue 531 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 474 optimal weight: 1.9990 chunk 306 optimal weight: 0.6980 chunk 458 optimal weight: 0.4980 chunk 231 optimal weight: 0.9980 chunk 150 optimal weight: 0.6980 chunk 148 optimal weight: 0.8980 chunk 487 optimal weight: 6.9990 chunk 522 optimal weight: 3.9990 chunk 379 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 603 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 8 ASN J 218 HIS K 24 GLN K 77 ASN ** M 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 26 ASN ** N 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 429 ASN N 531 ASN N 560 GLN ** O 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 383 GLN ** O 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 586 GLN Q 297 ASN R 221 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 65426 Z= 0.139 Angle : 0.532 16.131 88551 Z= 0.267 Chirality : 0.041 0.174 9656 Planarity : 0.004 0.064 11363 Dihedral : 8.562 148.881 9413 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.54 % Favored : 95.45 % Rotamer: Outliers : 1.77 % Allowed : 17.35 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.09), residues: 7933 helix: 0.89 (0.10), residues: 3032 sheet: 0.37 (0.18), residues: 960 loop : -1.67 (0.09), residues: 3941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 49 HIS 0.008 0.001 HIS O 480 PHE 0.018 0.001 PHE O 576 TYR 0.038 0.001 TYR F 312 ARG 0.011 0.000 ARG Q 468 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1440 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 1322 time to evaluate : 5.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 SER cc_start: 0.8396 (m) cc_final: 0.8109 (t) REVERT: A 74 ASP cc_start: 0.6715 (m-30) cc_final: 0.6479 (m-30) REVERT: A 293 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7340 (tm-30) REVERT: A 316 ARG cc_start: 0.6528 (mtt-85) cc_final: 0.6239 (mtt-85) REVERT: A 335 GLU cc_start: 0.7235 (pp20) cc_final: 0.6987 (pp20) REVERT: A 338 GLU cc_start: 0.6083 (mp0) cc_final: 0.5684 (mp0) REVERT: B 72 GLN cc_start: 0.7375 (tp40) cc_final: 0.6902 (tm-30) REVERT: B 88 GLU cc_start: 0.6968 (mt-10) cc_final: 0.6686 (mt-10) REVERT: B 97 LYS cc_start: 0.8269 (ttmm) cc_final: 0.8050 (ttmm) REVERT: B 128 GLU cc_start: 0.7228 (tm-30) cc_final: 0.6914 (tm-30) REVERT: B 132 GLU cc_start: 0.8243 (mm-30) cc_final: 0.8008 (mm-30) REVERT: B 242 GLU cc_start: 0.7859 (tt0) cc_final: 0.7516 (tt0) REVERT: C 106 GLU cc_start: 0.7471 (tp30) cc_final: 0.7168 (tp30) REVERT: C 352 GLU cc_start: 0.6807 (mp0) cc_final: 0.6277 (mp0) REVERT: C 353 LYS cc_start: 0.7316 (mtmm) cc_final: 0.7022 (mtmm) REVERT: D 50 LYS cc_start: 0.7939 (mmmt) cc_final: 0.7655 (ttmm) REVERT: D 97 LYS cc_start: 0.8543 (ttmm) cc_final: 0.8321 (ttmm) REVERT: D 107 GLU cc_start: 0.7457 (tm-30) cc_final: 0.7156 (tt0) REVERT: D 110 LYS cc_start: 0.8264 (mttp) cc_final: 0.7943 (mttp) REVERT: D 118 GLU cc_start: 0.7933 (tp30) cc_final: 0.7581 (tp30) REVERT: D 197 TYR cc_start: 0.8304 (m-10) cc_final: 0.7767 (m-80) REVERT: D 363 PHE cc_start: 0.7920 (m-80) cc_final: 0.7630 (m-80) REVERT: E 54 GLN cc_start: 0.8420 (tm-30) cc_final: 0.8150 (tm-30) REVERT: E 250 ASP cc_start: 0.7535 (m-30) cc_final: 0.7237 (m-30) REVERT: E 342 LYS cc_start: 0.7539 (tttm) cc_final: 0.7242 (tttm) REVERT: E 382 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6785 (pm20) REVERT: F 296 SER cc_start: 0.8885 (m) cc_final: 0.8651 (m) REVERT: G 43 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8000 (ptmt) REVERT: G 55 ASN cc_start: 0.7598 (m-40) cc_final: 0.7349 (m110) REVERT: G 110 LYS cc_start: 0.7852 (mppt) cc_final: 0.7509 (tppt) REVERT: G 142 LYS cc_start: 0.7845 (ttpp) cc_final: 0.7468 (ttpp) REVERT: G 178 GLU cc_start: 0.6729 (tt0) cc_final: 0.5779 (mt-10) REVERT: G 250 ASP cc_start: 0.7996 (t0) cc_final: 0.7709 (t0) REVERT: G 303 PHE cc_start: 0.6679 (m-10) cc_final: 0.6430 (m-10) REVERT: G 316 ARG cc_start: 0.7232 (mtm110) cc_final: 0.7032 (mtm110) REVERT: G 342 LYS cc_start: 0.6706 (tptp) cc_final: 0.6439 (tptp) REVERT: H 72 GLN cc_start: 0.6791 (pp30) cc_final: 0.6547 (pp30) REVERT: H 110 LYS cc_start: 0.8387 (mmmm) cc_final: 0.8084 (mtpp) REVERT: H 159 GLN cc_start: 0.8586 (mt0) cc_final: 0.8328 (mt0) REVERT: H 205 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.7301 (m-80) REVERT: H 364 ASN cc_start: 0.7662 (t0) cc_final: 0.7430 (t0) REVERT: I 74 ASP cc_start: 0.7795 (m-30) cc_final: 0.7502 (t0) REVERT: I 128 GLU cc_start: 0.7658 (tp30) cc_final: 0.7360 (tp30) REVERT: I 300 THR cc_start: 0.8536 (m) cc_final: 0.8192 (p) REVERT: J 46 LYS cc_start: 0.8109 (mtpp) cc_final: 0.7860 (mtpp) REVERT: J 54 GLN cc_start: 0.8013 (tt0) cc_final: 0.7805 (tt0) REVERT: J 108 PHE cc_start: 0.8399 (m-80) cc_final: 0.8121 (m-80) REVERT: J 116 TYR cc_start: 0.6842 (OUTLIER) cc_final: 0.6504 (m-80) REVERT: J 126 THR cc_start: 0.8709 (m) cc_final: 0.8478 (p) REVERT: J 142 LYS cc_start: 0.7637 (tppt) cc_final: 0.7295 (tttp) REVERT: J 189 SER cc_start: 0.8335 (p) cc_final: 0.8066 (m) REVERT: J 316 ARG cc_start: 0.8361 (mmm160) cc_final: 0.8087 (mmm160) REVERT: K 9 LYS cc_start: 0.8390 (mmmt) cc_final: 0.8117 (mmtt) REVERT: K 76 ASP cc_start: 0.7014 (m-30) cc_final: 0.6589 (m-30) REVERT: K 106 GLU cc_start: 0.7602 (pm20) cc_final: 0.7216 (pm20) REVERT: K 128 GLU cc_start: 0.7023 (tm-30) cc_final: 0.6756 (tm-30) REVERT: K 129 GLN cc_start: 0.8265 (mm-40) cc_final: 0.8064 (mt0) REVERT: K 286 GLU cc_start: 0.6064 (mm-30) cc_final: 0.5393 (mm-30) REVERT: K 353 LYS cc_start: 0.7784 (mptt) cc_final: 0.7573 (mptt) REVERT: K 361 MET cc_start: 0.7608 (mtm) cc_final: 0.7292 (pmm) REVERT: L 50 LYS cc_start: 0.8204 (mttm) cc_final: 0.7853 (mttm) REVERT: L 51 SER cc_start: 0.8164 (m) cc_final: 0.7902 (m) REVERT: L 88 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.6974 (mp0) REVERT: L 99 ARG cc_start: 0.6819 (OUTLIER) cc_final: 0.5741 (ttp-170) REVERT: L 104 GLU cc_start: 0.6748 (tt0) cc_final: 0.6393 (tt0) REVERT: L 118 GLU cc_start: 0.7714 (tp30) cc_final: 0.7391 (tp30) REVERT: L 227 HIS cc_start: 0.7041 (m90) cc_final: 0.6777 (m90) REVERT: L 323 LEU cc_start: 0.7821 (mt) cc_final: 0.7459 (mt) REVERT: M 59 ILE cc_start: 0.7253 (pt) cc_final: 0.6995 (mt) REVERT: M 149 GLU cc_start: 0.7047 (pp20) cc_final: 0.6657 (mt-10) REVERT: M 157 LYS cc_start: 0.7582 (mttm) cc_final: 0.7203 (mmtt) REVERT: M 254 LYS cc_start: 0.8102 (tppp) cc_final: 0.7697 (tppp) REVERT: M 294 LYS cc_start: 0.7855 (tmtt) cc_final: 0.7612 (tmtt) REVERT: M 352 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7253 (mm-30) REVERT: M 444 ASP cc_start: 0.6744 (t0) cc_final: 0.6517 (t0) REVERT: M 468 ARG cc_start: 0.6729 (ttm110) cc_final: 0.6528 (ttm110) REVERT: N 114 GLU cc_start: 0.7049 (tt0) cc_final: 0.6752 (tt0) REVERT: N 268 LYS cc_start: 0.8260 (mtpt) cc_final: 0.8009 (mtpt) REVERT: N 309 LEU cc_start: 0.8183 (mt) cc_final: 0.7752 (tt) REVERT: N 343 PHE cc_start: 0.7801 (t80) cc_final: 0.7493 (t80) REVERT: N 352 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7326 (mm-30) REVERT: N 353 PHE cc_start: 0.6822 (m-80) cc_final: 0.6590 (m-80) REVERT: N 380 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8134 (mp) REVERT: O 64 ARG cc_start: 0.6826 (ptp-110) cc_final: 0.5936 (ptt180) REVERT: O 268 LYS cc_start: 0.7943 (mtmt) cc_final: 0.7570 (mtpp) REVERT: O 327 ASP cc_start: 0.7230 (t0) cc_final: 0.6752 (t0) REVERT: O 380 ILE cc_start: 0.8197 (tp) cc_final: 0.7933 (tp) REVERT: O 416 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6853 (tm-30) REVERT: O 424 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7557 (mm-30) REVERT: O 448 MET cc_start: 0.6784 (tpt) cc_final: 0.6337 (tpt) REVERT: P 176 LEU cc_start: 0.5735 (OUTLIER) cc_final: 0.4736 (mt) REVERT: P 183 LYS cc_start: 0.7825 (mmmm) cc_final: 0.6794 (mtpp) REVERT: P 246 TYR cc_start: 0.7644 (t80) cc_final: 0.7355 (t80) REVERT: P 379 LYS cc_start: 0.7864 (ptpt) cc_final: 0.7579 (ptpp) REVERT: P 441 LEU cc_start: 0.7895 (tp) cc_final: 0.7632 (tp) REVERT: P 459 GLU cc_start: 0.7679 (tp30) cc_final: 0.7125 (tp30) REVERT: P 495 LYS cc_start: 0.7124 (OUTLIER) cc_final: 0.6762 (mtpt) REVERT: P 508 LYS cc_start: 0.7715 (mttp) cc_final: 0.7155 (mmtp) REVERT: P 586 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8259 (tm-30) REVERT: Q 50 ASP cc_start: 0.7446 (t0) cc_final: 0.6835 (t0) REVERT: Q 64 ARG cc_start: 0.7230 (tpt-90) cc_final: 0.7026 (tpt-90) REVERT: Q 146 LYS cc_start: 0.7908 (mppt) cc_final: 0.7638 (mppt) REVERT: Q 160 LYS cc_start: 0.6947 (mmtm) cc_final: 0.6563 (mppt) REVERT: Q 211 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7189 (mm-30) REVERT: Q 448 MET cc_start: 0.6954 (mmp) cc_final: 0.6631 (mmp) REVERT: Q 455 GLU cc_start: 0.7602 (pt0) cc_final: 0.6786 (pt0) REVERT: Q 516 GLN cc_start: 0.7276 (pp30) cc_final: 0.6970 (pp30) REVERT: Q 520 GLU cc_start: 0.6870 (mp0) cc_final: 0.6142 (mp0) REVERT: Q 541 ARG cc_start: 0.7471 (mtm-85) cc_final: 0.7181 (mtm-85) REVERT: Q 592 LYS cc_start: 0.7833 (mmmt) cc_final: 0.7529 (mmmt) REVERT: R 22 ARG cc_start: 0.6465 (mtt90) cc_final: 0.6006 (mtt90) REVERT: R 105 GLU cc_start: 0.6446 (pm20) cc_final: 0.6003 (pp20) REVERT: R 382 GLN cc_start: 0.7540 (pp30) cc_final: 0.7027 (pp30) REVERT: R 416 GLU cc_start: -0.0337 (OUTLIER) cc_final: -0.2024 (mp0) REVERT: R 473 VAL cc_start: 0.7232 (t) cc_final: 0.6959 (p) REVERT: R 540 GLU cc_start: 0.6885 (tp30) cc_final: 0.6292 (tp30) outliers start: 118 outliers final: 83 residues processed: 1378 average time/residue: 0.6315 time to fit residues: 1435.2720 Evaluate side-chains 1385 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 1291 time to evaluate : 5.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 405 ASN Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 129 GLN Chi-restraints excluded: chain H residue 205 PHE Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain I residue 266 GLN Chi-restraints excluded: chain J residue 116 TYR Chi-restraints excluded: chain J residue 234 GLN Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 358 LEU Chi-restraints excluded: chain J residue 389 LEU Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 300 THR Chi-restraints excluded: chain K residue 342 LYS Chi-restraints excluded: chain L residue 9 LYS Chi-restraints excluded: chain L residue 45 MET Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 99 ARG Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 269 ILE Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain M residue 413 MET Chi-restraints excluded: chain M residue 420 PHE Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 26 ASN Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 124 SER Chi-restraints excluded: chain N residue 203 ILE Chi-restraints excluded: chain N residue 301 GLU Chi-restraints excluded: chain N residue 349 LEU Chi-restraints excluded: chain N residue 380 ILE Chi-restraints excluded: chain N residue 414 SER Chi-restraints excluded: chain N residue 429 ASN Chi-restraints excluded: chain N residue 544 GLN Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 258 TYR Chi-restraints excluded: chain O residue 288 ILE Chi-restraints excluded: chain O residue 317 THR Chi-restraints excluded: chain O residue 411 LYS Chi-restraints excluded: chain O residue 441 LEU Chi-restraints excluded: chain O residue 443 GLN Chi-restraints excluded: chain O residue 472 THR Chi-restraints excluded: chain O residue 473 VAL Chi-restraints excluded: chain O residue 478 GLU Chi-restraints excluded: chain O residue 520 GLU Chi-restraints excluded: chain O residue 544 GLN Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 176 LEU Chi-restraints excluded: chain P residue 495 LYS Chi-restraints excluded: chain P residue 574 SER Chi-restraints excluded: chain P residue 586 GLN Chi-restraints excluded: chain P residue 597 VAL Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 193 LYS Chi-restraints excluded: chain Q residue 297 ASN Chi-restraints excluded: chain Q residue 425 LYS Chi-restraints excluded: chain Q residue 449 LEU Chi-restraints excluded: chain Q residue 584 ILE Chi-restraints excluded: chain R residue 14 TYR Chi-restraints excluded: chain R residue 416 GLU Chi-restraints excluded: chain R residue 456 MET Chi-restraints excluded: chain R residue 469 SER Chi-restraints excluded: chain R residue 476 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 697 optimal weight: 0.5980 chunk 735 optimal weight: 0.6980 chunk 670 optimal weight: 10.0000 chunk 714 optimal weight: 0.0000 chunk 734 optimal weight: 0.0570 chunk 430 optimal weight: 0.8980 chunk 311 optimal weight: 2.9990 chunk 561 optimal weight: 0.0030 chunk 219 optimal weight: 6.9990 chunk 646 optimal weight: 3.9990 chunk 676 optimal weight: 1.9990 overall best weight: 0.2712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN C 8 ASN G 227 HIS J 78 ASN J 218 HIS J 278 HIS K 77 ASN N 26 ASN N 277 GLN N 560 GLN ** O 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 383 GLN ** O 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 187 ASN Q 221 ASN Q 297 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 65426 Z= 0.131 Angle : 0.526 15.982 88551 Z= 0.263 Chirality : 0.040 0.165 9656 Planarity : 0.003 0.061 11363 Dihedral : 8.323 143.141 9413 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.63 % Favored : 95.36 % Rotamer: Outliers : 1.47 % Allowed : 17.91 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.10), residues: 7933 helix: 0.99 (0.10), residues: 3037 sheet: 0.49 (0.18), residues: 960 loop : -1.57 (0.09), residues: 3936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 49 HIS 0.008 0.000 HIS O 480 PHE 0.018 0.001 PHE O 576 TYR 0.036 0.001 TYR O 246 ARG 0.009 0.000 ARG H 289 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1408 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 1310 time to evaluate : 5.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 SER cc_start: 0.8371 (m) cc_final: 0.8103 (t) REVERT: A 74 ASP cc_start: 0.6709 (m-30) cc_final: 0.6487 (m-30) REVERT: A 293 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7329 (tm-30) REVERT: A 335 GLU cc_start: 0.7204 (pp20) cc_final: 0.6948 (pp20) REVERT: A 338 GLU cc_start: 0.6247 (mp0) cc_final: 0.5733 (mp0) REVERT: B 12 GLU cc_start: 0.7404 (mp0) cc_final: 0.6938 (mp0) REVERT: B 72 GLN cc_start: 0.7293 (tp40) cc_final: 0.6817 (tm-30) REVERT: B 88 GLU cc_start: 0.6942 (mt-10) cc_final: 0.6709 (mt-10) REVERT: B 128 GLU cc_start: 0.7225 (tm-30) cc_final: 0.6914 (tm-30) REVERT: B 242 GLU cc_start: 0.7846 (tt0) cc_final: 0.7266 (tt0) REVERT: C 106 GLU cc_start: 0.7475 (tp30) cc_final: 0.7155 (tp30) REVERT: C 353 LYS cc_start: 0.7321 (mtmm) cc_final: 0.7000 (mtmm) REVERT: D 50 LYS cc_start: 0.7935 (mmmt) cc_final: 0.7642 (ttmm) REVERT: D 97 LYS cc_start: 0.8560 (ttmm) cc_final: 0.8336 (ttmm) REVERT: D 106 GLU cc_start: 0.7490 (pp20) cc_final: 0.6852 (pp20) REVERT: D 107 GLU cc_start: 0.7429 (tm-30) cc_final: 0.6787 (tm-30) REVERT: D 110 LYS cc_start: 0.8257 (mttp) cc_final: 0.7929 (mttp) REVERT: D 197 TYR cc_start: 0.8330 (m-10) cc_final: 0.7770 (m-80) REVERT: D 335 GLU cc_start: 0.7553 (pm20) cc_final: 0.7255 (pm20) REVERT: D 363 PHE cc_start: 0.7891 (m-80) cc_final: 0.7573 (m-80) REVERT: E 54 GLN cc_start: 0.8411 (tm-30) cc_final: 0.8150 (tm-30) REVERT: E 250 ASP cc_start: 0.7495 (m-30) cc_final: 0.7200 (m-30) REVERT: E 338 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7670 (tm-30) REVERT: E 342 LYS cc_start: 0.7547 (tttm) cc_final: 0.7265 (tttm) REVERT: E 382 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6643 (pm20) REVERT: F 55 ASN cc_start: 0.8027 (m-40) cc_final: 0.7465 (m110) REVERT: G 43 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.7966 (ptmt) REVERT: G 45 MET cc_start: 0.6835 (mpp) cc_final: 0.5660 (mmm) REVERT: G 55 ASN cc_start: 0.7510 (m-40) cc_final: 0.7269 (m110) REVERT: G 110 LYS cc_start: 0.7843 (mppt) cc_final: 0.7502 (tppt) REVERT: G 142 LYS cc_start: 0.7816 (ttpp) cc_final: 0.7436 (ttpp) REVERT: G 178 GLU cc_start: 0.6660 (tt0) cc_final: 0.5643 (mt-10) REVERT: G 250 ASP cc_start: 0.8000 (t0) cc_final: 0.7703 (t0) REVERT: G 303 PHE cc_start: 0.6675 (m-10) cc_final: 0.6463 (m-10) REVERT: H 72 GLN cc_start: 0.6773 (pp30) cc_final: 0.6528 (pp30) REVERT: H 110 LYS cc_start: 0.8354 (mmmm) cc_final: 0.8051 (mtpp) REVERT: H 159 GLN cc_start: 0.8589 (mt0) cc_final: 0.8345 (mt0) REVERT: H 205 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.7338 (m-10) REVERT: H 364 ASN cc_start: 0.7665 (t0) cc_final: 0.7424 (t0) REVERT: I 74 ASP cc_start: 0.7770 (m-30) cc_final: 0.7472 (t0) REVERT: I 182 ILE cc_start: 0.7791 (pt) cc_final: 0.7454 (mt) REVERT: I 300 THR cc_start: 0.8535 (m) cc_final: 0.8230 (p) REVERT: J 54 GLN cc_start: 0.8069 (tt0) cc_final: 0.7865 (tt0) REVERT: J 100 ARG cc_start: 0.6697 (mtp85) cc_final: 0.6404 (mtp85) REVERT: J 108 PHE cc_start: 0.8356 (m-80) cc_final: 0.8062 (m-80) REVERT: J 116 TYR cc_start: 0.6805 (OUTLIER) cc_final: 0.6524 (m-80) REVERT: J 142 LYS cc_start: 0.7474 (tppt) cc_final: 0.7188 (tttp) REVERT: J 316 ARG cc_start: 0.8375 (mmm160) cc_final: 0.8081 (mmm160) REVERT: K 9 LYS cc_start: 0.8540 (mmmt) cc_final: 0.8264 (mmtt) REVERT: K 76 ASP cc_start: 0.7041 (m-30) cc_final: 0.6620 (m-30) REVERT: K 106 GLU cc_start: 0.7623 (pm20) cc_final: 0.7089 (pm20) REVERT: K 128 GLU cc_start: 0.6996 (tm-30) cc_final: 0.6750 (tm-30) REVERT: K 353 LYS cc_start: 0.7786 (mptt) cc_final: 0.7567 (mptt) REVERT: K 361 MET cc_start: 0.7526 (mtm) cc_final: 0.7249 (pmm) REVERT: L 50 LYS cc_start: 0.8186 (mttm) cc_final: 0.7844 (mttm) REVERT: L 51 SER cc_start: 0.8153 (m) cc_final: 0.7893 (m) REVERT: L 88 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7018 (mp0) REVERT: L 93 LEU cc_start: 0.8311 (tp) cc_final: 0.8081 (tt) REVERT: L 104 GLU cc_start: 0.6728 (tt0) cc_final: 0.6371 (tt0) REVERT: L 118 GLU cc_start: 0.7712 (tp30) cc_final: 0.7394 (tp30) REVERT: L 227 HIS cc_start: 0.7029 (m90) cc_final: 0.6765 (m90) REVERT: M 59 ILE cc_start: 0.7265 (pt) cc_final: 0.7010 (mt) REVERT: M 149 GLU cc_start: 0.6977 (pp20) cc_final: 0.6617 (mt-10) REVERT: M 157 LYS cc_start: 0.7523 (mttm) cc_final: 0.7255 (mmtt) REVERT: M 181 TYR cc_start: 0.4098 (m-10) cc_final: 0.3827 (m-10) REVERT: M 254 LYS cc_start: 0.8063 (tppp) cc_final: 0.7647 (tppp) REVERT: M 294 LYS cc_start: 0.7833 (tmtt) cc_final: 0.7571 (tmtt) REVERT: M 352 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7251 (mm-30) REVERT: M 444 ASP cc_start: 0.6698 (t0) cc_final: 0.6481 (t0) REVERT: M 457 PHE cc_start: 0.7136 (t80) cc_final: 0.6912 (t80) REVERT: M 468 ARG cc_start: 0.6616 (ttm110) cc_final: 0.6409 (ttm110) REVERT: N 114 GLU cc_start: 0.7055 (tt0) cc_final: 0.6760 (tt0) REVERT: N 268 LYS cc_start: 0.8259 (mtpt) cc_final: 0.7999 (mtpt) REVERT: N 302 LYS cc_start: 0.4554 (mttp) cc_final: 0.3365 (mttt) REVERT: N 309 LEU cc_start: 0.8181 (mt) cc_final: 0.7794 (tt) REVERT: N 350 VAL cc_start: 0.8558 (p) cc_final: 0.8336 (m) REVERT: N 352 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7215 (mm-30) REVERT: N 353 PHE cc_start: 0.6772 (m-80) cc_final: 0.6556 (m-80) REVERT: N 380 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8139 (mp) REVERT: N 506 LYS cc_start: 0.8324 (tptp) cc_final: 0.8105 (tppt) REVERT: O 64 ARG cc_start: 0.6788 (ptp-110) cc_final: 0.5900 (ptt180) REVERT: O 229 GLU cc_start: 0.6574 (pp20) cc_final: 0.6167 (pp20) REVERT: O 268 LYS cc_start: 0.7941 (mtmt) cc_final: 0.7564 (mtpp) REVERT: O 327 ASP cc_start: 0.7291 (t0) cc_final: 0.6818 (t0) REVERT: O 380 ILE cc_start: 0.8096 (tp) cc_final: 0.7831 (tp) REVERT: O 416 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6838 (tm-30) REVERT: O 424 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7535 (mm-30) REVERT: O 448 MET cc_start: 0.6857 (tpt) cc_final: 0.6257 (tpt) REVERT: P 19 GLU cc_start: 0.6587 (mp0) cc_final: 0.6274 (mp0) REVERT: P 134 ASN cc_start: 0.8210 (t0) cc_final: 0.7942 (t0) REVERT: P 176 LEU cc_start: 0.5680 (OUTLIER) cc_final: 0.4709 (mt) REVERT: P 183 LYS cc_start: 0.7745 (mmmm) cc_final: 0.7203 (mmmm) REVERT: P 246 TYR cc_start: 0.7585 (t80) cc_final: 0.7365 (t80) REVERT: P 255 LYS cc_start: 0.5498 (tttp) cc_final: 0.5281 (tptt) REVERT: P 441 LEU cc_start: 0.7870 (tp) cc_final: 0.7615 (tp) REVERT: P 459 GLU cc_start: 0.7666 (tp30) cc_final: 0.7126 (tp30) REVERT: P 495 LYS cc_start: 0.7097 (OUTLIER) cc_final: 0.6800 (mtpt) REVERT: P 508 LYS cc_start: 0.7711 (mttp) cc_final: 0.7256 (mmtp) REVERT: P 586 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8245 (tm-30) REVERT: Q 50 ASP cc_start: 0.7438 (t0) cc_final: 0.6819 (t0) REVERT: Q 64 ARG cc_start: 0.7245 (tpt-90) cc_final: 0.7025 (tpt-90) REVERT: Q 146 LYS cc_start: 0.7845 (mppt) cc_final: 0.7587 (mppt) REVERT: Q 160 LYS cc_start: 0.6899 (mmtm) cc_final: 0.6512 (mppt) REVERT: Q 211 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7181 (mm-30) REVERT: Q 444 ASP cc_start: 0.7869 (m-30) cc_final: 0.7587 (m-30) REVERT: Q 448 MET cc_start: 0.7000 (mmp) cc_final: 0.6689 (mmp) REVERT: Q 455 GLU cc_start: 0.7562 (pt0) cc_final: 0.6826 (pt0) REVERT: Q 516 GLN cc_start: 0.7239 (pp30) cc_final: 0.6955 (pp30) REVERT: Q 520 GLU cc_start: 0.6840 (mp0) cc_final: 0.6087 (mp0) REVERT: Q 541 ARG cc_start: 0.7425 (mtm-85) cc_final: 0.7131 (mtm-85) REVERT: Q 547 ARG cc_start: 0.7836 (ptp-170) cc_final: 0.7606 (ptm160) REVERT: Q 592 LYS cc_start: 0.7850 (mmmt) cc_final: 0.7540 (mmmt) REVERT: R 22 ARG cc_start: 0.6449 (mtt90) cc_final: 0.5997 (mtt90) REVERT: R 105 GLU cc_start: 0.6444 (pm20) cc_final: 0.5994 (pp20) REVERT: R 205 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7381 (mp) REVERT: R 382 GLN cc_start: 0.7465 (pp30) cc_final: 0.6976 (pp30) REVERT: R 416 GLU cc_start: -0.0384 (OUTLIER) cc_final: -0.2107 (mp0) REVERT: R 473 VAL cc_start: 0.7228 (t) cc_final: 0.6967 (p) REVERT: R 540 GLU cc_start: 0.6878 (tp30) cc_final: 0.6292 (tp30) outliers start: 98 outliers final: 72 residues processed: 1358 average time/residue: 0.6428 time to fit residues: 1442.2196 Evaluate side-chains 1368 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 1285 time to evaluate : 5.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 405 ASN Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 129 GLN Chi-restraints excluded: chain H residue 205 PHE Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain I residue 240 VAL Chi-restraints excluded: chain I residue 266 GLN Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain J residue 116 TYR Chi-restraints excluded: chain J residue 234 GLN Chi-restraints excluded: chain J residue 358 LEU Chi-restraints excluded: chain J residue 389 LEU Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 300 THR Chi-restraints excluded: chain L residue 45 MET Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 269 ILE Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain M residue 420 PHE Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 26 ASN Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 124 SER Chi-restraints excluded: chain N residue 203 ILE Chi-restraints excluded: chain N residue 348 THR Chi-restraints excluded: chain N residue 349 LEU Chi-restraints excluded: chain N residue 380 ILE Chi-restraints excluded: chain N residue 544 GLN Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 258 TYR Chi-restraints excluded: chain O residue 288 ILE Chi-restraints excluded: chain O residue 441 LEU Chi-restraints excluded: chain O residue 443 GLN Chi-restraints excluded: chain O residue 472 THR Chi-restraints excluded: chain O residue 473 VAL Chi-restraints excluded: chain O residue 478 GLU Chi-restraints excluded: chain O residue 544 GLN Chi-restraints excluded: chain P residue 176 LEU Chi-restraints excluded: chain P residue 495 LYS Chi-restraints excluded: chain P residue 574 SER Chi-restraints excluded: chain P residue 586 GLN Chi-restraints excluded: chain P residue 597 VAL Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 193 LYS Chi-restraints excluded: chain Q residue 425 LYS Chi-restraints excluded: chain Q residue 449 LEU Chi-restraints excluded: chain Q residue 584 ILE Chi-restraints excluded: chain R residue 14 TYR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 416 GLU Chi-restraints excluded: chain R residue 456 MET Chi-restraints excluded: chain R residue 469 SER Chi-restraints excluded: chain R residue 476 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 712 optimal weight: 4.9990 chunk 469 optimal weight: 5.9990 chunk 756 optimal weight: 6.9990 chunk 461 optimal weight: 0.7980 chunk 358 optimal weight: 2.9990 chunk 525 optimal weight: 0.9990 chunk 793 optimal weight: 0.0980 chunk 729 optimal weight: 5.9990 chunk 631 optimal weight: 3.9990 chunk 65 optimal weight: 0.0970 chunk 487 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN C 24 GLN K 77 ASN N 26 ASN ** N 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 560 GLN O 32 GLN ** O 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 383 GLN ** O 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 586 GLN Q 187 ASN Q 297 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 65426 Z= 0.182 Angle : 0.555 16.211 88551 Z= 0.278 Chirality : 0.041 0.221 9656 Planarity : 0.004 0.064 11363 Dihedral : 8.354 141.351 9413 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.31 % Favored : 94.68 % Rotamer: Outliers : 1.47 % Allowed : 18.21 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -0.48 (0.09), residues: 7933 helix: 0.97 (0.10), residues: 3015 sheet: 0.41 (0.17), residues: 979 loop : -1.59 (0.09), residues: 3939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 49 HIS 0.007 0.001 HIS O 480 PHE 0.016 0.001 PHE O 576 TYR 0.034 0.001 TYR F 312 ARG 0.011 0.000 ARG G 316 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15866 Ramachandran restraints generated. 7933 Oldfield, 0 Emsley, 7933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1418 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 1320 time to evaluate : 5.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 SER cc_start: 0.8367 (m) cc_final: 0.8105 (t) REVERT: A 74 ASP cc_start: 0.6731 (m-30) cc_final: 0.6504 (m-30) REVERT: A 131 ARG cc_start: 0.8196 (ptm-80) cc_final: 0.7877 (ptm-80) REVERT: A 293 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7347 (tm-30) REVERT: A 335 GLU cc_start: 0.7215 (pp20) cc_final: 0.6943 (pp20) REVERT: A 338 GLU cc_start: 0.6118 (mp0) cc_final: 0.5655 (mp0) REVERT: B 12 GLU cc_start: 0.7426 (mp0) cc_final: 0.6977 (mp0) REVERT: B 72 GLN cc_start: 0.7368 (tp40) cc_final: 0.6880 (tm-30) REVERT: B 88 GLU cc_start: 0.6986 (mt-10) cc_final: 0.6702 (mt-10) REVERT: B 128 GLU cc_start: 0.7247 (tm-30) cc_final: 0.6933 (tm-30) REVERT: B 242 GLU cc_start: 0.7874 (tt0) cc_final: 0.7147 (tt0) REVERT: C 106 GLU cc_start: 0.7517 (tp30) cc_final: 0.7216 (tp30) REVERT: C 130 PHE cc_start: 0.8037 (t80) cc_final: 0.7690 (t80) REVERT: D 50 LYS cc_start: 0.7956 (mmmt) cc_final: 0.7645 (ttmm) REVERT: D 97 LYS cc_start: 0.8527 (ttmm) cc_final: 0.8302 (ttmm) REVERT: D 107 GLU cc_start: 0.7452 (tm-30) cc_final: 0.6818 (tm-30) REVERT: D 110 LYS cc_start: 0.8268 (mttp) cc_final: 0.7940 (mttp) REVERT: D 197 TYR cc_start: 0.8299 (m-10) cc_final: 0.7742 (m-80) REVERT: D 335 GLU cc_start: 0.7678 (pm20) cc_final: 0.7444 (pm20) REVERT: D 363 PHE cc_start: 0.7911 (m-80) cc_final: 0.7612 (m-80) REVERT: E 54 GLN cc_start: 0.8425 (tm-30) cc_final: 0.8156 (tm-30) REVERT: E 250 ASP cc_start: 0.7526 (m-30) cc_final: 0.7228 (m-30) REVERT: E 338 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7673 (tm-30) REVERT: E 342 LYS cc_start: 0.7574 (tttm) cc_final: 0.7305 (tttm) REVERT: E 382 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6722 (pm20) REVERT: G 43 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8096 (ptmt) REVERT: G 45 MET cc_start: 0.6823 (mpp) cc_final: 0.5496 (mmt) REVERT: G 55 ASN cc_start: 0.7519 (m-40) cc_final: 0.7264 (m110) REVERT: G 110 LYS cc_start: 0.7903 (mppt) cc_final: 0.7565 (tppt) REVERT: G 142 LYS cc_start: 0.7834 (ttpp) cc_final: 0.7459 (ttpp) REVERT: G 178 GLU cc_start: 0.6833 (tt0) cc_final: 0.5829 (mt-10) REVERT: G 250 ASP cc_start: 0.8014 (t0) cc_final: 0.7668 (t0) REVERT: G 303 PHE cc_start: 0.6686 (m-10) cc_final: 0.6485 (m-10) REVERT: H 72 GLN cc_start: 0.6798 (pp30) cc_final: 0.6550 (pp30) REVERT: H 110 LYS cc_start: 0.8355 (mmmm) cc_final: 0.8052 (mtpp) REVERT: H 159 GLN cc_start: 0.8597 (mt0) cc_final: 0.8342 (mt0) REVERT: H 205 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.7262 (m-80) REVERT: H 364 ASN cc_start: 0.7664 (t0) cc_final: 0.7428 (t0) REVERT: I 74 ASP cc_start: 0.7791 (m-30) cc_final: 0.7524 (t0) REVERT: I 182 ILE cc_start: 0.7736 (pt) cc_final: 0.7463 (mt) REVERT: I 266 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8025 (mp10) REVERT: I 300 THR cc_start: 0.8591 (m) cc_final: 0.8244 (p) REVERT: J 43 LYS cc_start: 0.7678 (mmmm) cc_final: 0.7423 (mmmt) REVERT: J 54 GLN cc_start: 0.8121 (tt0) cc_final: 0.7903 (tt0) REVERT: J 108 PHE cc_start: 0.8400 (m-80) cc_final: 0.8117 (m-80) REVERT: J 116 TYR cc_start: 0.6822 (OUTLIER) cc_final: 0.6570 (m-80) REVERT: J 142 LYS cc_start: 0.7589 (tppt) cc_final: 0.7279 (tttp) REVERT: J 189 SER cc_start: 0.8366 (p) cc_final: 0.8068 (m) REVERT: J 287 MET cc_start: 0.7186 (OUTLIER) cc_final: 0.6323 (mtt) REVERT: J 316 ARG cc_start: 0.8378 (mmm160) cc_final: 0.8083 (mmm160) REVERT: K 76 ASP cc_start: 0.7010 (m-30) cc_final: 0.6606 (m-30) REVERT: K 106 GLU cc_start: 0.7685 (pm20) cc_final: 0.7280 (pm20) REVERT: K 128 GLU cc_start: 0.7043 (tm-30) cc_final: 0.6792 (tm-30) REVERT: K 353 LYS cc_start: 0.7798 (mptt) cc_final: 0.7574 (mptt) REVERT: K 361 MET cc_start: 0.7562 (mtm) cc_final: 0.7284 (pmm) REVERT: L 50 LYS cc_start: 0.8207 (mttm) cc_final: 0.7852 (mttm) REVERT: L 51 SER cc_start: 0.8165 (m) cc_final: 0.7902 (m) REVERT: L 88 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6980 (mp0) REVERT: L 93 LEU cc_start: 0.8388 (tp) cc_final: 0.8138 (tt) REVERT: L 104 GLU cc_start: 0.6741 (tt0) cc_final: 0.6377 (tt0) REVERT: L 118 GLU cc_start: 0.7711 (tp30) cc_final: 0.7394 (tp30) REVERT: L 227 HIS cc_start: 0.7076 (m90) cc_final: 0.6792 (m90) REVERT: M 59 ILE cc_start: 0.7325 (pt) cc_final: 0.7052 (mt) REVERT: M 149 GLU cc_start: 0.7013 (pp20) cc_final: 0.6705 (mt-10) REVERT: M 157 LYS cc_start: 0.7543 (mttm) cc_final: 0.7142 (mmtt) REVERT: M 254 LYS cc_start: 0.8089 (tppp) cc_final: 0.7663 (tppp) REVERT: M 294 LYS cc_start: 0.7889 (tmtt) cc_final: 0.7623 (tmtt) REVERT: M 352 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7311 (mm-30) REVERT: M 444 ASP cc_start: 0.6732 (t0) cc_final: 0.6521 (t0) REVERT: N 114 GLU cc_start: 0.7076 (tt0) cc_final: 0.6781 (tt0) REVERT: N 193 LYS cc_start: 0.8216 (ttmm) cc_final: 0.7901 (ttmm) REVERT: N 268 LYS cc_start: 0.8301 (mtpt) cc_final: 0.8067 (mtpt) REVERT: N 309 LEU cc_start: 0.8194 (mt) cc_final: 0.7788 (tt) REVERT: N 350 VAL cc_start: 0.8597 (p) cc_final: 0.8385 (m) REVERT: N 352 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7193 (mm-30) REVERT: N 353 PHE cc_start: 0.6787 (m-80) cc_final: 0.6567 (m-80) REVERT: N 380 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8202 (mp) REVERT: N 506 LYS cc_start: 0.8340 (tptp) cc_final: 0.8111 (tppt) REVERT: O 229 GLU cc_start: 0.6594 (pp20) cc_final: 0.6197 (pp20) REVERT: O 268 LYS cc_start: 0.7973 (mtmt) cc_final: 0.7595 (mtpp) REVERT: O 327 ASP cc_start: 0.7295 (t0) cc_final: 0.6826 (t0) REVERT: O 380 ILE cc_start: 0.8118 (tp) cc_final: 0.7852 (tp) REVERT: O 416 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6842 (tm-30) REVERT: O 424 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7588 (mm-30) REVERT: O 448 MET cc_start: 0.6901 (tpt) cc_final: 0.6310 (tpt) REVERT: O 506 LYS cc_start: 0.6006 (ttmm) cc_final: 0.5768 (mtpp) REVERT: P 19 GLU cc_start: 0.6622 (mp0) cc_final: 0.6327 (mp0) REVERT: P 176 LEU cc_start: 0.5857 (OUTLIER) cc_final: 0.4871 (mt) REVERT: P 183 LYS cc_start: 0.7826 (mmmm) cc_final: 0.7288 (mmmm) REVERT: P 246 TYR cc_start: 0.7564 (t80) cc_final: 0.7238 (t80) REVERT: P 255 LYS cc_start: 0.5617 (tttp) cc_final: 0.5359 (tptt) REVERT: P 441 LEU cc_start: 0.7842 (tp) cc_final: 0.7584 (tp) REVERT: P 459 GLU cc_start: 0.7673 (tp30) cc_final: 0.7143 (tp30) REVERT: P 495 LYS cc_start: 0.7157 (OUTLIER) cc_final: 0.6817 (mtpt) REVERT: P 508 LYS cc_start: 0.7775 (mttp) cc_final: 0.7310 (mmtp) REVERT: P 586 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8018 (tm-30) REVERT: Q 64 ARG cc_start: 0.7259 (tpt-90) cc_final: 0.7019 (tpt-90) REVERT: Q 146 LYS cc_start: 0.7901 (mppt) cc_final: 0.7634 (mppt) REVERT: Q 160 LYS cc_start: 0.6896 (mmtm) cc_final: 0.6499 (mppt) REVERT: Q 448 MET cc_start: 0.7049 (mmp) cc_final: 0.6729 (mmp) REVERT: Q 455 GLU cc_start: 0.7568 (pt0) cc_final: 0.6912 (pt0) REVERT: Q 516 GLN cc_start: 0.7253 (pp30) cc_final: 0.6958 (pp30) REVERT: Q 520 GLU cc_start: 0.6883 (mp0) cc_final: 0.6133 (mp0) REVERT: Q 541 ARG cc_start: 0.7452 (mtm-85) cc_final: 0.7187 (mtm-85) REVERT: Q 592 LYS cc_start: 0.7857 (mmmt) cc_final: 0.7546 (mmmt) REVERT: R 22 ARG cc_start: 0.6471 (mtt90) cc_final: 0.6006 (mtt90) REVERT: R 105 GLU cc_start: 0.6462 (pm20) cc_final: 0.5524 (tp30) REVERT: R 146 LYS cc_start: 0.5510 (tptp) cc_final: 0.5242 (tptt) REVERT: R 205 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7447 (mp) REVERT: R 382 GLN cc_start: 0.7470 (pp30) cc_final: 0.7001 (pp30) REVERT: R 416 GLU cc_start: -0.0354 (OUTLIER) cc_final: -0.2083 (mp0) REVERT: R 473 VAL cc_start: 0.7242 (t) cc_final: 0.6973 (p) REVERT: R 540 GLU cc_start: 0.6872 (tp30) cc_final: 0.6311 (tp30) outliers start: 98 outliers final: 80 residues processed: 1364 average time/residue: 0.6240 time to fit residues: 1405.4639 Evaluate side-chains 1392 residues out of total 6848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 1299 time to evaluate : 5.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 405 ASN Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 129 GLN Chi-restraints excluded: chain H residue 205 PHE Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 240 VAL Chi-restraints excluded: chain I residue 266 GLN Chi-restraints excluded: chain I residue 283 VAL Chi-restraints excluded: chain J residue 116 TYR Chi-restraints excluded: chain J residue 234 GLN Chi-restraints excluded: chain J residue 287 MET Chi-restraints excluded: chain J residue 358 LEU Chi-restraints excluded: chain J residue 389 LEU Chi-restraints excluded: chain K residue 152 ILE Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 300 THR Chi-restraints excluded: chain L residue 45 MET Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 269 ILE Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain M residue 420 PHE Chi-restraints excluded: chain M residue 538 THR Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 26 ASN Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 124 SER Chi-restraints excluded: chain N residue 203 ILE Chi-restraints excluded: chain N residue 348 THR Chi-restraints excluded: chain N residue 349 LEU Chi-restraints excluded: chain N residue 380 ILE Chi-restraints excluded: chain N residue 414 SER Chi-restraints excluded: chain N residue 498 GLU Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 32 GLN Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 150 LEU Chi-restraints excluded: chain O residue 258 TYR Chi-restraints excluded: chain O residue 288 ILE Chi-restraints excluded: chain O residue 317 THR Chi-restraints excluded: chain O residue 441 LEU Chi-restraints excluded: chain O residue 443 GLN Chi-restraints excluded: chain O residue 472 THR Chi-restraints excluded: chain O residue 473 VAL Chi-restraints excluded: chain O residue 478 GLU Chi-restraints excluded: chain O residue 544 GLN Chi-restraints excluded: chain P residue 176 LEU Chi-restraints excluded: chain P residue 495 LYS Chi-restraints excluded: chain P residue 574 SER Chi-restraints excluded: chain P residue 586 GLN Chi-restraints excluded: chain P residue 597 VAL Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 297 ASN Chi-restraints excluded: chain Q residue 425 LYS Chi-restraints excluded: chain Q residue 449 LEU Chi-restraints excluded: chain Q residue 582 ILE Chi-restraints excluded: chain Q residue 584 ILE Chi-restraints excluded: chain R residue 14 TYR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 256 ILE Chi-restraints excluded: chain R residue 416 GLU Chi-restraints excluded: chain R residue 456 MET Chi-restraints excluded: chain R residue 469 SER Chi-restraints excluded: chain R residue 476 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 387 optimal weight: 0.8980 chunk 501 optimal weight: 10.0000 chunk 672 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 582 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 632 optimal weight: 0.2980 chunk 264 optimal weight: 0.9990 chunk 649 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 8 ASN J 274 ASN K 77 ASN K 129 GLN N 26 ASN ** N 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 560 GLN O 32 GLN ** O 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 383 GLN ** O 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 586 GLN Q 187 ASN Q 297 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.177618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.142743 restraints weight = 94850.864| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 3.00 r_work: 0.3657 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 65426 Z= 0.164 Angle : 0.551 16.233 88551 Z= 0.276 Chirality : 0.041 0.213 9656 Planarity : 0.004 0.063 11363 Dihedral : 8.297 140.311 9413 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.98 % Favored : 95.01 % Rotamer: Outliers : 1.59 % Allowed : 18.29 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: -0.46 (0.09), residues: 7933 helix: 0.97 (0.10), residues: 3022 sheet: 0.53 (0.18), residues: 939 loop : -1.58 (0.09), residues: 3972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 49 HIS 0.007 0.001 HIS O 480 PHE 0.024 0.001 PHE M 457 TYR 0.035 0.001 TYR F 312 ARG 0.010 0.000 ARG G 316 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20276.74 seconds wall clock time: 351 minutes 45.53 seconds (21105.53 seconds total)