Starting phenix.real_space_refine on Fri Jan 19 13:23:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uaf_42062/01_2024/8uaf_42062_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uaf_42062/01_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uaf_42062/01_2024/8uaf_42062.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uaf_42062/01_2024/8uaf_42062.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uaf_42062/01_2024/8uaf_42062_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uaf_42062/01_2024/8uaf_42062_neut_updated.pdb" } 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 Residue "C TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 315": "NH1" <-> "NH2" Residue "O PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 24.42, per 1000 atoms: 0.38 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.87 Conformation dependent library (CDL) restraints added in 8.7 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... running ksdssp... Secondary structure from input PDB file: 340 helices and 55 sheets defined 38.5% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.17 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 Processing helix chain 'A' and resid 34 through 37 removed outlier: 3.546A pdb=" N SER A 37 " --> pdb=" O ALA A 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 34 through 37' Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 59 through 64 removed outlier: 3.626A pdb=" N LEU A 63 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 64 " --> pdb=" O GLY A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 83 through 99 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 103 through 121 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) Processing helix chain 'A' and resid 127 through 131 removed outlier: 4.396A pdb=" N ARG A 131 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 153 removed outlier: 3.633A pdb=" N LYS A 142 " --> pdb=" O ASP A 139 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N TYR A 143 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU A 146 " --> pdb=" O TYR A 143 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 147 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 153 " --> pdb=" O LYS A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 180 Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 245 through 251 Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.803A pdb=" N ILE A 317 " --> pdb=" O HIS A 313 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LEU A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 345 Processing helix chain 'A' and resid 350 through 359 Processing helix chain 'A' and resid 372 through 375 removed outlier: 3.627A pdb=" N ALA A 375 " --> pdb=" O GLY A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 372 through 375' Processing helix chain 'A' and resid 377 through 383 removed outlier: 3.571A pdb=" N HIS A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 405 Processing helix chain 'B' and resid 12 through 24 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) removed outlier: 3.945A pdb=" N GLN B 24 " --> pdb=" O TYR B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 37 removed outlier: 3.603A pdb=" N SER B 37 " --> pdb=" O ALA B 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 34 through 37' Processing helix chain 'B' and resid 45 through 55 removed outlier: 3.893A pdb=" N TRP B 49 " --> pdb=" O MET B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 65 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 72 through 77 removed outlier: 3.621A pdb=" N ASP B 76 " --> pdb=" O GLN B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 99 removed outlier: 3.707A pdb=" N ARG B 99 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 123 removed outlier: 4.732A pdb=" N GLU B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) 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) removed outlier: 3.889A pdb=" N ALA B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 131 removed outlier: 4.349A pdb=" N ARG B 131 " --> pdb=" O GLU B 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 131' Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 139 through 153 removed outlier: 3.960A pdb=" N LYS B 142 " --> pdb=" O ASP B 139 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TYR B 143 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER B 153 " --> pdb=" O LYS B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 180 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 245 through 251 Processing helix chain 'B' and resid 253 through 258 Processing helix chain 'B' and resid 275 through 277 No H-bonds generated for 'chain 'B' and resid 275 through 277' Processing helix chain 'B' and resid 283 through 294 Processing helix chain 'B' and resid 312 through 323 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) removed outlier: 3.968A pdb=" N LEU B 322 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LEU B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 344 Processing helix chain 'B' and resid 350 through 359 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 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 377 through 383 Processing helix chain 'C' and resid 12 through 24 removed outlier: 3.906A pdb=" N GLN C 24 " --> pdb=" O TYR C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 40 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) Processing helix chain 'C' and resid 45 through 55 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 58 through 65 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 73 through 77 Processing helix chain 'C' and resid 83 through 99 Processing helix chain 'C' and resid 102 through 123 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 127 through 130 Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 142 through 153 removed outlier: 3.830A pdb=" N GLU C 146 " --> pdb=" O LYS C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 180 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 202 removed outlier: 3.862A pdb=" N PHE C 201 " --> pdb=" O PRO C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 251 Processing helix chain 'C' and resid 254 through 258 Processing helix chain 'C' and resid 280 through 294 removed outlier: 3.677A pdb=" N TYR C 284 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 323 removed outlier: 3.721A pdb=" N LEU C 322 " --> pdb=" O ILE C 318 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 345 Processing helix chain 'C' and resid 350 through 359 Processing helix chain 'C' and resid 377 through 382 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) No H-bonds generated for 'chain 'C' and resid 377 through 382' Processing helix chain 'C' and resid 396 through 406 Processing helix chain 'D' and resid 12 through 24 removed outlier: 3.545A pdb=" N CYS D 23 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN D 24 " --> pdb=" O TYR D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 40 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 45 through 54 Processing helix chain 'D' and resid 58 through 64 removed outlier: 4.126A pdb=" N ALA D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 76 Processing helix chain 'D' and resid 82 through 99 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 102 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 135 through 137 No H-bonds generated for 'chain 'D' and resid 135 through 137' Processing helix chain 'D' and resid 142 through 153 Processing helix chain 'D' and resid 172 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 200 through 202 No H-bonds generated for 'chain 'D' and resid 200 through 202' Processing helix chain 'D' and resid 245 through 252 Processing helix chain 'D' and resid 254 through 258 Processing helix chain 'D' and resid 283 through 296 removed outlier: 3.638A pdb=" N SER D 296 " --> pdb=" O GLY D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 323 removed outlier: 4.465A pdb=" N LEU D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 344 Processing helix chain 'D' and resid 350 through 359 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) Processing helix chain 'D' and resid 372 through 375 Processing helix chain 'D' and resid 377 through 383 Processing helix chain 'E' and resid 12 through 24 removed outlier: 4.177A pdb=" N GLN E 24 " --> pdb=" O TYR E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 37 removed outlier: 4.026A pdb=" N SER E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 34 through 37' Processing helix chain 'E' and resid 45 through 55 Processing helix chain 'E' and resid 58 through 63 removed outlier: 3.842A pdb=" N ALA E 62 " --> pdb=" O GLU E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 77 removed outlier: 3.879A pdb=" N ASP E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 98 removed outlier: 4.321A pdb=" N ILE E 86 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP E 87 " --> pdb=" O LEU E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 122 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 139 through 154 removed outlier: 3.523A pdb=" N LYS E 142 " --> pdb=" O ASP E 139 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N TYR E 143 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS E 144 " --> pdb=" O PHE E 141 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS E 145 " --> pdb=" O LYS E 142 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER E 153 " --> pdb=" O LYS E 150 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN E 154 " --> pdb=" O LEU E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 180 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) Processing helix chain 'E' and resid 245 through 251 Processing helix chain 'E' and resid 253 through 258 Processing helix chain 'E' and resid 281 through 295 removed outlier: 3.801A pdb=" N GLU E 286 " --> pdb=" O PHE E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 321 Processing helix chain 'E' and resid 336 through 345 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 350 through 359 Processing helix chain 'E' and resid 372 through 375 Processing helix chain 'E' and resid 377 through 383 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) Processing helix chain 'E' and resid 396 through 405 removed outlier: 3.639A pdb=" N GLU E 401 " --> pdb=" O ASP E 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 22 Processing helix chain 'F' and resid 38 through 40 No H-bonds generated for 'chain 'F' and resid 38 through 40' Processing helix chain 'F' and resid 45 through 55 Processing helix chain 'F' and resid 57 through 65 Processing helix chain 'F' and resid 72 through 77 Processing helix chain 'F' and resid 82 through 98 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 104 through 122 removed outlier: 4.283A pdb=" N ALA F 122 " --> pdb=" O GLU F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 131 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) No H-bonds generated for 'chain 'F' and resid 127 through 131' Processing helix chain 'F' and resid 143 through 153 Processing helix chain 'F' and resid 172 through 178 Processing helix chain 'F' and resid 245 through 251 Processing helix chain 'F' and resid 253 through 257 Processing helix chain 'F' and resid 283 through 296 removed outlier: 3.603A pdb=" N ILE F 295 " --> pdb=" O PHE F 291 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER F 296 " --> pdb=" O GLY F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 323 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) removed outlier: 4.648A pdb=" N LEU F 323 " --> pdb=" O LEU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 344 removed outlier: 4.244A pdb=" N LYS F 342 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL F 343 " --> pdb=" O ALA F 339 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER F 344 " --> pdb=" O ILE F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 359 removed outlier: 3.569A pdb=" N LYS F 353 " --> pdb=" O GLU F 350 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA F 354 " --> pdb=" O ALA F 351 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ILE F 355 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 383 Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.691A pdb=" N TYR G 20 " --> pdb=" O ARG G 16 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN G 24 " --> pdb=" O TYR G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 36 No H-bonds generated for 'chain 'G' and resid 34 through 36' Processing helix chain 'G' and resid 38 through 40 No H-bonds generated for 'chain 'G' and resid 38 through 40' Processing helix chain 'G' and resid 45 through 53 Processing helix chain 'G' and resid 61 through 65 removed outlier: 3.954A pdb=" N ASP G 65 " --> pdb=" O ALA G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 77 Processing helix chain 'G' and resid 82 through 98 removed outlier: 3.781A pdb=" N ILE G 86 " --> pdb=" O VAL G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 123 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) removed outlier: 3.889A pdb=" N ARG G 109 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LYS G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE G 111 " --> pdb=" O GLU G 107 " (cutoff:3.500A) 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 127 through 129 No H-bonds generated for 'chain 'G' and resid 127 through 129' Processing helix chain 'G' and resid 144 through 152 Processing helix chain 'G' and resid 173 through 180 Processing helix chain 'G' and resid 198 through 202 removed outlier: 4.287A pdb=" N PHE G 201 " --> pdb=" O PRO G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 251 Processing helix chain 'G' and resid 253 through 257 removed outlier: 3.601A pdb=" N ILE G 257 " --> pdb=" O ILE G 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 253 through 257' Processing helix chain 'G' and resid 278 through 294 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) Processing helix chain 'G' and resid 313 through 323 removed outlier: 4.687A pdb=" N LEU G 323 " --> pdb=" O LEU G 319 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 344 Processing helix chain 'G' and resid 350 through 360 removed outlier: 3.763A pdb=" N LEU G 358 " --> pdb=" O ALA G 354 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS G 359 " --> pdb=" O ILE G 355 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASN G 360 " --> pdb=" O VAL G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 378 through 383 Processing helix chain 'G' and resid 396 through 405 Processing helix chain 'H' and resid 12 through 24 removed outlier: 3.683A pdb=" N GLN H 24 " --> pdb=" O TYR H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 37 No H-bonds generated for 'chain 'H' and resid 35 through 37' Processing helix chain 'H' and resid 45 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 57 through 64 Processing helix chain 'H' and resid 74 through 77 No H-bonds generated for 'chain 'H' and resid 74 through 77' Processing helix chain 'H' and resid 82 through 99 Processing helix chain 'H' and resid 103 through 114 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) Processing helix chain 'H' and resid 117 through 120 No H-bonds generated for 'chain 'H' and resid 117 through 120' Processing helix chain 'H' and resid 139 through 154 removed outlier: 3.836A pdb=" N LYS H 142 " --> pdb=" O ASP H 139 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N TYR H 143 " --> pdb=" O ALA H 140 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER H 153 " --> pdb=" O LYS H 150 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN H 154 " --> pdb=" O LEU H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 180 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 245 through 251 Processing helix chain 'H' and resid 254 through 258 Processing helix chain 'H' and resid 283 through 296 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) removed outlier: 3.998A pdb=" N SER H 296 " --> pdb=" O GLY H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 312 through 323 removed outlier: 3.557A pdb=" N LEU H 322 " --> pdb=" O ILE H 318 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LEU H 323 " --> pdb=" O LEU H 319 " (cutoff:3.500A) Processing helix chain 'H' and resid 336 through 344 removed outlier: 3.509A pdb=" N ILE H 340 " --> pdb=" O LEU H 336 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 359 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) Processing helix chain 'H' and resid 373 through 375 No H-bonds generated for 'chain 'H' and resid 373 through 375' Processing helix chain 'H' and resid 377 through 383 removed outlier: 3.536A pdb=" N HIS H 383 " --> pdb=" O SER H 379 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 22 removed outlier: 3.725A pdb=" N SER I 17 " --> pdb=" O ASP I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 55 removed outlier: 3.529A pdb=" N PHE I 52 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS I 53 " --> pdb=" O TRP I 49 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLN I 54 " --> pdb=" O LYS I 50 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASN I 55 " --> pdb=" O SER I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 65 Processing helix chain 'I' and resid 72 through 77 Processing helix chain 'I' and resid 83 through 99 removed outlier: 3.537A pdb=" N SER I 94 " --> pdb=" O THR I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 124 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) removed outlier: 4.460A pdb=" N LEU I 124 " --> pdb=" O THR I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 131 removed outlier: 3.971A pdb=" N ARG I 131 " --> pdb=" O GLU I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 154 removed outlier: 3.650A pdb=" N LYS I 142 " --> pdb=" O ASP I 139 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N TYR I 143 " --> pdb=" O ALA I 140 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS I 144 " --> pdb=" O PHE I 141 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER I 153 " --> pdb=" O LYS I 150 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN I 154 " --> pdb=" O LEU I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 180 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 245 through 251 Processing helix chain 'I' and resid 253 through 258 Processing helix chain 'I' and resid 278 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 312 through 323 removed outlier: 3.634A pdb=" N ALA I 321 " --> pdb=" O ILE I 317 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU I 322 " --> pdb=" O ILE I 318 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LEU I 323 " --> pdb=" O LEU I 319 " (cutoff:3.500A) Processing helix chain 'I' and resid 336 through 345 Processing helix chain 'I' and resid 350 through 357 Processing helix chain 'I' and resid 377 through 383 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) No H-bonds generated for 'chain 'I' and resid 377 through 383' Processing helix chain 'I' and resid 397 through 405 Processing helix chain 'J' and resid 12 through 24 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) removed outlier: 4.337A pdb=" N GLN J 24 " --> pdb=" O TYR J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 40 No H-bonds generated for 'chain 'J' and resid 38 through 40' Processing helix chain 'J' and resid 45 through 55 Processing helix chain 'J' and resid 57 through 60 No H-bonds generated for 'chain 'J' and resid 57 through 60' Processing helix chain 'J' and resid 73 through 77 Processing helix chain 'J' and resid 82 through 99 Processing helix chain 'J' and resid 102 through 123 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) Processing helix chain 'J' and resid 127 through 131 removed outlier: 3.893A pdb=" N ARG J 131 " --> pdb=" O GLU J 128 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 137 No H-bonds generated for 'chain 'J' and resid 135 through 137' Processing helix chain 'J' and resid 139 through 153 removed outlier: 4.814A pdb=" N TYR J 143 " --> pdb=" O ALA J 140 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N HIS J 144 " --> pdb=" O PHE J 141 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS J 145 " --> pdb=" O LYS J 142 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER J 153 " --> pdb=" O LYS J 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 174 through 180 Processing helix chain 'J' and resid 198 through 201 removed outlier: 3.796A pdb=" N PHE J 201 " --> pdb=" O PRO J 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 198 through 201' Processing helix chain 'J' and resid 245 through 251 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 253 through 257 Processing helix chain 'J' and resid 283 through 296 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) removed outlier: 3.574A pdb=" N SER J 296 " --> pdb=" O GLY J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 312 through 323 removed outlier: 3.584A pdb=" N LEU J 322 " --> pdb=" O ILE J 318 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N LEU J 323 " --> pdb=" O LEU J 319 " (cutoff:3.500A) Processing helix chain 'J' and resid 336 through 345 Processing helix chain 'J' and resid 350 through 359 Processing helix chain 'J' and resid 372 through 375 Processing helix chain 'J' and resid 377 through 383 Processing helix chain 'K' and resid 12 through 24 removed outlier: 4.081A pdb=" N GLN K 24 " --> pdb=" O TYR K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 40 removed outlier: 4.506A pdb=" N GLY K 39 " --> pdb=" O ALA K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 55 Processing helix chain 'K' and resid 58 through 65 removed outlier: 3.882A pdb=" N GLY K 61 " --> pdb=" O GLU K 58 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA K 62 " --> pdb=" O LEU K 59 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU K 63 " --> pdb=" O LEU K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 77 Processing helix chain 'K' and resid 82 through 99 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 102 through 123 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) removed outlier: 4.427A pdb=" N ALA K 122 " --> pdb=" O GLU K 118 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA K 123 " --> pdb=" O VAL K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 131 removed outlier: 4.184A pdb=" N ARG K 131 " --> pdb=" O GLU K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 153 removed outlier: 4.188A pdb=" N GLU K 146 " --> pdb=" O LYS K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 180 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 245 through 251 Processing helix chain 'K' and resid 253 through 257 Processing helix chain 'K' and resid 281 through 296 removed outlier: 3.518A pdb=" N GLY K 292 " --> pdb=" O PHE K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 313 through 323 removed outlier: 4.028A pdb=" N LEU K 322 " --> pdb=" O ILE K 318 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU K 323 " --> pdb=" O LEU K 319 " (cutoff:3.500A) Processing helix chain 'K' and resid 336 through 345 removed outlier: 3.694A pdb=" N LYS K 345 " --> pdb=" O THR K 341 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 360 Processing helix chain 'K' and resid 372 through 375 removed outlier: 3.659A pdb=" N ALA K 375 " --> pdb=" O GLY K 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 372 through 375' Processing helix chain 'K' and resid 377 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 405 Processing helix chain 'L' and resid 12 through 23 Processing helix chain 'L' and resid 38 through 40 No H-bonds generated for 'chain 'L' and resid 38 through 40' Processing helix chain 'L' and resid 45 through 55 Processing helix chain 'L' and resid 57 through 65 Processing helix chain 'L' and resid 72 through 76 removed outlier: 3.843A pdb=" N ASP L 76 " --> pdb=" O GLN L 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 72 through 76' Processing helix chain 'L' and resid 82 through 98 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 123 removed outlier: 4.001A pdb=" N GLU L 106 " --> pdb=" O ASP L 103 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU L 107 " --> pdb=" O GLU L 104 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N PHE L 108 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 131 removed outlier: 4.208A pdb=" N ARG L 131 " --> pdb=" O GLU L 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 128 through 131' Processing helix chain 'L' and resid 139 through 141 No H-bonds generated for 'chain 'L' and resid 139 through 141' Processing helix chain 'L' and resid 144 through 154 removed outlier: 3.718A pdb=" N ASN L 154 " --> pdb=" O LYS L 150 " (cutoff:3.500A) Processing helix chain 'L' and resid 173 through 180 Processing helix chain 'L' and resid 198 through 201 removed outlier: 3.525A pdb=" N PHE L 201 " --> pdb=" O PRO L 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 198 through 201' Processing helix chain 'L' and resid 245 through 251 Processing helix chain 'L' and resid 253 through 257 Processing helix chain 'L' and resid 282 through 295 Processing helix chain 'L' and resid 312 through 323 removed outlier: 3.928A pdb=" N LEU L 322 " --> pdb=" O ILE L 318 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LEU L 323 " --> pdb=" O LEU L 319 " (cutoff:3.500A) Processing helix chain 'L' and resid 336 through 344 Processing helix chain 'L' and resid 350 through 360 Processing helix chain 'L' and resid 372 through 375 Processing helix chain 'L' and resid 377 through 383 Processing helix chain 'M' and resid 130 through 136 removed outlier: 3.515A pdb=" N ILE M 135 " --> pdb=" O ASP M 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 144 No H-bonds generated for 'chain 'M' and resid 141 through 144' Processing helix chain 'M' and resid 165 through 168 No H-bonds generated for 'chain 'M' and resid 165 through 168' Processing helix chain 'M' and resid 184 through 197 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 211 through 213 No H-bonds generated for 'chain 'M' and resid 211 through 213' Processing helix chain 'M' and resid 258 through 261 removed outlier: 3.761A pdb=" N LEU M 261 " --> pdb=" O TYR M 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 258 through 261' Processing helix chain 'M' and resid 263 through 270 removed outlier: 3.860A pdb=" N ILE M 267 " --> pdb=" O PHE M 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 277 through 287 Processing helix chain 'M' and resid 322 through 329 Processing helix chain 'M' and resid 343 through 355 removed outlier: 3.519A pdb=" N LEU M 346 " --> pdb=" O PHE M 343 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS M 355 " --> pdb=" O GLU M 352 " (cutoff:3.500A) Processing helix chain 'M' and resid 368 through 372 Processing helix chain 'M' and resid 375 through 384 Processing helix chain 'M' and resid 408 through 421 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 446 through 464 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 479 through 481 No H-bonds generated for 'chain 'M' and resid 479 through 481' Processing helix chain 'M' and resid 523 through 527 Processing helix chain 'M' and resid 544 through 549 Processing helix chain 'M' and resid 559 through 563 removed outlier: 3.981A pdb=" N SER M 562 " --> pdb=" O LYS M 559 " (cutoff:3.500A) Processing helix chain 'M' and resid 598 through 602 Processing helix chain 'N' and resid 31 through 33 No H-bonds generated for 'chain 'N' and resid 31 through 33' Processing helix chain 'N' and resid 130 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 144 through 146 No H-bonds generated for 'chain 'N' and resid 144 through 146' Processing helix chain 'N' and resid 165 through 168 No H-bonds generated for 'chain 'N' and resid 165 through 168' Processing helix chain 'N' and resid 183 through 197 removed outlier: 3.604A pdb=" N LYS N 197 " --> pdb=" O LYS N 193 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 270 removed outlier: 3.619A pdb=" N LEU N 261 " --> pdb=" O TYR N 258 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY N 262 " --> pdb=" O GLN N 259 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE N 263 " --> pdb=" O ALA N 260 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ALA N 264 " --> pdb=" O LEU N 261 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY N 265 " --> pdb=" O GLY N 262 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU N 266 " --> pdb=" O PHE N 263 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS N 268 " --> pdb=" O GLY N 265 " (cutoff:3.500A) Processing helix chain 'N' and resid 278 through 290 removed outlier: 3.807A pdb=" N ASN N 283 " --> pdb=" O PRO N 279 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE N 288 " --> pdb=" O ALA N 284 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASN N 289 " --> pdb=" O LEU N 285 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ARG N 290 " --> pdb=" O SER N 286 " (cutoff:3.500A) Processing helix chain 'N' and resid 320 through 331 removed outlier: 4.244A pdb=" N ALA N 323 " --> pdb=" O SER N 320 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLU N 324 " --> pdb=" O LYS N 321 " (cutoff:3.500A) Processing helix chain 'N' and resid 343 through 355 removed outlier: 3.545A pdb=" N LEU N 349 " --> pdb=" O LEU N 346 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL N 350 " --> pdb=" O ALA N 347 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS N 355 " --> pdb=" O GLU N 352 " (cutoff:3.500A) Processing helix chain 'N' and resid 375 through 385 Processing helix chain 'N' and resid 388 through 391 No H-bonds generated for 'chain 'N' and resid 388 through 391' Processing helix chain 'N' and resid 408 through 421 removed outlier: 3.681A pdb=" N GLU N 416 " --> pdb=" O ALA N 412 " (cutoff:3.500A) Processing helix chain 'N' and resid 443 through 464 removed outlier: 3.644A pdb=" N ALA N 446 " --> pdb=" O GLN N 443 " (cutoff:3.500A) Proline residue: N 447 - end of helix Processing helix chain 'N' and resid 479 through 481 No H-bonds generated for 'chain 'N' and resid 479 through 481' Processing helix chain 'N' and resid 499 through 502 No H-bonds generated for 'chain 'N' and resid 499 through 502' Processing helix chain 'N' and resid 518 through 520 No H-bonds generated for 'chain 'N' and resid 518 through 520' Processing helix chain 'N' and resid 523 through 528 Processing helix chain 'N' and resid 540 through 548 Processing helix chain 'N' and resid 558 through 563 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) Processing helix chain 'O' and resid 130 through 136 Processing helix chain 'O' and resid 144 through 146 No H-bonds generated for 'chain 'O' and resid 144 through 146' Processing helix chain 'O' and resid 165 through 168 No H-bonds generated for 'chain 'O' and resid 165 through 168' Processing helix chain 'O' and resid 183 through 197 Processing helix chain 'O' and resid 213 through 216 Processing helix chain 'O' and resid 262 through 270 Processing helix chain 'O' and resid 277 through 286 Processing helix chain 'O' and resid 323 through 331 Processing helix chain 'O' and resid 343 through 354 removed outlier: 3.544A pdb=" N LEU O 346 " --> pdb=" O PHE O 343 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR O 348 " --> pdb=" O SER O 345 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE O 353 " --> pdb=" O VAL O 350 " (cutoff:3.500A) Processing helix chain 'O' and resid 368 through 384 Proline residue: O 376 - end of helix Processing helix chain 'O' and resid 410 through 420 removed outlier: 3.794A pdb=" N PHE O 420 " --> pdb=" O GLU O 416 " (cutoff:3.500A) Processing helix chain 'O' and resid 446 through 464 removed outlier: 3.727A pdb=" N SER O 451 " --> pdb=" O PRO O 447 " (cutoff:3.500A) Processing helix chain 'O' and resid 479 through 481 No H-bonds generated for 'chain 'O' and resid 479 through 481' Processing helix chain 'O' and resid 496 through 506 removed outlier: 3.543A pdb=" N LEU O 500 " --> pdb=" O ALA O 496 " (cutoff:3.500A) Processing helix chain 'O' and resid 523 through 528 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 523 through 528' Processing helix chain 'O' and resid 540 through 549 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 555 through 557 No H-bonds generated for 'chain 'O' and resid 555 through 557' Processing helix chain 'O' and resid 561 through 563 No H-bonds generated for 'chain 'O' and resid 561 through 563' Processing helix chain 'O' and resid 598 through 602 Processing helix chain 'P' and resid 130 through 137 Processing helix chain 'P' and resid 142 through 146 Proline residue: P 145 - end of helix No H-bonds generated for 'chain 'P' and resid 142 through 146' Processing helix chain 'P' and resid 166 through 169 No H-bonds generated for 'chain 'P' and resid 166 through 169' Processing helix chain 'P' and resid 183 through 197 Processing helix chain 'P' and resid 214 through 216 No H-bonds generated for 'chain 'P' and resid 214 through 216' Processing helix chain 'P' and resid 265 through 268 No H-bonds generated for 'chain 'P' and resid 265 through 268' Processing helix chain 'P' and resid 277 through 288 removed outlier: 3.502A pdb=" N ALA P 287 " --> pdb=" O ASN P 283 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE P 288 " --> pdb=" O ALA P 284 " (cutoff:3.500A) Processing helix chain 'P' and resid 343 through 353 removed outlier: 3.700A pdb=" N LEU P 346 " --> pdb=" O PHE P 343 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE P 353 " --> pdb=" O VAL P 350 " (cutoff:3.500A) Processing helix chain 'P' and resid 375 through 386 removed outlier: 3.665A pdb=" N LYS P 379 " --> pdb=" O PRO P 376 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE P 380 " --> pdb=" O LEU P 377 " (cutoff:3.500A) Processing helix chain 'P' and resid 390 through 392 No H-bonds generated for 'chain 'P' and resid 390 through 392' Processing helix chain 'P' and resid 408 through 417 Processing helix chain 'P' and resid 446 through 464 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) Processing helix chain 'P' and resid 498 through 503 Processing helix chain 'P' and resid 518 through 520 No H-bonds generated for 'chain 'P' and resid 518 through 520' Processing helix chain 'P' and resid 523 through 526 No H-bonds generated for 'chain 'P' and resid 523 through 526' Processing helix chain 'P' and resid 540 through 549 removed outlier: 3.790A pdb=" N ALA P 549 " --> pdb=" O ALA P 545 " (cutoff:3.500A) Processing helix chain 'P' and resid 556 through 563 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) removed outlier: 3.844A pdb=" N GLY P 563 " --> pdb=" O LYS P 559 " (cutoff:3.500A) Processing helix chain 'P' and resid 600 through 602 No H-bonds generated for 'chain 'P' and resid 600 through 602' Processing helix chain 'Q' and resid 130 through 136 Processing helix chain 'Q' and resid 141 through 144 removed outlier: 3.868A pdb=" N LEU Q 144 " --> pdb=" O LYS Q 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 141 through 144' Processing helix chain 'Q' and resid 165 through 169 Processing helix chain 'Q' and resid 183 through 197 Processing helix chain 'Q' and resid 214 through 216 No H-bonds generated for 'chain 'Q' and resid 214 through 216' Processing helix chain 'Q' and resid 263 through 269 Processing helix chain 'Q' and resid 278 through 287 removed outlier: 3.567A pdb=" N ALA Q 287 " --> pdb=" O ASN Q 283 " (cutoff:3.500A) Processing helix chain 'Q' and resid 322 through 331 Processing helix chain 'Q' and resid 343 through 353 removed outlier: 3.526A pdb=" N LEU Q 346 " --> pdb=" O PHE Q 343 " (cutoff:3.500A) Processing helix chain 'Q' and resid 368 through 384 removed outlier: 4.118A pdb=" N ASN Q 373 " --> pdb=" O PHE Q 369 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N VAL Q 374 " --> pdb=" O GLY Q 370 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU Q 375 " --> pdb=" O PHE Q 371 " (cutoff:3.500A) Proline residue: Q 376 - end of helix Processing helix chain 'Q' and resid 388 through 391 No H-bonds generated for 'chain 'Q' and resid 388 through 391' Processing helix chain 'Q' and resid 408 through 420 removed outlier: 3.611A pdb=" N GLU Q 416 " --> pdb=" O ALA Q 412 " (cutoff:3.500A) Processing helix chain 'Q' and resid 443 through 464 Proline residue: Q 447 - end of helix removed outlier: 3.784A pdb=" N ARG Q 463 " --> pdb=" O GLU Q 459 " (cutoff:3.500A) Processing helix chain 'Q' and resid 499 through 504 Processing helix chain 'Q' and resid 518 through 520 No H-bonds generated for 'chain 'Q' and resid 518 through 520' Processing helix chain 'Q' and resid 523 through 528 removed outlier: 3.991A pdb=" N ALA Q 527 " --> pdb=" O PRO Q 523 " (cutoff:3.500A) Processing helix chain 'Q' and resid 540 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 558 through 563 removed outlier: 3.555A pdb=" N SER Q 562 " --> pdb=" O LYS Q 559 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 136 Processing helix chain 'R' and resid 141 through 144 No H-bonds generated for 'chain 'R' and resid 141 through 144' Processing helix chain 'R' and resid 165 through 169 Processing helix chain 'R' and resid 183 through 197 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) Processing helix chain 'R' and resid 263 through 270 Processing helix chain 'R' and resid 277 through 286 Processing helix chain 'R' and resid 320 through 331 removed outlier: 3.880A pdb=" N ALA R 323 " --> pdb=" O SER R 320 " (cutoff:3.500A) Processing helix chain 'R' and resid 343 through 352 removed outlier: 3.843A pdb=" N ALA R 347 " --> pdb=" O PHE R 343 " (cutoff:3.500A) Processing helix chain 'R' and resid 368 through 385 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 391 through 393 No H-bonds generated for 'chain 'R' and resid 391 through 393' Processing helix chain 'R' and resid 408 through 419 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 446 through 464 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) Processing helix chain 'R' and resid 479 through 482 No H-bonds generated for 'chain 'R' and resid 479 through 482' Processing helix chain 'R' and resid 492 through 506 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) Processing helix chain 'R' and resid 523 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 540 through 549 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 555 through 563 removed outlier: 3.751A pdb=" N SER R 562 " --> pdb=" O LEU R 558 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLY R 563 " --> pdb=" O LYS R 559 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 3 through 5 removed outlier: 8.741A pdb=" N THR A 367 " --> pdb=" O PHE A 327 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL A 329 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N VAL A 369 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE A 331 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR A 300 " --> pdb=" O HIS A 328 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N VAL A 330 " --> pdb=" O THR A 300 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU A 302 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N TYR A 332 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE A 304 " --> pdb=" O TYR A 332 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN A 27 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N PHE A 303 " --> pdb=" O ASN A 27 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLY A 29 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA A 163 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N ILE A 164 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TYR A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N THR A 166 " --> pdb=" O TYR A 222 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR A 224 " --> pdb=" O THR A 166 " (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= B, first strand: chain 'A' and resid 232 through 234 Processing sheet with id= C, 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) Processing sheet with id= D, first strand: chain 'B' and resid 163 through 165 Processing sheet with id= E, first strand: chain 'B' and resid 183 through 185 Processing sheet with id= F, first strand: chain 'B' and resid 232 through 234 Processing sheet with id= G, first strand: chain 'C' and resid 366 through 369 removed outlier: 8.767A pdb=" N THR C 367 " --> pdb=" O PHE C 327 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL C 329 " --> pdb=" O THR C 367 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N VAL C 369 " --> pdb=" O VAL C 329 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE C 331 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR C 300 " --> pdb=" O HIS C 328 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N VAL C 330 " --> pdb=" O THR C 300 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU C 302 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N TYR C 332 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ILE C 304 " --> pdb=" O TYR C 332 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA C 163 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N LEU C 32 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE C 165 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N ILE C 164 " --> pdb=" O HIS C 220 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TYR C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR C 166 " --> pdb=" O TYR C 222 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TYR C 224 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLN C 183 " --> pdb=" O ALA C 221 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU C 223 " --> pdb=" O GLN C 183 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N PHE C 185 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LYS C 225 " --> pdb=" O PHE C 185 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 232 through 234 Processing sheet with id= I, first strand: chain 'D' and resid 3 through 5 removed outlier: 8.611A pdb=" N THR D 367 " --> pdb=" O PHE D 327 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL D 329 " --> pdb=" O THR D 367 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N VAL D 369 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE D 331 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR D 300 " --> pdb=" O HIS D 328 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N VAL D 330 " --> pdb=" O THR D 300 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU D 302 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N TYR D 332 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ILE D 304 " --> pdb=" O TYR D 332 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASN D 27 " --> pdb=" O ALA D 301 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N PHE D 303 " --> pdb=" O ASN D 27 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY D 29 " --> pdb=" O PHE D 303 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ASN D 305 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU D 31 " --> pdb=" O ASN D 305 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ALA D 163 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N LEU D 32 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N PHE D 165 " --> pdb=" O LEU D 32 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 183 through 185 Processing sheet with id= K, first strand: chain 'D' and resid 232 through 234 Processing sheet with id= L, first strand: chain 'E' and resid 183 through 185 removed outlier: 3.760A pdb=" N ALA E 221 " --> pdb=" O GLN E 183 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE E 164 " --> pdb=" O TYR E 222 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA E 163 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N HIS E 328 " --> pdb=" O LEU E 302 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ILE E 304 " --> pdb=" O HIS E 328 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL E 330 " --> pdb=" O ILE E 304 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 232 through 234 Processing sheet with id= N, first strand: chain 'F' and resid 3 through 5 removed outlier: 8.624A pdb=" N THR F 367 " --> pdb=" O PHE F 327 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL F 329 " --> pdb=" O THR F 367 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N VAL F 369 " --> pdb=" O VAL F 329 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE F 331 " --> pdb=" O VAL F 369 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR F 300 " --> pdb=" O HIS F 328 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N VAL F 330 " --> pdb=" O THR F 300 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU F 302 " --> pdb=" O VAL F 330 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N TYR F 332 " --> pdb=" O LEU F 302 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE F 304 " --> pdb=" O TYR F 332 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASN F 27 " --> pdb=" O ALA F 301 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N PHE F 303 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLY F 29 " --> pdb=" O PHE F 303 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ASN F 305 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU F 31 " --> pdb=" O ASN F 305 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA F 163 " --> pdb=" O VAL F 28 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR F 222 " --> pdb=" O PRO F 162 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR F 166 " --> pdb=" O TYR F 224 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLN F 183 " --> pdb=" O ALA F 221 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU F 223 " --> pdb=" O GLN F 183 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N PHE F 185 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LYS F 225 " --> pdb=" O PHE F 185 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 232 through 234 Processing sheet with id= P, first strand: chain 'G' and resid 163 through 165 removed outlier: 3.846A pdb=" N ALA G 163 " --> pdb=" O VAL G 28 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL G 330 " --> pdb=" O LEU G 302 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 183 through 185 removed outlier: 3.536A pdb=" N PHE G 185 " --> pdb=" O ALA G 221 " (cutoff:3.500A) Processing sheet with id= R, 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= S, 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: 6.905A pdb=" N THR H 300 " --> pdb=" O HIS H 328 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N VAL H 330 " --> pdb=" O THR H 300 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU H 302 " --> pdb=" O VAL H 330 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N TYR H 332 " --> pdb=" O LEU H 302 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ILE H 304 " --> pdb=" O TYR H 332 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ASN H 27 " --> pdb=" O ALA H 301 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N PHE H 303 " --> pdb=" O ASN H 27 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLY H 29 " --> pdb=" O PHE H 303 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ASN H 305 " --> pdb=" O GLY H 29 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU H 31 " --> pdb=" O ASN H 305 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA H 163 " --> pdb=" O VAL H 30 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N LEU H 32 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE H 165 " --> pdb=" O LEU H 32 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N ILE H 164 " --> pdb=" O HIS H 220 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TYR H 222 " --> pdb=" O ILE H 164 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N THR H 166 " --> pdb=" O TYR H 222 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TYR H 224 " --> pdb=" O THR H 166 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLN H 183 " --> pdb=" O ALA H 221 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU H 223 " --> pdb=" O GLN H 183 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N PHE H 185 " --> pdb=" O LEU H 223 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N LYS H 225 " --> pdb=" O PHE H 185 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 3 through 5 removed outlier: 8.526A pdb=" N THR I 367 " --> pdb=" O PHE I 327 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL I 329 " --> pdb=" O THR I 367 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N VAL I 369 " --> pdb=" O VAL I 329 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE I 331 " --> pdb=" O VAL I 369 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR I 300 " --> pdb=" O HIS I 328 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N VAL I 330 " --> pdb=" O THR I 300 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU I 302 " --> pdb=" O VAL I 330 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N TYR I 332 " --> pdb=" O LEU I 302 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ILE I 304 " --> pdb=" O TYR I 332 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN I 27 " --> pdb=" O ALA I 301 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N PHE I 303 " --> pdb=" O ASN I 27 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY I 29 " --> pdb=" O PHE I 303 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA I 163 " --> pdb=" O VAL I 30 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TYR I 222 " --> pdb=" O ILE I 164 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N THR I 166 " --> pdb=" O TYR I 222 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N TYR I 224 " --> pdb=" O THR I 166 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 3 through 5 removed outlier: 8.385A pdb=" N THR J 367 " --> pdb=" O PHE J 327 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL J 329 " --> pdb=" O THR J 367 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N VAL J 369 " --> pdb=" O VAL J 329 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE J 331 " --> pdb=" O VAL J 369 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR J 300 " --> pdb=" O HIS J 328 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N VAL J 330 " --> pdb=" O THR J 300 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU J 302 " --> pdb=" O VAL J 330 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N TYR J 332 " --> pdb=" O LEU J 302 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ILE J 304 " --> pdb=" O TYR J 332 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASN J 27 " --> pdb=" O ALA J 301 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N PHE J 303 " --> pdb=" O ASN J 27 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY J 29 " --> pdb=" O PHE J 303 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA J 163 " --> pdb=" O VAL J 30 " (cutoff:3.500A) removed outlier: 9.256A pdb=" N ILE J 164 " --> pdb=" O HIS J 220 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TYR J 222 " --> pdb=" O ILE J 164 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N THR J 166 " --> pdb=" O TYR J 222 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TYR J 224 " --> pdb=" O THR J 166 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLN J 183 " --> pdb=" O ALA J 221 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU J 223 " --> pdb=" O GLN J 183 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHE J 185 " --> pdb=" O LEU J 223 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N LYS J 225 " --> pdb=" O PHE J 185 " (cutoff:3.500A) Processing sheet with id= V, 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= W, first strand: chain 'K' and resid 3 through 5 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: 6.800A pdb=" N THR K 300 " --> pdb=" O HIS K 328 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N VAL K 330 " --> pdb=" O THR K 300 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU K 302 " --> pdb=" O VAL K 330 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N TYR K 332 " --> pdb=" O LEU K 302 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ILE K 304 " --> pdb=" O TYR K 332 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN K 27 " --> pdb=" O ALA K 301 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N PHE K 303 " --> pdb=" O ASN K 27 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLY K 29 " --> pdb=" O PHE K 303 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N ASN K 305 " --> pdb=" O GLY K 29 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU K 31 " --> pdb=" O ASN K 305 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA K 163 " --> pdb=" O VAL K 30 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N LEU K 32 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N PHE K 165 " --> pdb=" O LEU K 32 " (cutoff:3.500A) removed outlier: 9.351A pdb=" N ILE K 164 " --> pdb=" O HIS K 220 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR K 222 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N THR K 166 " --> pdb=" O TYR K 222 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TYR K 224 " --> pdb=" O THR K 166 " (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= X, first strand: chain 'K' and resid 232 through 234 Processing sheet with id= Y, first strand: chain 'L' and resid 183 through 185 removed outlier: 3.563A pdb=" N ALA L 163 " --> pdb=" O VAL L 28 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'L' and resid 232 through 234 Processing sheet with id= AA, first strand: chain 'M' and resid 67 through 70 removed outlier: 3.720A pdb=" N ASP M 67 " --> pdb=" O ILE M 95 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE M 95 " --> pdb=" O ASP M 67 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA M 69 " --> pdb=" O GLN M 93 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ARG M 92 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU M 27 " --> pdb=" O ARG M 92 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY M 17 " --> pdb=" O ARG M 24 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASN M 26 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL M 15 " --> pdb=" O ASN M 26 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'M' and resid 35 through 37 Processing sheet with id= AC, first strand: chain 'M' and resid 125 through 127 removed outlier: 3.634A pdb=" N VAL M 61 " --> pdb=" O PHE M 54 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA M 56 " --> pdb=" O ILE M 59 " (cutoff:3.500A) 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: 3.535A pdb=" N PHE M 101 " --> pdb=" O ILE M 112 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'M' and resid 252 through 254 removed outlier: 4.152A pdb=" N LYS M 254 " --> pdb=" O ILE M 226 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL M 433 " --> pdb=" O LYS M 223 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N THR M 225 " --> pdb=" O VAL M 433 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE M 435 " --> pdb=" O THR M 225 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU M 227 " --> pdb=" O ILE M 435 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASN M 437 " --> pdb=" O LEU M 227 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE M 203 " --> pdb=" O HIS M 434 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL M 436 " --> pdb=" O ILE M 203 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE M 205 " --> pdb=" O VAL M 436 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL M 473 " --> pdb=" O VAL M 204 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N PHE M 206 " --> pdb=" O VAL M 473 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU M 475 " --> pdb=" O PHE M 206 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER M 510 " --> pdb=" O THR M 472 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU M 173 " --> pdb=" O VAL M 513 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N THR M 515 " --> pdb=" O LEU M 173 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL M 175 " --> pdb=" O THR M 515 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN M 531 " --> pdb=" O ALA M 174 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N LEU M 176 " --> pdb=" O ASN M 531 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE M 533 " --> pdb=" O LEU M 176 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE M 572 " --> pdb=" O TRP M 532 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL M 148 " --> pdb=" O ALA M 163 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA M 163 " --> pdb=" O VAL M 148 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE M 161 " --> pdb=" O LEU M 150 " (cutoff:3.500A) Processing sheet with id= AE, 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= AF, first strand: chain 'N' and resid 67 through 70 removed outlier: 3.685A pdb=" N ASP N 67 " --> pdb=" O ILE N 95 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE N 95 " --> pdb=" O ASP N 67 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA N 69 " --> pdb=" O GLN N 93 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ARG N 92 " --> pdb=" O LEU N 27 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG N 22 " --> pdb=" O GLU N 19 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY N 17 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN N 26 " --> pdb=" O VAL N 15 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N VAL N 15 " --> pdb=" O ASN N 26 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'N' and resid 35 through 37 Processing sheet with id= AH, first strand: chain 'N' and resid 125 through 127 removed outlier: 3.905A pdb=" N GLY N 100 " --> pdb=" O VAL N 62 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ARG N 64 " --> pdb=" O ALA N 98 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ALA N 98 " --> pdb=" O ARG N 64 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'N' and resid 222 through 226 removed outlier: 6.978A pdb=" N VAL N 433 " --> pdb=" O LYS N 223 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N THR N 225 " --> pdb=" O VAL N 433 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE N 435 " --> pdb=" O THR N 225 " (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: 6.573A pdb=" N VAL N 473 " --> pdb=" O VAL N 204 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N PHE N 206 " --> pdb=" O VAL N 473 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU N 475 " --> pdb=" O PHE N 206 " (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: 7.246A pdb=" N LEU N 173 " --> pdb=" O VAL N 513 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASN N 531 " --> pdb=" O ALA N 174 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LEU N 176 " --> pdb=" O ASN N 531 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N PHE N 533 " --> pdb=" O LEU N 176 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE N 572 " --> pdb=" O TRP N 532 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL N 570 " --> pdb=" O SER N 534 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL N 580 " --> pdb=" O ALA N 571 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL N 152 " --> pdb=" O SER N 583 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE N 161 " --> pdb=" O LEU N 150 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'N' and resid 299 through 301 removed outlier: 3.681A pdb=" N PHE N 308 " --> pdb=" O LEU N 300 " (cutoff:3.500A) Processing sheet with id= AK, 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= AL, first strand: chain 'O' and resid 67 through 70 removed outlier: 3.741A pdb=" N ASP O 67 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE O 95 " --> pdb=" O ASP O 67 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY O 17 " --> pdb=" O ARG O 24 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASN O 26 " --> pdb=" O VAL O 15 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL O 15 " --> pdb=" O ASN O 26 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'O' and resid 51 through 53 removed outlier: 3.846A pdb=" N GLY O 100 " --> pdb=" O VAL O 62 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ARG O 64 " --> pdb=" O ALA O 98 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA O 98 " --> pdb=" O ARG O 64 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS O 103 " --> pdb=" O VAL O 110 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'O' and resid 531 through 534 removed outlier: 3.547A pdb=" N PHE O 572 " --> pdb=" O TRP O 532 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL O 580 " --> pdb=" O ALA O 571 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE O 161 " --> pdb=" O LEU O 150 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'O' and resid 510 through 514 removed outlier: 3.953A pdb=" N GLU O 477 " --> pdb=" O PHE O 206 " (cutoff:3.500A) Processing sheet with id= AP, 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= AQ, first strand: chain 'P' and resid 67 through 70 removed outlier: 5.313A pdb=" N ARG P 92 " --> pdb=" O LEU P 27 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU P 27 " --> pdb=" O ARG P 92 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE P 23 " --> pdb=" O ALA P 96 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY P 17 " --> pdb=" O ARG P 24 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ASN P 26 " --> pdb=" O VAL P 15 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N VAL P 15 " --> pdb=" O ASN P 26 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'P' and resid 124 through 127 removed outlier: 4.697A pdb=" N SER P 124 " --> pdb=" O ASP P 55 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE P 59 " --> pdb=" O ALA P 56 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU P 60 " --> pdb=" O VAL P 102 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ARG P 64 " --> pdb=" O ALA P 98 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ALA P 98 " --> pdb=" O ARG P 64 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'P' and resid 151 through 153 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= AT, first strand: chain 'P' and resid 173 through 176 removed outlier: 3.636A pdb=" N THR P 515 " --> pdb=" O VAL P 175 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR P 472 " --> pdb=" O SER P 510 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N ILE P 512 " --> pdb=" O THR P 472 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU P 474 " --> pdb=" O ILE P 512 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N SER P 514 " --> pdb=" O LEU P 474 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU P 476 " --> pdb=" O SER P 514 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'Q' and resid 13 through 18 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) 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) Processing sheet with id= AV, first strand: chain 'Q' and resid 101 through 104 removed outlier: 3.985A pdb=" N PHE Q 101 " --> pdb=" O ILE Q 112 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE Q 112 " --> pdb=" O PHE Q 101 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS Q 103 " --> pdb=" O VAL Q 110 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL Q 110 " --> pdb=" O LYS Q 103 " (cutoff:3.500A) No H-bonds generated for sheet with id= AV Processing sheet with id= AW, first strand: chain 'Q' and resid 532 through 534 removed outlier: 3.555A pdb=" N TRP Q 532 " --> pdb=" O PHE Q 572 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE Q 572 " --> pdb=" O TRP Q 532 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA Q 571 " --> pdb=" O VAL Q 580 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL Q 580 " --> pdb=" O ALA Q 571 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ILE Q 161 " --> pdb=" O LEU Q 150 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'Q' and resid 173 through 175 Processing sheet with id= AY, first strand: chain 'Q' and resid 473 through 476 removed outlier: 3.616A pdb=" N VAL Q 436 " --> pdb=" O ILE Q 205 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE Q 435 " --> pdb=" O LYS Q 223 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'R' and resid 512 through 515 removed outlier: 7.223A pdb=" N LEU R 173 " --> pdb=" O VAL R 513 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N THR R 515 " --> pdb=" O LEU R 173 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL R 175 " --> pdb=" O THR R 515 " (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= BA, 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= BA Processing sheet with id= BB, first strand: chain 'R' and resid 472 through 474 Processing sheet with id= BC, 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) 1752 hydrogen bonds defined for protein. 4662 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 23.43 Time building geometry restraints manager: 18.76 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: 94.82 - 104.22: 765 104.22 - 113.62: 35790 113.62 - 123.02: 47672 123.02 - 132.41: 4228 132.41 - 141.81: 96 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: 31055 2.99 - 3.63: 85482 3.63 - 4.26: 124991 4.26 - 4.90: 215110 Nonbonded interactions: 456696 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 2.440 nonbonded pdb=" OD1 ASN E 254 " pdb=" ND2 ASN E 258 " model vdw 2.204 2.520 ... (remaining 456691 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 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: 1.460 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: 0.060 Extract box with map and model: 8.840 Check model and map are aligned: 0.710 Set scattering table: 0.440 Process input model: 126.240 Find NCS groups from input model: 4.070 Set up NCS constraints: 0.240 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: 144.420 ------------------------------------------------------------------------------- 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= 0.334 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 fitting. rotamer outliers: 0 poor density : 1508 time to evaluate : 5.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 0.6445 time to fit residues: 1584.1920 Evaluate side-chains 1342 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1342 time to evaluate : 5.148 ------------------------------------------------------------------------------- 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: 0.9990 chunk 603 optimal weight: 2.9990 chunk 334 optimal weight: 10.0000 chunk 206 optimal weight: 0.0040 chunk 406 optimal weight: 4.9990 chunk 322 optimal weight: 0.3980 chunk 623 optimal weight: 0.6980 chunk 241 optimal weight: 5.9990 chunk 379 optimal weight: 2.9990 chunk 464 optimal weight: 8.9990 chunk 722 optimal weight: 0.8980 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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 C 24 GLN C 135 GLN C 227 HIS D 24 GLN D 227 HIS D 299 GLN D 360 ASN G 135 GLN G 199 GLN I 227 HIS I 299 GLN I 315 ASN I 365 GLN J 24 GLN K 234 GLN ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 32 GLN M 209 ASN M 214 GLN M 539 ASN N 200 ASN N 585 ASN P 38 HIS P 429 ASN P 586 GLN ** Q 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 214 GLN Q 221 ASN R 373 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.1140 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= 0.141 Angle : 0.542 12.284 88551 Z= 0.264 Chirality : 0.042 0.373 9656 Planarity : 0.004 0.049 11363 Dihedral : 11.695 146.086 9413 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.91 % Allowed : 8.10 % Favored : 90.98 % 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: -0.77 (0.09), residues: 7933 helix: 0.48 (0.10), residues: 2990 sheet: 0.40 (0.17), residues: 945 loop : -1.55 (0.09), residues: 3998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 532 HIS 0.006 0.001 HIS Q 481 PHE 0.020 0.001 PHE P 101 TYR 0.027 0.001 TYR R 497 ARG 0.008 0.000 ARG Q 463 *********************** 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 1432 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1371 time to evaluate : 5.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 SER cc_start: 0.8338 (m) cc_final: 0.8069 (t) REVERT: A 293 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7179 (tm-30) REVERT: A 374 LYS cc_start: 0.7796 (mttt) cc_final: 0.7525 (mttt) REVERT: B 202 ASP cc_start: 0.7640 (m-30) cc_final: 0.7432 (m-30) REVERT: B 250 ASP cc_start: 0.7911 (m-30) cc_final: 0.7695 (m-30) REVERT: B 256 ILE cc_start: 0.8386 (tt) cc_final: 0.8172 (tt) REVERT: B 312 TYR cc_start: 0.7731 (t80) cc_final: 0.7480 (t80) REVERT: C 102 GLU cc_start: 0.7226 (mp0) cc_final: 0.6713 (mp0) REVERT: C 105 GLU cc_start: 0.7786 (tt0) cc_final: 0.7535 (tt0) REVERT: C 106 GLU cc_start: 0.7208 (tp30) cc_final: 0.6982 (tp30) REVERT: C 142 LYS cc_start: 0.7904 (ttmt) cc_final: 0.7692 (ttmt) REVERT: C 352 GLU cc_start: 0.6652 (mp0) cc_final: 0.6151 (mp0) REVERT: D 50 LYS cc_start: 0.7895 (mmmt) cc_final: 0.7595 (ttmm) REVERT: D 74 ASP cc_start: 0.7467 (m-30) cc_final: 0.7044 (m-30) REVERT: D 97 LYS cc_start: 0.8456 (ttmm) cc_final: 0.8242 (ttmm) REVERT: D 106 GLU cc_start: 0.7444 (pp20) cc_final: 0.7028 (pp20) REVERT: D 107 GLU cc_start: 0.7396 (tm-30) cc_final: 0.6733 (tm-30) REVERT: D 110 LYS cc_start: 0.8071 (mttp) cc_final: 0.7729 (mttp) REVERT: D 197 TYR cc_start: 0.8237 (m-10) cc_final: 0.7676 (m-80) REVERT: D 227 HIS cc_start: 0.7254 (m90) cc_final: 0.6875 (m90) REVERT: D 259 LYS cc_start: 0.7922 (tppp) cc_final: 0.7663 (tppp) REVERT: D 335 GLU cc_start: 0.7537 (pm20) cc_final: 0.7154 (pm20) REVERT: E 46 LYS cc_start: 0.7499 (mttt) cc_final: 0.7249 (mttm) REVERT: E 54 GLN cc_start: 0.8415 (tm-30) cc_final: 0.7948 (tm-30) REVERT: E 128 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7501 (tt0) REVERT: E 250 ASP cc_start: 0.7660 (m-30) cc_final: 0.7231 (m-30) REVERT: E 316 ARG cc_start: 0.7758 (tpt-90) cc_final: 0.7108 (tmm-80) REVERT: E 342 LYS cc_start: 0.7679 (tttm) cc_final: 0.7449 (tttm) REVERT: F 21 SER cc_start: 0.8368 (t) cc_final: 0.8058 (t) REVERT: F 296 SER cc_start: 0.8967 (m) cc_final: 0.8681 (m) REVERT: F 312 TYR cc_start: 0.6124 (t80) cc_final: 0.5661 (t80) REVERT: G 58 GLU cc_start: 0.7376 (tm-30) cc_final: 0.6819 (tm-30) REVERT: G 110 LYS cc_start: 0.7577 (mppt) cc_final: 0.7297 (tppt) REVERT: G 142 LYS cc_start: 0.7915 (ttpp) cc_final: 0.7474 (ttpp) REVERT: G 178 GLU cc_start: 0.6994 (tt0) cc_final: 0.6755 (tt0) REVERT: G 250 ASP cc_start: 0.8106 (t0) cc_final: 0.7851 (t0) REVERT: G 259 LYS cc_start: 0.7942 (tptp) cc_final: 0.6810 (tptp) REVERT: G 262 PHE cc_start: 0.7028 (p90) cc_final: 0.6398 (p90) REVERT: H 110 LYS cc_start: 0.8254 (ttmm) cc_final: 0.7961 (mtpp) REVERT: H 364 ASN cc_start: 0.7706 (t0) cc_final: 0.7344 (t0) REVERT: J 100 ARG cc_start: 0.6621 (mtp85) cc_final: 0.6374 (mtp85) REVERT: J 108 PHE cc_start: 0.8582 (m-80) cc_final: 0.8292 (m-80) REVERT: J 126 THR cc_start: 0.8803 (m) cc_final: 0.8580 (p) REVERT: J 376 TYR cc_start: 0.8306 (m-10) cc_final: 0.8053 (m-80) REVERT: K 76 ASP cc_start: 0.6972 (m-30) cc_final: 0.6532 (m-30) REVERT: K 106 GLU cc_start: 0.7441 (pm20) cc_final: 0.7014 (pm20) REVERT: K 128 GLU cc_start: 0.7028 (tm-30) cc_final: 0.6767 (tm-30) REVERT: K 266 GLN cc_start: 0.7588 (mt0) cc_final: 0.7380 (mt0) REVERT: K 361 MET cc_start: 0.7884 (ptp) cc_final: 0.7642 (mtm) REVERT: L 50 LYS cc_start: 0.8174 (mttm) cc_final: 0.7807 (mttm) REVERT: L 104 GLU cc_start: 0.6930 (tt0) cc_final: 0.6605 (tt0) REVERT: L 202 ASP cc_start: 0.6971 (m-30) cc_final: 0.6749 (m-30) REVERT: L 323 LEU cc_start: 0.7871 (mt) cc_final: 0.7497 (mt) REVERT: M 70 PHE cc_start: 0.6721 (m-80) cc_final: 0.6280 (m-10) REVERT: M 97 TYR cc_start: 0.5456 (m-80) cc_final: 0.5116 (m-80) REVERT: M 183 LYS cc_start: 0.7255 (pttt) cc_final: 0.6627 (ptmt) REVERT: M 254 LYS cc_start: 0.7920 (tppp) cc_final: 0.7619 (tppp) REVERT: M 294 LYS cc_start: 0.7992 (ptmm) cc_final: 0.7777 (ptmm) REVERT: M 308 PHE cc_start: 0.7994 (t80) cc_final: 0.7594 (t80) REVERT: M 318 ASN cc_start: 0.8690 (t0) cc_final: 0.8355 (t0) REVERT: M 352 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7531 (mm-30) REVERT: M 390 PHE cc_start: 0.8341 (t80) cc_final: 0.8105 (t80) REVERT: M 395 ASN cc_start: 0.7126 (t0) cc_final: 0.6917 (t0) REVERT: M 516 GLN cc_start: 0.7523 (pt0) cc_final: 0.7304 (pt0) REVERT: N 114 GLU cc_start: 0.7057 (tt0) cc_final: 0.6799 (tt0) REVERT: N 193 LYS cc_start: 0.8211 (ttmm) cc_final: 0.7913 (ttmm) REVERT: N 268 LYS cc_start: 0.8264 (mtpt) cc_final: 0.8028 (mtpt) REVERT: N 277 GLN cc_start: 0.7357 (mt0) cc_final: 0.7095 (mt0) REVERT: N 297 ASN cc_start: 0.6950 (OUTLIER) cc_final: 0.6745 (p0) REVERT: N 353 PHE cc_start: 0.7114 (m-80) cc_final: 0.6894 (m-80) REVERT: N 425 LYS cc_start: 0.8171 (ttpt) cc_final: 0.7955 (ttmt) REVERT: N 467 GLU cc_start: 0.8113 (tp30) cc_final: 0.7711 (tp30) REVERT: O 64 ARG cc_start: 0.7272 (ptp-110) cc_final: 0.6050 (ptt180) REVERT: O 186 PHE cc_start: 0.8347 (t80) cc_final: 0.8103 (t80) REVERT: O 268 LYS cc_start: 0.7910 (mtmt) cc_final: 0.7605 (mtpp) REVERT: O 327 ASP cc_start: 0.7202 (t0) cc_final: 0.6755 (t0) REVERT: O 380 ILE cc_start: 0.8108 (tp) cc_final: 0.7861 (tp) REVERT: O 448 MET cc_start: 0.6594 (tpt) cc_final: 0.6321 (tpt) REVERT: P 68 MET cc_start: 0.5393 (mmp) cc_final: 0.5157 (mmp) REVERT: P 183 LYS cc_start: 0.7687 (mmmm) cc_final: 0.7458 (mmmm) REVERT: P 246 TYR cc_start: 0.7547 (t80) cc_final: 0.7175 (t80) REVERT: P 277 GLN cc_start: 0.7426 (mt0) cc_final: 0.7208 (mp10) REVERT: P 281 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8396 (mt) REVERT: P 427 GLN cc_start: 0.7202 (OUTLIER) cc_final: 0.6982 (pt0) REVERT: P 459 GLU cc_start: 0.7662 (tp30) cc_final: 0.7103 (tp30) REVERT: P 508 LYS cc_start: 0.7817 (mttp) cc_final: 0.7448 (mmtp) REVERT: P 524 THR cc_start: 0.7215 (t) cc_final: 0.5363 (p) REVERT: Q 137 TYR cc_start: 0.8346 (m-80) cc_final: 0.7988 (m-80) REVERT: Q 146 LYS cc_start: 0.7799 (mppt) cc_final: 0.7483 (mppt) REVERT: Q 192 ARG cc_start: 0.6656 (ttt180) cc_final: 0.5925 (ptm-80) REVERT: Q 424 GLU cc_start: 0.6425 (tm-30) cc_final: 0.6057 (tm-30) REVERT: Q 444 ASP cc_start: 0.7662 (m-30) cc_final: 0.7399 (m-30) REVERT: Q 448 MET cc_start: 0.6668 (mmp) cc_final: 0.6381 (mmp) REVERT: Q 455 GLU cc_start: 0.7710 (pt0) cc_final: 0.6913 (pt0) REVERT: Q 459 GLU cc_start: 0.7363 (mt-10) cc_final: 0.7077 (mt-10) REVERT: Q 520 GLU cc_start: 0.6685 (mp0) cc_final: 0.6250 (mp0) REVERT: Q 536 ARG cc_start: 0.6209 (tpt-90) cc_final: 0.5454 (tpt-90) REVERT: Q 592 LYS cc_start: 0.7797 (mmmt) cc_final: 0.7235 (mmmt) REVERT: R 221 ASN cc_start: 0.7646 (t0) cc_final: 0.7296 (t0) REVERT: R 259 GLN cc_start: 0.6898 (pp30) cc_final: 0.6646 (pm20) outliers start: 61 outliers final: 37 residues processed: 1390 average time/residue: 0.6276 time to fit residues: 1419.8330 Evaluate side-chains 1371 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1331 time to evaluate : 5.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 400 VAL Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain I residue 65 ASP Chi-restraints excluded: chain I residue 266 GLN Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain J residue 186 ASN Chi-restraints excluded: chain J residue 389 LEU Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 211 GLU Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain M residue 281 LEU 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 297 ASN 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 97 TYR 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 427 GLN Chi-restraints excluded: chain P residue 510 SER 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 Chi-restraints excluded: chain R residue 438 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 401 optimal weight: 0.7980 chunk 224 optimal weight: 6.9990 chunk 601 optimal weight: 6.9990 chunk 492 optimal weight: 4.9990 chunk 199 optimal weight: 0.8980 chunk 724 optimal weight: 9.9990 chunk 782 optimal weight: 6.9990 chunk 644 optimal weight: 0.7980 chunk 718 optimal weight: 7.9990 chunk 246 optimal weight: 4.9990 chunk 580 optimal weight: 7.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- 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** C 24 GLN C 258 ASN D 24 GLN ** G 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN ** H 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 364 ASN I 247 GLN I 315 ASN I 365 GLN J 24 GLN J 135 GLN J 254 ASN K 77 ASN ** K 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 360 ASN ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 214 GLN O 383 GLN P 429 ASN ** Q 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 214 GLN Q 277 GLN ** R 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 65426 Z= 0.365 Angle : 0.630 12.539 88551 Z= 0.320 Chirality : 0.045 0.231 9656 Planarity : 0.004 0.054 11363 Dihedral : 10.591 143.563 9413 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.04 % Allowed : 11.47 % Favored : 86.49 % 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: -1.19 (0.09), residues: 7933 helix: 0.14 (0.10), residues: 2929 sheet: 0.14 (0.18), residues: 938 loop : -1.76 (0.09), residues: 4066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 49 HIS 0.009 0.001 HIS P 224 PHE 0.027 0.002 PHE P 101 TYR 0.027 0.002 TYR E 224 ARG 0.008 0.001 ARG Q 463 *********************** 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 1529 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1393 time to evaluate : 5.134 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 293 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7311 (tm-30) REVERT: A 319 LEU cc_start: 0.8308 (mt) cc_final: 0.8029 (mp) REVERT: A 338 GLU cc_start: 0.6004 (mp0) cc_final: 0.5742 (mp0) REVERT: B 88 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6826 (mt-10) REVERT: B 97 LYS cc_start: 0.8216 (ttmm) cc_final: 0.8003 (ttmm) REVERT: B 128 GLU cc_start: 0.7070 (tm-30) cc_final: 0.6831 (tm-30) REVERT: B 242 GLU cc_start: 0.7877 (tt0) cc_final: 0.7431 (tt0) REVERT: B 250 ASP cc_start: 0.7901 (m-30) cc_final: 0.7604 (m-30) REVERT: B 256 ILE cc_start: 0.8387 (tt) cc_final: 0.8062 (tt) REVERT: C 106 GLU cc_start: 0.7494 (tp30) cc_final: 0.7253 (tp30) REVERT: C 352 GLU cc_start: 0.6699 (mp0) cc_final: 0.6233 (mp0) REVERT: D 50 LYS cc_start: 0.7941 (mmmt) cc_final: 0.7644 (ttmm) REVERT: D 74 ASP cc_start: 0.7515 (m-30) cc_final: 0.7134 (m-30) REVERT: D 97 LYS cc_start: 0.8488 (ttmm) cc_final: 0.8273 (ttmm) REVERT: D 110 LYS cc_start: 0.8241 (mttp) cc_final: 0.7861 (mttp) REVERT: D 197 TYR cc_start: 0.8228 (m-10) cc_final: 0.7749 (m-80) REVERT: D 335 GLU cc_start: 0.7744 (pm20) cc_final: 0.7270 (pm20) REVERT: E 54 GLN cc_start: 0.8441 (tm-30) cc_final: 0.8051 (tm-30) REVERT: E 66 LYS cc_start: 0.7926 (tptm) cc_final: 0.7325 (tptt) REVERT: E 128 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7443 (tt0) REVERT: E 342 LYS cc_start: 0.7751 (tttm) cc_final: 0.7537 (tttm) REVERT: F 21 SER cc_start: 0.8395 (t) cc_final: 0.8059 (t) REVERT: G 46 LYS cc_start: 0.5935 (tppt) cc_final: 0.5535 (tppp) REVERT: G 58 GLU cc_start: 0.7436 (tm-30) cc_final: 0.6920 (tm-30) REVERT: G 110 LYS cc_start: 0.7659 (mppt) cc_final: 0.7348 (tppt) REVERT: G 142 LYS cc_start: 0.8020 (ttpp) cc_final: 0.7636 (ttpp) REVERT: G 250 ASP cc_start: 0.8151 (t0) cc_final: 0.7860 (t0) REVERT: G 259 LYS cc_start: 0.7964 (tptp) cc_final: 0.6904 (tptp) REVERT: G 262 PHE cc_start: 0.7001 (p90) cc_final: 0.6581 (p90) REVERT: H 110 LYS cc_start: 0.8338 (ttmm) cc_final: 0.8029 (mtpp) REVERT: H 291 PHE cc_start: 0.7688 (t80) cc_final: 0.7289 (t80) REVERT: H 364 ASN cc_start: 0.7633 (OUTLIER) cc_final: 0.7203 (t0) REVERT: J 189 SER cc_start: 0.8348 (p) cc_final: 0.8140 (m) REVERT: J 316 ARG cc_start: 0.8336 (mmm160) cc_final: 0.8039 (mmm160) REVERT: K 76 ASP cc_start: 0.7056 (m-30) cc_final: 0.6618 (m-30) REVERT: K 106 GLU cc_start: 0.7542 (pm20) cc_final: 0.6879 (pm20) REVERT: K 128 GLU cc_start: 0.7109 (tm-30) cc_final: 0.6873 (tm-30) REVERT: K 135 GLN cc_start: 0.8412 (mm-40) cc_final: 0.8048 (mm-40) REVERT: K 353 LYS cc_start: 0.7712 (mptt) cc_final: 0.7117 (mptt) REVERT: K 361 MET cc_start: 0.8122 (ptp) cc_final: 0.7854 (mtm) REVERT: K 401 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6666 (tm-30) REVERT: L 9 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8265 (ttpp) REVERT: L 14 ASP cc_start: 0.6978 (m-30) cc_final: 0.6758 (m-30) REVERT: L 50 LYS cc_start: 0.8252 (mttm) cc_final: 0.7881 (mttm) REVERT: L 88 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7029 (mp0) REVERT: L 104 GLU cc_start: 0.6905 (tt0) cc_final: 0.6571 (tt0) REVERT: L 118 GLU cc_start: 0.7433 (tp30) cc_final: 0.7148 (tp30) REVERT: L 222 TYR cc_start: 0.8427 (m-80) cc_final: 0.8204 (m-80) REVERT: L 227 HIS cc_start: 0.7060 (m90) cc_final: 0.6811 (m90) REVERT: L 251 GLU cc_start: 0.7276 (tt0) cc_final: 0.7053 (tt0) REVERT: L 323 LEU cc_start: 0.7975 (mt) cc_final: 0.7644 (mt) REVERT: M 97 TYR cc_start: 0.5481 (m-80) cc_final: 0.4968 (m-80) REVERT: M 149 GLU cc_start: 0.6885 (pp20) cc_final: 0.6608 (pp20) REVERT: M 254 LYS cc_start: 0.8111 (tppp) cc_final: 0.7694 (tppp) REVERT: M 294 LYS cc_start: 0.8002 (ptmm) cc_final: 0.7644 (ptmm) REVERT: M 299 TYR cc_start: 0.8222 (p90) cc_final: 0.7756 (p90) REVERT: M 308 PHE cc_start: 0.8066 (t80) cc_final: 0.7629 (t80) REVERT: M 318 ASN cc_start: 0.8845 (t0) cc_final: 0.8562 (t0) REVERT: M 352 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7561 (mm-30) REVERT: M 391 LYS cc_start: 0.7789 (ptpt) cc_final: 0.7587 (ptpt) REVERT: M 468 ARG cc_start: 0.7182 (ttm110) cc_final: 0.6653 (ttp-110) REVERT: M 516 GLN cc_start: 0.7650 (pt0) cc_final: 0.7369 (pt0) REVERT: N 22 ARG cc_start: 0.7475 (mtt180) cc_final: 0.7262 (mtp-110) REVERT: N 114 GLU cc_start: 0.7218 (tt0) cc_final: 0.6902 (tt0) REVERT: N 193 LYS cc_start: 0.8310 (ttmm) cc_final: 0.7979 (ttmm) REVERT: N 268 LYS cc_start: 0.8361 (mtpt) cc_final: 0.8135 (mtpt) REVERT: N 277 GLN cc_start: 0.7557 (mt0) cc_final: 0.7148 (mt0) REVERT: N 353 PHE cc_start: 0.7178 (m-80) cc_final: 0.6932 (m-80) REVERT: N 425 LYS cc_start: 0.8288 (ttpt) cc_final: 0.7968 (ttmt) REVERT: N 457 PHE cc_start: 0.8253 (t80) cc_final: 0.8008 (t80) REVERT: N 467 GLU cc_start: 0.8110 (tp30) cc_final: 0.7622 (tp30) REVERT: O 186 PHE cc_start: 0.8354 (t80) cc_final: 0.8025 (t80) REVERT: O 268 LYS cc_start: 0.8006 (mtmt) cc_final: 0.7644 (mtpp) REVERT: O 327 ASP cc_start: 0.7198 (t0) cc_final: 0.6748 (t0) REVERT: O 380 ILE cc_start: 0.8252 (tp) cc_final: 0.8024 (tp) REVERT: O 416 GLU cc_start: 0.7300 (tm-30) cc_final: 0.6801 (tm-30) REVERT: O 448 MET cc_start: 0.6907 (tpt) cc_final: 0.6594 (tpt) REVERT: O 601 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8055 (mm-30) REVERT: P 183 LYS cc_start: 0.7998 (mmmm) cc_final: 0.7346 (mtpp) REVERT: P 211 GLU cc_start: 0.7272 (mt-10) cc_final: 0.7058 (mm-30) REVERT: P 246 TYR cc_start: 0.7608 (t80) cc_final: 0.7237 (t80) REVERT: P 283 ASN cc_start: 0.8495 (OUTLIER) cc_final: 0.8219 (p0) REVERT: P 389 ARG cc_start: 0.8289 (mmt90) cc_final: 0.8085 (mmt90) REVERT: P 459 GLU cc_start: 0.7719 (tp30) cc_final: 0.7153 (tp30) REVERT: P 467 GLU cc_start: 0.7401 (tp30) cc_final: 0.6903 (tp30) REVERT: P 495 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.6788 (mtpt) REVERT: P 502 LYS cc_start: 0.7503 (mmtt) cc_final: 0.6874 (mmtt) REVERT: P 508 LYS cc_start: 0.7986 (mttp) cc_final: 0.7494 (mmtp) REVERT: P 524 THR cc_start: 0.7401 (t) cc_final: 0.5298 (p) REVERT: Q 68 MET cc_start: 0.7944 (tpp) cc_final: 0.7720 (tpp) REVERT: Q 146 LYS cc_start: 0.7976 (mppt) cc_final: 0.7658 (mppt) REVERT: Q 424 GLU cc_start: 0.6686 (tm-30) cc_final: 0.6258 (tm-30) REVERT: Q 444 ASP cc_start: 0.7743 (m-30) cc_final: 0.7415 (m-30) REVERT: Q 448 MET cc_start: 0.6813 (mmp) cc_final: 0.6499 (mmp) REVERT: Q 455 GLU cc_start: 0.7670 (pt0) cc_final: 0.6812 (pt0) REVERT: Q 456 MET cc_start: 0.5578 (mtm) cc_final: 0.5326 (mtm) REVERT: Q 459 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7016 (mt-10) REVERT: Q 520 GLU cc_start: 0.6863 (mp0) cc_final: 0.6429 (mp0) REVERT: Q 541 ARG cc_start: 0.7258 (mtm-85) cc_final: 0.6981 (mtm-85) REVERT: Q 547 ARG cc_start: 0.7968 (ptm160) cc_final: 0.7600 (ptm160) REVERT: R 22 ARG cc_start: 0.6629 (mtt90) cc_final: 0.6132 (mtp85) REVERT: R 205 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7400 (mp) REVERT: R 221 ASN cc_start: 0.7676 (t0) cc_final: 0.7275 (t0) REVERT: R 271 ARG cc_start: 0.7866 (ptp90) cc_final: 0.7665 (ptp90) REVERT: R 382 GLN cc_start: 0.7550 (pp30) cc_final: 0.7036 (pp30) REVERT: R 550 MET cc_start: 0.6711 (ppp) cc_final: 0.6473 (ppp) outliers start: 136 outliers final: 90 residues processed: 1438 average time/residue: 0.6303 time to fit residues: 1481.6055 Evaluate side-chains 1429 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1332 time to evaluate : 5.175 ------------------------------------------------------------------------------- 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 47 ASP 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 E residue 37 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 378 ASN Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 340 ILE Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 5 GLN 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 364 ASN Chi-restraints excluded: chain I residue 253 ILE 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 166 THR Chi-restraints excluded: chain J residue 186 ASN 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 47 ASP Chi-restraints excluded: chain K residue 243 VAL Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 295 ILE Chi-restraints excluded: chain K residue 323 LEU Chi-restraints excluded: chain K residue 401 GLU 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 L residue 293 GLU Chi-restraints excluded: chain L residue 335 GLU Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 196 GLU Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 297 ASN Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain M residue 448 MET 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 94 ILE Chi-restraints excluded: chain N residue 130 SER 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 515 THR 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 97 TYR Chi-restraints excluded: chain O residue 124 SER 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 396 LEU Chi-restraints excluded: chain O residue 472 THR Chi-restraints excluded: chain O residue 473 VAL Chi-restraints excluded: chain P residue 123 SER Chi-restraints excluded: chain P residue 267 ILE Chi-restraints excluded: chain P residue 283 ASN Chi-restraints excluded: chain P residue 495 LYS Chi-restraints excluded: chain P residue 510 SER 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 283 ASN 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 205 ILE 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: 8.9990 chunk 544 optimal weight: 0.5980 chunk 375 optimal weight: 0.7980 chunk 80 optimal weight: 0.0050 chunk 345 optimal weight: 3.9990 chunk 486 optimal weight: 0.9980 chunk 726 optimal weight: 0.8980 chunk 769 optimal weight: 0.0670 chunk 379 optimal weight: 0.8980 chunk 688 optimal weight: 2.9990 chunk 207 optimal weight: 9.9990 overall best weight: 0.4732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 GLN B 313 HIS C 24 GLN C 159 GLN D 360 ASN G 54 GLN G 55 ASN I 247 GLN J 5 GLN J 24 GLN K 77 ASN ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 429 ASN N 531 ASN N 560 GLN O 383 GLN P 427 GLN P 586 GLN ** Q 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 277 GLN Q 297 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 65426 Z= 0.124 Angle : 0.501 13.701 88551 Z= 0.250 Chirality : 0.040 0.185 9656 Planarity : 0.003 0.049 11363 Dihedral : 9.421 144.670 9413 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.51 % Allowed : 13.74 % Favored : 84.75 % 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: -0.94 (0.09), residues: 7933 helix: 0.36 (0.10), residues: 2963 sheet: 0.41 (0.17), residues: 942 loop : -1.69 (0.09), residues: 4028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP E 49 HIS 0.004 0.001 HIS I 267 PHE 0.016 0.001 PHE M 457 TYR 0.023 0.001 TYR Q 548 ARG 0.006 0.000 ARG B 290 *********************** 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 1463 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1362 time to evaluate : 5.228 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 293 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7284 (tm-30) REVERT: A 316 ARG cc_start: 0.6516 (mtp180) cc_final: 0.6287 (mtp85) REVERT: A 374 LYS cc_start: 0.7696 (mttt) cc_final: 0.7495 (mttt) REVERT: B 88 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6743 (mt-10) REVERT: B 128 GLU cc_start: 0.7013 (tm-30) cc_final: 0.6744 (tm-30) REVERT: B 242 GLU cc_start: 0.7809 (tt0) cc_final: 0.7268 (tt0) REVERT: B 250 ASP cc_start: 0.7786 (m-30) cc_final: 0.7489 (m-30) REVERT: B 256 ILE cc_start: 0.8337 (tt) cc_final: 0.8068 (tt) REVERT: B 257 ILE cc_start: 0.8628 (mm) cc_final: 0.8361 (mt) REVERT: C 105 GLU cc_start: 0.7696 (tt0) cc_final: 0.7433 (tt0) REVERT: C 106 GLU cc_start: 0.7383 (tp30) cc_final: 0.7040 (tp30) REVERT: C 352 GLU cc_start: 0.6714 (mp0) cc_final: 0.6231 (mp0) REVERT: C 353 LYS cc_start: 0.7351 (mtmm) cc_final: 0.7020 (mtmm) REVERT: D 50 LYS cc_start: 0.7887 (mmmt) cc_final: 0.7604 (ttmm) REVERT: D 74 ASP cc_start: 0.7516 (m-30) cc_final: 0.7119 (m-30) REVERT: D 110 LYS cc_start: 0.8210 (mttp) cc_final: 0.7804 (mttp) REVERT: D 197 TYR cc_start: 0.8251 (m-10) cc_final: 0.7655 (m-80) REVERT: D 259 LYS cc_start: 0.7703 (tppp) cc_final: 0.7499 (tppp) REVERT: D 335 GLU cc_start: 0.7687 (pm20) cc_final: 0.7463 (pm20) REVERT: E 54 GLN cc_start: 0.8421 (tm-30) cc_final: 0.7931 (tm-30) REVERT: E 66 LYS cc_start: 0.7936 (tptm) cc_final: 0.7454 (tptt) REVERT: E 196 PHE cc_start: 0.8449 (t80) cc_final: 0.8228 (t80) REVERT: E 250 ASP cc_start: 0.7692 (m-30) cc_final: 0.7247 (m-30) REVERT: E 342 LYS cc_start: 0.7657 (tttm) cc_final: 0.7417 (tttm) REVERT: F 21 SER cc_start: 0.8334 (t) cc_final: 0.8013 (t) REVERT: G 58 GLU cc_start: 0.7374 (tm-30) cc_final: 0.6815 (tm-30) REVERT: G 110 LYS cc_start: 0.7634 (mppt) cc_final: 0.7324 (tppt) REVERT: G 142 LYS cc_start: 0.7975 (ttpp) cc_final: 0.7588 (ttpp) REVERT: G 250 ASP cc_start: 0.8109 (t0) cc_final: 0.7833 (t0) REVERT: G 259 LYS cc_start: 0.7981 (tptp) cc_final: 0.6888 (tptp) REVERT: G 262 PHE cc_start: 0.6945 (p90) cc_final: 0.6594 (p90) REVERT: H 58 GLU cc_start: 0.7427 (tp30) cc_final: 0.7201 (tp30) REVERT: H 72 GLN cc_start: 0.6674 (pp30) cc_final: 0.6466 (pp30) REVERT: I 135 GLN cc_start: 0.8312 (mm-40) cc_final: 0.8043 (mm-40) REVERT: J 108 PHE cc_start: 0.8507 (m-80) cc_final: 0.8069 (m-80) REVERT: J 117 LYS cc_start: 0.6367 (ptmt) cc_final: 0.5781 (mmtt) REVERT: J 126 THR cc_start: 0.8815 (m) cc_final: 0.8539 (p) REVERT: J 143 TYR cc_start: 0.6798 (m-80) cc_final: 0.5976 (m-80) REVERT: J 184 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6417 (pp) REVERT: J 189 SER cc_start: 0.8333 (p) cc_final: 0.8069 (m) REVERT: K 9 LYS cc_start: 0.8226 (tttt) cc_final: 0.7976 (mmtt) REVERT: K 76 ASP cc_start: 0.7016 (m-30) cc_final: 0.6576 (m-30) REVERT: K 106 GLU cc_start: 0.7487 (pm20) cc_final: 0.6939 (pm20) REVERT: K 128 GLU cc_start: 0.7044 (tm-30) cc_final: 0.6784 (tm-30) REVERT: K 130 PHE cc_start: 0.8126 (t80) cc_final: 0.7899 (t80) REVERT: K 353 LYS cc_start: 0.7657 (mptt) cc_final: 0.7128 (mptt) REVERT: K 401 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6606 (tm-30) REVERT: L 50 LYS cc_start: 0.8252 (mttm) cc_final: 0.7886 (mttm) REVERT: L 88 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6792 (mp0) REVERT: L 104 GLU cc_start: 0.6762 (tt0) cc_final: 0.6561 (tt0) REVERT: L 118 GLU cc_start: 0.7419 (tp30) cc_final: 0.7096 (tp30) REVERT: L 222 TYR cc_start: 0.8355 (m-80) cc_final: 0.7914 (m-80) REVERT: L 227 HIS cc_start: 0.6999 (m90) cc_final: 0.6752 (m90) REVERT: L 251 GLU cc_start: 0.7191 (tt0) cc_final: 0.6937 (tt0) REVERT: L 323 LEU cc_start: 0.7880 (mt) cc_final: 0.7516 (mt) REVERT: M 97 TYR cc_start: 0.5518 (m-80) cc_final: 0.5090 (m-80) REVERT: M 254 LYS cc_start: 0.8048 (tppp) cc_final: 0.7650 (tppp) REVERT: M 294 LYS cc_start: 0.7905 (ptmm) cc_final: 0.7622 (ptmm) REVERT: M 299 TYR cc_start: 0.8183 (p90) cc_final: 0.7823 (p90) REVERT: M 308 PHE cc_start: 0.7937 (t80) cc_final: 0.7551 (t80) REVERT: M 318 ASN cc_start: 0.8761 (t0) cc_final: 0.8370 (t0) REVERT: M 319 GLN cc_start: 0.7998 (pm20) cc_final: 0.7203 (mt0) REVERT: M 352 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7486 (mm-30) REVERT: M 468 ARG cc_start: 0.6886 (ttm110) cc_final: 0.6564 (ttm110) REVERT: M 516 GLN cc_start: 0.7574 (pt0) cc_final: 0.7297 (pt0) REVERT: N 114 GLU cc_start: 0.7062 (tt0) cc_final: 0.6780 (tt0) REVERT: N 268 LYS cc_start: 0.8314 (mtpt) cc_final: 0.8052 (mtpt) REVERT: N 277 GLN cc_start: 0.7475 (mt0) cc_final: 0.7073 (mt0) REVERT: N 353 PHE cc_start: 0.7114 (m-80) cc_final: 0.6914 (m-80) REVERT: N 425 LYS cc_start: 0.8264 (ttpt) cc_final: 0.8027 (ttmt) REVERT: N 467 GLU cc_start: 0.8081 (tp30) cc_final: 0.7683 (tp30) REVERT: O 186 PHE cc_start: 0.8262 (t80) cc_final: 0.7986 (t80) REVERT: O 268 LYS cc_start: 0.7948 (mtmt) cc_final: 0.7570 (mtpp) REVERT: O 327 ASP cc_start: 0.7277 (t0) cc_final: 0.6818 (t0) REVERT: O 380 ILE cc_start: 0.8202 (tp) cc_final: 0.7968 (tp) REVERT: O 416 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6727 (tm-30) REVERT: O 448 MET cc_start: 0.6619 (tpt) cc_final: 0.6323 (tpt) REVERT: O 477 GLU cc_start: 0.8168 (tp30) cc_final: 0.7070 (mm-30) REVERT: O 601 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8224 (mm-30) REVERT: P 183 LYS cc_start: 0.7726 (mmmm) cc_final: 0.6807 (mtpp) REVERT: P 246 TYR cc_start: 0.7455 (t80) cc_final: 0.7194 (t80) REVERT: P 277 GLN cc_start: 0.7528 (mt0) cc_final: 0.7297 (mp10) REVERT: P 459 GLU cc_start: 0.7667 (tp30) cc_final: 0.7105 (tp30) REVERT: P 467 GLU cc_start: 0.7259 (tp30) cc_final: 0.6786 (tp30) REVERT: P 495 LYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6741 (mtpt) REVERT: P 508 LYS cc_start: 0.7867 (mttp) cc_final: 0.7412 (mmtp) REVERT: P 524 THR cc_start: 0.7333 (t) cc_final: 0.5565 (p) REVERT: Q 68 MET cc_start: 0.7855 (tpp) cc_final: 0.7653 (tpp) REVERT: Q 146 LYS cc_start: 0.7804 (mppt) cc_final: 0.7527 (mppt) REVERT: Q 192 ARG cc_start: 0.6617 (ttt180) cc_final: 0.6259 (ttt90) REVERT: Q 211 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7017 (mm-30) REVERT: Q 444 ASP cc_start: 0.7720 (m-30) cc_final: 0.7407 (m-30) REVERT: Q 448 MET cc_start: 0.6699 (mmp) cc_final: 0.6427 (mmp) REVERT: Q 455 GLU cc_start: 0.7552 (pt0) cc_final: 0.6849 (pt0) REVERT: Q 459 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7142 (mt-10) REVERT: Q 516 GLN cc_start: 0.7270 (pp30) cc_final: 0.6967 (pp30) REVERT: Q 520 GLU cc_start: 0.6811 (mp0) cc_final: 0.6396 (mp0) REVERT: Q 536 ARG cc_start: 0.6358 (tpt-90) cc_final: 0.5390 (tpt-90) REVERT: Q 592 LYS cc_start: 0.7633 (mmmt) cc_final: 0.7389 (mmmt) REVERT: R 22 ARG cc_start: 0.6644 (mtt90) cc_final: 0.6159 (mtp85) REVERT: R 105 GLU cc_start: 0.6410 (pm20) cc_final: 0.5692 (pp20) REVERT: R 117 ARG cc_start: 0.5873 (tpt170) cc_final: 0.5589 (tpt-90) REVERT: R 205 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7393 (mp) REVERT: R 221 ASN cc_start: 0.7757 (t0) cc_final: 0.7363 (t0) REVERT: R 259 GLN cc_start: 0.6846 (pp30) cc_final: 0.6570 (pm20) REVERT: R 271 ARG cc_start: 0.7993 (ptp90) cc_final: 0.7343 (mtm-85) REVERT: R 382 GLN cc_start: 0.7432 (pp30) cc_final: 0.6903 (pp30) outliers start: 101 outliers final: 66 residues processed: 1397 average time/residue: 0.6282 time to fit residues: 1433.9198 Evaluate side-chains 1411 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1340 time to evaluate : 5.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 335 GLU 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 37 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 274 ASN Chi-restraints excluded: chain E residue 406 LEU 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 G residue 43 LYS Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 227 HIS Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain I residue 266 GLN Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 186 ASN Chi-restraints excluded: chain J residue 234 GLN Chi-restraints excluded: chain J residue 373 SER 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 207 ASN Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 342 LYS Chi-restraints excluded: chain K residue 401 GLU 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 311 ASP Chi-restraints excluded: chain L residue 335 GLU Chi-restraints excluded: chain M residue 196 GLU Chi-restraints excluded: chain M residue 211 GLU Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 429 ASN Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 203 ILE Chi-restraints excluded: chain N residue 414 SER Chi-restraints excluded: chain N residue 498 GLU Chi-restraints excluded: chain N residue 515 THR Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 97 TYR 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 473 VAL Chi-restraints excluded: chain O residue 544 GLN Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain P residue 495 LYS Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain P residue 574 SER Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 93 GLN 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 584 ILE Chi-restraints excluded: chain R residue 14 TYR Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 476 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 640 optimal weight: 2.9990 chunk 436 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 572 optimal weight: 8.9990 chunk 317 optimal weight: 1.9990 chunk 656 optimal weight: 4.9990 chunk 531 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 392 optimal weight: 3.9990 chunk 690 optimal weight: 9.9990 chunk 194 optimal weight: 0.0040 overall best weight: 2.6000 ------------------------------------------------------------------------------- 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 72 GLN D 360 ASN G 55 ASN G 365 GLN ** H 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 315 ASN J 24 GLN J 378 ASN K 77 ASN L 8 ASN L 24 GLN ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 560 GLN O 383 GLN P 427 GLN ** Q 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 277 GLN R 429 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 65426 Z= 0.377 Angle : 0.623 14.255 88551 Z= 0.316 Chirality : 0.045 0.193 9656 Planarity : 0.004 0.055 11363 Dihedral : 9.447 150.839 9413 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.47 % Allowed : 14.96 % Favored : 82.56 % 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: -1.31 (0.09), residues: 7933 helix: 0.04 (0.10), residues: 2946 sheet: 0.10 (0.18), residues: 921 loop : -1.84 (0.09), residues: 4066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 49 HIS 0.010 0.001 HIS P 224 PHE 0.026 0.002 PHE P 101 TYR 0.028 0.002 TYR E 224 ARG 0.009 0.001 ARG O 22 *********************** 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 1524 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1359 time to evaluate : 5.154 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 293 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7355 (tm-30) REVERT: B 88 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6798 (mt-10) REVERT: B 97 LYS cc_start: 0.8211 (ttmm) cc_final: 0.7999 (ttmm) REVERT: B 128 GLU cc_start: 0.7104 (tm-30) cc_final: 0.6833 (tm-30) REVERT: B 250 ASP cc_start: 0.7873 (m-30) cc_final: 0.7581 (m-30) REVERT: C 106 GLU cc_start: 0.7580 (tp30) cc_final: 0.7285 (tp30) REVERT: C 352 GLU cc_start: 0.6799 (mp0) cc_final: 0.6304 (mp0) REVERT: D 50 LYS cc_start: 0.7922 (mmmt) cc_final: 0.7652 (ttmm) REVERT: D 74 ASP cc_start: 0.7559 (m-30) cc_final: 0.7167 (m-30) REVERT: D 110 LYS cc_start: 0.8235 (mttp) cc_final: 0.7905 (mttp) REVERT: D 197 TYR cc_start: 0.8266 (m-10) cc_final: 0.7727 (m-80) REVERT: D 335 GLU cc_start: 0.7802 (pm20) cc_final: 0.7355 (pm20) REVERT: D 363 PHE cc_start: 0.8039 (m-10) cc_final: 0.7698 (m-80) REVERT: E 54 GLN cc_start: 0.8434 (tm-30) cc_final: 0.7984 (tm-30) REVERT: E 66 LYS cc_start: 0.7978 (tptm) cc_final: 0.7460 (tptt) REVERT: E 342 LYS cc_start: 0.7752 (tttm) cc_final: 0.7529 (tttm) REVERT: F 21 SER cc_start: 0.8377 (t) cc_final: 0.8031 (t) REVERT: G 43 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8002 (ptmt) REVERT: G 107 GLU cc_start: 0.7414 (tp30) cc_final: 0.7205 (tp30) REVERT: G 110 LYS cc_start: 0.7698 (mppt) cc_final: 0.7436 (tppt) REVERT: G 142 LYS cc_start: 0.8036 (ttpp) cc_final: 0.7670 (ttpp) REVERT: G 250 ASP cc_start: 0.8157 (t0) cc_final: 0.7866 (t0) REVERT: G 262 PHE cc_start: 0.6915 (p90) cc_final: 0.6626 (p90) REVERT: H 58 GLU cc_start: 0.7596 (tp30) cc_final: 0.7370 (tp30) REVERT: H 205 PHE cc_start: 0.8859 (OUTLIER) cc_final: 0.6767 (m-80) REVERT: H 291 PHE cc_start: 0.7633 (t80) cc_final: 0.7253 (t80) REVERT: I 142 LYS cc_start: 0.7577 (ptpp) cc_final: 0.7102 (mtmm) REVERT: J 100 ARG cc_start: 0.7157 (mtp85) cc_final: 0.6789 (mtp85) REVERT: J 143 TYR cc_start: 0.6852 (m-80) cc_final: 0.5919 (m-80) REVERT: J 184 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6466 (pp) REVERT: J 189 SER cc_start: 0.8357 (p) cc_final: 0.8149 (m) REVERT: J 287 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.6438 (mtt) REVERT: J 316 ARG cc_start: 0.8331 (mmm160) cc_final: 0.8023 (mmm160) REVERT: K 76 ASP cc_start: 0.7063 (m-30) cc_final: 0.6590 (m-30) REVERT: K 106 GLU cc_start: 0.7589 (pm20) cc_final: 0.7226 (pm20) REVERT: K 128 GLU cc_start: 0.7132 (tm-30) cc_final: 0.6902 (tm-30) REVERT: K 353 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7309 (mptt) REVERT: K 401 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6643 (tm-30) REVERT: L 14 ASP cc_start: 0.6970 (m-30) cc_final: 0.6722 (m-30) REVERT: L 50 LYS cc_start: 0.8222 (mttm) cc_final: 0.7837 (mttm) REVERT: L 88 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: L 104 GLU cc_start: 0.6864 (tt0) cc_final: 0.6591 (tt0) REVERT: L 118 GLU cc_start: 0.7347 (tp30) cc_final: 0.7002 (tp30) REVERT: L 227 HIS cc_start: 0.7027 (m90) cc_final: 0.6799 (m90) REVERT: L 251 GLU cc_start: 0.7276 (tt0) cc_final: 0.7018 (tt0) REVERT: L 323 LEU cc_start: 0.7948 (mt) cc_final: 0.7617 (mt) REVERT: M 70 PHE cc_start: 0.6845 (m-80) cc_final: 0.6262 (m-80) REVERT: M 254 LYS cc_start: 0.8141 (tppp) cc_final: 0.7703 (tppp) REVERT: M 294 LYS cc_start: 0.7965 (ptmm) cc_final: 0.7514 (ptmm) REVERT: M 299 TYR cc_start: 0.8265 (p90) cc_final: 0.7704 (p90) REVERT: M 308 PHE cc_start: 0.8065 (t80) cc_final: 0.7751 (t80) REVERT: M 319 GLN cc_start: 0.8009 (pm20) cc_final: 0.7320 (mt0) REVERT: M 352 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7448 (mm-30) REVERT: M 421 PHE cc_start: 0.6550 (m-10) cc_final: 0.6347 (m-10) REVERT: M 468 ARG cc_start: 0.7178 (ttm110) cc_final: 0.6694 (ttp-110) REVERT: M 516 GLN cc_start: 0.7663 (pt0) cc_final: 0.7363 (pt0) REVERT: N 114 GLU cc_start: 0.7214 (tt0) cc_final: 0.6906 (tt0) REVERT: N 268 LYS cc_start: 0.8396 (mtpt) cc_final: 0.8164 (mtpt) REVERT: N 277 GLN cc_start: 0.7706 (mt0) cc_final: 0.7238 (mt0) REVERT: N 353 PHE cc_start: 0.7212 (m-80) cc_final: 0.6975 (m-80) REVERT: N 425 LYS cc_start: 0.8314 (ttpt) cc_final: 0.8078 (ttmt) REVERT: N 467 GLU cc_start: 0.8100 (tp30) cc_final: 0.7661 (tp30) REVERT: O 64 ARG cc_start: 0.7023 (ptp-110) cc_final: 0.6808 (ptp-110) REVERT: O 186 PHE cc_start: 0.8332 (t80) cc_final: 0.8023 (t80) REVERT: O 254 LYS cc_start: 0.8728 (tptp) cc_final: 0.8494 (tptp) REVERT: O 268 LYS cc_start: 0.8029 (mtmt) cc_final: 0.7616 (mtpp) REVERT: O 327 ASP cc_start: 0.7289 (t0) cc_final: 0.6893 (t0) REVERT: O 380 ILE cc_start: 0.8302 (tp) cc_final: 0.8063 (tp) REVERT: O 416 GLU cc_start: 0.7289 (tm-30) cc_final: 0.6834 (tm-30) REVERT: O 448 MET cc_start: 0.6903 (tpt) cc_final: 0.6565 (tpt) REVERT: P 110 VAL cc_start: 0.7299 (OUTLIER) cc_final: 0.7082 (m) REVERT: P 176 LEU cc_start: 0.6316 (OUTLIER) cc_final: 0.5351 (mt) REVERT: P 246 TYR cc_start: 0.7587 (t80) cc_final: 0.7295 (t80) REVERT: P 277 GLN cc_start: 0.7758 (mt0) cc_final: 0.7401 (mp-120) REVERT: P 459 GLU cc_start: 0.7731 (tp30) cc_final: 0.7165 (tp30) REVERT: P 502 LYS cc_start: 0.7505 (mmtt) cc_final: 0.6878 (mmtt) REVERT: P 508 LYS cc_start: 0.7986 (mttp) cc_final: 0.7552 (mmtp) REVERT: P 524 THR cc_start: 0.7394 (t) cc_final: 0.5284 (p) REVERT: P 542 ASP cc_start: 0.5296 (OUTLIER) cc_final: 0.4349 (m-30) REVERT: Q 146 LYS cc_start: 0.8000 (mppt) cc_final: 0.7700 (mppt) REVERT: Q 211 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7219 (mm-30) REVERT: Q 444 ASP cc_start: 0.7701 (m-30) cc_final: 0.7415 (m-30) REVERT: Q 448 MET cc_start: 0.6841 (mmp) cc_final: 0.6515 (mmp) REVERT: Q 455 GLU cc_start: 0.7628 (pt0) cc_final: 0.6850 (pt0) REVERT: Q 459 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7053 (mt-10) REVERT: Q 516 GLN cc_start: 0.7307 (pp30) cc_final: 0.6840 (pp30) REVERT: Q 517 ARG cc_start: 0.7399 (mmm-85) cc_final: 0.6886 (mmm-85) REVERT: Q 520 GLU cc_start: 0.6990 (mp0) cc_final: 0.6538 (mp0) REVERT: Q 534 SER cc_start: 0.7906 (t) cc_final: 0.7677 (t) REVERT: Q 592 LYS cc_start: 0.7661 (mmmt) cc_final: 0.7446 (mmmt) REVERT: R 22 ARG cc_start: 0.6689 (mtt90) cc_final: 0.6144 (mtp85) REVERT: R 205 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7428 (mp) REVERT: R 221 ASN cc_start: 0.7908 (t0) cc_final: 0.7477 (t0) REVERT: R 259 GLN cc_start: 0.6852 (pp30) cc_final: 0.6609 (pm20) REVERT: R 271 ARG cc_start: 0.8063 (ptp90) cc_final: 0.7225 (mtm-85) REVERT: R 382 GLN cc_start: 0.7580 (pp30) cc_final: 0.7108 (pp30) REVERT: R 550 MET cc_start: 0.6656 (ppp) cc_final: 0.6428 (ppp) outliers start: 165 outliers final: 120 residues processed: 1427 average time/residue: 0.6693 time to fit residues: 1576.8885 Evaluate side-chains 1470 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1339 time to evaluate : 5.234 ------------------------------------------------------------------------------- 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 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 47 ASP Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 274 ASN 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 295 ILE Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain F residue 378 ASN 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 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 152 ILE Chi-restraints excluded: chain H residue 202 ASP Chi-restraints excluded: chain H residue 205 PHE Chi-restraints excluded: chain H residue 227 HIS Chi-restraints excluded: chain H residue 256 ILE 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 314 ILE Chi-restraints excluded: chain J residue 116 TYR Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 186 ASN 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 373 SER 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 295 ILE Chi-restraints excluded: chain K residue 323 LEU Chi-restraints excluded: chain K residue 353 LYS Chi-restraints excluded: chain K residue 401 GLU 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 125 LEU Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 168 ASN Chi-restraints excluded: chain L residue 293 GLU Chi-restraints excluded: chain L residue 335 GLU Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 196 GLU Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 297 ASN 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 131 ASP Chi-restraints excluded: chain N residue 165 VAL 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 506 LYS Chi-restraints excluded: chain N residue 515 THR 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 97 TYR 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 402 LEU Chi-restraints excluded: chain O residue 433 VAL 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 O residue 544 GLN Chi-restraints excluded: chain P residue 12 ILE Chi-restraints excluded: chain P residue 110 VAL Chi-restraints excluded: chain P residue 123 SER Chi-restraints excluded: chain P residue 176 LEU Chi-restraints excluded: chain P residue 267 ILE Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain P residue 510 SER Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain P residue 542 ASP Chi-restraints excluded: chain P residue 574 SER Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 283 ASN Chi-restraints excluded: chain Q residue 425 LYS Chi-restraints excluded: chain Q residue 449 LEU Chi-restraints excluded: chain Q residue 468 ARG Chi-restraints excluded: chain Q residue 483 LEU Chi-restraints excluded: chain Q residue 550 MET 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 205 ILE Chi-restraints excluded: chain R residue 469 SER Chi-restraints excluded: chain R residue 476 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 258 optimal weight: 0.8980 chunk 692 optimal weight: 0.0050 chunk 152 optimal weight: 0.9990 chunk 451 optimal weight: 0.0030 chunk 189 optimal weight: 8.9990 chunk 770 optimal weight: 40.0000 chunk 639 optimal weight: 0.0570 chunk 356 optimal weight: 0.9990 chunk 64 optimal weight: 30.0000 chunk 254 optimal weight: 0.0170 chunk 404 optimal weight: 1.9990 overall best weight: 0.1960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 GLN C 81 ASN D 5 GLN D 360 ASN H 364 ASN I 247 GLN J 5 GLN J 24 GLN K 24 GLN K 77 ASN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 560 GLN O 383 GLN P 47 GLN P 427 GLN P 586 GLN Q 187 ASN Q 277 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 65426 Z= 0.121 Angle : 0.503 15.423 88551 Z= 0.250 Chirality : 0.040 0.170 9656 Planarity : 0.003 0.050 11363 Dihedral : 8.731 145.552 9413 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.97 % Favored : 96.02 % Rotamer: Outliers : 1.66 % Allowed : 16.70 % Favored : 81.64 % 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: 0.37 (0.10), residues: 2943 sheet: 0.42 (0.18), residues: 924 loop : -1.68 (0.09), residues: 4066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 49 HIS 0.007 0.001 HIS O 480 PHE 0.018 0.001 PHE O 576 TYR 0.027 0.001 TYR Q 548 ARG 0.013 0.000 ARG O 22 *********************** 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 1447 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1336 time to evaluate : 5.494 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 293 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7317 (tm-30) REVERT: A 316 ARG cc_start: 0.6418 (mtp180) cc_final: 0.6143 (mtp85) REVERT: A 338 GLU cc_start: 0.5884 (mp0) cc_final: 0.5533 (mp0) REVERT: B 88 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6672 (mt-10) REVERT: B 128 GLU cc_start: 0.7046 (tm-30) cc_final: 0.6753 (tm-30) REVERT: B 250 ASP cc_start: 0.7789 (m-30) cc_final: 0.7528 (m-30) REVERT: B 345 LYS cc_start: 0.7860 (ptpt) cc_final: 0.7657 (ptpp) REVERT: C 100 ARG cc_start: 0.7237 (ttt-90) cc_final: 0.6802 (tmt-80) REVERT: C 105 GLU cc_start: 0.7729 (tt0) cc_final: 0.7396 (mt-10) REVERT: C 106 GLU cc_start: 0.7417 (tp30) cc_final: 0.7028 (tp30) REVERT: C 352 GLU cc_start: 0.6668 (mp0) cc_final: 0.6191 (mp0) REVERT: C 353 LYS cc_start: 0.7334 (mtmm) cc_final: 0.7009 (mtmm) REVERT: D 50 LYS cc_start: 0.7897 (mmmt) cc_final: 0.7607 (ttmm) REVERT: D 110 LYS cc_start: 0.8215 (mttp) cc_final: 0.7892 (mttp) REVERT: D 197 TYR cc_start: 0.8294 (m-10) cc_final: 0.7712 (m-80) REVERT: D 322 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7926 (mt) REVERT: D 335 GLU cc_start: 0.7749 (pm20) cc_final: 0.7540 (pm20) REVERT: D 363 PHE cc_start: 0.7883 (m-80) cc_final: 0.7531 (m-80) REVERT: E 54 GLN cc_start: 0.8408 (tm-30) cc_final: 0.8002 (tm-30) REVERT: E 66 LYS cc_start: 0.7951 (tptm) cc_final: 0.7447 (tptt) REVERT: E 196 PHE cc_start: 0.8466 (t80) cc_final: 0.8263 (t80) REVERT: E 250 ASP cc_start: 0.7691 (m-30) cc_final: 0.7231 (m-30) REVERT: E 342 LYS cc_start: 0.7665 (tttm) cc_final: 0.7420 (tttm) REVERT: E 382 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6699 (pm20) REVERT: F 21 SER cc_start: 0.8301 (t) cc_final: 0.7996 (t) REVERT: F 361 MET cc_start: 0.6840 (mtt) cc_final: 0.6381 (mtt) REVERT: G 43 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8014 (ptmt) REVERT: G 58 GLU cc_start: 0.7347 (tm-30) cc_final: 0.6844 (tm-30) REVERT: G 110 LYS cc_start: 0.7645 (mppt) cc_final: 0.7365 (tppt) REVERT: G 142 LYS cc_start: 0.7978 (ttpp) cc_final: 0.7602 (ttpp) REVERT: G 250 ASP cc_start: 0.8095 (t0) cc_final: 0.7827 (t0) REVERT: G 259 LYS cc_start: 0.8002 (tptp) cc_final: 0.6892 (tptp) REVERT: G 262 PHE cc_start: 0.6915 (p90) cc_final: 0.6612 (p90) REVERT: G 303 PHE cc_start: 0.6808 (m-10) cc_final: 0.6543 (m-10) REVERT: H 58 GLU cc_start: 0.7577 (tp30) cc_final: 0.7328 (tp30) REVERT: H 110 LYS cc_start: 0.8377 (mmmm) cc_final: 0.8049 (mtpp) REVERT: H 205 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.6917 (m-80) REVERT: J 100 ARG cc_start: 0.6802 (mtp85) cc_final: 0.6505 (mtp85) REVERT: J 108 PHE cc_start: 0.8482 (m-80) cc_final: 0.8127 (m-80) REVERT: J 116 TYR cc_start: 0.6851 (OUTLIER) cc_final: 0.6480 (m-80) REVERT: J 126 THR cc_start: 0.8768 (m) cc_final: 0.8540 (p) REVERT: J 143 TYR cc_start: 0.6494 (m-80) cc_final: 0.5643 (m-80) REVERT: J 189 SER cc_start: 0.8327 (p) cc_final: 0.8058 (m) REVERT: K 9 LYS cc_start: 0.8253 (tttt) cc_final: 0.8037 (mmtt) REVERT: K 56 TYR cc_start: 0.8266 (m-80) cc_final: 0.7889 (m-80) REVERT: K 76 ASP cc_start: 0.6958 (m-30) cc_final: 0.6508 (m-30) REVERT: K 106 GLU cc_start: 0.7483 (pm20) cc_final: 0.6968 (pm20) REVERT: K 128 GLU cc_start: 0.7043 (tm-30) cc_final: 0.6800 (tm-30) REVERT: K 129 GLN cc_start: 0.8279 (mm-40) cc_final: 0.8043 (mt0) REVERT: K 353 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7353 (mptt) REVERT: L 28 VAL cc_start: 0.8326 (p) cc_final: 0.8121 (m) REVERT: L 50 LYS cc_start: 0.8177 (mttm) cc_final: 0.7808 (mttm) REVERT: L 88 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6935 (mp0) REVERT: L 104 GLU cc_start: 0.6786 (tt0) cc_final: 0.6557 (tt0) REVERT: L 118 GLU cc_start: 0.7317 (tp30) cc_final: 0.6929 (tp30) REVERT: L 227 HIS cc_start: 0.6972 (m90) cc_final: 0.6734 (m90) REVERT: L 251 GLU cc_start: 0.7156 (tt0) cc_final: 0.6881 (tt0) REVERT: L 323 LEU cc_start: 0.7828 (mt) cc_final: 0.7458 (mt) REVERT: M 254 LYS cc_start: 0.8079 (tppp) cc_final: 0.7675 (tppp) REVERT: M 294 LYS cc_start: 0.7861 (ptmm) cc_final: 0.7425 (ptmm) REVERT: M 299 TYR cc_start: 0.8226 (p90) cc_final: 0.7731 (p90) REVERT: M 308 PHE cc_start: 0.7921 (t80) cc_final: 0.7643 (t80) REVERT: M 319 GLN cc_start: 0.7977 (pm20) cc_final: 0.7327 (mt0) REVERT: M 352 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7330 (mm-30) REVERT: M 468 ARG cc_start: 0.6912 (ttm110) cc_final: 0.6604 (ttm110) REVERT: M 516 GLN cc_start: 0.7561 (pt0) cc_final: 0.7247 (pt0) REVERT: N 114 GLU cc_start: 0.7052 (tt0) cc_final: 0.6775 (tt0) REVERT: N 268 LYS cc_start: 0.8318 (mtpt) cc_final: 0.8061 (mtpt) REVERT: N 277 GLN cc_start: 0.7503 (mt0) cc_final: 0.7213 (mt0) REVERT: N 353 PHE cc_start: 0.7116 (m-80) cc_final: 0.6889 (m-80) REVERT: N 425 LYS cc_start: 0.8256 (ttpt) cc_final: 0.8030 (ttmt) REVERT: N 467 GLU cc_start: 0.8093 (tp30) cc_final: 0.7711 (tp30) REVERT: N 560 GLN cc_start: 0.7900 (mt0) cc_final: 0.7527 (mt0) REVERT: O 254 LYS cc_start: 0.8622 (tptp) cc_final: 0.8324 (tptp) REVERT: O 268 LYS cc_start: 0.7956 (mtmt) cc_final: 0.7733 (mtpp) REVERT: O 327 ASP cc_start: 0.7285 (t0) cc_final: 0.6839 (t0) REVERT: O 380 ILE cc_start: 0.8246 (tp) cc_final: 0.7990 (tp) REVERT: O 416 GLU cc_start: 0.7247 (tm-30) cc_final: 0.6815 (tm-30) REVERT: O 424 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7666 (mm-30) REVERT: O 448 MET cc_start: 0.6547 (tpt) cc_final: 0.6216 (tpt) REVERT: O 455 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7691 (mm-30) REVERT: O 601 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8068 (mm-30) REVERT: P 183 LYS cc_start: 0.7734 (mmmm) cc_final: 0.6768 (mtpp) REVERT: P 246 TYR cc_start: 0.7434 (t80) cc_final: 0.7217 (t80) REVERT: P 277 GLN cc_start: 0.7603 (mt0) cc_final: 0.7325 (mp10) REVERT: P 441 LEU cc_start: 0.7914 (tp) cc_final: 0.7664 (tp) REVERT: P 508 LYS cc_start: 0.7852 (mttp) cc_final: 0.7372 (mmtp) REVERT: P 524 THR cc_start: 0.7291 (t) cc_final: 0.5470 (p) REVERT: P 586 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8124 (tm-30) REVERT: Q 50 ASP cc_start: 0.7534 (t0) cc_final: 0.6903 (t0) REVERT: Q 146 LYS cc_start: 0.7825 (mppt) cc_final: 0.7542 (mppt) REVERT: Q 192 ARG cc_start: 0.6589 (ttt180) cc_final: 0.6099 (ttt90) REVERT: Q 211 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7196 (mm-30) REVERT: Q 444 ASP cc_start: 0.7661 (m-30) cc_final: 0.7364 (m-30) REVERT: Q 448 MET cc_start: 0.6862 (mmp) cc_final: 0.6579 (mmp) REVERT: Q 455 GLU cc_start: 0.7599 (pt0) cc_final: 0.6770 (pt0) REVERT: Q 459 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7242 (mt-10) REVERT: Q 516 GLN cc_start: 0.7290 (pp30) cc_final: 0.6976 (pp30) REVERT: Q 520 GLU cc_start: 0.6930 (mp0) cc_final: 0.6288 (mp0) REVERT: R 22 ARG cc_start: 0.6669 (mtt90) cc_final: 0.6135 (mtp85) REVERT: R 205 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7399 (mp) REVERT: R 221 ASN cc_start: 0.7928 (t0) cc_final: 0.7511 (t0) REVERT: R 382 GLN cc_start: 0.7456 (pp30) cc_final: 0.6969 (pp30) REVERT: R 540 GLU cc_start: 0.6855 (tp30) cc_final: 0.6268 (tp30) REVERT: R 550 MET cc_start: 0.6609 (ppp) cc_final: 0.6367 (ppp) outliers start: 111 outliers final: 69 residues processed: 1380 average time/residue: 0.6703 time to fit residues: 1516.7699 Evaluate side-chains 1395 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1317 time to evaluate : 5.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 359 LYS 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 120 THR Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 205 PHE Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 364 ASN Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain I residue 8 ASN Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 266 GLN Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain J residue 116 TYR Chi-restraints excluded: chain J residue 186 ASN Chi-restraints excluded: chain J residue 234 GLN Chi-restraints excluded: chain J residue 389 LEU Chi-restraints excluded: chain K residue 47 ASP Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 353 LYS 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 168 ASN Chi-restraints excluded: chain L residue 293 GLU Chi-restraints excluded: chain L residue 311 ASP Chi-restraints excluded: chain M residue 281 LEU 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 94 ILE Chi-restraints excluded: chain N residue 203 ILE Chi-restraints excluded: chain N residue 414 SER Chi-restraints excluded: chain N residue 498 GLU Chi-restraints excluded: chain N residue 515 THR Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 97 TYR 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 473 VAL Chi-restraints excluded: chain O residue 478 GLU Chi-restraints excluded: chain O residue 544 GLN Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain P residue 574 SER Chi-restraints excluded: chain P residue 586 GLN Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 93 GLN Chi-restraints excluded: chain Q residue 134 ASN Chi-restraints excluded: chain Q residue 193 LYS Chi-restraints excluded: chain Q residue 425 LYS Chi-restraints excluded: chain Q residue 468 ARG 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 205 ILE Chi-restraints excluded: chain R residue 476 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 742 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 438 optimal weight: 0.0570 chunk 562 optimal weight: 0.0040 chunk 435 optimal weight: 3.9990 chunk 648 optimal weight: 4.9990 chunk 430 optimal weight: 2.9990 chunk 767 optimal weight: 20.0000 chunk 480 optimal weight: 4.9990 chunk 467 optimal weight: 0.8980 chunk 354 optimal weight: 3.9990 overall best weight: 0.9512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN B 72 GLN ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN B 360 ASN G 55 ASN H 364 ASN I 315 ASN J 5 GLN K 24 GLN K 360 ASN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 383 GLN P 38 HIS P 47 GLN P 586 GLN Q 187 ASN Q 277 GLN Q 297 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 65426 Z= 0.169 Angle : 0.511 14.860 88551 Z= 0.255 Chirality : 0.040 0.186 9656 Planarity : 0.003 0.048 11363 Dihedral : 8.686 144.410 9413 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.28 % Favored : 94.71 % Rotamer: Outliers : 1.89 % Allowed : 16.81 % Favored : 81.31 % 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: 0.36 (0.10), residues: 2958 sheet: 0.42 (0.18), residues: 928 loop : -1.70 (0.09), residues: 4047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 49 HIS 0.007 0.001 HIS O 480 PHE 0.020 0.001 PHE R 462 TYR 0.027 0.001 TYR Q 548 ARG 0.011 0.000 ARG O 22 *********************** 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 1449 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1323 time to evaluate : 5.244 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 72 GLN cc_start: 0.6692 (OUTLIER) cc_final: 0.6224 (pm20) REVERT: A 131 ARG cc_start: 0.8210 (ptm-80) cc_final: 0.7872 (ptm-80) REVERT: A 293 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7330 (tm-30) REVERT: A 316 ARG cc_start: 0.6484 (mtp180) cc_final: 0.6205 (mtp85) REVERT: A 338 GLU cc_start: 0.5920 (mp0) cc_final: 0.5544 (mp0) REVERT: B 47 ASP cc_start: 0.7500 (m-30) cc_final: 0.7293 (m-30) REVERT: B 88 GLU cc_start: 0.6980 (mt-10) cc_final: 0.6710 (mt-10) REVERT: B 128 GLU cc_start: 0.7074 (tm-30) cc_final: 0.6763 (tm-30) REVERT: B 132 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8123 (mm-30) REVERT: B 250 ASP cc_start: 0.7816 (m-30) cc_final: 0.7591 (m-30) REVERT: B 290 ARG cc_start: 0.6885 (mmt-90) cc_final: 0.6685 (mmt-90) REVERT: B 345 LYS cc_start: 0.7954 (ptpt) cc_final: 0.7749 (ptpp) REVERT: C 100 ARG cc_start: 0.7269 (ttt-90) cc_final: 0.6863 (tmt-80) REVERT: C 106 GLU cc_start: 0.7449 (tp30) cc_final: 0.7168 (tp30) REVERT: C 352 GLU cc_start: 0.6710 (mp0) cc_final: 0.6213 (mp0) REVERT: D 50 LYS cc_start: 0.7904 (mmmt) cc_final: 0.7614 (ttmm) REVERT: D 110 LYS cc_start: 0.8230 (mttp) cc_final: 0.7902 (mttp) REVERT: D 197 TYR cc_start: 0.8269 (m-10) cc_final: 0.7735 (m-80) REVERT: D 322 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7959 (mt) REVERT: D 335 GLU cc_start: 0.7753 (pm20) cc_final: 0.7540 (pm20) REVERT: D 363 PHE cc_start: 0.7913 (m-80) cc_final: 0.7553 (m-80) REVERT: E 54 GLN cc_start: 0.8415 (tm-30) cc_final: 0.8004 (tm-30) REVERT: E 250 ASP cc_start: 0.7747 (m-30) cc_final: 0.7308 (m-30) REVERT: E 342 LYS cc_start: 0.7688 (tttm) cc_final: 0.7455 (tttm) REVERT: E 382 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6689 (pm20) REVERT: G 43 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8037 (ptmt) REVERT: G 58 GLU cc_start: 0.7352 (tm-30) cc_final: 0.6844 (tm-30) REVERT: G 110 LYS cc_start: 0.7756 (mppt) cc_final: 0.7463 (tppt) REVERT: G 142 LYS cc_start: 0.8005 (ttpp) cc_final: 0.7651 (ttpp) REVERT: G 250 ASP cc_start: 0.8118 (t0) cc_final: 0.7845 (t0) REVERT: G 259 LYS cc_start: 0.8042 (tptp) cc_final: 0.6908 (tptp) REVERT: G 262 PHE cc_start: 0.6882 (p90) cc_final: 0.6585 (p90) REVERT: G 303 PHE cc_start: 0.6866 (m-10) cc_final: 0.6650 (m-10) REVERT: H 58 GLU cc_start: 0.7588 (tp30) cc_final: 0.7319 (tp30) REVERT: H 205 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.6885 (m-80) REVERT: J 116 TYR cc_start: 0.6885 (OUTLIER) cc_final: 0.6533 (m-80) REVERT: J 126 THR cc_start: 0.8748 (m) cc_final: 0.8521 (p) REVERT: J 143 TYR cc_start: 0.6552 (m-80) cc_final: 0.5699 (m-80) REVERT: J 184 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6488 (pp) REVERT: J 189 SER cc_start: 0.8340 (p) cc_final: 0.8071 (m) REVERT: J 316 ARG cc_start: 0.8349 (mmm160) cc_final: 0.8011 (mmm160) REVERT: K 9 LYS cc_start: 0.8259 (tttt) cc_final: 0.8023 (mmtt) REVERT: K 76 ASP cc_start: 0.7016 (m-30) cc_final: 0.6549 (m-30) REVERT: K 106 GLU cc_start: 0.7516 (pm20) cc_final: 0.6976 (pm20) REVERT: K 128 GLU cc_start: 0.7053 (tm-30) cc_final: 0.6809 (tm-30) REVERT: K 129 GLN cc_start: 0.8306 (mm-40) cc_final: 0.8035 (mt0) REVERT: K 353 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7309 (mptt) REVERT: K 401 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.6567 (tm-30) REVERT: L 14 ASP cc_start: 0.6842 (m-30) cc_final: 0.6617 (m-30) REVERT: L 50 LYS cc_start: 0.8129 (mttm) cc_final: 0.7762 (mttm) REVERT: L 88 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7245 (mp0) REVERT: L 104 GLU cc_start: 0.6841 (tt0) cc_final: 0.6594 (tt0) REVERT: L 118 GLU cc_start: 0.7287 (tp30) cc_final: 0.6935 (tp30) REVERT: L 227 HIS cc_start: 0.6995 (m90) cc_final: 0.6767 (m90) REVERT: L 251 GLU cc_start: 0.7179 (tt0) cc_final: 0.6908 (tt0) REVERT: L 323 LEU cc_start: 0.7852 (mt) cc_final: 0.7477 (mt) REVERT: M 254 LYS cc_start: 0.8096 (tppp) cc_final: 0.7688 (tppp) REVERT: M 294 LYS cc_start: 0.7845 (ptmm) cc_final: 0.7369 (ptmm) REVERT: M 299 TYR cc_start: 0.8241 (p90) cc_final: 0.7698 (p90) REVERT: M 308 PHE cc_start: 0.7965 (t80) cc_final: 0.7694 (t80) REVERT: M 319 GLN cc_start: 0.7996 (pm20) cc_final: 0.7337 (mt0) REVERT: M 352 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7621 (mm-30) REVERT: M 468 ARG cc_start: 0.6979 (ttm110) cc_final: 0.6675 (ttm110) REVERT: M 516 GLN cc_start: 0.7602 (pt0) cc_final: 0.7278 (pt0) REVERT: N 114 GLU cc_start: 0.7121 (tt0) cc_final: 0.6850 (tt0) REVERT: N 268 LYS cc_start: 0.8316 (mtpt) cc_final: 0.8055 (mtpt) REVERT: N 277 GLN cc_start: 0.7507 (mt0) cc_final: 0.7110 (mt0) REVERT: N 353 PHE cc_start: 0.7122 (m-80) cc_final: 0.6878 (m-80) REVERT: N 425 LYS cc_start: 0.8296 (ttpt) cc_final: 0.8063 (ttmt) REVERT: N 467 GLU cc_start: 0.8102 (tp30) cc_final: 0.7732 (tp30) REVERT: N 560 GLN cc_start: 0.7929 (mt0) cc_final: 0.7557 (mt0) REVERT: O 254 LYS cc_start: 0.8692 (tptp) cc_final: 0.8453 (tptp) REVERT: O 268 LYS cc_start: 0.7987 (mtmt) cc_final: 0.7762 (mtpp) REVERT: O 327 ASP cc_start: 0.7285 (t0) cc_final: 0.6841 (t0) REVERT: O 380 ILE cc_start: 0.8250 (tp) cc_final: 0.7989 (tp) REVERT: O 416 GLU cc_start: 0.7277 (tm-30) cc_final: 0.6851 (tm-30) REVERT: O 448 MET cc_start: 0.6607 (tpt) cc_final: 0.6224 (tpt) REVERT: O 455 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7740 (mm-30) REVERT: O 477 GLU cc_start: 0.8353 (tp30) cc_final: 0.7212 (mm-30) REVERT: P 246 TYR cc_start: 0.7498 (t80) cc_final: 0.7204 (t80) REVERT: P 277 GLN cc_start: 0.7627 (mt0) cc_final: 0.7357 (mp10) REVERT: P 328 LEU cc_start: 0.7885 (tt) cc_final: 0.7398 (mp) REVERT: P 459 GLU cc_start: 0.7689 (tp30) cc_final: 0.7131 (tp30) REVERT: P 508 LYS cc_start: 0.7904 (mttp) cc_final: 0.7467 (mmtp) REVERT: P 524 THR cc_start: 0.7298 (t) cc_final: 0.5350 (p) REVERT: Q 50 ASP cc_start: 0.7572 (t0) cc_final: 0.6920 (t0) REVERT: Q 146 LYS cc_start: 0.7865 (mppt) cc_final: 0.7569 (mppt) REVERT: Q 192 ARG cc_start: 0.6611 (ttt180) cc_final: 0.6119 (ttt90) REVERT: Q 254 LYS cc_start: 0.7069 (tptt) cc_final: 0.6834 (tptp) REVERT: Q 444 ASP cc_start: 0.7682 (m-30) cc_final: 0.7375 (m-30) REVERT: Q 448 MET cc_start: 0.6775 (mmp) cc_final: 0.6491 (mmp) REVERT: Q 455 GLU cc_start: 0.7610 (pt0) cc_final: 0.6775 (pt0) REVERT: Q 459 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7217 (mt-10) REVERT: Q 516 GLN cc_start: 0.7290 (pp30) cc_final: 0.6975 (pp30) REVERT: Q 520 GLU cc_start: 0.6950 (mp0) cc_final: 0.6300 (mp0) REVERT: R 22 ARG cc_start: 0.6686 (mtt90) cc_final: 0.6146 (mtp85) REVERT: R 205 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7424 (mp) REVERT: R 221 ASN cc_start: 0.7940 (t0) cc_final: 0.7689 (t0) REVERT: R 271 ARG cc_start: 0.8018 (ptp90) cc_final: 0.7272 (mtm-85) REVERT: R 382 GLN cc_start: 0.7454 (pp30) cc_final: 0.6965 (pp30) REVERT: R 540 GLU cc_start: 0.6860 (tp30) cc_final: 0.6280 (tp30) REVERT: R 550 MET cc_start: 0.6629 (ppp) cc_final: 0.6372 (ppp) outliers start: 126 outliers final: 94 residues processed: 1369 average time/residue: 0.6165 time to fit residues: 1383.2599 Evaluate side-chains 1413 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1308 time to evaluate : 5.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 274 ASN 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 359 LYS Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 373 SER Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 405 ASN Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 129 GLN Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 202 ASP Chi-restraints excluded: chain H residue 205 PHE Chi-restraints excluded: chain H residue 227 HIS Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 364 ASN 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 116 TYR Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 186 ASN Chi-restraints excluded: chain J residue 234 GLN Chi-restraints excluded: chain J residue 389 LEU Chi-restraints excluded: chain K residue 47 ASP Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 342 LYS Chi-restraints excluded: chain K residue 353 LYS Chi-restraints excluded: chain K residue 401 GLU 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 166 THR Chi-restraints excluded: chain L residue 168 ASN Chi-restraints excluded: chain L residue 335 GLU Chi-restraints excluded: chain M residue 196 GLU Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 297 ASN 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 45 VAL Chi-restraints excluded: chain N residue 124 SER Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 203 ILE Chi-restraints excluded: chain N residue 414 SER Chi-restraints excluded: chain N residue 473 VAL Chi-restraints excluded: chain N residue 481 HIS Chi-restraints excluded: chain N residue 498 GLU Chi-restraints excluded: chain N residue 515 THR 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 97 TYR 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 433 VAL Chi-restraints excluded: chain O residue 441 LEU 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 539 ASN Chi-restraints excluded: chain O residue 544 GLN Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 134 ASN 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 468 ARG 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 456 MET Chi-restraints excluded: chain R residue 476 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 474 optimal weight: 0.8980 chunk 306 optimal weight: 0.6980 chunk 458 optimal weight: 0.8980 chunk 231 optimal weight: 0.1980 chunk 150 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 487 optimal weight: 0.9980 chunk 522 optimal weight: 4.9990 chunk 379 optimal weight: 0.0980 chunk 71 optimal weight: 2.9990 chunk 603 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN ** D 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 364 ASN I 315 ASN K 24 GLN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 383 GLN P 47 GLN 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: 0.7165 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 65426 Z= 0.133 Angle : 0.500 15.778 88551 Z= 0.248 Chirality : 0.040 0.168 9656 Planarity : 0.003 0.048 11363 Dihedral : 8.489 143.730 9413 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.73 % Favored : 95.26 % Rotamer: Outliers : 1.80 % Allowed : 17.26 % Favored : 80.95 % 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: -0.87 (0.09), residues: 7933 helix: 0.42 (0.10), residues: 2953 sheet: 0.46 (0.18), residues: 933 loop : -1.64 (0.09), residues: 4047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 49 HIS 0.006 0.000 HIS O 480 PHE 0.017 0.001 PHE R 462 TYR 0.026 0.001 TYR Q 548 ARG 0.009 0.000 ARG O 22 *********************** 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 1436 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1316 time to evaluate : 5.245 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 131 ARG cc_start: 0.8190 (ptm-80) cc_final: 0.7866 (ptm-80) REVERT: A 293 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7330 (tm-30) REVERT: A 316 ARG cc_start: 0.6463 (mtp180) cc_final: 0.6177 (mtp85) REVERT: A 338 GLU cc_start: 0.5957 (mp0) cc_final: 0.5547 (mp0) REVERT: B 88 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6722 (mt-10) REVERT: B 128 GLU cc_start: 0.7152 (tm-30) cc_final: 0.6843 (tm-30) REVERT: B 132 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8081 (mm-30) REVERT: B 242 GLU cc_start: 0.7410 (tt0) cc_final: 0.6941 (tt0) REVERT: B 250 ASP cc_start: 0.7793 (m-30) cc_final: 0.7585 (m-30) REVERT: B 290 ARG cc_start: 0.6899 (mmt-90) cc_final: 0.6685 (mmt-90) REVERT: C 100 ARG cc_start: 0.7252 (ttt-90) cc_final: 0.6845 (tmt-80) REVERT: C 106 GLU cc_start: 0.7441 (tp30) cc_final: 0.7150 (tp30) REVERT: C 352 GLU cc_start: 0.6694 (mp0) cc_final: 0.6195 (mp0) REVERT: D 50 LYS cc_start: 0.7898 (mmmt) cc_final: 0.7605 (ttmm) REVERT: D 110 LYS cc_start: 0.8220 (mttp) cc_final: 0.7890 (mttp) REVERT: D 197 TYR cc_start: 0.8295 (m-10) cc_final: 0.7753 (m-80) REVERT: D 322 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7932 (mt) REVERT: D 335 GLU cc_start: 0.7743 (pm20) cc_final: 0.7533 (pm20) REVERT: D 363 PHE cc_start: 0.7891 (m-80) cc_final: 0.7532 (m-80) REVERT: E 54 GLN cc_start: 0.8401 (tm-30) cc_final: 0.7998 (tm-30) REVERT: E 250 ASP cc_start: 0.7685 (m-30) cc_final: 0.7235 (m-30) REVERT: E 342 LYS cc_start: 0.7679 (tttm) cc_final: 0.7433 (tttm) REVERT: E 382 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6710 (pm20) REVERT: G 43 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8050 (ptmt) REVERT: G 46 LYS cc_start: 0.5616 (ttmm) cc_final: 0.5381 (tppp) REVERT: G 58 GLU cc_start: 0.7338 (tm-30) cc_final: 0.6824 (tm-30) REVERT: G 110 LYS cc_start: 0.7694 (mppt) cc_final: 0.7403 (tppt) REVERT: G 142 LYS cc_start: 0.8002 (ttpp) cc_final: 0.7626 (ttpp) REVERT: G 250 ASP cc_start: 0.8097 (t0) cc_final: 0.7832 (t0) REVERT: G 303 PHE cc_start: 0.6849 (m-10) cc_final: 0.6636 (m-10) REVERT: H 58 GLU cc_start: 0.7570 (tp30) cc_final: 0.7298 (tp30) REVERT: H 159 GLN cc_start: 0.8550 (mt0) cc_final: 0.8289 (mt0) REVERT: H 205 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.7008 (m-80) REVERT: J 108 PHE cc_start: 0.8452 (m-80) cc_final: 0.8136 (m-80) REVERT: J 116 TYR cc_start: 0.6848 (OUTLIER) cc_final: 0.6524 (m-80) REVERT: J 126 THR cc_start: 0.8696 (m) cc_final: 0.8465 (p) REVERT: J 143 TYR cc_start: 0.6496 (m-80) cc_final: 0.5673 (m-80) REVERT: J 184 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6471 (pp) REVERT: J 189 SER cc_start: 0.8335 (p) cc_final: 0.8062 (m) REVERT: K 9 LYS cc_start: 0.8254 (tttt) cc_final: 0.8022 (mmtt) REVERT: K 76 ASP cc_start: 0.6998 (m-30) cc_final: 0.6542 (m-30) REVERT: K 106 GLU cc_start: 0.7509 (pm20) cc_final: 0.7118 (pm20) REVERT: K 128 GLU cc_start: 0.7015 (tm-30) cc_final: 0.6753 (tm-30) REVERT: K 353 LYS cc_start: 0.7675 (mptt) cc_final: 0.7304 (mptt) REVERT: K 401 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6553 (tm-30) REVERT: L 50 LYS cc_start: 0.8108 (mttm) cc_final: 0.7751 (mttm) REVERT: L 88 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: L 104 GLU cc_start: 0.6783 (tt0) cc_final: 0.6513 (tt0) REVERT: L 118 GLU cc_start: 0.7256 (tp30) cc_final: 0.6914 (tp30) REVERT: L 227 HIS cc_start: 0.6977 (m90) cc_final: 0.6765 (m90) REVERT: L 251 GLU cc_start: 0.7159 (tt0) cc_final: 0.6903 (tt0) REVERT: L 323 LEU cc_start: 0.7819 (mt) cc_final: 0.7444 (mt) REVERT: M 70 PHE cc_start: 0.6735 (m-80) cc_final: 0.6112 (m-80) REVERT: M 254 LYS cc_start: 0.8057 (tppp) cc_final: 0.7636 (tppp) REVERT: M 294 LYS cc_start: 0.7813 (ptmm) cc_final: 0.7341 (ptmm) REVERT: M 299 TYR cc_start: 0.8245 (p90) cc_final: 0.7691 (p90) REVERT: M 308 PHE cc_start: 0.7935 (t80) cc_final: 0.7674 (t80) REVERT: M 333 ARG cc_start: 0.7313 (mmt-90) cc_final: 0.6995 (mmm160) REVERT: M 352 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7606 (mm-30) REVERT: M 468 ARG cc_start: 0.6934 (ttm110) cc_final: 0.6628 (ttm110) REVERT: N 114 GLU cc_start: 0.7071 (tt0) cc_final: 0.6796 (tt0) REVERT: N 193 LYS cc_start: 0.8206 (ttmm) cc_final: 0.7876 (ttmm) REVERT: N 268 LYS cc_start: 0.8298 (mtpt) cc_final: 0.8042 (mtpt) REVERT: N 277 GLN cc_start: 0.7482 (mt0) cc_final: 0.7137 (mt0) REVERT: N 353 PHE cc_start: 0.7110 (m-80) cc_final: 0.6871 (m-80) REVERT: N 425 LYS cc_start: 0.8291 (ttpt) cc_final: 0.8060 (ttmt) REVERT: N 467 GLU cc_start: 0.8091 (tp30) cc_final: 0.7730 (tp30) REVERT: N 560 GLN cc_start: 0.7921 (mt0) cc_final: 0.7549 (mt0) REVERT: O 21 GLU cc_start: 0.7258 (mt-10) cc_final: 0.7006 (mt-10) REVERT: O 254 LYS cc_start: 0.8708 (tptp) cc_final: 0.8467 (tptp) REVERT: O 268 LYS cc_start: 0.7968 (mtmt) cc_final: 0.7740 (mtpp) REVERT: O 327 ASP cc_start: 0.7280 (t0) cc_final: 0.6839 (t0) REVERT: O 380 ILE cc_start: 0.8179 (tp) cc_final: 0.7915 (tp) REVERT: O 416 GLU cc_start: 0.7267 (tm-30) cc_final: 0.6860 (tm-30) REVERT: O 448 MET cc_start: 0.6543 (tpt) cc_final: 0.6146 (tpt) REVERT: O 477 GLU cc_start: 0.8307 (tp30) cc_final: 0.7167 (mm-30) REVERT: O 601 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8127 (mm-30) REVERT: P 246 TYR cc_start: 0.7474 (t80) cc_final: 0.7258 (t80) REVERT: P 255 LYS cc_start: 0.5953 (tptt) cc_final: 0.5369 (tptt) REVERT: P 277 GLN cc_start: 0.7592 (mt0) cc_final: 0.7335 (mp10) REVERT: P 441 LEU cc_start: 0.7910 (tp) cc_final: 0.7654 (tp) REVERT: P 459 GLU cc_start: 0.7675 (tp30) cc_final: 0.7130 (tp30) REVERT: P 508 LYS cc_start: 0.7880 (mttp) cc_final: 0.7388 (mmtp) REVERT: P 524 THR cc_start: 0.7235 (t) cc_final: 0.5443 (p) REVERT: P 581 ARG cc_start: 0.6320 (ttp-170) cc_final: 0.5961 (ttp-170) REVERT: P 586 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8007 (tm-30) REVERT: Q 50 ASP cc_start: 0.7558 (t0) cc_final: 0.6885 (t0) REVERT: Q 146 LYS cc_start: 0.7822 (mppt) cc_final: 0.7531 (mppt) REVERT: Q 192 ARG cc_start: 0.6587 (ttt180) cc_final: 0.6095 (ttt90) REVERT: Q 444 ASP cc_start: 0.7663 (m-30) cc_final: 0.7352 (m-30) REVERT: Q 448 MET cc_start: 0.6889 (mmp) cc_final: 0.6588 (mmp) REVERT: Q 455 GLU cc_start: 0.7576 (pt0) cc_final: 0.6768 (pt0) REVERT: Q 459 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7162 (mt-10) REVERT: Q 516 GLN cc_start: 0.7275 (pp30) cc_final: 0.6975 (pp30) REVERT: Q 520 GLU cc_start: 0.6946 (mp0) cc_final: 0.6293 (mp0) REVERT: R 22 ARG cc_start: 0.6687 (mtt90) cc_final: 0.6194 (mtp85) REVERT: R 205 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7421 (mp) REVERT: R 221 ASN cc_start: 0.7990 (t0) cc_final: 0.7736 (t0) REVERT: R 382 GLN cc_start: 0.7447 (pp30) cc_final: 0.6910 (pp30) REVERT: R 540 GLU cc_start: 0.6871 (tp30) cc_final: 0.6264 (tp30) REVERT: R 550 MET cc_start: 0.6594 (ppp) cc_final: 0.6337 (ppp) outliers start: 120 outliers final: 93 residues processed: 1362 average time/residue: 0.6455 time to fit residues: 1444.6703 Evaluate side-chains 1397 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 1294 time to evaluate : 5.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 167 THR 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 44 THR Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 274 ASN 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 359 LYS Chi-restraints excluded: chain F residue 361 MET 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 381 VAL Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 129 GLN Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 202 ASP Chi-restraints excluded: chain H residue 205 PHE Chi-restraints excluded: chain H residue 311 ASP Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 364 ASN Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain I residue 266 GLN Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain J residue 116 TYR Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 186 ASN Chi-restraints excluded: chain J residue 389 LEU Chi-restraints excluded: chain K residue 47 ASP Chi-restraints excluded: chain K residue 207 ASN Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 401 GLU 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 166 THR Chi-restraints excluded: chain L residue 168 ASN Chi-restraints excluded: chain L residue 293 GLU Chi-restraints excluded: chain L residue 335 GLU Chi-restraints excluded: chain M residue 32 GLN Chi-restraints excluded: chain M residue 196 GLU Chi-restraints excluded: chain M residue 281 LEU 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 45 VAL Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 124 SER Chi-restraints excluded: chain N residue 160 LYS Chi-restraints excluded: chain N residue 203 ILE Chi-restraints excluded: chain N residue 414 SER Chi-restraints excluded: chain N residue 481 HIS Chi-restraints excluded: chain N residue 498 GLU Chi-restraints excluded: chain N residue 515 THR Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 28 HIS Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 97 TYR Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 258 TYR Chi-restraints excluded: chain O residue 317 THR Chi-restraints excluded: chain O residue 433 VAL Chi-restraints excluded: chain O residue 441 LEU 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 539 ASN Chi-restraints excluded: chain O residue 544 GLN Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain P residue 574 SER Chi-restraints excluded: chain P residue 586 GLN Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 93 GLN Chi-restraints excluded: chain Q residue 134 ASN 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 468 ARG 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 456 MET 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: 1.9990 chunk 735 optimal weight: 4.9990 chunk 670 optimal weight: 5.9990 chunk 714 optimal weight: 0.0020 chunk 734 optimal weight: 9.9990 chunk 430 optimal weight: 3.9990 chunk 311 optimal weight: 3.9990 chunk 561 optimal weight: 0.9990 chunk 219 optimal weight: 20.0000 chunk 646 optimal weight: 2.9990 chunk 676 optimal weight: 2.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 GLN ** D 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 ASN G 55 ASN ** H 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 315 ASN J 24 GLN K 24 GLN K 129 GLN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 383 GLN P 427 GLN P 586 GLN Q 187 ASN Q 297 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 65426 Z= 0.273 Angle : 0.570 15.960 88551 Z= 0.286 Chirality : 0.043 0.284 9656 Planarity : 0.004 0.048 11363 Dihedral : 8.672 146.002 9413 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.25 % Favored : 93.74 % Rotamer: Outliers : 2.16 % Allowed : 17.21 % Favored : 80.63 % 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: -1.07 (0.09), residues: 7933 helix: 0.27 (0.10), residues: 2943 sheet: 0.27 (0.17), residues: 934 loop : -1.74 (0.09), residues: 4056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 49 HIS 0.007 0.001 HIS P 224 PHE 0.023 0.002 PHE P 101 TYR 0.024 0.002 TYR I 270 ARG 0.010 0.000 ARG O 22 *********************** 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 1504 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1360 time to evaluate : 5.242 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 54 GLN cc_start: 0.7495 (tm-30) cc_final: 0.7131 (tm-30) REVERT: A 227 HIS cc_start: 0.7648 (m90) cc_final: 0.7391 (m90) REVERT: A 293 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7337 (tm-30) REVERT: A 316 ARG cc_start: 0.6509 (mtp180) cc_final: 0.6249 (mtp85) REVERT: A 338 GLU cc_start: 0.5999 (mp0) cc_final: 0.5617 (mp0) REVERT: B 88 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6748 (mt-10) REVERT: B 97 LYS cc_start: 0.8252 (ttmm) cc_final: 0.8033 (ttmm) REVERT: B 128 GLU cc_start: 0.7097 (tm-30) cc_final: 0.6815 (tm-30) REVERT: B 132 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8059 (mm-30) REVERT: B 242 GLU cc_start: 0.7863 (tt0) cc_final: 0.7396 (tt0) REVERT: B 250 ASP cc_start: 0.7856 (m-30) cc_final: 0.7611 (m-30) REVERT: B 290 ARG cc_start: 0.6913 (mmt-90) cc_final: 0.6664 (mmt-90) REVERT: C 100 ARG cc_start: 0.7300 (ttt-90) cc_final: 0.6929 (tmt-80) REVERT: C 106 GLU cc_start: 0.7573 (tp30) cc_final: 0.7258 (tp30) REVERT: C 352 GLU cc_start: 0.6756 (mp0) cc_final: 0.6249 (mp0) REVERT: D 50 LYS cc_start: 0.7919 (mmmt) cc_final: 0.7628 (ttmm) REVERT: D 106 GLU cc_start: 0.7404 (pp20) cc_final: 0.7140 (pm20) REVERT: D 110 LYS cc_start: 0.8239 (mttp) cc_final: 0.8018 (mttp) REVERT: D 197 TYR cc_start: 0.8261 (m-10) cc_final: 0.7728 (m-80) REVERT: D 335 GLU cc_start: 0.7782 (pm20) cc_final: 0.7579 (pm20) REVERT: D 363 PHE cc_start: 0.7986 (m-80) cc_final: 0.7662 (m-80) REVERT: E 54 GLN cc_start: 0.8431 (tm-30) cc_final: 0.8148 (tm-30) REVERT: E 250 ASP cc_start: 0.7759 (m-30) cc_final: 0.7311 (m-30) REVERT: E 342 LYS cc_start: 0.7739 (tttm) cc_final: 0.7497 (tttm) REVERT: G 43 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8103 (ptmt) REVERT: G 46 LYS cc_start: 0.5686 (ttmm) cc_final: 0.5187 (tppp) REVERT: G 58 GLU cc_start: 0.7381 (tm-30) cc_final: 0.6879 (tm-30) REVERT: G 110 LYS cc_start: 0.7741 (mppt) cc_final: 0.7467 (tppt) REVERT: G 142 LYS cc_start: 0.8059 (ttpp) cc_final: 0.7711 (ttpp) REVERT: G 250 ASP cc_start: 0.8142 (t0) cc_final: 0.7870 (t0) REVERT: G 303 PHE cc_start: 0.6888 (m-10) cc_final: 0.6686 (m-10) REVERT: H 58 GLU cc_start: 0.7618 (tp30) cc_final: 0.7339 (tp30) REVERT: H 159 GLN cc_start: 0.8574 (mt0) cc_final: 0.8305 (mt0) REVERT: H 205 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.6831 (m-80) REVERT: I 50 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7996 (mmmt) REVERT: I 74 ASP cc_start: 0.7870 (m-30) cc_final: 0.7625 (t0) REVERT: J 108 PHE cc_start: 0.8518 (m-80) cc_final: 0.8147 (m-80) REVERT: J 143 TYR cc_start: 0.6646 (m-80) cc_final: 0.5775 (m-80) REVERT: J 184 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6439 (pp) REVERT: J 189 SER cc_start: 0.8392 (p) cc_final: 0.8117 (m) REVERT: J 287 MET cc_start: 0.7192 (OUTLIER) cc_final: 0.6349 (mtt) REVERT: J 316 ARG cc_start: 0.8356 (mmm160) cc_final: 0.8030 (mmm160) REVERT: K 76 ASP cc_start: 0.7023 (m-30) cc_final: 0.6582 (m-30) REVERT: K 106 GLU cc_start: 0.7579 (pm20) cc_final: 0.7089 (pm20) REVERT: K 128 GLU cc_start: 0.7110 (tm-30) cc_final: 0.6874 (tm-30) REVERT: K 353 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7315 (mptt) REVERT: K 401 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6590 (tm-30) REVERT: L 14 ASP cc_start: 0.6887 (m-30) cc_final: 0.6646 (m-30) REVERT: L 50 LYS cc_start: 0.8127 (mttm) cc_final: 0.7759 (mttm) REVERT: L 88 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: L 104 GLU cc_start: 0.6847 (tt0) cc_final: 0.6527 (tt0) REVERT: L 118 GLU cc_start: 0.7318 (tp30) cc_final: 0.6963 (tp30) REVERT: L 227 HIS cc_start: 0.7038 (m90) cc_final: 0.6814 (m90) REVERT: L 323 LEU cc_start: 0.7923 (mt) cc_final: 0.7589 (mt) REVERT: M 254 LYS cc_start: 0.8123 (tppp) cc_final: 0.7683 (tppp) REVERT: M 294 LYS cc_start: 0.7866 (ptmm) cc_final: 0.7609 (ptmm) REVERT: M 319 GLN cc_start: 0.8008 (pm20) cc_final: 0.7362 (mt0) REVERT: M 333 ARG cc_start: 0.7382 (mmt-90) cc_final: 0.7052 (mmm160) REVERT: M 352 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7618 (mm-30) REVERT: M 468 ARG cc_start: 0.7058 (ttm110) cc_final: 0.6521 (ttp-110) REVERT: M 516 GLN cc_start: 0.7646 (pt0) cc_final: 0.7331 (pt0) REVERT: N 114 GLU cc_start: 0.7156 (tt0) cc_final: 0.6877 (tt0) REVERT: N 193 LYS cc_start: 0.8248 (ttmm) cc_final: 0.7917 (ttmm) REVERT: N 268 LYS cc_start: 0.8346 (mtpt) cc_final: 0.8105 (mtpt) REVERT: N 277 GLN cc_start: 0.7667 (mt0) cc_final: 0.7315 (mt0) REVERT: N 353 PHE cc_start: 0.7205 (m-80) cc_final: 0.6955 (m-80) REVERT: N 425 LYS cc_start: 0.8331 (ttpt) cc_final: 0.8022 (ttmt) REVERT: N 467 GLU cc_start: 0.8106 (tp30) cc_final: 0.7721 (tp30) REVERT: N 520 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7157 (mm-30) REVERT: N 559 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7932 (mmmm) REVERT: N 560 GLN cc_start: 0.7983 (mt0) cc_final: 0.7610 (mt0) REVERT: O 254 LYS cc_start: 0.8719 (tptp) cc_final: 0.8471 (tptp) REVERT: O 268 LYS cc_start: 0.8033 (mtmt) cc_final: 0.7803 (mtpp) REVERT: O 327 ASP cc_start: 0.7287 (t0) cc_final: 0.6845 (t0) REVERT: O 380 ILE cc_start: 0.8266 (tp) cc_final: 0.8003 (tp) REVERT: O 416 GLU cc_start: 0.7289 (tm-30) cc_final: 0.6883 (tm-30) REVERT: O 448 MET cc_start: 0.6659 (tpt) cc_final: 0.6242 (tpt) REVERT: O 506 LYS cc_start: 0.5989 (ttmm) cc_final: 0.5718 (mtpp) REVERT: P 176 LEU cc_start: 0.6112 (OUTLIER) cc_final: 0.5140 (mt) REVERT: P 246 TYR cc_start: 0.7576 (t80) cc_final: 0.7313 (t80) REVERT: P 441 LEU cc_start: 0.7968 (tp) cc_final: 0.7726 (tp) REVERT: P 459 GLU cc_start: 0.7705 (tp30) cc_final: 0.7163 (tp30) REVERT: P 484 ARG cc_start: 0.5750 (mtt180) cc_final: 0.5416 (mtt-85) REVERT: P 508 LYS cc_start: 0.7965 (mttp) cc_final: 0.7554 (mmtp) REVERT: P 524 THR cc_start: 0.7349 (t) cc_final: 0.5438 (p) REVERT: Q 50 ASP cc_start: 0.7713 (t0) cc_final: 0.7063 (t0) REVERT: Q 146 LYS cc_start: 0.7932 (mppt) cc_final: 0.7643 (mppt) REVERT: Q 254 LYS cc_start: 0.7098 (tptt) cc_final: 0.6889 (tptp) REVERT: Q 297 ASN cc_start: 0.5267 (OUTLIER) cc_final: 0.5064 (m110) REVERT: Q 444 ASP cc_start: 0.7639 (m-30) cc_final: 0.7323 (m-30) REVERT: Q 448 MET cc_start: 0.6935 (mmp) cc_final: 0.6610 (mmp) REVERT: Q 455 GLU cc_start: 0.7644 (pt0) cc_final: 0.6709 (pt0) REVERT: Q 459 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7211 (mt-10) REVERT: Q 516 GLN cc_start: 0.7276 (pp30) cc_final: 0.6946 (pp30) REVERT: Q 520 GLU cc_start: 0.7005 (mp0) cc_final: 0.6341 (mp0) REVERT: R 22 ARG cc_start: 0.6733 (mtt90) cc_final: 0.6218 (mtp85) REVERT: R 205 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7421 (mp) REVERT: R 221 ASN cc_start: 0.8026 (t0) cc_final: 0.7763 (t0) REVERT: R 382 GLN cc_start: 0.7516 (pp30) cc_final: 0.6991 (pp30) REVERT: R 540 GLU cc_start: 0.6946 (tp30) cc_final: 0.6344 (tp30) REVERT: R 550 MET cc_start: 0.6615 (ppp) cc_final: 0.6369 (ppp) outliers start: 144 outliers final: 116 residues processed: 1418 average time/residue: 0.6491 time to fit residues: 1520.6831 Evaluate side-chains 1461 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1333 time to evaluate : 5.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 167 THR 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 11 ASN Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 274 ASN 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 359 LYS Chi-restraints excluded: chain F residue 361 MET 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 44 THR Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain G residue 405 ASN Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 129 GLN Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 202 ASP 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 50 LYS 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 116 TYR Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 186 ASN Chi-restraints excluded: chain J residue 234 GLN Chi-restraints excluded: chain J residue 287 MET Chi-restraints excluded: chain J residue 389 LEU Chi-restraints excluded: chain K residue 47 ASP Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 300 THR Chi-restraints excluded: chain K residue 353 LYS Chi-restraints excluded: chain K residue 401 GLU Chi-restraints excluded: chain L residue 45 MET Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 95 VAL 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 168 ASN Chi-restraints excluded: chain L residue 293 GLU Chi-restraints excluded: chain L residue 335 GLU Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 196 GLU Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 297 ASN 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 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 414 SER Chi-restraints excluded: chain N residue 417 VAL Chi-restraints excluded: chain N residue 451 SER Chi-restraints excluded: chain N residue 473 VAL Chi-restraints excluded: chain N residue 515 THR Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain N residue 559 LYS 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 97 TYR 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 433 VAL Chi-restraints excluded: chain O residue 441 LEU 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 539 ASN Chi-restraints excluded: chain O residue 544 GLN Chi-restraints excluded: chain P residue 176 LEU Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain P residue 586 GLN Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 134 ASN 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 468 ARG 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 115 ASP Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 456 MET 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: 8.9990 chunk 469 optimal weight: 0.6980 chunk 756 optimal weight: 7.9990 chunk 461 optimal weight: 2.9990 chunk 358 optimal weight: 2.9990 chunk 525 optimal weight: 0.8980 chunk 793 optimal weight: 8.9990 chunk 729 optimal weight: 0.0470 chunk 631 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 487 optimal weight: 7.9990 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 GLN ** H 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 315 ASN J 5 GLN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 383 GLN P 427 GLN P 586 GLN Q 187 ASN Q 297 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 65426 Z= 0.215 Angle : 0.553 16.230 88551 Z= 0.275 Chirality : 0.042 0.381 9656 Planarity : 0.004 0.049 11363 Dihedral : 8.572 144.754 9413 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.53 % Favored : 94.45 % Rotamer: Outliers : 2.04 % Allowed : 17.59 % Favored : 80.38 % 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: -1.07 (0.09), residues: 7933 helix: 0.27 (0.10), residues: 2938 sheet: 0.20 (0.17), residues: 947 loop : -1.73 (0.09), residues: 4048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 49 HIS 0.007 0.001 HIS O 480 PHE 0.021 0.001 PHE R 462 TYR 0.023 0.001 TYR Q 548 ARG 0.009 0.000 ARG O 22 ********************** 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 1456 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1320 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 GLN cc_start: 0.7489 (tm-30) cc_final: 0.7131 (tm-30) REVERT: A 131 ARG cc_start: 0.8235 (ptm-80) cc_final: 0.7894 (ptm-80) REVERT: A 293 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7349 (tm-30) REVERT: A 316 ARG cc_start: 0.6495 (mtp180) cc_final: 0.6258 (mtp85) REVERT: A 338 GLU cc_start: 0.5974 (mp0) cc_final: 0.5607 (mp0) REVERT: B 88 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6736 (mt-10) REVERT: B 97 LYS cc_start: 0.8249 (ttmm) cc_final: 0.8032 (ttmm) REVERT: B 128 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6831 (tm-30) REVERT: B 250 ASP cc_start: 0.7821 (m-30) cc_final: 0.7590 (m-30) REVERT: B 290 ARG cc_start: 0.6885 (mmt-90) cc_final: 0.6643 (mmt-90) REVERT: C 100 ARG cc_start: 0.7291 (ttt-90) cc_final: 0.6848 (tmt-80) REVERT: C 106 GLU cc_start: 0.7557 (tp30) cc_final: 0.7244 (tp30) REVERT: C 352 GLU cc_start: 0.6713 (mp0) cc_final: 0.6221 (mp0) REVERT: D 50 LYS cc_start: 0.7912 (mmmt) cc_final: 0.7622 (ttmm) REVERT: D 106 GLU cc_start: 0.7397 (pp20) cc_final: 0.7163 (pm20) REVERT: D 107 GLU cc_start: 0.7378 (tm-30) cc_final: 0.7021 (tt0) REVERT: D 110 LYS cc_start: 0.8250 (mttp) cc_final: 0.8011 (mttp) REVERT: D 197 TYR cc_start: 0.8265 (m-10) cc_final: 0.7736 (m-80) REVERT: D 335 GLU cc_start: 0.7780 (pm20) cc_final: 0.7560 (pm20) REVERT: D 363 PHE cc_start: 0.7938 (m-80) cc_final: 0.7655 (m-80) REVERT: E 54 GLN cc_start: 0.8416 (tm-30) cc_final: 0.7999 (tm-30) REVERT: E 250 ASP cc_start: 0.7760 (m-30) cc_final: 0.7300 (m-30) REVERT: E 342 LYS cc_start: 0.7685 (tttm) cc_final: 0.7446 (tttm) REVERT: G 43 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8097 (ptmt) REVERT: G 46 LYS cc_start: 0.5658 (ttmm) cc_final: 0.5169 (tppp) REVERT: G 110 LYS cc_start: 0.7746 (mppt) cc_final: 0.7475 (tppt) REVERT: G 142 LYS cc_start: 0.8059 (ttpp) cc_final: 0.7702 (ttpp) REVERT: G 224 TYR cc_start: 0.7479 (m-80) cc_final: 0.6099 (m-80) REVERT: G 250 ASP cc_start: 0.8132 (t0) cc_final: 0.7866 (t0) REVERT: G 303 PHE cc_start: 0.6873 (m-10) cc_final: 0.6666 (m-10) REVERT: H 58 GLU cc_start: 0.7645 (tp30) cc_final: 0.7374 (tp30) REVERT: H 60 LEU cc_start: 0.8111 (tp) cc_final: 0.7818 (tp) REVERT: H 154 ASN cc_start: 0.8673 (t0) cc_final: 0.8450 (m-40) REVERT: H 159 GLN cc_start: 0.8568 (mt0) cc_final: 0.8320 (mt0) REVERT: H 205 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.6837 (m-80) REVERT: I 50 LYS cc_start: 0.8260 (mmtm) cc_final: 0.7844 (mmmt) REVERT: I 74 ASP cc_start: 0.7854 (m-30) cc_final: 0.7585 (t0) REVERT: J 108 PHE cc_start: 0.8513 (m-80) cc_final: 0.8147 (m-80) REVERT: J 116 TYR cc_start: 0.6937 (OUTLIER) cc_final: 0.6638 (m-80) REVERT: J 143 TYR cc_start: 0.6619 (m-80) cc_final: 0.5757 (m-80) REVERT: J 184 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6432 (pp) REVERT: J 189 SER cc_start: 0.8369 (p) cc_final: 0.8097 (m) REVERT: J 287 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6311 (mtt) REVERT: J 316 ARG cc_start: 0.8352 (mmm160) cc_final: 0.8021 (mmm160) REVERT: K 76 ASP cc_start: 0.7021 (m-30) cc_final: 0.6597 (m-30) REVERT: K 106 GLU cc_start: 0.7586 (pm20) cc_final: 0.7101 (pm20) REVERT: K 128 GLU cc_start: 0.7099 (tm-30) cc_final: 0.6847 (tm-30) REVERT: K 286 GLU cc_start: 0.6232 (mm-30) cc_final: 0.5520 (mm-30) REVERT: K 353 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7324 (mptt) REVERT: K 401 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6577 (tm-30) REVERT: L 14 ASP cc_start: 0.6855 (m-30) cc_final: 0.6602 (m-30) REVERT: L 50 LYS cc_start: 0.8123 (mttm) cc_final: 0.7756 (mttm) REVERT: L 88 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: L 104 GLU cc_start: 0.6800 (tt0) cc_final: 0.6519 (tt0) REVERT: L 118 GLU cc_start: 0.7305 (tp30) cc_final: 0.6954 (tp30) REVERT: L 227 HIS cc_start: 0.7001 (m90) cc_final: 0.6767 (m90) REVERT: L 323 LEU cc_start: 0.7888 (mt) cc_final: 0.7532 (mt) REVERT: M 254 LYS cc_start: 0.8142 (tppp) cc_final: 0.7711 (tppp) REVERT: M 294 LYS cc_start: 0.7876 (ptmm) cc_final: 0.7613 (ptmm) REVERT: M 308 PHE cc_start: 0.7977 (t80) cc_final: 0.7691 (t80) REVERT: M 319 GLN cc_start: 0.8027 (pm20) cc_final: 0.7416 (mt0) REVERT: M 333 ARG cc_start: 0.7309 (mmt-90) cc_final: 0.6992 (mmm160) REVERT: M 352 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7600 (mm-30) REVERT: M 468 ARG cc_start: 0.7061 (ttm110) cc_final: 0.6524 (ttp-110) REVERT: M 516 GLN cc_start: 0.7630 (pt0) cc_final: 0.7322 (pt0) REVERT: N 114 GLU cc_start: 0.7137 (tt0) cc_final: 0.6860 (tt0) REVERT: N 193 LYS cc_start: 0.8240 (ttmm) cc_final: 0.7907 (ttmm) REVERT: N 268 LYS cc_start: 0.8326 (mtpt) cc_final: 0.8102 (mtpt) REVERT: N 277 GLN cc_start: 0.7655 (mt0) cc_final: 0.7322 (mt0) REVERT: N 353 PHE cc_start: 0.7217 (m-80) cc_final: 0.6953 (m-80) REVERT: N 425 LYS cc_start: 0.8349 (ttpt) cc_final: 0.8031 (ttmt) REVERT: N 467 GLU cc_start: 0.8107 (tp30) cc_final: 0.7725 (tp30) REVERT: N 559 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.7904 (mmmm) REVERT: N 560 GLN cc_start: 0.7971 (mt0) cc_final: 0.7587 (mt0) REVERT: O 186 PHE cc_start: 0.8268 (t80) cc_final: 0.8015 (t80) REVERT: O 254 LYS cc_start: 0.8715 (tptp) cc_final: 0.8463 (tptp) REVERT: O 268 LYS cc_start: 0.8026 (mtmt) cc_final: 0.7794 (mtpp) REVERT: O 327 ASP cc_start: 0.7279 (t0) cc_final: 0.6843 (t0) REVERT: O 380 ILE cc_start: 0.8202 (tp) cc_final: 0.7925 (tp) REVERT: O 416 GLU cc_start: 0.7293 (tm-30) cc_final: 0.6866 (tm-30) REVERT: O 448 MET cc_start: 0.6630 (tpt) cc_final: 0.6201 (tpt) REVERT: P 246 TYR cc_start: 0.7535 (t80) cc_final: 0.7255 (t80) REVERT: P 277 GLN cc_start: 0.7619 (mt0) cc_final: 0.7336 (mp10) REVERT: P 441 LEU cc_start: 0.7898 (tp) cc_final: 0.7656 (tp) REVERT: P 459 GLU cc_start: 0.7704 (tp30) cc_final: 0.7160 (tp30) REVERT: P 484 ARG cc_start: 0.5747 (mtt180) cc_final: 0.5145 (mtt-85) REVERT: P 508 LYS cc_start: 0.7932 (mttp) cc_final: 0.7520 (mmtp) REVERT: P 524 THR cc_start: 0.7350 (t) cc_final: 0.5428 (p) REVERT: Q 50 ASP cc_start: 0.7621 (t0) cc_final: 0.6955 (t0) REVERT: Q 146 LYS cc_start: 0.7895 (mppt) cc_final: 0.7609 (mppt) REVERT: Q 297 ASN cc_start: 0.5238 (OUTLIER) cc_final: 0.5031 (m110) REVERT: Q 444 ASP cc_start: 0.7645 (m-30) cc_final: 0.7306 (m-30) REVERT: Q 448 MET cc_start: 0.6917 (mmp) cc_final: 0.6617 (mmp) REVERT: Q 455 GLU cc_start: 0.7597 (pt0) cc_final: 0.6684 (pt0) REVERT: Q 459 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7198 (mt-10) REVERT: Q 516 GLN cc_start: 0.7266 (pp30) cc_final: 0.6860 (pp30) REVERT: Q 520 GLU cc_start: 0.6997 (mp0) cc_final: 0.6323 (mp0) REVERT: Q 543 LEU cc_start: 0.5191 (OUTLIER) cc_final: 0.4463 (mt) REVERT: R 22 ARG cc_start: 0.6733 (mtt90) cc_final: 0.6222 (mtp85) REVERT: R 205 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7441 (mp) REVERT: R 221 ASN cc_start: 0.8073 (t0) cc_final: 0.7799 (t0) REVERT: R 382 GLN cc_start: 0.7490 (pp30) cc_final: 0.6975 (pp30) REVERT: R 416 GLU cc_start: -0.0283 (OUTLIER) cc_final: -0.1562 (mp0) REVERT: R 502 LYS cc_start: 0.6828 (tmtt) cc_final: 0.6483 (tptp) REVERT: R 540 GLU cc_start: 0.6931 (tp30) cc_final: 0.6333 (tp30) REVERT: R 550 MET cc_start: 0.6606 (ppp) cc_final: 0.6357 (ppp) outliers start: 136 outliers final: 110 residues processed: 1381 average time/residue: 0.6227 time to fit residues: 1411.7323 Evaluate side-chains 1434 residues out of total 6848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1311 time to evaluate : 5.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 167 THR 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 11 ASN Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 274 ASN 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 359 LYS Chi-restraints excluded: chain F residue 361 MET 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 173 LEU Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain G residue 405 ASN Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 202 ASP Chi-restraints excluded: chain H residue 205 PHE Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain H residue 311 ASP Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain I residue 240 VAL Chi-restraints excluded: chain I residue 257 ILE 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 116 TYR Chi-restraints excluded: chain J residue 184 LEU Chi-restraints excluded: chain J residue 186 ASN Chi-restraints excluded: chain J residue 234 GLN Chi-restraints excluded: chain J residue 287 MET 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 279 THR Chi-restraints excluded: chain K residue 300 THR Chi-restraints excluded: chain K residue 353 LYS Chi-restraints excluded: chain K residue 401 GLU Chi-restraints excluded: chain L residue 45 MET Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 95 VAL 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 168 ASN Chi-restraints excluded: chain L residue 293 GLU Chi-restraints excluded: chain L residue 311 ASP Chi-restraints excluded: chain L residue 335 GLU Chi-restraints excluded: chain M residue 196 GLU Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 297 ASN 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 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 414 SER Chi-restraints excluded: chain N residue 473 VAL Chi-restraints excluded: chain N residue 515 THR Chi-restraints excluded: chain N residue 550 MET Chi-restraints excluded: chain N residue 559 LYS 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 97 TYR 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 433 VAL Chi-restraints excluded: chain O residue 441 LEU 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 539 ASN Chi-restraints excluded: chain O residue 544 GLN Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain P residue 538 THR Chi-restraints excluded: chain P residue 574 SER Chi-restraints excluded: chain P residue 586 GLN Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 134 ASN 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 468 ARG Chi-restraints excluded: chain Q residue 543 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 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 476 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 796 random chunks: chunk 387 optimal weight: 0.9990 chunk 501 optimal weight: 20.0000 chunk 672 optimal weight: 4.9990 chunk 193 optimal weight: 0.7980 chunk 582 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 632 optimal weight: 0.9980 chunk 264 optimal weight: 0.4980 chunk 649 optimal weight: 1.9990 chunk 80 optimal weight: 0.0270 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 GLN ** H 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 315 ASN J 5 GLN K 24 GLN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 383 GLN P 427 GLN Q 187 ASN ** Q 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.175471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.140324 restraints weight = 94650.937| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.97 r_work: 0.3617 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.146 65426 Z= 0.208 Angle : 0.626 59.190 88551 Z= 0.335 Chirality : 0.042 0.593 9656 Planarity : 0.004 0.150 11363 Dihedral : 8.568 144.695 9413 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.58 % Favored : 94.40 % Rotamer: Outliers : 2.04 % Allowed : 17.68 % Favored : 80.29 % Cbeta Deviations : 0.04 % 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: -1.07 (0.09), residues: 7933 helix: 0.28 (0.10), residues: 2938 sheet: 0.19 (0.17), residues: 954 loop : -1.73 (0.09), residues: 4041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 49 HIS 0.006 0.001 HIS O 480 PHE 0.023 0.001 PHE E 288 TYR 0.022 0.001 TYR Q 548 ARG 0.007 0.000 ARG O 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20833.38 seconds wall clock time: 362 minutes 32.07 seconds (21752.07 seconds total)