Starting phenix.real_space_refine on Sat Mar 7 10:58:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tfa_25867/03_2026/7tfa_25867.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tfa_25867/03_2026/7tfa_25867.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tfa_25867/03_2026/7tfa_25867.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tfa_25867/03_2026/7tfa_25867.map" model { file = "/net/cci-nas-00/data/ceres_data/7tfa_25867/03_2026/7tfa_25867.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tfa_25867/03_2026/7tfa_25867.cif" } resolution = 2.07 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.001 sd= 0.082 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 Mg 24 5.21 5 S 228 5.16 5 C 27096 2.51 5 N 7296 2.21 5 O 7872 1.98 5 H 120 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42636 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 82 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 82 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 82 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "F" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "G" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 82 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 82 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 82 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "K" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "L" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "M" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 82 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 82 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 82 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 82 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "R" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "S" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "T" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "U" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 82 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 82 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "X" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "J" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "K" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "L" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "Q" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "R" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "S" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "T" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "W" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "X" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N LEU B 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU B 248 " occ=0.97 residue: pdb=" N LEU E 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU E 248 " occ=0.97 residue: pdb=" N LEU F 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU F 248 " occ=0.97 residue: pdb=" N LEU J 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU J 248 " occ=0.97 residue: pdb=" N LEU K 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU K 248 " occ=0.97 residue: pdb=" N LEU L 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU L 248 " occ=0.97 residue: pdb=" N LEU Q 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU Q 248 " occ=0.97 residue: pdb=" N LEU R 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU R 248 " occ=0.97 residue: pdb=" N LEU S 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU S 248 " occ=0.97 residue: pdb=" N LEU T 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU T 248 " occ=0.97 residue: pdb=" N LEU W 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU W 248 " occ=0.97 residue: pdb=" N LEU X 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU X 248 " occ=0.97 Time building chain proxies: 9.69, per 1000 atoms: 0.23 Number of scatterers: 42636 At special positions: 0 Unit cell: (157.52, 148.72, 122.32, 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 228 16.00 Mg 24 11.99 O 7872 8.00 N 7296 7.00 C 27096 6.00 H 120 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.9 seconds 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10200 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 24 sheets defined 43.8% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 6 through 11 removed outlier: 4.202A pdb=" N ARG A 9 " --> pdb=" O GLU A 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 16 Processing helix chain 'B' and resid 40 through 46 Processing helix chain 'B' and resid 53 through 61 removed outlier: 6.591A pdb=" N TYR B 59 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL B 60 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 119 Processing helix chain 'B' and resid 165 through 178 Processing helix chain 'B' and resid 202 through 223 Processing helix chain 'B' and resid 266 through 279 Processing helix chain 'B' and resid 279 through 288 removed outlier: 4.506A pdb=" N ALA B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ILE B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 297 removed outlier: 3.607A pdb=" N ARG B 296 " --> pdb=" O ASN B 292 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 297 " --> pdb=" O SER B 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 292 through 297' Processing helix chain 'B' and resid 324 through 328 removed outlier: 3.808A pdb=" N THR B 328 " --> pdb=" O GLY B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 359 Processing helix chain 'B' and resid 374 through 381 Processing helix chain 'B' and resid 389 through 400 Processing helix chain 'B' and resid 401 through 408 removed outlier: 3.553A pdb=" N ASP B 405 " --> pdb=" O GLU B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 428 removed outlier: 3.577A pdb=" N ALA B 413 " --> pdb=" O ASP B 409 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR B 414 " --> pdb=" O HIS B 410 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR B 428 " --> pdb=" O ASP B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 438 Processing helix chain 'C' and resid 6 through 11 removed outlier: 4.234A pdb=" N ARG C 9 " --> pdb=" O GLU C 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 11 removed outlier: 4.077A pdb=" N ARG D 9 " --> pdb=" O GLU D 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 16 Processing helix chain 'E' and resid 40 through 46 Processing helix chain 'E' and resid 53 through 61 removed outlier: 6.739A pdb=" N TYR E 59 " --> pdb=" O ILE E 56 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL E 60 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG E 61 " --> pdb=" O GLY E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 119 Processing helix chain 'E' and resid 165 through 178 Processing helix chain 'E' and resid 202 through 223 Processing helix chain 'E' and resid 266 through 279 Processing helix chain 'E' and resid 279 through 288 removed outlier: 4.521A pdb=" N ALA E 285 " --> pdb=" O ARG E 281 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE E 286 " --> pdb=" O ALA E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 297 removed outlier: 3.581A pdb=" N ARG E 296 " --> pdb=" O ASN E 292 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU E 297 " --> pdb=" O SER E 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 292 through 297' Processing helix chain 'E' and resid 324 through 328 removed outlier: 3.838A pdb=" N THR E 328 " --> pdb=" O GLY E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 359 Processing helix chain 'E' and resid 374 through 381 Processing helix chain 'E' and resid 389 through 400 Processing helix chain 'E' and resid 401 through 408 removed outlier: 3.580A pdb=" N ASP E 405 " --> pdb=" O GLU E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 428 removed outlier: 3.568A pdb=" N ALA E 413 " --> pdb=" O ASP E 409 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR E 414 " --> pdb=" O HIS E 410 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR E 428 " --> pdb=" O ASP E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 438 Processing helix chain 'F' and resid 4 through 16 Processing helix chain 'F' and resid 40 through 46 Processing helix chain 'F' and resid 53 through 61 removed outlier: 6.662A pdb=" N TYR F 59 " --> pdb=" O ILE F 56 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL F 60 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG F 61 " --> pdb=" O GLY F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 119 Processing helix chain 'F' and resid 165 through 178 Processing helix chain 'F' and resid 202 through 223 Processing helix chain 'F' and resid 266 through 279 Processing helix chain 'F' and resid 279 through 288 removed outlier: 4.522A pdb=" N ALA F 285 " --> pdb=" O ARG F 281 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ILE F 286 " --> pdb=" O ALA F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 297 removed outlier: 3.602A pdb=" N ARG F 296 " --> pdb=" O ASN F 292 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU F 297 " --> pdb=" O SER F 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 292 through 297' Processing helix chain 'F' and resid 324 through 328 removed outlier: 3.796A pdb=" N THR F 328 " --> pdb=" O GLY F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 359 Processing helix chain 'F' and resid 374 through 381 Processing helix chain 'F' and resid 389 through 400 Processing helix chain 'F' and resid 401 through 408 removed outlier: 3.691A pdb=" N ASP F 405 " --> pdb=" O GLU F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 428 removed outlier: 3.554A pdb=" N ALA F 413 " --> pdb=" O ASP F 409 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR F 414 " --> pdb=" O HIS F 410 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR F 428 " --> pdb=" O ASP F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 438 Processing helix chain 'G' and resid 6 through 11 removed outlier: 4.263A pdb=" N ARG G 9 " --> pdb=" O GLU G 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 11 removed outlier: 4.274A pdb=" N ARG H 9 " --> pdb=" O GLU H 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 11 removed outlier: 4.099A pdb=" N ARG I 9 " --> pdb=" O GLU I 6 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 16 Processing helix chain 'J' and resid 40 through 46 Processing helix chain 'J' and resid 53 through 61 removed outlier: 6.590A pdb=" N TYR J 59 " --> pdb=" O ILE J 56 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL J 60 " --> pdb=" O GLU J 57 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG J 61 " --> pdb=" O GLY J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 105 through 119 Processing helix chain 'J' and resid 165 through 178 Processing helix chain 'J' and resid 202 through 223 Processing helix chain 'J' and resid 266 through 279 Processing helix chain 'J' and resid 279 through 288 removed outlier: 4.509A pdb=" N ALA J 285 " --> pdb=" O ARG J 281 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ILE J 286 " --> pdb=" O ALA J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.609A pdb=" N ARG J 296 " --> pdb=" O ASN J 292 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU J 297 " --> pdb=" O SER J 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 292 through 297' Processing helix chain 'J' and resid 324 through 328 removed outlier: 3.808A pdb=" N THR J 328 " --> pdb=" O GLY J 325 " (cutoff:3.500A) Processing helix chain 'J' and resid 340 through 359 Processing helix chain 'J' and resid 374 through 381 Processing helix chain 'J' and resid 389 through 400 Processing helix chain 'J' and resid 401 through 408 removed outlier: 3.554A pdb=" N ASP J 405 " --> pdb=" O GLU J 401 " (cutoff:3.500A) Processing helix chain 'J' and resid 408 through 428 removed outlier: 3.582A pdb=" N ALA J 413 " --> pdb=" O ASP J 409 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR J 414 " --> pdb=" O HIS J 410 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR J 428 " --> pdb=" O ASP J 424 " (cutoff:3.500A) Processing helix chain 'J' and resid 431 through 438 Processing helix chain 'K' and resid 4 through 16 Processing helix chain 'K' and resid 40 through 46 Processing helix chain 'K' and resid 53 through 61 removed outlier: 6.728A pdb=" N TYR K 59 " --> pdb=" O ILE K 56 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL K 60 " --> pdb=" O GLU K 57 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG K 61 " --> pdb=" O GLY K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 119 Processing helix chain 'K' and resid 165 through 178 Processing helix chain 'K' and resid 202 through 223 Processing helix chain 'K' and resid 266 through 279 Processing helix chain 'K' and resid 279 through 288 removed outlier: 4.512A pdb=" N ALA K 285 " --> pdb=" O ARG K 281 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ILE K 286 " --> pdb=" O ALA K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 292 through 297 removed outlier: 3.582A pdb=" N ARG K 296 " --> pdb=" O ASN K 292 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU K 297 " --> pdb=" O SER K 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 292 through 297' Processing helix chain 'K' and resid 324 through 328 removed outlier: 3.839A pdb=" N THR K 328 " --> pdb=" O GLY K 325 " (cutoff:3.500A) Processing helix chain 'K' and resid 340 through 359 Processing helix chain 'K' and resid 374 through 381 Processing helix chain 'K' and resid 389 through 400 Processing helix chain 'K' and resid 401 through 408 removed outlier: 3.607A pdb=" N ASP K 405 " --> pdb=" O GLU K 401 " (cutoff:3.500A) Processing helix chain 'K' and resid 408 through 428 removed outlier: 3.568A pdb=" N ALA K 413 " --> pdb=" O ASP K 409 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR K 414 " --> pdb=" O HIS K 410 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR K 428 " --> pdb=" O ASP K 424 " (cutoff:3.500A) Processing helix chain 'K' and resid 431 through 438 Processing helix chain 'L' and resid 4 through 16 Processing helix chain 'L' and resid 40 through 46 Processing helix chain 'L' and resid 53 through 61 removed outlier: 6.589A pdb=" N TYR L 59 " --> pdb=" O ILE L 56 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL L 60 " --> pdb=" O GLU L 57 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG L 61 " --> pdb=" O GLY L 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 119 Processing helix chain 'L' and resid 165 through 178 removed outlier: 3.541A pdb=" N GLU L 169 " --> pdb=" O ASN L 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 223 Processing helix chain 'L' and resid 266 through 279 Processing helix chain 'L' and resid 279 through 288 removed outlier: 4.523A pdb=" N ALA L 285 " --> pdb=" O ARG L 281 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ILE L 286 " --> pdb=" O ALA L 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 292 through 297 removed outlier: 3.602A pdb=" N ARG L 296 " --> pdb=" O ASN L 292 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU L 297 " --> pdb=" O SER L 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 292 through 297' Processing helix chain 'L' and resid 324 through 328 removed outlier: 3.796A pdb=" N THR L 328 " --> pdb=" O GLY L 325 " (cutoff:3.500A) Processing helix chain 'L' and resid 340 through 359 Processing helix chain 'L' and resid 374 through 381 Processing helix chain 'L' and resid 389 through 400 Processing helix chain 'L' and resid 402 through 408 Processing helix chain 'L' and resid 408 through 428 removed outlier: 3.566A pdb=" N ALA L 413 " --> pdb=" O ASP L 409 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR L 414 " --> pdb=" O HIS L 410 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR L 428 " --> pdb=" O ASP L 424 " (cutoff:3.500A) Processing helix chain 'L' and resid 431 through 438 Processing helix chain 'M' and resid 6 through 11 removed outlier: 4.273A pdb=" N ARG M 9 " --> pdb=" O GLU M 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 6 through 11 removed outlier: 4.126A pdb=" N ARG N 9 " --> pdb=" O GLU N 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 6 through 11 removed outlier: 4.152A pdb=" N ARG O 9 " --> pdb=" O GLU O 6 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 11 removed outlier: 4.173A pdb=" N ARG P 9 " --> pdb=" O GLU P 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 16 Processing helix chain 'Q' and resid 40 through 46 Processing helix chain 'Q' and resid 53 through 61 removed outlier: 6.728A pdb=" N TYR Q 59 " --> pdb=" O ILE Q 56 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL Q 60 " --> pdb=" O GLU Q 57 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG Q 61 " --> pdb=" O GLY Q 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 119 Processing helix chain 'Q' and resid 165 through 178 Processing helix chain 'Q' and resid 202 through 223 Processing helix chain 'Q' and resid 266 through 279 Processing helix chain 'Q' and resid 279 through 288 removed outlier: 4.520A pdb=" N ALA Q 285 " --> pdb=" O ARG Q 281 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ILE Q 286 " --> pdb=" O ALA Q 282 " (cutoff:3.500A) Processing helix chain 'Q' and resid 292 through 297 removed outlier: 3.581A pdb=" N ARG Q 296 " --> pdb=" O ASN Q 292 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU Q 297 " --> pdb=" O SER Q 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 292 through 297' Processing helix chain 'Q' and resid 324 through 328 removed outlier: 3.838A pdb=" N THR Q 328 " --> pdb=" O GLY Q 325 " (cutoff:3.500A) Processing helix chain 'Q' and resid 340 through 358 Processing helix chain 'Q' and resid 374 through 381 Processing helix chain 'Q' and resid 389 through 400 Processing helix chain 'Q' and resid 401 through 408 removed outlier: 3.579A pdb=" N ASP Q 405 " --> pdb=" O GLU Q 401 " (cutoff:3.500A) Processing helix chain 'Q' and resid 408 through 428 removed outlier: 3.570A pdb=" N ALA Q 413 " --> pdb=" O ASP Q 409 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR Q 414 " --> pdb=" O HIS Q 410 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR Q 428 " --> pdb=" O ASP Q 424 " (cutoff:3.500A) Processing helix chain 'Q' and resid 431 through 438 Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 40 through 46 Processing helix chain 'R' and resid 53 through 61 removed outlier: 6.667A pdb=" N TYR R 59 " --> pdb=" O ILE R 56 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL R 60 " --> pdb=" O GLU R 57 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG R 61 " --> pdb=" O GLY R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 119 Processing helix chain 'R' and resid 165 through 178 removed outlier: 3.549A pdb=" N GLU R 169 " --> pdb=" O ASN R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 202 through 223 Processing helix chain 'R' and resid 266 through 279 Processing helix chain 'R' and resid 279 through 288 removed outlier: 4.525A pdb=" N ALA R 285 " --> pdb=" O ARG R 281 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ILE R 286 " --> pdb=" O ALA R 282 " (cutoff:3.500A) Processing helix chain 'R' and resid 292 through 297 removed outlier: 3.602A pdb=" N ARG R 296 " --> pdb=" O ASN R 292 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU R 297 " --> pdb=" O SER R 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 292 through 297' Processing helix chain 'R' and resid 324 through 328 removed outlier: 3.795A pdb=" N THR R 328 " --> pdb=" O GLY R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 340 through 359 Processing helix chain 'R' and resid 374 through 381 Processing helix chain 'R' and resid 389 through 400 Processing helix chain 'R' and resid 401 through 408 removed outlier: 3.691A pdb=" N ASP R 405 " --> pdb=" O GLU R 401 " (cutoff:3.500A) Processing helix chain 'R' and resid 408 through 428 removed outlier: 3.554A pdb=" N ALA R 413 " --> pdb=" O ASP R 409 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR R 414 " --> pdb=" O HIS R 410 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR R 428 " --> pdb=" O ASP R 424 " (cutoff:3.500A) Processing helix chain 'R' and resid 431 through 438 Processing helix chain 'S' and resid 4 through 16 Processing helix chain 'S' and resid 40 through 46 Processing helix chain 'S' and resid 53 through 61 removed outlier: 6.596A pdb=" N TYR S 59 " --> pdb=" O ILE S 56 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL S 60 " --> pdb=" O GLU S 57 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG S 61 " --> pdb=" O GLY S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 105 through 119 Processing helix chain 'S' and resid 165 through 178 Processing helix chain 'S' and resid 202 through 223 Processing helix chain 'S' and resid 266 through 279 Processing helix chain 'S' and resid 279 through 288 removed outlier: 4.492A pdb=" N ALA S 285 " --> pdb=" O ARG S 281 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ILE S 286 " --> pdb=" O ALA S 282 " (cutoff:3.500A) Processing helix chain 'S' and resid 292 through 297 removed outlier: 3.609A pdb=" N ARG S 296 " --> pdb=" O ASN S 292 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU S 297 " --> pdb=" O SER S 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 292 through 297' Processing helix chain 'S' and resid 324 through 328 removed outlier: 3.790A pdb=" N THR S 328 " --> pdb=" O GLY S 325 " (cutoff:3.500A) Processing helix chain 'S' and resid 340 through 359 Processing helix chain 'S' and resid 374 through 381 Processing helix chain 'S' and resid 389 through 400 Processing helix chain 'S' and resid 401 through 408 removed outlier: 3.555A pdb=" N ASP S 405 " --> pdb=" O GLU S 401 " (cutoff:3.500A) Processing helix chain 'S' and resid 408 through 428 removed outlier: 3.576A pdb=" N ALA S 413 " --> pdb=" O ASP S 409 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR S 414 " --> pdb=" O HIS S 410 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR S 428 " --> pdb=" O ASP S 424 " (cutoff:3.500A) Processing helix chain 'S' and resid 431 through 438 Processing helix chain 'T' and resid 4 through 16 Processing helix chain 'T' and resid 40 through 46 Processing helix chain 'T' and resid 53 through 61 removed outlier: 6.589A pdb=" N TYR T 59 " --> pdb=" O ILE T 56 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL T 60 " --> pdb=" O GLU T 57 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG T 61 " --> pdb=" O GLY T 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 105 through 119 Processing helix chain 'T' and resid 165 through 178 removed outlier: 3.542A pdb=" N GLU T 169 " --> pdb=" O ASN T 165 " (cutoff:3.500A) Processing helix chain 'T' and resid 202 through 223 Processing helix chain 'T' and resid 266 through 279 Processing helix chain 'T' and resid 279 through 288 removed outlier: 4.509A pdb=" N ALA T 285 " --> pdb=" O ARG T 281 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ILE T 286 " --> pdb=" O ALA T 282 " (cutoff:3.500A) Processing helix chain 'T' and resid 292 through 297 removed outlier: 3.597A pdb=" N ARG T 296 " --> pdb=" O ASN T 292 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU T 297 " --> pdb=" O SER T 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 292 through 297' Processing helix chain 'T' and resid 324 through 328 removed outlier: 3.795A pdb=" N THR T 328 " --> pdb=" O GLY T 325 " (cutoff:3.500A) Processing helix chain 'T' and resid 340 through 359 Processing helix chain 'T' and resid 374 through 381 Processing helix chain 'T' and resid 389 through 400 Processing helix chain 'T' and resid 402 through 408 Processing helix chain 'T' and resid 408 through 428 removed outlier: 3.568A pdb=" N ALA T 413 " --> pdb=" O ASP T 409 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR T 414 " --> pdb=" O HIS T 410 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR T 428 " --> pdb=" O ASP T 424 " (cutoff:3.500A) Processing helix chain 'T' and resid 431 through 438 Processing helix chain 'U' and resid 6 through 11 removed outlier: 4.293A pdb=" N ARG U 9 " --> pdb=" O GLU U 6 " (cutoff:3.500A) Processing helix chain 'V' and resid 6 through 11 removed outlier: 4.281A pdb=" N ARG V 9 " --> pdb=" O GLU V 6 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 16 Processing helix chain 'W' and resid 40 through 46 Processing helix chain 'W' and resid 53 through 61 removed outlier: 6.587A pdb=" N TYR W 59 " --> pdb=" O ILE W 56 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL W 60 " --> pdb=" O GLU W 57 " (cutoff:3.500A) Processing helix chain 'W' and resid 105 through 119 Processing helix chain 'W' and resid 165 through 178 Processing helix chain 'W' and resid 202 through 223 Processing helix chain 'W' and resid 266 through 279 Processing helix chain 'W' and resid 279 through 288 removed outlier: 4.496A pdb=" N ALA W 285 " --> pdb=" O ARG W 281 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ILE W 286 " --> pdb=" O ALA W 282 " (cutoff:3.500A) Processing helix chain 'W' and resid 292 through 297 removed outlier: 3.607A pdb=" N ARG W 296 " --> pdb=" O ASN W 292 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU W 297 " --> pdb=" O SER W 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 292 through 297' Processing helix chain 'W' and resid 324 through 328 removed outlier: 3.809A pdb=" N THR W 328 " --> pdb=" O GLY W 325 " (cutoff:3.500A) Processing helix chain 'W' and resid 340 through 359 Processing helix chain 'W' and resid 374 through 381 Processing helix chain 'W' and resid 389 through 400 Processing helix chain 'W' and resid 401 through 408 removed outlier: 3.555A pdb=" N ASP W 405 " --> pdb=" O GLU W 401 " (cutoff:3.500A) Processing helix chain 'W' and resid 408 through 428 removed outlier: 3.589A pdb=" N ALA W 413 " --> pdb=" O ASP W 409 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR W 414 " --> pdb=" O HIS W 410 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR W 428 " --> pdb=" O ASP W 424 " (cutoff:3.500A) Processing helix chain 'W' and resid 431 through 438 Processing helix chain 'X' and resid 4 through 16 Processing helix chain 'X' and resid 40 through 46 Processing helix chain 'X' and resid 53 through 61 removed outlier: 6.751A pdb=" N TYR X 59 " --> pdb=" O ILE X 56 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL X 60 " --> pdb=" O GLU X 57 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG X 61 " --> pdb=" O GLY X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 105 through 119 Processing helix chain 'X' and resid 165 through 178 Processing helix chain 'X' and resid 202 through 223 Processing helix chain 'X' and resid 266 through 279 Processing helix chain 'X' and resid 279 through 288 removed outlier: 4.478A pdb=" N ALA X 285 " --> pdb=" O ARG X 281 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ILE X 286 " --> pdb=" O ALA X 282 " (cutoff:3.500A) Processing helix chain 'X' and resid 292 through 297 removed outlier: 3.589A pdb=" N ARG X 296 " --> pdb=" O ASN X 292 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU X 297 " --> pdb=" O SER X 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 292 through 297' Processing helix chain 'X' and resid 324 through 328 removed outlier: 3.701A pdb=" N THR X 328 " --> pdb=" O GLY X 325 " (cutoff:3.500A) Processing helix chain 'X' and resid 340 through 359 Processing helix chain 'X' and resid 374 through 381 Processing helix chain 'X' and resid 389 through 400 Processing helix chain 'X' and resid 401 through 408 removed outlier: 3.595A pdb=" N ASP X 405 " --> pdb=" O GLU X 401 " (cutoff:3.500A) Processing helix chain 'X' and resid 408 through 428 removed outlier: 3.546A pdb=" N ALA X 413 " --> pdb=" O ASP X 409 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR X 414 " --> pdb=" O HIS X 410 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR X 428 " --> pdb=" O ASP X 424 " (cutoff:3.500A) Processing helix chain 'X' and resid 431 through 438 Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 37 removed outlier: 4.829A pdb=" N VAL B 17 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ALA B 88 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE B 19 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU B 90 " --> pdb=" O PHE B 19 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ARG B 21 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N CYS B 92 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLN B 23 " --> pdb=" O CYS B 92 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ILE B 94 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N THR B 25 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 11.856A pdb=" N VAL B 87 " --> pdb=" O TRP B 76 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N TRP B 76 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 10.234A pdb=" N ARG B 89 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N ASP B 74 " --> pdb=" O ARG B 89 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE B 91 " --> pdb=" O ASP B 72 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N MET B 49 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 124 through 138 removed outlier: 7.190A pdb=" N LEU B 135 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLU B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LYS B 137 " --> pdb=" O THR B 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 144 through 148 current: chain 'B' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 192 through 197 current: chain 'B' and resid 318 through 319 Processing sheet with id=AA3, first strand: chain 'E' and resid 31 through 37 removed outlier: 4.793A pdb=" N VAL E 17 " --> pdb=" O ARG E 86 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ALA E 88 " --> pdb=" O VAL E 17 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE E 19 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LEU E 90 " --> pdb=" O PHE E 19 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ARG E 21 " --> pdb=" O LEU E 90 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N CYS E 92 " --> pdb=" O ARG E 21 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLN E 23 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ILE E 94 " --> pdb=" O GLN E 23 " (cutoff:3.500A) removed outlier: 10.364A pdb=" N THR E 25 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 11.868A pdb=" N VAL E 87 " --> pdb=" O TRP E 76 " (cutoff:3.500A) removed outlier: 10.521A pdb=" N TRP E 76 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 10.271A pdb=" N ARG E 89 " --> pdb=" O ASP E 74 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ASP E 74 " --> pdb=" O ARG E 89 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ILE E 91 " --> pdb=" O ASP E 72 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N MET E 49 " --> pdb=" O LEU E 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 124 through 138 removed outlier: 7.237A pdb=" N LEU E 135 " --> pdb=" O GLU E 147 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLU E 147 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LYS E 137 " --> pdb=" O THR E 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 144 through 148 current: chain 'E' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 192 through 197 current: chain 'E' and resid 318 through 319 Processing sheet with id=AA5, first strand: chain 'F' and resid 31 through 37 removed outlier: 4.814A pdb=" N VAL F 17 " --> pdb=" O ARG F 86 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ALA F 88 " --> pdb=" O VAL F 17 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N PHE F 19 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LEU F 90 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ARG F 21 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N CYS F 92 " --> pdb=" O ARG F 21 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLN F 23 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ILE F 94 " --> pdb=" O GLN F 23 " (cutoff:3.500A) removed outlier: 10.383A pdb=" N THR F 25 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 11.848A pdb=" N VAL F 87 " --> pdb=" O TRP F 76 " (cutoff:3.500A) removed outlier: 10.503A pdb=" N TRP F 76 " --> pdb=" O VAL F 87 " (cutoff:3.500A) removed outlier: 10.268A pdb=" N ARG F 89 " --> pdb=" O ASP F 74 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ASP F 74 " --> pdb=" O ARG F 89 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ILE F 91 " --> pdb=" O ASP F 72 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N MET F 49 " --> pdb=" O LEU F 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 124 through 138 removed outlier: 7.246A pdb=" N LEU F 135 " --> pdb=" O GLU F 147 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLU F 147 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LYS F 137 " --> pdb=" O THR F 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 144 through 148 current: chain 'F' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 192 through 197 current: chain 'F' and resid 318 through 319 Processing sheet with id=AA7, first strand: chain 'J' and resid 31 through 37 removed outlier: 4.828A pdb=" N VAL J 17 " --> pdb=" O ARG J 86 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ALA J 88 " --> pdb=" O VAL J 17 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE J 19 " --> pdb=" O ALA J 88 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU J 90 " --> pdb=" O PHE J 19 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ARG J 21 " --> pdb=" O LEU J 90 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N CYS J 92 " --> pdb=" O ARG J 21 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLN J 23 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ILE J 94 " --> pdb=" O GLN J 23 " (cutoff:3.500A) removed outlier: 10.334A pdb=" N THR J 25 " --> pdb=" O ILE J 94 " (cutoff:3.500A) removed outlier: 11.858A pdb=" N VAL J 87 " --> pdb=" O TRP J 76 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N TRP J 76 " --> pdb=" O VAL J 87 " (cutoff:3.500A) removed outlier: 10.233A pdb=" N ARG J 89 " --> pdb=" O ASP J 74 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ASP J 74 " --> pdb=" O ARG J 89 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE J 91 " --> pdb=" O ASP J 72 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N MET J 49 " --> pdb=" O LEU J 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 124 through 138 removed outlier: 7.191A pdb=" N LEU J 135 " --> pdb=" O GLU J 147 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLU J 147 " --> pdb=" O LEU J 135 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LYS J 137 " --> pdb=" O THR J 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 144 through 148 current: chain 'J' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 192 through 197 current: chain 'J' and resid 318 through 319 Processing sheet with id=AA9, first strand: chain 'K' and resid 31 through 37 removed outlier: 4.812A pdb=" N VAL K 17 " --> pdb=" O ARG K 86 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ALA K 88 " --> pdb=" O VAL K 17 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE K 19 " --> pdb=" O ALA K 88 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU K 90 " --> pdb=" O PHE K 19 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ARG K 21 " --> pdb=" O LEU K 90 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N CYS K 92 " --> pdb=" O ARG K 21 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN K 23 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE K 94 " --> pdb=" O GLN K 23 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N THR K 25 " --> pdb=" O ILE K 94 " (cutoff:3.500A) removed outlier: 11.865A pdb=" N VAL K 87 " --> pdb=" O TRP K 76 " (cutoff:3.500A) removed outlier: 10.525A pdb=" N TRP K 76 " --> pdb=" O VAL K 87 " (cutoff:3.500A) removed outlier: 10.273A pdb=" N ARG K 89 " --> pdb=" O ASP K 74 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ASP K 74 " --> pdb=" O ARG K 89 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ILE K 91 " --> pdb=" O ASP K 72 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N MET K 49 " --> pdb=" O LEU K 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 124 through 138 removed outlier: 7.221A pdb=" N LEU K 135 " --> pdb=" O GLU K 147 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLU K 147 " --> pdb=" O LEU K 135 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LYS K 137 " --> pdb=" O THR K 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 144 through 148 current: chain 'K' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 192 through 197 current: chain 'K' and resid 318 through 319 Processing sheet with id=AB2, first strand: chain 'L' and resid 31 through 37 removed outlier: 4.818A pdb=" N VAL L 17 " --> pdb=" O ARG L 86 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ALA L 88 " --> pdb=" O VAL L 17 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE L 19 " --> pdb=" O ALA L 88 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU L 90 " --> pdb=" O PHE L 19 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ARG L 21 " --> pdb=" O LEU L 90 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N CYS L 92 " --> pdb=" O ARG L 21 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLN L 23 " --> pdb=" O CYS L 92 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N ILE L 94 " --> pdb=" O GLN L 23 " (cutoff:3.500A) removed outlier: 10.374A pdb=" N THR L 25 " --> pdb=" O ILE L 94 " (cutoff:3.500A) removed outlier: 11.850A pdb=" N VAL L 87 " --> pdb=" O TRP L 76 " (cutoff:3.500A) removed outlier: 10.504A pdb=" N TRP L 76 " --> pdb=" O VAL L 87 " (cutoff:3.500A) removed outlier: 10.269A pdb=" N ARG L 89 " --> pdb=" O ASP L 74 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ASP L 74 " --> pdb=" O ARG L 89 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ILE L 91 " --> pdb=" O ASP L 72 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N MET L 49 " --> pdb=" O LEU L 69 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 124 through 138 removed outlier: 7.245A pdb=" N LEU L 135 " --> pdb=" O GLU L 147 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLU L 147 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LYS L 137 " --> pdb=" O THR L 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 144 through 148 current: chain 'L' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 192 through 197 current: chain 'L' and resid 318 through 319 Processing sheet with id=AB4, first strand: chain 'Q' and resid 31 through 37 removed outlier: 4.809A pdb=" N VAL Q 17 " --> pdb=" O ARG Q 86 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ALA Q 88 " --> pdb=" O VAL Q 17 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE Q 19 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N LEU Q 90 " --> pdb=" O PHE Q 19 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ARG Q 21 " --> pdb=" O LEU Q 90 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N CYS Q 92 " --> pdb=" O ARG Q 21 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN Q 23 " --> pdb=" O CYS Q 92 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ILE Q 94 " --> pdb=" O GLN Q 23 " (cutoff:3.500A) removed outlier: 10.359A pdb=" N THR Q 25 " --> pdb=" O ILE Q 94 " (cutoff:3.500A) removed outlier: 11.861A pdb=" N VAL Q 87 " --> pdb=" O TRP Q 76 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N TRP Q 76 " --> pdb=" O VAL Q 87 " (cutoff:3.500A) removed outlier: 10.270A pdb=" N ARG Q 89 " --> pdb=" O ASP Q 74 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N ASP Q 74 " --> pdb=" O ARG Q 89 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE Q 91 " --> pdb=" O ASP Q 72 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N MET Q 49 " --> pdb=" O LEU Q 69 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Q' and resid 124 through 138 removed outlier: 7.236A pdb=" N LEU Q 135 " --> pdb=" O GLU Q 147 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLU Q 147 " --> pdb=" O LEU Q 135 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LYS Q 137 " --> pdb=" O THR Q 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 144 through 148 current: chain 'Q' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 192 through 197 current: chain 'Q' and resid 318 through 319 Processing sheet with id=AB6, first strand: chain 'R' and resid 31 through 37 removed outlier: 4.815A pdb=" N VAL R 17 " --> pdb=" O ARG R 86 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ALA R 88 " --> pdb=" O VAL R 17 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N PHE R 19 " --> pdb=" O ALA R 88 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LEU R 90 " --> pdb=" O PHE R 19 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ARG R 21 " --> pdb=" O LEU R 90 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N CYS R 92 " --> pdb=" O ARG R 21 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN R 23 " --> pdb=" O CYS R 92 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ILE R 94 " --> pdb=" O GLN R 23 " (cutoff:3.500A) removed outlier: 10.383A pdb=" N THR R 25 " --> pdb=" O ILE R 94 " (cutoff:3.500A) removed outlier: 11.848A pdb=" N VAL R 87 " --> pdb=" O TRP R 76 " (cutoff:3.500A) removed outlier: 10.502A pdb=" N TRP R 76 " --> pdb=" O VAL R 87 " (cutoff:3.500A) removed outlier: 10.268A pdb=" N ARG R 89 " --> pdb=" O ASP R 74 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ASP R 74 " --> pdb=" O ARG R 89 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE R 91 " --> pdb=" O ASP R 72 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N MET R 49 " --> pdb=" O LEU R 69 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'R' and resid 124 through 138 removed outlier: 7.243A pdb=" N LEU R 135 " --> pdb=" O GLU R 147 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLU R 147 " --> pdb=" O LEU R 135 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LYS R 137 " --> pdb=" O THR R 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 144 through 148 current: chain 'R' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 192 through 197 current: chain 'R' and resid 318 through 319 Processing sheet with id=AB8, first strand: chain 'S' and resid 31 through 37 removed outlier: 4.835A pdb=" N VAL S 17 " --> pdb=" O ARG S 86 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ALA S 88 " --> pdb=" O VAL S 17 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N PHE S 19 " --> pdb=" O ALA S 88 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU S 90 " --> pdb=" O PHE S 19 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ARG S 21 " --> pdb=" O LEU S 90 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N CYS S 92 " --> pdb=" O ARG S 21 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN S 23 " --> pdb=" O CYS S 92 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ILE S 94 " --> pdb=" O GLN S 23 " (cutoff:3.500A) removed outlier: 10.344A pdb=" N THR S 25 " --> pdb=" O ILE S 94 " (cutoff:3.500A) removed outlier: 11.870A pdb=" N VAL S 87 " --> pdb=" O TRP S 76 " (cutoff:3.500A) removed outlier: 10.519A pdb=" N TRP S 76 " --> pdb=" O VAL S 87 " (cutoff:3.500A) removed outlier: 10.238A pdb=" N ARG S 89 " --> pdb=" O ASP S 74 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ASP S 74 " --> pdb=" O ARG S 89 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE S 91 " --> pdb=" O ASP S 72 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N MET S 49 " --> pdb=" O LEU S 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'S' and resid 124 through 138 removed outlier: 7.182A pdb=" N LEU S 135 " --> pdb=" O GLU S 147 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLU S 147 " --> pdb=" O LEU S 135 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LYS S 137 " --> pdb=" O THR S 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 144 through 148 current: chain 'S' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 192 through 197 current: chain 'S' and resid 318 through 319 Processing sheet with id=AC1, first strand: chain 'T' and resid 31 through 37 removed outlier: 4.819A pdb=" N VAL T 17 " --> pdb=" O ARG T 86 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ALA T 88 " --> pdb=" O VAL T 17 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE T 19 " --> pdb=" O ALA T 88 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LEU T 90 " --> pdb=" O PHE T 19 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ARG T 21 " --> pdb=" O LEU T 90 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N CYS T 92 " --> pdb=" O ARG T 21 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLN T 23 " --> pdb=" O CYS T 92 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ILE T 94 " --> pdb=" O GLN T 23 " (cutoff:3.500A) removed outlier: 10.372A pdb=" N THR T 25 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 11.850A pdb=" N VAL T 87 " --> pdb=" O TRP T 76 " (cutoff:3.500A) removed outlier: 10.503A pdb=" N TRP T 76 " --> pdb=" O VAL T 87 " (cutoff:3.500A) removed outlier: 10.268A pdb=" N ARG T 89 " --> pdb=" O ASP T 74 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ASP T 74 " --> pdb=" O ARG T 89 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ILE T 91 " --> pdb=" O ASP T 72 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N MET T 49 " --> pdb=" O LEU T 69 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'T' and resid 124 through 138 removed outlier: 7.247A pdb=" N LEU T 135 " --> pdb=" O GLU T 147 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLU T 147 " --> pdb=" O LEU T 135 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LYS T 137 " --> pdb=" O THR T 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 144 through 148 current: chain 'T' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 192 through 197 current: chain 'T' and resid 318 through 319 Processing sheet with id=AC3, first strand: chain 'W' and resid 31 through 37 removed outlier: 4.828A pdb=" N VAL W 17 " --> pdb=" O ARG W 86 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ALA W 88 " --> pdb=" O VAL W 17 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE W 19 " --> pdb=" O ALA W 88 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU W 90 " --> pdb=" O PHE W 19 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ARG W 21 " --> pdb=" O LEU W 90 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N CYS W 92 " --> pdb=" O ARG W 21 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLN W 23 " --> pdb=" O CYS W 92 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ILE W 94 " --> pdb=" O GLN W 23 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N THR W 25 " --> pdb=" O ILE W 94 " (cutoff:3.500A) removed outlier: 11.857A pdb=" N VAL W 87 " --> pdb=" O TRP W 76 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N TRP W 76 " --> pdb=" O VAL W 87 " (cutoff:3.500A) removed outlier: 10.233A pdb=" N ARG W 89 " --> pdb=" O ASP W 74 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ASP W 74 " --> pdb=" O ARG W 89 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE W 91 " --> pdb=" O ASP W 72 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N MET W 49 " --> pdb=" O LEU W 69 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'W' and resid 124 through 138 removed outlier: 7.193A pdb=" N LEU W 135 " --> pdb=" O GLU W 147 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLU W 147 " --> pdb=" O LEU W 135 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LYS W 137 " --> pdb=" O THR W 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 144 through 148 current: chain 'W' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 192 through 197 current: chain 'W' and resid 318 through 319 Processing sheet with id=AC5, first strand: chain 'X' and resid 31 through 37 removed outlier: 4.813A pdb=" N VAL X 17 " --> pdb=" O ARG X 86 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ALA X 88 " --> pdb=" O VAL X 17 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N PHE X 19 " --> pdb=" O ALA X 88 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LEU X 90 " --> pdb=" O PHE X 19 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ARG X 21 " --> pdb=" O LEU X 90 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N CYS X 92 " --> pdb=" O ARG X 21 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLN X 23 " --> pdb=" O CYS X 92 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ILE X 94 " --> pdb=" O GLN X 23 " (cutoff:3.500A) removed outlier: 10.371A pdb=" N THR X 25 " --> pdb=" O ILE X 94 " (cutoff:3.500A) removed outlier: 11.855A pdb=" N VAL X 87 " --> pdb=" O TRP X 76 " (cutoff:3.500A) removed outlier: 10.503A pdb=" N TRP X 76 " --> pdb=" O VAL X 87 " (cutoff:3.500A) removed outlier: 10.258A pdb=" N ARG X 89 " --> pdb=" O ASP X 74 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ASP X 74 " --> pdb=" O ARG X 89 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE X 91 " --> pdb=" O ASP X 72 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N MET X 49 " --> pdb=" O LEU X 69 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'X' and resid 124 through 138 removed outlier: 7.228A pdb=" N LEU X 135 " --> pdb=" O GLU X 147 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLU X 147 " --> pdb=" O LEU X 135 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LYS X 137 " --> pdb=" O THR X 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 144 through 148 current: chain 'X' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 192 through 197 current: chain 'X' and resid 318 through 319 1642 hydrogen bonds defined for protein. 4668 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: 7.62 Time building geometry restraints manager: 4.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.97 - 1.14: 120 1.14 - 1.30: 7140 1.30 - 1.47: 17363 1.47 - 1.64: 18553 1.64 - 1.81: 408 Bond restraints: 43584 Sorted by residual: bond pdb=" NE2 GLN X 503 " pdb="HE21 GLN X 503 " ideal model delta sigma weight residual 0.860 1.017 -0.157 2.00e-02 2.50e+03 6.15e+01 bond pdb=" NE2 GLN S 503 " pdb="HE22 GLN S 503 " ideal model delta sigma weight residual 0.860 1.017 -0.157 2.00e-02 2.50e+03 6.14e+01 bond pdb=" NE2 GLN K 503 " pdb="HE21 GLN K 503 " ideal model delta sigma weight residual 0.860 1.017 -0.157 2.00e-02 2.50e+03 6.12e+01 bond pdb=" NE2 GLN W 503 " pdb="HE22 GLN W 503 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.12e+01 bond pdb=" NE2 GLN L 503 " pdb="HE22 GLN L 503 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.11e+01 ... (remaining 43579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 57799 1.59 - 3.17: 1127 3.17 - 4.76: 253 4.76 - 6.34: 48 6.34 - 7.93: 5 Bond angle restraints: 59232 Sorted by residual: angle pdb=" N LEU F 162 " pdb=" CA LEU F 162 " pdb=" C LEU F 162 " ideal model delta sigma weight residual 114.75 109.79 4.96 1.26e+00 6.30e-01 1.55e+01 angle pdb=" C ASP T 161 " pdb=" CA ASP T 161 " pdb=" CB ASP T 161 " ideal model delta sigma weight residual 116.34 110.92 5.42 1.40e+00 5.10e-01 1.50e+01 angle pdb=" C ASP L 161 " pdb=" CA ASP L 161 " pdb=" CB ASP L 161 " ideal model delta sigma weight residual 116.34 110.92 5.42 1.40e+00 5.10e-01 1.50e+01 angle pdb=" N LEU L 162 " pdb=" CA LEU L 162 " pdb=" C LEU L 162 " ideal model delta sigma weight residual 114.31 109.35 4.96 1.29e+00 6.01e-01 1.48e+01 angle pdb=" N LEU T 162 " pdb=" CA LEU T 162 " pdb=" C LEU T 162 " ideal model delta sigma weight residual 114.31 109.40 4.91 1.29e+00 6.01e-01 1.45e+01 ... (remaining 59227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 22553 16.95 - 33.90: 2470 33.90 - 50.85: 873 50.85 - 67.80: 249 67.80 - 84.75: 87 Dihedral angle restraints: 26232 sinusoidal: 10404 harmonic: 15828 Sorted by residual: dihedral pdb=" CA TYR S 371 " pdb=" C TYR S 371 " pdb=" N VAL S 372 " pdb=" CA VAL S 372 " ideal model delta harmonic sigma weight residual 180.00 157.40 22.60 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA TYR J 371 " pdb=" C TYR J 371 " pdb=" N VAL J 372 " pdb=" CA VAL J 372 " ideal model delta harmonic sigma weight residual 180.00 157.63 22.37 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA TYR W 371 " pdb=" C TYR W 371 " pdb=" N VAL W 372 " pdb=" CA VAL W 372 " ideal model delta harmonic sigma weight residual 180.00 157.64 22.36 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 26229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 5517 0.055 - 0.109: 752 0.109 - 0.164: 182 0.164 - 0.219: 4 0.219 - 0.274: 1 Chirality restraints: 6456 Sorted by residual: chirality pdb=" CA LEU F 157 " pdb=" N LEU F 157 " pdb=" C LEU F 157 " pdb=" CB LEU F 157 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA ARG L 168 " pdb=" N ARG L 168 " pdb=" C ARG L 168 " pdb=" CB ARG L 168 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CA ARG T 168 " pdb=" N ARG T 168 " pdb=" C ARG T 168 " pdb=" CB ARG T 168 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 6453 not shown) Planarity restraints: 7716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN W 503 " -0.314 2.00e-02 2.50e+03 3.32e-01 1.66e+03 pdb=" CD GLN W 503 " 0.025 2.00e-02 2.50e+03 pdb=" OE1 GLN W 503 " 0.301 2.00e-02 2.50e+03 pdb=" NE2 GLN W 503 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN W 503 " 0.479 2.00e-02 2.50e+03 pdb="HE22 GLN W 503 " -0.493 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN J 503 " 0.299 2.00e-02 2.50e+03 3.10e-01 1.44e+03 pdb=" CD GLN J 503 " -0.024 2.00e-02 2.50e+03 pdb=" OE1 GLN J 503 " -0.286 2.00e-02 2.50e+03 pdb=" NE2 GLN J 503 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN J 503 " -0.443 2.00e-02 2.50e+03 pdb="HE22 GLN J 503 " 0.456 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN S 503 " 0.293 2.00e-02 2.50e+03 3.01e-01 1.36e+03 pdb=" CD GLN S 503 " -0.024 2.00e-02 2.50e+03 pdb=" OE1 GLN S 503 " -0.279 2.00e-02 2.50e+03 pdb=" NE2 GLN S 503 " -0.003 2.00e-02 2.50e+03 pdb="HE21 GLN S 503 " -0.429 2.00e-02 2.50e+03 pdb="HE22 GLN S 503 " 0.442 2.00e-02 2.50e+03 ... (remaining 7713 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.39: 185 2.39 - 2.94: 19108 2.94 - 3.49: 51487 3.49 - 4.05: 84184 4.05 - 4.60: 126311 Nonbonded interactions: 281275 Sorted by model distance: nonbonded pdb=" O GLY Q 239 " pdb=" H1 GLN Q 503 " model vdw 1.836 2.450 nonbonded pdb=" O GLY X 239 " pdb=" H1 GLN X 503 " model vdw 1.838 2.450 nonbonded pdb=" O GLY K 239 " pdb=" H1 GLN K 503 " model vdw 1.840 2.450 nonbonded pdb=" O GLY E 239 " pdb=" H1 GLN E 503 " model vdw 1.841 2.450 nonbonded pdb=" O GLY T 239 " pdb=" H1 GLN T 503 " model vdw 1.848 2.450 ... (remaining 281270 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'X' } 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=0.97 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.270 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 36.530 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.130 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:6.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 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 : 0.003 0.038 43464 Z= 0.159 Angle : 0.566 7.929 58968 Z= 0.314 Chirality : 0.041 0.274 6456 Planarity : 0.003 0.034 7716 Dihedral : 17.351 84.748 16020 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.62 % Favored : 96.36 % Rotamer: Outliers : 2.16 % Allowed : 18.78 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.12), residues: 5364 helix: 1.31 (0.11), residues: 2136 sheet: -0.78 (0.17), residues: 876 loop : -0.33 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 86 TYR 0.016 0.001 TYR R 294 PHE 0.007 0.001 PHE E 212 TRP 0.007 0.001 TRP Q 423 HIS 0.002 0.000 HIS W 243 Details of bonding type rmsd covalent geometry : bond 0.00288 (43464) covalent geometry : angle 0.56639 (58968) hydrogen bonds : bond 0.15481 ( 1642) hydrogen bonds : angle 6.06059 ( 4668) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1118 residues out of total 4668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 1023 time to evaluate : 1.653 Fit side-chains REVERT: A 4 GLN cc_start: 0.4742 (mp10) cc_final: 0.4058 (mt0) REVERT: B 5 ARG cc_start: 0.6222 (mtp-110) cc_final: 0.5553 (ttt90) REVERT: B 33 ASN cc_start: 0.6583 (OUTLIER) cc_final: 0.6093 (p0) REVERT: B 35 GLU cc_start: 0.5595 (mm-30) cc_final: 0.5167 (mp0) REVERT: B 42 GLU cc_start: 0.5317 (pm20) cc_final: 0.5059 (pm20) REVERT: B 48 LYS cc_start: 0.6647 (mtpt) cc_final: 0.6023 (mmtp) REVERT: B 57 GLU cc_start: 0.6542 (mt-10) cc_final: 0.6338 (mt-10) REVERT: B 63 GLU cc_start: 0.6230 (pt0) cc_final: 0.5891 (mt-10) REVERT: B 72 ASP cc_start: 0.6720 (t70) cc_final: 0.6480 (t0) REVERT: B 86 ARG cc_start: 0.6033 (mmt90) cc_final: 0.4837 (mmm160) REVERT: B 116 GLU cc_start: 0.6300 (pt0) cc_final: 0.6059 (pt0) REVERT: B 126 ASN cc_start: 0.7261 (t0) cc_final: 0.6858 (t0) REVERT: B 180 GLU cc_start: 0.6351 (mm-30) cc_final: 0.5832 (mt-10) REVERT: B 221 ARG cc_start: 0.5457 (ttp-170) cc_final: 0.4781 (tpp-160) REVERT: B 273 MET cc_start: 0.7143 (mtp) cc_final: 0.6753 (mtp) REVERT: B 278 LYS cc_start: 0.6836 (ttmm) cc_final: 0.6525 (tppp) REVERT: B 313 ASN cc_start: 0.6969 (t0) cc_final: 0.6125 (m-40) REVERT: B 328 THR cc_start: 0.7473 (t) cc_final: 0.7223 (m) REVERT: B 359 GLN cc_start: 0.6631 (mt0) cc_final: 0.6343 (mt0) REVERT: B 391 LYS cc_start: 0.5401 (tptp) cc_final: 0.4707 (ttpt) REVERT: B 396 GLU cc_start: 0.6244 (mm-30) cc_final: 0.5923 (mm-30) REVERT: B 398 ILE cc_start: 0.6423 (OUTLIER) cc_final: 0.5562 (pt) REVERT: B 417 GLU cc_start: 0.5913 (tt0) cc_final: 0.5516 (mt-10) REVERT: B 424 ASP cc_start: 0.6534 (t70) cc_final: 0.6188 (t70) REVERT: B 425 MET cc_start: 0.6979 (mmt) cc_final: 0.6501 (mmp) REVERT: C 4 GLN cc_start: 0.4782 (mp-120) cc_final: 0.4427 (mm110) REVERT: C 6 GLU cc_start: 0.5392 (OUTLIER) cc_final: 0.5119 (mm-30) REVERT: D 4 GLN cc_start: 0.4715 (mm-40) cc_final: 0.4135 (tp40) REVERT: E 2 SER cc_start: 0.5968 (p) cc_final: 0.5714 (p) REVERT: E 5 ARG cc_start: 0.6163 (mtp-110) cc_final: 0.5538 (ttt90) REVERT: E 10 ARG cc_start: 0.6183 (ttp-110) cc_final: 0.5875 (ttp80) REVERT: E 33 ASN cc_start: 0.6702 (OUTLIER) cc_final: 0.6285 (p0) REVERT: E 35 GLU cc_start: 0.5328 (mm-30) cc_final: 0.5101 (mp0) REVERT: E 42 GLU cc_start: 0.5335 (pm20) cc_final: 0.4997 (pm20) REVERT: E 48 LYS cc_start: 0.6399 (mtpt) cc_final: 0.5932 (mttt) REVERT: E 57 GLU cc_start: 0.6529 (mp0) cc_final: 0.6185 (mm-30) REVERT: E 62 ILE cc_start: 0.6683 (tp) cc_final: 0.6319 (pt) REVERT: E 63 GLU cc_start: 0.6096 (pt0) cc_final: 0.5841 (mt-10) REVERT: E 67 MET cc_start: 0.7102 (mtp) cc_final: 0.6657 (mtt) REVERT: E 72 ASP cc_start: 0.6407 (t70) cc_final: 0.6158 (t0) REVERT: E 73 LEU cc_start: 0.6373 (mt) cc_final: 0.6094 (mt) REVERT: E 86 ARG cc_start: 0.5992 (mmt90) cc_final: 0.4830 (mmm160) REVERT: E 115 LYS cc_start: 0.6305 (tptp) cc_final: 0.4738 (mmtm) REVERT: E 126 ASN cc_start: 0.7319 (t0) cc_final: 0.7056 (t0) REVERT: E 180 GLU cc_start: 0.6375 (mm-30) cc_final: 0.5977 (mt-10) REVERT: E 221 ARG cc_start: 0.6031 (ttp-170) cc_final: 0.5005 (tpp-160) REVERT: E 283 MET cc_start: 0.6590 (mtm) cc_final: 0.6231 (mtm) REVERT: E 313 ASN cc_start: 0.6864 (t0) cc_final: 0.6561 (t0) REVERT: E 328 THR cc_start: 0.7564 (OUTLIER) cc_final: 0.7118 (p) REVERT: E 358 ARG cc_start: 0.6459 (mtp180) cc_final: 0.5796 (mtm180) REVERT: E 391 LYS cc_start: 0.5333 (tptp) cc_final: 0.4609 (ttpt) REVERT: E 398 ILE cc_start: 0.6097 (OUTLIER) cc_final: 0.5316 (pt) REVERT: E 399 ARG cc_start: 0.6379 (mtm110) cc_final: 0.6013 (mtp-110) REVERT: E 424 ASP cc_start: 0.6712 (t70) cc_final: 0.6488 (t70) REVERT: F 5 ARG cc_start: 0.6065 (mtp-110) cc_final: 0.5637 (ttp80) REVERT: F 10 ARG cc_start: 0.6133 (ttp-110) cc_final: 0.5701 (ttp-110) REVERT: F 33 ASN cc_start: 0.6633 (OUTLIER) cc_final: 0.6054 (p0) REVERT: F 35 GLU cc_start: 0.5370 (mm-30) cc_final: 0.5045 (mp0) REVERT: F 50 MET cc_start: 0.5155 (ptp) cc_final: 0.4383 (ttp) REVERT: F 57 GLU cc_start: 0.6633 (mt-10) cc_final: 0.6190 (mp0) REVERT: F 62 ILE cc_start: 0.6476 (tp) cc_final: 0.6157 (pp) REVERT: F 63 GLU cc_start: 0.6549 (pt0) cc_final: 0.5861 (mt-10) REVERT: F 67 MET cc_start: 0.7040 (mtt) cc_final: 0.6490 (mtt) REVERT: F 86 ARG cc_start: 0.5702 (mmt90) cc_final: 0.4612 (mmm160) REVERT: F 93 ASP cc_start: 0.6242 (m-30) cc_final: 0.6016 (m-30) REVERT: F 115 LYS cc_start: 0.6102 (tptp) cc_final: 0.4484 (mmtm) REVERT: F 116 GLU cc_start: 0.6232 (pt0) cc_final: 0.5995 (pt0) REVERT: F 125 MET cc_start: 0.5995 (ttt) cc_final: 0.5338 (ttt) REVERT: F 126 ASN cc_start: 0.7429 (t0) cc_final: 0.7159 (t0) REVERT: F 160 MET cc_start: 0.4361 (ptt) cc_final: 0.4150 (ptp) REVERT: F 180 GLU cc_start: 0.6345 (mm-30) cc_final: 0.5911 (mt-10) REVERT: F 182 GLU cc_start: 0.7019 (tp30) cc_final: 0.6735 (tp30) REVERT: F 196 ASP cc_start: 0.6129 (m-30) cc_final: 0.5666 (m-30) REVERT: F 221 ARG cc_start: 0.5854 (ttp-170) cc_final: 0.4812 (tpp-160) REVERT: F 328 THR cc_start: 0.7448 (t) cc_final: 0.7159 (m) REVERT: F 358 ARG cc_start: 0.6160 (mtp180) cc_final: 0.5541 (mtm180) REVERT: F 396 GLU cc_start: 0.6033 (mm-30) cc_final: 0.5643 (mm-30) REVERT: F 398 ILE cc_start: 0.6113 (OUTLIER) cc_final: 0.5382 (pt) REVERT: F 399 ARG cc_start: 0.6501 (mtm110) cc_final: 0.6125 (mtp180) REVERT: F 417 GLU cc_start: 0.5727 (tt0) cc_final: 0.5403 (mt-10) REVERT: F 424 ASP cc_start: 0.6897 (t70) cc_final: 0.6666 (t70) REVERT: F 436 ASP cc_start: 0.6608 (m-30) cc_final: 0.6285 (m-30) REVERT: H 4 GLN cc_start: 0.4911 (mp-120) cc_final: 0.4109 (mt0) REVERT: I 4 GLN cc_start: 0.4749 (mp-120) cc_final: 0.4127 (tp40) REVERT: J 5 ARG cc_start: 0.6229 (mtp-110) cc_final: 0.5563 (ttt90) REVERT: J 33 ASN cc_start: 0.6613 (OUTLIER) cc_final: 0.6055 (p0) REVERT: J 35 GLU cc_start: 0.5585 (mm-30) cc_final: 0.5219 (mp0) REVERT: J 42 GLU cc_start: 0.5319 (pm20) cc_final: 0.5060 (pm20) REVERT: J 48 LYS cc_start: 0.6639 (mtpt) cc_final: 0.5889 (mmtm) REVERT: J 57 GLU cc_start: 0.6534 (mt-10) cc_final: 0.6277 (mt-10) REVERT: J 63 GLU cc_start: 0.6250 (pt0) cc_final: 0.5916 (mt-10) REVERT: J 72 ASP cc_start: 0.6723 (t70) cc_final: 0.6485 (t0) REVERT: J 86 ARG cc_start: 0.6035 (mmt90) cc_final: 0.4850 (mmm160) REVERT: J 116 GLU cc_start: 0.6291 (pt0) cc_final: 0.6061 (pt0) REVERT: J 126 ASN cc_start: 0.7258 (t0) cc_final: 0.6853 (t0) REVERT: J 180 GLU cc_start: 0.6352 (mm-30) cc_final: 0.5831 (mt-10) REVERT: J 221 ARG cc_start: 0.5409 (ttp-170) cc_final: 0.4918 (tpp-160) REVERT: J 273 MET cc_start: 0.7157 (mtp) cc_final: 0.6768 (mtp) REVERT: J 278 LYS cc_start: 0.6822 (ttmm) cc_final: 0.6511 (tppp) REVERT: J 313 ASN cc_start: 0.6968 (t0) cc_final: 0.6127 (m-40) REVERT: J 328 THR cc_start: 0.7472 (t) cc_final: 0.7223 (m) REVERT: J 359 GLN cc_start: 0.6629 (mt0) cc_final: 0.6351 (mt0) REVERT: J 391 LYS cc_start: 0.5399 (tptp) cc_final: 0.4703 (ttpt) REVERT: J 396 GLU cc_start: 0.6206 (mm-30) cc_final: 0.5884 (mm-30) REVERT: J 398 ILE cc_start: 0.6367 (OUTLIER) cc_final: 0.5505 (pt) REVERT: J 417 GLU cc_start: 0.5916 (tt0) cc_final: 0.5524 (mt-10) REVERT: J 424 ASP cc_start: 0.6533 (t70) cc_final: 0.6172 (t70) REVERT: J 425 MET cc_start: 0.6975 (mmt) cc_final: 0.6497 (mmp) REVERT: K 2 SER cc_start: 0.6142 (p) cc_final: 0.5895 (p) REVERT: K 5 ARG cc_start: 0.6201 (mtp-110) cc_final: 0.5598 (ttt90) REVERT: K 10 ARG cc_start: 0.6220 (ttp-110) cc_final: 0.5891 (ttp80) REVERT: K 33 ASN cc_start: 0.6689 (OUTLIER) cc_final: 0.6266 (p0) REVERT: K 35 GLU cc_start: 0.5430 (mm-30) cc_final: 0.5173 (mp0) REVERT: K 42 GLU cc_start: 0.5386 (pm20) cc_final: 0.5034 (pm20) REVERT: K 48 LYS cc_start: 0.6383 (mtpt) cc_final: 0.5924 (mttt) REVERT: K 62 ILE cc_start: 0.6721 (tp) cc_final: 0.6365 (pt) REVERT: K 63 GLU cc_start: 0.6148 (pt0) cc_final: 0.5908 (mt-10) REVERT: K 67 MET cc_start: 0.7230 (mtp) cc_final: 0.6731 (mtt) REVERT: K 72 ASP cc_start: 0.6504 (t70) cc_final: 0.6287 (t0) REVERT: K 73 LEU cc_start: 0.6385 (mt) cc_final: 0.6121 (mt) REVERT: K 86 ARG cc_start: 0.5998 (mmt90) cc_final: 0.4843 (mmm160) REVERT: K 115 LYS cc_start: 0.6337 (tptp) cc_final: 0.4777 (mmtm) REVERT: K 126 ASN cc_start: 0.7335 (t0) cc_final: 0.7068 (t0) REVERT: K 180 GLU cc_start: 0.6337 (mm-30) cc_final: 0.5888 (mt-10) REVERT: K 221 ARG cc_start: 0.5704 (tpt-90) cc_final: 0.4937 (tpp-160) REVERT: K 283 MET cc_start: 0.6563 (mtm) cc_final: 0.6255 (mtm) REVERT: K 313 ASN cc_start: 0.6904 (t0) cc_final: 0.6601 (t0) REVERT: K 328 THR cc_start: 0.7543 (OUTLIER) cc_final: 0.7119 (p) REVERT: K 358 ARG cc_start: 0.6403 (mtp180) cc_final: 0.5627 (mtp180) REVERT: K 359 GLN cc_start: 0.6648 (mt0) cc_final: 0.6374 (mt0) REVERT: K 391 LYS cc_start: 0.5336 (tptp) cc_final: 0.4633 (ttpt) REVERT: K 398 ILE cc_start: 0.6142 (OUTLIER) cc_final: 0.5366 (pt) REVERT: K 399 ARG cc_start: 0.6367 (mtm110) cc_final: 0.6079 (mtp180) REVERT: K 424 ASP cc_start: 0.6722 (t70) cc_final: 0.6481 (t70) REVERT: K 425 MET cc_start: 0.6994 (mmt) cc_final: 0.6583 (mmp) REVERT: L 5 ARG cc_start: 0.6069 (mtp-110) cc_final: 0.5640 (ttp80) REVERT: L 10 ARG cc_start: 0.6132 (ttp-110) cc_final: 0.5675 (ttp-110) REVERT: L 33 ASN cc_start: 0.6625 (OUTLIER) cc_final: 0.6087 (p0) REVERT: L 35 GLU cc_start: 0.5389 (mm-30) cc_final: 0.5084 (mp0) REVERT: L 50 MET cc_start: 0.5135 (ptp) cc_final: 0.4370 (ttp) REVERT: L 57 GLU cc_start: 0.6457 (mt-10) cc_final: 0.5963 (mp0) REVERT: L 62 ILE cc_start: 0.6441 (tp) cc_final: 0.6136 (pp) REVERT: L 63 GLU cc_start: 0.6571 (pt0) cc_final: 0.5894 (mt-10) REVERT: L 67 MET cc_start: 0.7039 (mtt) cc_final: 0.6443 (mtt) REVERT: L 86 ARG cc_start: 0.5705 (mmt90) cc_final: 0.4616 (mmm160) REVERT: L 93 ASP cc_start: 0.6172 (m-30) cc_final: 0.5933 (m-30) REVERT: L 115 LYS cc_start: 0.6101 (tptp) cc_final: 0.4481 (mmtm) REVERT: L 116 GLU cc_start: 0.6234 (pt0) cc_final: 0.5994 (pt0) REVERT: L 125 MET cc_start: 0.5997 (ttt) cc_final: 0.5343 (ttt) REVERT: L 126 ASN cc_start: 0.7430 (t0) cc_final: 0.7078 (t0) REVERT: L 180 GLU cc_start: 0.6345 (mm-30) cc_final: 0.5913 (mt-10) REVERT: L 182 GLU cc_start: 0.7015 (tp30) cc_final: 0.6728 (tp30) REVERT: L 196 ASP cc_start: 0.6147 (m-30) cc_final: 0.5667 (m-30) REVERT: L 221 ARG cc_start: 0.5853 (ttp-170) cc_final: 0.4817 (tpp-160) REVERT: L 328 THR cc_start: 0.7459 (t) cc_final: 0.7169 (m) REVERT: L 358 ARG cc_start: 0.6161 (mtp180) cc_final: 0.5555 (mtm180) REVERT: L 391 LYS cc_start: 0.5481 (tptp) cc_final: 0.4734 (ttpp) REVERT: L 396 GLU cc_start: 0.6018 (mm-30) cc_final: 0.5638 (mm-30) REVERT: L 398 ILE cc_start: 0.6108 (OUTLIER) cc_final: 0.5378 (pt) REVERT: L 399 ARG cc_start: 0.6478 (mtm110) cc_final: 0.6116 (mtp180) REVERT: L 417 GLU cc_start: 0.5660 (tt0) cc_final: 0.5337 (mt-10) REVERT: L 424 ASP cc_start: 0.6923 (t70) cc_final: 0.6689 (t70) REVERT: L 436 ASP cc_start: 0.6549 (m-30) cc_final: 0.6222 (m-30) REVERT: M 4 GLN cc_start: 0.4874 (mp-120) cc_final: 0.4522 (mm110) REVERT: N 4 GLN cc_start: 0.4700 (mp-120) cc_final: 0.4217 (tp40) REVERT: O 4 GLN cc_start: 0.4737 (mp10) cc_final: 0.4086 (tp-100) REVERT: P 4 GLN cc_start: 0.4718 (mm-40) cc_final: 0.4132 (mt0) REVERT: Q 2 SER cc_start: 0.6002 (p) cc_final: 0.5749 (p) REVERT: Q 5 ARG cc_start: 0.6150 (mtp-110) cc_final: 0.5522 (ttt90) REVERT: Q 10 ARG cc_start: 0.6162 (ttp-110) cc_final: 0.5855 (ttp80) REVERT: Q 33 ASN cc_start: 0.6707 (OUTLIER) cc_final: 0.6302 (p0) REVERT: Q 42 GLU cc_start: 0.5331 (pm20) cc_final: 0.4992 (pm20) REVERT: Q 48 LYS cc_start: 0.6356 (mtpt) cc_final: 0.5898 (mttt) REVERT: Q 62 ILE cc_start: 0.6691 (tp) cc_final: 0.6349 (pt) REVERT: Q 63 GLU cc_start: 0.6184 (pt0) cc_final: 0.5839 (mt-10) REVERT: Q 67 MET cc_start: 0.7223 (mtp) cc_final: 0.6784 (mtt) REVERT: Q 72 ASP cc_start: 0.6411 (t70) cc_final: 0.6167 (t0) REVERT: Q 73 LEU cc_start: 0.6383 (mt) cc_final: 0.6103 (mt) REVERT: Q 86 ARG cc_start: 0.5996 (mmt90) cc_final: 0.4824 (mmm160) REVERT: Q 115 LYS cc_start: 0.6282 (tptp) cc_final: 0.4721 (mmtm) REVERT: Q 126 ASN cc_start: 0.7319 (t0) cc_final: 0.7056 (t0) REVERT: Q 180 GLU cc_start: 0.6370 (mm-30) cc_final: 0.5979 (mt-10) REVERT: Q 221 ARG cc_start: 0.6091 (ttp-170) cc_final: 0.4982 (tpp-160) REVERT: Q 283 MET cc_start: 0.6556 (mtm) cc_final: 0.6214 (mtm) REVERT: Q 313 ASN cc_start: 0.6862 (t0) cc_final: 0.6561 (t0) REVERT: Q 328 THR cc_start: 0.7562 (OUTLIER) cc_final: 0.7113 (p) REVERT: Q 358 ARG cc_start: 0.5771 (mtp180) cc_final: 0.5451 (mtm180) REVERT: Q 359 GLN cc_start: 0.6573 (mt0) cc_final: 0.6365 (mt0) REVERT: Q 391 LYS cc_start: 0.5362 (tptp) cc_final: 0.4636 (ttpt) REVERT: Q 398 ILE cc_start: 0.6115 (OUTLIER) cc_final: 0.5344 (pt) REVERT: Q 399 ARG cc_start: 0.6387 (mtm110) cc_final: 0.6021 (mtp-110) REVERT: Q 424 ASP cc_start: 0.6730 (t70) cc_final: 0.6506 (t70) REVERT: R 5 ARG cc_start: 0.6061 (mtp-110) cc_final: 0.5502 (ttt90) REVERT: R 10 ARG cc_start: 0.6123 (ttp-110) cc_final: 0.5666 (ttp-110) REVERT: R 33 ASN cc_start: 0.6633 (OUTLIER) cc_final: 0.6094 (p0) REVERT: R 35 GLU cc_start: 0.5366 (mm-30) cc_final: 0.5065 (mp0) REVERT: R 50 MET cc_start: 0.5153 (ptp) cc_final: 0.4385 (ttp) REVERT: R 57 GLU cc_start: 0.6556 (mt-10) cc_final: 0.6114 (mp0) REVERT: R 62 ILE cc_start: 0.6407 (tp) cc_final: 0.6070 (pp) REVERT: R 63 GLU cc_start: 0.6530 (pt0) cc_final: 0.5882 (mt-10) REVERT: R 67 MET cc_start: 0.7041 (mtt) cc_final: 0.6491 (mtt) REVERT: R 86 ARG cc_start: 0.5714 (mmt90) cc_final: 0.4628 (mmm160) REVERT: R 93 ASP cc_start: 0.6214 (m-30) cc_final: 0.5985 (m-30) REVERT: R 115 LYS cc_start: 0.6093 (tptp) cc_final: 0.4474 (mmtm) REVERT: R 116 GLU cc_start: 0.6217 (pt0) cc_final: 0.5986 (pt0) REVERT: R 125 MET cc_start: 0.5956 (ttt) cc_final: 0.5272 (ttt) REVERT: R 180 GLU cc_start: 0.6349 (mm-30) cc_final: 0.5918 (mt-10) REVERT: R 182 GLU cc_start: 0.7032 (tp30) cc_final: 0.6741 (tp30) REVERT: R 196 ASP cc_start: 0.6076 (m-30) cc_final: 0.5600 (m-30) REVERT: R 221 ARG cc_start: 0.5842 (ttp-170) cc_final: 0.4820 (tpp-160) REVERT: R 328 THR cc_start: 0.7446 (t) cc_final: 0.7155 (m) REVERT: R 358 ARG cc_start: 0.6174 (mtp180) cc_final: 0.5656 (mtm180) REVERT: R 396 GLU cc_start: 0.6019 (mm-30) cc_final: 0.5626 (mm-30) REVERT: R 398 ILE cc_start: 0.6109 (OUTLIER) cc_final: 0.5377 (pt) REVERT: R 399 ARG cc_start: 0.6500 (mtm110) cc_final: 0.6124 (mtp180) REVERT: R 417 GLU cc_start: 0.5723 (tt0) cc_final: 0.5400 (mt-10) REVERT: R 424 ASP cc_start: 0.6906 (t70) cc_final: 0.6674 (t70) REVERT: R 436 ASP cc_start: 0.6612 (m-30) cc_final: 0.6289 (m-30) REVERT: S 5 ARG cc_start: 0.6274 (mtp-110) cc_final: 0.5638 (ttm-80) REVERT: S 7 ASP cc_start: 0.5542 (m-30) cc_final: 0.5314 (m-30) REVERT: S 33 ASN cc_start: 0.6565 (OUTLIER) cc_final: 0.6056 (p0) REVERT: S 35 GLU cc_start: 0.5472 (mm-30) cc_final: 0.5167 (mp0) REVERT: S 42 GLU cc_start: 0.5330 (pm20) cc_final: 0.4984 (pm20) REVERT: S 48 LYS cc_start: 0.6486 (mtpt) cc_final: 0.5883 (mmtp) REVERT: S 86 ARG cc_start: 0.5963 (mmt90) cc_final: 0.4764 (mmm160) REVERT: S 115 LYS cc_start: 0.6259 (tptp) cc_final: 0.4574 (mmtm) REVERT: S 116 GLU cc_start: 0.6282 (pt0) cc_final: 0.5996 (pt0) REVERT: S 126 ASN cc_start: 0.7263 (t0) cc_final: 0.6872 (t0) REVERT: S 180 GLU cc_start: 0.6215 (mm-30) cc_final: 0.5773 (mt-10) REVERT: S 221 ARG cc_start: 0.5391 (ttp-170) cc_final: 0.4817 (tpp-160) REVERT: S 278 LYS cc_start: 0.6865 (ttmm) cc_final: 0.6534 (tppp) REVERT: S 313 ASN cc_start: 0.7090 (t0) cc_final: 0.6152 (m-40) REVERT: S 328 THR cc_start: 0.7520 (t) cc_final: 0.7308 (m) REVERT: S 359 GLN cc_start: 0.6575 (mt0) cc_final: 0.6290 (mt0) REVERT: S 391 LYS cc_start: 0.5362 (tptp) cc_final: 0.4671 (ttpt) REVERT: S 396 GLU cc_start: 0.6177 (mm-30) cc_final: 0.5865 (mm-30) REVERT: S 398 ILE cc_start: 0.6272 (OUTLIER) cc_final: 0.5401 (pt) REVERT: S 417 GLU cc_start: 0.5759 (tt0) cc_final: 0.5316 (mt-10) REVERT: S 420 GLU cc_start: 0.5821 (tm-30) cc_final: 0.5416 (tp30) REVERT: S 424 ASP cc_start: 0.6583 (t70) cc_final: 0.6284 (t70) REVERT: T 5 ARG cc_start: 0.6075 (mtp-110) cc_final: 0.5522 (ttt90) REVERT: T 10 ARG cc_start: 0.6154 (ttp-110) cc_final: 0.5696 (ttp-110) REVERT: T 33 ASN cc_start: 0.6644 (OUTLIER) cc_final: 0.6107 (p0) REVERT: T 35 GLU cc_start: 0.5383 (mm-30) cc_final: 0.5078 (mp0) REVERT: T 48 LYS cc_start: 0.6452 (mtpt) cc_final: 0.5690 (mmtm) REVERT: T 50 MET cc_start: 0.5129 (ptp) cc_final: 0.4375 (tpp) REVERT: T 57 GLU cc_start: 0.6405 (mt-10) cc_final: 0.5930 (mp0) REVERT: T 62 ILE cc_start: 0.6384 (tp) cc_final: 0.6042 (pp) REVERT: T 63 GLU cc_start: 0.6484 (pt0) cc_final: 0.5770 (mt-10) REVERT: T 67 MET cc_start: 0.7050 (mtt) cc_final: 0.6410 (mtt) REVERT: T 86 ARG cc_start: 0.5718 (mmt90) cc_final: 0.4633 (mmm160) REVERT: T 93 ASP cc_start: 0.6132 (m-30) cc_final: 0.5893 (m-30) REVERT: T 115 LYS cc_start: 0.5984 (tptp) cc_final: 0.4370 (mmtm) REVERT: T 116 GLU cc_start: 0.6243 (pt0) cc_final: 0.6004 (pt0) REVERT: T 125 MET cc_start: 0.6001 (ttt) cc_final: 0.5353 (ttt) REVERT: T 180 GLU cc_start: 0.6345 (mm-30) cc_final: 0.5913 (mt-10) REVERT: T 182 GLU cc_start: 0.7017 (tp30) cc_final: 0.6728 (tp30) REVERT: T 196 ASP cc_start: 0.6127 (m-30) cc_final: 0.5682 (m-30) REVERT: T 221 ARG cc_start: 0.5850 (ttp-170) cc_final: 0.4810 (tpp-160) REVERT: T 328 THR cc_start: 0.7465 (t) cc_final: 0.7179 (m) REVERT: T 358 ARG cc_start: 0.6164 (mtp180) cc_final: 0.5560 (mtm180) REVERT: T 391 LYS cc_start: 0.5478 (tptp) cc_final: 0.4731 (ttpp) REVERT: T 396 GLU cc_start: 0.6030 (mm-30) cc_final: 0.5651 (mm-30) REVERT: T 398 ILE cc_start: 0.6121 (OUTLIER) cc_final: 0.5386 (pt) REVERT: T 399 ARG cc_start: 0.6484 (mtm110) cc_final: 0.6122 (mtp180) REVERT: T 417 GLU cc_start: 0.5725 (tt0) cc_final: 0.5402 (mt-10) REVERT: T 424 ASP cc_start: 0.6918 (t70) cc_final: 0.6689 (t70) REVERT: T 436 ASP cc_start: 0.6614 (m-30) cc_final: 0.6288 (m-30) REVERT: U 4 GLN cc_start: 0.4535 (OUTLIER) cc_final: 0.3947 (mt0) REVERT: V 4 GLN cc_start: 0.4902 (mp-120) cc_final: 0.4078 (tp40) REVERT: W 5 ARG cc_start: 0.6221 (mtp-110) cc_final: 0.5553 (ttt90) REVERT: W 33 ASN cc_start: 0.6614 (OUTLIER) cc_final: 0.6059 (p0) REVERT: W 35 GLU cc_start: 0.5578 (mm-30) cc_final: 0.5212 (mp0) REVERT: W 42 GLU cc_start: 0.5298 (pm20) cc_final: 0.5040 (pm20) REVERT: W 48 LYS cc_start: 0.6648 (mtpt) cc_final: 0.6032 (mmtp) REVERT: W 63 GLU cc_start: 0.6207 (pt0) cc_final: 0.5923 (mt-10) REVERT: W 72 ASP cc_start: 0.6720 (t70) cc_final: 0.6481 (t0) REVERT: W 86 ARG cc_start: 0.6035 (mmt90) cc_final: 0.4843 (mmm160) REVERT: W 116 GLU cc_start: 0.6288 (pt0) cc_final: 0.6046 (pt0) REVERT: W 126 ASN cc_start: 0.7247 (t0) cc_final: 0.6844 (t0) REVERT: W 180 GLU cc_start: 0.6348 (mm-30) cc_final: 0.5831 (mt-10) REVERT: W 221 ARG cc_start: 0.5395 (ttp-170) cc_final: 0.4930 (tpp-160) REVERT: W 273 MET cc_start: 0.7146 (mtp) cc_final: 0.6752 (mtp) REVERT: W 278 LYS cc_start: 0.6790 (ttmm) cc_final: 0.6478 (tppp) REVERT: W 313 ASN cc_start: 0.6966 (t0) cc_final: 0.6114 (m-40) REVERT: W 328 THR cc_start: 0.7470 (t) cc_final: 0.7219 (m) REVERT: W 359 GLN cc_start: 0.6614 (mt0) cc_final: 0.6324 (mt0) REVERT: W 391 LYS cc_start: 0.5401 (tptp) cc_final: 0.4708 (ttpt) REVERT: W 396 GLU cc_start: 0.6202 (mm-30) cc_final: 0.5883 (mm-30) REVERT: W 398 ILE cc_start: 0.6332 (OUTLIER) cc_final: 0.5458 (pt) REVERT: W 417 GLU cc_start: 0.5895 (tt0) cc_final: 0.5504 (mt-10) REVERT: W 424 ASP cc_start: 0.6521 (t70) cc_final: 0.6178 (t70) REVERT: W 425 MET cc_start: 0.6956 (mmt) cc_final: 0.6477 (mmp) REVERT: X 2 SER cc_start: 0.6164 (p) cc_final: 0.5913 (p) REVERT: X 5 ARG cc_start: 0.6112 (mtp-110) cc_final: 0.5516 (ttt90) REVERT: X 10 ARG cc_start: 0.6194 (ttp-110) cc_final: 0.5861 (ttp80) REVERT: X 33 ASN cc_start: 0.6730 (OUTLIER) cc_final: 0.6331 (p0) REVERT: X 35 GLU cc_start: 0.5392 (mm-30) cc_final: 0.4941 (mp0) REVERT: X 42 GLU cc_start: 0.5269 (pm20) cc_final: 0.4923 (pm20) REVERT: X 48 LYS cc_start: 0.6318 (mtpt) cc_final: 0.5868 (mttt) REVERT: X 62 ILE cc_start: 0.6710 (tp) cc_final: 0.6369 (pt) REVERT: X 67 MET cc_start: 0.7057 (mtp) cc_final: 0.6627 (mtt) REVERT: X 86 ARG cc_start: 0.6009 (mmt90) cc_final: 0.4828 (mmm160) REVERT: X 115 LYS cc_start: 0.6278 (tptp) cc_final: 0.4730 (mmtm) REVERT: X 116 GLU cc_start: 0.6239 (pt0) cc_final: 0.5991 (pt0) REVERT: X 126 ASN cc_start: 0.7320 (t0) cc_final: 0.7019 (t0) REVERT: X 180 GLU cc_start: 0.6340 (mm-30) cc_final: 0.5899 (mt-10) REVERT: X 221 ARG cc_start: 0.5461 (ttp-170) cc_final: 0.4836 (tpm170) REVERT: X 283 MET cc_start: 0.6562 (mtm) cc_final: 0.6182 (mtm) REVERT: X 313 ASN cc_start: 0.7038 (t0) cc_final: 0.6733 (t0) REVERT: X 328 THR cc_start: 0.7492 (t) cc_final: 0.7286 (m) REVERT: X 357 LYS cc_start: 0.6763 (mtmp) cc_final: 0.6506 (mtpp) REVERT: X 358 ARG cc_start: 0.6468 (mtp180) cc_final: 0.5709 (mtm180) REVERT: X 373 MET cc_start: 0.6826 (ptm) cc_final: 0.6607 (ptm) REVERT: X 391 LYS cc_start: 0.5274 (tptp) cc_final: 0.4572 (ttpt) REVERT: X 398 ILE cc_start: 0.6108 (OUTLIER) cc_final: 0.5333 (pt) REVERT: X 399 ARG cc_start: 0.6448 (mtm110) cc_final: 0.6171 (mtp180) REVERT: X 424 ASP cc_start: 0.6699 (t70) cc_final: 0.6472 (t70) outliers start: 95 outliers final: 20 residues processed: 1075 average time/residue: 0.9608 time to fit residues: 1206.9957 Evaluate side-chains 837 residues out of total 4668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 788 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain J residue 33 ASN Chi-restraints excluded: chain J residue 334 ASN Chi-restraints excluded: chain J residue 398 ILE Chi-restraints excluded: chain J residue 403 ILE Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 328 THR Chi-restraints excluded: chain K residue 334 ASN Chi-restraints excluded: chain K residue 398 ILE Chi-restraints excluded: chain K residue 403 ILE Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 237 VAL Chi-restraints excluded: chain L residue 398 ILE Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain Q residue 33 ASN Chi-restraints excluded: chain Q residue 328 THR Chi-restraints excluded: chain Q residue 398 ILE Chi-restraints excluded: chain Q residue 403 ILE Chi-restraints excluded: chain R residue 33 ASN Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 398 ILE Chi-restraints excluded: chain S residue 33 ASN Chi-restraints excluded: chain S residue 65 SER Chi-restraints excluded: chain S residue 398 ILE Chi-restraints excluded: chain S residue 403 ILE Chi-restraints excluded: chain T residue 33 ASN Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 398 ILE Chi-restraints excluded: chain U residue 4 GLN Chi-restraints excluded: chain W residue 33 ASN Chi-restraints excluded: chain W residue 334 ASN Chi-restraints excluded: chain W residue 398 ILE Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain X residue 33 ASN Chi-restraints excluded: chain X residue 398 ILE Chi-restraints excluded: chain X residue 403 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 394 optimal weight: 9.9990 chunk 430 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 265 optimal weight: 7.9990 chunk 523 optimal weight: 5.9990 chunk 497 optimal weight: 7.9990 chunk 414 optimal weight: 8.9990 chunk 310 optimal weight: 8.9990 chunk 488 optimal weight: 0.3980 chunk 366 optimal weight: 0.8980 chunk 223 optimal weight: 0.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 GLN F 223 HIS J 23 GLN ** J 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 210 GLN L 223 HIS P 4 GLN R 210 GLN R 223 HIS S 23 GLN S 165 ASN T 210 GLN T 223 HIS W 23 GLN ** W 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.186172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.168657 restraints weight = 34443.305| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 0.82 r_work: 0.3749 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3658 rms_B_bonded: 2.18 restraints_weight: 0.2500 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3657 r_free = 0.3657 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3657 r_free = 0.3657 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 43464 Z= 0.194 Angle : 0.635 5.608 58968 Z= 0.343 Chirality : 0.045 0.149 6456 Planarity : 0.006 0.056 7716 Dihedral : 6.276 55.958 6068 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.39 % Allowed : 16.37 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.11), residues: 5364 helix: 1.06 (0.11), residues: 2196 sheet: -1.43 (0.17), residues: 756 loop : -0.41 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 167 TYR 0.028 0.003 TYR S 294 PHE 0.020 0.002 PHE X 197 TRP 0.015 0.002 TRP S 423 HIS 0.008 0.002 HIS F 193 Details of bonding type rmsd covalent geometry : bond 0.00427 (43464) covalent geometry : angle 0.63519 (58968) hydrogen bonds : bond 0.06100 ( 1642) hydrogen bonds : angle 5.18958 ( 4668) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1001 residues out of total 4668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 808 time to evaluate : 1.534 Fit side-chains REVERT: A 4 GLN cc_start: 0.6351 (mp10) cc_final: 0.6015 (mt0) REVERT: B 5 ARG cc_start: 0.7284 (mtp-110) cc_final: 0.7013 (ttt180) REVERT: B 15 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7269 (mm-30) REVERT: B 86 ARG cc_start: 0.7438 (mmt90) cc_final: 0.6988 (mmm160) REVERT: B 126 ASN cc_start: 0.8509 (t0) cc_final: 0.8291 (t0) REVERT: B 222 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7606 (mt0) REVERT: B 391 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8150 (ttmt) REVERT: B 420 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7507 (mm-30) REVERT: C 4 GLN cc_start: 0.6199 (mp-120) cc_final: 0.5993 (tp40) REVERT: E 62 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7977 (pt) REVERT: E 86 ARG cc_start: 0.7495 (mmt90) cc_final: 0.7065 (mmm160) REVERT: E 96 LYS cc_start: 0.7959 (mttm) cc_final: 0.7722 (mmmt) REVERT: E 115 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7027 (mmtm) REVERT: E 116 GLU cc_start: 0.7125 (pt0) cc_final: 0.6871 (pt0) REVERT: E 126 ASN cc_start: 0.8609 (t0) cc_final: 0.8407 (t0) REVERT: E 221 ARG cc_start: 0.8249 (ttp-170) cc_final: 0.7759 (tpp-160) REVERT: E 358 ARG cc_start: 0.7558 (mtp180) cc_final: 0.7214 (mtm180) REVERT: E 425 MET cc_start: 0.8936 (mmt) cc_final: 0.8729 (mmp) REVERT: F 48 LYS cc_start: 0.7955 (mtpt) cc_final: 0.7709 (mttp) REVERT: F 86 ARG cc_start: 0.7505 (mmt90) cc_final: 0.7081 (mmm160) REVERT: F 93 ASP cc_start: 0.7474 (m-30) cc_final: 0.7269 (m-30) REVERT: F 96 LYS cc_start: 0.7986 (mttm) cc_final: 0.7701 (mmmt) REVERT: F 115 LYS cc_start: 0.7778 (tptp) cc_final: 0.6872 (mmtm) REVERT: F 116 GLU cc_start: 0.7276 (pt0) cc_final: 0.6998 (pt0) REVERT: F 221 ARG cc_start: 0.8024 (ttp-170) cc_final: 0.7505 (tpp-160) REVERT: F 350 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7741 (tpt90) REVERT: F 358 ARG cc_start: 0.7465 (mtp180) cc_final: 0.7117 (mtm180) REVERT: G 4 GLN cc_start: 0.6258 (mm110) cc_final: 0.5934 (mt0) REVERT: H 4 GLN cc_start: 0.6371 (mp-120) cc_final: 0.5980 (mt0) REVERT: I 4 GLN cc_start: 0.6350 (mp-120) cc_final: 0.5876 (mt0) REVERT: J 5 ARG cc_start: 0.7270 (mtp-110) cc_final: 0.7017 (ttt180) REVERT: J 42 GLU cc_start: 0.7376 (pm20) cc_final: 0.7171 (pm20) REVERT: J 86 ARG cc_start: 0.7423 (mmt90) cc_final: 0.6975 (mmm160) REVERT: J 126 ASN cc_start: 0.8506 (t0) cc_final: 0.8286 (t0) REVERT: J 222 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7606 (mt0) REVERT: J 391 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8135 (ttmt) REVERT: J 420 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7493 (mm-30) REVERT: K 5 ARG cc_start: 0.7096 (mtp-110) cc_final: 0.6893 (ttp80) REVERT: K 62 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7981 (pt) REVERT: K 86 ARG cc_start: 0.7498 (mmt90) cc_final: 0.7063 (mmm160) REVERT: K 115 LYS cc_start: 0.7885 (tptp) cc_final: 0.7033 (mmtm) REVERT: K 116 GLU cc_start: 0.7116 (pt0) cc_final: 0.6845 (pt0) REVERT: K 126 ASN cc_start: 0.8616 (t0) cc_final: 0.8414 (t0) REVERT: K 221 ARG cc_start: 0.8083 (tpt-90) cc_final: 0.7805 (tpp-160) REVERT: K 358 ARG cc_start: 0.7541 (mtp180) cc_final: 0.7171 (mtm180) REVERT: K 373 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.6264 (ptm) REVERT: K 379 ILE cc_start: 0.6676 (OUTLIER) cc_final: 0.6214 (mt) REVERT: L 48 LYS cc_start: 0.7960 (mtpt) cc_final: 0.7720 (mttp) REVERT: L 86 ARG cc_start: 0.7488 (mmt90) cc_final: 0.7064 (mmm160) REVERT: L 96 LYS cc_start: 0.7982 (mttm) cc_final: 0.7692 (mmmt) REVERT: L 115 LYS cc_start: 0.7808 (tptp) cc_final: 0.6888 (mmtm) REVERT: L 221 ARG cc_start: 0.8032 (ttp-170) cc_final: 0.7516 (tpp-160) REVERT: L 358 ARG cc_start: 0.7443 (mtp180) cc_final: 0.7088 (mtm180) REVERT: M 4 GLN cc_start: 0.6163 (mp-120) cc_final: 0.5921 (tp40) REVERT: O 4 GLN cc_start: 0.6313 (mp10) cc_final: 0.5915 (mt0) REVERT: P 4 GLN cc_start: 0.6453 (mm110) cc_final: 0.6190 (mt0) REVERT: Q 35 GLU cc_start: 0.7357 (mp0) cc_final: 0.7154 (mp0) REVERT: Q 62 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7986 (pt) REVERT: Q 86 ARG cc_start: 0.7477 (mmt90) cc_final: 0.7047 (mmm160) REVERT: Q 96 LYS cc_start: 0.7966 (mttm) cc_final: 0.7728 (mmmt) REVERT: Q 115 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7040 (mmtm) REVERT: Q 116 GLU cc_start: 0.7094 (pt0) cc_final: 0.6836 (pt0) REVERT: Q 126 ASN cc_start: 0.8609 (t0) cc_final: 0.8409 (t0) REVERT: Q 221 ARG cc_start: 0.8270 (ttp-170) cc_final: 0.7785 (tpp-160) REVERT: Q 358 ARG cc_start: 0.7416 (mtp180) cc_final: 0.7085 (mtm180) REVERT: Q 425 MET cc_start: 0.8934 (mmt) cc_final: 0.8728 (mmp) REVERT: R 5 ARG cc_start: 0.7044 (mtp-110) cc_final: 0.6838 (ttt90) REVERT: R 48 LYS cc_start: 0.7962 (mtpt) cc_final: 0.7722 (mttp) REVERT: R 86 ARG cc_start: 0.7486 (mmt90) cc_final: 0.7070 (mmm160) REVERT: R 93 ASP cc_start: 0.7469 (m-30) cc_final: 0.7188 (m-30) REVERT: R 96 LYS cc_start: 0.7995 (mttm) cc_final: 0.7717 (mmmt) REVERT: R 115 LYS cc_start: 0.7796 (tptp) cc_final: 0.6899 (mmtm) REVERT: R 116 GLU cc_start: 0.7267 (pt0) cc_final: 0.6990 (pt0) REVERT: R 221 ARG cc_start: 0.8026 (ttp-170) cc_final: 0.7505 (tpp-160) REVERT: R 350 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7737 (tpt90) REVERT: R 358 ARG cc_start: 0.7435 (mtp180) cc_final: 0.7085 (mtm180) REVERT: S 48 LYS cc_start: 0.8118 (mtpt) cc_final: 0.7831 (mttp) REVERT: S 86 ARG cc_start: 0.7435 (mmt90) cc_final: 0.6972 (mmm160) REVERT: S 126 ASN cc_start: 0.8490 (t0) cc_final: 0.8260 (t0) REVERT: S 165 ASN cc_start: 0.6349 (t160) cc_final: 0.6055 (t0) REVERT: S 273 MET cc_start: 0.8624 (mtp) cc_final: 0.7892 (mtp) REVERT: S 391 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8130 (ttmt) REVERT: S 417 GLU cc_start: 0.8198 (tt0) cc_final: 0.7979 (mt-10) REVERT: S 420 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7585 (tp30) REVERT: T 48 LYS cc_start: 0.7956 (mtpt) cc_final: 0.7716 (mttp) REVERT: T 49 MET cc_start: 0.8200 (mmm) cc_final: 0.7971 (mmm) REVERT: T 86 ARG cc_start: 0.7504 (mmt90) cc_final: 0.7090 (mmm160) REVERT: T 96 LYS cc_start: 0.7984 (mttm) cc_final: 0.7697 (mmmt) REVERT: T 115 LYS cc_start: 0.7784 (tptp) cc_final: 0.6865 (mmtm) REVERT: T 221 ARG cc_start: 0.8044 (ttp-170) cc_final: 0.7530 (tpp-160) REVERT: T 358 ARG cc_start: 0.7466 (mtp180) cc_final: 0.7107 (mtm180) REVERT: U 4 GLN cc_start: 0.6282 (mm110) cc_final: 0.5789 (mt0) REVERT: V 4 GLN cc_start: 0.6449 (mp-120) cc_final: 0.6134 (mt0) REVERT: W 5 ARG cc_start: 0.7271 (mtp-110) cc_final: 0.7013 (ttt180) REVERT: W 42 GLU cc_start: 0.7371 (pm20) cc_final: 0.7158 (pm20) REVERT: W 86 ARG cc_start: 0.7419 (mmt90) cc_final: 0.6982 (mmm160) REVERT: W 126 ASN cc_start: 0.8507 (t0) cc_final: 0.8287 (t0) REVERT: W 222 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7618 (mt0) REVERT: W 391 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8141 (ttmt) REVERT: W 420 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7522 (mm-30) REVERT: W 425 MET cc_start: 0.8861 (mmt) cc_final: 0.8647 (mmp) REVERT: X 15 GLU cc_start: 0.7279 (mm-30) cc_final: 0.7070 (mm-30) REVERT: X 62 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7962 (pt) REVERT: X 86 ARG cc_start: 0.7496 (mmt90) cc_final: 0.7077 (mmm160) REVERT: X 115 LYS cc_start: 0.7899 (tptp) cc_final: 0.7082 (mmtm) REVERT: X 126 ASN cc_start: 0.8628 (t0) cc_final: 0.8420 (t0) REVERT: X 221 ARG cc_start: 0.8113 (ttp-170) cc_final: 0.7818 (tpp-160) REVERT: X 317 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7203 (tpt) REVERT: X 358 ARG cc_start: 0.7547 (mtp180) cc_final: 0.7120 (mtm180) REVERT: X 360 MET cc_start: 0.8727 (mtt) cc_final: 0.8506 (mtt) REVERT: X 425 MET cc_start: 0.8944 (mmt) cc_final: 0.8739 (mmp) outliers start: 193 outliers final: 70 residues processed: 892 average time/residue: 0.9037 time to fit residues: 950.8599 Evaluate side-chains 851 residues out of total 4668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 759 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 222 GLN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 317 MET Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 373 MET Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain F residue 2 SER Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 350 ARG Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 160 MET Chi-restraints excluded: chain J residue 222 GLN Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 391 LYS Chi-restraints excluded: chain J residue 398 ILE Chi-restraints excluded: chain J residue 403 ILE Chi-restraints excluded: chain J residue 420 GLU Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 328 THR Chi-restraints excluded: chain K residue 373 MET Chi-restraints excluded: chain K residue 379 ILE Chi-restraints excluded: chain K residue 398 ILE Chi-restraints excluded: chain K residue 403 ILE Chi-restraints excluded: chain L residue 2 SER Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 237 VAL Chi-restraints excluded: chain L residue 326 LEU Chi-restraints excluded: chain L residue 403 ILE Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 115 LYS Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain Q residue 328 THR Chi-restraints excluded: chain Q residue 373 MET Chi-restraints excluded: chain Q residue 398 ILE Chi-restraints excluded: chain Q residue 403 ILE Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 350 ARG Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain S residue 2 SER Chi-restraints excluded: chain S residue 15 GLU Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 65 SER Chi-restraints excluded: chain S residue 160 MET Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain S residue 317 MET Chi-restraints excluded: chain S residue 391 LYS Chi-restraints excluded: chain S residue 398 ILE Chi-restraints excluded: chain S residue 403 ILE Chi-restraints excluded: chain S residue 420 GLU Chi-restraints excluded: chain T residue 2 SER Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 326 LEU Chi-restraints excluded: chain T residue 403 ILE Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 222 GLN Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 391 LYS Chi-restraints excluded: chain W residue 398 ILE Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain W residue 420 GLU Chi-restraints excluded: chain X residue 36 ILE Chi-restraints excluded: chain X residue 62 ILE Chi-restraints excluded: chain X residue 237 VAL Chi-restraints excluded: chain X residue 317 MET Chi-restraints excluded: chain X residue 326 LEU Chi-restraints excluded: chain X residue 398 ILE Chi-restraints excluded: chain X residue 403 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 451 optimal weight: 9.9990 chunk 184 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 406 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 492 optimal weight: 0.9980 chunk 491 optimal weight: 4.9990 chunk 479 optimal weight: 1.9990 chunk 124 optimal weight: 0.0060 chunk 296 optimal weight: 10.0000 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN E 33 ASN ** E 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN F 126 ASN ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 ASN ** J 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 313 ASN ** K 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 ASN L 126 ASN Q 33 ASN R 33 ASN R 126 ASN S 33 ASN S 313 ASN T 33 ASN W 33 ASN ** W 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 313 ASN X 33 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.186398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.169932 restraints weight = 34627.611| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 0.76 r_work: 0.3768 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3679 r_free = 0.3679 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3679 r_free = 0.3679 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 43464 Z= 0.134 Angle : 0.522 5.241 58968 Z= 0.280 Chirality : 0.041 0.140 6456 Planarity : 0.005 0.047 7716 Dihedral : 5.601 56.580 6016 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.60 % Allowed : 16.60 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.11), residues: 5364 helix: 1.26 (0.11), residues: 2196 sheet: -1.11 (0.16), residues: 876 loop : -0.30 (0.13), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 10 TYR 0.025 0.002 TYR S 294 PHE 0.013 0.001 PHE B 179 TRP 0.013 0.002 TRP W 423 HIS 0.005 0.001 HIS S 193 Details of bonding type rmsd covalent geometry : bond 0.00290 (43464) covalent geometry : angle 0.52237 (58968) hydrogen bonds : bond 0.05101 ( 1642) hydrogen bonds : angle 4.86557 ( 4668) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 947 residues out of total 4668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 789 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 GLN cc_start: 0.6442 (mp10) cc_final: 0.6112 (mt0) REVERT: B 5 ARG cc_start: 0.7261 (mtp-110) cc_final: 0.6991 (ttt180) REVERT: B 86 ARG cc_start: 0.7440 (mmt90) cc_final: 0.6967 (mmm160) REVERT: B 126 ASN cc_start: 0.8462 (t0) cc_final: 0.8219 (t0) REVERT: B 222 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7579 (mt0) REVERT: B 317 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.6866 (tpt) REVERT: B 420 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7407 (mm-30) REVERT: C 4 GLN cc_start: 0.6401 (mp-120) cc_final: 0.6052 (mt0) REVERT: C 6 GLU cc_start: 0.6506 (tp30) cc_final: 0.5846 (mm-30) REVERT: E 62 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7929 (pt) REVERT: E 86 ARG cc_start: 0.7408 (mmt90) cc_final: 0.7040 (mmm160) REVERT: E 96 LYS cc_start: 0.7919 (mttm) cc_final: 0.7680 (mmmt) REVERT: E 115 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7022 (mmtm) REVERT: E 116 GLU cc_start: 0.6929 (pt0) cc_final: 0.6615 (pt0) REVERT: E 221 ARG cc_start: 0.8178 (ttp-170) cc_final: 0.7731 (tpp-160) REVERT: E 317 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.6857 (tpt) REVERT: E 334 ASN cc_start: 0.6761 (m-40) cc_final: 0.6524 (m110) REVERT: E 358 ARG cc_start: 0.7505 (mtp180) cc_final: 0.7137 (mtm180) REVERT: E 391 LYS cc_start: 0.8386 (tptp) cc_final: 0.8184 (ttmt) REVERT: F 86 ARG cc_start: 0.7469 (mmt90) cc_final: 0.7022 (mmm160) REVERT: F 93 ASP cc_start: 0.7404 (m-30) cc_final: 0.7200 (m-30) REVERT: F 96 LYS cc_start: 0.7932 (mttm) cc_final: 0.7668 (mmmt) REVERT: F 115 LYS cc_start: 0.7702 (tptp) cc_final: 0.6878 (mmtm) REVERT: F 160 MET cc_start: 0.6387 (OUTLIER) cc_final: 0.5889 (ptt) REVERT: F 221 ARG cc_start: 0.7953 (ttp-170) cc_final: 0.7497 (tpp-160) REVERT: F 358 ARG cc_start: 0.7425 (mtp180) cc_final: 0.7083 (mtm180) REVERT: F 403 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7492 (pp) REVERT: G 4 GLN cc_start: 0.6254 (mm110) cc_final: 0.5908 (mt0) REVERT: H 4 GLN cc_start: 0.6441 (mp-120) cc_final: 0.6033 (mt0) REVERT: H 6 GLU cc_start: 0.6411 (tp30) cc_final: 0.5953 (mm-30) REVERT: I 4 GLN cc_start: 0.6446 (mp-120) cc_final: 0.5993 (mt0) REVERT: J 5 ARG cc_start: 0.7234 (mtp-110) cc_final: 0.6982 (ttt180) REVERT: J 86 ARG cc_start: 0.7423 (mmt90) cc_final: 0.7023 (mmm160) REVERT: J 126 ASN cc_start: 0.8449 (t0) cc_final: 0.8200 (t0) REVERT: J 222 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7590 (mt0) REVERT: J 317 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.6857 (tpt) REVERT: J 420 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7416 (mm-30) REVERT: K 62 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7935 (pt) REVERT: K 86 ARG cc_start: 0.7427 (mmt90) cc_final: 0.7051 (mmm160) REVERT: K 115 LYS cc_start: 0.7854 (tptp) cc_final: 0.6950 (mmtm) REVERT: K 116 GLU cc_start: 0.6906 (pt0) cc_final: 0.6597 (pt0) REVERT: K 221 ARG cc_start: 0.7956 (tpt-90) cc_final: 0.7605 (tpp-160) REVERT: K 317 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.6888 (tpt) REVERT: K 358 ARG cc_start: 0.7487 (mtp180) cc_final: 0.7127 (mtm180) REVERT: K 373 MET cc_start: 0.7199 (OUTLIER) cc_final: 0.6196 (ptm) REVERT: K 391 LYS cc_start: 0.8388 (tptp) cc_final: 0.8183 (ttmt) REVERT: L 86 ARG cc_start: 0.7472 (mmt90) cc_final: 0.7007 (mmm160) REVERT: L 96 LYS cc_start: 0.7927 (mttm) cc_final: 0.7666 (mmmt) REVERT: L 115 LYS cc_start: 0.7717 (tptp) cc_final: 0.6851 (mmtm) REVERT: L 221 ARG cc_start: 0.7949 (ttp-170) cc_final: 0.7512 (tpp-160) REVERT: L 350 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7726 (tpt90) REVERT: L 358 ARG cc_start: 0.7408 (mtp180) cc_final: 0.7089 (mtm180) REVERT: M 4 GLN cc_start: 0.6410 (mp-120) cc_final: 0.6085 (mt0) REVERT: M 6 GLU cc_start: 0.6401 (tp30) cc_final: 0.5813 (mm-30) REVERT: O 4 GLN cc_start: 0.6451 (mp10) cc_final: 0.6073 (mt0) REVERT: P 4 GLN cc_start: 0.6501 (mm110) cc_final: 0.6197 (mt0) REVERT: Q 62 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7932 (pt) REVERT: Q 86 ARG cc_start: 0.7398 (mmt90) cc_final: 0.7015 (mmm160) REVERT: Q 96 LYS cc_start: 0.7908 (mttm) cc_final: 0.7692 (mmmt) REVERT: Q 115 LYS cc_start: 0.7874 (tptp) cc_final: 0.7021 (mmtm) REVERT: Q 116 GLU cc_start: 0.6918 (pt0) cc_final: 0.6626 (pt0) REVERT: Q 221 ARG cc_start: 0.8160 (ttp-170) cc_final: 0.7702 (tpp-160) REVERT: Q 358 ARG cc_start: 0.7465 (mtp180) cc_final: 0.7129 (mtm180) REVERT: Q 391 LYS cc_start: 0.8392 (tptp) cc_final: 0.8182 (ttmt) REVERT: R 5 ARG cc_start: 0.7012 (mtp-110) cc_final: 0.6791 (ttp80) REVERT: R 86 ARG cc_start: 0.7467 (mmt90) cc_final: 0.7015 (mmm160) REVERT: R 93 ASP cc_start: 0.7420 (m-30) cc_final: 0.7217 (m-30) REVERT: R 96 LYS cc_start: 0.7942 (mttm) cc_final: 0.7682 (mmmt) REVERT: R 115 LYS cc_start: 0.7703 (tptp) cc_final: 0.6873 (mmtm) REVERT: R 221 ARG cc_start: 0.7954 (ttp-170) cc_final: 0.7505 (tpp-160) REVERT: R 358 ARG cc_start: 0.7418 (mtp180) cc_final: 0.7052 (mtm180) REVERT: R 403 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7497 (pp) REVERT: S 86 ARG cc_start: 0.7407 (mmt90) cc_final: 0.7013 (mmm160) REVERT: S 126 ASN cc_start: 0.8452 (t0) cc_final: 0.8195 (t0) REVERT: S 165 ASN cc_start: 0.6372 (t160) cc_final: 0.6040 (t0) REVERT: S 326 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7212 (tp) REVERT: S 417 GLU cc_start: 0.8126 (tt0) cc_final: 0.7910 (mt-10) REVERT: S 420 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7569 (tp30) REVERT: T 86 ARG cc_start: 0.7484 (mmt90) cc_final: 0.7016 (mmm160) REVERT: T 96 LYS cc_start: 0.7927 (mttm) cc_final: 0.7666 (mmmt) REVERT: T 115 LYS cc_start: 0.7681 (tptp) cc_final: 0.6840 (mmtm) REVERT: T 221 ARG cc_start: 0.7961 (ttp-170) cc_final: 0.7526 (tpp-160) REVERT: T 350 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7730 (tpt90) REVERT: T 358 ARG cc_start: 0.7431 (mtp180) cc_final: 0.7110 (mtm180) REVERT: U 4 GLN cc_start: 0.6339 (mm110) cc_final: 0.5896 (mt0) REVERT: V 4 GLN cc_start: 0.6558 (mp-120) cc_final: 0.6129 (mt0) REVERT: W 5 ARG cc_start: 0.7247 (mtp-110) cc_final: 0.6997 (ttt180) REVERT: W 86 ARG cc_start: 0.7407 (mmt90) cc_final: 0.7016 (mmm160) REVERT: W 126 ASN cc_start: 0.8464 (t0) cc_final: 0.8221 (t0) REVERT: W 222 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7597 (mt0) REVERT: W 420 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7436 (mm-30) REVERT: X 62 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7939 (pt) REVERT: X 86 ARG cc_start: 0.7424 (mmt90) cc_final: 0.7010 (mmm160) REVERT: X 115 LYS cc_start: 0.7845 (tptp) cc_final: 0.7028 (mmtm) REVERT: X 221 ARG cc_start: 0.8060 (ttp-170) cc_final: 0.7666 (tpp-160) REVERT: X 358 ARG cc_start: 0.7528 (mtp180) cc_final: 0.7158 (mtm180) REVERT: X 373 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.5363 (ptm) REVERT: X 391 LYS cc_start: 0.8392 (tptp) cc_final: 0.8180 (ttmt) outliers start: 158 outliers final: 72 residues processed: 870 average time/residue: 0.8835 time to fit residues: 910.0880 Evaluate side-chains 868 residues out of total 4668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 772 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 222 GLN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 317 MET Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain F residue 2 SER Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 160 MET Chi-restraints excluded: chain F residue 312 SER Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 395 SER Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 160 MET Chi-restraints excluded: chain J residue 222 GLN Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 317 MET Chi-restraints excluded: chain J residue 326 LEU Chi-restraints excluded: chain J residue 373 MET Chi-restraints excluded: chain J residue 395 SER Chi-restraints excluded: chain J residue 403 ILE Chi-restraints excluded: chain J residue 420 GLU Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 96 LYS Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 317 MET Chi-restraints excluded: chain K residue 373 MET Chi-restraints excluded: chain K residue 403 ILE Chi-restraints excluded: chain L residue 2 SER Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 312 SER Chi-restraints excluded: chain L residue 326 LEU Chi-restraints excluded: chain L residue 350 ARG Chi-restraints excluded: chain L residue 395 SER Chi-restraints excluded: chain L residue 403 ILE Chi-restraints excluded: chain O residue 3 ILE Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain Q residue 326 LEU Chi-restraints excluded: chain Q residue 403 ILE Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 312 SER Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 395 SER Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain S residue 2 SER Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 65 SER Chi-restraints excluded: chain S residue 160 MET Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain S residue 317 MET Chi-restraints excluded: chain S residue 326 LEU Chi-restraints excluded: chain S residue 373 MET Chi-restraints excluded: chain S residue 395 SER Chi-restraints excluded: chain S residue 403 ILE Chi-restraints excluded: chain S residue 420 GLU Chi-restraints excluded: chain T residue 2 SER Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 62 ILE Chi-restraints excluded: chain T residue 326 LEU Chi-restraints excluded: chain T residue 350 ARG Chi-restraints excluded: chain T residue 395 SER Chi-restraints excluded: chain T residue 403 ILE Chi-restraints excluded: chain W residue 2 SER Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 222 GLN Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 326 LEU Chi-restraints excluded: chain W residue 373 MET Chi-restraints excluded: chain W residue 395 SER Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain W residue 420 GLU Chi-restraints excluded: chain X residue 36 ILE Chi-restraints excluded: chain X residue 62 ILE Chi-restraints excluded: chain X residue 96 LYS Chi-restraints excluded: chain X residue 237 VAL Chi-restraints excluded: chain X residue 373 MET Chi-restraints excluded: chain X residue 403 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 74 optimal weight: 0.0670 chunk 163 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 149 optimal weight: 8.9990 chunk 462 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 239 optimal weight: 0.6980 chunk 481 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 394 optimal weight: 0.8980 chunk 284 optimal weight: 3.9990 overall best weight: 1.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN B 210 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN ** E 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN F 126 ASN F 165 ASN J 33 ASN J 210 GLN ** J 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 ASN L 33 ASN L 126 ASN L 165 ASN L 313 ASN Q 33 ASN R 33 ASN R 126 ASN R 165 ASN S 33 ASN S 210 GLN T 33 ASN T 126 ASN T 165 ASN W 33 ASN W 165 ASN W 210 GLN ** W 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 33 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.185321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.169069 restraints weight = 34413.870| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 0.74 r_work: 0.3760 rms_B_bonded: 1.10 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 1.92 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3672 r_free = 0.3672 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3672 r_free = 0.3672 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 43464 Z= 0.142 Angle : 0.540 5.379 58968 Z= 0.288 Chirality : 0.042 0.141 6456 Planarity : 0.005 0.050 7716 Dihedral : 5.567 57.634 5993 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.28 % Allowed : 15.60 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.11), residues: 5364 helix: 1.25 (0.11), residues: 2196 sheet: -1.16 (0.16), residues: 876 loop : -0.29 (0.13), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 10 TYR 0.026 0.002 TYR S 294 PHE 0.012 0.002 PHE W 179 TRP 0.013 0.002 TRP S 423 HIS 0.006 0.001 HIS S 193 Details of bonding type rmsd covalent geometry : bond 0.00309 (43464) covalent geometry : angle 0.53979 (58968) hydrogen bonds : bond 0.05186 ( 1642) hydrogen bonds : angle 4.86866 ( 4668) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 950 residues out of total 4668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 762 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 GLN cc_start: 0.6504 (mp10) cc_final: 0.6134 (mt0) REVERT: B 86 ARG cc_start: 0.7424 (mmt90) cc_final: 0.7033 (mmm160) REVERT: B 126 ASN cc_start: 0.8524 (t0) cc_final: 0.8274 (t0) REVERT: B 222 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7579 (mt0) REVERT: B 317 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.6879 (tpt) REVERT: B 420 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7392 (mm-30) REVERT: C 4 GLN cc_start: 0.6549 (mp-120) cc_final: 0.6196 (mt0) REVERT: C 6 GLU cc_start: 0.6466 (tp30) cc_final: 0.5828 (mm-30) REVERT: E 62 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7940 (pt) REVERT: E 86 ARG cc_start: 0.7435 (mmt90) cc_final: 0.7075 (mmm160) REVERT: E 96 LYS cc_start: 0.7925 (mttm) cc_final: 0.7681 (mmmt) REVERT: E 115 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7017 (mmtm) REVERT: E 116 GLU cc_start: 0.6945 (pt0) cc_final: 0.6638 (pt0) REVERT: E 221 ARG cc_start: 0.8237 (ttp-170) cc_final: 0.7779 (tpp-160) REVERT: E 317 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.6912 (tpt) REVERT: E 334 ASN cc_start: 0.6734 (m-40) cc_final: 0.6489 (m110) REVERT: E 358 ARG cc_start: 0.7486 (mtp180) cc_final: 0.7134 (mtm180) REVERT: F 86 ARG cc_start: 0.7491 (mmt90) cc_final: 0.7025 (mmm160) REVERT: F 93 ASP cc_start: 0.7428 (m-30) cc_final: 0.7198 (m-30) REVERT: F 96 LYS cc_start: 0.7922 (mttm) cc_final: 0.7678 (mmmt) REVERT: F 115 LYS cc_start: 0.7695 (tptp) cc_final: 0.6860 (mmtm) REVERT: F 221 ARG cc_start: 0.8003 (ttp-170) cc_final: 0.7530 (tpp-160) REVERT: F 350 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7709 (tpt90) REVERT: F 358 ARG cc_start: 0.7399 (mtp180) cc_final: 0.7055 (mtm180) REVERT: F 403 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7541 (pp) REVERT: F 420 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7317 (mm-30) REVERT: G 4 GLN cc_start: 0.6335 (mm110) cc_final: 0.5981 (mt0) REVERT: G 6 GLU cc_start: 0.6527 (tp30) cc_final: 0.5773 (mm-30) REVERT: H 4 GLN cc_start: 0.6632 (mp-120) cc_final: 0.6219 (mt0) REVERT: H 6 GLU cc_start: 0.6459 (tp30) cc_final: 0.6024 (mm-30) REVERT: I 4 GLN cc_start: 0.6673 (mp-120) cc_final: 0.6247 (mt0) REVERT: J 86 ARG cc_start: 0.7405 (mmt90) cc_final: 0.7020 (mmm160) REVERT: J 126 ASN cc_start: 0.8519 (t0) cc_final: 0.8268 (t0) REVERT: J 222 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7598 (mt0) REVERT: J 317 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.6845 (tpt) REVERT: J 420 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7421 (mm-30) REVERT: K 62 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7956 (pt) REVERT: K 86 ARG cc_start: 0.7422 (mmt90) cc_final: 0.7052 (mmm160) REVERT: K 115 LYS cc_start: 0.7838 (tptp) cc_final: 0.7014 (mmtm) REVERT: K 116 GLU cc_start: 0.6933 (pt0) cc_final: 0.6617 (pt0) REVERT: K 317 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.6915 (tpt) REVERT: K 358 ARG cc_start: 0.7488 (mtp180) cc_final: 0.7122 (mtm180) REVERT: K 373 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6243 (ptm) REVERT: K 391 LYS cc_start: 0.8419 (tptp) cc_final: 0.8206 (ttmt) REVERT: L 86 ARG cc_start: 0.7483 (mmt90) cc_final: 0.6994 (mmm160) REVERT: L 96 LYS cc_start: 0.7937 (mttm) cc_final: 0.7670 (mmmt) REVERT: L 115 LYS cc_start: 0.7703 (tptp) cc_final: 0.6848 (mmtm) REVERT: L 221 ARG cc_start: 0.7980 (ttp-170) cc_final: 0.7532 (tpp-160) REVERT: L 350 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7733 (tpt90) REVERT: L 358 ARG cc_start: 0.7410 (mtp180) cc_final: 0.7091 (mtm180) REVERT: L 403 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7518 (pp) REVERT: L 420 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7359 (mm-30) REVERT: M 4 GLN cc_start: 0.6466 (mp-120) cc_final: 0.6060 (mt0) REVERT: M 6 GLU cc_start: 0.6437 (tp30) cc_final: 0.5965 (mm-30) REVERT: O 4 GLN cc_start: 0.6602 (mp10) cc_final: 0.6140 (mt0) REVERT: P 4 GLN cc_start: 0.6566 (mm110) cc_final: 0.6247 (mt0) REVERT: Q 62 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7958 (pt) REVERT: Q 86 ARG cc_start: 0.7411 (mmt90) cc_final: 0.7045 (mmm160) REVERT: Q 96 LYS cc_start: 0.7916 (mttm) cc_final: 0.7691 (mmmt) REVERT: Q 115 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7022 (mmtm) REVERT: Q 116 GLU cc_start: 0.6943 (pt0) cc_final: 0.6645 (pt0) REVERT: Q 165 ASN cc_start: 0.6819 (t0) cc_final: 0.6529 (t160) REVERT: Q 221 ARG cc_start: 0.8175 (ttp-170) cc_final: 0.7719 (tpp-160) REVERT: Q 358 ARG cc_start: 0.7529 (mtp180) cc_final: 0.7199 (mtm180) REVERT: R 86 ARG cc_start: 0.7495 (mmt90) cc_final: 0.7022 (mmm160) REVERT: R 93 ASP cc_start: 0.7405 (m-30) cc_final: 0.7179 (m-30) REVERT: R 96 LYS cc_start: 0.7940 (mttm) cc_final: 0.7688 (mmmt) REVERT: R 115 LYS cc_start: 0.7689 (tptp) cc_final: 0.6844 (mmtm) REVERT: R 221 ARG cc_start: 0.7984 (ttp-170) cc_final: 0.7520 (tpp-160) REVERT: R 350 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7708 (tpt90) REVERT: R 358 ARG cc_start: 0.7416 (mtp180) cc_final: 0.7044 (mtm180) REVERT: R 403 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7540 (pp) REVERT: R 420 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7326 (mm-30) REVERT: S 5 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.6957 (ttt-90) REVERT: S 36 ILE cc_start: 0.6967 (OUTLIER) cc_final: 0.6765 (tp) REVERT: S 86 ARG cc_start: 0.7401 (mmt90) cc_final: 0.6988 (mmm160) REVERT: S 126 ASN cc_start: 0.8515 (t0) cc_final: 0.8254 (t0) REVERT: S 165 ASN cc_start: 0.6354 (t160) cc_final: 0.6148 (t0) REVERT: S 417 GLU cc_start: 0.8136 (tt0) cc_final: 0.7908 (mt-10) REVERT: S 420 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7577 (tp30) REVERT: T 86 ARG cc_start: 0.7478 (mmt90) cc_final: 0.6996 (mmm160) REVERT: T 96 LYS cc_start: 0.7945 (mttm) cc_final: 0.7678 (mmmt) REVERT: T 115 LYS cc_start: 0.7672 (tptp) cc_final: 0.6831 (mmtm) REVERT: T 221 ARG cc_start: 0.7997 (ttp-170) cc_final: 0.7539 (tpp-160) REVERT: T 350 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7731 (tpt90) REVERT: T 358 ARG cc_start: 0.7424 (mtp180) cc_final: 0.7102 (mtm180) REVERT: T 403 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7518 (pp) REVERT: T 420 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7379 (mm-30) REVERT: U 4 GLN cc_start: 0.6362 (mm110) cc_final: 0.5917 (mt0) REVERT: U 6 GLU cc_start: 0.6534 (tp30) cc_final: 0.5831 (mm-30) REVERT: V 4 GLN cc_start: 0.6657 (mp-120) cc_final: 0.6206 (mt0) REVERT: V 6 GLU cc_start: 0.6467 (tp30) cc_final: 0.6012 (mm-30) REVERT: W 86 ARG cc_start: 0.7398 (mmt90) cc_final: 0.7019 (mmm160) REVERT: W 126 ASN cc_start: 0.8534 (t0) cc_final: 0.8283 (t0) REVERT: W 165 ASN cc_start: 0.6819 (t0) cc_final: 0.6535 (t160) REVERT: W 222 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7596 (mt0) REVERT: W 420 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7431 (mm-30) REVERT: X 62 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7918 (pt) REVERT: X 86 ARG cc_start: 0.7416 (mmt90) cc_final: 0.7051 (mmm160) REVERT: X 115 LYS cc_start: 0.7804 (tptp) cc_final: 0.7025 (mmtm) REVERT: X 165 ASN cc_start: 0.6846 (t0) cc_final: 0.6531 (t160) REVERT: X 221 ARG cc_start: 0.8103 (ttp-170) cc_final: 0.7759 (tpp-160) REVERT: X 317 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7052 (tpt) REVERT: X 358 ARG cc_start: 0.7518 (mtp180) cc_final: 0.7147 (mtm180) REVERT: X 373 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.5437 (ptm) REVERT: X 391 LYS cc_start: 0.8416 (tptp) cc_final: 0.8197 (ttmt) outliers start: 188 outliers final: 92 residues processed: 854 average time/residue: 0.8586 time to fit residues: 868.5626 Evaluate side-chains 888 residues out of total 4668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 762 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 222 GLN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 317 MET Chi-restraints excluded: chain E residue 395 SER Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain F residue 2 SER Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 312 SER Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 350 ARG Chi-restraints excluded: chain F residue 395 SER Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain F residue 420 GLU Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 160 MET Chi-restraints excluded: chain J residue 222 GLN Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 317 MET Chi-restraints excluded: chain J residue 326 LEU Chi-restraints excluded: chain J residue 373 MET Chi-restraints excluded: chain J residue 395 SER Chi-restraints excluded: chain J residue 403 ILE Chi-restraints excluded: chain J residue 420 GLU Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 96 LYS Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 317 MET Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain K residue 373 MET Chi-restraints excluded: chain K residue 395 SER Chi-restraints excluded: chain K residue 398 ILE Chi-restraints excluded: chain K residue 403 ILE Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 237 VAL Chi-restraints excluded: chain L residue 312 SER Chi-restraints excluded: chain L residue 326 LEU Chi-restraints excluded: chain L residue 350 ARG Chi-restraints excluded: chain L residue 395 SER Chi-restraints excluded: chain L residue 398 ILE Chi-restraints excluded: chain L residue 403 ILE Chi-restraints excluded: chain L residue 420 GLU Chi-restraints excluded: chain O residue 3 ILE Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 115 LYS Chi-restraints excluded: chain Q residue 172 LEU Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain Q residue 395 SER Chi-restraints excluded: chain Q residue 398 ILE Chi-restraints excluded: chain Q residue 403 ILE Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 312 SER Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 350 ARG Chi-restraints excluded: chain R residue 395 SER Chi-restraints excluded: chain R residue 398 ILE Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain R residue 420 GLU Chi-restraints excluded: chain S residue 2 SER Chi-restraints excluded: chain S residue 5 ARG Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 65 SER Chi-restraints excluded: chain S residue 160 MET Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain S residue 250 LYS Chi-restraints excluded: chain S residue 317 MET Chi-restraints excluded: chain S residue 326 LEU Chi-restraints excluded: chain S residue 373 MET Chi-restraints excluded: chain S residue 395 SER Chi-restraints excluded: chain S residue 403 ILE Chi-restraints excluded: chain S residue 420 GLU Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 62 ILE Chi-restraints excluded: chain T residue 138 THR Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 312 SER Chi-restraints excluded: chain T residue 326 LEU Chi-restraints excluded: chain T residue 350 ARG Chi-restraints excluded: chain T residue 395 SER Chi-restraints excluded: chain T residue 398 ILE Chi-restraints excluded: chain T residue 403 ILE Chi-restraints excluded: chain T residue 420 GLU Chi-restraints excluded: chain W residue 2 SER Chi-restraints excluded: chain W residue 222 GLN Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 326 LEU Chi-restraints excluded: chain W residue 373 MET Chi-restraints excluded: chain W residue 395 SER Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain W residue 420 GLU Chi-restraints excluded: chain X residue 36 ILE Chi-restraints excluded: chain X residue 62 ILE Chi-restraints excluded: chain X residue 96 LYS Chi-restraints excluded: chain X residue 172 LEU Chi-restraints excluded: chain X residue 237 VAL Chi-restraints excluded: chain X residue 317 MET Chi-restraints excluded: chain X residue 373 MET Chi-restraints excluded: chain X residue 395 SER Chi-restraints excluded: chain X residue 398 ILE Chi-restraints excluded: chain X residue 403 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 162 optimal weight: 6.9990 chunk 494 optimal weight: 1.9990 chunk 233 optimal weight: 0.0030 chunk 46 optimal weight: 10.0000 chunk 389 optimal weight: 6.9990 chunk 257 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 286 optimal weight: 0.7980 chunk 340 optimal weight: 7.9990 overall best weight: 2.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN ** E 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN F 126 ASN F 246 GLN J 33 ASN ** J 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 ASN L 33 ASN L 126 ASN L 246 GLN Q 33 ASN R 33 ASN R 126 ASN R 246 GLN S 33 ASN ** S 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 33 ASN T 126 ASN T 246 GLN W 33 ASN ** W 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 33 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.183197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.166384 restraints weight = 34460.801| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 0.79 r_work: 0.3727 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3638 r_free = 0.3638 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3638 r_free = 0.3638 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 43464 Z= 0.194 Angle : 0.628 6.069 58968 Z= 0.337 Chirality : 0.045 0.178 6456 Planarity : 0.006 0.089 7716 Dihedral : 5.862 55.805 5993 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.79 % Favored : 95.19 % Rotamer: Outliers : 4.94 % Allowed : 15.19 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.11), residues: 5364 helix: 0.99 (0.11), residues: 2196 sheet: -1.70 (0.16), residues: 756 loop : -0.43 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 10 TYR 0.032 0.003 TYR B 294 PHE 0.017 0.002 PHE J 179 TRP 0.017 0.003 TRP S 423 HIS 0.007 0.002 HIS S 193 Details of bonding type rmsd covalent geometry : bond 0.00428 (43464) covalent geometry : angle 0.62841 (58968) hydrogen bonds : bond 0.05968 ( 1642) hydrogen bonds : angle 5.13073 ( 4668) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 971 residues out of total 4668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 754 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 GLN cc_start: 0.6573 (mp10) cc_final: 0.6170 (mt0) REVERT: B 86 ARG cc_start: 0.7471 (mmt90) cc_final: 0.7067 (mmm160) REVERT: B 126 ASN cc_start: 0.8541 (t0) cc_final: 0.8293 (t0) REVERT: B 157 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7913 (tt) REVERT: B 165 ASN cc_start: 0.6867 (t0) cc_final: 0.6600 (t160) REVERT: B 222 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7680 (mt0) REVERT: B 317 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.7444 (ttt) REVERT: B 420 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7467 (mm-30) REVERT: C 4 GLN cc_start: 0.6702 (mp-120) cc_final: 0.6269 (mt0) REVERT: C 6 GLU cc_start: 0.6476 (tp30) cc_final: 0.5867 (mm-30) REVERT: E 62 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7947 (pt) REVERT: E 86 ARG cc_start: 0.7476 (mmt90) cc_final: 0.7119 (mmm160) REVERT: E 96 LYS cc_start: 0.7955 (mttm) cc_final: 0.7705 (mmmt) REVERT: E 115 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7095 (mmtm) REVERT: E 116 GLU cc_start: 0.7108 (pt0) cc_final: 0.6855 (pt0) REVERT: E 221 ARG cc_start: 0.8265 (ttp-170) cc_final: 0.7794 (tpp-160) REVERT: E 358 ARG cc_start: 0.7498 (mtp180) cc_final: 0.7138 (mtm180) REVERT: F 86 ARG cc_start: 0.7588 (mmt90) cc_final: 0.7099 (mmm160) REVERT: F 93 ASP cc_start: 0.7490 (m-30) cc_final: 0.7234 (m-30) REVERT: F 96 LYS cc_start: 0.7970 (mttm) cc_final: 0.7714 (mmmt) REVERT: F 115 LYS cc_start: 0.7744 (tptp) cc_final: 0.6928 (mmtm) REVERT: F 221 ARG cc_start: 0.8101 (ttp-170) cc_final: 0.7794 (tpp-160) REVERT: F 350 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7733 (tpt90) REVERT: F 358 ARG cc_start: 0.7453 (mtp180) cc_final: 0.7092 (mtm180) REVERT: F 403 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7564 (pp) REVERT: G 4 GLN cc_start: 0.6326 (mm110) cc_final: 0.5981 (mt0) REVERT: G 6 GLU cc_start: 0.6543 (tp30) cc_final: 0.5800 (mm-30) REVERT: H 4 GLN cc_start: 0.6706 (mp-120) cc_final: 0.6261 (mt0) REVERT: H 6 GLU cc_start: 0.6426 (tp30) cc_final: 0.6001 (mm-30) REVERT: I 4 GLN cc_start: 0.6764 (mp-120) cc_final: 0.6341 (mt0) REVERT: J 86 ARG cc_start: 0.7472 (mmt90) cc_final: 0.7066 (mmm160) REVERT: J 126 ASN cc_start: 0.8525 (t0) cc_final: 0.8270 (t0) REVERT: J 157 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7896 (tt) REVERT: J 222 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7676 (mt0) REVERT: J 317 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.7427 (ttt) REVERT: J 420 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7472 (mm-30) REVERT: K 5 ARG cc_start: 0.7405 (mtp85) cc_final: 0.7134 (mtp85) REVERT: K 62 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7966 (pt) REVERT: K 86 ARG cc_start: 0.7493 (mmt90) cc_final: 0.7129 (mmm160) REVERT: K 115 LYS cc_start: 0.7872 (tptp) cc_final: 0.7066 (mmtm) REVERT: K 116 GLU cc_start: 0.7063 (pt0) cc_final: 0.6799 (pt0) REVERT: K 317 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7287 (ttt) REVERT: K 358 ARG cc_start: 0.7538 (mtp180) cc_final: 0.7167 (mtm180) REVERT: L 86 ARG cc_start: 0.7571 (mmt90) cc_final: 0.7070 (mmm160) REVERT: L 96 LYS cc_start: 0.7965 (mttm) cc_final: 0.7709 (mmmt) REVERT: L 115 LYS cc_start: 0.7777 (tptp) cc_final: 0.6939 (mmtm) REVERT: L 221 ARG cc_start: 0.8075 (ttp-170) cc_final: 0.7837 (tpp-160) REVERT: L 350 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7744 (tpt90) REVERT: L 358 ARG cc_start: 0.7459 (mtp180) cc_final: 0.7131 (mtm180) REVERT: L 403 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7582 (pp) REVERT: M 4 GLN cc_start: 0.6693 (mp-120) cc_final: 0.6211 (mt0) REVERT: M 6 GLU cc_start: 0.6447 (tp30) cc_final: 0.6024 (mm-30) REVERT: O 4 GLN cc_start: 0.6687 (mp10) cc_final: 0.6228 (mt0) REVERT: P 4 GLN cc_start: 0.6606 (mm110) cc_final: 0.6255 (mt0) REVERT: Q 62 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7965 (pt) REVERT: Q 86 ARG cc_start: 0.7473 (mmt90) cc_final: 0.7115 (mmm160) REVERT: Q 96 LYS cc_start: 0.7960 (mttm) cc_final: 0.7718 (mmmt) REVERT: Q 115 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7082 (mmtm) REVERT: Q 116 GLU cc_start: 0.7088 (pt0) cc_final: 0.6837 (pt0) REVERT: Q 221 ARG cc_start: 0.8228 (ttp-170) cc_final: 0.7759 (tpp-160) REVERT: Q 358 ARG cc_start: 0.7601 (mtp180) cc_final: 0.7288 (mtm180) REVERT: R 86 ARG cc_start: 0.7593 (mmt90) cc_final: 0.7087 (mmm160) REVERT: R 93 ASP cc_start: 0.7478 (m-30) cc_final: 0.7250 (m-30) REVERT: R 96 LYS cc_start: 0.7968 (mttm) cc_final: 0.7724 (mmmt) REVERT: R 115 LYS cc_start: 0.7756 (tptp) cc_final: 0.6935 (mmtm) REVERT: R 221 ARG cc_start: 0.8077 (ttp-170) cc_final: 0.7793 (tpp-160) REVERT: R 350 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7738 (tpt90) REVERT: R 358 ARG cc_start: 0.7441 (mtp180) cc_final: 0.7080 (mtm180) REVERT: R 403 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7566 (pp) REVERT: S 5 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7015 (ttt-90) REVERT: S 86 ARG cc_start: 0.7467 (mmt90) cc_final: 0.7062 (mmm160) REVERT: S 126 ASN cc_start: 0.8545 (t0) cc_final: 0.8293 (t0) REVERT: S 157 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7922 (tt) REVERT: S 326 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7430 (mp) REVERT: S 417 GLU cc_start: 0.8179 (tt0) cc_final: 0.7932 (mt-10) REVERT: S 420 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7613 (tp30) REVERT: S 425 MET cc_start: 0.8838 (mmt) cc_final: 0.8613 (mmp) REVERT: T 86 ARG cc_start: 0.7572 (mmt90) cc_final: 0.7065 (mmm160) REVERT: T 96 LYS cc_start: 0.7970 (mttm) cc_final: 0.7709 (mmmt) REVERT: T 115 LYS cc_start: 0.7748 (tptp) cc_final: 0.6922 (mmtm) REVERT: T 221 ARG cc_start: 0.8091 (ttp-170) cc_final: 0.7844 (tpp-160) REVERT: T 350 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7745 (tpt90) REVERT: T 358 ARG cc_start: 0.7480 (mtp180) cc_final: 0.7146 (mtm180) REVERT: T 370 ILE cc_start: 0.5050 (OUTLIER) cc_final: 0.4723 (tp) REVERT: T 403 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7592 (pp) REVERT: U 4 GLN cc_start: 0.6433 (mm110) cc_final: 0.6018 (mt0) REVERT: U 6 GLU cc_start: 0.6522 (tp30) cc_final: 0.5810 (mm-30) REVERT: V 4 GLN cc_start: 0.6713 (mp-120) cc_final: 0.6228 (mt0) REVERT: V 6 GLU cc_start: 0.6406 (tp30) cc_final: 0.5984 (mm-30) REVERT: W 86 ARG cc_start: 0.7459 (mmt90) cc_final: 0.7061 (mmm160) REVERT: W 126 ASN cc_start: 0.8541 (t0) cc_final: 0.8289 (t0) REVERT: W 157 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7875 (tt) REVERT: W 165 ASN cc_start: 0.7210 (t0) cc_final: 0.6807 (t0) REVERT: W 222 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7683 (mt0) REVERT: W 420 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7502 (mm-30) REVERT: X 62 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7954 (pt) REVERT: X 86 ARG cc_start: 0.7497 (mmt90) cc_final: 0.7139 (mmm160) REVERT: X 115 LYS cc_start: 0.7831 (tptp) cc_final: 0.7086 (mmtm) REVERT: X 221 ARG cc_start: 0.8185 (ttp-170) cc_final: 0.7775 (tpp-160) REVERT: X 317 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7368 (ttt) REVERT: X 358 ARG cc_start: 0.7580 (mtp180) cc_final: 0.7194 (mtm180) REVERT: X 373 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.5403 (ptm) outliers start: 217 outliers final: 112 residues processed: 871 average time/residue: 0.8568 time to fit residues: 885.6485 Evaluate side-chains 890 residues out of total 4668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 745 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 222 GLN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 317 MET Chi-restraints excluded: chain E residue 395 SER Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain F residue 2 SER Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 312 SER Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 350 ARG Chi-restraints excluded: chain F residue 395 SER Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 160 MET Chi-restraints excluded: chain J residue 222 GLN Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 317 MET Chi-restraints excluded: chain J residue 326 LEU Chi-restraints excluded: chain J residue 373 MET Chi-restraints excluded: chain J residue 395 SER Chi-restraints excluded: chain J residue 403 ILE Chi-restraints excluded: chain J residue 420 GLU Chi-restraints excluded: chain K residue 15 GLU Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 96 LYS Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain K residue 221 ARG Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 317 MET Chi-restraints excluded: chain K residue 395 SER Chi-restraints excluded: chain K residue 398 ILE Chi-restraints excluded: chain K residue 403 ILE Chi-restraints excluded: chain L residue 2 SER Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 138 THR Chi-restraints excluded: chain L residue 203 VAL Chi-restraints excluded: chain L residue 237 VAL Chi-restraints excluded: chain L residue 312 SER Chi-restraints excluded: chain L residue 326 LEU Chi-restraints excluded: chain L residue 350 ARG Chi-restraints excluded: chain L residue 395 SER Chi-restraints excluded: chain L residue 398 ILE Chi-restraints excluded: chain L residue 403 ILE Chi-restraints excluded: chain O residue 3 ILE Chi-restraints excluded: chain Q residue 15 GLU Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 115 LYS Chi-restraints excluded: chain Q residue 172 LEU Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain Q residue 395 SER Chi-restraints excluded: chain Q residue 398 ILE Chi-restraints excluded: chain Q residue 403 ILE Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 312 SER Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 350 ARG Chi-restraints excluded: chain R residue 395 SER Chi-restraints excluded: chain R residue 398 ILE Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain S residue 2 SER Chi-restraints excluded: chain S residue 5 ARG Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 65 SER Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 157 LEU Chi-restraints excluded: chain S residue 160 MET Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain S residue 317 MET Chi-restraints excluded: chain S residue 326 LEU Chi-restraints excluded: chain S residue 373 MET Chi-restraints excluded: chain S residue 395 SER Chi-restraints excluded: chain S residue 403 ILE Chi-restraints excluded: chain S residue 420 GLU Chi-restraints excluded: chain T residue 2 SER Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 62 ILE Chi-restraints excluded: chain T residue 138 THR Chi-restraints excluded: chain T residue 203 VAL Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 312 SER Chi-restraints excluded: chain T residue 326 LEU Chi-restraints excluded: chain T residue 350 ARG Chi-restraints excluded: chain T residue 370 ILE Chi-restraints excluded: chain T residue 395 SER Chi-restraints excluded: chain T residue 398 ILE Chi-restraints excluded: chain T residue 403 ILE Chi-restraints excluded: chain W residue 2 SER Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain W residue 138 THR Chi-restraints excluded: chain W residue 157 LEU Chi-restraints excluded: chain W residue 222 GLN Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 326 LEU Chi-restraints excluded: chain W residue 373 MET Chi-restraints excluded: chain W residue 395 SER Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain W residue 420 GLU Chi-restraints excluded: chain X residue 36 ILE Chi-restraints excluded: chain X residue 62 ILE Chi-restraints excluded: chain X residue 96 LYS Chi-restraints excluded: chain X residue 172 LEU Chi-restraints excluded: chain X residue 237 VAL Chi-restraints excluded: chain X residue 317 MET Chi-restraints excluded: chain X residue 373 MET Chi-restraints excluded: chain X residue 395 SER Chi-restraints excluded: chain X residue 398 ILE Chi-restraints excluded: chain X residue 403 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 364 optimal weight: 0.9980 chunk 343 optimal weight: 9.9990 chunk 503 optimal weight: 4.9990 chunk 27 optimal weight: 0.0070 chunk 147 optimal weight: 0.8980 chunk 15 optimal weight: 0.0270 chunk 224 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 239 optimal weight: 0.8980 chunk 136 optimal weight: 10.0000 chunk 274 optimal weight: 3.9990 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN B 165 ASN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 165 ASN E 210 GLN ** E 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN F 126 ASN F 313 ASN J 33 ASN J 165 ASN ** J 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 ASN K 210 GLN K 243 HIS L 33 ASN L 126 ASN Q 33 ASN Q 210 GLN ** Q 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 33 ASN R 126 ASN R 313 ASN S 33 ASN T 33 ASN T 126 ASN T 313 ASN W 33 ASN ** W 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 33 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.188288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.171697 restraints weight = 34848.924| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 0.79 r_work: 0.3794 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3706 r_free = 0.3706 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3706 r_free = 0.3706 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 43464 Z= 0.078 Angle : 0.420 4.236 58968 Z= 0.223 Chirality : 0.038 0.131 6456 Planarity : 0.003 0.039 7716 Dihedral : 5.034 59.958 5993 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.64 % Allowed : 17.53 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.12), residues: 5364 helix: 1.71 (0.11), residues: 2184 sheet: -1.17 (0.16), residues: 900 loop : -0.23 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 5 TYR 0.018 0.001 TYR W 294 PHE 0.006 0.001 PHE J 179 TRP 0.009 0.001 TRP S 423 HIS 0.003 0.001 HIS W 226 Details of bonding type rmsd covalent geometry : bond 0.00169 (43464) covalent geometry : angle 0.41977 (58968) hydrogen bonds : bond 0.03783 ( 1642) hydrogen bonds : angle 4.36741 ( 4668) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 4668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 761 time to evaluate : 1.722 Fit side-chains REVERT: A 4 GLN cc_start: 0.6537 (mp10) cc_final: 0.6125 (mt0) REVERT: B 86 ARG cc_start: 0.7417 (mmt90) cc_final: 0.6965 (mmm160) REVERT: B 126 ASN cc_start: 0.8491 (t0) cc_final: 0.8286 (t0) REVERT: B 157 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7670 (tt) REVERT: B 165 ASN cc_start: 0.6518 (t160) cc_final: 0.6167 (t0) REVERT: B 222 GLN cc_start: 0.7805 (tt0) cc_final: 0.7444 (mt0) REVERT: B 242 MET cc_start: 0.7649 (ttp) cc_final: 0.7245 (ttp) REVERT: B 326 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7244 (tp) REVERT: B 403 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7619 (mm) REVERT: B 420 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7439 (mm-30) REVERT: C 4 GLN cc_start: 0.6643 (mp-120) cc_final: 0.6217 (mt0) REVERT: C 6 GLU cc_start: 0.6490 (OUTLIER) cc_final: 0.5891 (mm-30) REVERT: E 86 ARG cc_start: 0.7402 (mmt90) cc_final: 0.7016 (mmm160) REVERT: E 96 LYS cc_start: 0.7915 (mttm) cc_final: 0.7709 (mmmt) REVERT: E 115 LYS cc_start: 0.7847 (tptp) cc_final: 0.6959 (mmtm) REVERT: E 221 ARG cc_start: 0.8197 (ttp-170) cc_final: 0.7768 (tpp-160) REVERT: E 358 ARG cc_start: 0.7473 (mtp180) cc_final: 0.7200 (mtm180) REVERT: E 373 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6442 (ptm) REVERT: E 391 LYS cc_start: 0.8371 (tptp) cc_final: 0.8154 (ttpt) REVERT: E 403 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7682 (mm) REVERT: F 86 ARG cc_start: 0.7499 (mmt90) cc_final: 0.7000 (mmm160) REVERT: F 93 ASP cc_start: 0.7216 (m-30) cc_final: 0.6940 (m-30) REVERT: F 96 LYS cc_start: 0.7947 (mttm) cc_final: 0.7693 (mmmt) REVERT: F 221 ARG cc_start: 0.7933 (ttp-170) cc_final: 0.7496 (tpp-160) REVERT: F 358 ARG cc_start: 0.7357 (mtp180) cc_final: 0.7020 (mtm180) REVERT: F 403 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.7253 (pp) REVERT: F 420 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7514 (mm-30) REVERT: G 4 GLN cc_start: 0.6326 (mm110) cc_final: 0.6018 (mt0) REVERT: G 6 GLU cc_start: 0.6547 (tp30) cc_final: 0.5766 (mm-30) REVERT: H 4 GLN cc_start: 0.6651 (mp-120) cc_final: 0.6159 (mt0) REVERT: H 6 GLU cc_start: 0.6476 (tp30) cc_final: 0.5988 (mm-30) REVERT: I 4 GLN cc_start: 0.6682 (mp-120) cc_final: 0.6288 (mt0) REVERT: J 86 ARG cc_start: 0.7414 (mmt90) cc_final: 0.6960 (mmm160) REVERT: J 157 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7711 (tt) REVERT: J 165 ASN cc_start: 0.6377 (t160) cc_final: 0.5952 (t0) REVERT: J 222 GLN cc_start: 0.7820 (tt0) cc_final: 0.7459 (mt0) REVERT: J 242 MET cc_start: 0.7661 (ttp) cc_final: 0.7265 (ttp) REVERT: J 326 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7238 (tp) REVERT: J 403 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7620 (mm) REVERT: J 420 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7424 (mm-30) REVERT: K 86 ARG cc_start: 0.7432 (mmt90) cc_final: 0.7032 (mmm160) REVERT: K 96 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7873 (mmmt) REVERT: K 358 ARG cc_start: 0.7521 (mtp180) cc_final: 0.7121 (mtm180) REVERT: K 373 MET cc_start: 0.6987 (OUTLIER) cc_final: 0.6319 (ptm) REVERT: K 391 LYS cc_start: 0.8380 (tptp) cc_final: 0.8157 (ttpt) REVERT: K 403 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7683 (mm) REVERT: L 86 ARG cc_start: 0.7474 (mmt90) cc_final: 0.6969 (mmm160) REVERT: L 96 LYS cc_start: 0.7953 (mttm) cc_final: 0.7695 (mmmt) REVERT: L 115 LYS cc_start: 0.7688 (tptp) cc_final: 0.6830 (mmtm) REVERT: L 221 ARG cc_start: 0.7925 (ttp-170) cc_final: 0.7511 (tpp-160) REVERT: L 350 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7668 (tpt90) REVERT: L 358 ARG cc_start: 0.7423 (mtp180) cc_final: 0.7075 (mtm180) REVERT: L 403 ILE cc_start: 0.7528 (OUTLIER) cc_final: 0.7269 (pp) REVERT: L 420 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7527 (mm-30) REVERT: M 4 GLN cc_start: 0.6688 (mp-120) cc_final: 0.6234 (mt0) REVERT: M 6 GLU cc_start: 0.6496 (tp30) cc_final: 0.6003 (mm-30) REVERT: O 4 GLN cc_start: 0.6629 (mp10) cc_final: 0.6216 (mt0) REVERT: P 4 GLN cc_start: 0.6597 (mm110) cc_final: 0.6248 (mt0) REVERT: Q 86 ARG cc_start: 0.7380 (mmt90) cc_final: 0.7006 (mmm160) REVERT: Q 96 LYS cc_start: 0.7915 (mttm) cc_final: 0.7710 (mmmt) REVERT: Q 115 LYS cc_start: 0.7882 (tptp) cc_final: 0.6970 (mmtm) REVERT: Q 221 ARG cc_start: 0.8202 (ttp-170) cc_final: 0.7784 (tpp-160) REVERT: Q 358 ARG cc_start: 0.7486 (mtp180) cc_final: 0.7172 (mtm180) REVERT: Q 373 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6517 (ptm) REVERT: Q 391 LYS cc_start: 0.8379 (tptp) cc_final: 0.8149 (ttpt) REVERT: Q 403 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7691 (mm) REVERT: R 86 ARG cc_start: 0.7475 (mmt90) cc_final: 0.6985 (mmm160) REVERT: R 93 ASP cc_start: 0.7208 (m-30) cc_final: 0.6939 (m-30) REVERT: R 96 LYS cc_start: 0.7949 (mttm) cc_final: 0.7715 (mmmt) REVERT: R 165 ASN cc_start: 0.6632 (t0) cc_final: 0.6359 (t160) REVERT: R 221 ARG cc_start: 0.7914 (ttp-170) cc_final: 0.7492 (tpp-160) REVERT: R 273 MET cc_start: 0.8642 (mtp) cc_final: 0.7967 (mtp) REVERT: R 358 ARG cc_start: 0.7411 (mtp180) cc_final: 0.7043 (mtm180) REVERT: R 403 ILE cc_start: 0.7557 (OUTLIER) cc_final: 0.7250 (pp) REVERT: R 420 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7510 (mm-30) REVERT: S 86 ARG cc_start: 0.7403 (mmt90) cc_final: 0.6954 (mmm160) REVERT: S 126 ASN cc_start: 0.8489 (t0) cc_final: 0.8280 (t0) REVERT: S 157 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7714 (tt) REVERT: S 165 ASN cc_start: 0.6503 (t160) cc_final: 0.6148 (t0) REVERT: S 242 MET cc_start: 0.7649 (ttp) cc_final: 0.7221 (ttp) REVERT: S 326 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7311 (tp) REVERT: S 403 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7617 (mm) REVERT: S 420 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7594 (tp30) REVERT: T 86 ARG cc_start: 0.7455 (mmt90) cc_final: 0.6951 (mmm160) REVERT: T 96 LYS cc_start: 0.7959 (mttm) cc_final: 0.7698 (mmmt) REVERT: T 115 LYS cc_start: 0.7665 (tptp) cc_final: 0.6807 (mmtm) REVERT: T 221 ARG cc_start: 0.7935 (ttp-170) cc_final: 0.7510 (tpp-160) REVERT: T 350 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7679 (tpt90) REVERT: T 358 ARG cc_start: 0.7451 (mtp180) cc_final: 0.7094 (mtm180) REVERT: T 403 ILE cc_start: 0.7537 (OUTLIER) cc_final: 0.7278 (pp) REVERT: T 420 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7560 (mm-30) REVERT: U 4 GLN cc_start: 0.6445 (mm110) cc_final: 0.5995 (mt0) REVERT: U 6 GLU cc_start: 0.6499 (tp30) cc_final: 0.5696 (mm-30) REVERT: V 4 GLN cc_start: 0.6667 (mp-120) cc_final: 0.6216 (mt0) REVERT: V 6 GLU cc_start: 0.6450 (tp30) cc_final: 0.6020 (mm-30) REVERT: W 86 ARG cc_start: 0.7418 (mmt90) cc_final: 0.6969 (mmm160) REVERT: W 157 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7554 (tt) REVERT: W 165 ASN cc_start: 0.6999 (t0) cc_final: 0.6673 (t160) REVERT: W 222 GLN cc_start: 0.7823 (tt0) cc_final: 0.7465 (mt0) REVERT: W 326 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7224 (tp) REVERT: W 403 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7623 (mm) REVERT: W 420 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7482 (mm-30) REVERT: X 86 ARG cc_start: 0.7400 (mmt90) cc_final: 0.7021 (mmm160) REVERT: X 96 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7799 (mmmt) REVERT: X 221 ARG cc_start: 0.8055 (ttp-170) cc_final: 0.7645 (tpp-160) REVERT: X 358 ARG cc_start: 0.7544 (mtp180) cc_final: 0.7119 (mtm180) REVERT: X 391 LYS cc_start: 0.8364 (tptp) cc_final: 0.8142 (ttpt) REVERT: X 403 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7581 (tt) outliers start: 116 outliers final: 14 residues processed: 822 average time/residue: 0.9117 time to fit residues: 882.1856 Evaluate side-chains 806 residues out of total 4668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 756 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain E residue 373 MET Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain F residue 420 GLU Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 326 LEU Chi-restraints excluded: chain J residue 403 ILE Chi-restraints excluded: chain J residue 420 GLU Chi-restraints excluded: chain K residue 96 LYS Chi-restraints excluded: chain K residue 373 MET Chi-restraints excluded: chain K residue 398 ILE Chi-restraints excluded: chain K residue 403 ILE Chi-restraints excluded: chain L residue 2 SER Chi-restraints excluded: chain L residue 138 THR Chi-restraints excluded: chain L residue 350 ARG Chi-restraints excluded: chain L residue 398 ILE Chi-restraints excluded: chain L residue 403 ILE Chi-restraints excluded: chain L residue 420 GLU Chi-restraints excluded: chain Q residue 373 MET Chi-restraints excluded: chain Q residue 398 ILE Chi-restraints excluded: chain Q residue 403 ILE Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 398 ILE Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain R residue 420 GLU Chi-restraints excluded: chain S residue 157 LEU Chi-restraints excluded: chain S residue 326 LEU Chi-restraints excluded: chain S residue 403 ILE Chi-restraints excluded: chain S residue 420 GLU Chi-restraints excluded: chain T residue 2 SER Chi-restraints excluded: chain T residue 350 ARG Chi-restraints excluded: chain T residue 398 ILE Chi-restraints excluded: chain T residue 403 ILE Chi-restraints excluded: chain T residue 420 GLU Chi-restraints excluded: chain W residue 157 LEU Chi-restraints excluded: chain W residue 326 LEU Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain W residue 420 GLU Chi-restraints excluded: chain X residue 96 LYS Chi-restraints excluded: chain X residue 398 ILE Chi-restraints excluded: chain X residue 403 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 399 optimal weight: 2.9990 chunk 536 optimal weight: 10.0000 chunk 359 optimal weight: 6.9990 chunk 214 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 529 optimal weight: 6.9990 chunk 278 optimal weight: 10.0000 chunk 168 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 186 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 126 ASN ** E 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN ** E 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN F 126 ASN F 313 ASN J 33 ASN ** J 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 ASN K 126 ASN K 210 GLN L 33 ASN L 126 ASN Q 33 ASN Q 126 ASN ** Q 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 210 GLN R 33 ASN R 126 ASN R 313 ASN S 33 ASN ** S 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 33 ASN T 126 ASN T 313 ASN W 33 ASN X 33 ASN X 126 ASN ** X 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.182069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.165088 restraints weight = 34455.841| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 0.79 r_work: 0.3722 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3633 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3633 r_free = 0.3633 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3633 r_free = 0.3633 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 43464 Z= 0.211 Angle : 0.645 6.479 58968 Z= 0.346 Chirality : 0.045 0.200 6456 Planarity : 0.007 0.103 7716 Dihedral : 5.842 56.352 5992 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.87 % Favored : 95.12 % Rotamer: Outliers : 4.23 % Allowed : 16.53 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.11), residues: 5364 helix: 1.15 (0.11), residues: 2196 sheet: -1.70 (0.16), residues: 756 loop : -0.34 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 296 TYR 0.034 0.003 TYR S 294 PHE 0.019 0.002 PHE B 179 TRP 0.016 0.003 TRP W 423 HIS 0.008 0.002 HIS B 193 Details of bonding type rmsd covalent geometry : bond 0.00467 (43464) covalent geometry : angle 0.64547 (58968) hydrogen bonds : bond 0.06137 ( 1642) hydrogen bonds : angle 5.11674 ( 4668) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 4668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 738 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 GLN cc_start: 0.6607 (mp10) cc_final: 0.6197 (mt0) REVERT: B 5 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.6833 (ttm-80) REVERT: B 86 ARG cc_start: 0.7471 (mmt90) cc_final: 0.7081 (mmm160) REVERT: B 157 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7925 (tt) REVERT: B 222 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7578 (mt0) REVERT: B 273 MET cc_start: 0.8648 (mtp) cc_final: 0.8172 (mtp) REVERT: B 420 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7489 (mm-30) REVERT: C 4 GLN cc_start: 0.6714 (mp-120) cc_final: 0.6242 (mt0) REVERT: C 6 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.6127 (mm-30) REVERT: E 86 ARG cc_start: 0.7484 (mmt90) cc_final: 0.7126 (mmm160) REVERT: E 96 LYS cc_start: 0.7954 (mttm) cc_final: 0.7702 (mmmt) REVERT: E 115 LYS cc_start: 0.7933 (tptp) cc_final: 0.7132 (mmtm) REVERT: E 221 ARG cc_start: 0.8265 (ttp-170) cc_final: 0.7794 (tpp-160) REVERT: E 317 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.6997 (tpt) REVERT: E 334 ASN cc_start: 0.6946 (m-40) cc_final: 0.6677 (m110) REVERT: E 358 ARG cc_start: 0.7511 (mtp180) cc_final: 0.7148 (mtm180) REVERT: E 373 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6105 (ptm) REVERT: F 86 ARG cc_start: 0.7630 (mmt90) cc_final: 0.7122 (mmm160) REVERT: F 96 LYS cc_start: 0.7990 (mttm) cc_final: 0.7709 (mmmt) REVERT: F 115 LYS cc_start: 0.7715 (tptp) cc_final: 0.6915 (mmtm) REVERT: F 221 ARG cc_start: 0.8065 (ttp-170) cc_final: 0.7795 (tpp-160) REVERT: F 326 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7319 (tp) REVERT: F 350 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7756 (tpt90) REVERT: F 358 ARG cc_start: 0.7470 (mtp180) cc_final: 0.7104 (mtm180) REVERT: F 403 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7605 (pp) REVERT: G 4 GLN cc_start: 0.6498 (mm110) cc_final: 0.6055 (mt0) REVERT: G 6 GLU cc_start: 0.6516 (tp30) cc_final: 0.5794 (mm-30) REVERT: H 4 GLN cc_start: 0.6728 (mp-120) cc_final: 0.6215 (mt0) REVERT: H 6 GLU cc_start: 0.6443 (tp30) cc_final: 0.5962 (mm-30) REVERT: I 4 GLN cc_start: 0.6747 (mp-120) cc_final: 0.6278 (mt0) REVERT: J 5 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.6784 (ttm-80) REVERT: J 86 ARG cc_start: 0.7454 (mmt90) cc_final: 0.7071 (mmm160) REVERT: J 157 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7940 (tt) REVERT: J 222 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7592 (mt0) REVERT: J 273 MET cc_start: 0.8652 (mtp) cc_final: 0.8188 (mtp) REVERT: J 420 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7486 (mm-30) REVERT: K 86 ARG cc_start: 0.7509 (mmt90) cc_final: 0.7129 (mmm160) REVERT: K 115 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7197 (mmtm) REVERT: K 317 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7015 (tpt) REVERT: K 358 ARG cc_start: 0.7545 (mtp180) cc_final: 0.7183 (mtm180) REVERT: K 373 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.6094 (ptm) REVERT: L 86 ARG cc_start: 0.7613 (mmt90) cc_final: 0.7101 (mmm160) REVERT: L 96 LYS cc_start: 0.7992 (mttm) cc_final: 0.7724 (mmmt) REVERT: L 115 LYS cc_start: 0.7732 (tptp) cc_final: 0.6909 (mmtm) REVERT: L 221 ARG cc_start: 0.8067 (ttp-170) cc_final: 0.7840 (tpp-160) REVERT: L 326 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7336 (tp) REVERT: L 350 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7796 (tpt90) REVERT: L 358 ARG cc_start: 0.7477 (mtp180) cc_final: 0.7138 (mtm180) REVERT: L 403 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7587 (pp) REVERT: M 4 GLN cc_start: 0.6717 (mp-120) cc_final: 0.6247 (mt0) REVERT: M 6 GLU cc_start: 0.6435 (tp30) cc_final: 0.6018 (mm-30) REVERT: O 4 GLN cc_start: 0.6703 (mp10) cc_final: 0.6243 (mt0) REVERT: P 4 GLN cc_start: 0.6617 (mm110) cc_final: 0.6239 (mt0) REVERT: Q 86 ARG cc_start: 0.7484 (mmt90) cc_final: 0.7123 (mmm160) REVERT: Q 96 LYS cc_start: 0.7956 (mttm) cc_final: 0.7713 (mmmt) REVERT: Q 115 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7115 (mmtm) REVERT: Q 221 ARG cc_start: 0.8221 (ttp-170) cc_final: 0.7759 (tpp-160) REVERT: Q 358 ARG cc_start: 0.7681 (mtp180) cc_final: 0.7252 (mtm180) REVERT: Q 373 MET cc_start: 0.6941 (OUTLIER) cc_final: 0.6080 (ptm) REVERT: R 86 ARG cc_start: 0.7628 (mmt90) cc_final: 0.7123 (mmm160) REVERT: R 93 ASP cc_start: 0.7485 (m-30) cc_final: 0.7271 (m-30) REVERT: R 96 LYS cc_start: 0.7989 (mttm) cc_final: 0.7716 (mmmt) REVERT: R 221 ARG cc_start: 0.8069 (ttp-170) cc_final: 0.7809 (tpp-160) REVERT: R 326 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7317 (tp) REVERT: R 358 ARG cc_start: 0.7446 (mtp180) cc_final: 0.7075 (mtm180) REVERT: R 403 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7603 (pp) REVERT: S 5 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.6876 (ttm-80) REVERT: S 35 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7300 (mt-10) REVERT: S 86 ARG cc_start: 0.7480 (mmt90) cc_final: 0.7086 (mmm160) REVERT: S 157 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7933 (tt) REVERT: S 420 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7618 (tp30) REVERT: T 86 ARG cc_start: 0.7602 (mmt90) cc_final: 0.7081 (mmm160) REVERT: T 96 LYS cc_start: 0.7993 (mttm) cc_final: 0.7724 (mmmt) REVERT: T 115 LYS cc_start: 0.7721 (tptp) cc_final: 0.6899 (mmtm) REVERT: T 221 ARG cc_start: 0.8074 (ttp-170) cc_final: 0.7850 (tpp-160) REVERT: T 326 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7333 (tp) REVERT: T 350 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7802 (tpt90) REVERT: T 358 ARG cc_start: 0.7498 (mtp180) cc_final: 0.7155 (mtm180) REVERT: T 403 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7604 (pp) REVERT: U 4 GLN cc_start: 0.6403 (mm110) cc_final: 0.6021 (mt0) REVERT: U 6 GLU cc_start: 0.6485 (tp30) cc_final: 0.5833 (mm-30) REVERT: V 4 GLN cc_start: 0.6741 (mp-120) cc_final: 0.6226 (mt0) REVERT: V 6 GLU cc_start: 0.6431 (tp30) cc_final: 0.6010 (mm-30) REVERT: W 5 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.6842 (ttm-80) REVERT: W 86 ARG cc_start: 0.7446 (mmt90) cc_final: 0.7073 (mmm160) REVERT: W 157 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7909 (tt) REVERT: W 222 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7593 (mt0) REVERT: W 273 MET cc_start: 0.8651 (mtp) cc_final: 0.8187 (mtp) REVERT: W 420 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7516 (mm-30) REVERT: X 86 ARG cc_start: 0.7499 (mmt90) cc_final: 0.7133 (mmm160) REVERT: X 221 ARG cc_start: 0.8218 (ttp-170) cc_final: 0.7789 (tpp-160) REVERT: X 358 ARG cc_start: 0.7589 (mtp180) cc_final: 0.7188 (mtm180) REVERT: X 373 MET cc_start: 0.7260 (OUTLIER) cc_final: 0.5462 (ptm) outliers start: 186 outliers final: 85 residues processed: 842 average time/residue: 0.8900 time to fit residues: 884.2325 Evaluate side-chains 852 residues out of total 4668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 731 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 5 ARG Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 222 GLN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 317 MET Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain E residue 373 MET Chi-restraints excluded: chain E residue 395 SER Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 312 SER Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 350 ARG Chi-restraints excluded: chain F residue 395 SER Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain J residue 5 ARG Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 222 GLN Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 326 LEU Chi-restraints excluded: chain J residue 373 MET Chi-restraints excluded: chain J residue 395 SER Chi-restraints excluded: chain J residue 403 ILE Chi-restraints excluded: chain J residue 420 GLU Chi-restraints excluded: chain K residue 96 LYS Chi-restraints excluded: chain K residue 115 LYS Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 317 MET Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain K residue 373 MET Chi-restraints excluded: chain K residue 395 SER Chi-restraints excluded: chain K residue 398 ILE Chi-restraints excluded: chain K residue 403 ILE Chi-restraints excluded: chain L residue 2 SER Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 138 THR Chi-restraints excluded: chain L residue 203 VAL Chi-restraints excluded: chain L residue 237 VAL Chi-restraints excluded: chain L residue 312 SER Chi-restraints excluded: chain L residue 326 LEU Chi-restraints excluded: chain L residue 350 ARG Chi-restraints excluded: chain L residue 395 SER Chi-restraints excluded: chain L residue 398 ILE Chi-restraints excluded: chain L residue 403 ILE Chi-restraints excluded: chain O residue 3 ILE Chi-restraints excluded: chain Q residue 115 LYS Chi-restraints excluded: chain Q residue 326 LEU Chi-restraints excluded: chain Q residue 373 MET Chi-restraints excluded: chain Q residue 395 SER Chi-restraints excluded: chain Q residue 398 ILE Chi-restraints excluded: chain Q residue 403 ILE Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 312 SER Chi-restraints excluded: chain R residue 326 LEU Chi-restraints excluded: chain R residue 395 SER Chi-restraints excluded: chain R residue 398 ILE Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain S residue 5 ARG Chi-restraints excluded: chain S residue 35 GLU Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 157 LEU Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain S residue 326 LEU Chi-restraints excluded: chain S residue 373 MET Chi-restraints excluded: chain S residue 395 SER Chi-restraints excluded: chain S residue 403 ILE Chi-restraints excluded: chain S residue 420 GLU Chi-restraints excluded: chain T residue 2 SER Chi-restraints excluded: chain T residue 138 THR Chi-restraints excluded: chain T residue 203 VAL Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 312 SER Chi-restraints excluded: chain T residue 326 LEU Chi-restraints excluded: chain T residue 350 ARG Chi-restraints excluded: chain T residue 395 SER Chi-restraints excluded: chain T residue 398 ILE Chi-restraints excluded: chain T residue 403 ILE Chi-restraints excluded: chain W residue 2 SER Chi-restraints excluded: chain W residue 5 ARG Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain W residue 138 THR Chi-restraints excluded: chain W residue 157 LEU Chi-restraints excluded: chain W residue 222 GLN Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 326 LEU Chi-restraints excluded: chain W residue 373 MET Chi-restraints excluded: chain W residue 395 SER Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain W residue 420 GLU Chi-restraints excluded: chain X residue 96 LYS Chi-restraints excluded: chain X residue 237 VAL Chi-restraints excluded: chain X residue 326 LEU Chi-restraints excluded: chain X residue 373 MET Chi-restraints excluded: chain X residue 395 SER Chi-restraints excluded: chain X residue 398 ILE Chi-restraints excluded: chain X residue 403 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 14 optimal weight: 1.9990 chunk 228 optimal weight: 0.6980 chunk 218 optimal weight: 7.9990 chunk 443 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 537 optimal weight: 0.9990 chunk 196 optimal weight: 7.9990 chunk 216 optimal weight: 0.9990 chunk 175 optimal weight: 0.4980 chunk 408 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN B 165 ASN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 165 ASN E 210 GLN ** E 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN F 126 ASN F 313 ASN J 33 ASN ** J 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 ASN K 165 ASN K 210 GLN L 33 ASN L 126 ASN ** L 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 33 ASN Q 165 ASN Q 210 GLN R 33 ASN R 126 ASN R 313 ASN S 33 ASN S 165 ASN T 33 ASN T 126 ASN T 313 ASN W 33 ASN ** W 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 33 ASN X 165 ASN X 210 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.187022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.170201 restraints weight = 34688.079| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 0.79 r_work: 0.3780 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3691 r_free = 0.3691 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3691 r_free = 0.3691 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 43464 Z= 0.088 Angle : 0.439 4.121 58968 Z= 0.234 Chirality : 0.038 0.132 6456 Planarity : 0.003 0.041 7716 Dihedral : 5.176 59.242 5992 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.53 % Allowed : 17.74 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.12), residues: 5364 helix: 1.68 (0.11), residues: 2184 sheet: -1.17 (0.16), residues: 900 loop : -0.17 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 5 TYR 0.020 0.001 TYR T 294 PHE 0.008 0.001 PHE B 179 TRP 0.010 0.001 TRP S 423 HIS 0.004 0.001 HIS B 193 Details of bonding type rmsd covalent geometry : bond 0.00186 (43464) covalent geometry : angle 0.43948 (58968) hydrogen bonds : bond 0.04073 ( 1642) hydrogen bonds : angle 4.47121 ( 4668) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 4668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 748 time to evaluate : 1.483 Fit side-chains REVERT: A 4 GLN cc_start: 0.6568 (mp10) cc_final: 0.6150 (mt0) REVERT: B 86 ARG cc_start: 0.7420 (mmt90) cc_final: 0.6959 (mmm160) REVERT: B 157 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7807 (tt) REVERT: B 179 PHE cc_start: 0.6669 (OUTLIER) cc_final: 0.5296 (m-80) REVERT: B 222 GLN cc_start: 0.7811 (tt0) cc_final: 0.7439 (mt0) REVERT: B 273 MET cc_start: 0.8554 (mtp) cc_final: 0.7969 (mtp) REVERT: B 317 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8176 (ttt) REVERT: B 403 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7570 (mm) REVERT: B 420 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7447 (mm-30) REVERT: C 3 ILE cc_start: 0.4904 (OUTLIER) cc_final: 0.4633 (pp) REVERT: C 4 GLN cc_start: 0.6696 (mp-120) cc_final: 0.6175 (mt0) REVERT: C 6 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.6078 (mm-30) REVERT: E 86 ARG cc_start: 0.7362 (mmt90) cc_final: 0.6979 (mmm160) REVERT: E 96 LYS cc_start: 0.7918 (mttm) cc_final: 0.7676 (mmmt) REVERT: E 115 LYS cc_start: 0.7894 (tptp) cc_final: 0.7110 (mmtm) REVERT: E 221 ARG cc_start: 0.8190 (ttp-170) cc_final: 0.7749 (tpp-160) REVERT: E 358 ARG cc_start: 0.7474 (mtp180) cc_final: 0.7184 (mtm180) REVERT: E 391 LYS cc_start: 0.8370 (tptp) cc_final: 0.8163 (ttmt) REVERT: F 86 ARG cc_start: 0.7462 (mmt90) cc_final: 0.6942 (mmm160) REVERT: F 96 LYS cc_start: 0.7931 (mttm) cc_final: 0.7654 (mmmt) REVERT: F 221 ARG cc_start: 0.7940 (ttp-170) cc_final: 0.7488 (tpp-160) REVERT: F 358 ARG cc_start: 0.7373 (mtp180) cc_final: 0.7025 (mtm180) REVERT: F 403 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7245 (pp) REVERT: F 420 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7456 (mm-30) REVERT: G 4 GLN cc_start: 0.6426 (mm110) cc_final: 0.5978 (mt0) REVERT: G 6 GLU cc_start: 0.6516 (tp30) cc_final: 0.5738 (mm-30) REVERT: H 4 GLN cc_start: 0.6678 (mp-120) cc_final: 0.6163 (mt0) REVERT: H 6 GLU cc_start: 0.6409 (tp30) cc_final: 0.5988 (mm-30) REVERT: I 4 GLN cc_start: 0.6672 (mp-120) cc_final: 0.6213 (mt0) REVERT: J 86 ARG cc_start: 0.7393 (mmt90) cc_final: 0.6935 (mmm160) REVERT: J 157 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7803 (tt) REVERT: J 165 ASN cc_start: 0.6497 (t160) cc_final: 0.6188 (t0) REVERT: J 179 PHE cc_start: 0.6676 (OUTLIER) cc_final: 0.5305 (m-80) REVERT: J 222 GLN cc_start: 0.7806 (tt0) cc_final: 0.7451 (mt0) REVERT: J 273 MET cc_start: 0.8557 (mtp) cc_final: 0.7980 (mtp) REVERT: J 317 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8176 (ttt) REVERT: J 403 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7567 (mm) REVERT: J 420 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7438 (mm-30) REVERT: K 86 ARG cc_start: 0.7392 (mmt90) cc_final: 0.6993 (mmm160) REVERT: K 96 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7779 (mmmt) REVERT: K 115 LYS cc_start: 0.7940 (tptt) cc_final: 0.7193 (mmtm) REVERT: K 358 ARG cc_start: 0.7453 (mtp180) cc_final: 0.7058 (mtm180) REVERT: K 391 LYS cc_start: 0.8380 (tptp) cc_final: 0.8169 (ttmt) REVERT: K 403 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7675 (mm) REVERT: L 86 ARG cc_start: 0.7459 (mmt90) cc_final: 0.6939 (mmm160) REVERT: L 96 LYS cc_start: 0.7940 (mttm) cc_final: 0.7656 (mmmt) REVERT: L 221 ARG cc_start: 0.7938 (ttp-170) cc_final: 0.7506 (tpp-160) REVERT: L 350 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7724 (tpt90) REVERT: L 358 ARG cc_start: 0.7416 (mtp180) cc_final: 0.7085 (mtm180) REVERT: L 403 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7358 (pp) REVERT: L 420 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7473 (mm-30) REVERT: M 4 GLN cc_start: 0.6674 (mp-120) cc_final: 0.6168 (mt0) REVERT: M 6 GLU cc_start: 0.6446 (tp30) cc_final: 0.5973 (mm-30) REVERT: O 4 GLN cc_start: 0.6641 (mp10) cc_final: 0.6204 (mt0) REVERT: O 6 GLU cc_start: 0.6343 (mm-30) cc_final: 0.6110 (mm-30) REVERT: P 4 GLN cc_start: 0.6586 (mm110) cc_final: 0.6236 (mt0) REVERT: Q 86 ARG cc_start: 0.7358 (mmt90) cc_final: 0.6976 (mmm160) REVERT: Q 96 LYS cc_start: 0.7917 (mttm) cc_final: 0.7679 (mmmt) REVERT: Q 115 LYS cc_start: 0.7946 (tptp) cc_final: 0.7129 (mmtm) REVERT: Q 221 ARG cc_start: 0.8189 (ttp-170) cc_final: 0.7759 (tpp-160) REVERT: Q 358 ARG cc_start: 0.7496 (mtp180) cc_final: 0.7172 (mtm180) REVERT: Q 391 LYS cc_start: 0.8383 (tptp) cc_final: 0.8162 (ttmt) REVERT: Q 403 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7677 (mm) REVERT: R 86 ARG cc_start: 0.7464 (mmt90) cc_final: 0.6946 (mmm160) REVERT: R 93 ASP cc_start: 0.7270 (m-30) cc_final: 0.7000 (m-30) REVERT: R 96 LYS cc_start: 0.7939 (mttm) cc_final: 0.7673 (mmmt) REVERT: R 221 ARG cc_start: 0.7935 (ttp-170) cc_final: 0.7498 (tpp-160) REVERT: R 273 MET cc_start: 0.8669 (mtp) cc_final: 0.7949 (mtp) REVERT: R 358 ARG cc_start: 0.7417 (mtp180) cc_final: 0.7030 (mtm180) REVERT: R 403 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7240 (pp) REVERT: R 420 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7498 (mm-30) REVERT: S 86 ARG cc_start: 0.7412 (mmt90) cc_final: 0.7014 (mmm160) REVERT: S 157 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7785 (tt) REVERT: S 165 ASN cc_start: 0.6883 (t0) cc_final: 0.6535 (t160) REVERT: S 391 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8052 (ttpt) REVERT: S 403 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7578 (mm) REVERT: S 420 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7565 (tp30) REVERT: T 86 ARG cc_start: 0.7444 (mmt90) cc_final: 0.6921 (mmm160) REVERT: T 96 LYS cc_start: 0.7931 (mttm) cc_final: 0.7647 (mmmt) REVERT: T 221 ARG cc_start: 0.7948 (ttp-170) cc_final: 0.7506 (tpp-160) REVERT: T 350 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7721 (tpt90) REVERT: T 358 ARG cc_start: 0.7440 (mtp180) cc_final: 0.7101 (mtm180) REVERT: T 403 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7368 (pp) REVERT: T 420 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7496 (mm-30) REVERT: U 4 GLN cc_start: 0.6466 (mm110) cc_final: 0.6021 (mt0) REVERT: U 6 GLU cc_start: 0.6475 (tp30) cc_final: 0.5672 (mm-30) REVERT: V 4 GLN cc_start: 0.6682 (mp-120) cc_final: 0.6179 (mt0) REVERT: V 6 GLU cc_start: 0.6411 (tp30) cc_final: 0.5975 (mm-30) REVERT: W 86 ARG cc_start: 0.7382 (mmt90) cc_final: 0.6937 (mmm160) REVERT: W 157 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7585 (tt) REVERT: W 179 PHE cc_start: 0.6688 (OUTLIER) cc_final: 0.5315 (m-80) REVERT: W 222 GLN cc_start: 0.7815 (tt0) cc_final: 0.7463 (mt0) REVERT: W 273 MET cc_start: 0.8554 (mtp) cc_final: 0.7973 (mtp) REVERT: W 391 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8043 (ttpt) REVERT: W 403 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7568 (mm) REVERT: W 420 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7461 (mm-30) REVERT: X 86 ARG cc_start: 0.7392 (mmt90) cc_final: 0.7001 (mmm160) REVERT: X 96 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7751 (mmmt) REVERT: X 221 ARG cc_start: 0.8064 (ttp-170) cc_final: 0.7612 (tpp-160) REVERT: X 358 ARG cc_start: 0.7542 (mtp180) cc_final: 0.7112 (mtm180) REVERT: X 391 LYS cc_start: 0.8374 (tptp) cc_final: 0.8168 (ttmt) outliers start: 111 outliers final: 36 residues processed: 817 average time/residue: 0.9118 time to fit residues: 876.9301 Evaluate side-chains 809 residues out of total 4668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 738 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 179 PHE Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain F residue 420 GLU Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 179 PHE Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 317 MET Chi-restraints excluded: chain J residue 326 LEU Chi-restraints excluded: chain J residue 373 MET Chi-restraints excluded: chain J residue 403 ILE Chi-restraints excluded: chain J residue 420 GLU Chi-restraints excluded: chain K residue 15 GLU Chi-restraints excluded: chain K residue 96 LYS Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 398 ILE Chi-restraints excluded: chain K residue 403 ILE Chi-restraints excluded: chain L residue 2 SER Chi-restraints excluded: chain L residue 138 THR Chi-restraints excluded: chain L residue 350 ARG Chi-restraints excluded: chain L residue 395 SER Chi-restraints excluded: chain L residue 398 ILE Chi-restraints excluded: chain L residue 403 ILE Chi-restraints excluded: chain L residue 420 GLU Chi-restraints excluded: chain O residue 3 ILE Chi-restraints excluded: chain Q residue 15 GLU Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain Q residue 398 ILE Chi-restraints excluded: chain Q residue 403 ILE Chi-restraints excluded: chain R residue 50 MET Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 395 SER Chi-restraints excluded: chain R residue 398 ILE Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain R residue 420 GLU Chi-restraints excluded: chain S residue 157 LEU Chi-restraints excluded: chain S residue 326 LEU Chi-restraints excluded: chain S residue 373 MET Chi-restraints excluded: chain S residue 391 LYS Chi-restraints excluded: chain S residue 403 ILE Chi-restraints excluded: chain S residue 420 GLU Chi-restraints excluded: chain T residue 2 SER Chi-restraints excluded: chain T residue 350 ARG Chi-restraints excluded: chain T residue 398 ILE Chi-restraints excluded: chain T residue 403 ILE Chi-restraints excluded: chain T residue 420 GLU Chi-restraints excluded: chain W residue 157 LEU Chi-restraints excluded: chain W residue 179 PHE Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 326 LEU Chi-restraints excluded: chain W residue 373 MET Chi-restraints excluded: chain W residue 391 LYS Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain W residue 420 GLU Chi-restraints excluded: chain X residue 96 LYS Chi-restraints excluded: chain X residue 373 MET Chi-restraints excluded: chain X residue 398 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 21 optimal weight: 8.9990 chunk 519 optimal weight: 3.9990 chunk 448 optimal weight: 2.9990 chunk 372 optimal weight: 6.9990 chunk 443 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 507 optimal weight: 7.9990 chunk 379 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 359 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN E 33 ASN E 126 ASN E 210 GLN ** E 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN F 126 ASN F 313 ASN J 33 ASN ** J 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 ASN K 210 GLN L 33 ASN L 126 ASN ** L 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 33 ASN Q 210 GLN ** Q 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 33 ASN R 126 ASN R 313 ASN S 33 ASN T 33 ASN T 126 ASN T 313 ASN ** T 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 33 ASN ** W 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 33 ASN X 210 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.182725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.165928 restraints weight = 34528.973| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 0.78 r_work: 0.3732 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 43464 Z= 0.174 Angle : 0.586 5.813 58968 Z= 0.314 Chirality : 0.043 0.148 6456 Planarity : 0.006 0.079 7716 Dihedral : 5.642 57.627 5990 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.85 % Favored : 95.13 % Rotamer: Outliers : 2.96 % Allowed : 17.55 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.11), residues: 5364 helix: 1.31 (0.11), residues: 2196 sheet: -1.65 (0.16), residues: 756 loop : -0.25 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG W 5 TYR 0.030 0.003 TYR J 294 PHE 0.016 0.002 PHE B 179 TRP 0.014 0.002 TRP W 423 HIS 0.007 0.002 HIS B 193 Details of bonding type rmsd covalent geometry : bond 0.00382 (43464) covalent geometry : angle 0.58615 (58968) hydrogen bonds : bond 0.05619 ( 1642) hydrogen bonds : angle 4.94814 ( 4668) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 4668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 735 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 GLN cc_start: 0.6599 (mp10) cc_final: 0.6200 (mt0) REVERT: B 86 ARG cc_start: 0.7504 (mmt90) cc_final: 0.7114 (mmm160) REVERT: B 157 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7883 (tt) REVERT: B 165 ASN cc_start: 0.7068 (t0) cc_final: 0.6674 (t0) REVERT: B 222 GLN cc_start: 0.7883 (tt0) cc_final: 0.7576 (mt0) REVERT: B 273 MET cc_start: 0.8642 (mtp) cc_final: 0.8117 (mtp) REVERT: B 420 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7477 (mm-30) REVERT: C 4 GLN cc_start: 0.6709 (mp-120) cc_final: 0.6228 (mt0) REVERT: C 6 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.6089 (mm-30) REVERT: E 86 ARG cc_start: 0.7449 (mmt90) cc_final: 0.7107 (mmm160) REVERT: E 96 LYS cc_start: 0.7957 (mttm) cc_final: 0.7696 (mmmt) REVERT: E 115 LYS cc_start: 0.7923 (tptp) cc_final: 0.7143 (mmtm) REVERT: E 221 ARG cc_start: 0.8229 (ttp-170) cc_final: 0.7780 (tpp-160) REVERT: E 358 ARG cc_start: 0.7532 (mtp180) cc_final: 0.7165 (mtm180) REVERT: F 86 ARG cc_start: 0.7596 (mmt90) cc_final: 0.7087 (mmm160) REVERT: F 96 LYS cc_start: 0.7973 (mttm) cc_final: 0.7707 (mmmt) REVERT: F 115 LYS cc_start: 0.7703 (tptp) cc_final: 0.6911 (mmtm) REVERT: F 221 ARG cc_start: 0.8052 (ttp-170) cc_final: 0.7792 (tpp-160) REVERT: F 358 ARG cc_start: 0.7416 (mtp180) cc_final: 0.7065 (mtm180) REVERT: F 403 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7521 (pp) REVERT: F 420 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7428 (mm-30) REVERT: G 4 GLN cc_start: 0.6553 (mm110) cc_final: 0.6099 (mt0) REVERT: G 6 GLU cc_start: 0.6508 (tp30) cc_final: 0.5737 (mm-30) REVERT: H 4 GLN cc_start: 0.6750 (mp-120) cc_final: 0.6257 (mt0) REVERT: H 6 GLU cc_start: 0.6452 (tp30) cc_final: 0.6068 (mm-30) REVERT: I 4 GLN cc_start: 0.6720 (mp-120) cc_final: 0.6251 (mt0) REVERT: J 86 ARG cc_start: 0.7463 (mmt90) cc_final: 0.7086 (mmm160) REVERT: J 157 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7908 (tt) REVERT: J 222 GLN cc_start: 0.7930 (tt0) cc_final: 0.7599 (mt0) REVERT: J 273 MET cc_start: 0.8645 (mtp) cc_final: 0.8126 (mtp) REVERT: J 420 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7476 (mm-30) REVERT: K 86 ARG cc_start: 0.7466 (mmt90) cc_final: 0.7106 (mmm160) REVERT: K 115 LYS cc_start: 0.7983 (tptt) cc_final: 0.7257 (mmtm) REVERT: K 317 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.6896 (tpt) REVERT: K 358 ARG cc_start: 0.7539 (mtp180) cc_final: 0.7162 (mtm180) REVERT: L 86 ARG cc_start: 0.7586 (mmt90) cc_final: 0.7068 (mmm160) REVERT: L 96 LYS cc_start: 0.7979 (mttm) cc_final: 0.7693 (mmmt) REVERT: L 115 LYS cc_start: 0.7726 (tptp) cc_final: 0.6911 (mmtm) REVERT: L 221 ARG cc_start: 0.8053 (ttp-170) cc_final: 0.7845 (tpp-160) REVERT: L 350 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7771 (tpt90) REVERT: L 358 ARG cc_start: 0.7463 (mtp180) cc_final: 0.7126 (mtm180) REVERT: L 403 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7528 (pp) REVERT: L 420 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7462 (mm-30) REVERT: M 4 GLN cc_start: 0.6772 (mp-120) cc_final: 0.6274 (mt0) REVERT: M 6 GLU cc_start: 0.6450 (tp30) cc_final: 0.5996 (mm-30) REVERT: O 4 GLN cc_start: 0.6662 (mp10) cc_final: 0.6198 (mt0) REVERT: P 4 GLN cc_start: 0.6646 (mm110) cc_final: 0.6277 (mt0) REVERT: Q 86 ARG cc_start: 0.7470 (mmt90) cc_final: 0.7124 (mmm160) REVERT: Q 96 LYS cc_start: 0.7950 (mttm) cc_final: 0.7702 (mmmt) REVERT: Q 115 LYS cc_start: 0.7954 (tptp) cc_final: 0.7139 (mmtm) REVERT: Q 165 ASN cc_start: 0.7087 (t0) cc_final: 0.6846 (t160) REVERT: Q 221 ARG cc_start: 0.8208 (ttp-170) cc_final: 0.7753 (tpp-160) REVERT: Q 358 ARG cc_start: 0.7679 (mtp180) cc_final: 0.7255 (mtm180) REVERT: R 86 ARG cc_start: 0.7587 (mmt90) cc_final: 0.7087 (mmm160) REVERT: R 93 ASP cc_start: 0.7443 (m-30) cc_final: 0.7214 (m-30) REVERT: R 96 LYS cc_start: 0.7974 (mttm) cc_final: 0.7712 (mmmt) REVERT: R 115 LYS cc_start: 0.7734 (tptp) cc_final: 0.6919 (mmtm) REVERT: R 221 ARG cc_start: 0.8044 (ttp-170) cc_final: 0.7798 (tpp-160) REVERT: R 358 ARG cc_start: 0.7433 (mtp180) cc_final: 0.7062 (mtm180) REVERT: R 403 ILE cc_start: 0.7894 (OUTLIER) cc_final: 0.7514 (pp) REVERT: S 86 ARG cc_start: 0.7445 (mmt90) cc_final: 0.7060 (mmm160) REVERT: S 157 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7895 (tt) REVERT: S 165 ASN cc_start: 0.7207 (t0) cc_final: 0.6821 (t0) REVERT: S 391 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8158 (ttmt) REVERT: S 420 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7617 (tp30) REVERT: T 86 ARG cc_start: 0.7578 (mmt90) cc_final: 0.7051 (mmm160) REVERT: T 96 LYS cc_start: 0.7973 (mttm) cc_final: 0.7688 (mmmt) REVERT: T 115 LYS cc_start: 0.7721 (tptp) cc_final: 0.6902 (mmtm) REVERT: T 221 ARG cc_start: 0.8054 (ttp-170) cc_final: 0.7843 (tpp-160) REVERT: T 350 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7769 (tpt90) REVERT: T 358 ARG cc_start: 0.7487 (mtp180) cc_final: 0.7144 (mtm180) REVERT: T 403 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7524 (pp) REVERT: U 4 GLN cc_start: 0.6428 (mm110) cc_final: 0.6047 (mt0) REVERT: U 6 GLU cc_start: 0.6491 (tp30) cc_final: 0.5778 (mm-30) REVERT: V 4 GLN cc_start: 0.6755 (mp-120) cc_final: 0.6270 (mt0) REVERT: V 6 GLU cc_start: 0.6460 (tp30) cc_final: 0.6005 (mm-30) REVERT: W 86 ARG cc_start: 0.7458 (mmt90) cc_final: 0.7081 (mmm160) REVERT: W 157 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7796 (tt) REVERT: W 222 GLN cc_start: 0.7935 (tt0) cc_final: 0.7602 (mt0) REVERT: W 273 MET cc_start: 0.8643 (mtp) cc_final: 0.8127 (mtp) REVERT: W 391 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8156 (ttmt) REVERT: W 420 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7498 (mm-30) REVERT: X 86 ARG cc_start: 0.7488 (mmt90) cc_final: 0.7120 (mmm160) REVERT: X 221 ARG cc_start: 0.8185 (ttp-170) cc_final: 0.7792 (tpp-160) REVERT: X 358 ARG cc_start: 0.7559 (mtp180) cc_final: 0.7169 (mtm180) outliers start: 130 outliers final: 69 residues processed: 824 average time/residue: 0.9017 time to fit residues: 875.5923 Evaluate side-chains 814 residues out of total 4668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 725 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 395 SER Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain F residue 420 GLU Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 326 LEU Chi-restraints excluded: chain J residue 373 MET Chi-restraints excluded: chain J residue 395 SER Chi-restraints excluded: chain J residue 403 ILE Chi-restraints excluded: chain J residue 420 GLU Chi-restraints excluded: chain K residue 15 GLU Chi-restraints excluded: chain K residue 96 LYS Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 221 ARG Chi-restraints excluded: chain K residue 317 MET Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain K residue 398 ILE Chi-restraints excluded: chain K residue 403 ILE Chi-restraints excluded: chain L residue 2 SER Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 138 THR Chi-restraints excluded: chain L residue 203 VAL Chi-restraints excluded: chain L residue 350 ARG Chi-restraints excluded: chain L residue 395 SER Chi-restraints excluded: chain L residue 398 ILE Chi-restraints excluded: chain L residue 403 ILE Chi-restraints excluded: chain L residue 420 GLU Chi-restraints excluded: chain O residue 3 ILE Chi-restraints excluded: chain Q residue 15 GLU Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain Q residue 398 ILE Chi-restraints excluded: chain Q residue 403 ILE Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 203 VAL Chi-restraints excluded: chain R residue 395 SER Chi-restraints excluded: chain R residue 398 ILE Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 157 LEU Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain S residue 326 LEU Chi-restraints excluded: chain S residue 373 MET Chi-restraints excluded: chain S residue 391 LYS Chi-restraints excluded: chain S residue 403 ILE Chi-restraints excluded: chain S residue 420 GLU Chi-restraints excluded: chain T residue 2 SER Chi-restraints excluded: chain T residue 138 THR Chi-restraints excluded: chain T residue 203 VAL Chi-restraints excluded: chain T residue 312 SER Chi-restraints excluded: chain T residue 350 ARG Chi-restraints excluded: chain T residue 395 SER Chi-restraints excluded: chain T residue 398 ILE Chi-restraints excluded: chain T residue 403 ILE Chi-restraints excluded: chain W residue 138 THR Chi-restraints excluded: chain W residue 157 LEU Chi-restraints excluded: chain W residue 160 MET Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 326 LEU Chi-restraints excluded: chain W residue 373 MET Chi-restraints excluded: chain W residue 391 LYS Chi-restraints excluded: chain W residue 395 SER Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain W residue 420 GLU Chi-restraints excluded: chain X residue 96 LYS Chi-restraints excluded: chain X residue 326 LEU Chi-restraints excluded: chain X residue 373 MET Chi-restraints excluded: chain X residue 398 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 206 optimal weight: 10.0000 chunk 502 optimal weight: 6.9990 chunk 528 optimal weight: 9.9990 chunk 253 optimal weight: 0.9980 chunk 368 optimal weight: 10.0000 chunk 405 optimal weight: 1.9990 chunk 297 optimal weight: 1.9990 chunk 213 optimal weight: 0.9990 chunk 333 optimal weight: 0.9990 chunk 105 optimal weight: 20.0000 chunk 235 optimal weight: 0.0070 overall best weight: 1.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 210 GLN ** E 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN F 126 ASN F 313 ASN J 33 ASN J 165 ASN ** J 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 ASN K 165 ASN K 210 GLN L 33 ASN L 126 ASN ** L 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 33 ASN Q 210 GLN ** Q 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 33 ASN R 126 ASN R 313 ASN ** R 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 33 ASN T 33 ASN T 126 ASN T 313 ASN ** T 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 33 ASN W 165 ASN X 33 ASN X 165 ASN X 210 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.186233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.169364 restraints weight = 34488.810| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 0.79 r_work: 0.3768 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3679 r_free = 0.3679 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3679 r_free = 0.3679 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 43464 Z= 0.097 Angle : 0.455 4.325 58968 Z= 0.243 Chirality : 0.039 0.134 6456 Planarity : 0.004 0.042 7716 Dihedral : 5.223 59.087 5990 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.09 % Allowed : 18.35 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.11), residues: 5364 helix: 1.65 (0.11), residues: 2196 sheet: -1.16 (0.15), residues: 900 loop : -0.13 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 324 TYR 0.021 0.002 TYR L 294 PHE 0.011 0.001 PHE J 179 TRP 0.010 0.001 TRP S 423 HIS 0.004 0.001 HIS B 193 Details of bonding type rmsd covalent geometry : bond 0.00207 (43464) covalent geometry : angle 0.45548 (58968) hydrogen bonds : bond 0.04277 ( 1642) hydrogen bonds : angle 4.51984 ( 4668) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 4668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 741 time to evaluate : 1.591 Fit side-chains REVERT: A 4 GLN cc_start: 0.6614 (mp10) cc_final: 0.6187 (mt0) REVERT: B 86 ARG cc_start: 0.7441 (mmt90) cc_final: 0.7006 (mmm160) REVERT: B 157 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7686 (tt) REVERT: B 165 ASN cc_start: 0.7045 (t0) cc_final: 0.6677 (t160) REVERT: B 222 GLN cc_start: 0.7844 (tt0) cc_final: 0.7488 (mt0) REVERT: B 273 MET cc_start: 0.8573 (mtp) cc_final: 0.7967 (mtp) REVERT: B 403 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7568 (mm) REVERT: B 420 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7467 (mm-30) REVERT: C 3 ILE cc_start: 0.5024 (OUTLIER) cc_final: 0.4747 (pp) REVERT: C 4 GLN cc_start: 0.6713 (mp-120) cc_final: 0.6228 (mt0) REVERT: C 6 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.6098 (mm-30) REVERT: D 4 GLN cc_start: 0.6982 (tp40) cc_final: 0.6589 (mt0) REVERT: E 86 ARG cc_start: 0.7413 (mmt90) cc_final: 0.7072 (mmm160) REVERT: E 96 LYS cc_start: 0.7935 (mttm) cc_final: 0.7689 (mmmt) REVERT: E 115 LYS cc_start: 0.7952 (tptp) cc_final: 0.7183 (mmtm) REVERT: E 221 ARG cc_start: 0.8207 (ttp-170) cc_final: 0.7795 (tpp-160) REVERT: E 358 ARG cc_start: 0.7517 (mtp180) cc_final: 0.7226 (mtm180) REVERT: F 86 ARG cc_start: 0.7512 (mmt90) cc_final: 0.6995 (mmm160) REVERT: F 96 LYS cc_start: 0.7948 (mttm) cc_final: 0.7688 (mmmt) REVERT: F 115 LYS cc_start: 0.7698 (tptp) cc_final: 0.6868 (mmtm) REVERT: F 221 ARG cc_start: 0.7985 (ttp-170) cc_final: 0.7533 (tpp-160) REVERT: F 358 ARG cc_start: 0.7392 (mtp180) cc_final: 0.7049 (mtm180) REVERT: F 403 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7240 (pp) REVERT: F 420 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7489 (mm-30) REVERT: G 4 GLN cc_start: 0.6477 (mm110) cc_final: 0.6015 (mt0) REVERT: G 6 GLU cc_start: 0.6495 (tp30) cc_final: 0.5718 (mm-30) REVERT: H 4 GLN cc_start: 0.6717 (mp-120) cc_final: 0.6209 (mt0) REVERT: H 6 GLU cc_start: 0.6432 (tp30) cc_final: 0.6022 (mm-30) REVERT: I 4 GLN cc_start: 0.6735 (mp-120) cc_final: 0.6250 (mt0) REVERT: J 86 ARG cc_start: 0.7414 (mmt90) cc_final: 0.6973 (mmm160) REVERT: J 157 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7796 (tt) REVERT: J 222 GLN cc_start: 0.7870 (tt0) cc_final: 0.7499 (mt0) REVERT: J 273 MET cc_start: 0.8577 (mtp) cc_final: 0.7978 (mtp) REVERT: J 403 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7564 (mm) REVERT: J 420 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7460 (mm-30) REVERT: K 86 ARG cc_start: 0.7437 (mmt90) cc_final: 0.7068 (mmm160) REVERT: K 96 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7807 (mmmt) REVERT: K 115 LYS cc_start: 0.7982 (tptt) cc_final: 0.7246 (mmtm) REVERT: K 358 ARG cc_start: 0.7487 (mtp180) cc_final: 0.7086 (mtm180) REVERT: L 86 ARG cc_start: 0.7499 (mmt90) cc_final: 0.6975 (mmm160) REVERT: L 96 LYS cc_start: 0.7950 (mttm) cc_final: 0.7689 (mmmt) REVERT: L 221 ARG cc_start: 0.7984 (ttp-170) cc_final: 0.7551 (tpp-160) REVERT: L 350 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7724 (tpt90) REVERT: L 358 ARG cc_start: 0.7446 (mtp180) cc_final: 0.7115 (mtm180) REVERT: L 403 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7357 (pp) REVERT: L 420 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7515 (mm-30) REVERT: M 4 GLN cc_start: 0.6731 (mp-120) cc_final: 0.6220 (mt0) REVERT: M 6 GLU cc_start: 0.6463 (tp30) cc_final: 0.6032 (mm-30) REVERT: O 4 GLN cc_start: 0.6681 (mp10) cc_final: 0.6230 (mt0) REVERT: P 4 GLN cc_start: 0.6717 (mm110) cc_final: 0.6305 (mt0) REVERT: Q 86 ARG cc_start: 0.7408 (mmt90) cc_final: 0.7073 (mmm160) REVERT: Q 96 LYS cc_start: 0.7935 (mttm) cc_final: 0.7691 (mmmt) REVERT: Q 115 LYS cc_start: 0.8008 (tptp) cc_final: 0.7213 (mmtm) REVERT: Q 221 ARG cc_start: 0.8215 (ttp-170) cc_final: 0.7796 (tpp-160) REVERT: Q 358 ARG cc_start: 0.7612 (mtp180) cc_final: 0.7195 (mtm180) REVERT: Q 391 LYS cc_start: 0.8405 (tptp) cc_final: 0.8198 (ttmt) REVERT: R 86 ARG cc_start: 0.7488 (mmt90) cc_final: 0.6995 (mmm160) REVERT: R 93 ASP cc_start: 0.7357 (m-30) cc_final: 0.7077 (m-30) REVERT: R 96 LYS cc_start: 0.7948 (mttm) cc_final: 0.7692 (mmmt) REVERT: R 221 ARG cc_start: 0.7969 (ttp-170) cc_final: 0.7534 (tpp-160) REVERT: R 358 ARG cc_start: 0.7428 (mtp180) cc_final: 0.7042 (mtm180) REVERT: R 403 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.7239 (pp) REVERT: S 86 ARG cc_start: 0.7457 (mmt90) cc_final: 0.6987 (mmm160) REVERT: S 157 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7702 (tt) REVERT: S 160 MET cc_start: 0.5864 (ptt) cc_final: 0.5644 (ptt) REVERT: S 165 ASN cc_start: 0.7095 (t0) cc_final: 0.6783 (t160) REVERT: S 403 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7573 (mm) REVERT: S 420 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7586 (tp30) REVERT: T 86 ARG cc_start: 0.7486 (mmt90) cc_final: 0.6959 (mmm160) REVERT: T 96 LYS cc_start: 0.7946 (mttm) cc_final: 0.7679 (mmmt) REVERT: T 221 ARG cc_start: 0.7984 (ttp-170) cc_final: 0.7542 (tpp-160) REVERT: T 350 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7732 (tpt90) REVERT: T 358 ARG cc_start: 0.7464 (mtp180) cc_final: 0.7129 (mtm180) REVERT: T 403 ILE cc_start: 0.7668 (OUTLIER) cc_final: 0.7368 (pp) REVERT: U 4 GLN cc_start: 0.6419 (mm110) cc_final: 0.6034 (mt0) REVERT: U 6 GLU cc_start: 0.6472 (tp30) cc_final: 0.5708 (mm-30) REVERT: V 4 GLN cc_start: 0.6756 (mp-120) cc_final: 0.6249 (mt0) REVERT: V 6 GLU cc_start: 0.6432 (tp30) cc_final: 0.6026 (mm-30) REVERT: W 86 ARG cc_start: 0.7415 (mmt90) cc_final: 0.6995 (mmm160) REVERT: W 157 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7666 (tt) REVERT: W 222 GLN cc_start: 0.7873 (tt0) cc_final: 0.7516 (mt0) REVERT: W 273 MET cc_start: 0.8577 (mtp) cc_final: 0.7980 (mtp) REVERT: W 403 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7568 (mm) REVERT: W 420 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7498 (mm-30) REVERT: X 86 ARG cc_start: 0.7446 (mmt90) cc_final: 0.7086 (mmm160) REVERT: X 96 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7784 (mmmt) REVERT: X 221 ARG cc_start: 0.8083 (ttp-170) cc_final: 0.7734 (tpp-160) REVERT: X 350 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7807 (tpt90) REVERT: X 358 ARG cc_start: 0.7514 (mtp180) cc_final: 0.7099 (mtm180) outliers start: 92 outliers final: 49 residues processed: 804 average time/residue: 0.8569 time to fit residues: 811.8536 Evaluate side-chains 814 residues out of total 4668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 740 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain E residue 395 SER Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 395 SER Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain F residue 420 GLU Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain J residue 2 SER Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 326 LEU Chi-restraints excluded: chain J residue 373 MET Chi-restraints excluded: chain J residue 403 ILE Chi-restraints excluded: chain J residue 420 GLU Chi-restraints excluded: chain K residue 15 GLU Chi-restraints excluded: chain K residue 96 LYS Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 395 SER Chi-restraints excluded: chain K residue 398 ILE Chi-restraints excluded: chain K residue 403 ILE Chi-restraints excluded: chain L residue 2 SER Chi-restraints excluded: chain L residue 138 THR Chi-restraints excluded: chain L residue 203 VAL Chi-restraints excluded: chain L residue 350 ARG Chi-restraints excluded: chain L residue 395 SER Chi-restraints excluded: chain L residue 398 ILE Chi-restraints excluded: chain L residue 403 ILE Chi-restraints excluded: chain L residue 420 GLU Chi-restraints excluded: chain O residue 3 ILE Chi-restraints excluded: chain Q residue 15 GLU Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain Q residue 398 ILE Chi-restraints excluded: chain Q residue 403 ILE Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 395 SER Chi-restraints excluded: chain R residue 398 ILE Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain S residue 157 LEU Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain S residue 326 LEU Chi-restraints excluded: chain S residue 373 MET Chi-restraints excluded: chain S residue 403 ILE Chi-restraints excluded: chain S residue 420 GLU Chi-restraints excluded: chain T residue 2 SER Chi-restraints excluded: chain T residue 203 VAL Chi-restraints excluded: chain T residue 312 SER Chi-restraints excluded: chain T residue 350 ARG Chi-restraints excluded: chain T residue 395 SER Chi-restraints excluded: chain T residue 398 ILE Chi-restraints excluded: chain T residue 403 ILE Chi-restraints excluded: chain W residue 157 LEU Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 326 LEU Chi-restraints excluded: chain W residue 373 MET Chi-restraints excluded: chain W residue 395 SER Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain W residue 420 GLU Chi-restraints excluded: chain X residue 96 LYS Chi-restraints excluded: chain X residue 350 ARG Chi-restraints excluded: chain X residue 373 MET Chi-restraints excluded: chain X residue 398 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 65 optimal weight: 0.7980 chunk 78 optimal weight: 0.0040 chunk 126 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 406 optimal weight: 4.9990 chunk 427 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 472 optimal weight: 8.9990 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN E 33 ASN ** E 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN F 126 ASN F 313 ASN J 33 ASN K 33 ASN L 33 ASN ** L 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 33 ASN ** Q 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 33 ASN R 126 ASN R 313 ASN ** R 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 33 ASN T 313 ASN ** T 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 33 ASN W 165 ASN X 33 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.185393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.168346 restraints weight = 34642.845| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 0.80 r_work: 0.3756 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 43464 Z= 0.114 Angle : 0.486 4.557 58968 Z= 0.259 Chirality : 0.040 0.137 6456 Planarity : 0.004 0.045 7716 Dihedral : 5.300 59.323 5990 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.44 % Allowed : 18.33 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.11), residues: 5364 helix: 1.62 (0.11), residues: 2196 sheet: -1.53 (0.16), residues: 780 loop : -0.15 (0.13), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 324 TYR 0.023 0.002 TYR R 294 PHE 0.012 0.001 PHE B 179 TRP 0.011 0.002 TRP S 423 HIS 0.005 0.001 HIS J 193 Details of bonding type rmsd covalent geometry : bond 0.00244 (43464) covalent geometry : angle 0.48647 (58968) hydrogen bonds : bond 0.04642 ( 1642) hydrogen bonds : angle 4.60040 ( 4668) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21085.15 seconds wall clock time: 357 minutes 39.01 seconds (21459.01 seconds total)