Starting phenix.real_space_refine on Sat Feb 24 02:27:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6evz_3964/02_2024/6evz_3964.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6evz_3964/02_2024/6evz_3964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6evz_3964/02_2024/6evz_3964.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6evz_3964/02_2024/6evz_3964.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6evz_3964/02_2024/6evz_3964.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6evz_3964/02_2024/6evz_3964.pdb" } resolution = 3.8 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= 0.010 sd= 0.061 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 30 5.49 5 Mg 6 5.21 5 S 276 5.16 5 C 25674 2.51 5 N 6978 2.21 5 O 7902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "E ARG 64": "NH1" <-> "NH2" Residue "E ARG 390": "NH1" <-> "NH2" Residue "J ARG 64": "NH1" <-> "NH2" Residue "J ARG 390": "NH1" <-> "NH2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C ARG 390": "NH1" <-> "NH2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "L ARG 390": "NH1" <-> "NH2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K ARG 390": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 40866 Number of models: 1 Model: "" Number of chains: 24 Chain: "F" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.26, per 1000 atoms: 0.50 Number of scatterers: 40866 At special positions: 0 Unit cell: (119.54, 172.36, 212.67, 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 276 16.00 P 30 15.00 Mg 6 11.99 O 7902 8.00 N 6978 7.00 C 25674 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.21 Conformation dependent library (CDL) restraints added in 7.2 seconds 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9576 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 30 sheets defined 45.1% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.16 Creating SS restraints... Processing helix chain 'F' and resid 10 through 29 removed outlier: 3.987A pdb=" N LYS F 19 " --> pdb=" O GLN F 15 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP F 26 " --> pdb=" O GLU F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 49 removed outlier: 3.694A pdb=" N VAL F 49 " --> pdb=" O ARG F 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 46 through 49' Processing helix chain 'F' and resid 70 through 77 removed outlier: 3.755A pdb=" N SER F 75 " --> pdb=" O GLY F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 106 Processing helix chain 'F' and resid 112 through 125 removed outlier: 4.119A pdb=" N ASP F 118 " --> pdb=" O ASP F 114 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL F 119 " --> pdb=" O SER F 115 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS F 122 " --> pdb=" O ASP F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 159 removed outlier: 3.848A pdb=" N ILE F 152 " --> pdb=" O GLY F 148 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU F 157 " --> pdb=" O SER F 153 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU F 158 " --> pdb=" O LYS F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 193 removed outlier: 4.039A pdb=" N SER F 188 " --> pdb=" O ASN F 184 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLN F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 214 removed outlier: 3.716A pdb=" N ILE F 210 " --> pdb=" O ALA F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 237 removed outlier: 3.721A pdb=" N HIS F 227 " --> pdb=" O GLY F 223 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU F 228 " --> pdb=" O ASP F 224 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL F 229 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR F 237 " --> pdb=" O MET F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 240 No H-bonds generated for 'chain 'F' and resid 238 through 240' Processing helix chain 'F' and resid 251 through 256 Processing helix chain 'F' and resid 285 through 294 removed outlier: 3.560A pdb=" N LEU F 289 " --> pdb=" O THR F 285 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR F 290 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE F 294 " --> pdb=" O THR F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 336 removed outlier: 3.606A pdb=" N VAL F 326 " --> pdb=" O SER F 322 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN F 334 " --> pdb=" O MET F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 390 removed outlier: 3.591A pdb=" N ILE F 381 " --> pdb=" O LEU F 377 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU F 383 " --> pdb=" O LYS F 379 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG F 390 " --> pdb=" O THR F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 400 Processing helix chain 'F' and resid 404 through 427 removed outlier: 3.851A pdb=" N PHE F 408 " --> pdb=" O ASP F 404 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA F 411 " --> pdb=" O GLU F 407 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU F 421 " --> pdb=" O ASP F 417 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN F 424 " --> pdb=" O SER F 420 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP F 427 " --> pdb=" O GLN F 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 29 removed outlier: 3.987A pdb=" N LYS G 19 " --> pdb=" O GLN G 15 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP G 26 " --> pdb=" O GLU G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 49 removed outlier: 3.695A pdb=" N VAL G 49 " --> pdb=" O ARG G 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 46 through 49' Processing helix chain 'G' and resid 70 through 77 removed outlier: 3.755A pdb=" N SER G 75 " --> pdb=" O GLY G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 106 Processing helix chain 'G' and resid 112 through 125 removed outlier: 4.120A pdb=" N ASP G 118 " --> pdb=" O ASP G 114 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL G 119 " --> pdb=" O SER G 115 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS G 122 " --> pdb=" O ASP G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 159 removed outlier: 3.848A pdb=" N ILE G 152 " --> pdb=" O GLY G 148 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU G 157 " --> pdb=" O SER G 153 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU G 158 " --> pdb=" O LYS G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 193 removed outlier: 4.039A pdb=" N SER G 188 " --> pdb=" O ASN G 184 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLN G 191 " --> pdb=" O LEU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 214 removed outlier: 3.717A pdb=" N ILE G 210 " --> pdb=" O ALA G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 237 removed outlier: 3.721A pdb=" N HIS G 227 " --> pdb=" O GLY G 223 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU G 228 " --> pdb=" O ASP G 224 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL G 229 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR G 237 " --> pdb=" O MET G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 240 No H-bonds generated for 'chain 'G' and resid 238 through 240' Processing helix chain 'G' and resid 251 through 256 Processing helix chain 'G' and resid 285 through 294 removed outlier: 3.561A pdb=" N LEU G 289 " --> pdb=" O THR G 285 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR G 290 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE G 294 " --> pdb=" O THR G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 336 removed outlier: 3.605A pdb=" N VAL G 326 " --> pdb=" O SER G 322 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN G 334 " --> pdb=" O MET G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 374 through 390 removed outlier: 3.590A pdb=" N ILE G 381 " --> pdb=" O LEU G 377 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU G 383 " --> pdb=" O LYS G 379 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG G 390 " --> pdb=" O THR G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 395 through 400 Processing helix chain 'G' and resid 404 through 427 removed outlier: 3.852A pdb=" N PHE G 408 " --> pdb=" O ASP G 404 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA G 411 " --> pdb=" O GLU G 407 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU G 421 " --> pdb=" O ASP G 417 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN G 424 " --> pdb=" O SER G 420 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP G 427 " --> pdb=" O GLN G 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 29 removed outlier: 3.987A pdb=" N LYS D 19 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 49 removed outlier: 3.695A pdb=" N VAL D 49 " --> pdb=" O ARG D 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 46 through 49' Processing helix chain 'D' and resid 70 through 77 removed outlier: 3.755A pdb=" N SER D 75 " --> pdb=" O GLY D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 112 through 125 removed outlier: 4.119A pdb=" N ASP D 118 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 159 removed outlier: 3.848A pdb=" N ILE D 152 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU D 158 " --> pdb=" O LYS D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 193 removed outlier: 4.039A pdb=" N SER D 188 " --> pdb=" O ASN D 184 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 214 removed outlier: 3.716A pdb=" N ILE D 210 " --> pdb=" O ALA D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 237 removed outlier: 3.722A pdb=" N HIS D 227 " --> pdb=" O GLY D 223 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL D 229 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 240 No H-bonds generated for 'chain 'D' and resid 238 through 240' Processing helix chain 'D' and resid 251 through 256 Processing helix chain 'D' and resid 285 through 294 removed outlier: 3.561A pdb=" N LEU D 289 " --> pdb=" O THR D 285 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR D 290 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE D 294 " --> pdb=" O THR D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 336 removed outlier: 3.606A pdb=" N VAL D 326 " --> pdb=" O SER D 322 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN D 334 " --> pdb=" O MET D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 390 removed outlier: 3.590A pdb=" N ILE D 381 " --> pdb=" O LEU D 377 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU D 383 " --> pdb=" O LYS D 379 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG D 390 " --> pdb=" O THR D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 404 through 427 removed outlier: 3.851A pdb=" N PHE D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 411 " --> pdb=" O GLU D 407 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU D 421 " --> pdb=" O ASP D 417 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN D 424 " --> pdb=" O SER D 420 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP D 427 " --> pdb=" O GLN D 423 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 29 removed outlier: 3.987A pdb=" N LYS I 19 " --> pdb=" O GLN I 15 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU I 22 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP I 26 " --> pdb=" O GLU I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 49 removed outlier: 3.695A pdb=" N VAL I 49 " --> pdb=" O ARG I 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 46 through 49' Processing helix chain 'I' and resid 70 through 77 removed outlier: 3.756A pdb=" N SER I 75 " --> pdb=" O GLY I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 106 Processing helix chain 'I' and resid 112 through 125 removed outlier: 4.119A pdb=" N ASP I 118 " --> pdb=" O ASP I 114 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL I 119 " --> pdb=" O SER I 115 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS I 122 " --> pdb=" O ASP I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 159 removed outlier: 3.848A pdb=" N ILE I 152 " --> pdb=" O GLY I 148 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU I 157 " --> pdb=" O SER I 153 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU I 158 " --> pdb=" O LYS I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 193 removed outlier: 4.039A pdb=" N SER I 188 " --> pdb=" O ASN I 184 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS I 190 " --> pdb=" O THR I 186 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLN I 191 " --> pdb=" O LEU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 214 removed outlier: 3.716A pdb=" N ILE I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 237 removed outlier: 3.721A pdb=" N HIS I 227 " --> pdb=" O GLY I 223 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU I 228 " --> pdb=" O ASP I 224 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL I 229 " --> pdb=" O LEU I 225 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR I 237 " --> pdb=" O MET I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 240 No H-bonds generated for 'chain 'I' and resid 238 through 240' Processing helix chain 'I' and resid 251 through 256 Processing helix chain 'I' and resid 285 through 294 removed outlier: 3.561A pdb=" N LEU I 289 " --> pdb=" O THR I 285 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR I 290 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE I 294 " --> pdb=" O THR I 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 322 through 336 removed outlier: 3.606A pdb=" N VAL I 326 " --> pdb=" O SER I 322 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN I 334 " --> pdb=" O MET I 330 " (cutoff:3.500A) Processing helix chain 'I' and resid 374 through 390 removed outlier: 3.591A pdb=" N ILE I 381 " --> pdb=" O LEU I 377 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU I 383 " --> pdb=" O LYS I 379 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG I 390 " --> pdb=" O THR I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 400 Processing helix chain 'I' and resid 404 through 427 removed outlier: 3.851A pdb=" N PHE I 408 " --> pdb=" O ASP I 404 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA I 411 " --> pdb=" O GLU I 407 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU I 421 " --> pdb=" O ASP I 417 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN I 424 " --> pdb=" O SER I 420 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP I 427 " --> pdb=" O GLN I 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 28 removed outlier: 3.573A pdb=" N ILE A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS A 25 " --> pdb=" O TRP A 21 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS A 28 " --> pdb=" O TYR A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.643A pdb=" N ASN A 50 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 47 through 51' Processing helix chain 'A' and resid 74 through 81 removed outlier: 4.028A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 114 through 127 removed outlier: 3.553A pdb=" N ASP A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.500A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.720A pdb=" N ILE A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 239 removed outlier: 3.821A pdb=" N LEU A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 244 removed outlier: 3.782A pdb=" N ARG A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 259 removed outlier: 3.695A pdb=" N ASN A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 292 Processing helix chain 'A' and resid 292 through 297 removed outlier: 3.681A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.668A pdb=" N ASN A 329 " --> pdb=" O PRO A 325 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 401 removed outlier: 3.924A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.110A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 410 " --> pdb=" O HIS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 437 removed outlier: 3.569A pdb=" N GLU A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 removed outlier: 3.986A pdb=" N LYS B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 49 removed outlier: 3.694A pdb=" N VAL B 49 " --> pdb=" O ARG B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 49' Processing helix chain 'B' and resid 70 through 77 removed outlier: 3.755A pdb=" N SER B 75 " --> pdb=" O GLY B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 112 through 125 removed outlier: 4.119A pdb=" N ASP B 118 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 159 removed outlier: 3.849A pdb=" N ILE B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 193 removed outlier: 4.039A pdb=" N SER B 188 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 removed outlier: 3.717A pdb=" N ILE B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.722A pdb=" N HIS B 227 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 240 No H-bonds generated for 'chain 'B' and resid 238 through 240' Processing helix chain 'B' and resid 251 through 256 Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.561A pdb=" N LEU B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR B 290 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 336 removed outlier: 3.607A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 390 removed outlier: 3.590A pdb=" N ILE B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU B 383 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG B 390 " --> pdb=" O THR B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.851A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 411 " --> pdb=" O GLU B 407 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 29 removed outlier: 3.986A pdb=" N LYS H 19 " --> pdb=" O GLN H 15 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP H 26 " --> pdb=" O GLU H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 49 removed outlier: 3.695A pdb=" N VAL H 49 " --> pdb=" O ARG H 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 46 through 49' Processing helix chain 'H' and resid 70 through 77 removed outlier: 3.755A pdb=" N SER H 75 " --> pdb=" O GLY H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 106 Processing helix chain 'H' and resid 112 through 125 removed outlier: 4.119A pdb=" N ASP H 118 " --> pdb=" O ASP H 114 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS H 122 " --> pdb=" O ASP H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 159 removed outlier: 3.849A pdb=" N ILE H 152 " --> pdb=" O GLY H 148 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU H 157 " --> pdb=" O SER H 153 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU H 158 " --> pdb=" O LYS H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 193 removed outlier: 4.039A pdb=" N SER H 188 " --> pdb=" O ASN H 184 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS H 190 " --> pdb=" O THR H 186 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLN H 191 " --> pdb=" O LEU H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 214 removed outlier: 3.717A pdb=" N ILE H 210 " --> pdb=" O ALA H 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 237 removed outlier: 3.722A pdb=" N HIS H 227 " --> pdb=" O GLY H 223 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU H 228 " --> pdb=" O ASP H 224 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL H 229 " --> pdb=" O LEU H 225 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR H 237 " --> pdb=" O MET H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 240 No H-bonds generated for 'chain 'H' and resid 238 through 240' Processing helix chain 'H' and resid 251 through 256 Processing helix chain 'H' and resid 285 through 294 removed outlier: 3.560A pdb=" N LEU H 289 " --> pdb=" O THR H 285 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR H 290 " --> pdb=" O VAL H 286 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE H 294 " --> pdb=" O THR H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 322 through 336 removed outlier: 3.606A pdb=" N VAL H 326 " --> pdb=" O SER H 322 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN H 334 " --> pdb=" O MET H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 374 through 390 removed outlier: 3.591A pdb=" N ILE H 381 " --> pdb=" O LEU H 377 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU H 383 " --> pdb=" O LYS H 379 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG H 390 " --> pdb=" O THR H 386 " (cutoff:3.500A) Processing helix chain 'H' and resid 395 through 400 Processing helix chain 'H' and resid 404 through 427 removed outlier: 3.850A pdb=" N PHE H 408 " --> pdb=" O ASP H 404 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA H 411 " --> pdb=" O GLU H 407 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU H 421 " --> pdb=" O ASP H 417 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN H 424 " --> pdb=" O SER H 420 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP H 427 " --> pdb=" O GLN H 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 28 removed outlier: 3.573A pdb=" N ILE E 16 " --> pdb=" O ALA E 12 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA E 19 " --> pdb=" O GLN E 15 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU E 22 " --> pdb=" O ASN E 18 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU E 23 " --> pdb=" O ALA E 19 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS E 25 " --> pdb=" O TRP E 21 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS E 28 " --> pdb=" O TYR E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 51 removed outlier: 3.643A pdb=" N ASN E 50 " --> pdb=" O ASP E 47 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR E 51 " --> pdb=" O SER E 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 47 through 51' Processing helix chain 'E' and resid 74 through 81 removed outlier: 4.028A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 114 through 127 removed outlier: 3.553A pdb=" N ASP E 120 " --> pdb=" O ASP E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 161 removed outlier: 4.500A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU E 155 " --> pdb=" O SER E 151 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER E 158 " --> pdb=" O MET E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 removed outlier: 3.721A pdb=" N ILE E 188 " --> pdb=" O PRO E 184 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 216 Processing helix chain 'E' and resid 223 through 239 removed outlier: 3.821A pdb=" N LEU E 230 " --> pdb=" O ASN E 226 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE E 234 " --> pdb=" O LEU E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 244 removed outlier: 3.782A pdb=" N ARG E 243 " --> pdb=" O THR E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 259 removed outlier: 3.696A pdb=" N ASN E 258 " --> pdb=" O GLU E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 292 Processing helix chain 'E' and resid 292 through 297 removed outlier: 3.680A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 336 removed outlier: 3.667A pdb=" N ASN E 329 " --> pdb=" O PRO E 325 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR E 334 " --> pdb=" O ALA E 330 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE E 335 " --> pdb=" O ALA E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 401 removed outlier: 3.925A pdb=" N LYS E 401 " --> pdb=" O LEU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 4.110A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY E 410 " --> pdb=" O HIS E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 437 removed outlier: 3.569A pdb=" N GLU E 423 " --> pdb=" O SER E 419 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR E 432 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU E 433 " --> pdb=" O GLU E 429 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL E 437 " --> pdb=" O GLU E 433 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 28 removed outlier: 3.572A pdb=" N ILE J 16 " --> pdb=" O ALA J 12 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA J 19 " --> pdb=" O GLN J 15 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU J 22 " --> pdb=" O ASN J 18 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU J 23 " --> pdb=" O ALA J 19 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS J 25 " --> pdb=" O TRP J 21 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU J 26 " --> pdb=" O GLU J 22 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS J 28 " --> pdb=" O TYR J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 51 removed outlier: 3.644A pdb=" N ASN J 50 " --> pdb=" O ASP J 47 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR J 51 " --> pdb=" O SER J 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 47 through 51' Processing helix chain 'J' and resid 74 through 81 removed outlier: 4.028A pdb=" N VAL J 78 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 108 Processing helix chain 'J' and resid 114 through 127 removed outlier: 3.554A pdb=" N ASP J 120 " --> pdb=" O ASP J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 161 removed outlier: 4.499A pdb=" N THR J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU J 155 " --> pdb=" O SER J 151 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER J 158 " --> pdb=" O MET J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 195 removed outlier: 3.720A pdb=" N ILE J 188 " --> pdb=" O PRO J 184 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR J 193 " --> pdb=" O LEU J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 216 Processing helix chain 'J' and resid 223 through 239 removed outlier: 3.821A pdb=" N LEU J 230 " --> pdb=" O ASN J 226 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE J 234 " --> pdb=" O LEU J 230 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 244 removed outlier: 3.782A pdb=" N ARG J 243 " --> pdb=" O THR J 239 " (cutoff:3.500A) Processing helix chain 'J' and resid 254 through 259 removed outlier: 3.695A pdb=" N ASN J 258 " --> pdb=" O GLU J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 292 Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.682A pdb=" N PHE J 296 " --> pdb=" O THR J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 324 through 336 removed outlier: 3.667A pdb=" N ASN J 329 " --> pdb=" O PRO J 325 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR J 334 " --> pdb=" O ALA J 330 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE J 335 " --> pdb=" O ALA J 331 " (cutoff:3.500A) Processing helix chain 'J' and resid 384 through 401 removed outlier: 3.924A pdb=" N LYS J 401 " --> pdb=" O LEU J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 404 through 410 removed outlier: 4.110A pdb=" N TYR J 408 " --> pdb=" O PHE J 404 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY J 410 " --> pdb=" O HIS J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 416 through 437 removed outlier: 3.569A pdb=" N GLU J 423 " --> pdb=" O SER J 419 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR J 432 " --> pdb=" O LEU J 428 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU J 433 " --> pdb=" O GLU J 429 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL J 437 " --> pdb=" O GLU J 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 28 removed outlier: 3.572A pdb=" N ILE C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU C 22 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 23 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS C 25 " --> pdb=" O TRP C 21 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS C 28 " --> pdb=" O TYR C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 51 removed outlier: 3.644A pdb=" N ASN C 50 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR C 51 " --> pdb=" O SER C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 47 through 51' Processing helix chain 'C' and resid 74 through 81 removed outlier: 4.027A pdb=" N VAL C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 114 through 127 removed outlier: 3.553A pdb=" N ASP C 120 " --> pdb=" O ASP C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 removed outlier: 4.500A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU C 155 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 removed outlier: 3.721A pdb=" N ILE C 188 " --> pdb=" O PRO C 184 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 223 through 239 removed outlier: 3.821A pdb=" N LEU C 230 " --> pdb=" O ASN C 226 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 244 removed outlier: 3.782A pdb=" N ARG C 243 " --> pdb=" O THR C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 259 removed outlier: 3.695A pdb=" N ASN C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 292 Processing helix chain 'C' and resid 292 through 297 removed outlier: 3.681A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 336 removed outlier: 3.667A pdb=" N ASN C 329 " --> pdb=" O PRO C 325 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR C 334 " --> pdb=" O ALA C 330 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE C 335 " --> pdb=" O ALA C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 401 removed outlier: 3.924A pdb=" N LYS C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 4.110A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY C 410 " --> pdb=" O HIS C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 437 removed outlier: 3.570A pdb=" N GLU C 423 " --> pdb=" O SER C 419 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU C 433 " --> pdb=" O GLU C 429 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 28 removed outlier: 3.573A pdb=" N ILE L 16 " --> pdb=" O ALA L 12 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA L 19 " --> pdb=" O GLN L 15 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU L 22 " --> pdb=" O ASN L 18 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU L 23 " --> pdb=" O ALA L 19 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS L 25 " --> pdb=" O TRP L 21 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU L 26 " --> pdb=" O GLU L 22 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS L 28 " --> pdb=" O TYR L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 51 removed outlier: 3.644A pdb=" N ASN L 50 " --> pdb=" O ASP L 47 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR L 51 " --> pdb=" O SER L 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 47 through 51' Processing helix chain 'L' and resid 74 through 81 removed outlier: 4.028A pdb=" N VAL L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 108 Processing helix chain 'L' and resid 114 through 127 removed outlier: 3.554A pdb=" N ASP L 120 " --> pdb=" O ASP L 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 161 removed outlier: 4.501A pdb=" N THR L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU L 155 " --> pdb=" O SER L 151 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER L 158 " --> pdb=" O MET L 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 195 removed outlier: 3.721A pdb=" N ILE L 188 " --> pdb=" O PRO L 184 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR L 193 " --> pdb=" O LEU L 189 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 216 Processing helix chain 'L' and resid 223 through 239 removed outlier: 3.822A pdb=" N LEU L 230 " --> pdb=" O ASN L 226 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE L 234 " --> pdb=" O LEU L 230 " (cutoff:3.500A) Processing helix chain 'L' and resid 239 through 244 removed outlier: 3.782A pdb=" N ARG L 243 " --> pdb=" O THR L 239 " (cutoff:3.500A) Processing helix chain 'L' and resid 254 through 259 removed outlier: 3.695A pdb=" N ASN L 258 " --> pdb=" O GLU L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 292 Processing helix chain 'L' and resid 292 through 297 removed outlier: 3.680A pdb=" N PHE L 296 " --> pdb=" O THR L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 324 through 336 removed outlier: 3.668A pdb=" N ASN L 329 " --> pdb=" O PRO L 325 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR L 334 " --> pdb=" O ALA L 330 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE L 335 " --> pdb=" O ALA L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 384 through 401 removed outlier: 3.925A pdb=" N LYS L 401 " --> pdb=" O LEU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 404 through 410 removed outlier: 4.110A pdb=" N TYR L 408 " --> pdb=" O PHE L 404 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY L 410 " --> pdb=" O HIS L 406 " (cutoff:3.500A) Processing helix chain 'L' and resid 416 through 437 removed outlier: 3.569A pdb=" N GLU L 423 " --> pdb=" O SER L 419 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR L 432 " --> pdb=" O LEU L 428 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU L 433 " --> pdb=" O GLU L 429 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL L 437 " --> pdb=" O GLU L 433 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 28 removed outlier: 3.572A pdb=" N ILE K 16 " --> pdb=" O ALA K 12 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA K 19 " --> pdb=" O GLN K 15 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU K 22 " --> pdb=" O ASN K 18 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU K 23 " --> pdb=" O ALA K 19 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS K 25 " --> pdb=" O TRP K 21 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU K 26 " --> pdb=" O GLU K 22 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS K 28 " --> pdb=" O TYR K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 51 removed outlier: 3.643A pdb=" N ASN K 50 " --> pdb=" O ASP K 47 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR K 51 " --> pdb=" O SER K 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 47 through 51' Processing helix chain 'K' and resid 74 through 81 removed outlier: 4.028A pdb=" N VAL K 78 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 114 through 127 removed outlier: 3.553A pdb=" N ASP K 120 " --> pdb=" O ASP K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 161 removed outlier: 4.499A pdb=" N THR K 150 " --> pdb=" O GLY K 146 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU K 155 " --> pdb=" O SER K 151 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER K 158 " --> pdb=" O MET K 154 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 195 removed outlier: 3.721A pdb=" N ILE K 188 " --> pdb=" O PRO K 184 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR K 193 " --> pdb=" O LEU K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 216 Processing helix chain 'K' and resid 223 through 239 removed outlier: 3.821A pdb=" N LEU K 230 " --> pdb=" O ASN K 226 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE K 234 " --> pdb=" O LEU K 230 " (cutoff:3.500A) Processing helix chain 'K' and resid 239 through 244 removed outlier: 3.782A pdb=" N ARG K 243 " --> pdb=" O THR K 239 " (cutoff:3.500A) Processing helix chain 'K' and resid 254 through 259 removed outlier: 3.695A pdb=" N ASN K 258 " --> pdb=" O GLU K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 292 Processing helix chain 'K' and resid 292 through 297 removed outlier: 3.680A pdb=" N PHE K 296 " --> pdb=" O THR K 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 324 through 336 removed outlier: 3.667A pdb=" N ASN K 329 " --> pdb=" O PRO K 325 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR K 334 " --> pdb=" O ALA K 330 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE K 335 " --> pdb=" O ALA K 331 " (cutoff:3.500A) Processing helix chain 'K' and resid 384 through 401 removed outlier: 3.925A pdb=" N LYS K 401 " --> pdb=" O LEU K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 410 removed outlier: 4.110A pdb=" N TYR K 408 " --> pdb=" O PHE K 404 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY K 410 " --> pdb=" O HIS K 406 " (cutoff:3.500A) Processing helix chain 'K' and resid 416 through 437 removed outlier: 3.569A pdb=" N GLU K 423 " --> pdb=" O SER K 419 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR K 432 " --> pdb=" O LEU K 428 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU K 433 " --> pdb=" O GLU K 429 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL K 437 " --> pdb=" O GLU K 433 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 90 through 92 removed outlier: 8.104A pdb=" N VAL F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU F 65 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE F 7 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N GLN F 131 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N ASN F 165 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE F 133 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N PHE F 167 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU F 135 " --> pdb=" O PHE F 167 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N VAL F 169 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N MET F 164 " --> pdb=" O GLU F 198 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N TYR F 200 " --> pdb=" O MET F 164 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR F 166 " --> pdb=" O TYR F 200 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE F 202 " --> pdb=" O THR F 166 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER F 168 " --> pdb=" O ILE F 202 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N THR F 199 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N CYS F 201 " --> pdb=" O PRO F 268 " (cutoff:3.500A) removed outlier: 10.690A pdb=" N PHE F 270 " --> pdb=" O CYS F 201 " (cutoff:3.500A) removed outlier: 13.851A pdb=" N ASP F 203 " --> pdb=" O PHE F 270 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA F 271 " --> pdb=" O ALA F 365 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL F 313 " --> pdb=" O LYS F 350 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ALA F 352 " --> pdb=" O VAL F 313 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA F 315 " --> pdb=" O ALA F 352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 51 through 53 Processing sheet with id=AA3, first strand: chain 'G' and resid 90 through 92 removed outlier: 8.104A pdb=" N VAL G 91 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU G 65 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLU G 3 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N PHE G 133 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL G 5 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU G 135 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE G 7 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLN G 131 " --> pdb=" O ILE G 163 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N ASN G 165 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE G 133 " --> pdb=" O ASN G 165 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N PHE G 167 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU G 135 " --> pdb=" O PHE G 167 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N VAL G 169 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N MET G 164 " --> pdb=" O GLU G 198 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N TYR G 200 " --> pdb=" O MET G 164 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR G 166 " --> pdb=" O TYR G 200 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE G 202 " --> pdb=" O THR G 166 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER G 168 " --> pdb=" O ILE G 202 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N THR G 199 " --> pdb=" O PHE G 266 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N CYS G 201 " --> pdb=" O PRO G 268 " (cutoff:3.500A) removed outlier: 10.689A pdb=" N PHE G 270 " --> pdb=" O CYS G 201 " (cutoff:3.500A) removed outlier: 13.851A pdb=" N ASP G 203 " --> pdb=" O PHE G 270 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA G 271 " --> pdb=" O ALA G 365 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL G 313 " --> pdb=" O LYS G 350 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ALA G 352 " --> pdb=" O VAL G 313 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA G 315 " --> pdb=" O ALA G 352 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 51 through 53 Processing sheet with id=AA5, first strand: chain 'D' and resid 90 through 92 removed outlier: 8.104A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLU D 3 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N PHE D 133 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N VAL D 5 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE D 7 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLN D 131 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N ASN D 165 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE D 133 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N PHE D 167 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU D 135 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N VAL D 169 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N MET D 164 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N TYR D 200 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR D 166 " --> pdb=" O TYR D 200 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE D 202 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER D 168 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N CYS D 201 " --> pdb=" O PRO D 268 " (cutoff:3.500A) removed outlier: 10.689A pdb=" N PHE D 270 " --> pdb=" O CYS D 201 " (cutoff:3.500A) removed outlier: 13.852A pdb=" N ASP D 203 " --> pdb=" O PHE D 270 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA D 271 " --> pdb=" O ALA D 365 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL D 313 " --> pdb=" O LYS D 350 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ALA D 352 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA D 315 " --> pdb=" O ALA D 352 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AA7, first strand: chain 'I' and resid 90 through 92 removed outlier: 8.104A pdb=" N VAL I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU I 65 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLN I 131 " --> pdb=" O ILE I 163 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N ASN I 165 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE I 133 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N PHE I 167 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU I 135 " --> pdb=" O PHE I 167 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N VAL I 169 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N MET I 164 " --> pdb=" O GLU I 198 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N TYR I 200 " --> pdb=" O MET I 164 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR I 166 " --> pdb=" O TYR I 200 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE I 202 " --> pdb=" O THR I 166 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER I 168 " --> pdb=" O ILE I 202 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N THR I 199 " --> pdb=" O PHE I 266 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N CYS I 201 " --> pdb=" O PRO I 268 " (cutoff:3.500A) removed outlier: 10.690A pdb=" N PHE I 270 " --> pdb=" O CYS I 201 " (cutoff:3.500A) removed outlier: 13.851A pdb=" N ASP I 203 " --> pdb=" O PHE I 270 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA I 271 " --> pdb=" O ALA I 365 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL I 313 " --> pdb=" O LYS I 350 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ALA I 352 " --> pdb=" O VAL I 313 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA I 315 " --> pdb=" O ALA I 352 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 51 through 53 Processing sheet with id=AA9, first strand: chain 'A' and resid 65 through 68 removed outlier: 7.054A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 53 through 55 removed outlier: 3.796A pdb=" N VAL A 62 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AB3, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.104A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.939A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N MET B 164 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 10.689A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 13.851A pdb=" N ASP B 203 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 271 " --> pdb=" O ALA B 365 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B 313 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ALA B 352 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA B 315 " --> pdb=" O ALA B 352 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AB5, first strand: chain 'H' and resid 90 through 92 removed outlier: 8.103A pdb=" N VAL H 91 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU H 65 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLU H 3 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N PHE H 133 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL H 5 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE H 7 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLN H 131 " --> pdb=" O ILE H 163 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N ASN H 165 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE H 133 " --> pdb=" O ASN H 165 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N PHE H 167 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU H 135 " --> pdb=" O PHE H 167 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N VAL H 169 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N MET H 164 " --> pdb=" O GLU H 198 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N TYR H 200 " --> pdb=" O MET H 164 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR H 166 " --> pdb=" O TYR H 200 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE H 202 " --> pdb=" O THR H 166 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER H 168 " --> pdb=" O ILE H 202 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N THR H 199 " --> pdb=" O PHE H 266 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N CYS H 201 " --> pdb=" O PRO H 268 " (cutoff:3.500A) removed outlier: 10.690A pdb=" N PHE H 270 " --> pdb=" O CYS H 201 " (cutoff:3.500A) removed outlier: 13.851A pdb=" N ASP H 203 " --> pdb=" O PHE H 270 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA H 271 " --> pdb=" O ALA H 365 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL H 313 " --> pdb=" O LYS H 350 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ALA H 352 " --> pdb=" O VAL H 313 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA H 315 " --> pdb=" O ALA H 352 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 51 through 53 Processing sheet with id=AB7, first strand: chain 'E' and resid 65 through 68 removed outlier: 7.054A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N SER E 170 " --> pdb=" O VAL E 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 53 through 55 removed outlier: 3.797A pdb=" N VAL E 62 " --> pdb=" O SER E 54 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 246 through 248 Processing sheet with id=AC1, first strand: chain 'J' and resid 65 through 68 removed outlier: 7.053A pdb=" N SER J 6 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL J 68 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N HIS J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS J 166 " --> pdb=" O CYS J 200 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N PHE J 202 " --> pdb=" O LYS J 166 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU J 168 " --> pdb=" O PHE J 202 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL J 204 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N SER J 170 " --> pdb=" O VAL J 204 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 53 through 55 removed outlier: 3.797A pdb=" N VAL J 62 " --> pdb=" O SER J 54 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 246 through 248 Processing sheet with id=AC4, first strand: chain 'C' and resid 65 through 68 removed outlier: 7.054A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS C 166 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N PHE C 202 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU C 168 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL C 204 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N SER C 170 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 53 through 55 removed outlier: 3.796A pdb=" N VAL C 62 " --> pdb=" O SER C 54 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 246 through 248 Processing sheet with id=AC7, first strand: chain 'L' and resid 65 through 68 removed outlier: 7.054A pdb=" N SER L 6 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL L 68 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N HIS L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS L 166 " --> pdb=" O CYS L 200 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N PHE L 202 " --> pdb=" O LYS L 166 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU L 168 " --> pdb=" O PHE L 202 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL L 204 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N SER L 170 " --> pdb=" O VAL L 204 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 53 through 55 removed outlier: 3.796A pdb=" N VAL L 62 " --> pdb=" O SER L 54 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 246 through 248 Processing sheet with id=AD1, first strand: chain 'K' and resid 65 through 68 removed outlier: 7.053A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS K 166 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N PHE K 202 " --> pdb=" O LYS K 166 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLU K 168 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL K 204 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N SER K 170 " --> pdb=" O VAL K 204 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 53 through 55 removed outlier: 3.796A pdb=" N VAL K 62 " --> pdb=" O SER K 54 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 246 through 248 1440 hydrogen bonds defined for protein. 4284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.03 Time building geometry restraints manager: 16.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13505 1.34 - 1.46: 6233 1.46 - 1.57: 21578 1.57 - 1.69: 48 1.69 - 1.80: 432 Bond restraints: 41796 Sorted by residual: bond pdb=" C5 GDP B 501 " pdb=" C4 GDP B 501 " ideal model delta sigma weight residual 1.490 1.375 0.115 2.00e-02 2.50e+03 3.30e+01 bond pdb=" C5 GDP F 501 " pdb=" C4 GDP F 501 " ideal model delta sigma weight residual 1.490 1.375 0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C5 GDP G 501 " pdb=" C4 GDP G 501 " ideal model delta sigma weight residual 1.490 1.376 0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" C5 GDP H 501 " pdb=" C4 GDP H 501 " ideal model delta sigma weight residual 1.490 1.376 0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" C5 GDP I 501 " pdb=" C4 GDP I 501 " ideal model delta sigma weight residual 1.490 1.376 0.114 2.00e-02 2.50e+03 3.24e+01 ... (remaining 41791 not shown) Histogram of bond angle deviations from ideal: 99.00 - 106.01: 1076 106.01 - 113.02: 22127 113.02 - 120.03: 14679 120.03 - 127.03: 18388 127.03 - 134.04: 514 Bond angle restraints: 56784 Sorted by residual: angle pdb=" N ILE H 84 " pdb=" CA ILE H 84 " pdb=" C ILE H 84 " ideal model delta sigma weight residual 113.42 108.69 4.73 1.17e+00 7.31e-01 1.63e+01 angle pdb=" N ILE D 84 " pdb=" CA ILE D 84 " pdb=" C ILE D 84 " ideal model delta sigma weight residual 113.42 108.70 4.72 1.17e+00 7.31e-01 1.63e+01 angle pdb=" N ILE I 84 " pdb=" CA ILE I 84 " pdb=" C ILE I 84 " ideal model delta sigma weight residual 113.42 108.71 4.71 1.17e+00 7.31e-01 1.62e+01 angle pdb=" N ILE F 84 " pdb=" CA ILE F 84 " pdb=" C ILE F 84 " ideal model delta sigma weight residual 113.42 108.74 4.68 1.17e+00 7.31e-01 1.60e+01 angle pdb=" N ILE B 84 " pdb=" CA ILE B 84 " pdb=" C ILE B 84 " ideal model delta sigma weight residual 113.42 108.74 4.68 1.17e+00 7.31e-01 1.60e+01 ... (remaining 56779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.55: 24574 32.55 - 65.09: 219 65.09 - 97.64: 25 97.64 - 130.18: 17 130.18 - 162.73: 17 Dihedral angle restraints: 24852 sinusoidal: 9924 harmonic: 14928 Sorted by residual: dihedral pdb=" C8 GTP E 501 " pdb=" C1' GTP E 501 " pdb=" N9 GTP E 501 " pdb=" O4' GTP E 501 " ideal model delta sinusoidal sigma weight residual 104.59 -58.14 162.73 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" C8 GTP J 501 " pdb=" C1' GTP J 501 " pdb=" N9 GTP J 501 " pdb=" O4' GTP J 501 " ideal model delta sinusoidal sigma weight residual 104.59 -57.05 161.65 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" C8 GTP L 501 " pdb=" C1' GTP L 501 " pdb=" N9 GTP L 501 " pdb=" O4' GTP L 501 " ideal model delta sinusoidal sigma weight residual 104.59 -56.30 160.89 1 2.00e+01 2.50e-03 4.67e+01 ... (remaining 24849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4235 0.045 - 0.089: 1441 0.089 - 0.134: 462 0.134 - 0.178: 48 0.178 - 0.223: 30 Chirality restraints: 6216 Sorted by residual: chirality pdb=" C2' GTP K 501 " pdb=" C1' GTP K 501 " pdb=" C3' GTP K 501 " pdb=" O2' GTP K 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.69 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C2' GTP A 501 " pdb=" C1' GTP A 501 " pdb=" C3' GTP A 501 " pdb=" O2' GTP A 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.69 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C2' GTP C 501 " pdb=" C1' GTP C 501 " pdb=" C3' GTP C 501 " pdb=" O2' GTP C 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.69 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 6213 not shown) Planarity restraints: 7398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GDP H 501 " 0.060 2.00e-02 2.50e+03 2.51e-02 1.90e+01 pdb=" N9 GDP H 501 " -0.011 2.00e-02 2.50e+03 pdb=" C8 GDP H 501 " -0.007 2.00e-02 2.50e+03 pdb=" N7 GDP H 501 " -0.015 2.00e-02 2.50e+03 pdb=" C5 GDP H 501 " -0.021 2.00e-02 2.50e+03 pdb=" C6 GDP H 501 " 0.009 2.00e-02 2.50e+03 pdb=" O6 GDP H 501 " 0.028 2.00e-02 2.50e+03 pdb=" N1 GDP H 501 " 0.021 2.00e-02 2.50e+03 pdb=" C2 GDP H 501 " -0.000 2.00e-02 2.50e+03 pdb=" N2 GDP H 501 " -0.004 2.00e-02 2.50e+03 pdb=" N3 GDP H 501 " -0.028 2.00e-02 2.50e+03 pdb=" C4 GDP H 501 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GDP I 501 " -0.054 2.00e-02 2.50e+03 2.29e-02 1.57e+01 pdb=" N9 GDP I 501 " 0.009 2.00e-02 2.50e+03 pdb=" C8 GDP I 501 " 0.009 2.00e-02 2.50e+03 pdb=" N7 GDP I 501 " 0.015 2.00e-02 2.50e+03 pdb=" C5 GDP I 501 " 0.019 2.00e-02 2.50e+03 pdb=" C6 GDP I 501 " -0.010 2.00e-02 2.50e+03 pdb=" O6 GDP I 501 " -0.023 2.00e-02 2.50e+03 pdb=" N1 GDP I 501 " -0.024 2.00e-02 2.50e+03 pdb=" C2 GDP I 501 " -0.002 2.00e-02 2.50e+03 pdb=" N2 GDP I 501 " 0.010 2.00e-02 2.50e+03 pdb=" N3 GDP I 501 " 0.023 2.00e-02 2.50e+03 pdb=" C4 GDP I 501 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GDP B 501 " 0.053 2.00e-02 2.50e+03 2.20e-02 1.45e+01 pdb=" N9 GDP B 501 " -0.010 2.00e-02 2.50e+03 pdb=" C8 GDP B 501 " -0.011 2.00e-02 2.50e+03 pdb=" N7 GDP B 501 " -0.015 2.00e-02 2.50e+03 pdb=" C5 GDP B 501 " -0.017 2.00e-02 2.50e+03 pdb=" C6 GDP B 501 " 0.010 2.00e-02 2.50e+03 pdb=" O6 GDP B 501 " 0.025 2.00e-02 2.50e+03 pdb=" N1 GDP B 501 " 0.020 2.00e-02 2.50e+03 pdb=" C2 GDP B 501 " 0.001 2.00e-02 2.50e+03 pdb=" N2 GDP B 501 " -0.009 2.00e-02 2.50e+03 pdb=" N3 GDP B 501 " -0.021 2.00e-02 2.50e+03 pdb=" C4 GDP B 501 " -0.025 2.00e-02 2.50e+03 ... (remaining 7395 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 420 2.65 - 3.21: 35314 3.21 - 3.78: 59256 3.78 - 4.34: 86796 4.34 - 4.90: 142232 Nonbonded interactions: 324018 Sorted by model distance: nonbonded pdb=" O2G GTP C 501 " pdb="MG MG C 502 " model vdw 2.091 2.170 nonbonded pdb=" O2G GTP L 501 " pdb="MG MG L 502 " model vdw 2.094 2.170 nonbonded pdb=" O2G GTP E 501 " pdb="MG MG E 502 " model vdw 2.097 2.170 nonbonded pdb=" O2G GTP J 501 " pdb="MG MG J 502 " model vdw 2.100 2.170 nonbonded pdb=" O2G GTP A 501 " pdb="MG MG A 502 " model vdw 2.101 2.170 ... (remaining 324013 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' selection = chain 'C' selection = chain 'E' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 2.870 Check model and map are aligned: 0.630 Set scattering table: 0.380 Process input model: 99.730 Find NCS groups from input model: 3.160 Set up NCS constraints: 0.350 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 : 0.006 0.115 41796 Z= 0.364 Angle : 0.919 11.606 56784 Z= 0.512 Chirality : 0.050 0.223 6216 Planarity : 0.007 0.055 7398 Dihedral : 11.513 162.731 15276 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.24 (0.09), residues: 5130 helix: -4.67 (0.04), residues: 2208 sheet: -1.45 (0.18), residues: 846 loop : -2.72 (0.11), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP F 101 HIS 0.013 0.002 HIS E 28 PHE 0.018 0.002 PHE J 138 TYR 0.026 0.002 TYR C 210 ARG 0.007 0.001 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1339 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1339 time to evaluate : 4.423 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: F 3 GLU cc_start: 0.7652 (mp0) cc_final: 0.7439 (mp0) REVERT: F 74 ASP cc_start: 0.7659 (t70) cc_final: 0.7080 (t0) REVERT: F 86 ARG cc_start: 0.7915 (mtp180) cc_final: 0.6830 (mmp-170) REVERT: F 129 CYS cc_start: 0.8275 (t) cc_final: 0.7614 (t) REVERT: F 225 LEU cc_start: 0.8775 (mp) cc_final: 0.8355 (mp) REVERT: F 253 LEU cc_start: 0.8667 (mt) cc_final: 0.8396 (mt) REVERT: F 351 THR cc_start: 0.9264 (m) cc_final: 0.8917 (p) REVERT: G 74 ASP cc_start: 0.7736 (t70) cc_final: 0.7142 (t0) REVERT: G 86 ARG cc_start: 0.7949 (mtp180) cc_final: 0.6943 (mmp-170) REVERT: G 151 LEU cc_start: 0.9096 (mt) cc_final: 0.8887 (mt) REVERT: G 213 ARG cc_start: 0.7451 (ttm110) cc_final: 0.7193 (ttm170) REVERT: G 224 ASP cc_start: 0.8059 (m-30) cc_final: 0.7815 (m-30) REVERT: G 225 LEU cc_start: 0.8648 (mp) cc_final: 0.8262 (mp) REVERT: G 253 LEU cc_start: 0.8725 (mt) cc_final: 0.8481 (mt) REVERT: G 404 ASP cc_start: 0.7709 (p0) cc_final: 0.7505 (p0) REVERT: D 74 ASP cc_start: 0.7720 (t70) cc_final: 0.7234 (t0) REVERT: D 103 LYS cc_start: 0.8794 (mttt) cc_final: 0.8509 (mtmt) REVERT: D 167 PHE cc_start: 0.8792 (m-80) cc_final: 0.8244 (m-10) REVERT: D 178 THR cc_start: 0.8845 (m) cc_final: 0.8587 (m) REVERT: D 407 GLU cc_start: 0.8482 (tp30) cc_final: 0.8219 (mm-30) REVERT: I 74 ASP cc_start: 0.7785 (t70) cc_final: 0.7319 (t0) REVERT: I 103 LYS cc_start: 0.8968 (mttt) cc_final: 0.8712 (mtmt) REVERT: I 164 MET cc_start: 0.8127 (tpt) cc_final: 0.7693 (tpt) REVERT: A 24 TYR cc_start: 0.8984 (m-80) cc_final: 0.8735 (m-10) REVERT: A 193 THR cc_start: 0.9172 (m) cc_final: 0.8848 (p) REVERT: A 235 VAL cc_start: 0.9284 (t) cc_final: 0.9049 (t) REVERT: A 302 MET cc_start: 0.7882 (mtt) cc_final: 0.7632 (mtt) REVERT: A 319 TYR cc_start: 0.9186 (m-80) cc_final: 0.8905 (m-80) REVERT: A 327 ASP cc_start: 0.8161 (m-30) cc_final: 0.7925 (m-30) REVERT: A 351 PHE cc_start: 0.8873 (m-80) cc_final: 0.8672 (m-80) REVERT: A 370 LYS cc_start: 0.8984 (tttp) cc_final: 0.8623 (tptt) REVERT: A 393 HIS cc_start: 0.8071 (t70) cc_final: 0.7701 (t70) REVERT: B 3 GLU cc_start: 0.7634 (mp0) cc_final: 0.7235 (mp0) REVERT: B 74 ASP cc_start: 0.7433 (t70) cc_final: 0.7193 (t0) REVERT: B 129 CYS cc_start: 0.8645 (t) cc_final: 0.8203 (t) REVERT: B 178 THR cc_start: 0.9121 (m) cc_final: 0.8799 (m) REVERT: B 246 LEU cc_start: 0.9019 (tp) cc_final: 0.8800 (tt) REVERT: B 329 GLN cc_start: 0.8302 (mm-40) cc_final: 0.8053 (mm-40) REVERT: B 332 ASN cc_start: 0.8340 (t0) cc_final: 0.7634 (t0) REVERT: B 340 TYR cc_start: 0.7823 (m-80) cc_final: 0.7612 (m-10) REVERT: B 379 LYS cc_start: 0.8527 (mtpt) cc_final: 0.8125 (tttm) REVERT: H 3 GLU cc_start: 0.8076 (mp0) cc_final: 0.7563 (mp0) REVERT: H 37 HIS cc_start: 0.6926 (m90) cc_final: 0.6716 (m170) REVERT: H 74 ASP cc_start: 0.7602 (t70) cc_final: 0.7222 (t0) REVERT: H 164 MET cc_start: 0.8143 (tpt) cc_final: 0.7937 (tpt) REVERT: H 213 ARG cc_start: 0.7695 (ttm110) cc_final: 0.7239 (mtp-110) REVERT: H 379 LYS cc_start: 0.8406 (mtpt) cc_final: 0.7997 (tttm) REVERT: E 24 TYR cc_start: 0.8822 (m-80) cc_final: 0.8477 (m-10) REVERT: E 93 ILE cc_start: 0.9225 (mt) cc_final: 0.8992 (mm) REVERT: E 154 MET cc_start: 0.8430 (mmm) cc_final: 0.8209 (mmt) REVERT: E 156 ARG cc_start: 0.7931 (mmt90) cc_final: 0.7360 (mmt180) REVERT: E 170 SER cc_start: 0.9232 (m) cc_final: 0.8942 (p) REVERT: E 221 ARG cc_start: 0.7444 (mtt90) cc_final: 0.7158 (mtm-85) REVERT: E 271 THR cc_start: 0.9041 (m) cc_final: 0.8834 (p) REVERT: E 319 TYR cc_start: 0.8973 (m-80) cc_final: 0.8369 (m-10) REVERT: E 377 MET cc_start: 0.8524 (ttp) cc_final: 0.8200 (ttt) REVERT: E 420 GLU cc_start: 0.7900 (tt0) cc_final: 0.7475 (tp30) REVERT: J 24 TYR cc_start: 0.8771 (m-80) cc_final: 0.8340 (m-10) REVERT: J 170 SER cc_start: 0.9262 (m) cc_final: 0.8980 (p) REVERT: J 254 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7205 (mm-30) REVERT: J 271 THR cc_start: 0.8816 (m) cc_final: 0.8535 (p) REVERT: J 297 GLU cc_start: 0.8709 (tt0) cc_final: 0.8485 (tt0) REVERT: J 393 HIS cc_start: 0.8495 (t70) cc_final: 0.8263 (t-90) REVERT: C 2 ARG cc_start: 0.7718 (mpp80) cc_final: 0.7513 (mtm180) REVERT: C 91 GLN cc_start: 0.8371 (mt0) cc_final: 0.7893 (mt0) REVERT: C 117 LEU cc_start: 0.8973 (tp) cc_final: 0.8742 (tt) REVERT: C 203 MET cc_start: 0.8670 (mmp) cc_final: 0.8455 (mmm) REVERT: C 230 LEU cc_start: 0.9003 (mp) cc_final: 0.8514 (tt) REVERT: C 327 ASP cc_start: 0.8269 (m-30) cc_final: 0.8041 (m-30) REVERT: C 415 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7195 (tp30) REVERT: C 425 MET cc_start: 0.8481 (tpp) cc_final: 0.8207 (tpp) REVERT: L 91 GLN cc_start: 0.8310 (mt0) cc_final: 0.7899 (mt0) REVERT: L 103 TYR cc_start: 0.8727 (t80) cc_final: 0.8280 (t80) REVERT: L 161 TYR cc_start: 0.8112 (m-80) cc_final: 0.7802 (m-80) REVERT: L 172 TYR cc_start: 0.8020 (t80) cc_final: 0.7488 (t80) REVERT: L 203 MET cc_start: 0.8570 (mmp) cc_final: 0.7850 (mmt) REVERT: L 254 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7532 (mm-30) REVERT: L 271 THR cc_start: 0.8764 (m) cc_final: 0.7822 (m) REVERT: L 304 LYS cc_start: 0.8567 (tppt) cc_final: 0.8339 (tppp) REVERT: L 393 HIS cc_start: 0.8310 (t70) cc_final: 0.7806 (t70) REVERT: K 103 TYR cc_start: 0.8369 (t80) cc_final: 0.8133 (t80) REVERT: K 216 ASN cc_start: 0.8846 (m110) cc_final: 0.8637 (t0) outliers start: 0 outliers final: 0 residues processed: 1339 average time/residue: 0.5626 time to fit residues: 1195.4754 Evaluate side-chains 724 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 724 time to evaluate : 4.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 430 optimal weight: 7.9990 chunk 386 optimal weight: 20.0000 chunk 214 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 260 optimal weight: 20.0000 chunk 206 optimal weight: 10.0000 chunk 399 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 243 optimal weight: 5.9990 chunk 297 optimal weight: 10.0000 chunk 463 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN F 137 HIS F 190 HIS F 204 ASN ** F 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 ASN F 375 GLN F 396 HIS F 426 GLN G 8 GLN G 14 ASN G 137 HIS ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 ASN ** G 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 335 ASN G 396 HIS G 423 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 HIS ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN D 226 ASN D 307 HIS D 396 HIS ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 ASN I 137 HIS ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 204 ASN I 226 ASN I 307 HIS I 375 GLN I 396 HIS I 426 GLN A 28 HIS A 61 HIS ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 HIS ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 266 HIS A 283 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN B 226 ASN ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN B 396 HIS B 423 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 HIS ** H 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 ASN H 226 ASN H 307 HIS H 396 HIS H 423 GLN E 28 HIS E 61 HIS E 88 HIS E 107 HIS E 139 HIS E 186 ASN E 192 HIS E 206 ASN E 258 ASN E 283 HIS J 28 HIS J 61 HIS J 88 HIS J 107 HIS J 139 HIS J 186 ASN J 192 HIS J 206 ASN J 258 ASN J 266 HIS J 283 HIS C 28 HIS C 61 HIS ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN C 206 ASN C 266 HIS L 28 HIS L 50 ASN L 61 HIS L 88 HIS L 107 HIS L 133 GLN ** L 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN L 192 HIS L 206 ASN L 258 ASN L 266 HIS ** L 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 HIS K 61 HIS K 88 HIS K 107 HIS ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN K 192 HIS K 206 ASN K 258 ASN K 283 HIS Total number of N/Q/H flips: 94 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 41796 Z= 0.340 Angle : 0.633 7.276 56784 Z= 0.332 Chirality : 0.047 0.156 6216 Planarity : 0.005 0.077 7398 Dihedral : 11.654 152.912 5760 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.07 % Allowed : 10.04 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.10), residues: 5130 helix: -2.64 (0.08), residues: 2160 sheet: -1.33 (0.18), residues: 852 loop : -2.11 (0.12), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 21 HIS 0.007 0.001 HIS H 190 PHE 0.015 0.002 PHE C 67 TYR 0.020 0.002 TYR L 24 ARG 0.008 0.001 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 782 time to evaluate : 4.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 74 ASP cc_start: 0.7732 (t70) cc_final: 0.7155 (t0) REVERT: F 86 ARG cc_start: 0.7947 (mtp180) cc_final: 0.6917 (mmp-170) REVERT: F 150 LEU cc_start: 0.9137 (tp) cc_final: 0.8727 (tp) REVERT: F 205 GLU cc_start: 0.7952 (tt0) cc_final: 0.7665 (tt0) REVERT: F 267 MET cc_start: 0.8510 (mtm) cc_final: 0.8300 (mtm) REVERT: F 292 GLN cc_start: 0.8466 (tt0) cc_final: 0.8126 (tt0) REVERT: F 323 MET cc_start: 0.8435 (tpp) cc_final: 0.7829 (mmm) REVERT: G 74 ASP cc_start: 0.7810 (t70) cc_final: 0.7248 (t0) REVERT: G 224 ASP cc_start: 0.8100 (m-30) cc_final: 0.7801 (m-30) REVERT: G 332 ASN cc_start: 0.7682 (t0) cc_final: 0.7182 (t0) REVERT: G 379 LYS cc_start: 0.8366 (mtpt) cc_final: 0.8154 (mtpt) REVERT: D 74 ASP cc_start: 0.7611 (t70) cc_final: 0.7232 (t0) REVERT: D 103 LYS cc_start: 0.9032 (mttt) cc_final: 0.8653 (mtmt) REVERT: D 178 THR cc_start: 0.8822 (m) cc_final: 0.8316 (p) REVERT: D 230 SER cc_start: 0.9311 (p) cc_final: 0.9110 (t) REVERT: D 330 MET cc_start: 0.8692 (mmp) cc_final: 0.8184 (mmp) REVERT: I 74 ASP cc_start: 0.7876 (t70) cc_final: 0.7475 (t0) REVERT: I 103 LYS cc_start: 0.9150 (mttt) cc_final: 0.8849 (mtmt) REVERT: I 113 VAL cc_start: 0.9440 (p) cc_final: 0.9233 (t) REVERT: I 257 MET cc_start: 0.8781 (mmm) cc_final: 0.8427 (mmm) REVERT: A 154 MET cc_start: 0.8244 (mmt) cc_final: 0.7896 (mmt) REVERT: A 279 GLU cc_start: 0.8599 (tp30) cc_final: 0.8215 (tp30) REVERT: A 327 ASP cc_start: 0.8472 (m-30) cc_final: 0.8182 (m-30) REVERT: A 367 ASP cc_start: 0.7985 (p0) cc_final: 0.7752 (p0) REVERT: B 3 GLU cc_start: 0.8228 (mp0) cc_final: 0.7680 (mp0) REVERT: B 69 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7448 (pt0) REVERT: B 74 ASP cc_start: 0.7525 (t70) cc_final: 0.7237 (t0) REVERT: B 178 THR cc_start: 0.9131 (m) cc_final: 0.8693 (p) REVERT: B 213 ARG cc_start: 0.8143 (mtp-110) cc_final: 0.7723 (mtm110) REVERT: B 332 ASN cc_start: 0.8269 (t0) cc_final: 0.7949 (t0) REVERT: B 363 MET cc_start: 0.8612 (ptp) cc_final: 0.8312 (ptp) REVERT: B 379 LYS cc_start: 0.8542 (mtpt) cc_final: 0.8194 (tptm) REVERT: H 3 GLU cc_start: 0.8088 (mp0) cc_final: 0.7636 (mp0) REVERT: H 332 ASN cc_start: 0.8013 (t0) cc_final: 0.7646 (t0) REVERT: H 336 LYS cc_start: 0.8069 (mttt) cc_final: 0.7863 (mttt) REVERT: H 379 LYS cc_start: 0.8577 (mtpt) cc_final: 0.8075 (tttm) REVERT: E 24 TYR cc_start: 0.8802 (m-80) cc_final: 0.8259 (m-10) REVERT: E 79 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8710 (mtt180) REVERT: E 124 LYS cc_start: 0.8877 (ttmm) cc_final: 0.8384 (ttmt) REVERT: E 170 SER cc_start: 0.9410 (m) cc_final: 0.9028 (p) REVERT: E 269 LEU cc_start: 0.8767 (pp) cc_final: 0.8211 (pp) REVERT: E 271 THR cc_start: 0.9080 (m) cc_final: 0.8199 (p) REVERT: E 319 TYR cc_start: 0.9159 (m-80) cc_final: 0.8491 (m-80) REVERT: J 24 TYR cc_start: 0.8767 (m-80) cc_final: 0.8495 (m-10) REVERT: J 93 ILE cc_start: 0.9398 (mt) cc_final: 0.9102 (mm) REVERT: J 254 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7351 (mm-30) REVERT: J 271 THR cc_start: 0.9050 (m) cc_final: 0.8351 (p) REVERT: C 90 GLU cc_start: 0.7254 (tp30) cc_final: 0.7004 (tp30) REVERT: C 91 GLN cc_start: 0.8527 (mt0) cc_final: 0.8065 (mt0) REVERT: C 123 ARG cc_start: 0.8241 (tpp80) cc_final: 0.7947 (tpp80) REVERT: C 124 LYS cc_start: 0.9129 (ttmm) cc_final: 0.8527 (ttmt) REVERT: C 127 ASP cc_start: 0.8299 (m-30) cc_final: 0.7913 (m-30) REVERT: C 393 HIS cc_start: 0.7924 (t70) cc_final: 0.7717 (t-90) REVERT: C 433 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7978 (mm-30) REVERT: L 91 GLN cc_start: 0.8521 (mt0) cc_final: 0.8109 (mt0) REVERT: L 154 MET cc_start: 0.8558 (mmm) cc_final: 0.8266 (mmm) REVERT: L 172 TYR cc_start: 0.8015 (t80) cc_final: 0.7457 (t80) REVERT: L 203 MET cc_start: 0.8869 (mmp) cc_final: 0.8033 (mmt) REVERT: L 254 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7580 (tp30) REVERT: L 429 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8302 (tt0) REVERT: K 254 GLU cc_start: 0.5549 (tp30) cc_final: 0.5330 (mm-30) outliers start: 91 outliers final: 59 residues processed: 837 average time/residue: 0.5422 time to fit residues: 740.6182 Evaluate side-chains 686 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 624 time to evaluate : 5.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 157 GLU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain I residue 198 GLU Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 233 MET Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 419 VAL Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 207 GLU Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 285 GLN Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 324 VAL Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 324 VAL Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain K residue 284 GLU Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 345 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 257 optimal weight: 0.0670 chunk 143 optimal weight: 10.0000 chunk 385 optimal weight: 9.9990 chunk 315 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 463 optimal weight: 10.0000 chunk 501 optimal weight: 4.9990 chunk 413 optimal weight: 0.2980 chunk 460 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 372 optimal weight: 7.9990 overall best weight: 3.0724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 8 GLN F 14 ASN F 190 HIS F 226 ASN ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 ASN G 83 GLN ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN D 14 ASN ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 GLN D 426 GLN I 8 GLN I 14 ASN I 99 ASN ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 HIS ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN B 8 GLN B 190 HIS ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 190 HIS E 186 ASN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 HIS ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN L 301 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 41796 Z= 0.187 Angle : 0.520 7.267 56784 Z= 0.265 Chirality : 0.044 0.136 6216 Planarity : 0.004 0.058 7398 Dihedral : 10.982 148.352 5760 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.12 % Allowed : 12.41 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.11), residues: 5130 helix: -1.37 (0.10), residues: 2214 sheet: -1.04 (0.18), residues: 846 loop : -1.79 (0.12), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 21 HIS 0.010 0.001 HIS F 190 PHE 0.020 0.001 PHE F 167 TYR 0.019 0.001 TYR L 24 ARG 0.005 0.000 ARG L 123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 687 time to evaluate : 4.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 150 LEU cc_start: 0.9119 (tp) cc_final: 0.8757 (tp) REVERT: F 230 SER cc_start: 0.9199 (p) cc_final: 0.8994 (t) REVERT: F 267 MET cc_start: 0.8482 (mtm) cc_final: 0.8276 (mtm) REVERT: F 292 GLN cc_start: 0.8494 (tt0) cc_final: 0.8129 (tt0) REVERT: F 332 ASN cc_start: 0.7534 (t0) cc_final: 0.7243 (t0) REVERT: G 74 ASP cc_start: 0.7645 (t70) cc_final: 0.7124 (t0) REVERT: G 178 THR cc_start: 0.9268 (m) cc_final: 0.8922 (p) REVERT: G 292 GLN cc_start: 0.8266 (tt0) cc_final: 0.7978 (tt0) REVERT: G 332 ASN cc_start: 0.7872 (t0) cc_final: 0.7354 (t0) REVERT: D 74 ASP cc_start: 0.7454 (t70) cc_final: 0.7063 (t0) REVERT: D 103 LYS cc_start: 0.8996 (mttt) cc_final: 0.8637 (mtmt) REVERT: D 257 MET cc_start: 0.8836 (mmm) cc_final: 0.8206 (mmm) REVERT: D 330 MET cc_start: 0.8735 (mmp) cc_final: 0.8523 (mmm) REVERT: I 74 ASP cc_start: 0.7588 (t70) cc_final: 0.7252 (t0) REVERT: I 103 LYS cc_start: 0.9134 (mttt) cc_final: 0.8833 (mtmt) REVERT: I 330 MET cc_start: 0.8661 (mmp) cc_final: 0.8179 (mmm) REVERT: A 279 GLU cc_start: 0.8635 (tp30) cc_final: 0.8251 (tp30) REVERT: A 327 ASP cc_start: 0.8472 (m-30) cc_final: 0.8181 (m-30) REVERT: A 351 PHE cc_start: 0.8841 (m-80) cc_final: 0.8593 (m-10) REVERT: A 367 ASP cc_start: 0.7888 (p0) cc_final: 0.7667 (p0) REVERT: B 233 MET cc_start: 0.7924 (mtm) cc_final: 0.7641 (ttp) REVERT: B 322 SER cc_start: 0.9183 (p) cc_final: 0.8880 (t) REVERT: B 332 ASN cc_start: 0.8377 (t0) cc_final: 0.7837 (t0) REVERT: B 363 MET cc_start: 0.8658 (ptp) cc_final: 0.8435 (ptp) REVERT: H 230 SER cc_start: 0.9316 (p) cc_final: 0.9115 (t) REVERT: H 323 MET cc_start: 0.8526 (mmm) cc_final: 0.8205 (mmm) REVERT: H 332 ASN cc_start: 0.7995 (t0) cc_final: 0.7622 (t0) REVERT: E 24 TYR cc_start: 0.8759 (m-80) cc_final: 0.8362 (m-10) REVERT: E 154 MET cc_start: 0.8528 (mmm) cc_final: 0.8119 (mmt) REVERT: E 170 SER cc_start: 0.9355 (m) cc_final: 0.9112 (p) REVERT: E 254 GLU cc_start: 0.7798 (mt-10) cc_final: 0.6846 (mp0) REVERT: E 319 TYR cc_start: 0.9093 (m-80) cc_final: 0.8428 (m-80) REVERT: E 430 LYS cc_start: 0.8800 (mmtp) cc_final: 0.8377 (tttt) REVERT: J 24 TYR cc_start: 0.8744 (m-80) cc_final: 0.8532 (m-10) REVERT: J 93 ILE cc_start: 0.9374 (mt) cc_final: 0.9090 (mm) REVERT: J 254 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7316 (mm-30) REVERT: J 296 PHE cc_start: 0.8501 (m-80) cc_final: 0.8235 (m-80) REVERT: J 319 TYR cc_start: 0.8970 (m-80) cc_final: 0.8663 (m-10) REVERT: C 80 THR cc_start: 0.8921 (m) cc_final: 0.8646 (t) REVERT: C 90 GLU cc_start: 0.7368 (tp30) cc_final: 0.7035 (tp30) REVERT: C 91 GLN cc_start: 0.8542 (mt0) cc_final: 0.8051 (mt0) REVERT: C 203 MET cc_start: 0.8853 (mmp) cc_final: 0.8567 (mmp) REVERT: C 319 TYR cc_start: 0.8995 (m-80) cc_final: 0.8706 (m-80) REVERT: C 433 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7804 (tp30) REVERT: L 91 GLN cc_start: 0.8502 (mt0) cc_final: 0.8108 (mt0) REVERT: L 154 MET cc_start: 0.8588 (mmm) cc_final: 0.8251 (mmm) REVERT: L 207 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7031 (tm-30) REVERT: L 254 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7499 (tp30) REVERT: L 429 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8284 (tt0) REVERT: L 430 LYS cc_start: 0.8792 (mmtp) cc_final: 0.8517 (ttpt) REVERT: K 36 MET cc_start: 0.9120 (ttp) cc_final: 0.8867 (ttp) REVERT: K 431 ASP cc_start: 0.7232 (m-30) cc_final: 0.7025 (m-30) outliers start: 93 outliers final: 66 residues processed: 747 average time/residue: 0.5211 time to fit residues: 642.3742 Evaluate side-chains 681 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 613 time to evaluate : 4.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 157 GLU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain I residue 198 GLU Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 368 ILE Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 337 ASN Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 419 VAL Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 207 GLU Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 285 GLN Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 324 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 207 GLU Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 324 VAL Chi-restraints excluded: chain L residue 335 ILE Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 133 GLN Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain K residue 218 ASP Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 345 ASP Chi-restraints excluded: chain K residue 353 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 458 optimal weight: 2.9990 chunk 348 optimal weight: 8.9990 chunk 240 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 221 optimal weight: 20.0000 chunk 311 optimal weight: 9.9990 chunk 465 optimal weight: 5.9990 chunk 492 optimal weight: 10.0000 chunk 243 optimal weight: 5.9990 chunk 441 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 14 ASN ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 ASN ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 GLN D 423 GLN D 426 GLN ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 375 GLN I 423 GLN I 426 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN C 31 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN ** L 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN K 266 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 41796 Z= 0.247 Angle : 0.536 6.934 56784 Z= 0.273 Chirality : 0.045 0.140 6216 Planarity : 0.004 0.054 7398 Dihedral : 10.667 146.688 5760 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.62 % Allowed : 12.75 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.11), residues: 5130 helix: -0.70 (0.11), residues: 2214 sheet: -0.93 (0.18), residues: 846 loop : -1.67 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 21 HIS 0.004 0.001 HIS A 107 PHE 0.022 0.001 PHE F 167 TYR 0.019 0.001 TYR L 24 ARG 0.006 0.000 ARG J 339 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 670 time to evaluate : 4.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 145 SER cc_start: 0.8774 (p) cc_final: 0.8549 (m) REVERT: F 178 THR cc_start: 0.9342 (m) cc_final: 0.8879 (p) REVERT: F 205 GLU cc_start: 0.8023 (tt0) cc_final: 0.7795 (tt0) REVERT: F 292 GLN cc_start: 0.8446 (tt0) cc_final: 0.7922 (tt0) REVERT: F 332 ASN cc_start: 0.7851 (t0) cc_final: 0.7649 (t0) REVERT: G 74 ASP cc_start: 0.7652 (t70) cc_final: 0.7151 (t0) REVERT: G 178 THR cc_start: 0.9376 (m) cc_final: 0.8986 (p) REVERT: G 292 GLN cc_start: 0.8254 (tt0) cc_final: 0.7960 (tt0) REVERT: G 335 ASN cc_start: 0.8389 (m-40) cc_final: 0.7791 (t0) REVERT: D 74 ASP cc_start: 0.7384 (t70) cc_final: 0.7042 (t0) REVERT: D 103 LYS cc_start: 0.9107 (mttt) cc_final: 0.8764 (mtmt) REVERT: D 292 GLN cc_start: 0.8300 (tt0) cc_final: 0.8038 (tt0) REVERT: D 330 MET cc_start: 0.8829 (mmp) cc_final: 0.8539 (mmm) REVERT: D 374 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8503 (pp) REVERT: I 74 ASP cc_start: 0.7528 (t70) cc_final: 0.7166 (t0) REVERT: I 257 MET cc_start: 0.8822 (mmm) cc_final: 0.8226 (mmm) REVERT: I 330 MET cc_start: 0.8770 (mmp) cc_final: 0.8553 (mmm) REVERT: I 383 GLU cc_start: 0.8295 (mm-30) cc_final: 0.8024 (mm-30) REVERT: A 80 THR cc_start: 0.8730 (m) cc_final: 0.8508 (t) REVERT: A 154 MET cc_start: 0.8305 (mmt) cc_final: 0.8062 (mmt) REVERT: A 279 GLU cc_start: 0.8680 (tp30) cc_final: 0.8198 (tp30) REVERT: A 327 ASP cc_start: 0.8392 (m-30) cc_final: 0.8118 (m-30) REVERT: A 367 ASP cc_start: 0.7954 (p0) cc_final: 0.7691 (p0) REVERT: B 69 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7602 (pt0) REVERT: B 233 MET cc_start: 0.7982 (mtm) cc_final: 0.7648 (ttp) REVERT: B 322 SER cc_start: 0.9081 (p) cc_final: 0.8827 (t) REVERT: B 332 ASN cc_start: 0.8450 (t0) cc_final: 0.8044 (t0) REVERT: B 363 MET cc_start: 0.8573 (ptp) cc_final: 0.8289 (ptp) REVERT: H 323 MET cc_start: 0.8388 (mmm) cc_final: 0.8071 (mmm) REVERT: E 24 TYR cc_start: 0.8809 (m-80) cc_final: 0.8482 (m-80) REVERT: E 79 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8748 (mtt180) REVERT: E 154 MET cc_start: 0.8540 (mmm) cc_final: 0.7825 (mmt) REVERT: E 170 SER cc_start: 0.9382 (m) cc_final: 0.8937 (p) REVERT: E 319 TYR cc_start: 0.9226 (m-80) cc_final: 0.8685 (m-80) REVERT: E 377 MET cc_start: 0.8904 (tmm) cc_final: 0.8257 (tmm) REVERT: E 429 GLU cc_start: 0.8794 (tp30) cc_final: 0.8405 (tt0) REVERT: E 430 LYS cc_start: 0.8698 (mmtp) cc_final: 0.8299 (tttt) REVERT: J 93 ILE cc_start: 0.9352 (mt) cc_final: 0.9098 (mm) REVERT: J 154 MET cc_start: 0.8577 (mmt) cc_final: 0.8325 (mmt) REVERT: J 254 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7368 (mm-30) REVERT: J 319 TYR cc_start: 0.9042 (m-80) cc_final: 0.8775 (m-10) REVERT: J 429 GLU cc_start: 0.8718 (tp30) cc_final: 0.8461 (tt0) REVERT: C 80 THR cc_start: 0.8958 (m) cc_final: 0.8682 (t) REVERT: C 90 GLU cc_start: 0.7525 (tp30) cc_final: 0.7226 (tp30) REVERT: C 91 GLN cc_start: 0.8513 (mt0) cc_final: 0.8095 (mt0) REVERT: C 433 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7731 (tp30) REVERT: L 80 THR cc_start: 0.9045 (m) cc_final: 0.8726 (t) REVERT: L 91 GLN cc_start: 0.8447 (mt0) cc_final: 0.8028 (mt0) REVERT: L 154 MET cc_start: 0.8673 (mmm) cc_final: 0.8313 (mmm) REVERT: L 172 TYR cc_start: 0.8104 (t80) cc_final: 0.7633 (t80) REVERT: L 203 MET cc_start: 0.8658 (mmp) cc_final: 0.8076 (mmp) REVERT: L 207 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6956 (tm-30) REVERT: L 221 ARG cc_start: 0.7963 (mtm-85) cc_final: 0.7653 (mpp80) REVERT: L 254 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7540 (tp30) REVERT: L 319 TYR cc_start: 0.9059 (m-80) cc_final: 0.8659 (m-10) REVERT: L 430 LYS cc_start: 0.8923 (mmtp) cc_final: 0.8568 (ttpt) REVERT: L 433 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7996 (tp30) REVERT: K 36 MET cc_start: 0.9181 (ttp) cc_final: 0.8923 (ttp) REVERT: K 296 PHE cc_start: 0.8878 (m-80) cc_final: 0.8564 (m-10) REVERT: K 420 GLU cc_start: 0.7700 (tp30) cc_final: 0.7495 (tp30) REVERT: K 431 ASP cc_start: 0.7318 (m-30) cc_final: 0.7069 (m-30) outliers start: 115 outliers final: 87 residues processed: 747 average time/residue: 0.5182 time to fit residues: 636.3171 Evaluate side-chains 715 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 624 time to evaluate : 4.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 157 GLU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 198 GLU Chi-restraints excluded: chain I residue 205 GLU Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 239 CYS Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 239 CYS Chi-restraints excluded: chain H residue 337 ASN Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 375 GLN Chi-restraints excluded: chain H residue 419 VAL Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 207 GLU Chi-restraints excluded: chain J residue 213 CYS Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 285 GLN Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 324 VAL Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 398 MET Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 207 GLU Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 324 VAL Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 133 GLN Chi-restraints excluded: chain K residue 160 ASP Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 353 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 428 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 410 optimal weight: 3.9990 chunk 279 optimal weight: 7.9990 chunk 7 optimal weight: 20.0000 chunk 367 optimal weight: 0.2980 chunk 203 optimal weight: 0.7980 chunk 420 optimal weight: 9.9990 chunk 340 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 251 optimal weight: 0.0470 chunk 442 optimal weight: 9.9990 chunk 124 optimal weight: 0.4980 overall best weight: 1.1280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 14 ASN ** F 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 GLN D 426 GLN ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 204 ASN I 375 GLN I 426 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 HIS E 186 ASN C 31 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 41796 Z= 0.122 Angle : 0.479 8.564 56784 Z= 0.238 Chirality : 0.042 0.136 6216 Planarity : 0.003 0.048 7398 Dihedral : 10.239 143.208 5760 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.96 % Allowed : 13.96 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.12), residues: 5130 helix: -0.24 (0.11), residues: 2214 sheet: -0.54 (0.18), residues: 828 loop : -1.49 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 344 HIS 0.003 0.000 HIS L 393 PHE 0.012 0.001 PHE F 167 TYR 0.016 0.001 TYR L 24 ARG 0.008 0.000 ARG H 282 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 692 time to evaluate : 5.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 136 THR cc_start: 0.9442 (m) cc_final: 0.8861 (p) REVERT: F 145 SER cc_start: 0.8742 (p) cc_final: 0.8399 (m) REVERT: F 150 LEU cc_start: 0.9072 (tp) cc_final: 0.8762 (tp) REVERT: F 205 GLU cc_start: 0.7889 (tt0) cc_final: 0.7586 (tt0) REVERT: F 267 MET cc_start: 0.8472 (mtm) cc_final: 0.8249 (mtm) REVERT: F 292 GLN cc_start: 0.8339 (tt0) cc_final: 0.7768 (tt0) REVERT: F 332 ASN cc_start: 0.7789 (t0) cc_final: 0.7575 (t0) REVERT: G 26 ASP cc_start: 0.8217 (t0) cc_final: 0.7937 (t0) REVERT: G 74 ASP cc_start: 0.7551 (t70) cc_final: 0.7010 (t0) REVERT: G 292 GLN cc_start: 0.8222 (tt0) cc_final: 0.7757 (tt0) REVERT: G 332 ASN cc_start: 0.8012 (t0) cc_final: 0.7736 (t0) REVERT: D 74 ASP cc_start: 0.7263 (t70) cc_final: 0.6928 (t0) REVERT: D 103 LYS cc_start: 0.9042 (mttt) cc_final: 0.8736 (mtmt) REVERT: D 330 MET cc_start: 0.8860 (mmp) cc_final: 0.8541 (mmm) REVERT: I 67 ASP cc_start: 0.8181 (t0) cc_final: 0.7895 (t0) REVERT: I 69 GLU cc_start: 0.7656 (pm20) cc_final: 0.7049 (pm20) REVERT: I 74 ASP cc_start: 0.7390 (t70) cc_final: 0.7047 (t0) REVERT: I 257 MET cc_start: 0.8786 (mmm) cc_final: 0.8215 (mmm) REVERT: I 330 MET cc_start: 0.8819 (mmp) cc_final: 0.8605 (mmm) REVERT: I 336 LYS cc_start: 0.8383 (mttt) cc_final: 0.8080 (mtmt) REVERT: A 154 MET cc_start: 0.8358 (mmt) cc_final: 0.8051 (mmt) REVERT: A 221 ARG cc_start: 0.8155 (mtm-85) cc_final: 0.7928 (mtt90) REVERT: A 279 GLU cc_start: 0.8745 (tp30) cc_final: 0.8311 (tp30) REVERT: A 327 ASP cc_start: 0.8317 (m-30) cc_final: 0.8046 (m-30) REVERT: A 351 PHE cc_start: 0.8644 (m-80) cc_final: 0.8387 (m-10) REVERT: A 367 ASP cc_start: 0.7835 (p0) cc_final: 0.7576 (p0) REVERT: A 431 ASP cc_start: 0.7341 (m-30) cc_final: 0.7070 (m-30) REVERT: A 433 GLU cc_start: 0.7992 (tp30) cc_final: 0.7779 (tp30) REVERT: B 233 MET cc_start: 0.7804 (mtm) cc_final: 0.7568 (ttp) REVERT: B 322 SER cc_start: 0.9129 (p) cc_final: 0.8907 (t) REVERT: B 332 ASN cc_start: 0.8402 (t0) cc_final: 0.7938 (t0) REVERT: B 363 MET cc_start: 0.8502 (ptp) cc_final: 0.8265 (ptp) REVERT: H 47 ILE cc_start: 0.9395 (tp) cc_final: 0.9153 (tp) REVERT: H 323 MET cc_start: 0.8345 (mmm) cc_final: 0.8129 (mmm) REVERT: E 24 TYR cc_start: 0.8733 (m-80) cc_final: 0.8483 (m-80) REVERT: E 154 MET cc_start: 0.8405 (mmm) cc_final: 0.7595 (mmt) REVERT: E 170 SER cc_start: 0.9345 (m) cc_final: 0.9016 (p) REVERT: E 269 LEU cc_start: 0.8995 (pp) cc_final: 0.8667 (pp) REVERT: E 319 TYR cc_start: 0.9173 (m-80) cc_final: 0.8675 (m-80) REVERT: E 377 MET cc_start: 0.8762 (tmm) cc_final: 0.7878 (tmm) REVERT: E 429 GLU cc_start: 0.8636 (tp30) cc_final: 0.8424 (tt0) REVERT: E 430 LYS cc_start: 0.8645 (mmtp) cc_final: 0.8288 (ttpt) REVERT: J 93 ILE cc_start: 0.9362 (mt) cc_final: 0.9118 (mm) REVERT: J 154 MET cc_start: 0.8517 (mmt) cc_final: 0.8238 (mmt) REVERT: J 254 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7384 (mm-30) REVERT: J 282 TYR cc_start: 0.8370 (m-10) cc_final: 0.7769 (m-10) REVERT: J 319 TYR cc_start: 0.9012 (m-80) cc_final: 0.8798 (m-10) REVERT: J 377 MET cc_start: 0.8978 (tmm) cc_final: 0.8387 (tmm) REVERT: J 430 LYS cc_start: 0.8684 (mmtp) cc_final: 0.8258 (tttt) REVERT: C 80 THR cc_start: 0.8906 (m) cc_final: 0.8667 (t) REVERT: C 91 GLN cc_start: 0.8475 (mt0) cc_final: 0.8067 (mt0) REVERT: C 161 TYR cc_start: 0.8039 (m-80) cc_final: 0.7786 (m-80) REVERT: C 377 MET cc_start: 0.9038 (ttp) cc_final: 0.8117 (tmm) REVERT: C 433 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7804 (tp30) REVERT: L 80 THR cc_start: 0.9011 (m) cc_final: 0.8705 (t) REVERT: L 91 GLN cc_start: 0.8472 (mt0) cc_final: 0.8040 (mt0) REVERT: L 154 MET cc_start: 0.8605 (mmm) cc_final: 0.8274 (mmm) REVERT: L 207 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6935 (tm-30) REVERT: L 221 ARG cc_start: 0.8089 (mtm-85) cc_final: 0.7661 (mpp80) REVERT: L 254 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7252 (tp30) REVERT: L 339 ARG cc_start: 0.7525 (ptt90) cc_final: 0.7112 (ttp-110) REVERT: L 353 VAL cc_start: 0.9427 (t) cc_final: 0.9202 (m) REVERT: L 377 MET cc_start: 0.8553 (ttp) cc_final: 0.8115 (tmm) REVERT: L 433 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7763 (tp30) REVERT: K 36 MET cc_start: 0.9100 (ttp) cc_final: 0.8877 (ttp) REVERT: K 124 LYS cc_start: 0.8915 (ttmm) cc_final: 0.8525 (ttpt) REVERT: K 203 MET cc_start: 0.8584 (mmp) cc_final: 0.8206 (mmp) REVERT: K 296 PHE cc_start: 0.8745 (m-80) cc_final: 0.8541 (m-10) REVERT: K 319 TYR cc_start: 0.8809 (m-80) cc_final: 0.8443 (m-10) REVERT: K 351 PHE cc_start: 0.8700 (m-80) cc_final: 0.8431 (m-80) REVERT: K 381 THR cc_start: 0.8501 (t) cc_final: 0.8057 (t) REVERT: K 420 GLU cc_start: 0.7788 (tp30) cc_final: 0.7521 (tp30) REVERT: K 431 ASP cc_start: 0.7292 (m-30) cc_final: 0.7021 (m-30) REVERT: K 433 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7637 (tp30) outliers start: 86 outliers final: 57 residues processed: 753 average time/residue: 0.5186 time to fit residues: 642.8665 Evaluate side-chains 699 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 641 time to evaluate : 4.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain I residue 198 GLU Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 337 ASN Chi-restraints excluded: chain H residue 380 ARG Chi-restraints excluded: chain H residue 419 VAL Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 207 GLU Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 285 GLN Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 207 GLU Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 160 ASP Chi-restraints excluded: chain K residue 353 VAL Chi-restraints excluded: chain K residue 363 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 165 optimal weight: 10.0000 chunk 443 optimal weight: 30.0000 chunk 97 optimal weight: 8.9990 chunk 289 optimal weight: 0.9990 chunk 121 optimal weight: 0.0980 chunk 493 optimal weight: 20.0000 chunk 409 optimal weight: 7.9990 chunk 228 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 163 optimal weight: 6.9990 chunk 259 optimal weight: 6.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 ASN ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 GLN D 426 GLN ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 375 GLN I 426 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 HIS E 186 ASN C 31 GLN C 88 HIS ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 41796 Z= 0.189 Angle : 0.506 8.759 56784 Z= 0.252 Chirality : 0.044 0.138 6216 Planarity : 0.003 0.049 7398 Dihedral : 10.102 144.147 5760 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.28 % Allowed : 14.48 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.12), residues: 5130 helix: 0.04 (0.11), residues: 2214 sheet: -0.40 (0.19), residues: 828 loop : -1.41 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 21 HIS 0.003 0.001 HIS F 6 PHE 0.017 0.001 PHE I 167 TYR 0.020 0.001 TYR J 24 ARG 0.007 0.000 ARG K 339 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 659 time to evaluate : 5.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 136 THR cc_start: 0.9405 (m) cc_final: 0.8901 (p) REVERT: F 145 SER cc_start: 0.8809 (p) cc_final: 0.8545 (m) REVERT: F 150 LEU cc_start: 0.9099 (tp) cc_final: 0.8789 (tp) REVERT: F 205 GLU cc_start: 0.7683 (tt0) cc_final: 0.7410 (tt0) REVERT: F 292 GLN cc_start: 0.8360 (tt0) cc_final: 0.8094 (tt0) REVERT: F 335 ASN cc_start: 0.8302 (m-40) cc_final: 0.7973 (t0) REVERT: G 26 ASP cc_start: 0.8218 (t0) cc_final: 0.7957 (t0) REVERT: G 74 ASP cc_start: 0.7545 (t70) cc_final: 0.7005 (t0) REVERT: G 178 THR cc_start: 0.9384 (m) cc_final: 0.9001 (p) REVERT: G 205 GLU cc_start: 0.8179 (tt0) cc_final: 0.7958 (tt0) REVERT: G 267 MET cc_start: 0.8436 (mtm) cc_final: 0.8199 (mtm) REVERT: G 292 GLN cc_start: 0.8271 (tt0) cc_final: 0.7887 (tt0) REVERT: G 332 ASN cc_start: 0.8114 (t0) cc_final: 0.7858 (t0) REVERT: G 335 ASN cc_start: 0.8302 (m-40) cc_final: 0.7793 (t0) REVERT: D 51 TYR cc_start: 0.8923 (m-80) cc_final: 0.8578 (m-80) REVERT: D 74 ASP cc_start: 0.7251 (t70) cc_final: 0.6924 (t0) REVERT: D 103 LYS cc_start: 0.9083 (mttt) cc_final: 0.8763 (mtmt) REVERT: D 291 GLN cc_start: 0.8691 (tp40) cc_final: 0.8206 (tp-100) REVERT: D 297 LYS cc_start: 0.8200 (ptpt) cc_final: 0.7970 (tmmt) REVERT: D 330 MET cc_start: 0.8897 (mmp) cc_final: 0.8623 (mmm) REVERT: D 374 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8484 (pp) REVERT: I 67 ASP cc_start: 0.8218 (t0) cc_final: 0.7814 (t0) REVERT: I 69 GLU cc_start: 0.7664 (pm20) cc_final: 0.6978 (pm20) REVERT: I 74 ASP cc_start: 0.7363 (t70) cc_final: 0.7046 (t0) REVERT: I 257 MET cc_start: 0.8732 (mmm) cc_final: 0.8094 (mmm) REVERT: I 336 LYS cc_start: 0.8519 (mttt) cc_final: 0.8229 (mtmt) REVERT: A 154 MET cc_start: 0.8411 (mmt) cc_final: 0.8064 (mmt) REVERT: A 221 ARG cc_start: 0.8135 (mtm-85) cc_final: 0.7911 (mtt90) REVERT: A 279 GLU cc_start: 0.8678 (tp30) cc_final: 0.8217 (tp30) REVERT: A 327 ASP cc_start: 0.8389 (m-30) cc_final: 0.8143 (m-30) REVERT: A 367 ASP cc_start: 0.7912 (p0) cc_final: 0.7630 (p0) REVERT: A 433 GLU cc_start: 0.7971 (tp30) cc_final: 0.7767 (tp30) REVERT: B 69 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7651 (pt0) REVERT: B 209 ASP cc_start: 0.8487 (t0) cc_final: 0.8280 (t0) REVERT: B 322 SER cc_start: 0.9048 (p) cc_final: 0.8825 (t) REVERT: B 332 ASN cc_start: 0.8455 (t0) cc_final: 0.8094 (t0) REVERT: B 363 MET cc_start: 0.8484 (ptp) cc_final: 0.8245 (ptp) REVERT: H 47 ILE cc_start: 0.9433 (tp) cc_final: 0.9193 (tp) REVERT: H 323 MET cc_start: 0.8402 (mmm) cc_final: 0.8180 (mmm) REVERT: H 335 ASN cc_start: 0.8407 (m-40) cc_final: 0.8179 (m-40) REVERT: E 24 TYR cc_start: 0.8767 (m-80) cc_final: 0.8533 (m-80) REVERT: E 79 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8862 (mtt180) REVERT: E 154 MET cc_start: 0.8653 (mmm) cc_final: 0.7976 (mmt) REVERT: E 170 SER cc_start: 0.9351 (m) cc_final: 0.9102 (t) REVERT: E 319 TYR cc_start: 0.9210 (m-80) cc_final: 0.8710 (m-80) REVERT: E 377 MET cc_start: 0.8798 (tmm) cc_final: 0.7881 (tmm) REVERT: E 429 GLU cc_start: 0.8719 (tp30) cc_final: 0.8488 (tt0) REVERT: E 430 LYS cc_start: 0.8683 (mmtp) cc_final: 0.8258 (tttt) REVERT: J 93 ILE cc_start: 0.9352 (mt) cc_final: 0.9104 (mm) REVERT: J 154 MET cc_start: 0.8603 (mmt) cc_final: 0.8261 (mmt) REVERT: J 254 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7375 (mm-30) REVERT: J 319 TYR cc_start: 0.9057 (m-80) cc_final: 0.8739 (m-10) REVERT: C 80 THR cc_start: 0.8926 (m) cc_final: 0.8672 (t) REVERT: C 91 GLN cc_start: 0.8452 (mt0) cc_final: 0.8106 (mt0) REVERT: C 161 TYR cc_start: 0.8009 (m-80) cc_final: 0.7643 (m-80) REVERT: C 413 MET cc_start: 0.8937 (tpp) cc_final: 0.8426 (ttm) REVERT: C 433 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7741 (tp30) REVERT: L 80 THR cc_start: 0.9005 (m) cc_final: 0.8675 (t) REVERT: L 91 GLN cc_start: 0.8455 (mt0) cc_final: 0.8044 (mt0) REVERT: L 120 ASP cc_start: 0.8233 (t70) cc_final: 0.7855 (t0) REVERT: L 124 LYS cc_start: 0.9012 (ttmm) cc_final: 0.8652 (mtpt) REVERT: L 154 MET cc_start: 0.8648 (mmm) cc_final: 0.8225 (mmm) REVERT: L 207 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6986 (tm-30) REVERT: L 220 GLU cc_start: 0.7769 (pm20) cc_final: 0.7559 (pm20) REVERT: L 248 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7973 (tt) REVERT: L 254 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7531 (tp30) REVERT: L 353 VAL cc_start: 0.9441 (t) cc_final: 0.8828 (m) REVERT: L 433 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7802 (tp30) REVERT: K 124 LYS cc_start: 0.8926 (ttmm) cc_final: 0.8543 (ttpt) REVERT: K 420 GLU cc_start: 0.7866 (tp30) cc_final: 0.7595 (tp30) REVERT: K 431 ASP cc_start: 0.7346 (m-30) cc_final: 0.7048 (m-30) REVERT: K 433 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7701 (tp30) outliers start: 100 outliers final: 78 residues processed: 729 average time/residue: 0.5315 time to fit residues: 641.2429 Evaluate side-chains 716 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 633 time to evaluate : 4.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain I residue 198 GLU Chi-restraints excluded: chain I residue 205 GLU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 337 ASN Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 207 GLU Chi-restraints excluded: chain J residue 213 CYS Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 285 GLN Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 334 THR Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain L residue 36 MET Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 207 GLU Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 324 VAL Chi-restraints excluded: chain L residue 340 SER Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 160 ASP Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 353 VAL Chi-restraints excluded: chain K residue 363 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 475 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 281 optimal weight: 0.7980 chunk 360 optimal weight: 6.9990 chunk 279 optimal weight: 8.9990 chunk 415 optimal weight: 9.9990 chunk 275 optimal weight: 6.9990 chunk 491 optimal weight: 9.9990 chunk 307 optimal weight: 9.9990 chunk 299 optimal weight: 9.9990 chunk 226 optimal weight: 9.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 14 ASN F 375 GLN F 426 GLN ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 HIS C 139 HIS L 31 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 41796 Z= 0.304 Angle : 0.569 9.048 56784 Z= 0.287 Chirality : 0.046 0.144 6216 Planarity : 0.004 0.053 7398 Dihedral : 10.222 148.873 5760 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.71 % Allowed : 14.55 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.12), residues: 5130 helix: 0.09 (0.11), residues: 2232 sheet: -0.56 (0.19), residues: 792 loop : -1.43 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 21 HIS 0.004 0.001 HIS B 307 PHE 0.032 0.002 PHE K 296 TYR 0.016 0.002 TYR L 24 ARG 0.008 0.000 ARG E 339 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 639 time to evaluate : 4.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 74 ASP cc_start: 0.7537 (t70) cc_final: 0.7014 (t0) REVERT: F 145 SER cc_start: 0.8896 (p) cc_final: 0.8674 (m) REVERT: F 205 GLU cc_start: 0.7890 (tt0) cc_final: 0.7647 (tt0) REVERT: F 212 PHE cc_start: 0.8081 (t80) cc_final: 0.7809 (t80) REVERT: F 300 MET cc_start: 0.8246 (mtt) cc_final: 0.8045 (mtt) REVERT: F 327 ASP cc_start: 0.7535 (m-30) cc_final: 0.7293 (m-30) REVERT: F 335 ASN cc_start: 0.8534 (m-40) cc_final: 0.8144 (t0) REVERT: G 26 ASP cc_start: 0.8261 (t0) cc_final: 0.7996 (t0) REVERT: G 74 ASP cc_start: 0.7593 (t70) cc_final: 0.7110 (t0) REVERT: G 205 GLU cc_start: 0.8289 (tt0) cc_final: 0.8070 (tt0) REVERT: G 267 MET cc_start: 0.8427 (mtm) cc_final: 0.8174 (mtm) REVERT: G 292 GLN cc_start: 0.8341 (tt0) cc_final: 0.7924 (tt0) REVERT: G 332 ASN cc_start: 0.8218 (t0) cc_final: 0.7973 (t0) REVERT: G 335 ASN cc_start: 0.8453 (m-40) cc_final: 0.8106 (t0) REVERT: D 74 ASP cc_start: 0.7322 (t70) cc_final: 0.6973 (t0) REVERT: D 103 LYS cc_start: 0.9115 (mttt) cc_final: 0.8804 (mtmt) REVERT: D 291 GLN cc_start: 0.8711 (tp40) cc_final: 0.8210 (tp-100) REVERT: D 297 LYS cc_start: 0.8437 (ptpt) cc_final: 0.8111 (tmmt) REVERT: D 330 MET cc_start: 0.8982 (mmp) cc_final: 0.8654 (mmm) REVERT: I 74 ASP cc_start: 0.7395 (t70) cc_final: 0.7069 (t0) REVERT: I 115 SER cc_start: 0.9403 (m) cc_final: 0.9139 (t) REVERT: I 257 MET cc_start: 0.8744 (mmm) cc_final: 0.8514 (mmm) REVERT: I 297 LYS cc_start: 0.8307 (ptpt) cc_final: 0.8105 (tmmt) REVERT: A 80 THR cc_start: 0.8832 (m) cc_final: 0.8510 (t) REVERT: A 154 MET cc_start: 0.8403 (mmt) cc_final: 0.8010 (mmt) REVERT: A 279 GLU cc_start: 0.8700 (tp30) cc_final: 0.8215 (tp30) REVERT: A 327 ASP cc_start: 0.8488 (m-30) cc_final: 0.8280 (m-30) REVERT: A 367 ASP cc_start: 0.7965 (p0) cc_final: 0.7735 (p0) REVERT: B 47 ILE cc_start: 0.9429 (tp) cc_final: 0.9219 (tp) REVERT: B 164 MET cc_start: 0.8135 (tpp) cc_final: 0.7781 (ttm) REVERT: B 233 MET cc_start: 0.8220 (ttp) cc_final: 0.7899 (ttp) REVERT: B 322 SER cc_start: 0.9066 (p) cc_final: 0.8772 (t) REVERT: B 332 ASN cc_start: 0.8445 (t0) cc_final: 0.8032 (t0) REVERT: B 363 MET cc_start: 0.8452 (ptp) cc_final: 0.8168 (ptp) REVERT: H 178 THR cc_start: 0.9445 (m) cc_final: 0.9016 (p) REVERT: H 332 ASN cc_start: 0.8224 (t0) cc_final: 0.7910 (t0) REVERT: E 24 TYR cc_start: 0.8812 (m-80) cc_final: 0.8543 (m-80) REVERT: E 79 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8816 (mtt180) REVERT: E 154 MET cc_start: 0.8742 (mmm) cc_final: 0.8107 (mmt) REVERT: E 170 SER cc_start: 0.9328 (m) cc_final: 0.9021 (t) REVERT: E 319 TYR cc_start: 0.9277 (m-80) cc_final: 0.8798 (m-80) REVERT: E 377 MET cc_start: 0.8816 (tmm) cc_final: 0.8497 (tmm) REVERT: E 429 GLU cc_start: 0.8748 (tp30) cc_final: 0.8392 (tt0) REVERT: E 430 LYS cc_start: 0.8703 (mmtp) cc_final: 0.8269 (tttt) REVERT: J 93 ILE cc_start: 0.9353 (mt) cc_final: 0.9149 (mm) REVERT: J 154 MET cc_start: 0.8669 (mmt) cc_final: 0.8385 (mmt) REVERT: J 254 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7687 (tp30) REVERT: J 319 TYR cc_start: 0.9167 (m-80) cc_final: 0.8842 (m-10) REVERT: J 377 MET cc_start: 0.8995 (tmm) cc_final: 0.8365 (tmm) REVERT: C 80 THR cc_start: 0.8933 (m) cc_final: 0.8683 (t) REVERT: C 91 GLN cc_start: 0.8446 (mt0) cc_final: 0.8026 (mt0) REVERT: C 172 TYR cc_start: 0.8174 (t80) cc_final: 0.7714 (t80) REVERT: C 279 GLU cc_start: 0.8678 (tp30) cc_final: 0.8004 (tt0) REVERT: C 413 MET cc_start: 0.8963 (tpp) cc_final: 0.8657 (ttm) REVERT: C 433 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7804 (tp30) REVERT: L 80 THR cc_start: 0.9027 (m) cc_final: 0.8695 (t) REVERT: L 91 GLN cc_start: 0.8459 (mt0) cc_final: 0.8056 (mt0) REVERT: L 120 ASP cc_start: 0.8251 (t70) cc_final: 0.7861 (t0) REVERT: L 124 LYS cc_start: 0.9041 (ttmm) cc_final: 0.8716 (ttpt) REVERT: L 172 TYR cc_start: 0.8158 (t80) cc_final: 0.7740 (t80) REVERT: L 207 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.6944 (tm-30) REVERT: L 248 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8036 (tt) REVERT: L 254 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7314 (tp30) REVERT: L 377 MET cc_start: 0.8630 (ttp) cc_final: 0.8111 (tmm) REVERT: L 379 SER cc_start: 0.8914 (m) cc_final: 0.8439 (p) REVERT: L 433 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7844 (tp30) REVERT: K 124 LYS cc_start: 0.8927 (ttmm) cc_final: 0.8545 (ttpp) REVERT: K 319 TYR cc_start: 0.8791 (m-80) cc_final: 0.8420 (m-10) REVERT: K 431 ASP cc_start: 0.7430 (m-30) cc_final: 0.7114 (m-30) REVERT: K 433 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7906 (tp30) outliers start: 119 outliers final: 100 residues processed: 716 average time/residue: 0.5167 time to fit residues: 610.4076 Evaluate side-chains 721 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 618 time to evaluate : 4.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 198 GLU Chi-restraints excluded: chain I residue 205 GLU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 337 ASN Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 340 SER Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 207 GLU Chi-restraints excluded: chain J residue 213 CYS Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 285 GLN Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 324 VAL Chi-restraints excluded: chain J residue 334 THR Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 36 MET Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 207 GLU Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 324 VAL Chi-restraints excluded: chain L residue 340 SER Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 160 ASP Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 353 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 428 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 304 optimal weight: 10.0000 chunk 196 optimal weight: 0.9980 chunk 293 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 96 optimal weight: 20.0000 chunk 95 optimal weight: 0.8980 chunk 312 optimal weight: 0.9980 chunk 334 optimal weight: 3.9990 chunk 243 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 386 optimal weight: 10.0000 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 41796 Z= 0.164 Angle : 0.503 9.450 56784 Z= 0.250 Chirality : 0.043 0.135 6216 Planarity : 0.003 0.047 7398 Dihedral : 9.894 147.129 5760 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.53 % Allowed : 14.89 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.12), residues: 5130 helix: 0.34 (0.11), residues: 2250 sheet: -0.35 (0.19), residues: 828 loop : -1.31 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 344 HIS 0.003 0.001 HIS F 396 PHE 0.026 0.001 PHE K 296 TYR 0.015 0.001 TYR L 103 ARG 0.009 0.000 ARG E 339 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 663 time to evaluate : 4.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 136 THR cc_start: 0.9412 (m) cc_final: 0.8923 (p) REVERT: F 145 SER cc_start: 0.8773 (p) cc_final: 0.8529 (m) REVERT: F 150 LEU cc_start: 0.9096 (tp) cc_final: 0.8800 (tp) REVERT: F 327 ASP cc_start: 0.7321 (m-30) cc_final: 0.7120 (m-30) REVERT: F 335 ASN cc_start: 0.8490 (m-40) cc_final: 0.8118 (t0) REVERT: G 26 ASP cc_start: 0.8195 (t0) cc_final: 0.7934 (t0) REVERT: G 65 LEU cc_start: 0.8736 (mp) cc_final: 0.8509 (mt) REVERT: G 74 ASP cc_start: 0.7479 (t70) cc_final: 0.7148 (t0) REVERT: G 136 THR cc_start: 0.9386 (m) cc_final: 0.8836 (p) REVERT: G 205 GLU cc_start: 0.8176 (tt0) cc_final: 0.7914 (tt0) REVERT: G 292 GLN cc_start: 0.8243 (tt0) cc_final: 0.7819 (tt0) REVERT: G 332 ASN cc_start: 0.8188 (t0) cc_final: 0.7881 (t0) REVERT: G 335 ASN cc_start: 0.8530 (m-40) cc_final: 0.8157 (t0) REVERT: D 51 TYR cc_start: 0.8829 (m-80) cc_final: 0.8595 (m-80) REVERT: D 74 ASP cc_start: 0.7233 (t70) cc_final: 0.6901 (t0) REVERT: D 103 LYS cc_start: 0.9091 (mttt) cc_final: 0.8787 (mtmt) REVERT: D 291 GLN cc_start: 0.8655 (tp40) cc_final: 0.8187 (tp-100) REVERT: D 297 LYS cc_start: 0.8359 (ptpt) cc_final: 0.8083 (tmmt) REVERT: D 330 MET cc_start: 0.8959 (mmp) cc_final: 0.8603 (mmm) REVERT: D 374 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8550 (pp) REVERT: I 67 ASP cc_start: 0.8135 (t0) cc_final: 0.7722 (t0) REVERT: I 74 ASP cc_start: 0.7326 (t70) cc_final: 0.7005 (t0) REVERT: I 115 SER cc_start: 0.9424 (m) cc_final: 0.9149 (t) REVERT: I 291 GLN cc_start: 0.8509 (tt0) cc_final: 0.7983 (tp-100) REVERT: I 297 LYS cc_start: 0.8352 (ptpt) cc_final: 0.8061 (tmmt) REVERT: A 80 THR cc_start: 0.8783 (m) cc_final: 0.8471 (t) REVERT: A 154 MET cc_start: 0.8396 (mmt) cc_final: 0.8011 (mmt) REVERT: A 279 GLU cc_start: 0.8640 (tp30) cc_final: 0.8263 (tp30) REVERT: A 319 TYR cc_start: 0.8850 (m-80) cc_final: 0.8467 (m-10) REVERT: A 367 ASP cc_start: 0.7938 (p0) cc_final: 0.7671 (p0) REVERT: B 167 PHE cc_start: 0.8916 (m-80) cc_final: 0.8324 (m-80) REVERT: B 233 MET cc_start: 0.8066 (ttp) cc_final: 0.7805 (ttp) REVERT: B 332 ASN cc_start: 0.8473 (t0) cc_final: 0.8092 (t0) REVERT: B 363 MET cc_start: 0.8515 (ptp) cc_final: 0.8271 (ptp) REVERT: H 323 MET cc_start: 0.8388 (mmm) cc_final: 0.8161 (mmm) REVERT: E 24 TYR cc_start: 0.8755 (m-80) cc_final: 0.8521 (m-80) REVERT: E 154 MET cc_start: 0.8702 (mmm) cc_final: 0.8039 (mmt) REVERT: E 170 SER cc_start: 0.9349 (m) cc_final: 0.9084 (t) REVERT: E 319 TYR cc_start: 0.9217 (m-80) cc_final: 0.8632 (m-80) REVERT: E 377 MET cc_start: 0.8848 (tmm) cc_final: 0.8548 (tmm) REVERT: E 430 LYS cc_start: 0.8660 (mmtp) cc_final: 0.8243 (tttt) REVERT: J 93 ILE cc_start: 0.9356 (mt) cc_final: 0.9103 (mm) REVERT: J 154 MET cc_start: 0.8612 (mmt) cc_final: 0.8283 (mmt) REVERT: J 254 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7649 (tp30) REVERT: J 319 TYR cc_start: 0.9124 (m-80) cc_final: 0.8806 (m-10) REVERT: J 377 MET cc_start: 0.8976 (tmm) cc_final: 0.8331 (tmm) REVERT: C 80 THR cc_start: 0.8905 (m) cc_final: 0.8673 (t) REVERT: C 91 GLN cc_start: 0.8415 (mt0) cc_final: 0.8127 (mt0) REVERT: C 172 TYR cc_start: 0.8150 (t80) cc_final: 0.7771 (t80) REVERT: C 279 GLU cc_start: 0.8702 (tp30) cc_final: 0.7984 (tt0) REVERT: C 413 MET cc_start: 0.8934 (tpp) cc_final: 0.8559 (ttm) REVERT: C 433 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7756 (tp30) REVERT: L 80 THR cc_start: 0.8992 (m) cc_final: 0.8659 (t) REVERT: L 91 GLN cc_start: 0.8457 (mt0) cc_final: 0.8026 (mt0) REVERT: L 120 ASP cc_start: 0.8212 (t70) cc_final: 0.7855 (t0) REVERT: L 124 LYS cc_start: 0.9017 (ttmm) cc_final: 0.8712 (ttpt) REVERT: L 172 TYR cc_start: 0.8145 (t80) cc_final: 0.7754 (t80) REVERT: L 207 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6935 (tm-30) REVERT: L 248 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7943 (tt) REVERT: L 254 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7374 (tp30) REVERT: L 353 VAL cc_start: 0.9433 (t) cc_final: 0.8820 (m) REVERT: L 379 SER cc_start: 0.8927 (m) cc_final: 0.8601 (p) REVERT: L 433 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7849 (tp30) REVERT: K 124 LYS cc_start: 0.8884 (ttmm) cc_final: 0.8540 (ttpt) REVERT: K 203 MET cc_start: 0.8711 (mmp) cc_final: 0.8319 (mmp) REVERT: K 319 TYR cc_start: 0.8726 (m-80) cc_final: 0.8385 (m-10) REVERT: K 431 ASP cc_start: 0.7375 (m-30) cc_final: 0.7077 (m-30) REVERT: K 433 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7760 (tp30) outliers start: 111 outliers final: 93 residues processed: 733 average time/residue: 0.5133 time to fit residues: 621.1221 Evaluate side-chains 729 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 633 time to evaluate : 5.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain G residue 239 CYS Chi-restraints excluded: chain G residue 312 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 198 GLU Chi-restraints excluded: chain I residue 205 GLU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 337 ASN Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 207 GLU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 285 GLN Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 324 VAL Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain L residue 36 MET Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 207 GLU Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 252 LEU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 303 VAL Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 160 ASP Chi-restraints excluded: chain K residue 218 ASP Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 335 ILE Chi-restraints excluded: chain K residue 363 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 447 optimal weight: 9.9990 chunk 470 optimal weight: 1.9990 chunk 429 optimal weight: 0.0770 chunk 458 optimal weight: 6.9990 chunk 275 optimal weight: 10.0000 chunk 199 optimal weight: 2.9990 chunk 359 optimal weight: 6.9990 chunk 140 optimal weight: 20.0000 chunk 413 optimal weight: 9.9990 chunk 433 optimal weight: 9.9990 chunk 456 optimal weight: 0.9980 overall best weight: 2.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 41796 Z= 0.169 Angle : 0.508 9.784 56784 Z= 0.252 Chirality : 0.043 0.136 6216 Planarity : 0.003 0.047 7398 Dihedral : 9.744 146.559 5760 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.19 % Allowed : 15.35 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.12), residues: 5130 helix: 0.42 (0.12), residues: 2250 sheet: -0.26 (0.19), residues: 828 loop : -1.28 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 344 HIS 0.003 0.001 HIS F 396 PHE 0.020 0.001 PHE I 167 TYR 0.014 0.001 TYR L 24 ARG 0.008 0.000 ARG E 339 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 645 time to evaluate : 4.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 136 THR cc_start: 0.9414 (m) cc_final: 0.8936 (p) REVERT: F 145 SER cc_start: 0.8806 (p) cc_final: 0.8572 (m) REVERT: F 150 LEU cc_start: 0.9093 (tp) cc_final: 0.8807 (tp) REVERT: F 163 ILE cc_start: 0.8675 (pt) cc_final: 0.8416 (pt) REVERT: F 213 ARG cc_start: 0.7310 (ttm170) cc_final: 0.7093 (mtp-110) REVERT: F 327 ASP cc_start: 0.7398 (m-30) cc_final: 0.7141 (m-30) REVERT: F 335 ASN cc_start: 0.8491 (m-40) cc_final: 0.8118 (t0) REVERT: G 136 THR cc_start: 0.9390 (m) cc_final: 0.8848 (p) REVERT: G 163 ILE cc_start: 0.8757 (pt) cc_final: 0.8500 (pt) REVERT: G 205 GLU cc_start: 0.8182 (tt0) cc_final: 0.7938 (tt0) REVERT: G 297 LYS cc_start: 0.8630 (mttp) cc_final: 0.7793 (tmmt) REVERT: G 332 ASN cc_start: 0.8196 (t0) cc_final: 0.7895 (t0) REVERT: G 335 ASN cc_start: 0.8539 (m-40) cc_final: 0.8177 (t0) REVERT: D 51 TYR cc_start: 0.8827 (m-80) cc_final: 0.8616 (m-80) REVERT: D 74 ASP cc_start: 0.7195 (t70) cc_final: 0.6871 (t0) REVERT: D 103 LYS cc_start: 0.9107 (mttt) cc_final: 0.8788 (mtmt) REVERT: D 291 GLN cc_start: 0.8669 (tp40) cc_final: 0.8166 (tp-100) REVERT: D 297 LYS cc_start: 0.8317 (ptpt) cc_final: 0.8065 (tmmt) REVERT: D 330 MET cc_start: 0.8951 (mmp) cc_final: 0.8651 (mmm) REVERT: D 374 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8508 (pp) REVERT: I 67 ASP cc_start: 0.8135 (t0) cc_final: 0.7747 (t0) REVERT: I 74 ASP cc_start: 0.7292 (t70) cc_final: 0.7001 (t0) REVERT: I 115 SER cc_start: 0.9435 (m) cc_final: 0.9162 (t) REVERT: I 291 GLN cc_start: 0.8500 (tt0) cc_final: 0.7986 (tp-100) REVERT: I 297 LYS cc_start: 0.8332 (ptpt) cc_final: 0.8096 (tmmt) REVERT: I 330 MET cc_start: 0.8444 (mmm) cc_final: 0.8055 (mtp) REVERT: A 80 THR cc_start: 0.8823 (m) cc_final: 0.8449 (t) REVERT: A 124 LYS cc_start: 0.8867 (ttmm) cc_final: 0.8495 (ttpp) REVERT: A 154 MET cc_start: 0.8348 (mmt) cc_final: 0.8025 (mmt) REVERT: A 279 GLU cc_start: 0.8651 (tp30) cc_final: 0.8265 (tp30) REVERT: A 319 TYR cc_start: 0.8828 (m-80) cc_final: 0.8354 (m-10) REVERT: A 367 ASP cc_start: 0.7943 (p0) cc_final: 0.7674 (p0) REVERT: B 167 PHE cc_start: 0.8926 (m-80) cc_final: 0.8331 (m-80) REVERT: B 233 MET cc_start: 0.8019 (ttp) cc_final: 0.7758 (ttp) REVERT: B 332 ASN cc_start: 0.8397 (t0) cc_final: 0.8011 (t0) REVERT: B 363 MET cc_start: 0.8507 (ptp) cc_final: 0.8258 (ptp) REVERT: H 247 ASN cc_start: 0.8486 (m-40) cc_final: 0.8021 (m110) REVERT: H 323 MET cc_start: 0.8410 (mmm) cc_final: 0.8209 (mmm) REVERT: E 24 TYR cc_start: 0.8758 (m-80) cc_final: 0.8526 (m-80) REVERT: E 154 MET cc_start: 0.8704 (mmm) cc_final: 0.8051 (mmt) REVERT: E 170 SER cc_start: 0.9345 (m) cc_final: 0.9083 (t) REVERT: E 319 TYR cc_start: 0.9228 (m-80) cc_final: 0.8670 (m-80) REVERT: E 377 MET cc_start: 0.8873 (tmm) cc_final: 0.8525 (tmm) REVERT: E 430 LYS cc_start: 0.8553 (mmtp) cc_final: 0.8182 (tttt) REVERT: J 93 ILE cc_start: 0.9361 (mt) cc_final: 0.9113 (mm) REVERT: J 154 MET cc_start: 0.8624 (mmt) cc_final: 0.8340 (mmt) REVERT: J 254 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7653 (tp30) REVERT: J 319 TYR cc_start: 0.9128 (m-80) cc_final: 0.8853 (m-10) REVERT: J 377 MET cc_start: 0.9008 (tmm) cc_final: 0.8320 (tmm) REVERT: C 80 THR cc_start: 0.8940 (m) cc_final: 0.8666 (t) REVERT: C 91 GLN cc_start: 0.8410 (mt0) cc_final: 0.8031 (mt0) REVERT: C 161 TYR cc_start: 0.8012 (m-80) cc_final: 0.7676 (m-80) REVERT: C 172 TYR cc_start: 0.8154 (t80) cc_final: 0.7744 (t80) REVERT: C 193 THR cc_start: 0.9171 (m) cc_final: 0.8907 (p) REVERT: C 279 GLU cc_start: 0.8717 (tp30) cc_final: 0.7994 (tt0) REVERT: C 413 MET cc_start: 0.8883 (tpp) cc_final: 0.8510 (ttm) REVERT: C 433 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7866 (tp30) REVERT: L 80 THR cc_start: 0.8987 (m) cc_final: 0.8655 (t) REVERT: L 91 GLN cc_start: 0.8460 (mt0) cc_final: 0.8019 (mt0) REVERT: L 120 ASP cc_start: 0.8251 (t70) cc_final: 0.7868 (t0) REVERT: L 124 LYS cc_start: 0.9003 (ttmm) cc_final: 0.8702 (ttpt) REVERT: L 145 THR cc_start: 0.9016 (m) cc_final: 0.8799 (m) REVERT: L 172 TYR cc_start: 0.8134 (t80) cc_final: 0.7721 (t80) REVERT: L 207 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6940 (tm-30) REVERT: L 248 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7913 (tt) REVERT: L 254 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7441 (tp30) REVERT: L 353 VAL cc_start: 0.9422 (t) cc_final: 0.8837 (m) REVERT: L 433 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7794 (tp30) REVERT: K 124 LYS cc_start: 0.8875 (ttmm) cc_final: 0.8519 (ttpt) REVERT: K 203 MET cc_start: 0.8671 (mmp) cc_final: 0.8461 (mmp) REVERT: K 319 TYR cc_start: 0.8752 (m-80) cc_final: 0.8364 (m-10) REVERT: K 351 PHE cc_start: 0.8693 (m-80) cc_final: 0.8373 (m-10) REVERT: K 431 ASP cc_start: 0.7385 (m-30) cc_final: 0.7082 (m-30) REVERT: K 433 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7760 (tp30) outliers start: 96 outliers final: 86 residues processed: 704 average time/residue: 0.5150 time to fit residues: 600.0930 Evaluate side-chains 724 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 635 time to evaluate : 4.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain G residue 239 CYS Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 198 GLU Chi-restraints excluded: chain I residue 205 GLU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 337 ASN Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 207 GLU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 324 VAL Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain L residue 36 MET Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 207 GLU Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 303 VAL Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 133 GLN Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 160 ASP Chi-restraints excluded: chain K residue 218 ASP Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 335 ILE Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 428 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 300 optimal weight: 0.0270 chunk 484 optimal weight: 2.9990 chunk 295 optimal weight: 8.9990 chunk 229 optimal weight: 0.9980 chunk 336 optimal weight: 9.9990 chunk 508 optimal weight: 6.9990 chunk 467 optimal weight: 10.0000 chunk 404 optimal weight: 8.9990 chunk 42 optimal weight: 20.0000 chunk 312 optimal weight: 4.9990 chunk 248 optimal weight: 0.9980 overall best weight: 2.0042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 41796 Z= 0.150 Angle : 0.501 10.073 56784 Z= 0.248 Chirality : 0.043 0.143 6216 Planarity : 0.003 0.047 7398 Dihedral : 9.529 145.116 5760 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.19 % Allowed : 15.39 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.12), residues: 5130 helix: 0.55 (0.12), residues: 2256 sheet: -0.19 (0.19), residues: 828 loop : -1.21 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 344 HIS 0.003 0.000 HIS F 396 PHE 0.024 0.001 PHE H 212 TYR 0.019 0.001 TYR C 24 ARG 0.009 0.000 ARG E 339 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 671 time to evaluate : 5.184 Fit side-chains revert: symmetry clash REVERT: F 136 THR cc_start: 0.9419 (m) cc_final: 0.8990 (p) REVERT: F 145 SER cc_start: 0.8774 (p) cc_final: 0.8534 (m) REVERT: F 150 LEU cc_start: 0.9090 (tp) cc_final: 0.8873 (tp) REVERT: F 163 ILE cc_start: 0.8739 (pt) cc_final: 0.8408 (pt) REVERT: F 213 ARG cc_start: 0.7293 (ttm170) cc_final: 0.7066 (mtp-110) REVERT: F 292 GLN cc_start: 0.8320 (tt0) cc_final: 0.6537 (tm-30) REVERT: F 327 ASP cc_start: 0.7373 (m-30) cc_final: 0.7116 (m-30) REVERT: F 335 ASN cc_start: 0.8458 (m-40) cc_final: 0.8113 (t0) REVERT: G 136 THR cc_start: 0.9365 (m) cc_final: 0.8889 (p) REVERT: G 163 ILE cc_start: 0.8743 (pt) cc_final: 0.8499 (pt) REVERT: G 205 GLU cc_start: 0.8081 (tt0) cc_final: 0.7820 (tt0) REVERT: G 292 GLN cc_start: 0.7592 (tt0) cc_final: 0.6659 (tm-30) REVERT: G 332 ASN cc_start: 0.8156 (t0) cc_final: 0.7846 (t0) REVERT: G 335 ASN cc_start: 0.8550 (m-40) cc_final: 0.8177 (t0) REVERT: D 51 TYR cc_start: 0.8798 (m-80) cc_final: 0.8466 (m-80) REVERT: D 74 ASP cc_start: 0.7143 (t70) cc_final: 0.6839 (t0) REVERT: D 103 LYS cc_start: 0.9099 (mttt) cc_final: 0.8795 (mtmt) REVERT: D 291 GLN cc_start: 0.8656 (tp40) cc_final: 0.8170 (tp-100) REVERT: D 297 LYS cc_start: 0.8235 (ptpt) cc_final: 0.8004 (tmmt) REVERT: D 330 MET cc_start: 0.8996 (mmp) cc_final: 0.8608 (mmm) REVERT: D 374 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8482 (pp) REVERT: I 67 ASP cc_start: 0.8122 (t0) cc_final: 0.7690 (t0) REVERT: I 74 ASP cc_start: 0.7272 (t70) cc_final: 0.6892 (t0) REVERT: I 113 VAL cc_start: 0.9280 (p) cc_final: 0.9068 (t) REVERT: I 167 PHE cc_start: 0.8658 (m-80) cc_final: 0.7971 (m-10) REVERT: I 247 ASN cc_start: 0.8535 (m-40) cc_final: 0.8299 (m-40) REVERT: I 291 GLN cc_start: 0.8374 (tt0) cc_final: 0.7940 (tp-100) REVERT: I 297 LYS cc_start: 0.8229 (ptpt) cc_final: 0.8024 (tmmt) REVERT: I 312 THR cc_start: 0.9349 (p) cc_final: 0.8483 (p) REVERT: I 330 MET cc_start: 0.8445 (mmm) cc_final: 0.8088 (mtp) REVERT: A 80 THR cc_start: 0.8837 (m) cc_final: 0.8445 (t) REVERT: A 124 LYS cc_start: 0.8847 (ttmm) cc_final: 0.8499 (ttpt) REVERT: A 154 MET cc_start: 0.8350 (mmt) cc_final: 0.8011 (mmt) REVERT: A 203 MET cc_start: 0.8499 (mmp) cc_final: 0.8027 (mmp) REVERT: A 279 GLU cc_start: 0.8681 (tp30) cc_final: 0.8320 (tp30) REVERT: A 319 TYR cc_start: 0.8855 (m-80) cc_final: 0.8536 (m-10) REVERT: A 367 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7658 (p0) REVERT: B 332 ASN cc_start: 0.8418 (t0) cc_final: 0.8008 (t0) REVERT: H 247 ASN cc_start: 0.8500 (m-40) cc_final: 0.8040 (m110) REVERT: E 24 TYR cc_start: 0.8748 (m-80) cc_final: 0.8514 (m-80) REVERT: E 154 MET cc_start: 0.8683 (mmm) cc_final: 0.8063 (mmt) REVERT: E 170 SER cc_start: 0.9324 (m) cc_final: 0.9073 (t) REVERT: E 319 TYR cc_start: 0.9210 (m-80) cc_final: 0.8761 (m-80) REVERT: E 377 MET cc_start: 0.8801 (tmm) cc_final: 0.8408 (tmm) REVERT: E 430 LYS cc_start: 0.8571 (mmtp) cc_final: 0.7968 (tmtt) REVERT: J 93 ILE cc_start: 0.9342 (mt) cc_final: 0.9101 (mm) REVERT: J 154 MET cc_start: 0.8614 (mmt) cc_final: 0.8318 (mmt) REVERT: J 205 ASP cc_start: 0.7689 (t0) cc_final: 0.7302 (t0) REVERT: J 254 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7525 (tp30) REVERT: J 319 TYR cc_start: 0.9105 (m-80) cc_final: 0.8777 (m-10) REVERT: J 377 MET cc_start: 0.8985 (tmm) cc_final: 0.8293 (tmm) REVERT: C 80 THR cc_start: 0.8931 (m) cc_final: 0.8651 (t) REVERT: C 91 GLN cc_start: 0.8386 (mt0) cc_final: 0.8014 (mt0) REVERT: C 161 TYR cc_start: 0.7935 (m-80) cc_final: 0.7557 (m-80) REVERT: C 172 TYR cc_start: 0.8164 (t80) cc_final: 0.7741 (t80) REVERT: C 193 THR cc_start: 0.9236 (m) cc_final: 0.8809 (p) REVERT: C 279 GLU cc_start: 0.8731 (tp30) cc_final: 0.7997 (tt0) REVERT: C 377 MET cc_start: 0.9138 (ttp) cc_final: 0.8858 (tmm) REVERT: C 413 MET cc_start: 0.8881 (tpp) cc_final: 0.8495 (ttm) REVERT: C 433 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7932 (tp30) REVERT: L 80 THR cc_start: 0.8987 (m) cc_final: 0.8618 (t) REVERT: L 91 GLN cc_start: 0.8445 (mt0) cc_final: 0.8032 (mt0) REVERT: L 120 ASP cc_start: 0.8257 (t70) cc_final: 0.7875 (t0) REVERT: L 124 LYS cc_start: 0.9003 (ttmm) cc_final: 0.8730 (ttpt) REVERT: L 145 THR cc_start: 0.8963 (m) cc_final: 0.8619 (m) REVERT: L 172 TYR cc_start: 0.8124 (t80) cc_final: 0.7677 (t80) REVERT: L 207 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6944 (tm-30) REVERT: L 248 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7869 (tt) REVERT: L 254 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7543 (tp30) REVERT: L 295 CYS cc_start: 0.8345 (m) cc_final: 0.8095 (m) REVERT: L 353 VAL cc_start: 0.9410 (t) cc_final: 0.8834 (m) REVERT: L 377 MET cc_start: 0.8673 (tmm) cc_final: 0.8469 (tmm) REVERT: L 433 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7776 (tp30) REVERT: K 124 LYS cc_start: 0.8862 (ttmm) cc_final: 0.8514 (ttpt) REVERT: K 203 MET cc_start: 0.8636 (mmp) cc_final: 0.8401 (mmp) REVERT: K 319 TYR cc_start: 0.8773 (m-80) cc_final: 0.8463 (m-10) REVERT: K 351 PHE cc_start: 0.8671 (m-80) cc_final: 0.8363 (m-10) REVERT: K 431 ASP cc_start: 0.7375 (m-30) cc_final: 0.7071 (m-30) REVERT: K 433 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7752 (tp30) outliers start: 96 outliers final: 85 residues processed: 728 average time/residue: 0.5097 time to fit residues: 613.3450 Evaluate side-chains 735 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 646 time to evaluate : 4.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain F residue 326 VAL Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain G residue 239 CYS Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain I residue 127 CYS Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 198 GLU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 374 ILE Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 337 ASN Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 207 GLU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 324 VAL Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain L residue 36 MET Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 207 GLU Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 303 VAL Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 133 GLN Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 154 MET Chi-restraints excluded: chain K residue 160 ASP Chi-restraints excluded: chain K residue 218 ASP Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 335 ILE Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 428 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 321 optimal weight: 4.9990 chunk 430 optimal weight: 0.9980 chunk 123 optimal weight: 9.9990 chunk 373 optimal weight: 20.0000 chunk 59 optimal weight: 0.8980 chunk 112 optimal weight: 10.0000 chunk 405 optimal weight: 8.9990 chunk 169 optimal weight: 20.0000 chunk 416 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.096218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.084407 restraints weight = 65158.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.087036 restraints weight = 35750.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.088883 restraints weight = 22913.714| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 41796 Z= 0.183 Angle : 0.522 11.104 56784 Z= 0.257 Chirality : 0.044 0.345 6216 Planarity : 0.003 0.049 7398 Dihedral : 9.425 145.343 5760 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.35 % Allowed : 15.71 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.12), residues: 5130 helix: 0.60 (0.12), residues: 2256 sheet: -0.21 (0.19), residues: 828 loop : -1.17 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 21 HIS 0.003 0.001 HIS F 396 PHE 0.019 0.001 PHE K 296 TYR 0.014 0.001 TYR C 24 ARG 0.009 0.000 ARG E 339 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10263.96 seconds wall clock time: 186 minutes 2.87 seconds (11162.87 seconds total)