Starting phenix.real_space_refine on Tue Sep 24 08:40:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfc_25869/09_2024/7tfc_25869.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfc_25869/09_2024/7tfc_25869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfc_25869/09_2024/7tfc_25869.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfc_25869/09_2024/7tfc_25869.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfc_25869/09_2024/7tfc_25869.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfc_25869/09_2024/7tfc_25869.cif" } resolution = 1.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.120 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 28 5.21 5 S 224 5.16 5 C 32130 2.51 5 N 8484 2.21 5 O 9450 1.98 5 H 140 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 50456 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3498 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 418} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3498 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 418} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3498 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 418} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3498 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 418} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3498 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 418} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "H" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3498 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 418} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "I" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3498 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 418} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "J" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3498 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 418} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "O" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3498 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 418} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "P" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3498 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 418} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "Q" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3498 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 418} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "R" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3498 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 418} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "S" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3498 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 418} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "T" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3498 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 24, 'TRANS': 418} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "U" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" 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: "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: "C" 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: "G" 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: "H" 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: "I" 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: "N" 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: "O" 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: "P" 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} Residues with excluded nonbonded symmetry interactions: 14 residue: pdb=" N LEU A 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU A 350 " occ=0.92 residue: pdb=" N LEU B 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU B 350 " occ=0.92 residue: pdb=" N LEU C 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU C 350 " occ=0.92 residue: pdb=" N LEU F 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU F 350 " occ=0.92 residue: pdb=" N LEU G 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU G 350 " occ=0.92 residue: pdb=" N LEU H 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU H 350 " occ=0.92 residue: pdb=" N LEU I 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU I 350 " occ=0.92 residue: pdb=" N LEU N 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU N 350 " occ=0.92 residue: pdb=" N LEU O 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU O 350 " occ=0.92 residue: pdb=" N LEU P 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU P 350 " occ=0.92 residue: pdb=" N LEU Q 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU Q 350 " occ=0.92 residue: pdb=" N LEU R 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU R 350 " occ=0.92 ... (remaining 2 not shown) Time building chain proxies: 23.15, per 1000 atoms: 0.46 Number of scatterers: 50456 At special positions: 0 Unit cell: (170.72, 168.96, 124.08, 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 224 16.00 Mg 28 11.99 O 9450 8.00 N 8484 7.00 C 32130 6.00 H 140 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: 9.36 Conformation dependent library (CDL) restraints added in 4.8 seconds 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11900 Finding SS restraints... Secondary structure from input PDB file: 262 helices and 44 sheets defined 45.0% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.54 Creating SS restraints... Processing helix chain 'A' and resid 5 through 17 Processing helix chain 'A' and resid 41 through 47 Processing helix chain 'A' and resid 55 through 62 removed outlier: 6.472A pdb=" N PHE A 60 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL A 61 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 121 Processing helix chain 'A' and resid 167 through 179 Processing helix chain 'A' and resid 204 through 225 Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'A' and resid 268 through 281 Processing helix chain 'A' and resid 281 through 290 removed outlier: 3.513A pdb=" N THR A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ALA A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N VAL A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 299 removed outlier: 3.719A pdb=" N ARG A 298 " --> pdb=" O ASN A 294 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 294 through 299' Processing helix chain 'A' and resid 326 through 330 removed outlier: 3.669A pdb=" N SER A 329 " --> pdb=" O ARG A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 361 Processing helix chain 'A' and resid 376 through 382 removed outlier: 4.061A pdb=" N GLU A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 402 removed outlier: 3.507A pdb=" N SER A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 409 through 430 removed outlier: 4.148A pdb=" N LEU A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 430 " --> pdb=" O ASP A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 441 removed outlier: 3.545A pdb=" N ARG A 437 " --> pdb=" O HIS A 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 17 Processing helix chain 'B' and resid 41 through 47 Processing helix chain 'B' and resid 55 through 62 removed outlier: 6.487A pdb=" N PHE B 60 " --> pdb=" O ILE B 57 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL B 61 " --> pdb=" O GLU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 121 Processing helix chain 'B' and resid 167 through 179 Processing helix chain 'B' and resid 204 through 225 Processing helix chain 'B' and resid 263 through 267 Processing helix chain 'B' and resid 268 through 281 Processing helix chain 'B' and resid 281 through 290 removed outlier: 5.234A pdb=" N ALA B 287 " --> pdb=" O THR B 283 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N VAL B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 299 removed outlier: 3.710A pdb=" N ARG B 298 " --> pdb=" O ASN B 294 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 299 " --> pdb=" O SER B 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 294 through 299' Processing helix chain 'B' and resid 326 through 330 removed outlier: 3.613A pdb=" N SER B 329 " --> pdb=" O ARG B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 361 Processing helix chain 'B' and resid 376 through 382 removed outlier: 4.117A pdb=" N GLU B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 402 removed outlier: 3.502A pdb=" N SER B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 408 Processing helix chain 'B' and resid 409 through 430 removed outlier: 4.128A pdb=" N LEU B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 441 removed outlier: 3.569A pdb=" N ARG B 437 " --> pdb=" O HIS B 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 17 Processing helix chain 'C' and resid 41 through 47 Processing helix chain 'C' and resid 55 through 62 removed outlier: 6.411A pdb=" N PHE C 60 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL C 61 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG C 62 " --> pdb=" O GLY C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 121 Processing helix chain 'C' and resid 167 through 179 Processing helix chain 'C' and resid 204 through 225 Processing helix chain 'C' and resid 263 through 267 Processing helix chain 'C' and resid 268 through 281 Processing helix chain 'C' and resid 281 through 290 removed outlier: 3.524A pdb=" N THR C 286 " --> pdb=" O ALA C 282 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ALA C 287 " --> pdb=" O THR C 283 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N VAL C 288 " --> pdb=" O SER C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 299 removed outlier: 3.705A pdb=" N ARG C 298 " --> pdb=" O ASN C 294 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 299 " --> pdb=" O SER C 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 294 through 299' Processing helix chain 'C' and resid 326 through 330 removed outlier: 3.686A pdb=" N SER C 329 " --> pdb=" O ARG C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 361 Processing helix chain 'C' and resid 371 through 375 Processing helix chain 'C' and resid 377 through 382 removed outlier: 4.277A pdb=" N GLU C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 402 removed outlier: 3.511A pdb=" N ASN C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 408 removed outlier: 3.537A pdb=" N LYS C 407 " --> pdb=" O GLU C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 430 removed outlier: 4.127A pdb=" N LEU C 413 " --> pdb=" O LEU C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 441 removed outlier: 3.543A pdb=" N ARG C 437 " --> pdb=" O HIS C 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 10 removed outlier: 4.247A pdb=" N ARG D 9 " --> pdb=" O ASP D 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 10 removed outlier: 3.551A pdb=" N SER E 8 " --> pdb=" O GLY E 5 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG E 9 " --> pdb=" O ASP E 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 17 Processing helix chain 'F' and resid 41 through 47 Processing helix chain 'F' and resid 55 through 62 removed outlier: 6.458A pdb=" N PHE F 60 " --> pdb=" O ILE F 57 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL F 61 " --> pdb=" O GLU F 58 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG F 62 " --> pdb=" O GLY F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 77 Processing helix chain 'F' and resid 107 through 121 Processing helix chain 'F' and resid 167 through 179 Processing helix chain 'F' and resid 204 through 225 Processing helix chain 'F' and resid 263 through 267 Processing helix chain 'F' and resid 268 through 281 Processing helix chain 'F' and resid 281 through 290 removed outlier: 3.517A pdb=" N THR F 286 " --> pdb=" O ALA F 282 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ALA F 287 " --> pdb=" O THR F 283 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N VAL F 288 " --> pdb=" O SER F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 299 removed outlier: 3.660A pdb=" N ARG F 298 " --> pdb=" O ASN F 294 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU F 299 " --> pdb=" O SER F 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 294 through 299' Processing helix chain 'F' and resid 326 through 330 removed outlier: 3.622A pdb=" N SER F 329 " --> pdb=" O ARG F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 361 Processing helix chain 'F' and resid 376 through 382 removed outlier: 4.116A pdb=" N GLU F 382 " --> pdb=" O GLU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 402 Processing helix chain 'F' and resid 402 through 408 Processing helix chain 'F' and resid 409 through 430 removed outlier: 4.190A pdb=" N LEU F 413 " --> pdb=" O LEU F 409 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR F 430 " --> pdb=" O ASP F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 441 removed outlier: 3.526A pdb=" N ARG F 437 " --> pdb=" O HIS F 433 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 17 Processing helix chain 'G' and resid 41 through 47 Processing helix chain 'G' and resid 55 through 62 removed outlier: 6.422A pdb=" N PHE G 60 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL G 61 " --> pdb=" O GLU G 58 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG G 62 " --> pdb=" O GLY G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 77 Processing helix chain 'G' and resid 107 through 121 Processing helix chain 'G' and resid 167 through 179 Processing helix chain 'G' and resid 204 through 225 Processing helix chain 'G' and resid 263 through 267 Processing helix chain 'G' and resid 268 through 281 Processing helix chain 'G' and resid 281 through 290 removed outlier: 3.531A pdb=" N THR G 286 " --> pdb=" O ALA G 282 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ALA G 287 " --> pdb=" O THR G 283 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N VAL G 288 " --> pdb=" O SER G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 299 removed outlier: 3.705A pdb=" N ARG G 298 " --> pdb=" O ASN G 294 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU G 299 " --> pdb=" O SER G 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 294 through 299' Processing helix chain 'G' and resid 326 through 330 removed outlier: 3.627A pdb=" N SER G 329 " --> pdb=" O ARG G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 361 Processing helix chain 'G' and resid 376 through 382 removed outlier: 4.069A pdb=" N GLU G 382 " --> pdb=" O GLU G 378 " (cutoff:3.500A) Processing helix chain 'G' and resid 391 through 402 Processing helix chain 'G' and resid 402 through 408 removed outlier: 3.524A pdb=" N LYS G 407 " --> pdb=" O GLU G 403 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 430 removed outlier: 4.163A pdb=" N LEU G 413 " --> pdb=" O LEU G 409 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 441 removed outlier: 3.553A pdb=" N ARG G 437 " --> pdb=" O HIS G 433 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 17 Processing helix chain 'H' and resid 41 through 47 Processing helix chain 'H' and resid 55 through 62 removed outlier: 6.453A pdb=" N PHE H 60 " --> pdb=" O ILE H 57 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL H 61 " --> pdb=" O GLU H 58 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG H 62 " --> pdb=" O GLY H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 77 Processing helix chain 'H' and resid 107 through 121 Processing helix chain 'H' and resid 167 through 179 Processing helix chain 'H' and resid 204 through 225 Processing helix chain 'H' and resid 263 through 267 Processing helix chain 'H' and resid 268 through 281 Processing helix chain 'H' and resid 281 through 290 removed outlier: 5.263A pdb=" N ALA H 287 " --> pdb=" O THR H 283 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N VAL H 288 " --> pdb=" O SER H 284 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 299 removed outlier: 3.739A pdb=" N ARG H 298 " --> pdb=" O ASN H 294 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU H 299 " --> pdb=" O SER H 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 294 through 299' Processing helix chain 'H' and resid 326 through 330 removed outlier: 3.601A pdb=" N SER H 329 " --> pdb=" O ARG H 326 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 361 Processing helix chain 'H' and resid 377 through 382 removed outlier: 4.190A pdb=" N GLU H 382 " --> pdb=" O GLU H 378 " (cutoff:3.500A) Processing helix chain 'H' and resid 391 through 402 Processing helix chain 'H' and resid 402 through 408 Processing helix chain 'H' and resid 409 through 430 removed outlier: 4.153A pdb=" N LEU H 413 " --> pdb=" O LEU H 409 " (cutoff:3.500A) Processing helix chain 'H' and resid 433 through 441 removed outlier: 3.544A pdb=" N ARG H 437 " --> pdb=" O HIS H 433 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 17 Processing helix chain 'I' and resid 41 through 47 Processing helix chain 'I' and resid 55 through 62 removed outlier: 6.491A pdb=" N PHE I 60 " --> pdb=" O ILE I 57 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL I 61 " --> pdb=" O GLU I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 77 Processing helix chain 'I' and resid 107 through 122 Processing helix chain 'I' and resid 167 through 179 Processing helix chain 'I' and resid 204 through 225 Processing helix chain 'I' and resid 263 through 267 Processing helix chain 'I' and resid 268 through 281 Processing helix chain 'I' and resid 281 through 290 removed outlier: 5.233A pdb=" N ALA I 287 " --> pdb=" O THR I 283 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N VAL I 288 " --> pdb=" O SER I 284 " (cutoff:3.500A) Processing helix chain 'I' and resid 294 through 299 removed outlier: 3.693A pdb=" N ARG I 298 " --> pdb=" O ASN I 294 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU I 299 " --> pdb=" O SER I 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 294 through 299' Processing helix chain 'I' and resid 326 through 330 removed outlier: 3.566A pdb=" N SER I 329 " --> pdb=" O ARG I 326 " (cutoff:3.500A) Processing helix chain 'I' and resid 342 through 361 Processing helix chain 'I' and resid 376 through 382 removed outlier: 4.113A pdb=" N GLU I 382 " --> pdb=" O GLU I 378 " (cutoff:3.500A) Processing helix chain 'I' and resid 391 through 402 removed outlier: 3.500A pdb=" N SER I 401 " --> pdb=" O GLU I 397 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN I 402 " --> pdb=" O GLU I 398 " (cutoff:3.500A) Processing helix chain 'I' and resid 402 through 408 Processing helix chain 'I' and resid 409 through 430 removed outlier: 4.104A pdb=" N LEU I 413 " --> pdb=" O LEU I 409 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR I 430 " --> pdb=" O ASP I 426 " (cutoff:3.500A) Processing helix chain 'I' and resid 433 through 441 removed outlier: 3.567A pdb=" N ARG I 437 " --> pdb=" O HIS I 433 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 10 removed outlier: 4.166A pdb=" N ARG J 9 " --> pdb=" O ASP J 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.636A pdb=" N SER K 8 " --> pdb=" O GLY K 5 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG K 9 " --> pdb=" O ASP K 6 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 10 removed outlier: 3.525A pdb=" N SER L 8 " --> pdb=" O GLY L 5 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG L 9 " --> pdb=" O ASP L 6 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 10 removed outlier: 3.559A pdb=" N SER M 8 " --> pdb=" O GLY M 5 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG M 9 " --> pdb=" O ASP M 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 17 Processing helix chain 'N' and resid 41 through 47 Processing helix chain 'N' and resid 55 through 62 removed outlier: 6.448A pdb=" N PHE N 60 " --> pdb=" O ILE N 57 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL N 61 " --> pdb=" O GLU N 58 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG N 62 " --> pdb=" O GLY N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 77 Processing helix chain 'N' and resid 107 through 121 Processing helix chain 'N' and resid 167 through 179 Processing helix chain 'N' and resid 204 through 225 Processing helix chain 'N' and resid 263 through 267 Processing helix chain 'N' and resid 268 through 281 Processing helix chain 'N' and resid 281 through 290 removed outlier: 3.516A pdb=" N THR N 286 " --> pdb=" O ALA N 282 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ALA N 287 " --> pdb=" O THR N 283 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N VAL N 288 " --> pdb=" O SER N 284 " (cutoff:3.500A) Processing helix chain 'N' and resid 294 through 299 removed outlier: 3.660A pdb=" N ARG N 298 " --> pdb=" O ASN N 294 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU N 299 " --> pdb=" O SER N 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 294 through 299' Processing helix chain 'N' and resid 326 through 330 removed outlier: 3.628A pdb=" N SER N 329 " --> pdb=" O ARG N 326 " (cutoff:3.500A) Processing helix chain 'N' and resid 342 through 361 Processing helix chain 'N' and resid 376 through 382 removed outlier: 4.114A pdb=" N GLU N 382 " --> pdb=" O GLU N 378 " (cutoff:3.500A) Processing helix chain 'N' and resid 391 through 402 Processing helix chain 'N' and resid 402 through 408 removed outlier: 3.512A pdb=" N LYS N 407 " --> pdb=" O GLU N 403 " (cutoff:3.500A) Processing helix chain 'N' and resid 409 through 430 removed outlier: 4.156A pdb=" N LEU N 413 " --> pdb=" O LEU N 409 " (cutoff:3.500A) Processing helix chain 'N' and resid 433 through 441 removed outlier: 3.524A pdb=" N ARG N 437 " --> pdb=" O HIS N 433 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 17 Processing helix chain 'O' and resid 41 through 47 Processing helix chain 'O' and resid 55 through 62 removed outlier: 6.422A pdb=" N PHE O 60 " --> pdb=" O ILE O 57 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL O 61 " --> pdb=" O GLU O 58 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG O 62 " --> pdb=" O GLY O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 77 Processing helix chain 'O' and resid 107 through 121 Processing helix chain 'O' and resid 167 through 179 Processing helix chain 'O' and resid 204 through 225 Processing helix chain 'O' and resid 263 through 267 Processing helix chain 'O' and resid 268 through 281 Processing helix chain 'O' and resid 281 through 290 removed outlier: 3.545A pdb=" N THR O 286 " --> pdb=" O ALA O 282 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ALA O 287 " --> pdb=" O THR O 283 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N VAL O 288 " --> pdb=" O SER O 284 " (cutoff:3.500A) Processing helix chain 'O' and resid 294 through 299 removed outlier: 3.711A pdb=" N ARG O 298 " --> pdb=" O ASN O 294 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU O 299 " --> pdb=" O SER O 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 294 through 299' Processing helix chain 'O' and resid 326 through 330 removed outlier: 3.649A pdb=" N SER O 329 " --> pdb=" O ARG O 326 " (cutoff:3.500A) Processing helix chain 'O' and resid 342 through 361 Processing helix chain 'O' and resid 376 through 382 removed outlier: 4.149A pdb=" N GLU O 382 " --> pdb=" O GLU O 378 " (cutoff:3.500A) Processing helix chain 'O' and resid 391 through 402 Processing helix chain 'O' and resid 402 through 408 removed outlier: 3.576A pdb=" N VAL O 406 " --> pdb=" O ASN O 402 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS O 407 " --> pdb=" O GLU O 403 " (cutoff:3.500A) Processing helix chain 'O' and resid 409 through 430 removed outlier: 4.147A pdb=" N LEU O 413 " --> pdb=" O LEU O 409 " (cutoff:3.500A) Processing helix chain 'O' and resid 433 through 441 removed outlier: 3.553A pdb=" N ARG O 437 " --> pdb=" O HIS O 433 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 17 Processing helix chain 'P' and resid 41 through 47 Processing helix chain 'P' and resid 55 through 62 removed outlier: 6.453A pdb=" N PHE P 60 " --> pdb=" O ILE P 57 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL P 61 " --> pdb=" O GLU P 58 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG P 62 " --> pdb=" O GLY P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 73 through 77 Processing helix chain 'P' and resid 107 through 121 Processing helix chain 'P' and resid 167 through 179 Processing helix chain 'P' and resid 204 through 225 Processing helix chain 'P' and resid 263 through 267 Processing helix chain 'P' and resid 268 through 281 Processing helix chain 'P' and resid 281 through 290 removed outlier: 5.270A pdb=" N ALA P 287 " --> pdb=" O THR P 283 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N VAL P 288 " --> pdb=" O SER P 284 " (cutoff:3.500A) Processing helix chain 'P' and resid 294 through 299 removed outlier: 3.735A pdb=" N ARG P 298 " --> pdb=" O ASN P 294 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU P 299 " --> pdb=" O SER P 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 294 through 299' Processing helix chain 'P' and resid 326 through 330 removed outlier: 3.577A pdb=" N SER P 329 " --> pdb=" O ARG P 326 " (cutoff:3.500A) Processing helix chain 'P' and resid 342 through 361 Processing helix chain 'P' and resid 376 through 382 removed outlier: 4.196A pdb=" N GLU P 382 " --> pdb=" O GLU P 378 " (cutoff:3.500A) Processing helix chain 'P' and resid 391 through 402 Processing helix chain 'P' and resid 402 through 408 removed outlier: 3.539A pdb=" N VAL P 406 " --> pdb=" O ASN P 402 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS P 407 " --> pdb=" O GLU P 403 " (cutoff:3.500A) Processing helix chain 'P' and resid 409 through 430 removed outlier: 4.158A pdb=" N LEU P 413 " --> pdb=" O LEU P 409 " (cutoff:3.500A) Processing helix chain 'P' and resid 433 through 441 removed outlier: 3.542A pdb=" N ARG P 437 " --> pdb=" O HIS P 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 17 Processing helix chain 'Q' and resid 41 through 47 Processing helix chain 'Q' and resid 55 through 62 removed outlier: 6.494A pdb=" N PHE Q 60 " --> pdb=" O ILE Q 57 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL Q 61 " --> pdb=" O GLU Q 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 73 through 77 Processing helix chain 'Q' and resid 107 through 122 Processing helix chain 'Q' and resid 167 through 179 Processing helix chain 'Q' and resid 204 through 225 Processing helix chain 'Q' and resid 263 through 267 Processing helix chain 'Q' and resid 268 through 281 Processing helix chain 'Q' and resid 281 through 290 removed outlier: 5.229A pdb=" N ALA Q 287 " --> pdb=" O THR Q 283 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N VAL Q 288 " --> pdb=" O SER Q 284 " (cutoff:3.500A) Processing helix chain 'Q' and resid 294 through 299 removed outlier: 3.692A pdb=" N ARG Q 298 " --> pdb=" O ASN Q 294 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU Q 299 " --> pdb=" O SER Q 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 294 through 299' Processing helix chain 'Q' and resid 326 through 330 removed outlier: 3.567A pdb=" N SER Q 329 " --> pdb=" O ARG Q 326 " (cutoff:3.500A) Processing helix chain 'Q' and resid 342 through 361 Processing helix chain 'Q' and resid 376 through 382 removed outlier: 4.119A pdb=" N GLU Q 382 " --> pdb=" O GLU Q 378 " (cutoff:3.500A) Processing helix chain 'Q' and resid 391 through 402 Processing helix chain 'Q' and resid 402 through 408 Processing helix chain 'Q' and resid 409 through 430 removed outlier: 4.114A pdb=" N LEU Q 413 " --> pdb=" O LEU Q 409 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR Q 430 " --> pdb=" O ASP Q 426 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 441 removed outlier: 3.566A pdb=" N ARG Q 437 " --> pdb=" O HIS Q 433 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 17 Processing helix chain 'R' and resid 41 through 47 Processing helix chain 'R' and resid 55 through 62 removed outlier: 6.467A pdb=" N PHE R 60 " --> pdb=" O ILE R 57 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL R 61 " --> pdb=" O GLU R 58 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG R 62 " --> pdb=" O GLY R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 121 Processing helix chain 'R' and resid 167 through 179 Processing helix chain 'R' and resid 204 through 225 Processing helix chain 'R' and resid 263 through 267 Processing helix chain 'R' and resid 268 through 281 Processing helix chain 'R' and resid 281 through 290 removed outlier: 3.514A pdb=" N THR R 286 " --> pdb=" O ALA R 282 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ALA R 287 " --> pdb=" O THR R 283 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N VAL R 288 " --> pdb=" O SER R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 299 removed outlier: 3.729A pdb=" N ARG R 298 " --> pdb=" O ASN R 294 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU R 299 " --> pdb=" O SER R 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 294 through 299' Processing helix chain 'R' and resid 326 through 330 removed outlier: 3.857A pdb=" N SER R 329 " --> pdb=" O ARG R 326 " (cutoff:3.500A) Processing helix chain 'R' and resid 342 through 361 Processing helix chain 'R' and resid 376 through 382 removed outlier: 4.063A pdb=" N GLU R 382 " --> pdb=" O GLU R 378 " (cutoff:3.500A) Processing helix chain 'R' and resid 391 through 402 removed outlier: 3.528A pdb=" N ASN R 402 " --> pdb=" O GLU R 398 " (cutoff:3.500A) Processing helix chain 'R' and resid 402 through 408 removed outlier: 3.654A pdb=" N LYS R 407 " --> pdb=" O GLU R 403 " (cutoff:3.500A) Processing helix chain 'R' and resid 409 through 430 removed outlier: 4.159A pdb=" N LEU R 413 " --> pdb=" O LEU R 409 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR R 430 " --> pdb=" O ASP R 426 " (cutoff:3.500A) Processing helix chain 'R' and resid 433 through 441 removed outlier: 3.530A pdb=" N ARG R 437 " --> pdb=" O HIS R 433 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 17 Processing helix chain 'S' and resid 41 through 47 Processing helix chain 'S' and resid 55 through 62 removed outlier: 6.498A pdb=" N PHE S 60 " --> pdb=" O ILE S 57 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL S 61 " --> pdb=" O GLU S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 107 through 121 Processing helix chain 'S' and resid 167 through 179 Processing helix chain 'S' and resid 204 through 225 Processing helix chain 'S' and resid 263 through 267 Processing helix chain 'S' and resid 268 through 281 Processing helix chain 'S' and resid 281 through 290 removed outlier: 3.502A pdb=" N THR S 286 " --> pdb=" O ALA S 282 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ALA S 287 " --> pdb=" O THR S 283 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N VAL S 288 " --> pdb=" O SER S 284 " (cutoff:3.500A) Processing helix chain 'S' and resid 294 through 299 removed outlier: 3.712A pdb=" N ARG S 298 " --> pdb=" O ASN S 294 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU S 299 " --> pdb=" O SER S 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 294 through 299' Processing helix chain 'S' and resid 326 through 330 removed outlier: 3.614A pdb=" N SER S 329 " --> pdb=" O ARG S 326 " (cutoff:3.500A) Processing helix chain 'S' and resid 342 through 361 Processing helix chain 'S' and resid 376 through 382 removed outlier: 4.130A pdb=" N GLU S 382 " --> pdb=" O GLU S 378 " (cutoff:3.500A) Processing helix chain 'S' and resid 391 through 402 removed outlier: 3.524A pdb=" N ASN S 402 " --> pdb=" O GLU S 398 " (cutoff:3.500A) Processing helix chain 'S' and resid 402 through 408 Processing helix chain 'S' and resid 409 through 430 removed outlier: 4.121A pdb=" N LEU S 413 " --> pdb=" O LEU S 409 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR S 430 " --> pdb=" O ASP S 426 " (cutoff:3.500A) Processing helix chain 'S' and resid 433 through 441 removed outlier: 3.567A pdb=" N ARG S 437 " --> pdb=" O HIS S 433 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 17 Processing helix chain 'T' and resid 41 through 47 Processing helix chain 'T' and resid 55 through 62 removed outlier: 6.411A pdb=" N PHE T 60 " --> pdb=" O ILE T 57 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL T 61 " --> pdb=" O GLU T 58 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG T 62 " --> pdb=" O GLY T 59 " (cutoff:3.500A) Processing helix chain 'T' and resid 107 through 122 Processing helix chain 'T' and resid 167 through 179 Processing helix chain 'T' and resid 204 through 225 Processing helix chain 'T' and resid 263 through 267 Processing helix chain 'T' and resid 268 through 281 Processing helix chain 'T' and resid 281 through 290 removed outlier: 3.545A pdb=" N THR T 286 " --> pdb=" O ALA T 282 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ALA T 287 " --> pdb=" O THR T 283 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N VAL T 288 " --> pdb=" O SER T 284 " (cutoff:3.500A) Processing helix chain 'T' and resid 294 through 299 removed outlier: 3.706A pdb=" N ARG T 298 " --> pdb=" O ASN T 294 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU T 299 " --> pdb=" O SER T 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 294 through 299' Processing helix chain 'T' and resid 326 through 330 removed outlier: 3.658A pdb=" N SER T 329 " --> pdb=" O ARG T 326 " (cutoff:3.500A) Processing helix chain 'T' and resid 342 through 361 Processing helix chain 'T' and resid 371 through 375 Processing helix chain 'T' and resid 377 through 382 removed outlier: 4.263A pdb=" N GLU T 382 " --> pdb=" O GLU T 378 " (cutoff:3.500A) Processing helix chain 'T' and resid 391 through 402 Processing helix chain 'T' and resid 402 through 408 removed outlier: 3.841A pdb=" N LYS T 407 " --> pdb=" O GLU T 403 " (cutoff:3.500A) Processing helix chain 'T' and resid 409 through 430 removed outlier: 4.113A pdb=" N LEU T 413 " --> pdb=" O LEU T 409 " (cutoff:3.500A) Processing helix chain 'T' and resid 433 through 441 removed outlier: 3.539A pdb=" N ARG T 437 " --> pdb=" O HIS T 433 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 10 removed outlier: 4.152A pdb=" N ARG U 9 " --> pdb=" O ASP U 6 " (cutoff:3.500A) Processing helix chain 'V' and resid 5 through 10 removed outlier: 3.579A pdb=" N SER V 8 " --> pdb=" O GLY V 5 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG V 9 " --> pdb=" O ASP V 6 " (cutoff:3.500A) Processing helix chain 'W' and resid 6 through 10 removed outlier: 4.264A pdb=" N ARG W 9 " --> pdb=" O ASP W 6 " (cutoff:3.500A) Processing helix chain 'X' and resid 6 through 10 removed outlier: 4.237A pdb=" N ARG X 9 " --> pdb=" O ASP X 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 6 through 10 removed outlier: 4.135A pdb=" N ARG Y 9 " --> pdb=" O ASP Y 6 " (cutoff:3.500A) Processing helix chain 'Z' and resid 5 through 10 removed outlier: 4.216A pdb=" N ARG Z 9 " --> pdb=" O ASP Z 6 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 10 removed outlier: 3.616A pdb=" N SER a 8 " --> pdb=" O GLY a 5 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ARG a 9 " --> pdb=" O ASP a 6 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 10 removed outlier: 4.161A pdb=" N ARG b 9 " --> pdb=" O ASP b 6 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 38 removed outlier: 3.514A pdb=" N VAL A 35 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL A 18 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ALA A 90 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TYR A 20 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N PHE A 92 " --> pdb=" O TYR A 20 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ARG A 22 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N CYS A 94 " --> pdb=" O ARG A 22 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLN A 24 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ILE A 93 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N THR A 76 " --> pdb=" O ILE A 93 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 126 through 140 removed outlier: 5.419A pdb=" N GLU A 149 " --> pdb=" O LYS A 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 146 through 150 current: chain 'A' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 194 through 199 current: chain 'A' and resid 255 through 256 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 255 through 256 current: chain 'A' and resid 320 through 321 Processing sheet with id=AA4, first strand: chain 'A' and resid 308 through 309 removed outlier: 4.192A pdb=" N VAL A 386 " --> pdb=" O VAL A 309 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 32 through 38 removed outlier: 5.528A pdb=" N LYS B 88 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N THR B 26 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ILE B 93 " --> pdb=" O THR B 76 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N THR B 76 " --> pdb=" O ILE B 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AA7, first strand: chain 'B' and resid 126 through 140 removed outlier: 5.420A pdb=" N GLU B 149 " --> pdb=" O LYS B 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 146 through 150 current: chain 'B' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 194 through 199 current: chain 'B' and resid 255 through 256 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 255 through 256 current: chain 'B' and resid 320 through 321 Processing sheet with id=AA8, first strand: chain 'C' and resid 32 through 38 removed outlier: 5.523A pdb=" N LYS C 88 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N THR C 26 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ILE C 93 " --> pdb=" O THR C 76 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N THR C 76 " --> pdb=" O ILE C 93 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 51 through 53 Processing sheet with id=AB1, first strand: chain 'C' and resid 126 through 140 removed outlier: 5.410A pdb=" N GLU C 149 " --> pdb=" O LYS C 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 146 through 150 current: chain 'C' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 194 through 199 current: chain 'C' and resid 255 through 256 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 255 through 256 current: chain 'C' and resid 320 through 321 Processing sheet with id=AB2, first strand: chain 'F' and resid 32 through 38 removed outlier: 3.511A pdb=" N VAL F 35 " --> pdb=" O LEU F 23 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LYS F 88 " --> pdb=" O VAL F 18 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 51 through 53 Processing sheet with id=AB4, first strand: chain 'F' and resid 126 through 140 removed outlier: 5.391A pdb=" N GLU F 149 " --> pdb=" O LYS F 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 146 through 150 current: chain 'F' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 194 through 199 current: chain 'F' and resid 255 through 256 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 255 through 256 current: chain 'F' and resid 320 through 321 Processing sheet with id=AB5, first strand: chain 'G' and resid 32 through 38 removed outlier: 5.507A pdb=" N LYS G 88 " --> pdb=" O VAL G 18 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 51 through 53 Processing sheet with id=AB7, first strand: chain 'G' and resid 126 through 140 removed outlier: 5.406A pdb=" N GLU G 149 " --> pdb=" O LYS G 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 146 through 150 current: chain 'G' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 194 through 199 current: chain 'G' and resid 255 through 256 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 255 through 256 current: chain 'G' and resid 320 through 321 Processing sheet with id=AB8, first strand: chain 'H' and resid 32 through 38 removed outlier: 4.764A pdb=" N VAL H 18 " --> pdb=" O LYS H 88 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ALA H 90 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR H 20 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N PHE H 92 " --> pdb=" O TYR H 20 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ARG H 22 " --> pdb=" O PHE H 92 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 51 through 53 Processing sheet with id=AC1, first strand: chain 'H' and resid 126 through 140 removed outlier: 5.399A pdb=" N GLU H 149 " --> pdb=" O LYS H 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 146 through 150 current: chain 'H' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 194 through 199 current: chain 'H' and resid 255 through 256 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 255 through 256 current: chain 'H' and resid 320 through 321 Processing sheet with id=AC2, first strand: chain 'I' and resid 32 through 38 removed outlier: 5.587A pdb=" N LYS I 88 " --> pdb=" O VAL I 18 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 51 through 53 Processing sheet with id=AC4, first strand: chain 'I' and resid 126 through 140 removed outlier: 5.388A pdb=" N GLU I 149 " --> pdb=" O LYS I 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 146 through 150 current: chain 'I' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 194 through 199 current: chain 'I' and resid 255 through 256 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 255 through 256 current: chain 'I' and resid 320 through 321 Processing sheet with id=AC5, first strand: chain 'N' and resid 32 through 38 removed outlier: 5.645A pdb=" N LYS N 88 " --> pdb=" O VAL N 18 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 51 through 53 Processing sheet with id=AC7, first strand: chain 'N' and resid 126 through 140 removed outlier: 5.390A pdb=" N GLU N 149 " --> pdb=" O LYS N 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 146 through 150 current: chain 'N' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 194 through 199 current: chain 'N' and resid 255 through 256 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 255 through 256 current: chain 'N' and resid 320 through 321 Processing sheet with id=AC8, first strand: chain 'O' and resid 32 through 38 removed outlier: 5.530A pdb=" N LYS O 88 " --> pdb=" O VAL O 18 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 51 through 53 Processing sheet with id=AD1, first strand: chain 'O' and resid 126 through 140 removed outlier: 5.420A pdb=" N GLU O 149 " --> pdb=" O LYS O 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 146 through 150 current: chain 'O' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 194 through 199 current: chain 'O' and resid 255 through 256 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 255 through 256 current: chain 'O' and resid 320 through 321 Processing sheet with id=AD2, first strand: chain 'P' and resid 32 through 38 removed outlier: 5.542A pdb=" N LYS P 88 " --> pdb=" O VAL P 18 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 51 through 53 Processing sheet with id=AD4, first strand: chain 'P' and resid 126 through 140 removed outlier: 5.393A pdb=" N GLU P 149 " --> pdb=" O LYS P 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 146 through 150 current: chain 'P' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 194 through 199 current: chain 'P' and resid 255 through 256 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 255 through 256 current: chain 'P' and resid 320 through 321 Processing sheet with id=AD5, first strand: chain 'Q' and resid 32 through 38 removed outlier: 4.816A pdb=" N VAL Q 18 " --> pdb=" O LYS Q 88 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ALA Q 90 " --> pdb=" O VAL Q 18 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR Q 20 " --> pdb=" O ALA Q 90 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N PHE Q 92 " --> pdb=" O TYR Q 20 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ARG Q 22 " --> pdb=" O PHE Q 92 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 51 through 53 Processing sheet with id=AD7, first strand: chain 'Q' and resid 126 through 140 removed outlier: 5.390A pdb=" N GLU Q 149 " --> pdb=" O LYS Q 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 146 through 150 current: chain 'Q' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 194 through 199 current: chain 'Q' and resid 255 through 256 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 255 through 256 current: chain 'Q' and resid 320 through 321 Processing sheet with id=AD8, first strand: chain 'R' and resid 32 through 38 removed outlier: 3.516A pdb=" N VAL R 35 " --> pdb=" O LEU R 23 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL R 18 " --> pdb=" O LYS R 88 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ALA R 90 " --> pdb=" O VAL R 18 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TYR R 20 " --> pdb=" O ALA R 90 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N PHE R 92 " --> pdb=" O TYR R 20 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ARG R 22 " --> pdb=" O PHE R 92 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N CYS R 94 " --> pdb=" O ARG R 22 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLN R 24 " --> pdb=" O CYS R 94 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ILE R 93 " --> pdb=" O THR R 76 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N THR R 76 " --> pdb=" O ILE R 93 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 51 through 53 Processing sheet with id=AE1, first strand: chain 'R' and resid 126 through 140 removed outlier: 5.420A pdb=" N GLU R 149 " --> pdb=" O LYS R 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 146 through 150 current: chain 'R' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 194 through 199 current: chain 'R' and resid 255 through 256 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 255 through 256 current: chain 'R' and resid 320 through 321 Processing sheet with id=AE2, first strand: chain 'R' and resid 308 through 309 removed outlier: 4.205A pdb=" N VAL R 386 " --> pdb=" O VAL R 309 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'S' and resid 32 through 38 removed outlier: 5.523A pdb=" N LYS S 88 " --> pdb=" O VAL S 18 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N THR S 26 " --> pdb=" O CYS S 94 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ILE S 93 " --> pdb=" O THR S 76 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N THR S 76 " --> pdb=" O ILE S 93 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'S' and resid 51 through 53 Processing sheet with id=AE5, first strand: chain 'S' and resid 126 through 140 removed outlier: 5.421A pdb=" N GLU S 149 " --> pdb=" O LYS S 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 146 through 150 current: chain 'S' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 194 through 199 current: chain 'S' and resid 255 through 256 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 255 through 256 current: chain 'S' and resid 320 through 321 Processing sheet with id=AE6, first strand: chain 'T' and resid 32 through 38 removed outlier: 5.514A pdb=" N LYS T 88 " --> pdb=" O VAL T 18 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N THR T 26 " --> pdb=" O CYS T 94 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ILE T 93 " --> pdb=" O THR T 76 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR T 76 " --> pdb=" O ILE T 93 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'T' and resid 51 through 53 Processing sheet with id=AE8, first strand: chain 'T' and resid 126 through 140 removed outlier: 5.407A pdb=" N GLU T 149 " --> pdb=" O LYS T 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 146 through 150 current: chain 'T' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 194 through 199 current: chain 'T' and resid 255 through 256 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 255 through 256 current: chain 'T' and resid 320 through 321 1909 hydrogen bonds defined for protein. 5367 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: 17.64 Time building geometry restraints manager: 11.25 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: 140 1.14 - 1.31: 8680 1.31 - 1.48: 20394 1.48 - 1.65: 21998 1.65 - 1.82: 378 Bond restraints: 51590 Sorted by residual: bond pdb=" NE2 GLN N 503 " pdb="HE21 GLN N 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 O 503 " pdb="HE21 GLN O 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 T 503 " pdb="HE22 GLN T 503 " ideal model delta sigma weight residual 0.860 1.017 -0.157 2.00e-02 2.50e+03 6.13e+01 bond pdb=" NE2 GLN I 503 " pdb="HE22 GLN I 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 F 503 " pdb="HE22 GLN F 503 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.12e+01 ... (remaining 51585 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 68205 1.47 - 2.94: 1368 2.94 - 4.42: 312 4.42 - 5.89: 56 5.89 - 7.36: 17 Bond angle restraints: 69958 Sorted by residual: angle pdb=" CA ARG T 370 " pdb=" CB ARG T 370 " pdb=" CG ARG T 370 " ideal model delta sigma weight residual 114.10 121.46 -7.36 2.00e+00 2.50e-01 1.36e+01 angle pdb=" CA ARG P 370 " pdb=" CB ARG P 370 " pdb=" CG ARG P 370 " ideal model delta sigma weight residual 114.10 121.41 -7.31 2.00e+00 2.50e-01 1.34e+01 angle pdb=" N GLU O 15 " pdb=" CA GLU O 15 " pdb=" CB GLU O 15 " ideal model delta sigma weight residual 110.20 115.60 -5.40 1.49e+00 4.50e-01 1.31e+01 angle pdb=" CA ARG H 370 " pdb=" CB ARG H 370 " pdb=" CG ARG H 370 " ideal model delta sigma weight residual 114.10 121.16 -7.06 2.00e+00 2.50e-01 1.24e+01 angle pdb=" CA ARG B 370 " pdb=" CB ARG B 370 " pdb=" CG ARG B 370 " ideal model delta sigma weight residual 114.10 121.11 -7.01 2.00e+00 2.50e-01 1.23e+01 ... (remaining 69953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 26758 17.98 - 35.95: 2965 35.95 - 53.93: 935 53.93 - 71.90: 173 71.90 - 89.88: 95 Dihedral angle restraints: 30926 sinusoidal: 12516 harmonic: 18410 Sorted by residual: dihedral pdb=" CA ASN C 34 " pdb=" C ASN C 34 " pdb=" N VAL C 35 " pdb=" CA VAL C 35 " ideal model delta harmonic sigma weight residual 180.00 161.93 18.07 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA ASN F 34 " pdb=" C ASN F 34 " pdb=" N VAL F 35 " pdb=" CA VAL F 35 " ideal model delta harmonic sigma weight residual 180.00 162.16 17.84 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ASN T 34 " pdb=" C ASN T 34 " pdb=" N VAL T 35 " pdb=" CA VAL T 35 " ideal model delta harmonic sigma weight residual 180.00 162.37 17.63 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 30923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 5070 0.035 - 0.070: 1790 0.070 - 0.105: 498 0.105 - 0.140: 181 0.140 - 0.176: 7 Chirality restraints: 7546 Sorted by residual: chirality pdb=" CA GLU H 15 " pdb=" N GLU H 15 " pdb=" C GLU H 15 " pdb=" CB GLU H 15 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CA GLU B 15 " pdb=" N GLU B 15 " pdb=" C GLU B 15 " pdb=" CB GLU B 15 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CA GLU I 15 " pdb=" N GLU I 15 " pdb=" C GLU I 15 " pdb=" CB GLU I 15 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.19e-01 ... (remaining 7543 not shown) Planarity restraints: 9184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN R 503 " -0.319 2.00e-02 2.50e+03 3.39e-01 1.73e+03 pdb=" CD GLN R 503 " 0.024 2.00e-02 2.50e+03 pdb=" OE1 GLN R 503 " 0.305 2.00e-02 2.50e+03 pdb=" NE2 GLN R 503 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN R 503 " 0.491 2.00e-02 2.50e+03 pdb="HE22 GLN R 503 " -0.504 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 503 " -0.307 2.00e-02 2.50e+03 3.21e-01 1.54e+03 pdb=" CD GLN A 503 " 0.023 2.00e-02 2.50e+03 pdb=" OE1 GLN A 503 " 0.293 2.00e-02 2.50e+03 pdb=" NE2 GLN A 503 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN A 503 " 0.461 2.00e-02 2.50e+03 pdb="HE22 GLN A 503 " -0.473 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN T 503 " -0.305 2.00e-02 2.50e+03 3.18e-01 1.52e+03 pdb=" CD GLN T 503 " 0.023 2.00e-02 2.50e+03 pdb=" OE1 GLN T 503 " 0.292 2.00e-02 2.50e+03 pdb=" NE2 GLN T 503 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN T 503 " 0.457 2.00e-02 2.50e+03 pdb="HE22 GLN T 503 " -0.469 2.00e-02 2.50e+03 ... (remaining 9181 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.37: 290 2.37 - 2.93: 22227 2.93 - 3.49: 59513 3.49 - 4.04: 100686 4.04 - 4.60: 149099 Nonbonded interactions: 331815 Sorted by model distance: nonbonded pdb=" O GLY I 241 " pdb=" H1 GLN I 503 " model vdw 1.813 2.450 nonbonded pdb=" O GLY Q 241 " pdb=" H1 GLN Q 503 " model vdw 1.816 2.450 nonbonded pdb=" O GLY F 241 " pdb=" H1 GLN F 503 " model vdw 1.827 2.450 nonbonded pdb=" O GLY N 241 " pdb=" H1 GLN N 503 " model vdw 1.834 2.450 nonbonded pdb=" O GLY T 241 " pdb=" H1 GLN T 503 " model vdw 1.851 2.450 ... (remaining 331810 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 'B' selection = chain 'C' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } 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=0.92 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: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.090 Extract box with map and model: 1.440 Check model and map are aligned: 0.360 Set scattering table: 0.360 Process input model: 88.910 Find NCS groups from input model: 2.550 Set up NCS constraints: 0.430 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: 0.020 Load rotamer database and sin/cos tables:9.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5908 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 : 0.002 0.038 51450 Z= 0.163 Angle : 0.532 7.362 69650 Z= 0.288 Chirality : 0.041 0.176 7546 Planarity : 0.004 0.037 9184 Dihedral : 17.585 89.876 19012 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.74 % Allowed : 21.93 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.11), residues: 6286 helix: 1.64 (0.11), residues: 2338 sheet: -0.37 (0.17), residues: 980 loop : 0.09 (0.12), residues: 2968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 425 HIS 0.005 0.001 HIS N 416 PHE 0.014 0.001 PHE A 285 TYR 0.017 0.001 TYR Q 296 ARG 0.009 0.001 ARG S 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1194 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1101 time to evaluate : 4.405 Fit side-chains revert: symmetry clash REVERT: A 3 LYS cc_start: 0.7120 (tttt) cc_final: 0.6667 (ttmm) REVERT: A 18 VAL cc_start: 0.4849 (OUTLIER) cc_final: 0.4362 (t) REVERT: A 32 ILE cc_start: 0.5775 (mp) cc_final: 0.5509 (mp) REVERT: A 44 LYS cc_start: 0.5824 (tttp) cc_final: 0.5580 (tttt) REVERT: A 49 LYS cc_start: 0.5914 (mmtt) cc_final: 0.5462 (mmmt) REVERT: A 102 THR cc_start: 0.6184 (m) cc_final: 0.5675 (p) REVERT: A 117 LYS cc_start: 0.5932 (tptm) cc_final: 0.5633 (tptm) REVERT: A 148 LEU cc_start: 0.6502 (mt) cc_final: 0.6224 (mt) REVERT: A 153 LYS cc_start: 0.6027 (ptpp) cc_final: 0.4946 (mmmt) REVERT: A 182 GLU cc_start: 0.5847 (mt-10) cc_final: 0.5548 (mt-10) REVERT: A 206 ARG cc_start: 0.5169 (ttt90) cc_final: 0.4877 (tpt-90) REVERT: A 244 MET cc_start: 0.6092 (ttp) cc_final: 0.5785 (ttp) REVERT: A 261 GLU cc_start: 0.5869 (pm20) cc_final: 0.5512 (pm20) REVERT: A 269 GLU cc_start: 0.5351 (mm-30) cc_final: 0.4665 (pm20) REVERT: A 328 ILE cc_start: 0.6850 (tp) cc_final: 0.6584 (tp) REVERT: A 329 SER cc_start: 0.7030 (m) cc_final: 0.6524 (p) REVERT: A 363 GLU cc_start: 0.6244 (tp30) cc_final: 0.5879 (tt0) REVERT: A 407 LYS cc_start: 0.6094 (mmtm) cc_final: 0.5610 (mppt) REVERT: A 411 GLU cc_start: 0.5741 (pt0) cc_final: 0.4852 (mm-30) REVERT: A 412 HIS cc_start: 0.6101 (t70) cc_final: 0.5876 (t-90) REVERT: A 431 GLN cc_start: 0.6602 (mm-40) cc_final: 0.5813 (mm-40) REVERT: A 438 GLU cc_start: 0.5255 (mt-10) cc_final: 0.4840 (mt-10) REVERT: A 441 MET cc_start: 0.6927 (tpp) cc_final: 0.6327 (tpp) REVERT: B 3 LYS cc_start: 0.6932 (tttt) cc_final: 0.6696 (tttm) REVERT: B 11 LYS cc_start: 0.5028 (tttp) cc_final: 0.4687 (ttpp) REVERT: B 18 VAL cc_start: 0.4796 (OUTLIER) cc_final: 0.4377 (t) REVERT: B 49 LYS cc_start: 0.5685 (mmtt) cc_final: 0.5192 (mmmt) REVERT: B 68 MET cc_start: 0.6444 (mmt) cc_final: 0.5774 (mmt) REVERT: B 105 GLU cc_start: 0.5993 (pm20) cc_final: 0.5768 (pm20) REVERT: B 117 LYS cc_start: 0.5820 (tptp) cc_final: 0.5527 (tptt) REVERT: B 148 LEU cc_start: 0.6454 (mt) cc_final: 0.6057 (mp) REVERT: B 182 GLU cc_start: 0.5779 (mt-10) cc_final: 0.5542 (mt-10) REVERT: B 200 LYS cc_start: 0.6014 (mtpp) cc_final: 0.5660 (ttmp) REVERT: B 206 ARG cc_start: 0.5054 (ttt90) cc_final: 0.4849 (tpt-90) REVERT: B 224 LYS cc_start: 0.5435 (ttmm) cc_final: 0.5098 (mttm) REVERT: B 260 ASP cc_start: 0.6415 (t0) cc_final: 0.6082 (t0) REVERT: B 269 GLU cc_start: 0.5269 (mm-30) cc_final: 0.4539 (pm20) REVERT: B 280 LYS cc_start: 0.6479 (tttt) cc_final: 0.6247 (tttm) REVERT: B 328 ILE cc_start: 0.7159 (tp) cc_final: 0.6872 (tp) REVERT: B 329 SER cc_start: 0.7245 (m) cc_final: 0.6438 (p) REVERT: B 363 GLU cc_start: 0.5978 (tp30) cc_final: 0.5697 (tt0) REVERT: B 397 GLU cc_start: 0.5973 (mm-30) cc_final: 0.5203 (mm-30) REVERT: B 403 GLU cc_start: 0.5812 (tm-30) cc_final: 0.5608 (pm20) REVERT: B 407 LYS cc_start: 0.6028 (mmtm) cc_final: 0.5478 (mppt) REVERT: B 409 LEU cc_start: 0.5246 (OUTLIER) cc_final: 0.5005 (pp) REVERT: B 411 GLU cc_start: 0.5407 (pt0) cc_final: 0.4734 (mm-30) REVERT: B 415 GLU cc_start: 0.5128 (mt-10) cc_final: 0.4409 (mm-30) REVERT: B 438 GLU cc_start: 0.5313 (mt-10) cc_final: 0.5083 (mt-10) REVERT: B 441 MET cc_start: 0.6858 (tpp) cc_final: 0.6289 (tpp) REVERT: C 11 LYS cc_start: 0.4545 (tttm) cc_final: 0.4289 (ttpp) REVERT: C 18 VAL cc_start: 0.4880 (OUTLIER) cc_final: 0.4401 (t) REVERT: C 49 LYS cc_start: 0.5876 (mmtt) cc_final: 0.5392 (mmmt) REVERT: C 102 THR cc_start: 0.6043 (m) cc_final: 0.5557 (p) REVERT: C 105 GLU cc_start: 0.5787 (pm20) cc_final: 0.5546 (pm20) REVERT: C 117 LYS cc_start: 0.5851 (tptm) cc_final: 0.5492 (tptm) REVERT: C 153 LYS cc_start: 0.5776 (mttm) cc_final: 0.4627 (mmmt) REVERT: C 200 LYS cc_start: 0.5857 (mtpp) cc_final: 0.5654 (ttmm) REVERT: C 206 ARG cc_start: 0.5074 (ttt90) cc_final: 0.4846 (tpt-90) REVERT: C 223 ARG cc_start: 0.5227 (ttm-80) cc_final: 0.4970 (ttt90) REVERT: C 269 GLU cc_start: 0.5542 (mm-30) cc_final: 0.4591 (pm20) REVERT: C 314 GLN cc_start: 0.6954 (tp40) cc_final: 0.6633 (tt0) REVERT: C 328 ILE cc_start: 0.6850 (OUTLIER) cc_final: 0.6616 (tp) REVERT: C 329 SER cc_start: 0.7210 (m) cc_final: 0.6510 (p) REVERT: C 332 VAL cc_start: 0.6847 (m) cc_final: 0.6617 (t) REVERT: C 363 GLU cc_start: 0.6016 (tp30) cc_final: 0.5528 (tt0) REVERT: C 405 MET cc_start: 0.6209 (mmp) cc_final: 0.5903 (mmp) REVERT: C 407 LYS cc_start: 0.6070 (mttm) cc_final: 0.5576 (mppt) REVERT: C 411 GLU cc_start: 0.5629 (pt0) cc_final: 0.5160 (tt0) REVERT: C 412 HIS cc_start: 0.5980 (t70) cc_final: 0.5719 (t-90) REVERT: C 415 GLU cc_start: 0.5038 (mt-10) cc_final: 0.4309 (mm-30) REVERT: C 427 MET cc_start: 0.5735 (mmp) cc_final: 0.5331 (mmm) REVERT: C 431 GLN cc_start: 0.6441 (mm-40) cc_final: 0.6223 (mm-40) REVERT: C 438 GLU cc_start: 0.5211 (mt-10) cc_final: 0.4959 (mt-10) REVERT: C 441 MET cc_start: 0.6850 (tpp) cc_final: 0.6340 (tpp) REVERT: F 11 LYS cc_start: 0.5087 (tttm) cc_final: 0.4757 (ttpp) REVERT: F 15 GLU cc_start: 0.4368 (OUTLIER) cc_final: 0.3650 (mm-30) REVERT: F 18 VAL cc_start: 0.4419 (OUTLIER) cc_final: 0.4035 (t) REVERT: F 28 ILE cc_start: 0.6150 (OUTLIER) cc_final: 0.5892 (mm) REVERT: F 49 LYS cc_start: 0.5855 (mmtt) cc_final: 0.5340 (mmmt) REVERT: F 68 MET cc_start: 0.6188 (mmt) cc_final: 0.5766 (mmt) REVERT: F 105 GLU cc_start: 0.5835 (pm20) cc_final: 0.5587 (pm20) REVERT: F 117 LYS cc_start: 0.6073 (tptm) cc_final: 0.5745 (tptm) REVERT: F 148 LEU cc_start: 0.6325 (mt) cc_final: 0.5977 (mp) REVERT: F 153 LYS cc_start: 0.5967 (OUTLIER) cc_final: 0.4858 (mmmt) REVERT: F 182 GLU cc_start: 0.5872 (mt-10) cc_final: 0.5523 (mt-10) REVERT: F 200 LYS cc_start: 0.5842 (mtpp) cc_final: 0.5526 (ttmp) REVERT: F 206 ARG cc_start: 0.5102 (ttp80) cc_final: 0.4774 (tpt-90) REVERT: F 223 ARG cc_start: 0.5569 (ttm-80) cc_final: 0.5231 (ttm-80) REVERT: F 224 LYS cc_start: 0.5420 (mtpt) cc_final: 0.5011 (mttt) REVERT: F 232 MET cc_start: 0.6371 (ttt) cc_final: 0.6168 (ttt) REVERT: F 244 MET cc_start: 0.6110 (ttp) cc_final: 0.5769 (ttp) REVERT: F 269 GLU cc_start: 0.5287 (mm-30) cc_final: 0.4458 (pm20) REVERT: F 280 LYS cc_start: 0.6363 (tttt) cc_final: 0.6158 (tttp) REVERT: F 328 ILE cc_start: 0.6877 (OUTLIER) cc_final: 0.6629 (tp) REVERT: F 329 SER cc_start: 0.7060 (m) cc_final: 0.6478 (p) REVERT: F 363 GLU cc_start: 0.5905 (tp30) cc_final: 0.5472 (tt0) REVERT: F 375 MET cc_start: 0.5798 (ptm) cc_final: 0.5456 (ptp) REVERT: F 401 SER cc_start: 0.7420 (OUTLIER) cc_final: 0.7156 (m) REVERT: F 407 LYS cc_start: 0.6238 (mmtm) cc_final: 0.5707 (mppt) REVERT: F 411 GLU cc_start: 0.5560 (pt0) cc_final: 0.4579 (mm-30) REVERT: F 415 GLU cc_start: 0.5411 (mt-10) cc_final: 0.4580 (mm-30) REVERT: F 438 GLU cc_start: 0.5460 (mt-10) cc_final: 0.5168 (mt-10) REVERT: F 441 MET cc_start: 0.6879 (tpp) cc_final: 0.6054 (tpp) REVERT: G 11 LYS cc_start: 0.4490 (tttm) cc_final: 0.4190 (ttpp) REVERT: G 18 VAL cc_start: 0.4824 (OUTLIER) cc_final: 0.4347 (t) REVERT: G 27 ASP cc_start: 0.5632 (p0) cc_final: 0.5405 (p0) REVERT: G 49 LYS cc_start: 0.5516 (mmtt) cc_final: 0.4998 (mmmt) REVERT: G 102 THR cc_start: 0.6171 (m) cc_final: 0.5583 (p) REVERT: G 105 GLU cc_start: 0.5950 (pm20) cc_final: 0.5567 (pm20) REVERT: G 182 GLU cc_start: 0.5824 (mt-10) cc_final: 0.5619 (mt-10) REVERT: G 206 ARG cc_start: 0.5142 (ttt90) cc_final: 0.4821 (tpt-90) REVERT: G 223 ARG cc_start: 0.5311 (ttm-80) cc_final: 0.4993 (tpt-90) REVERT: G 314 GLN cc_start: 0.6631 (tt0) cc_final: 0.6430 (tt0) REVERT: G 328 ILE cc_start: 0.6990 (OUTLIER) cc_final: 0.6743 (tp) REVERT: G 329 SER cc_start: 0.7023 (m) cc_final: 0.6482 (p) REVERT: G 363 GLU cc_start: 0.5926 (tp30) cc_final: 0.5701 (tt0) REVERT: G 403 GLU cc_start: 0.6098 (tp30) cc_final: 0.5126 (mp0) REVERT: G 411 GLU cc_start: 0.5505 (pt0) cc_final: 0.4713 (mm-30) REVERT: G 426 ASP cc_start: 0.6197 (t70) cc_final: 0.5977 (t70) REVERT: G 427 MET cc_start: 0.5847 (mmp) cc_final: 0.5608 (mmp) REVERT: G 438 GLU cc_start: 0.5501 (mt-10) cc_final: 0.5220 (mt-10) REVERT: H 11 LYS cc_start: 0.5118 (tttm) cc_final: 0.4652 (ttpp) REVERT: H 18 VAL cc_start: 0.4752 (OUTLIER) cc_final: 0.4232 (t) REVERT: H 27 ASP cc_start: 0.5615 (p0) cc_final: 0.5413 (p0) REVERT: H 32 ILE cc_start: 0.5560 (mp) cc_final: 0.5270 (mm) REVERT: H 49 LYS cc_start: 0.5694 (mmtt) cc_final: 0.5292 (mmmt) REVERT: H 69 TYR cc_start: 0.6698 (m-80) cc_final: 0.6493 (m-80) REVERT: H 102 THR cc_start: 0.6465 (m) cc_final: 0.5871 (p) REVERT: H 105 GLU cc_start: 0.5858 (pm20) cc_final: 0.5622 (pm20) REVERT: H 117 LYS cc_start: 0.6081 (tptm) cc_final: 0.5880 (tptm) REVERT: H 153 LYS cc_start: 0.5405 (OUTLIER) cc_final: 0.4615 (mmmt) REVERT: H 200 LYS cc_start: 0.5857 (mtpm) cc_final: 0.5556 (ttmm) REVERT: H 206 ARG cc_start: 0.5238 (ttt90) cc_final: 0.4783 (tpt-90) REVERT: H 223 ARG cc_start: 0.5338 (ttm-80) cc_final: 0.5006 (tpt-90) REVERT: H 252 LYS cc_start: 0.6824 (tttt) cc_final: 0.6587 (tttm) REVERT: H 280 LYS cc_start: 0.6440 (tttt) cc_final: 0.6208 (tttm) REVERT: H 315 ASN cc_start: 0.6805 (t0) cc_final: 0.6435 (t0) REVERT: H 328 ILE cc_start: 0.7007 (tp) cc_final: 0.6732 (tp) REVERT: H 329 SER cc_start: 0.7104 (m) cc_final: 0.6438 (p) REVERT: H 363 GLU cc_start: 0.5912 (tp30) cc_final: 0.5632 (tt0) REVERT: H 407 LYS cc_start: 0.5864 (mmtm) cc_final: 0.5375 (mppt) REVERT: H 411 GLU cc_start: 0.5654 (pt0) cc_final: 0.5102 (mm-30) REVERT: H 415 GLU cc_start: 0.5143 (mt-10) cc_final: 0.4398 (mm-30) REVERT: H 431 GLN cc_start: 0.6624 (mm-40) cc_final: 0.6327 (mm-40) REVERT: H 438 GLU cc_start: 0.5392 (mt-10) cc_final: 0.5102 (mt-10) REVERT: H 441 MET cc_start: 0.6842 (tpp) cc_final: 0.6386 (tpp) REVERT: I 10 GLU cc_start: 0.6229 (mt-10) cc_final: 0.5951 (mt-10) REVERT: I 11 LYS cc_start: 0.4854 (tttp) cc_final: 0.4552 (ttpp) REVERT: I 18 VAL cc_start: 0.4846 (OUTLIER) cc_final: 0.4277 (t) REVERT: I 19 LYS cc_start: 0.5996 (mmtt) cc_final: 0.5750 (mmmt) REVERT: I 27 ASP cc_start: 0.5691 (p0) cc_final: 0.5476 (p0) REVERT: I 28 ILE cc_start: 0.5865 (mm) cc_final: 0.5636 (mm) REVERT: I 49 LYS cc_start: 0.5532 (mmtt) cc_final: 0.5134 (mmmt) REVERT: I 63 ILE cc_start: 0.6326 (mt) cc_final: 0.5818 (mm) REVERT: I 68 MET cc_start: 0.6437 (mmt) cc_final: 0.5961 (mmt) REVERT: I 117 LYS cc_start: 0.6397 (tptm) cc_final: 0.6185 (tptm) REVERT: I 153 LYS cc_start: 0.5973 (mttm) cc_final: 0.4970 (mmmt) REVERT: I 182 GLU cc_start: 0.5773 (mt-10) cc_final: 0.5422 (mt-10) REVERT: I 200 LYS cc_start: 0.5953 (mtpm) cc_final: 0.5696 (ttmm) REVERT: I 206 ARG cc_start: 0.5019 (ttp80) cc_final: 0.4622 (tpt-90) REVERT: I 224 LYS cc_start: 0.5549 (ttmm) cc_final: 0.5155 (mttm) REVERT: I 265 LEU cc_start: 0.5866 (mt) cc_final: 0.5618 (mt) REVERT: I 269 GLU cc_start: 0.5210 (mm-30) cc_final: 0.4521 (pm20) REVERT: I 280 LYS cc_start: 0.6408 (tttt) cc_final: 0.6198 (tttm) REVERT: I 314 GLN cc_start: 0.6921 (tp40) cc_final: 0.6508 (tt0) REVERT: I 329 SER cc_start: 0.7096 (m) cc_final: 0.6395 (p) REVERT: I 363 GLU cc_start: 0.5890 (tp30) cc_final: 0.5416 (tt0) REVERT: I 375 MET cc_start: 0.4573 (OUTLIER) cc_final: 0.4250 (mtm) REVERT: I 407 LYS cc_start: 0.5770 (mmtm) cc_final: 0.5095 (mppt) REVERT: I 411 GLU cc_start: 0.5341 (pt0) cc_final: 0.4708 (mm-30) REVERT: I 412 HIS cc_start: 0.6156 (t70) cc_final: 0.5716 (t-90) REVERT: I 415 GLU cc_start: 0.4967 (mt-10) cc_final: 0.4228 (mm-30) REVERT: I 427 MET cc_start: 0.5439 (mmp) cc_final: 0.5219 (mmp) REVERT: I 431 GLN cc_start: 0.6505 (mm-40) cc_final: 0.6155 (mm-40) REVERT: I 438 GLU cc_start: 0.5461 (mt-10) cc_final: 0.5160 (mt-10) REVERT: I 441 MET cc_start: 0.6769 (tpp) cc_final: 0.6145 (tpp) REVERT: N 11 LYS cc_start: 0.5090 (tttm) cc_final: 0.4727 (ttpp) REVERT: N 15 GLU cc_start: 0.4436 (OUTLIER) cc_final: 0.3728 (mm-30) REVERT: N 18 VAL cc_start: 0.4463 (OUTLIER) cc_final: 0.4028 (t) REVERT: N 49 LYS cc_start: 0.5860 (mmtt) cc_final: 0.5346 (mmmt) REVERT: N 68 MET cc_start: 0.6172 (mmt) cc_final: 0.5820 (mmt) REVERT: N 105 GLU cc_start: 0.5920 (pm20) cc_final: 0.5690 (pm20) REVERT: N 117 LYS cc_start: 0.6117 (tptm) cc_final: 0.5775 (tptm) REVERT: N 148 LEU cc_start: 0.6345 (mt) cc_final: 0.5990 (mp) REVERT: N 153 LYS cc_start: 0.5996 (mttm) cc_final: 0.4896 (mmmt) REVERT: N 182 GLU cc_start: 0.5853 (mt-10) cc_final: 0.5502 (mt-10) REVERT: N 200 LYS cc_start: 0.5774 (mtpp) cc_final: 0.5469 (ttmp) REVERT: N 206 ARG cc_start: 0.5102 (ttp80) cc_final: 0.4774 (tpt-90) REVERT: N 223 ARG cc_start: 0.5583 (ttm-80) cc_final: 0.5245 (ttm-80) REVERT: N 224 LYS cc_start: 0.5414 (mtpt) cc_final: 0.5005 (mttt) REVERT: N 232 MET cc_start: 0.6375 (ttt) cc_final: 0.6171 (ttt) REVERT: N 244 MET cc_start: 0.6117 (ttp) cc_final: 0.5776 (ttp) REVERT: N 260 ASP cc_start: 0.6431 (t0) cc_final: 0.6225 (t0) REVERT: N 269 GLU cc_start: 0.5284 (mm-30) cc_final: 0.4455 (pm20) REVERT: N 328 ILE cc_start: 0.6914 (tp) cc_final: 0.6666 (tp) REVERT: N 329 SER cc_start: 0.6994 (m) cc_final: 0.6415 (p) REVERT: N 363 GLU cc_start: 0.6023 (tp30) cc_final: 0.5489 (tt0) REVERT: N 375 MET cc_start: 0.5817 (ptm) cc_final: 0.5494 (ptp) REVERT: N 401 SER cc_start: 0.7429 (OUTLIER) cc_final: 0.7129 (m) REVERT: N 407 LYS cc_start: 0.6205 (mttm) cc_final: 0.5658 (mtmt) REVERT: N 411 GLU cc_start: 0.5666 (pt0) cc_final: 0.4683 (mm-30) REVERT: N 415 GLU cc_start: 0.5499 (mt-10) cc_final: 0.4630 (mm-30) REVERT: N 438 GLU cc_start: 0.5450 (mt-10) cc_final: 0.5159 (mt-10) REVERT: N 441 MET cc_start: 0.6887 (tpp) cc_final: 0.6063 (tpp) REVERT: O 10 GLU cc_start: 0.6176 (mt-10) cc_final: 0.5952 (mt-10) REVERT: O 18 VAL cc_start: 0.4821 (OUTLIER) cc_final: 0.4329 (t) REVERT: O 19 LYS cc_start: 0.5890 (mmtt) cc_final: 0.5493 (mmmt) REVERT: O 27 ASP cc_start: 0.5625 (p0) cc_final: 0.5398 (p0) REVERT: O 49 LYS cc_start: 0.5530 (mmtt) cc_final: 0.5013 (mmmt) REVERT: O 102 THR cc_start: 0.6177 (m) cc_final: 0.5578 (p) REVERT: O 105 GLU cc_start: 0.5966 (pm20) cc_final: 0.5581 (pm20) REVERT: O 153 LYS cc_start: 0.6163 (mttm) cc_final: 0.5114 (mmmt) REVERT: O 206 ARG cc_start: 0.5155 (ttt90) cc_final: 0.4837 (tpt-90) REVERT: O 223 ARG cc_start: 0.5359 (ttm-80) cc_final: 0.5023 (ttm-80) REVERT: O 224 LYS cc_start: 0.5518 (mtpt) cc_final: 0.5288 (mtpp) REVERT: O 328 ILE cc_start: 0.6990 (OUTLIER) cc_final: 0.6743 (tp) REVERT: O 329 SER cc_start: 0.7011 (m) cc_final: 0.6471 (p) REVERT: O 363 GLU cc_start: 0.5922 (tp30) cc_final: 0.5689 (tt0) REVERT: O 401 SER cc_start: 0.7176 (OUTLIER) cc_final: 0.6895 (p) REVERT: O 411 GLU cc_start: 0.5454 (pt0) cc_final: 0.4700 (mm-30) REVERT: O 426 ASP cc_start: 0.6198 (t70) cc_final: 0.5965 (t70) REVERT: O 427 MET cc_start: 0.5738 (mmp) cc_final: 0.5525 (mmp) REVERT: O 438 GLU cc_start: 0.5485 (mt-10) cc_final: 0.5250 (mt-10) REVERT: P 11 LYS cc_start: 0.5032 (tttm) cc_final: 0.4712 (ttpp) REVERT: P 18 VAL cc_start: 0.4771 (OUTLIER) cc_final: 0.4279 (t) REVERT: P 19 LYS cc_start: 0.5831 (mmtt) cc_final: 0.5613 (mmmt) REVERT: P 27 ASP cc_start: 0.5619 (p0) cc_final: 0.5413 (p0) REVERT: P 32 ILE cc_start: 0.5531 (mp) cc_final: 0.5239 (mm) REVERT: P 49 LYS cc_start: 0.5715 (mmtt) cc_final: 0.5313 (mmmt) REVERT: P 69 TYR cc_start: 0.6697 (m-80) cc_final: 0.6492 (m-80) REVERT: P 102 THR cc_start: 0.6462 (m) cc_final: 0.5860 (p) REVERT: P 105 GLU cc_start: 0.5808 (pm20) cc_final: 0.5597 (pm20) REVERT: P 153 LYS cc_start: 0.5854 (ptpt) cc_final: 0.4845 (mmmt) REVERT: P 200 LYS cc_start: 0.5970 (mtpp) cc_final: 0.5729 (ttmm) REVERT: P 206 ARG cc_start: 0.5236 (ttt90) cc_final: 0.4778 (tpt-90) REVERT: P 223 ARG cc_start: 0.5346 (ttm-80) cc_final: 0.5009 (tpt-90) REVERT: P 252 LYS cc_start: 0.6822 (tttt) cc_final: 0.6586 (tttm) REVERT: P 280 LYS cc_start: 0.6444 (tttt) cc_final: 0.6214 (tttm) REVERT: P 329 SER cc_start: 0.7070 (m) cc_final: 0.6086 (p) REVERT: P 363 GLU cc_start: 0.5888 (tp30) cc_final: 0.5581 (tt0) REVERT: P 375 MET cc_start: 0.5926 (ptt) cc_final: 0.5708 (ptt) REVERT: P 407 LYS cc_start: 0.5970 (mmtm) cc_final: 0.5420 (mttt) REVERT: P 411 GLU cc_start: 0.5613 (pt0) cc_final: 0.5061 (mm-30) REVERT: P 415 GLU cc_start: 0.5149 (mt-10) cc_final: 0.4407 (mm-30) REVERT: P 431 GLN cc_start: 0.6617 (mm-40) cc_final: 0.6313 (mm-40) REVERT: P 438 GLU cc_start: 0.5396 (mt-10) cc_final: 0.5106 (mt-10) REVERT: P 441 MET cc_start: 0.6858 (tpp) cc_final: 0.6218 (tpp) REVERT: Q 10 GLU cc_start: 0.6141 (mt-10) cc_final: 0.5877 (mt-10) REVERT: Q 18 VAL cc_start: 0.4722 (OUTLIER) cc_final: 0.4397 (t) REVERT: Q 19 LYS cc_start: 0.5985 (mmtt) cc_final: 0.5751 (mmmt) REVERT: Q 27 ASP cc_start: 0.5655 (p0) cc_final: 0.5448 (p0) REVERT: Q 28 ILE cc_start: 0.5921 (mm) cc_final: 0.5679 (mm) REVERT: Q 49 LYS cc_start: 0.5548 (mmtt) cc_final: 0.5128 (mmmt) REVERT: Q 63 ILE cc_start: 0.6324 (mt) cc_final: 0.5825 (mm) REVERT: Q 68 MET cc_start: 0.6472 (mmt) cc_final: 0.5997 (mmt) REVERT: Q 105 GLU cc_start: 0.5848 (pm20) cc_final: 0.5623 (pm20) REVERT: Q 117 LYS cc_start: 0.6350 (tptm) cc_final: 0.6132 (tptm) REVERT: Q 153 LYS cc_start: 0.5966 (mttm) cc_final: 0.4960 (mmmt) REVERT: Q 182 GLU cc_start: 0.5823 (mt-10) cc_final: 0.5448 (mt-10) REVERT: Q 200 LYS cc_start: 0.5958 (mtpm) cc_final: 0.5702 (ttmm) REVERT: Q 206 ARG cc_start: 0.5038 (ttp80) cc_final: 0.4641 (tpt-90) REVERT: Q 224 LYS cc_start: 0.5545 (ttmm) cc_final: 0.5151 (mttm) REVERT: Q 265 LEU cc_start: 0.5890 (mt) cc_final: 0.5647 (mt) REVERT: Q 269 GLU cc_start: 0.5215 (mm-30) cc_final: 0.4527 (pm20) REVERT: Q 280 LYS cc_start: 0.6432 (tttt) cc_final: 0.6222 (tttm) REVERT: Q 314 GLN cc_start: 0.6864 (tp40) cc_final: 0.6498 (tt0) REVERT: Q 329 SER cc_start: 0.7098 (m) cc_final: 0.6400 (p) REVERT: Q 363 GLU cc_start: 0.5875 (tp30) cc_final: 0.5438 (tt0) REVERT: Q 375 MET cc_start: 0.4575 (mtp) cc_final: 0.4251 (mtm) REVERT: Q 407 LYS cc_start: 0.5917 (mmtm) cc_final: 0.5383 (mppt) REVERT: Q 411 GLU cc_start: 0.5324 (pt0) cc_final: 0.4683 (mm-30) REVERT: Q 412 HIS cc_start: 0.6143 (t70) cc_final: 0.5818 (t70) REVERT: Q 415 GLU cc_start: 0.4933 (mt-10) cc_final: 0.4207 (mm-30) REVERT: Q 427 MET cc_start: 0.5536 (mmp) cc_final: 0.5304 (mmp) REVERT: Q 431 GLN cc_start: 0.6508 (mm-40) cc_final: 0.6153 (mm-40) REVERT: Q 438 GLU cc_start: 0.5495 (mt-10) cc_final: 0.5191 (mt-10) REVERT: Q 441 MET cc_start: 0.6770 (tpp) cc_final: 0.6145 (tpp) REVERT: R 3 LYS cc_start: 0.7208 (tttt) cc_final: 0.6691 (ttmm) REVERT: R 10 GLU cc_start: 0.5577 (mt-10) cc_final: 0.5332 (mt-10) REVERT: R 11 LYS cc_start: 0.4775 (tttp) cc_final: 0.4480 (ttpp) REVERT: R 18 VAL cc_start: 0.4824 (OUTLIER) cc_final: 0.4335 (t) REVERT: R 32 ILE cc_start: 0.5756 (mp) cc_final: 0.5502 (mp) REVERT: R 44 LYS cc_start: 0.5830 (tttp) cc_final: 0.5585 (tttt) REVERT: R 49 LYS cc_start: 0.5888 (mmtt) cc_final: 0.5453 (mmmt) REVERT: R 102 THR cc_start: 0.6155 (m) cc_final: 0.5645 (p) REVERT: R 117 LYS cc_start: 0.5840 (tptm) cc_final: 0.5559 (tptm) REVERT: R 148 LEU cc_start: 0.6490 (mt) cc_final: 0.6210 (mt) REVERT: R 153 LYS cc_start: 0.6003 (ptpp) cc_final: 0.4916 (mmmt) REVERT: R 182 GLU cc_start: 0.5840 (mt-10) cc_final: 0.5533 (mt-10) REVERT: R 206 ARG cc_start: 0.5164 (ttt90) cc_final: 0.4871 (tpt-90) REVERT: R 261 GLU cc_start: 0.5841 (pm20) cc_final: 0.5553 (pm20) REVERT: R 328 ILE cc_start: 0.6832 (tp) cc_final: 0.6570 (tp) REVERT: R 329 SER cc_start: 0.7077 (m) cc_final: 0.6541 (p) REVERT: R 363 GLU cc_start: 0.6221 (tp30) cc_final: 0.5867 (tt0) REVERT: R 375 MET cc_start: 0.5661 (ptt) cc_final: 0.5285 (pmt) REVERT: R 407 LYS cc_start: 0.5981 (mmtm) cc_final: 0.5501 (mppt) REVERT: R 411 GLU cc_start: 0.5876 (mm-30) cc_final: 0.5001 (tt0) REVERT: R 415 GLU cc_start: 0.5493 (mt-10) cc_final: 0.4717 (mm-30) REVERT: R 431 GLN cc_start: 0.6614 (mm-40) cc_final: 0.5820 (mm-40) REVERT: R 438 GLU cc_start: 0.5299 (mt-10) cc_final: 0.4873 (mt-10) REVERT: R 441 MET cc_start: 0.6888 (tpp) cc_final: 0.6381 (tpp) REVERT: S 3 LYS cc_start: 0.6946 (tttt) cc_final: 0.6491 (ttmt) REVERT: S 11 LYS cc_start: 0.5218 (tttp) cc_final: 0.4837 (ttpp) REVERT: S 15 GLU cc_start: 0.4519 (OUTLIER) cc_final: 0.3973 (mm-30) REVERT: S 18 VAL cc_start: 0.4874 (OUTLIER) cc_final: 0.4461 (t) REVERT: S 44 LYS cc_start: 0.5780 (tttp) cc_final: 0.5578 (tttt) REVERT: S 49 LYS cc_start: 0.5685 (mmtt) cc_final: 0.5191 (mmmt) REVERT: S 63 ILE cc_start: 0.6409 (mm) cc_final: 0.6146 (mm) REVERT: S 68 MET cc_start: 0.6461 (mmt) cc_final: 0.5796 (mmt) REVERT: S 105 GLU cc_start: 0.6006 (pm20) cc_final: 0.5781 (pm20) REVERT: S 117 LYS cc_start: 0.5824 (tptp) cc_final: 0.5534 (tptt) REVERT: S 148 LEU cc_start: 0.6464 (mt) cc_final: 0.6058 (mp) REVERT: S 153 LYS cc_start: 0.5543 (mmpt) cc_final: 0.5086 (mmmt) REVERT: S 200 LYS cc_start: 0.6016 (mtpp) cc_final: 0.5645 (ttmp) REVERT: S 206 ARG cc_start: 0.5029 (ttt90) cc_final: 0.4823 (tpt-90) REVERT: S 223 ARG cc_start: 0.5095 (ttm-80) cc_final: 0.4888 (ttt90) REVERT: S 269 GLU cc_start: 0.5263 (mm-30) cc_final: 0.4530 (pm20) REVERT: S 280 LYS cc_start: 0.6527 (tttt) cc_final: 0.6299 (tttm) REVERT: S 328 ILE cc_start: 0.7158 (tp) cc_final: 0.6870 (tp) REVERT: S 329 SER cc_start: 0.7224 (m) cc_final: 0.6419 (p) REVERT: S 363 GLU cc_start: 0.5981 (tp30) cc_final: 0.5714 (tt0) REVERT: S 375 MET cc_start: 0.5907 (pmm) cc_final: 0.5090 (pmt) REVERT: S 397 GLU cc_start: 0.6013 (mm-30) cc_final: 0.5239 (mm-30) REVERT: S 403 GLU cc_start: 0.5875 (tm-30) cc_final: 0.5597 (pm20) REVERT: S 407 LYS cc_start: 0.5994 (mmtm) cc_final: 0.5464 (mppt) REVERT: S 409 LEU cc_start: 0.5229 (OUTLIER) cc_final: 0.4989 (pp) REVERT: S 411 GLU cc_start: 0.5410 (pt0) cc_final: 0.4707 (mm-30) REVERT: S 415 GLU cc_start: 0.5140 (mt-10) cc_final: 0.4423 (mm-30) REVERT: S 427 MET cc_start: 0.5745 (mmp) cc_final: 0.5535 (mmp) REVERT: S 438 GLU cc_start: 0.5347 (mt-10) cc_final: 0.5119 (mt-10) REVERT: S 441 MET cc_start: 0.6862 (tpp) cc_final: 0.6179 (tpp) REVERT: T 11 LYS cc_start: 0.4760 (ttpp) cc_final: 0.4425 (ttpp) REVERT: T 18 VAL cc_start: 0.4834 (OUTLIER) cc_final: 0.4373 (t) REVERT: T 49 LYS cc_start: 0.5949 (mmtt) cc_final: 0.5479 (mmmt) REVERT: T 105 GLU cc_start: 0.5816 (pm20) cc_final: 0.5560 (pm20) REVERT: T 117 LYS cc_start: 0.5857 (tptm) cc_final: 0.5501 (tptm) REVERT: T 153 LYS cc_start: 0.5850 (mttm) cc_final: 0.4660 (mmmt) REVERT: T 200 LYS cc_start: 0.5817 (mtpp) cc_final: 0.5584 (ttmm) REVERT: T 206 ARG cc_start: 0.5096 (ttt90) cc_final: 0.4856 (tpt-90) REVERT: T 223 ARG cc_start: 0.5228 (ttm-80) cc_final: 0.4965 (ttt90) REVERT: T 269 GLU cc_start: 0.5399 (mm-30) cc_final: 0.4496 (pm20) REVERT: T 314 GLN cc_start: 0.6934 (tp40) cc_final: 0.6616 (tt0) REVERT: T 328 ILE cc_start: 0.6889 (OUTLIER) cc_final: 0.6643 (tp) REVERT: T 329 SER cc_start: 0.7209 (m) cc_final: 0.6506 (p) REVERT: T 332 VAL cc_start: 0.6883 (m) cc_final: 0.6642 (t) REVERT: T 363 GLU cc_start: 0.6043 (tp30) cc_final: 0.5531 (tt0) REVERT: T 375 MET cc_start: 0.5276 (pmt) cc_final: 0.4948 (pmm) REVERT: T 411 GLU cc_start: 0.5582 (pt0) cc_final: 0.5146 (tt0) REVERT: T 412 HIS cc_start: 0.5983 (t70) cc_final: 0.5729 (t-90) REVERT: T 415 GLU cc_start: 0.5037 (mt-10) cc_final: 0.4300 (mm-30) REVERT: T 427 MET cc_start: 0.5753 (mmp) cc_final: 0.5307 (mmm) REVERT: T 431 GLN cc_start: 0.6448 (mm-40) cc_final: 0.6226 (mm-40) REVERT: T 438 GLU cc_start: 0.5209 (mt-10) cc_final: 0.4961 (mt-10) REVERT: T 441 MET cc_start: 0.6843 (tpp) cc_final: 0.6326 (tpp) REVERT: U 7 MET cc_start: 0.5074 (mtm) cc_final: 0.4824 (mtm) outliers start: 93 outliers final: 25 residues processed: 1160 average time/residue: 1.5510 time to fit residues: 2185.6756 Evaluate side-chains 903 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 847 time to evaluate : 4.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 153 LYS Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 401 SER Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 153 LYS Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 375 MET Chi-restraints excluded: chain N residue 15 GLU Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 401 SER Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 328 ILE Chi-restraints excluded: chain O residue 370 ARG Chi-restraints excluded: chain O residue 401 SER Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 35 VAL Chi-restraints excluded: chain Q residue 239 VAL Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain S residue 15 GLU Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 409 LEU Chi-restraints excluded: chain T residue 18 VAL Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 83 THR Chi-restraints excluded: chain T residue 240 ASN Chi-restraints excluded: chain T residue 328 ILE Chi-restraints excluded: chain V residue 9 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 531 optimal weight: 10.0000 chunk 477 optimal weight: 3.9990 chunk 264 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 322 optimal weight: 10.0000 chunk 255 optimal weight: 6.9990 chunk 493 optimal weight: 8.9990 chunk 191 optimal weight: 2.9990 chunk 300 optimal weight: 4.9990 chunk 367 optimal weight: 10.0000 chunk 572 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 212 GLN A 443 GLN B 34 ASN B 212 GLN B 443 GLN C 34 ASN C 75 ASN C 443 GLN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 GLN G 34 ASN G 75 ASN G 212 GLN G 443 GLN H 17 ASN H 34 ASN H 212 GLN H 228 HIS H 443 GLN I 34 ASN I 75 ASN I 212 GLN N 34 ASN O 34 ASN O 75 ASN O 212 GLN O 443 GLN P 34 ASN P 212 GLN P 443 GLN Q 34 ASN Q 75 ASN Q 212 GLN R 34 ASN R 212 GLN S 34 ASN S 212 GLN S 443 GLN T 34 ASN T 75 ASN T 439 GLN T 443 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5972 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 51450 Z= 0.379 Angle : 0.755 10.439 69650 Z= 0.409 Chirality : 0.051 0.229 7546 Planarity : 0.008 0.113 9184 Dihedral : 6.630 56.549 6931 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.28 % Allowed : 18.07 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.10), residues: 6286 helix: 1.47 (0.10), residues: 2296 sheet: -0.28 (0.17), residues: 840 loop : -0.22 (0.11), residues: 3150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP P 425 HIS 0.009 0.003 HIS Q 188 PHE 0.038 0.004 PHE C 199 TYR 0.048 0.004 TYR F 296 ARG 0.013 0.001 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 923 time to evaluate : 4.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.7149 (tttt) cc_final: 0.6518 (ttmm) REVERT: A 11 LYS cc_start: 0.5021 (tttp) cc_final: 0.4774 (ttpp) REVERT: A 32 ILE cc_start: 0.5701 (mp) cc_final: 0.5426 (mp) REVERT: A 49 LYS cc_start: 0.5860 (mmtt) cc_final: 0.5325 (mmmt) REVERT: A 102 THR cc_start: 0.6205 (m) cc_final: 0.5819 (p) REVERT: A 117 LYS cc_start: 0.5831 (tptm) cc_final: 0.5511 (tptm) REVERT: A 148 LEU cc_start: 0.6563 (mt) cc_final: 0.6322 (mt) REVERT: A 153 LYS cc_start: 0.6184 (ptpp) cc_final: 0.5083 (mmmt) REVERT: A 182 GLU cc_start: 0.5933 (mt-10) cc_final: 0.5581 (mt-10) REVERT: A 200 LYS cc_start: 0.5983 (ttmm) cc_final: 0.4970 (tptt) REVERT: A 206 ARG cc_start: 0.4977 (ttt90) cc_final: 0.4689 (tpt-90) REVERT: A 261 GLU cc_start: 0.5711 (pm20) cc_final: 0.5488 (pm20) REVERT: A 314 GLN cc_start: 0.6809 (OUTLIER) cc_final: 0.6325 (tt0) REVERT: A 329 SER cc_start: 0.6988 (m) cc_final: 0.6429 (p) REVERT: A 407 LYS cc_start: 0.5846 (mmtm) cc_final: 0.5333 (mtpt) REVERT: A 411 GLU cc_start: 0.5520 (pt0) cc_final: 0.4873 (mm-30) REVERT: A 427 MET cc_start: 0.5688 (mmm) cc_final: 0.5310 (mmp) REVERT: A 438 GLU cc_start: 0.5458 (mt-10) cc_final: 0.5031 (mt-10) REVERT: A 441 MET cc_start: 0.6959 (tpp) cc_final: 0.6634 (tpp) REVERT: B 3 LYS cc_start: 0.6856 (tttt) cc_final: 0.6654 (tttm) REVERT: B 10 GLU cc_start: 0.6150 (OUTLIER) cc_final: 0.5507 (mt-10) REVERT: B 19 LYS cc_start: 0.5898 (mmtt) cc_final: 0.5641 (mmmt) REVERT: B 49 LYS cc_start: 0.5803 (mmtt) cc_final: 0.5249 (mmmt) REVERT: B 68 MET cc_start: 0.6317 (mmt) cc_final: 0.5769 (mmt) REVERT: B 105 GLU cc_start: 0.6175 (pm20) cc_final: 0.5863 (pm20) REVERT: B 117 LYS cc_start: 0.5747 (tptp) cc_final: 0.5478 (tptm) REVERT: B 153 LYS cc_start: 0.6118 (OUTLIER) cc_final: 0.5046 (mmmt) REVERT: B 166 GLU cc_start: 0.4208 (OUTLIER) cc_final: 0.3995 (tm-30) REVERT: B 182 GLU cc_start: 0.6015 (mt-10) cc_final: 0.5712 (mt-10) REVERT: B 200 LYS cc_start: 0.5928 (mtpp) cc_final: 0.4886 (tptt) REVERT: B 224 LYS cc_start: 0.5573 (ttmm) cc_final: 0.5305 (mttm) REVERT: B 314 GLN cc_start: 0.6787 (OUTLIER) cc_final: 0.6173 (tt0) REVERT: B 329 SER cc_start: 0.6899 (m) cc_final: 0.6065 (p) REVERT: B 397 GLU cc_start: 0.5884 (mm-30) cc_final: 0.5058 (mm-30) REVERT: B 411 GLU cc_start: 0.5361 (OUTLIER) cc_final: 0.4764 (mm-30) REVERT: B 415 GLU cc_start: 0.5099 (mt-10) cc_final: 0.4420 (mm-30) REVERT: B 441 MET cc_start: 0.6908 (tpp) cc_final: 0.6504 (tpp) REVERT: C 11 LYS cc_start: 0.4512 (tttm) cc_final: 0.4278 (ttpp) REVERT: C 15 GLU cc_start: 0.4283 (OUTLIER) cc_final: 0.3885 (mm-30) REVERT: C 49 LYS cc_start: 0.5981 (mmtt) cc_final: 0.5528 (mmmt) REVERT: C 102 THR cc_start: 0.6315 (m) cc_final: 0.5932 (p) REVERT: C 105 GLU cc_start: 0.6023 (pm20) cc_final: 0.5766 (pm20) REVERT: C 117 LYS cc_start: 0.5869 (tptm) cc_final: 0.5535 (tptm) REVERT: C 153 LYS cc_start: 0.5987 (mttm) cc_final: 0.4829 (mmmt) REVERT: C 200 LYS cc_start: 0.5645 (mtpp) cc_final: 0.4927 (tptp) REVERT: C 223 ARG cc_start: 0.5065 (ttm-80) cc_final: 0.4687 (tpt170) REVERT: C 224 LYS cc_start: 0.5699 (mtmt) cc_final: 0.5318 (mttm) REVERT: C 269 GLU cc_start: 0.5203 (mm-30) cc_final: 0.4386 (pm20) REVERT: C 314 GLN cc_start: 0.6912 (tt0) cc_final: 0.6639 (tt0) REVERT: C 329 SER cc_start: 0.7024 (m) cc_final: 0.6259 (p) REVERT: C 363 GLU cc_start: 0.5972 (tp30) cc_final: 0.5481 (tt0) REVERT: C 375 MET cc_start: 0.5491 (OUTLIER) cc_final: 0.4898 (pmm) REVERT: C 403 GLU cc_start: 0.5751 (tp30) cc_final: 0.5074 (pm20) REVERT: C 409 LEU cc_start: 0.5514 (OUTLIER) cc_final: 0.4897 (mt) REVERT: C 411 GLU cc_start: 0.5352 (pt0) cc_final: 0.4590 (mm-30) REVERT: C 415 GLU cc_start: 0.5082 (mt-10) cc_final: 0.4302 (mm-30) REVERT: C 438 GLU cc_start: 0.5192 (mt-10) cc_final: 0.4869 (mt-10) REVERT: C 441 MET cc_start: 0.6848 (tpp) cc_final: 0.6219 (tpp) REVERT: D 7 MET cc_start: 0.4908 (OUTLIER) cc_final: 0.4654 (mtt) REVERT: F 10 GLU cc_start: 0.5759 (OUTLIER) cc_final: 0.5272 (mt-10) REVERT: F 49 LYS cc_start: 0.5759 (mmtt) cc_final: 0.5298 (mmmt) REVERT: F 68 MET cc_start: 0.6335 (mmt) cc_final: 0.5781 (mmt) REVERT: F 105 GLU cc_start: 0.6021 (pm20) cc_final: 0.5773 (pm20) REVERT: F 148 LEU cc_start: 0.6363 (mt) cc_final: 0.6026 (mp) REVERT: F 153 LYS cc_start: 0.5995 (mttm) cc_final: 0.5024 (mmmt) REVERT: F 182 GLU cc_start: 0.5918 (mt-10) cc_final: 0.5552 (mt-10) REVERT: F 200 LYS cc_start: 0.5503 (mtpp) cc_final: 0.4633 (tptt) REVERT: F 206 ARG cc_start: 0.4955 (ttp80) cc_final: 0.4664 (tpt-90) REVERT: F 223 ARG cc_start: 0.5072 (ttm-80) cc_final: 0.4814 (ttm-80) REVERT: F 224 LYS cc_start: 0.5434 (mtpt) cc_final: 0.5075 (mttm) REVERT: F 232 MET cc_start: 0.6583 (ttt) cc_final: 0.6238 (ttt) REVERT: F 269 GLU cc_start: 0.5302 (mm-30) cc_final: 0.4525 (pm20) REVERT: F 329 SER cc_start: 0.6912 (m) cc_final: 0.6304 (p) REVERT: F 363 GLU cc_start: 0.5934 (tp30) cc_final: 0.5426 (tt0) REVERT: F 375 MET cc_start: 0.5622 (ptm) cc_final: 0.4938 (ptp) REVERT: F 403 GLU cc_start: 0.5841 (tp30) cc_final: 0.5140 (mp0) REVERT: F 411 GLU cc_start: 0.5605 (pt0) cc_final: 0.4870 (mm-30) REVERT: F 415 GLU cc_start: 0.5358 (mt-10) cc_final: 0.4582 (mm-30) REVERT: F 438 GLU cc_start: 0.5362 (mt-10) cc_final: 0.5122 (mt-10) REVERT: F 441 MET cc_start: 0.6862 (tpp) cc_final: 0.6196 (tpp) REVERT: G 27 ASP cc_start: 0.5610 (p0) cc_final: 0.5372 (p0) REVERT: G 49 LYS cc_start: 0.5640 (mmtt) cc_final: 0.5134 (mmmt) REVERT: G 102 THR cc_start: 0.6527 (m) cc_final: 0.6058 (p) REVERT: G 105 GLU cc_start: 0.6029 (pm20) cc_final: 0.5556 (pm20) REVERT: G 182 GLU cc_start: 0.5865 (mt-10) cc_final: 0.5648 (mt-10) REVERT: G 200 LYS cc_start: 0.6069 (ttmm) cc_final: 0.5055 (tptt) REVERT: G 206 ARG cc_start: 0.5140 (OUTLIER) cc_final: 0.4692 (tpt-90) REVERT: G 223 ARG cc_start: 0.5066 (ttm-80) cc_final: 0.4776 (tpt170) REVERT: G 329 SER cc_start: 0.7086 (m) cc_final: 0.6494 (p) REVERT: G 411 GLU cc_start: 0.5592 (pt0) cc_final: 0.4838 (mm-30) REVERT: G 415 GLU cc_start: 0.5239 (mt-10) cc_final: 0.4436 (mm-30) REVERT: G 438 GLU cc_start: 0.5516 (mt-10) cc_final: 0.5218 (mt-10) REVERT: H 7 GLU cc_start: 0.4449 (OUTLIER) cc_final: 0.4224 (mm-30) REVERT: H 10 GLU cc_start: 0.5999 (OUTLIER) cc_final: 0.5744 (mt-10) REVERT: H 27 ASP cc_start: 0.5669 (p0) cc_final: 0.5362 (p0) REVERT: H 49 LYS cc_start: 0.5729 (mmtt) cc_final: 0.5210 (mmmt) REVERT: H 117 LYS cc_start: 0.5982 (tptm) cc_final: 0.5724 (tptm) REVERT: H 153 LYS cc_start: 0.5805 (OUTLIER) cc_final: 0.4886 (mmmt) REVERT: H 200 LYS cc_start: 0.5827 (mtpm) cc_final: 0.4866 (tptt) REVERT: H 206 ARG cc_start: 0.5205 (ttt90) cc_final: 0.4776 (tpt-90) REVERT: H 223 ARG cc_start: 0.5315 (ttm-80) cc_final: 0.5003 (tpt-90) REVERT: H 329 SER cc_start: 0.7179 (m) cc_final: 0.6386 (p) REVERT: H 407 LYS cc_start: 0.5809 (mmtm) cc_final: 0.5432 (mtpt) REVERT: H 411 GLU cc_start: 0.5626 (pt0) cc_final: 0.5262 (mm-30) REVERT: H 415 GLU cc_start: 0.5185 (mt-10) cc_final: 0.4387 (tm-30) REVERT: H 438 GLU cc_start: 0.5447 (mt-10) cc_final: 0.5226 (mt-10) REVERT: H 441 MET cc_start: 0.6916 (tpp) cc_final: 0.6227 (tpp) REVERT: I 3 LYS cc_start: 0.6793 (tttt) cc_final: 0.6430 (ttmt) REVERT: I 10 GLU cc_start: 0.5946 (mt-10) cc_final: 0.5489 (mt-10) REVERT: I 19 LYS cc_start: 0.5954 (mmtt) cc_final: 0.5620 (mmmt) REVERT: I 49 LYS cc_start: 0.5792 (mmtt) cc_final: 0.5251 (mmmt) REVERT: I 63 ILE cc_start: 0.6270 (mt) cc_final: 0.5646 (mm) REVERT: I 68 MET cc_start: 0.6435 (mmt) cc_final: 0.6166 (mmt) REVERT: I 153 LYS cc_start: 0.6067 (mttm) cc_final: 0.5065 (mmmt) REVERT: I 182 GLU cc_start: 0.5873 (mt-10) cc_final: 0.5492 (mt-10) REVERT: I 200 LYS cc_start: 0.5754 (mtpm) cc_final: 0.4865 (tppt) REVERT: I 206 ARG cc_start: 0.4991 (ttp80) cc_final: 0.4562 (tpt-90) REVERT: I 223 ARG cc_start: 0.5332 (ttm-80) cc_final: 0.4998 (mtp85) REVERT: I 224 LYS cc_start: 0.5708 (ttmm) cc_final: 0.5265 (mttm) REVERT: I 269 GLU cc_start: 0.5005 (mm-30) cc_final: 0.4444 (pm20) REVERT: I 314 GLN cc_start: 0.6863 (tp40) cc_final: 0.6388 (tt0) REVERT: I 329 SER cc_start: 0.7080 (m) cc_final: 0.6274 (p) REVERT: I 363 GLU cc_start: 0.5988 (tp30) cc_final: 0.5454 (tt0) REVERT: I 411 GLU cc_start: 0.5393 (pt0) cc_final: 0.4909 (mm-30) REVERT: I 415 GLU cc_start: 0.5084 (mt-10) cc_final: 0.4267 (tm-30) REVERT: I 438 GLU cc_start: 0.5328 (mt-10) cc_final: 0.5053 (mt-10) REVERT: I 441 MET cc_start: 0.6836 (tpp) cc_final: 0.6334 (tpp) REVERT: N 10 GLU cc_start: 0.5777 (OUTLIER) cc_final: 0.5289 (mt-10) REVERT: N 49 LYS cc_start: 0.5792 (mmtt) cc_final: 0.5316 (mmmt) REVERT: N 68 MET cc_start: 0.6324 (mmt) cc_final: 0.5762 (mmt) REVERT: N 105 GLU cc_start: 0.6069 (pm20) cc_final: 0.5828 (pm20) REVERT: N 148 LEU cc_start: 0.6362 (mt) cc_final: 0.6026 (mp) REVERT: N 153 LYS cc_start: 0.6009 (mttm) cc_final: 0.4892 (mmmt) REVERT: N 182 GLU cc_start: 0.5910 (mt-10) cc_final: 0.5548 (mt-10) REVERT: N 200 LYS cc_start: 0.5506 (mtpp) cc_final: 0.4625 (tptt) REVERT: N 206 ARG cc_start: 0.4955 (ttp80) cc_final: 0.4665 (tpt-90) REVERT: N 223 ARG cc_start: 0.5073 (ttm-80) cc_final: 0.4815 (ttm-80) REVERT: N 224 LYS cc_start: 0.5427 (mtpt) cc_final: 0.5069 (mttm) REVERT: N 232 MET cc_start: 0.6585 (ttt) cc_final: 0.6240 (ttt) REVERT: N 269 GLU cc_start: 0.5301 (mm-30) cc_final: 0.4522 (pm20) REVERT: N 329 SER cc_start: 0.6920 (m) cc_final: 0.6300 (p) REVERT: N 363 GLU cc_start: 0.5992 (tp30) cc_final: 0.5478 (tt0) REVERT: N 375 MET cc_start: 0.5662 (ptm) cc_final: 0.4993 (ptp) REVERT: N 403 GLU cc_start: 0.6049 (tp30) cc_final: 0.5808 (mm-30) REVERT: N 411 GLU cc_start: 0.5568 (pt0) cc_final: 0.4839 (mm-30) REVERT: N 415 GLU cc_start: 0.5312 (mt-10) cc_final: 0.4567 (mm-30) REVERT: N 438 GLU cc_start: 0.5357 (mt-10) cc_final: 0.5123 (mt-10) REVERT: N 441 MET cc_start: 0.6861 (tpp) cc_final: 0.6192 (tpp) REVERT: O 3 LYS cc_start: 0.6842 (tttt) cc_final: 0.6626 (tttm) REVERT: O 10 GLU cc_start: 0.5949 (mt-10) cc_final: 0.5726 (mt-10) REVERT: O 27 ASP cc_start: 0.5602 (p0) cc_final: 0.5365 (p0) REVERT: O 49 LYS cc_start: 0.5635 (mmtt) cc_final: 0.5126 (mmmt) REVERT: O 102 THR cc_start: 0.6524 (m) cc_final: 0.6054 (p) REVERT: O 105 GLU cc_start: 0.6045 (pm20) cc_final: 0.5571 (pm20) REVERT: O 200 LYS cc_start: 0.6081 (ttmm) cc_final: 0.5073 (tptt) REVERT: O 206 ARG cc_start: 0.5169 (OUTLIER) cc_final: 0.4785 (tpt-90) REVERT: O 223 ARG cc_start: 0.5070 (ttm-80) cc_final: 0.4780 (tpt170) REVERT: O 224 LYS cc_start: 0.5587 (mtpt) cc_final: 0.5296 (mtpp) REVERT: O 314 GLN cc_start: 0.6836 (OUTLIER) cc_final: 0.6305 (tt0) REVERT: O 329 SER cc_start: 0.7068 (m) cc_final: 0.6475 (p) REVERT: O 407 LYS cc_start: 0.6091 (mttm) cc_final: 0.5842 (mmtm) REVERT: O 411 GLU cc_start: 0.5606 (pt0) cc_final: 0.4825 (mm-30) REVERT: O 415 GLU cc_start: 0.5212 (mt-10) cc_final: 0.4416 (mm-30) REVERT: O 438 GLU cc_start: 0.5518 (mt-10) cc_final: 0.5236 (mt-10) REVERT: P 10 GLU cc_start: 0.6056 (OUTLIER) cc_final: 0.5175 (mp0) REVERT: P 27 ASP cc_start: 0.5651 (p0) cc_final: 0.5349 (p0) REVERT: P 49 LYS cc_start: 0.5730 (mmtt) cc_final: 0.5211 (mmmt) REVERT: P 153 LYS cc_start: 0.5722 (ptpt) cc_final: 0.4706 (mmmt) REVERT: P 200 LYS cc_start: 0.5836 (mtpp) cc_final: 0.4953 (tptt) REVERT: P 206 ARG cc_start: 0.5214 (ttt90) cc_final: 0.4733 (tpt-90) REVERT: P 223 ARG cc_start: 0.5286 (ttm-80) cc_final: 0.4968 (tpt-90) REVERT: P 329 SER cc_start: 0.7178 (m) cc_final: 0.6322 (p) REVERT: P 407 LYS cc_start: 0.5903 (mmtm) cc_final: 0.5454 (mtpt) REVERT: P 411 GLU cc_start: 0.5621 (pt0) cc_final: 0.5260 (mm-30) REVERT: P 415 GLU cc_start: 0.5192 (mt-10) cc_final: 0.4390 (tm-30) REVERT: P 438 GLU cc_start: 0.5452 (mt-10) cc_final: 0.5230 (mt-10) REVERT: P 441 MET cc_start: 0.6951 (tpp) cc_final: 0.6271 (tpp) REVERT: Q 3 LYS cc_start: 0.6807 (tttt) cc_final: 0.6432 (ttmt) REVERT: Q 10 GLU cc_start: 0.5980 (mt-10) cc_final: 0.5670 (mt-10) REVERT: Q 18 VAL cc_start: 0.5109 (OUTLIER) cc_final: 0.4872 (t) REVERT: Q 19 LYS cc_start: 0.6041 (mmtt) cc_final: 0.5813 (mmmt) REVERT: Q 27 ASP cc_start: 0.5718 (p0) cc_final: 0.5517 (p0) REVERT: Q 49 LYS cc_start: 0.5796 (mmtt) cc_final: 0.5259 (mmmt) REVERT: Q 63 ILE cc_start: 0.6318 (mt) cc_final: 0.5748 (mm) REVERT: Q 68 MET cc_start: 0.6443 (mmt) cc_final: 0.6184 (mmt) REVERT: Q 105 GLU cc_start: 0.5873 (pm20) cc_final: 0.5628 (pm20) REVERT: Q 153 LYS cc_start: 0.6056 (mttm) cc_final: 0.5050 (mmmt) REVERT: Q 182 GLU cc_start: 0.5883 (mt-10) cc_final: 0.5506 (mt-10) REVERT: Q 200 LYS cc_start: 0.5754 (mtpm) cc_final: 0.4871 (tppt) REVERT: Q 206 ARG cc_start: 0.5020 (ttp80) cc_final: 0.4591 (tpt-90) REVERT: Q 224 LYS cc_start: 0.5551 (ttmm) cc_final: 0.5232 (mttm) REVERT: Q 269 GLU cc_start: 0.5023 (mm-30) cc_final: 0.4452 (pm20) REVERT: Q 314 GLN cc_start: 0.6848 (tp40) cc_final: 0.6422 (tt0) REVERT: Q 329 SER cc_start: 0.7088 (m) cc_final: 0.6287 (p) REVERT: Q 363 GLU cc_start: 0.5989 (tp30) cc_final: 0.5453 (tt0) REVERT: Q 403 GLU cc_start: 0.5574 (tp30) cc_final: 0.5031 (pm20) REVERT: Q 407 LYS cc_start: 0.5548 (mmtm) cc_final: 0.4991 (mtpt) REVERT: Q 411 GLU cc_start: 0.5347 (pt0) cc_final: 0.4874 (mm-30) REVERT: Q 415 GLU cc_start: 0.5079 (mt-10) cc_final: 0.4228 (tm-30) REVERT: Q 438 GLU cc_start: 0.5290 (mt-10) cc_final: 0.5032 (mt-10) REVERT: Q 441 MET cc_start: 0.6834 (tpp) cc_final: 0.6332 (tpp) REVERT: R 3 LYS cc_start: 0.7116 (tttt) cc_final: 0.6448 (ttmm) REVERT: R 11 LYS cc_start: 0.4582 (tttp) cc_final: 0.4242 (ttpp) REVERT: R 15 GLU cc_start: 0.4283 (OUTLIER) cc_final: 0.3792 (mm-30) REVERT: R 18 VAL cc_start: 0.4969 (OUTLIER) cc_final: 0.4729 (t) REVERT: R 32 ILE cc_start: 0.5713 (mp) cc_final: 0.5437 (mp) REVERT: R 49 LYS cc_start: 0.5858 (mmtt) cc_final: 0.5356 (mmmt) REVERT: R 102 THR cc_start: 0.6377 (m) cc_final: 0.5936 (p) REVERT: R 117 LYS cc_start: 0.5772 (tptm) cc_final: 0.5445 (tptm) REVERT: R 148 LEU cc_start: 0.6576 (mt) cc_final: 0.6328 (mt) REVERT: R 153 LYS cc_start: 0.6210 (ptpp) cc_final: 0.5043 (mmmt) REVERT: R 182 GLU cc_start: 0.5887 (mt-10) cc_final: 0.5562 (mt-10) REVERT: R 200 LYS cc_start: 0.5974 (ttmm) cc_final: 0.5032 (tptt) REVERT: R 206 ARG cc_start: 0.4973 (ttt90) cc_final: 0.4683 (tpt-90) REVERT: R 314 GLN cc_start: 0.6853 (OUTLIER) cc_final: 0.6367 (tt0) REVERT: R 329 SER cc_start: 0.6957 (m) cc_final: 0.6398 (p) REVERT: R 401 SER cc_start: 0.7177 (p) cc_final: 0.6929 (p) REVERT: R 407 LYS cc_start: 0.6029 (mmtm) cc_final: 0.5455 (mppt) REVERT: R 411 GLU cc_start: 0.5853 (mm-30) cc_final: 0.5167 (tt0) REVERT: R 415 GLU cc_start: 0.5212 (mt-10) cc_final: 0.4520 (mm-30) REVERT: R 427 MET cc_start: 0.5695 (mmm) cc_final: 0.5331 (mmp) REVERT: R 438 GLU cc_start: 0.5390 (mt-10) cc_final: 0.4998 (mt-10) REVERT: R 441 MET cc_start: 0.6985 (tpp) cc_final: 0.6476 (tpp) REVERT: S 3 LYS cc_start: 0.6751 (tttt) cc_final: 0.6191 (ttmt) REVERT: S 10 GLU cc_start: 0.6138 (OUTLIER) cc_final: 0.5675 (mt-10) REVERT: S 19 LYS cc_start: 0.5902 (mmtt) cc_final: 0.5634 (mmmt) REVERT: S 49 LYS cc_start: 0.5754 (mmtt) cc_final: 0.5187 (mmmt) REVERT: S 68 MET cc_start: 0.6330 (mmt) cc_final: 0.5781 (mmt) REVERT: S 105 GLU cc_start: 0.6101 (pm20) cc_final: 0.5796 (pm20) REVERT: S 153 LYS cc_start: 0.5744 (mmpt) cc_final: 0.5340 (mmmt) REVERT: S 166 GLU cc_start: 0.4229 (OUTLIER) cc_final: 0.3977 (tm-30) REVERT: S 200 LYS cc_start: 0.5917 (mtpp) cc_final: 0.4978 (tptt) REVERT: S 223 ARG cc_start: 0.4990 (ttm-80) cc_final: 0.4779 (ttt90) REVERT: S 314 GLN cc_start: 0.6776 (OUTLIER) cc_final: 0.6163 (tt0) REVERT: S 329 SER cc_start: 0.6899 (m) cc_final: 0.6067 (p) REVERT: S 397 GLU cc_start: 0.5684 (mm-30) cc_final: 0.4898 (mm-30) REVERT: S 411 GLU cc_start: 0.5368 (OUTLIER) cc_final: 0.4781 (mm-30) REVERT: S 415 GLU cc_start: 0.5112 (mt-10) cc_final: 0.4433 (mm-30) REVERT: S 441 MET cc_start: 0.6902 (tpp) cc_final: 0.6474 (tpp) REVERT: T 11 LYS cc_start: 0.4762 (ttpp) cc_final: 0.4372 (ttpp) REVERT: T 15 GLU cc_start: 0.4620 (OUTLIER) cc_final: 0.4193 (mm-30) REVERT: T 49 LYS cc_start: 0.6007 (mmtt) cc_final: 0.5553 (mmmt) REVERT: T 117 LYS cc_start: 0.5955 (tptm) cc_final: 0.5626 (tptm) REVERT: T 153 LYS cc_start: 0.5958 (mttm) cc_final: 0.4790 (mmmt) REVERT: T 184 GLU cc_start: 0.6109 (tt0) cc_final: 0.5892 (tt0) REVERT: T 200 LYS cc_start: 0.5654 (mtpp) cc_final: 0.4847 (tptt) REVERT: T 223 ARG cc_start: 0.5058 (ttm-80) cc_final: 0.4697 (tpt170) REVERT: T 269 GLU cc_start: 0.5263 (mm-30) cc_final: 0.4485 (pm20) REVERT: T 314 GLN cc_start: 0.6895 (tt0) cc_final: 0.6622 (tt0) REVERT: T 329 SER cc_start: 0.6968 (m) cc_final: 0.6216 (p) REVERT: T 363 GLU cc_start: 0.5987 (tp30) cc_final: 0.5488 (tt0) REVERT: T 409 LEU cc_start: 0.5529 (OUTLIER) cc_final: 0.4902 (mt) REVERT: T 411 GLU cc_start: 0.5352 (pt0) cc_final: 0.4609 (mm-30) REVERT: T 415 GLU cc_start: 0.5085 (mt-10) cc_final: 0.4310 (mm-30) REVERT: T 438 GLU cc_start: 0.5192 (mt-10) cc_final: 0.4866 (mt-10) REVERT: T 441 MET cc_start: 0.6841 (tpp) cc_final: 0.6313 (tpp) REVERT: V 7 MET cc_start: 0.4966 (OUTLIER) cc_final: 0.4347 (ttm) outliers start: 175 outliers final: 55 residues processed: 1023 average time/residue: 1.4386 time to fit residues: 1808.2077 Evaluate side-chains 926 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 841 time to evaluate : 4.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 411 GLU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 9 ARG Chi-restraints excluded: chain E residue 7 MET Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 114 ARG Chi-restraints excluded: chain G residue 206 ARG Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 153 LYS Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 328 ILE Chi-restraints excluded: chain H residue 409 LEU Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain L residue 7 MET Chi-restraints excluded: chain N residue 10 GLU Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 114 ARG Chi-restraints excluded: chain O residue 206 ARG Chi-restraints excluded: chain O residue 314 GLN Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 239 VAL Chi-restraints excluded: chain P residue 409 LEU Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 35 VAL Chi-restraints excluded: chain Q residue 83 THR Chi-restraints excluded: chain Q residue 239 VAL Chi-restraints excluded: chain Q residue 409 LEU Chi-restraints excluded: chain R residue 15 GLU Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 314 GLN Chi-restraints excluded: chain R residue 409 LEU Chi-restraints excluded: chain S residue 10 GLU Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 102 THR Chi-restraints excluded: chain S residue 166 GLU Chi-restraints excluded: chain S residue 239 VAL Chi-restraints excluded: chain S residue 264 ASP Chi-restraints excluded: chain S residue 314 GLN Chi-restraints excluded: chain S residue 409 LEU Chi-restraints excluded: chain S residue 411 GLU Chi-restraints excluded: chain T residue 15 GLU Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 83 THR Chi-restraints excluded: chain T residue 409 LEU Chi-restraints excluded: chain V residue 7 MET Chi-restraints excluded: chain Z residue 7 MET Chi-restraints excluded: chain a residue 7 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 317 optimal weight: 0.8980 chunk 177 optimal weight: 0.9990 chunk 476 optimal weight: 0.3980 chunk 389 optimal weight: 0.0870 chunk 157 optimal weight: 1.9990 chunk 573 optimal weight: 3.9990 chunk 619 optimal weight: 6.9990 chunk 510 optimal weight: 0.9990 chunk 568 optimal weight: 2.9990 chunk 195 optimal weight: 9.9990 chunk 459 optimal weight: 1.9990 overall best weight: 0.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN B 443 GLN C 34 ASN C 75 ASN C 167 ASN C 315 ASN C 443 GLN F 24 GLN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN F 167 ASN F 443 GLN G 24 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN G 167 ASN G 443 GLN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 ASN H 443 GLN I 34 ASN I 75 ASN I 167 ASN I 266 GLN N 24 GLN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 ASN N 167 ASN O 24 GLN ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 ASN O 315 ASN O 443 GLN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 167 ASN P 443 GLN Q 34 ASN Q 75 ASN Q 167 ASN Q 266 GLN R 24 GLN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 167 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 ASN S 266 GLN S 443 GLN ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 ASN T 443 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5940 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 51450 Z= 0.117 Angle : 0.435 4.165 69650 Z= 0.239 Chirality : 0.040 0.134 7546 Planarity : 0.003 0.049 9184 Dihedral : 5.306 50.282 6875 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.99 % Allowed : 17.85 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.11), residues: 6286 helix: 2.03 (0.10), residues: 2324 sheet: -0.21 (0.15), residues: 1120 loop : 0.09 (0.12), residues: 2842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP T 425 HIS 0.003 0.001 HIS I 416 PHE 0.016 0.001 PHE I 285 TYR 0.024 0.001 TYR I 296 ARG 0.003 0.000 ARG H 335 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 977 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 871 time to evaluate : 4.418 Fit side-chains REVERT: A 3 LYS cc_start: 0.7128 (tttt) cc_final: 0.6709 (ttmm) REVERT: A 11 LYS cc_start: 0.5019 (tttp) cc_final: 0.4781 (ttpp) REVERT: A 32 ILE cc_start: 0.5755 (mp) cc_final: 0.5449 (mp) REVERT: A 35 VAL cc_start: 0.7004 (OUTLIER) cc_final: 0.6707 (t) REVERT: A 49 LYS cc_start: 0.5762 (mmtt) cc_final: 0.5216 (mmmt) REVERT: A 102 THR cc_start: 0.6116 (m) cc_final: 0.5768 (p) REVERT: A 117 LYS cc_start: 0.5957 (tptm) cc_final: 0.5596 (tptm) REVERT: A 148 LEU cc_start: 0.6515 (mt) cc_final: 0.6240 (mt) REVERT: A 182 GLU cc_start: 0.6000 (mt-10) cc_final: 0.5595 (mt-10) REVERT: A 200 LYS cc_start: 0.6080 (ttmm) cc_final: 0.4990 (tptt) REVERT: A 206 ARG cc_start: 0.5100 (ttt90) cc_final: 0.4871 (tpt-90) REVERT: A 261 GLU cc_start: 0.5720 (pm20) cc_final: 0.5499 (pm20) REVERT: A 314 GLN cc_start: 0.6838 (OUTLIER) cc_final: 0.6372 (tt0) REVERT: A 329 SER cc_start: 0.6971 (m) cc_final: 0.6384 (p) REVERT: A 407 LYS cc_start: 0.5843 (mmtm) cc_final: 0.5440 (mtpt) REVERT: A 411 GLU cc_start: 0.5318 (pt0) cc_final: 0.4597 (mm-30) REVERT: A 438 GLU cc_start: 0.5253 (mt-10) cc_final: 0.4894 (mt-10) REVERT: A 441 MET cc_start: 0.6927 (tpp) cc_final: 0.6506 (tpp) REVERT: B 3 LYS cc_start: 0.6749 (tttt) cc_final: 0.6242 (ttmt) REVERT: B 10 GLU cc_start: 0.5988 (OUTLIER) cc_final: 0.5392 (mt-10) REVERT: B 49 LYS cc_start: 0.5841 (mmtt) cc_final: 0.5323 (mmmt) REVERT: B 68 MET cc_start: 0.6282 (mmt) cc_final: 0.5707 (mmt) REVERT: B 102 THR cc_start: 0.6177 (m) cc_final: 0.5893 (p) REVERT: B 105 GLU cc_start: 0.6062 (pm20) cc_final: 0.5465 (mp0) REVERT: B 117 LYS cc_start: 0.5787 (tptp) cc_final: 0.5433 (tptm) REVERT: B 153 LYS cc_start: 0.6076 (mttm) cc_final: 0.5025 (mmmt) REVERT: B 182 GLU cc_start: 0.6032 (mt-10) cc_final: 0.5740 (mt-10) REVERT: B 200 LYS cc_start: 0.5931 (mtpp) cc_final: 0.4844 (tptt) REVERT: B 224 LYS cc_start: 0.5612 (ttmm) cc_final: 0.5305 (mttm) REVERT: B 314 GLN cc_start: 0.6890 (OUTLIER) cc_final: 0.6249 (tt0) REVERT: B 329 SER cc_start: 0.6961 (m) cc_final: 0.6121 (p) REVERT: B 397 GLU cc_start: 0.5953 (mm-30) cc_final: 0.5099 (mm-30) REVERT: B 407 LYS cc_start: 0.6112 (mmtm) cc_final: 0.5477 (mtpt) REVERT: B 411 GLU cc_start: 0.5226 (pt0) cc_final: 0.4835 (mm-30) REVERT: B 415 GLU cc_start: 0.5128 (mt-10) cc_final: 0.4364 (tm-30) REVERT: B 441 MET cc_start: 0.6874 (tpp) cc_final: 0.6503 (tpp) REVERT: C 11 LYS cc_start: 0.4746 (tttm) cc_final: 0.4500 (ttpp) REVERT: C 15 GLU cc_start: 0.4099 (OUTLIER) cc_final: 0.3569 (mm-30) REVERT: C 49 LYS cc_start: 0.6015 (mmtt) cc_final: 0.5567 (mmmt) REVERT: C 63 ILE cc_start: 0.6120 (mt) cc_final: 0.5559 (mm) REVERT: C 102 THR cc_start: 0.6181 (m) cc_final: 0.5822 (p) REVERT: C 117 LYS cc_start: 0.5947 (tptm) cc_final: 0.5633 (tptm) REVERT: C 153 LYS cc_start: 0.5974 (mttm) cc_final: 0.4833 (mmmt) REVERT: C 200 LYS cc_start: 0.5761 (mtpp) cc_final: 0.5076 (tptt) REVERT: C 223 ARG cc_start: 0.5159 (ttm-80) cc_final: 0.4818 (tpt170) REVERT: C 269 GLU cc_start: 0.5223 (mm-30) cc_final: 0.4454 (pm20) REVERT: C 280 LYS cc_start: 0.5972 (tttt) cc_final: 0.5765 (tttm) REVERT: C 314 GLN cc_start: 0.6962 (tt0) cc_final: 0.6689 (tt0) REVERT: C 329 SER cc_start: 0.7115 (m) cc_final: 0.6305 (p) REVERT: C 363 GLU cc_start: 0.6032 (tp30) cc_final: 0.5488 (tt0) REVERT: C 403 GLU cc_start: 0.5568 (tp30) cc_final: 0.4863 (pm20) REVERT: C 411 GLU cc_start: 0.5267 (pt0) cc_final: 0.4538 (mm-30) REVERT: C 438 GLU cc_start: 0.5136 (mt-10) cc_final: 0.4827 (mt-10) REVERT: C 441 MET cc_start: 0.6789 (tpp) cc_final: 0.6172 (tpp) REVERT: F 5 THR cc_start: 0.5587 (p) cc_final: 0.5144 (t) REVERT: F 10 GLU cc_start: 0.5796 (OUTLIER) cc_final: 0.5353 (mt-10) REVERT: F 35 VAL cc_start: 0.7115 (OUTLIER) cc_final: 0.6895 (t) REVERT: F 49 LYS cc_start: 0.5694 (mmtt) cc_final: 0.5234 (mmmt) REVERT: F 68 MET cc_start: 0.6260 (mmt) cc_final: 0.5733 (mmt) REVERT: F 102 THR cc_start: 0.6218 (m) cc_final: 0.5766 (p) REVERT: F 105 GLU cc_start: 0.5993 (pm20) cc_final: 0.5781 (pm20) REVERT: F 148 LEU cc_start: 0.6373 (mt) cc_final: 0.6060 (mp) REVERT: F 153 LYS cc_start: 0.6033 (mttm) cc_final: 0.4978 (mmmt) REVERT: F 182 GLU cc_start: 0.5958 (mt-10) cc_final: 0.5599 (mt-10) REVERT: F 200 LYS cc_start: 0.5550 (mtpp) cc_final: 0.4692 (tptt) REVERT: F 206 ARG cc_start: 0.4851 (ttp80) cc_final: 0.4500 (tpt-90) REVERT: F 224 LYS cc_start: 0.5451 (OUTLIER) cc_final: 0.5124 (mtpp) REVERT: F 232 MET cc_start: 0.6336 (ttt) cc_final: 0.6063 (ttt) REVERT: F 269 GLU cc_start: 0.5151 (mm-30) cc_final: 0.4511 (pm20) REVERT: F 280 LYS cc_start: 0.6144 (tttt) cc_final: 0.5912 (tttm) REVERT: F 329 SER cc_start: 0.6925 (m) cc_final: 0.6279 (p) REVERT: F 363 GLU cc_start: 0.5939 (tp30) cc_final: 0.5451 (tt0) REVERT: F 375 MET cc_start: 0.5393 (ptm) cc_final: 0.4980 (ptp) REVERT: F 403 GLU cc_start: 0.5549 (tp30) cc_final: 0.4943 (mp0) REVERT: F 411 GLU cc_start: 0.5376 (pt0) cc_final: 0.4622 (mm-30) REVERT: F 438 GLU cc_start: 0.5280 (mt-10) cc_final: 0.4960 (mt-10) REVERT: F 441 MET cc_start: 0.6835 (tpp) cc_final: 0.6140 (tpp) REVERT: G 27 ASP cc_start: 0.5424 (p0) cc_final: 0.4999 (p0) REVERT: G 49 LYS cc_start: 0.5671 (mmtt) cc_final: 0.5143 (mmmt) REVERT: G 102 THR cc_start: 0.6345 (m) cc_final: 0.5946 (p) REVERT: G 105 GLU cc_start: 0.5970 (pm20) cc_final: 0.5466 (pm20) REVERT: G 206 ARG cc_start: 0.5031 (ttt90) cc_final: 0.4626 (tpt-90) REVERT: G 223 ARG cc_start: 0.5364 (ttm-80) cc_final: 0.5013 (tpt170) REVERT: G 329 SER cc_start: 0.7029 (m) cc_final: 0.6417 (p) REVERT: G 375 MET cc_start: 0.6291 (ptt) cc_final: 0.5829 (ptt) REVERT: G 411 GLU cc_start: 0.5421 (pt0) cc_final: 0.4593 (mm-30) REVERT: G 415 GLU cc_start: 0.5132 (mt-10) cc_final: 0.4445 (mm-30) REVERT: G 438 GLU cc_start: 0.5476 (mt-10) cc_final: 0.5198 (mt-10) REVERT: H 3 LYS cc_start: 0.6949 (tttt) cc_final: 0.6724 (ttmm) REVERT: H 27 ASP cc_start: 0.5750 (p0) cc_final: 0.5418 (p0) REVERT: H 32 ILE cc_start: 0.5794 (mt) cc_final: 0.5499 (mm) REVERT: H 49 LYS cc_start: 0.5734 (mmtt) cc_final: 0.5204 (mmmt) REVERT: H 102 THR cc_start: 0.6372 (m) cc_final: 0.5937 (p) REVERT: H 105 GLU cc_start: 0.5847 (pm20) cc_final: 0.5440 (mp0) REVERT: H 117 LYS cc_start: 0.5962 (tptm) cc_final: 0.5712 (tptm) REVERT: H 153 LYS cc_start: 0.5774 (OUTLIER) cc_final: 0.4839 (mmmt) REVERT: H 200 LYS cc_start: 0.5906 (mtpm) cc_final: 0.4891 (tptt) REVERT: H 206 ARG cc_start: 0.5140 (ttt90) cc_final: 0.4732 (tpt-90) REVERT: H 223 ARG cc_start: 0.5260 (ttm-80) cc_final: 0.4745 (ttm-80) REVERT: H 329 SER cc_start: 0.7093 (m) cc_final: 0.6265 (p) REVERT: H 369 ASP cc_start: 0.4951 (OUTLIER) cc_final: 0.4221 (m-30) REVERT: H 411 GLU cc_start: 0.5312 (pt0) cc_final: 0.4884 (mm-30) REVERT: H 415 GLU cc_start: 0.5185 (mt-10) cc_final: 0.4535 (tm-30) REVERT: H 438 GLU cc_start: 0.5462 (mt-10) cc_final: 0.5239 (mt-10) REVERT: H 441 MET cc_start: 0.6924 (tpp) cc_final: 0.6169 (tpp) REVERT: I 3 LYS cc_start: 0.6851 (tttt) cc_final: 0.6489 (ttmt) REVERT: I 10 GLU cc_start: 0.5811 (mt-10) cc_final: 0.5349 (mt-10) REVERT: I 49 LYS cc_start: 0.5742 (mmtt) cc_final: 0.5289 (mmmt) REVERT: I 63 ILE cc_start: 0.6309 (mt) cc_final: 0.5755 (mm) REVERT: I 105 GLU cc_start: 0.5973 (pm20) cc_final: 0.5673 (pm20) REVERT: I 122 LEU cc_start: 0.6431 (OUTLIER) cc_final: 0.6204 (mp) REVERT: I 153 LYS cc_start: 0.5978 (mttm) cc_final: 0.4949 (mmmt) REVERT: I 182 GLU cc_start: 0.5916 (mt-10) cc_final: 0.5518 (mt-10) REVERT: I 206 ARG cc_start: 0.4952 (ttp80) cc_final: 0.4481 (tpt-90) REVERT: I 223 ARG cc_start: 0.5111 (ttm-80) cc_final: 0.4687 (tpt170) REVERT: I 224 LYS cc_start: 0.5727 (ttmm) cc_final: 0.5502 (mtpp) REVERT: I 269 GLU cc_start: 0.4992 (mm-30) cc_final: 0.4450 (pm20) REVERT: I 280 LYS cc_start: 0.6168 (tttt) cc_final: 0.5940 (tttm) REVERT: I 314 GLN cc_start: 0.6970 (tp40) cc_final: 0.6545 (tt0) REVERT: I 329 SER cc_start: 0.7207 (m) cc_final: 0.6366 (p) REVERT: I 363 GLU cc_start: 0.5997 (tp30) cc_final: 0.5447 (tt0) REVERT: I 411 GLU cc_start: 0.5212 (pt0) cc_final: 0.4723 (mm-30) REVERT: I 415 GLU cc_start: 0.4929 (mt-10) cc_final: 0.4095 (tm-30) REVERT: I 438 GLU cc_start: 0.5414 (mt-10) cc_final: 0.5201 (mt-10) REVERT: I 441 MET cc_start: 0.6748 (tpp) cc_final: 0.6024 (tpp) REVERT: N 5 THR cc_start: 0.5595 (p) cc_final: 0.5151 (t) REVERT: N 10 GLU cc_start: 0.5773 (OUTLIER) cc_final: 0.5330 (mt-10) REVERT: N 49 LYS cc_start: 0.5748 (mmtt) cc_final: 0.5285 (mmmt) REVERT: N 68 MET cc_start: 0.6232 (mmt) cc_final: 0.5723 (mmt) REVERT: N 102 THR cc_start: 0.6207 (m) cc_final: 0.5762 (p) REVERT: N 105 GLU cc_start: 0.6019 (pm20) cc_final: 0.5515 (mp0) REVERT: N 148 LEU cc_start: 0.6380 (mt) cc_final: 0.6058 (mp) REVERT: N 153 LYS cc_start: 0.6037 (mttm) cc_final: 0.4929 (mmmt) REVERT: N 182 GLU cc_start: 0.5963 (mt-10) cc_final: 0.5607 (mt-10) REVERT: N 200 LYS cc_start: 0.5554 (mtpp) cc_final: 0.4701 (tptt) REVERT: N 206 ARG cc_start: 0.4852 (ttp80) cc_final: 0.4501 (tpt-90) REVERT: N 224 LYS cc_start: 0.5445 (OUTLIER) cc_final: 0.5119 (mtpp) REVERT: N 232 MET cc_start: 0.6351 (ttt) cc_final: 0.6085 (ttt) REVERT: N 269 GLU cc_start: 0.5147 (mm-30) cc_final: 0.4508 (pm20) REVERT: N 280 LYS cc_start: 0.6142 (tttt) cc_final: 0.5911 (tttm) REVERT: N 329 SER cc_start: 0.6929 (m) cc_final: 0.6274 (p) REVERT: N 363 GLU cc_start: 0.5949 (tp30) cc_final: 0.5460 (tt0) REVERT: N 375 MET cc_start: 0.5414 (ptm) cc_final: 0.4772 (ptp) REVERT: N 403 GLU cc_start: 0.5899 (tp30) cc_final: 0.4946 (mp0) REVERT: N 411 GLU cc_start: 0.5368 (pt0) cc_final: 0.4596 (mm-30) REVERT: N 438 GLU cc_start: 0.5269 (mt-10) cc_final: 0.4947 (mt-10) REVERT: N 441 MET cc_start: 0.6844 (tpp) cc_final: 0.6262 (tpp) REVERT: O 3 LYS cc_start: 0.6715 (tttt) cc_final: 0.6514 (tttm) REVERT: O 10 GLU cc_start: 0.5885 (mt-10) cc_final: 0.5677 (mt-10) REVERT: O 27 ASP cc_start: 0.5418 (p0) cc_final: 0.4995 (p0) REVERT: O 49 LYS cc_start: 0.5659 (mmtt) cc_final: 0.5138 (mmmt) REVERT: O 102 THR cc_start: 0.6342 (m) cc_final: 0.5941 (p) REVERT: O 105 GLU cc_start: 0.5985 (pm20) cc_final: 0.5483 (pm20) REVERT: O 206 ARG cc_start: 0.5067 (OUTLIER) cc_final: 0.4658 (tpt-90) REVERT: O 223 ARG cc_start: 0.5361 (ttm-80) cc_final: 0.5017 (tpt170) REVERT: O 329 SER cc_start: 0.7011 (m) cc_final: 0.6398 (p) REVERT: O 411 GLU cc_start: 0.5394 (pt0) cc_final: 0.4761 (mm-30) REVERT: O 415 GLU cc_start: 0.5125 (mt-10) cc_final: 0.4320 (tm-30) REVERT: O 438 GLU cc_start: 0.5476 (mt-10) cc_final: 0.5201 (mt-10) REVERT: P 10 GLU cc_start: 0.5895 (OUTLIER) cc_final: 0.5252 (mt-10) REVERT: P 27 ASP cc_start: 0.5599 (p0) cc_final: 0.5270 (p0) REVERT: P 32 ILE cc_start: 0.5767 (mt) cc_final: 0.5470 (mm) REVERT: P 49 LYS cc_start: 0.5735 (mmtt) cc_final: 0.5203 (mmmt) REVERT: P 102 THR cc_start: 0.6356 (m) cc_final: 0.5906 (p) REVERT: P 105 GLU cc_start: 0.5798 (pm20) cc_final: 0.5500 (mp0) REVERT: P 153 LYS cc_start: 0.5841 (ptpt) cc_final: 0.4766 (mmmt) REVERT: P 200 LYS cc_start: 0.5917 (mtpp) cc_final: 0.4931 (tptt) REVERT: P 206 ARG cc_start: 0.5137 (ttt90) cc_final: 0.4726 (tpt-90) REVERT: P 223 ARG cc_start: 0.5282 (ttm-80) cc_final: 0.4726 (ttm-80) REVERT: P 329 SER cc_start: 0.7163 (m) cc_final: 0.6292 (p) REVERT: P 411 GLU cc_start: 0.5343 (pt0) cc_final: 0.4946 (mm-30) REVERT: P 415 GLU cc_start: 0.5196 (mt-10) cc_final: 0.4554 (tm-30) REVERT: P 438 GLU cc_start: 0.5468 (mt-10) cc_final: 0.5244 (mt-10) REVERT: P 441 MET cc_start: 0.6930 (tpp) cc_final: 0.6173 (tpp) REVERT: Q 3 LYS cc_start: 0.6852 (tttt) cc_final: 0.6509 (ttmt) REVERT: Q 10 GLU cc_start: 0.5805 (mt-10) cc_final: 0.5502 (mt-10) REVERT: Q 27 ASP cc_start: 0.5447 (p0) cc_final: 0.5215 (p0) REVERT: Q 49 LYS cc_start: 0.5751 (mmtt) cc_final: 0.5298 (mmmt) REVERT: Q 63 ILE cc_start: 0.6312 (mt) cc_final: 0.5762 (mm) REVERT: Q 102 THR cc_start: 0.6641 (m) cc_final: 0.6256 (p) REVERT: Q 122 LEU cc_start: 0.6412 (OUTLIER) cc_final: 0.6186 (mp) REVERT: Q 153 LYS cc_start: 0.5965 (mttm) cc_final: 0.4934 (mmmt) REVERT: Q 182 GLU cc_start: 0.5957 (mt-10) cc_final: 0.5541 (mt-10) REVERT: Q 206 ARG cc_start: 0.4965 (ttp80) cc_final: 0.4495 (tpt-90) REVERT: Q 269 GLU cc_start: 0.4996 (mm-30) cc_final: 0.4455 (pm20) REVERT: Q 280 LYS cc_start: 0.6185 (tttt) cc_final: 0.5956 (tttm) REVERT: Q 314 GLN cc_start: 0.6901 (tp40) cc_final: 0.6498 (tt0) REVERT: Q 329 SER cc_start: 0.7155 (m) cc_final: 0.6326 (p) REVERT: Q 363 GLU cc_start: 0.5969 (tp30) cc_final: 0.5404 (tt0) REVERT: Q 403 GLU cc_start: 0.5578 (tp30) cc_final: 0.5159 (pm20) REVERT: Q 407 LYS cc_start: 0.5365 (mmtm) cc_final: 0.4860 (mtpt) REVERT: Q 411 GLU cc_start: 0.5188 (pt0) cc_final: 0.4715 (mm-30) REVERT: Q 415 GLU cc_start: 0.4923 (mt-10) cc_final: 0.4090 (tm-30) REVERT: Q 441 MET cc_start: 0.6746 (tpp) cc_final: 0.6020 (tpp) REVERT: R 3 LYS cc_start: 0.7124 (tttt) cc_final: 0.6718 (ttmm) REVERT: R 11 LYS cc_start: 0.4620 (tttp) cc_final: 0.4273 (ttpp) REVERT: R 15 GLU cc_start: 0.4199 (OUTLIER) cc_final: 0.3643 (mm-30) REVERT: R 32 ILE cc_start: 0.5767 (mp) cc_final: 0.5460 (mp) REVERT: R 35 VAL cc_start: 0.7009 (OUTLIER) cc_final: 0.6710 (t) REVERT: R 49 LYS cc_start: 0.5807 (mmtt) cc_final: 0.5268 (mmmt) REVERT: R 102 THR cc_start: 0.6101 (m) cc_final: 0.5755 (p) REVERT: R 117 LYS cc_start: 0.5970 (tptm) cc_final: 0.5611 (tptm) REVERT: R 148 LEU cc_start: 0.6512 (mt) cc_final: 0.6258 (mt) REVERT: R 182 GLU cc_start: 0.5939 (mt-10) cc_final: 0.5627 (mt-10) REVERT: R 200 LYS cc_start: 0.6089 (ttmm) cc_final: 0.5102 (tptp) REVERT: R 206 ARG cc_start: 0.5097 (ttt90) cc_final: 0.4865 (tpt-90) REVERT: R 314 GLN cc_start: 0.6835 (OUTLIER) cc_final: 0.6380 (tt0) REVERT: R 329 SER cc_start: 0.6925 (m) cc_final: 0.6372 (p) REVERT: R 407 LYS cc_start: 0.6045 (mmtm) cc_final: 0.5533 (mtpt) REVERT: R 409 LEU cc_start: 0.5447 (OUTLIER) cc_final: 0.5111 (pp) REVERT: R 415 GLU cc_start: 0.5175 (mt-10) cc_final: 0.4873 (mt-10) REVERT: R 438 GLU cc_start: 0.5290 (mt-10) cc_final: 0.4884 (mt-10) REVERT: R 441 MET cc_start: 0.6897 (tpp) cc_final: 0.6611 (tpp) REVERT: S 3 LYS cc_start: 0.6740 (tttt) cc_final: 0.6232 (ttmt) REVERT: S 7 GLU cc_start: 0.4761 (mm-30) cc_final: 0.4541 (mm-30) REVERT: S 10 GLU cc_start: 0.6063 (OUTLIER) cc_final: 0.5622 (mt-10) REVERT: S 11 LYS cc_start: 0.5095 (tttp) cc_final: 0.4685 (ttpp) REVERT: S 49 LYS cc_start: 0.5746 (mmtt) cc_final: 0.5235 (mmmt) REVERT: S 63 ILE cc_start: 0.6288 (mm) cc_final: 0.6063 (mm) REVERT: S 68 MET cc_start: 0.6291 (mmt) cc_final: 0.5712 (mmt) REVERT: S 102 THR cc_start: 0.6188 (m) cc_final: 0.5902 (p) REVERT: S 105 GLU cc_start: 0.6078 (pm20) cc_final: 0.5813 (pm20) REVERT: S 153 LYS cc_start: 0.5656 (mmpt) cc_final: 0.5264 (mmmt) REVERT: S 200 LYS cc_start: 0.5933 (mtpp) cc_final: 0.4977 (tptt) REVERT: S 223 ARG cc_start: 0.5133 (ttm-80) cc_final: 0.4884 (ttt90) REVERT: S 280 LYS cc_start: 0.6082 (tttt) cc_final: 0.5858 (tttm) REVERT: S 314 GLN cc_start: 0.6881 (OUTLIER) cc_final: 0.6239 (tt0) REVERT: S 329 SER cc_start: 0.6989 (m) cc_final: 0.6142 (p) REVERT: S 397 GLU cc_start: 0.5648 (mm-30) cc_final: 0.4842 (mm-30) REVERT: S 403 GLU cc_start: 0.5819 (tp30) cc_final: 0.5364 (pm20) REVERT: S 407 LYS cc_start: 0.6007 (mmtm) cc_final: 0.5385 (mtpt) REVERT: S 411 GLU cc_start: 0.5230 (pt0) cc_final: 0.4839 (mm-30) REVERT: S 415 GLU cc_start: 0.5140 (mt-10) cc_final: 0.4377 (tm-30) REVERT: S 441 MET cc_start: 0.6870 (tpp) cc_final: 0.6482 (tpp) REVERT: T 11 LYS cc_start: 0.4659 (ttpp) cc_final: 0.4349 (tttp) REVERT: T 15 GLU cc_start: 0.4621 (OUTLIER) cc_final: 0.4118 (mm-30) REVERT: T 49 LYS cc_start: 0.6022 (mmtt) cc_final: 0.5575 (mmmt) REVERT: T 63 ILE cc_start: 0.6109 (mt) cc_final: 0.5557 (mm) REVERT: T 117 LYS cc_start: 0.5947 (tptm) cc_final: 0.5668 (tptm) REVERT: T 153 LYS cc_start: 0.5975 (mttm) cc_final: 0.4837 (mmmt) REVERT: T 223 ARG cc_start: 0.5166 (ttm-80) cc_final: 0.4781 (tpt170) REVERT: T 269 GLU cc_start: 0.5129 (mm-30) cc_final: 0.4916 (mm-30) REVERT: T 314 GLN cc_start: 0.6944 (tt0) cc_final: 0.6663 (tt0) REVERT: T 329 SER cc_start: 0.7090 (m) cc_final: 0.6299 (p) REVERT: T 363 GLU cc_start: 0.6038 (tp30) cc_final: 0.5504 (tt0) REVERT: T 369 ASP cc_start: 0.5388 (OUTLIER) cc_final: 0.4892 (m-30) REVERT: T 411 GLU cc_start: 0.5318 (pt0) cc_final: 0.4584 (mm-30) REVERT: T 438 GLU cc_start: 0.5138 (mt-10) cc_final: 0.4831 (mt-10) REVERT: T 441 MET cc_start: 0.6770 (tpp) cc_final: 0.6146 (tpp) outliers start: 106 outliers final: 29 residues processed: 918 average time/residue: 1.5523 time to fit residues: 1733.4751 Evaluate side-chains 876 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 823 time to evaluate : 4.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain H residue 153 LYS Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 167 ASN Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain L residue 7 MET Chi-restraints excluded: chain M residue 7 MET Chi-restraints excluded: chain N residue 10 GLU Chi-restraints excluded: chain N residue 167 ASN Chi-restraints excluded: chain N residue 224 LYS Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 206 ARG Chi-restraints excluded: chain O residue 239 VAL Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain Q residue 83 THR Chi-restraints excluded: chain Q residue 122 LEU Chi-restraints excluded: chain Q residue 167 ASN Chi-restraints excluded: chain R residue 15 GLU Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 314 GLN Chi-restraints excluded: chain R residue 409 LEU Chi-restraints excluded: chain S residue 10 GLU Chi-restraints excluded: chain S residue 224 LYS Chi-restraints excluded: chain S residue 314 GLN Chi-restraints excluded: chain S residue 409 LEU Chi-restraints excluded: chain T residue 15 GLU Chi-restraints excluded: chain T residue 83 THR Chi-restraints excluded: chain T residue 224 LYS Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain U residue 7 MET Chi-restraints excluded: chain W residue 7 MET Chi-restraints excluded: chain X residue 7 MET Chi-restraints excluded: chain Y residue 7 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 566 optimal weight: 1.9990 chunk 430 optimal weight: 5.9990 chunk 297 optimal weight: 0.3980 chunk 63 optimal weight: 4.9990 chunk 273 optimal weight: 8.9990 chunk 384 optimal weight: 9.9990 chunk 575 optimal weight: 1.9990 chunk 608 optimal weight: 6.9990 chunk 300 optimal weight: 3.9990 chunk 545 optimal weight: 6.9990 chunk 164 optimal weight: 0.2980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 GLN A 167 ASN A 315 ASN B 24 GLN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN C 34 ASN C 75 ASN C 167 ASN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN F 443 GLN G 24 GLN G 34 ASN G 75 ASN H 34 ASN H 167 ASN H 443 GLN I 17 ASN I 24 GLN I 34 ASN I 41 GLN I 167 ASN I 266 GLN N 24 GLN N 34 ASN N 75 ASN O 24 GLN O 34 ASN O 75 ASN P 34 ASN P 167 ASN P 443 GLN Q 24 GLN Q 34 ASN Q 167 ASN Q 266 GLN R 17 ASN R 24 GLN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 41 GLN R 167 ASN R 315 ASN S 24 GLN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 ASN S 266 GLN S 443 GLN T 34 ASN T 75 ASN T 167 ASN X 4 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5959 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 51450 Z= 0.176 Angle : 0.505 5.294 69650 Z= 0.276 Chirality : 0.042 0.149 7546 Planarity : 0.004 0.060 9184 Dihedral : 5.223 51.897 6861 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.93 % Allowed : 17.29 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.11), residues: 6286 helix: 1.98 (0.10), residues: 2324 sheet: -0.48 (0.16), residues: 980 loop : -0.09 (0.11), residues: 2982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 425 HIS 0.006 0.002 HIS F 416 PHE 0.021 0.002 PHE R 285 TYR 0.033 0.002 TYR T 296 ARG 0.005 0.000 ARG R 170 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 947 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 844 time to evaluate : 4.418 Fit side-chains REVERT: A 3 LYS cc_start: 0.6895 (tttt) cc_final: 0.6474 (ttmm) REVERT: A 11 LYS cc_start: 0.5022 (tttp) cc_final: 0.4766 (ttpp) REVERT: A 32 ILE cc_start: 0.5744 (mp) cc_final: 0.5437 (mp) REVERT: A 35 VAL cc_start: 0.7095 (OUTLIER) cc_final: 0.6809 (t) REVERT: A 49 LYS cc_start: 0.5789 (mmtt) cc_final: 0.5225 (mmmt) REVERT: A 102 THR cc_start: 0.6179 (m) cc_final: 0.5829 (p) REVERT: A 117 LYS cc_start: 0.5873 (tptm) cc_final: 0.5524 (tptm) REVERT: A 148 LEU cc_start: 0.6520 (mt) cc_final: 0.6283 (mt) REVERT: A 182 GLU cc_start: 0.5884 (mt-10) cc_final: 0.5575 (mt-10) REVERT: A 200 LYS cc_start: 0.5975 (ttmm) cc_final: 0.4870 (tptt) REVERT: A 206 ARG cc_start: 0.5082 (ttt90) cc_final: 0.4868 (tpt-90) REVERT: A 314 GLN cc_start: 0.6773 (OUTLIER) cc_final: 0.6317 (tt0) REVERT: A 329 SER cc_start: 0.6925 (m) cc_final: 0.6312 (p) REVERT: A 403 GLU cc_start: 0.5858 (OUTLIER) cc_final: 0.5220 (tp30) REVERT: A 407 LYS cc_start: 0.5736 (mmtm) cc_final: 0.5229 (mtpt) REVERT: A 411 GLU cc_start: 0.5355 (pt0) cc_final: 0.4677 (mm-30) REVERT: A 438 GLU cc_start: 0.5279 (mt-10) cc_final: 0.4899 (mt-10) REVERT: A 441 MET cc_start: 0.6945 (tpp) cc_final: 0.6502 (tpp) REVERT: B 3 LYS cc_start: 0.6723 (tttt) cc_final: 0.6225 (ttmt) REVERT: B 10 GLU cc_start: 0.6001 (OUTLIER) cc_final: 0.5414 (mt-10) REVERT: B 49 LYS cc_start: 0.5861 (mmtt) cc_final: 0.5354 (mmmt) REVERT: B 68 MET cc_start: 0.6305 (mmt) cc_final: 0.5812 (mmt) REVERT: B 102 THR cc_start: 0.6364 (m) cc_final: 0.6048 (p) REVERT: B 105 GLU cc_start: 0.6055 (pm20) cc_final: 0.5715 (pm20) REVERT: B 117 LYS cc_start: 0.5659 (tptp) cc_final: 0.5394 (tptm) REVERT: B 153 LYS cc_start: 0.6025 (mttm) cc_final: 0.4962 (mmmt) REVERT: B 182 GLU cc_start: 0.6054 (mt-10) cc_final: 0.5751 (mt-10) REVERT: B 200 LYS cc_start: 0.5860 (mtpp) cc_final: 0.4895 (tptt) REVERT: B 224 LYS cc_start: 0.5603 (ttmm) cc_final: 0.5257 (mtmt) REVERT: B 314 GLN cc_start: 0.6900 (OUTLIER) cc_final: 0.6259 (tt0) REVERT: B 329 SER cc_start: 0.6901 (m) cc_final: 0.6074 (p) REVERT: B 397 GLU cc_start: 0.5883 (mm-30) cc_final: 0.5030 (mm-30) REVERT: B 407 LYS cc_start: 0.6139 (mmtm) cc_final: 0.5487 (mtpt) REVERT: B 411 GLU cc_start: 0.5270 (OUTLIER) cc_final: 0.4862 (mm-30) REVERT: B 415 GLU cc_start: 0.5169 (mt-10) cc_final: 0.4385 (tm-30) REVERT: B 441 MET cc_start: 0.6862 (tpp) cc_final: 0.6539 (tpp) REVERT: C 11 LYS cc_start: 0.4733 (tttm) cc_final: 0.4500 (ttpp) REVERT: C 15 GLU cc_start: 0.4417 (OUTLIER) cc_final: 0.3907 (mm-30) REVERT: C 49 LYS cc_start: 0.5860 (mmtt) cc_final: 0.5408 (mmmt) REVERT: C 63 ILE cc_start: 0.6149 (mt) cc_final: 0.5581 (mm) REVERT: C 102 THR cc_start: 0.6237 (m) cc_final: 0.5865 (p) REVERT: C 117 LYS cc_start: 0.5866 (tptm) cc_final: 0.5549 (tptm) REVERT: C 153 LYS cc_start: 0.5967 (mttm) cc_final: 0.4817 (mmmt) REVERT: C 200 LYS cc_start: 0.5764 (mtpp) cc_final: 0.5144 (tptp) REVERT: C 223 ARG cc_start: 0.5000 (ttm-80) cc_final: 0.4604 (tpt170) REVERT: C 269 GLU cc_start: 0.5221 (mm-30) cc_final: 0.4417 (pm20) REVERT: C 280 LYS cc_start: 0.6007 (tttt) cc_final: 0.5806 (tttm) REVERT: C 314 GLN cc_start: 0.6789 (tt0) cc_final: 0.6526 (tt0) REVERT: C 329 SER cc_start: 0.6975 (m) cc_final: 0.6164 (p) REVERT: C 363 GLU cc_start: 0.6048 (tp30) cc_final: 0.5533 (tt0) REVERT: C 403 GLU cc_start: 0.5661 (tp30) cc_final: 0.4964 (pm20) REVERT: C 411 GLU cc_start: 0.5234 (pt0) cc_final: 0.4516 (mm-30) REVERT: C 438 GLU cc_start: 0.5126 (mt-10) cc_final: 0.4875 (mt-10) REVERT: C 441 MET cc_start: 0.6755 (tpp) cc_final: 0.6218 (tpp) REVERT: F 10 GLU cc_start: 0.5753 (OUTLIER) cc_final: 0.5300 (mt-10) REVERT: F 35 VAL cc_start: 0.7152 (OUTLIER) cc_final: 0.6920 (t) REVERT: F 49 LYS cc_start: 0.5708 (mmtt) cc_final: 0.5261 (mmmt) REVERT: F 102 THR cc_start: 0.6281 (OUTLIER) cc_final: 0.5805 (p) REVERT: F 148 LEU cc_start: 0.6416 (mt) cc_final: 0.6114 (mp) REVERT: F 153 LYS cc_start: 0.5940 (mttm) cc_final: 0.4881 (mmmt) REVERT: F 182 GLU cc_start: 0.5927 (mt-10) cc_final: 0.5547 (mt-10) REVERT: F 200 LYS cc_start: 0.5545 (mtpp) cc_final: 0.4677 (tptt) REVERT: F 206 ARG cc_start: 0.4929 (ttp80) cc_final: 0.4573 (tpt-90) REVERT: F 224 LYS cc_start: 0.5423 (OUTLIER) cc_final: 0.5120 (mtpp) REVERT: F 232 MET cc_start: 0.6478 (ttt) cc_final: 0.6182 (ttt) REVERT: F 269 GLU cc_start: 0.5198 (mm-30) cc_final: 0.4507 (pm20) REVERT: F 280 LYS cc_start: 0.6176 (tttt) cc_final: 0.5943 (tttm) REVERT: F 329 SER cc_start: 0.6840 (m) cc_final: 0.6191 (p) REVERT: F 363 GLU cc_start: 0.5950 (tp30) cc_final: 0.5442 (tt0) REVERT: F 375 MET cc_start: 0.5269 (ptm) cc_final: 0.4858 (ptp) REVERT: F 403 GLU cc_start: 0.5566 (tp30) cc_final: 0.5360 (pm20) REVERT: F 411 GLU cc_start: 0.5340 (pt0) cc_final: 0.4704 (mm-30) REVERT: F 438 GLU cc_start: 0.5357 (mt-10) cc_final: 0.5083 (mt-10) REVERT: F 441 MET cc_start: 0.6814 (tpp) cc_final: 0.6300 (tpp) REVERT: G 27 ASP cc_start: 0.5457 (p0) cc_final: 0.4936 (p0) REVERT: G 49 LYS cc_start: 0.5717 (mmtt) cc_final: 0.5165 (mmmt) REVERT: G 102 THR cc_start: 0.6402 (m) cc_final: 0.5985 (p) REVERT: G 200 LYS cc_start: 0.6062 (ttmm) cc_final: 0.5147 (tptt) REVERT: G 206 ARG cc_start: 0.5071 (OUTLIER) cc_final: 0.4662 (tpt-90) REVERT: G 223 ARG cc_start: 0.5335 (ttm-80) cc_final: 0.5008 (tpt170) REVERT: G 261 GLU cc_start: 0.6165 (OUTLIER) cc_final: 0.5845 (mm-30) REVERT: G 329 SER cc_start: 0.7023 (m) cc_final: 0.6378 (p) REVERT: G 411 GLU cc_start: 0.5497 (pt0) cc_final: 0.4873 (mm-30) REVERT: G 415 GLU cc_start: 0.5154 (mt-10) cc_final: 0.4253 (tm-30) REVERT: H 3 LYS cc_start: 0.6967 (tttt) cc_final: 0.6706 (ttmm) REVERT: H 27 ASP cc_start: 0.5580 (p0) cc_final: 0.5266 (p0) REVERT: H 32 ILE cc_start: 0.5759 (mt) cc_final: 0.5460 (mm) REVERT: H 49 LYS cc_start: 0.5772 (mmtt) cc_final: 0.5248 (mmmt) REVERT: H 102 THR cc_start: 0.6456 (m) cc_final: 0.6026 (p) REVERT: H 117 LYS cc_start: 0.5960 (tptm) cc_final: 0.5712 (tptm) REVERT: H 153 LYS cc_start: 0.5800 (OUTLIER) cc_final: 0.4828 (mmmt) REVERT: H 200 LYS cc_start: 0.5921 (mtpm) cc_final: 0.4921 (tptt) REVERT: H 206 ARG cc_start: 0.5156 (ttt90) cc_final: 0.4748 (tpt-90) REVERT: H 223 ARG cc_start: 0.5283 (ttm-80) cc_final: 0.4722 (ttm-80) REVERT: H 252 LYS cc_start: 0.6826 (tttt) cc_final: 0.6606 (tttm) REVERT: H 329 SER cc_start: 0.7071 (m) cc_final: 0.6239 (p) REVERT: H 411 GLU cc_start: 0.5339 (pt0) cc_final: 0.4892 (mm-30) REVERT: H 415 GLU cc_start: 0.5129 (mt-10) cc_final: 0.4462 (tm-30) REVERT: H 438 GLU cc_start: 0.5499 (mt-10) cc_final: 0.5275 (mt-10) REVERT: H 441 MET cc_start: 0.6894 (tpp) cc_final: 0.6219 (tpp) REVERT: I 3 LYS cc_start: 0.6721 (tttt) cc_final: 0.6341 (ttmt) REVERT: I 10 GLU cc_start: 0.5886 (mt-10) cc_final: 0.5589 (mt-10) REVERT: I 49 LYS cc_start: 0.5678 (mmtt) cc_final: 0.5216 (mmmt) REVERT: I 63 ILE cc_start: 0.6334 (mt) cc_final: 0.5770 (mm) REVERT: I 122 LEU cc_start: 0.6529 (OUTLIER) cc_final: 0.6311 (mp) REVERT: I 153 LYS cc_start: 0.5988 (mttm) cc_final: 0.4939 (mmmt) REVERT: I 182 GLU cc_start: 0.5918 (mt-10) cc_final: 0.5521 (mt-10) REVERT: I 200 LYS cc_start: 0.6020 (ttmm) cc_final: 0.4935 (tppt) REVERT: I 206 ARG cc_start: 0.4958 (ttp80) cc_final: 0.4486 (tpt-90) REVERT: I 223 ARG cc_start: 0.5162 (ttm-80) cc_final: 0.4725 (tpt170) REVERT: I 224 LYS cc_start: 0.5821 (ttmm) cc_final: 0.5596 (mtpp) REVERT: I 280 LYS cc_start: 0.6113 (tttt) cc_final: 0.5881 (tttm) REVERT: I 314 GLN cc_start: 0.6941 (tp40) cc_final: 0.6517 (tt0) REVERT: I 329 SER cc_start: 0.7130 (m) cc_final: 0.6283 (p) REVERT: I 363 GLU cc_start: 0.6053 (tp30) cc_final: 0.5530 (tt0) REVERT: I 411 GLU cc_start: 0.5316 (pt0) cc_final: 0.5001 (mm-30) REVERT: I 415 GLU cc_start: 0.5022 (mt-10) cc_final: 0.4159 (tm-30) REVERT: I 441 MET cc_start: 0.6883 (tpp) cc_final: 0.6453 (tpp) REVERT: N 10 GLU cc_start: 0.5773 (OUTLIER) cc_final: 0.5321 (mt-10) REVERT: N 49 LYS cc_start: 0.5789 (mmtt) cc_final: 0.5322 (mmmt) REVERT: N 102 THR cc_start: 0.6268 (OUTLIER) cc_final: 0.5803 (p) REVERT: N 105 GLU cc_start: 0.6068 (pm20) cc_final: 0.5588 (mp0) REVERT: N 148 LEU cc_start: 0.6388 (mt) cc_final: 0.6083 (mp) REVERT: N 153 LYS cc_start: 0.5949 (mttm) cc_final: 0.4857 (mmmt) REVERT: N 182 GLU cc_start: 0.5923 (mt-10) cc_final: 0.5541 (mt-10) REVERT: N 200 LYS cc_start: 0.5545 (mtpp) cc_final: 0.4678 (tptt) REVERT: N 206 ARG cc_start: 0.4931 (ttp80) cc_final: 0.4575 (tpt-90) REVERT: N 224 LYS cc_start: 0.5404 (OUTLIER) cc_final: 0.5098 (mtpp) REVERT: N 232 MET cc_start: 0.6481 (ttt) cc_final: 0.6192 (ttt) REVERT: N 269 GLU cc_start: 0.5194 (mm-30) cc_final: 0.4504 (pm20) REVERT: N 280 LYS cc_start: 0.6176 (tttt) cc_final: 0.5943 (tttm) REVERT: N 329 SER cc_start: 0.6836 (m) cc_final: 0.6185 (p) REVERT: N 363 GLU cc_start: 0.5960 (tp30) cc_final: 0.5447 (tt0) REVERT: N 375 MET cc_start: 0.5338 (ptm) cc_final: 0.4925 (ptp) REVERT: N 403 GLU cc_start: 0.5921 (tp30) cc_final: 0.4985 (mp0) REVERT: N 411 GLU cc_start: 0.5364 (pt0) cc_final: 0.4715 (mm-30) REVERT: N 438 GLU cc_start: 0.5345 (mt-10) cc_final: 0.5071 (mt-10) REVERT: N 441 MET cc_start: 0.6819 (tpp) cc_final: 0.6306 (tpp) REVERT: O 10 GLU cc_start: 0.5875 (mt-10) cc_final: 0.5651 (mt-10) REVERT: O 27 ASP cc_start: 0.5447 (p0) cc_final: 0.4932 (p0) REVERT: O 49 LYS cc_start: 0.5720 (mmtt) cc_final: 0.5165 (mmmt) REVERT: O 102 THR cc_start: 0.6398 (m) cc_final: 0.5980 (p) REVERT: O 206 ARG cc_start: 0.5123 (OUTLIER) cc_final: 0.4715 (tpt-90) REVERT: O 223 ARG cc_start: 0.5353 (ttm-80) cc_final: 0.5019 (tpt170) REVERT: O 314 GLN cc_start: 0.6895 (OUTLIER) cc_final: 0.6373 (tt0) REVERT: O 329 SER cc_start: 0.7007 (m) cc_final: 0.6357 (p) REVERT: O 411 GLU cc_start: 0.5527 (pt0) cc_final: 0.4894 (mm-30) REVERT: O 415 GLU cc_start: 0.5143 (mt-10) cc_final: 0.4238 (tm-30) REVERT: P 3 LYS cc_start: 0.6913 (tttt) cc_final: 0.6700 (ttmm) REVERT: P 10 GLU cc_start: 0.5939 (OUTLIER) cc_final: 0.5317 (mt-10) REVERT: P 27 ASP cc_start: 0.5553 (p0) cc_final: 0.5244 (p0) REVERT: P 32 ILE cc_start: 0.5754 (mt) cc_final: 0.5456 (mm) REVERT: P 49 LYS cc_start: 0.5756 (mmtt) cc_final: 0.5237 (mmmt) REVERT: P 102 THR cc_start: 0.6450 (m) cc_final: 0.6013 (p) REVERT: P 153 LYS cc_start: 0.5807 (OUTLIER) cc_final: 0.4798 (mmmt) REVERT: P 200 LYS cc_start: 0.5860 (mtpp) cc_final: 0.4985 (tptt) REVERT: P 206 ARG cc_start: 0.5112 (ttt90) cc_final: 0.4702 (tpt-90) REVERT: P 223 ARG cc_start: 0.5299 (ttm-80) cc_final: 0.4724 (ttm-80) REVERT: P 329 SER cc_start: 0.7155 (m) cc_final: 0.6294 (p) REVERT: P 411 GLU cc_start: 0.5314 (pt0) cc_final: 0.4906 (mm-30) REVERT: P 415 GLU cc_start: 0.5177 (mt-10) cc_final: 0.4531 (tm-30) REVERT: P 438 GLU cc_start: 0.5511 (mt-10) cc_final: 0.5284 (mt-10) REVERT: P 441 MET cc_start: 0.6900 (tpp) cc_final: 0.6219 (tpp) REVERT: Q 3 LYS cc_start: 0.6735 (tttt) cc_final: 0.6359 (ttmt) REVERT: Q 10 GLU cc_start: 0.5880 (mt-10) cc_final: 0.5578 (mt-10) REVERT: Q 27 ASP cc_start: 0.5559 (p0) cc_final: 0.5321 (p0) REVERT: Q 49 LYS cc_start: 0.5680 (mmtt) cc_final: 0.5220 (mmmt) REVERT: Q 63 ILE cc_start: 0.6336 (mt) cc_final: 0.5775 (mm) REVERT: Q 102 THR cc_start: 0.6672 (m) cc_final: 0.6271 (p) REVERT: Q 122 LEU cc_start: 0.6512 (OUTLIER) cc_final: 0.6299 (mp) REVERT: Q 153 LYS cc_start: 0.5975 (mttm) cc_final: 0.4959 (mmmt) REVERT: Q 182 GLU cc_start: 0.5943 (mt-10) cc_final: 0.5540 (mt-10) REVERT: Q 200 LYS cc_start: 0.6023 (ttmm) cc_final: 0.4939 (tppt) REVERT: Q 206 ARG cc_start: 0.4977 (ttp80) cc_final: 0.4503 (tpt-90) REVERT: Q 280 LYS cc_start: 0.6131 (tttt) cc_final: 0.5898 (tttm) REVERT: Q 314 GLN cc_start: 0.6911 (tp40) cc_final: 0.6471 (tt0) REVERT: Q 329 SER cc_start: 0.7131 (m) cc_final: 0.6286 (p) REVERT: Q 363 GLU cc_start: 0.6019 (tp30) cc_final: 0.5508 (tt0) REVERT: Q 403 GLU cc_start: 0.5518 (tp30) cc_final: 0.5115 (pm20) REVERT: Q 407 LYS cc_start: 0.5380 (mmtm) cc_final: 0.4913 (mtpt) REVERT: Q 411 GLU cc_start: 0.5283 (pt0) cc_final: 0.4977 (mm-30) REVERT: Q 415 GLU cc_start: 0.5017 (mt-10) cc_final: 0.4154 (tm-30) REVERT: Q 441 MET cc_start: 0.6880 (tpp) cc_final: 0.6450 (tpp) REVERT: R 3 LYS cc_start: 0.7036 (tttt) cc_final: 0.6616 (ttmm) REVERT: R 10 GLU cc_start: 0.5999 (mt-10) cc_final: 0.5787 (mt-10) REVERT: R 11 LYS cc_start: 0.4614 (tttp) cc_final: 0.4324 (ttpp) REVERT: R 15 GLU cc_start: 0.4239 (OUTLIER) cc_final: 0.3744 (mm-30) REVERT: R 32 ILE cc_start: 0.5756 (mp) cc_final: 0.5449 (mp) REVERT: R 35 VAL cc_start: 0.7100 (OUTLIER) cc_final: 0.6814 (t) REVERT: R 49 LYS cc_start: 0.5813 (mmtt) cc_final: 0.5280 (mmmt) REVERT: R 102 THR cc_start: 0.6228 (m) cc_final: 0.5846 (p) REVERT: R 117 LYS cc_start: 0.5854 (tptm) cc_final: 0.5502 (tptm) REVERT: R 148 LEU cc_start: 0.6495 (mt) cc_final: 0.6249 (mt) REVERT: R 182 GLU cc_start: 0.5923 (mt-10) cc_final: 0.5614 (mt-10) REVERT: R 200 LYS cc_start: 0.6046 (ttmm) cc_final: 0.5088 (tptp) REVERT: R 206 ARG cc_start: 0.5078 (ttt90) cc_final: 0.4862 (tpt-90) REVERT: R 314 GLN cc_start: 0.6823 (OUTLIER) cc_final: 0.6366 (tt0) REVERT: R 329 SER cc_start: 0.6907 (m) cc_final: 0.6307 (p) REVERT: R 407 LYS cc_start: 0.5909 (mmtm) cc_final: 0.5399 (mtpt) REVERT: R 409 LEU cc_start: 0.5539 (OUTLIER) cc_final: 0.5252 (pp) REVERT: R 411 GLU cc_start: 0.5751 (mm-30) cc_final: 0.5067 (tt0) REVERT: R 438 GLU cc_start: 0.5287 (mt-10) cc_final: 0.4924 (mt-10) REVERT: R 441 MET cc_start: 0.6879 (tpp) cc_final: 0.6652 (tpp) REVERT: S 3 LYS cc_start: 0.6744 (tttt) cc_final: 0.6539 (tttm) REVERT: S 10 GLU cc_start: 0.6070 (OUTLIER) cc_final: 0.5622 (mt-10) REVERT: S 11 LYS cc_start: 0.5098 (tttp) cc_final: 0.4703 (ttpp) REVERT: S 49 LYS cc_start: 0.5785 (mmtt) cc_final: 0.5267 (mmmt) REVERT: S 63 ILE cc_start: 0.6295 (mm) cc_final: 0.6061 (mm) REVERT: S 68 MET cc_start: 0.6288 (mmt) cc_final: 0.5806 (mmt) REVERT: S 102 THR cc_start: 0.6367 (m) cc_final: 0.6054 (p) REVERT: S 105 GLU cc_start: 0.6067 (pm20) cc_final: 0.5808 (pm20) REVERT: S 153 LYS cc_start: 0.5670 (mmpt) cc_final: 0.5418 (mmmt) REVERT: S 189 GLU cc_start: 0.6418 (OUTLIER) cc_final: 0.5992 (tp30) REVERT: S 200 LYS cc_start: 0.5844 (mtpp) cc_final: 0.4802 (tptt) REVERT: S 223 ARG cc_start: 0.5129 (ttm-80) cc_final: 0.4888 (ttt90) REVERT: S 314 GLN cc_start: 0.6888 (OUTLIER) cc_final: 0.6247 (tt0) REVERT: S 329 SER cc_start: 0.6903 (m) cc_final: 0.6077 (p) REVERT: S 397 GLU cc_start: 0.5653 (mm-30) cc_final: 0.4871 (mm-30) REVERT: S 407 LYS cc_start: 0.6001 (mmtm) cc_final: 0.5376 (mtpt) REVERT: S 411 GLU cc_start: 0.5276 (OUTLIER) cc_final: 0.4868 (mm-30) REVERT: S 415 GLU cc_start: 0.5181 (mt-10) cc_final: 0.4399 (tm-30) REVERT: S 441 MET cc_start: 0.6866 (tpp) cc_final: 0.6550 (tpp) REVERT: T 11 LYS cc_start: 0.4730 (ttpp) cc_final: 0.4384 (ttpp) REVERT: T 15 GLU cc_start: 0.4518 (OUTLIER) cc_final: 0.4084 (mm-30) REVERT: T 49 LYS cc_start: 0.5870 (mmtt) cc_final: 0.5416 (mmmt) REVERT: T 63 ILE cc_start: 0.6119 (mt) cc_final: 0.5551 (mm) REVERT: T 117 LYS cc_start: 0.5939 (tptm) cc_final: 0.5641 (tptm) REVERT: T 153 LYS cc_start: 0.6008 (mttm) cc_final: 0.4845 (mmmt) REVERT: T 189 GLU cc_start: 0.6255 (OUTLIER) cc_final: 0.5781 (tp30) REVERT: T 200 LYS cc_start: 0.5914 (ttmm) cc_final: 0.4998 (tptt) REVERT: T 223 ARG cc_start: 0.5029 (ttm-80) cc_final: 0.4645 (tpt170) REVERT: T 269 GLU cc_start: 0.5173 (mm-30) cc_final: 0.4410 (pm20) REVERT: T 280 LYS cc_start: 0.6026 (tttt) cc_final: 0.5813 (tttm) REVERT: T 314 GLN cc_start: 0.6769 (tt0) cc_final: 0.6508 (tt0) REVERT: T 329 SER cc_start: 0.6986 (m) cc_final: 0.6186 (p) REVERT: T 363 GLU cc_start: 0.6056 (tp30) cc_final: 0.5539 (tt0) REVERT: T 411 GLU cc_start: 0.5243 (pt0) cc_final: 0.4514 (mm-30) REVERT: T 438 GLU cc_start: 0.5113 (mt-10) cc_final: 0.4855 (mt-10) REVERT: T 441 MET cc_start: 0.6745 (tpp) cc_final: 0.6207 (tpp) outliers start: 103 outliers final: 27 residues processed: 900 average time/residue: 1.5685 time to fit residues: 1712.9927 Evaluate side-chains 891 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 831 time to evaluate : 4.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 411 GLU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain E residue 7 MET Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 206 ARG Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 261 GLU Chi-restraints excluded: chain H residue 153 LYS Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain L residue 7 MET Chi-restraints excluded: chain N residue 10 GLU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 224 LYS Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 206 ARG Chi-restraints excluded: chain O residue 239 VAL Chi-restraints excluded: chain O residue 314 GLN Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 153 LYS Chi-restraints excluded: chain Q residue 122 LEU Chi-restraints excluded: chain R residue 15 GLU Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 314 GLN Chi-restraints excluded: chain R residue 409 LEU Chi-restraints excluded: chain S residue 10 GLU Chi-restraints excluded: chain S residue 189 GLU Chi-restraints excluded: chain S residue 224 LYS Chi-restraints excluded: chain S residue 239 VAL Chi-restraints excluded: chain S residue 314 GLN Chi-restraints excluded: chain S residue 409 LEU Chi-restraints excluded: chain S residue 411 GLU Chi-restraints excluded: chain T residue 15 GLU Chi-restraints excluded: chain T residue 189 GLU Chi-restraints excluded: chain T residue 224 LYS Chi-restraints excluded: chain T residue 409 LEU Chi-restraints excluded: chain U residue 7 MET Chi-restraints excluded: chain W residue 7 MET Chi-restraints excluded: chain Y residue 7 MET Chi-restraints excluded: chain Z residue 7 MET Chi-restraints excluded: chain b residue 7 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 507 optimal weight: 10.0000 chunk 345 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 453 optimal weight: 3.9990 chunk 251 optimal weight: 2.9990 chunk 519 optimal weight: 3.9990 chunk 420 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 310 optimal weight: 0.4980 chunk 546 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 34 ASN A 167 ASN A 315 ASN B 17 ASN B 34 ASN B 167 ASN C 34 ASN C 75 ASN C 167 ASN C 439 GLN F 24 GLN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN F 167 ASN F 443 GLN G 17 ASN G 34 ASN G 75 ASN H 34 ASN H 443 GLN I 34 ASN I 266 GLN J 4 GLN N 24 GLN N 34 ASN N 75 ASN N 167 ASN O 34 ASN O 75 ASN P 17 ASN P 34 ASN P 443 GLN Q 34 ASN Q 266 GLN R 34 ASN R 167 ASN S 34 ASN S 167 ASN S 245 HIS S 443 GLN T 34 ASN T 75 ASN T 167 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5972 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 51450 Z= 0.280 Angle : 0.633 6.692 69650 Z= 0.345 Chirality : 0.046 0.168 7546 Planarity : 0.006 0.100 9184 Dihedral : 5.805 56.849 6859 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.72 % Favored : 95.15 % Rotamer: Outliers : 2.68 % Allowed : 16.40 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.10), residues: 6286 helix: 1.58 (0.10), residues: 2296 sheet: -0.33 (0.17), residues: 812 loop : -0.41 (0.11), residues: 3178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP G 425 HIS 0.008 0.002 HIS F 416 PHE 0.026 0.003 PHE R 285 TYR 0.043 0.003 TYR T 296 ARG 0.008 0.001 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 999 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 856 time to evaluate : 4.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.4997 (tttp) cc_final: 0.4749 (ttpp) REVERT: A 32 ILE cc_start: 0.5748 (mp) cc_final: 0.5460 (mp) REVERT: A 35 VAL cc_start: 0.7075 (OUTLIER) cc_final: 0.6833 (t) REVERT: A 49 LYS cc_start: 0.5852 (mmtt) cc_final: 0.5263 (mmmt) REVERT: A 102 THR cc_start: 0.6252 (m) cc_final: 0.5890 (p) REVERT: A 117 LYS cc_start: 0.5847 (tptm) cc_final: 0.5525 (tptm) REVERT: A 148 LEU cc_start: 0.6508 (mt) cc_final: 0.6271 (mt) REVERT: A 182 GLU cc_start: 0.5985 (mt-10) cc_final: 0.5683 (mt-10) REVERT: A 200 LYS cc_start: 0.5945 (ttmm) cc_final: 0.4919 (tptm) REVERT: A 206 ARG cc_start: 0.5118 (ttt90) cc_final: 0.4916 (tpt-90) REVERT: A 314 GLN cc_start: 0.6819 (OUTLIER) cc_final: 0.6271 (tt0) REVERT: A 329 SER cc_start: 0.6791 (m) cc_final: 0.6183 (p) REVERT: A 369 ASP cc_start: 0.5603 (OUTLIER) cc_final: 0.4957 (m-30) REVERT: A 403 GLU cc_start: 0.5835 (OUTLIER) cc_final: 0.5199 (tp30) REVERT: A 407 LYS cc_start: 0.5746 (mmtm) cc_final: 0.5262 (mtpt) REVERT: A 411 GLU cc_start: 0.5505 (pt0) cc_final: 0.4875 (mm-30) REVERT: A 441 MET cc_start: 0.6931 (tpp) cc_final: 0.6651 (tpp) REVERT: B 3 LYS cc_start: 0.6538 (tttt) cc_final: 0.6203 (ttmt) REVERT: B 10 GLU cc_start: 0.6051 (OUTLIER) cc_final: 0.5476 (mt-10) REVERT: B 32 ILE cc_start: 0.5705 (mt) cc_final: 0.5392 (mm) REVERT: B 49 LYS cc_start: 0.5826 (mmtt) cc_final: 0.5339 (mmmt) REVERT: B 102 THR cc_start: 0.6399 (OUTLIER) cc_final: 0.5943 (p) REVERT: B 105 GLU cc_start: 0.6070 (pm20) cc_final: 0.5752 (pm20) REVERT: B 117 LYS cc_start: 0.5689 (tptp) cc_final: 0.5421 (tptm) REVERT: B 153 LYS cc_start: 0.6038 (mttm) cc_final: 0.4976 (mmmt) REVERT: B 182 GLU cc_start: 0.6066 (mt-10) cc_final: 0.5713 (mt-10) REVERT: B 200 LYS cc_start: 0.5869 (mtpp) cc_final: 0.4915 (tptt) REVERT: B 224 LYS cc_start: 0.5689 (ttmm) cc_final: 0.5467 (mtpp) REVERT: B 261 GLU cc_start: 0.6198 (OUTLIER) cc_final: 0.5903 (mm-30) REVERT: B 314 GLN cc_start: 0.6798 (OUTLIER) cc_final: 0.6147 (tt0) REVERT: B 329 SER cc_start: 0.6902 (m) cc_final: 0.6102 (p) REVERT: B 407 LYS cc_start: 0.6128 (mmtm) cc_final: 0.5441 (mtpt) REVERT: B 411 GLU cc_start: 0.5385 (OUTLIER) cc_final: 0.4787 (mm-30) REVERT: B 415 GLU cc_start: 0.5216 (mt-10) cc_final: 0.4453 (mm-30) REVERT: B 441 MET cc_start: 0.6861 (tpp) cc_final: 0.6636 (tpp) REVERT: C 11 LYS cc_start: 0.4772 (tttm) cc_final: 0.4451 (ttpp) REVERT: C 15 GLU cc_start: 0.4410 (OUTLIER) cc_final: 0.3939 (mm-30) REVERT: C 49 LYS cc_start: 0.5820 (mmtt) cc_final: 0.5367 (mmmt) REVERT: C 102 THR cc_start: 0.6312 (m) cc_final: 0.5917 (p) REVERT: C 114 ARG cc_start: 0.6697 (OUTLIER) cc_final: 0.5863 (ttm170) REVERT: C 117 LYS cc_start: 0.5778 (tptm) cc_final: 0.5435 (tptm) REVERT: C 153 LYS cc_start: 0.6026 (mttm) cc_final: 0.5053 (mmmt) REVERT: C 200 LYS cc_start: 0.5704 (mtpp) cc_final: 0.4919 (tptt) REVERT: C 223 ARG cc_start: 0.5016 (ttm-80) cc_final: 0.4614 (tpt170) REVERT: C 269 GLU cc_start: 0.5325 (mm-30) cc_final: 0.4466 (pm20) REVERT: C 280 LYS cc_start: 0.6014 (tttt) cc_final: 0.5809 (tttm) REVERT: C 314 GLN cc_start: 0.6910 (OUTLIER) cc_final: 0.6640 (tt0) REVERT: C 329 SER cc_start: 0.6942 (m) cc_final: 0.6144 (p) REVERT: C 363 GLU cc_start: 0.5957 (tp30) cc_final: 0.5438 (tt0) REVERT: C 403 GLU cc_start: 0.5646 (tp30) cc_final: 0.5091 (pm20) REVERT: C 411 GLU cc_start: 0.5366 (pt0) cc_final: 0.4635 (mm-30) REVERT: C 441 MET cc_start: 0.6768 (tpp) cc_final: 0.6373 (tpp) REVERT: F 10 GLU cc_start: 0.5676 (OUTLIER) cc_final: 0.5200 (mt-10) REVERT: F 49 LYS cc_start: 0.5758 (mmtt) cc_final: 0.5302 (mmmt) REVERT: F 148 LEU cc_start: 0.6373 (mt) cc_final: 0.6044 (mp) REVERT: F 153 LYS cc_start: 0.5929 (mttm) cc_final: 0.4841 (mmmt) REVERT: F 182 GLU cc_start: 0.5914 (mt-10) cc_final: 0.5498 (mt-10) REVERT: F 200 LYS cc_start: 0.5612 (mtpp) cc_final: 0.4646 (tptt) REVERT: F 206 ARG cc_start: 0.4890 (ttp80) cc_final: 0.4509 (tpt-90) REVERT: F 224 LYS cc_start: 0.5466 (OUTLIER) cc_final: 0.5154 (mtpp) REVERT: F 232 MET cc_start: 0.6472 (ttt) cc_final: 0.6250 (ttt) REVERT: F 269 GLU cc_start: 0.5343 (mm-30) cc_final: 0.4566 (pm20) REVERT: F 280 LYS cc_start: 0.6254 (tttt) cc_final: 0.5961 (tttm) REVERT: F 329 SER cc_start: 0.6889 (m) cc_final: 0.6225 (p) REVERT: F 363 GLU cc_start: 0.5931 (tp30) cc_final: 0.5408 (tt0) REVERT: F 403 GLU cc_start: 0.5635 (tp30) cc_final: 0.5423 (pm20) REVERT: F 411 GLU cc_start: 0.5438 (pt0) cc_final: 0.4800 (mm-30) REVERT: F 441 MET cc_start: 0.6713 (tpp) cc_final: 0.6374 (tpp) REVERT: G 27 ASP cc_start: 0.5534 (p0) cc_final: 0.5316 (p0) REVERT: G 49 LYS cc_start: 0.5647 (mmtt) cc_final: 0.5119 (mmmt) REVERT: G 102 THR cc_start: 0.6364 (m) cc_final: 0.5934 (p) REVERT: G 200 LYS cc_start: 0.6014 (ttmm) cc_final: 0.5018 (tptt) REVERT: G 206 ARG cc_start: 0.5162 (OUTLIER) cc_final: 0.4773 (tpt-90) REVERT: G 223 ARG cc_start: 0.5070 (ttm-80) cc_final: 0.4743 (tpt170) REVERT: G 261 GLU cc_start: 0.6280 (OUTLIER) cc_final: 0.5920 (mm-30) REVERT: G 329 SER cc_start: 0.6997 (m) cc_final: 0.6322 (p) REVERT: G 411 GLU cc_start: 0.5622 (pt0) cc_final: 0.5002 (mm-30) REVERT: G 415 GLU cc_start: 0.5197 (mt-10) cc_final: 0.4262 (tm-30) REVERT: H 27 ASP cc_start: 0.5425 (p0) cc_final: 0.5147 (p0) REVERT: H 32 ILE cc_start: 0.5714 (mt) cc_final: 0.5407 (mm) REVERT: H 49 LYS cc_start: 0.5738 (mmtt) cc_final: 0.5230 (mmmt) REVERT: H 102 THR cc_start: 0.6510 (m) cc_final: 0.6076 (p) REVERT: H 105 GLU cc_start: 0.5891 (pm20) cc_final: 0.5522 (mp0) REVERT: H 117 LYS cc_start: 0.5946 (tptm) cc_final: 0.5708 (tptm) REVERT: H 153 LYS cc_start: 0.5942 (OUTLIER) cc_final: 0.4963 (mmmt) REVERT: H 200 LYS cc_start: 0.5876 (mtpm) cc_final: 0.4835 (tptt) REVERT: H 206 ARG cc_start: 0.5169 (ttt90) cc_final: 0.4755 (tpt-90) REVERT: H 223 ARG cc_start: 0.5269 (ttm-80) cc_final: 0.4948 (tpt-90) REVERT: H 329 SER cc_start: 0.7109 (m) cc_final: 0.6293 (p) REVERT: H 411 GLU cc_start: 0.5463 (pt0) cc_final: 0.5028 (mm-30) REVERT: H 415 GLU cc_start: 0.5173 (mt-10) cc_final: 0.4365 (tm-30) REVERT: H 441 MET cc_start: 0.6745 (tpp) cc_final: 0.6164 (tpp) REVERT: I 10 GLU cc_start: 0.5859 (mt-10) cc_final: 0.5582 (mt-10) REVERT: I 49 LYS cc_start: 0.5674 (mmtt) cc_final: 0.5212 (mmmt) REVERT: I 153 LYS cc_start: 0.5939 (mttm) cc_final: 0.4925 (mmmt) REVERT: I 182 GLU cc_start: 0.5981 (mt-10) cc_final: 0.5563 (mt-10) REVERT: I 200 LYS cc_start: 0.5976 (ttmm) cc_final: 0.4958 (tppt) REVERT: I 206 ARG cc_start: 0.4970 (ttp80) cc_final: 0.4530 (tpt-90) REVERT: I 223 ARG cc_start: 0.5310 (ttm-80) cc_final: 0.4833 (tpt170) REVERT: I 224 LYS cc_start: 0.5824 (ttmm) cc_final: 0.5580 (mtpp) REVERT: I 269 GLU cc_start: 0.5089 (mm-30) cc_final: 0.4548 (pm20) REVERT: I 314 GLN cc_start: 0.6838 (tp40) cc_final: 0.6422 (tt0) REVERT: I 329 SER cc_start: 0.7027 (m) cc_final: 0.6196 (p) REVERT: I 363 GLU cc_start: 0.6014 (tp30) cc_final: 0.5392 (tt0) REVERT: I 411 GLU cc_start: 0.5360 (OUTLIER) cc_final: 0.5043 (mm-30) REVERT: I 415 GLU cc_start: 0.5006 (mt-10) cc_final: 0.4168 (tm-30) REVERT: I 441 MET cc_start: 0.6780 (tpp) cc_final: 0.6310 (tpp) REVERT: N 10 GLU cc_start: 0.5757 (OUTLIER) cc_final: 0.5280 (mt-10) REVERT: N 49 LYS cc_start: 0.5794 (mmtt) cc_final: 0.5331 (mmmt) REVERT: N 148 LEU cc_start: 0.6354 (mt) cc_final: 0.6024 (mp) REVERT: N 153 LYS cc_start: 0.5928 (mttm) cc_final: 0.4947 (mmmt) REVERT: N 182 GLU cc_start: 0.5908 (mt-10) cc_final: 0.5493 (mt-10) REVERT: N 200 LYS cc_start: 0.5617 (mtpp) cc_final: 0.4653 (tptt) REVERT: N 206 ARG cc_start: 0.4891 (ttp80) cc_final: 0.4509 (tpt-90) REVERT: N 224 LYS cc_start: 0.5461 (OUTLIER) cc_final: 0.5151 (mtpp) REVERT: N 232 MET cc_start: 0.6477 (ttt) cc_final: 0.6258 (ttt) REVERT: N 269 GLU cc_start: 0.5339 (mm-30) cc_final: 0.4562 (pm20) REVERT: N 280 LYS cc_start: 0.6253 (tttt) cc_final: 0.5963 (tttm) REVERT: N 329 SER cc_start: 0.6879 (m) cc_final: 0.6219 (p) REVERT: N 363 GLU cc_start: 0.5945 (tp30) cc_final: 0.5418 (tt0) REVERT: N 403 GLU cc_start: 0.6050 (tp30) cc_final: 0.5162 (mp0) REVERT: N 411 GLU cc_start: 0.5476 (pt0) cc_final: 0.4836 (mm-30) REVERT: N 415 GLU cc_start: 0.5447 (mt-10) cc_final: 0.4651 (mm-30) REVERT: N 441 MET cc_start: 0.6712 (tpp) cc_final: 0.6359 (tpp) REVERT: O 10 GLU cc_start: 0.5903 (mt-10) cc_final: 0.5642 (mt-10) REVERT: O 27 ASP cc_start: 0.5524 (p0) cc_final: 0.5307 (p0) REVERT: O 49 LYS cc_start: 0.5668 (mmtt) cc_final: 0.5139 (mmmt) REVERT: O 102 THR cc_start: 0.6365 (m) cc_final: 0.5939 (p) REVERT: O 200 LYS cc_start: 0.6025 (ttmm) cc_final: 0.5045 (tptt) REVERT: O 206 ARG cc_start: 0.5168 (OUTLIER) cc_final: 0.4790 (tpt-90) REVERT: O 223 ARG cc_start: 0.5071 (ttm-80) cc_final: 0.4746 (tpt170) REVERT: O 314 GLN cc_start: 0.6846 (OUTLIER) cc_final: 0.6074 (tt0) REVERT: O 329 SER cc_start: 0.6979 (m) cc_final: 0.6301 (p) REVERT: O 411 GLU cc_start: 0.5619 (pt0) cc_final: 0.5006 (mm-30) REVERT: O 415 GLU cc_start: 0.5217 (mt-10) cc_final: 0.4304 (tm-30) REVERT: P 10 GLU cc_start: 0.5915 (OUTLIER) cc_final: 0.5330 (mt-10) REVERT: P 27 ASP cc_start: 0.5396 (p0) cc_final: 0.5116 (p0) REVERT: P 32 ILE cc_start: 0.5711 (mt) cc_final: 0.5402 (mm) REVERT: P 49 LYS cc_start: 0.5621 (mmtt) cc_final: 0.5124 (mmmt) REVERT: P 102 THR cc_start: 0.6464 (m) cc_final: 0.6025 (p) REVERT: P 105 GLU cc_start: 0.5893 (pm20) cc_final: 0.5532 (mp0) REVERT: P 153 LYS cc_start: 0.5686 (OUTLIER) cc_final: 0.4686 (mmmt) REVERT: P 200 LYS cc_start: 0.5784 (mtpp) cc_final: 0.4954 (tptt) REVERT: P 206 ARG cc_start: 0.5165 (ttt90) cc_final: 0.4751 (tpt-90) REVERT: P 223 ARG cc_start: 0.5291 (ttm-80) cc_final: 0.4975 (tpt-90) REVERT: P 329 SER cc_start: 0.7130 (m) cc_final: 0.6314 (p) REVERT: P 411 GLU cc_start: 0.5493 (pt0) cc_final: 0.5056 (mm-30) REVERT: P 415 GLU cc_start: 0.5234 (mt-10) cc_final: 0.4424 (tm-30) REVERT: P 441 MET cc_start: 0.6813 (tpp) cc_final: 0.6205 (tpp) REVERT: Q 3 LYS cc_start: 0.6762 (tttt) cc_final: 0.6444 (ttmt) REVERT: Q 27 ASP cc_start: 0.5575 (p0) cc_final: 0.5369 (p0) REVERT: Q 49 LYS cc_start: 0.5687 (mmtt) cc_final: 0.5226 (mmmt) REVERT: Q 102 THR cc_start: 0.6671 (m) cc_final: 0.6260 (p) REVERT: Q 153 LYS cc_start: 0.5927 (mttm) cc_final: 0.4911 (mmmt) REVERT: Q 182 GLU cc_start: 0.5996 (mt-10) cc_final: 0.5581 (mt-10) REVERT: Q 200 LYS cc_start: 0.5980 (ttmm) cc_final: 0.4961 (tppt) REVERT: Q 206 ARG cc_start: 0.4982 (ttp80) cc_final: 0.4542 (tpt-90) REVERT: Q 269 GLU cc_start: 0.5094 (mm-30) cc_final: 0.4553 (pm20) REVERT: Q 280 LYS cc_start: 0.6101 (tttt) cc_final: 0.5869 (tttm) REVERT: Q 314 GLN cc_start: 0.6812 (tp40) cc_final: 0.6367 (tt0) REVERT: Q 329 SER cc_start: 0.7028 (m) cc_final: 0.6197 (p) REVERT: Q 363 GLU cc_start: 0.6015 (tp30) cc_final: 0.5393 (tt0) REVERT: Q 403 GLU cc_start: 0.5415 (tp30) cc_final: 0.5075 (pm20) REVERT: Q 411 GLU cc_start: 0.5340 (pt0) cc_final: 0.5029 (mm-30) REVERT: Q 415 GLU cc_start: 0.5003 (mt-10) cc_final: 0.4164 (tm-30) REVERT: Q 441 MET cc_start: 0.6778 (tpp) cc_final: 0.6329 (tpp) REVERT: R 11 LYS cc_start: 0.4554 (tttp) cc_final: 0.4268 (ttpp) REVERT: R 15 GLU cc_start: 0.4243 (OUTLIER) cc_final: 0.3765 (mm-30) REVERT: R 32 ILE cc_start: 0.5760 (mp) cc_final: 0.5479 (mp) REVERT: R 35 VAL cc_start: 0.7067 (OUTLIER) cc_final: 0.6822 (t) REVERT: R 49 LYS cc_start: 0.5828 (mmtt) cc_final: 0.5253 (mmmt) REVERT: R 102 THR cc_start: 0.6319 (m) cc_final: 0.5930 (p) REVERT: R 117 LYS cc_start: 0.5826 (tptm) cc_final: 0.5518 (tptm) REVERT: R 148 LEU cc_start: 0.6505 (mt) cc_final: 0.6257 (mt) REVERT: R 182 GLU cc_start: 0.5921 (mt-10) cc_final: 0.5655 (mt-10) REVERT: R 200 LYS cc_start: 0.5938 (ttmm) cc_final: 0.5007 (tptp) REVERT: R 206 ARG cc_start: 0.5115 (ttt90) cc_final: 0.4910 (tpt-90) REVERT: R 314 GLN cc_start: 0.6838 (OUTLIER) cc_final: 0.6326 (tt0) REVERT: R 329 SER cc_start: 0.6823 (m) cc_final: 0.6205 (p) REVERT: R 403 GLU cc_start: 0.5853 (tp30) cc_final: 0.5351 (mp0) REVERT: R 407 LYS cc_start: 0.5969 (mmtm) cc_final: 0.5340 (mtpt) REVERT: R 409 LEU cc_start: 0.5549 (OUTLIER) cc_final: 0.4881 (mt) REVERT: R 411 GLU cc_start: 0.5824 (mm-30) cc_final: 0.5138 (tt0) REVERT: R 441 MET cc_start: 0.6884 (tpp) cc_final: 0.6429 (tpp) REVERT: S 3 LYS cc_start: 0.6520 (tttt) cc_final: 0.6184 (ttmt) REVERT: S 10 GLU cc_start: 0.5925 (OUTLIER) cc_final: 0.5530 (mt-10) REVERT: S 11 LYS cc_start: 0.4790 (tttp) cc_final: 0.4455 (ttpp) REVERT: S 49 LYS cc_start: 0.5766 (mmtt) cc_final: 0.5271 (mmmt) REVERT: S 102 THR cc_start: 0.6421 (OUTLIER) cc_final: 0.5969 (p) REVERT: S 105 GLU cc_start: 0.6071 (pm20) cc_final: 0.5704 (pm20) REVERT: S 200 LYS cc_start: 0.5856 (mtpp) cc_final: 0.4916 (tptt) REVERT: S 223 ARG cc_start: 0.5001 (ttm-80) cc_final: 0.4738 (ttt90) REVERT: S 314 GLN cc_start: 0.6786 (OUTLIER) cc_final: 0.6137 (tt0) REVERT: S 329 SER cc_start: 0.6902 (m) cc_final: 0.6103 (p) REVERT: S 397 GLU cc_start: 0.5728 (mm-30) cc_final: 0.4931 (mm-30) REVERT: S 403 GLU cc_start: 0.5787 (tp30) cc_final: 0.5574 (tp30) REVERT: S 407 LYS cc_start: 0.6074 (mmtm) cc_final: 0.5433 (mtpt) REVERT: S 411 GLU cc_start: 0.5367 (OUTLIER) cc_final: 0.4764 (mm-30) REVERT: S 415 GLU cc_start: 0.5228 (mt-10) cc_final: 0.4466 (mm-30) REVERT: S 441 MET cc_start: 0.6832 (tpp) cc_final: 0.6630 (tpp) REVERT: T 11 LYS cc_start: 0.4726 (ttpp) cc_final: 0.4362 (ttpp) REVERT: T 15 GLU cc_start: 0.4551 (OUTLIER) cc_final: 0.4156 (mm-30) REVERT: T 49 LYS cc_start: 0.5831 (mmtt) cc_final: 0.5381 (mmmt) REVERT: T 63 ILE cc_start: 0.6132 (mt) cc_final: 0.5538 (mm) REVERT: T 114 ARG cc_start: 0.6705 (OUTLIER) cc_final: 0.5870 (ttm170) REVERT: T 117 LYS cc_start: 0.6039 (tptm) cc_final: 0.5717 (tptm) REVERT: T 153 LYS cc_start: 0.5998 (mttm) cc_final: 0.4984 (mmmt) REVERT: T 189 GLU cc_start: 0.6336 (OUTLIER) cc_final: 0.5712 (tp30) REVERT: T 200 LYS cc_start: 0.5833 (ttmm) cc_final: 0.5021 (tptp) REVERT: T 223 ARG cc_start: 0.5016 (ttm-80) cc_final: 0.4625 (tpt170) REVERT: T 269 GLU cc_start: 0.5388 (mm-30) cc_final: 0.4572 (pm20) REVERT: T 280 LYS cc_start: 0.6009 (tttt) cc_final: 0.5803 (tttm) REVERT: T 314 GLN cc_start: 0.6890 (OUTLIER) cc_final: 0.6621 (tt0) REVERT: T 329 SER cc_start: 0.6941 (m) cc_final: 0.6147 (p) REVERT: T 363 GLU cc_start: 0.5965 (tp30) cc_final: 0.5435 (tt0) REVERT: T 411 GLU cc_start: 0.5406 (pt0) cc_final: 0.4668 (mm-30) REVERT: T 441 MET cc_start: 0.6703 (tpp) cc_final: 0.6330 (tpp) outliers start: 143 outliers final: 51 residues processed: 936 average time/residue: 1.5548 time to fit residues: 1769.9438 Evaluate side-chains 924 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 837 time to evaluate : 4.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 411 GLU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain E residue 7 MET Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 206 ARG Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 261 GLU Chi-restraints excluded: chain H residue 153 LYS Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain H residue 409 LEU Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 114 ARG Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 411 GLU Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain L residue 7 MET Chi-restraints excluded: chain N residue 10 GLU Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 224 LYS Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 206 ARG Chi-restraints excluded: chain O residue 239 VAL Chi-restraints excluded: chain O residue 314 GLN Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 153 LYS Chi-restraints excluded: chain P residue 239 VAL Chi-restraints excluded: chain P residue 409 LEU Chi-restraints excluded: chain Q residue 83 THR Chi-restraints excluded: chain Q residue 114 ARG Chi-restraints excluded: chain Q residue 239 VAL Chi-restraints excluded: chain Q residue 409 LEU Chi-restraints excluded: chain R residue 15 GLU Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 314 GLN Chi-restraints excluded: chain R residue 409 LEU Chi-restraints excluded: chain S residue 10 GLU Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 102 THR Chi-restraints excluded: chain S residue 224 LYS Chi-restraints excluded: chain S residue 239 VAL Chi-restraints excluded: chain S residue 314 GLN Chi-restraints excluded: chain S residue 409 LEU Chi-restraints excluded: chain S residue 411 GLU Chi-restraints excluded: chain T residue 15 GLU Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 83 THR Chi-restraints excluded: chain T residue 114 ARG Chi-restraints excluded: chain T residue 189 GLU Chi-restraints excluded: chain T residue 314 GLN Chi-restraints excluded: chain T residue 409 LEU Chi-restraints excluded: chain U residue 7 MET Chi-restraints excluded: chain W residue 7 MET Chi-restraints excluded: chain Y residue 7 MET Chi-restraints excluded: chain Z residue 7 MET Chi-restraints excluded: chain a residue 7 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 204 optimal weight: 9.9990 chunk 548 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 357 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 609 optimal weight: 0.0870 chunk 506 optimal weight: 0.0020 chunk 282 optimal weight: 0.0050 chunk 50 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 320 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN A 315 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN C 34 ASN C 75 ASN C 167 ASN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN F 167 ASN F 443 GLN G 24 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN G 167 ASN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 ASN H 315 ASN H 443 GLN I 34 ASN I 167 ASN I 266 GLN N 24 GLN N 34 ASN N 75 ASN N 167 ASN O 24 GLN ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 ASN O 167 ASN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 167 ASN P 443 GLN Q 34 ASN Q 167 ASN Q 266 GLN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 167 ASN S 17 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 ASN S 266 GLN T 34 ASN T 75 ASN T 167 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5945 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 51450 Z= 0.120 Angle : 0.439 4.591 69650 Z= 0.242 Chirality : 0.040 0.132 7546 Planarity : 0.003 0.052 9184 Dihedral : 5.039 51.150 6858 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.74 % Allowed : 16.89 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.11), residues: 6286 helix: 2.13 (0.10), residues: 2310 sheet: -0.29 (0.15), residues: 1092 loop : -0.13 (0.12), residues: 2884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP T 425 HIS 0.004 0.001 HIS A 416 PHE 0.016 0.001 PHE I 285 TYR 0.027 0.001 TYR T 296 ARG 0.004 0.000 ARG T 170 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 935 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 842 time to evaluate : 4.445 Fit side-chains REVERT: A 3 LYS cc_start: 0.7082 (ttmt) cc_final: 0.6823 (ttmm) REVERT: A 11 LYS cc_start: 0.4993 (tttp) cc_final: 0.4742 (ttpp) REVERT: A 32 ILE cc_start: 0.5764 (mp) cc_final: 0.5441 (mp) REVERT: A 49 LYS cc_start: 0.5828 (mmtt) cc_final: 0.5230 (mmmt) REVERT: A 102 THR cc_start: 0.6208 (m) cc_final: 0.5854 (p) REVERT: A 117 LYS cc_start: 0.5854 (tptm) cc_final: 0.5499 (tptm) REVERT: A 148 LEU cc_start: 0.6491 (mt) cc_final: 0.6246 (mt) REVERT: A 182 GLU cc_start: 0.6007 (mt-10) cc_final: 0.5742 (mt-10) REVERT: A 200 LYS cc_start: 0.5986 (ttmm) cc_final: 0.4808 (tptt) REVERT: A 206 ARG cc_start: 0.5073 (ttt90) cc_final: 0.4864 (tpt-90) REVERT: A 314 GLN cc_start: 0.6773 (OUTLIER) cc_final: 0.6265 (tt0) REVERT: A 329 SER cc_start: 0.6885 (m) cc_final: 0.6280 (p) REVERT: A 363 GLU cc_start: 0.6131 (tp30) cc_final: 0.5740 (tt0) REVERT: A 369 ASP cc_start: 0.5372 (OUTLIER) cc_final: 0.4723 (m-30) REVERT: A 403 GLU cc_start: 0.5817 (OUTLIER) cc_final: 0.5244 (tp30) REVERT: A 407 LYS cc_start: 0.5767 (mmtm) cc_final: 0.5372 (mtpt) REVERT: A 409 LEU cc_start: 0.5329 (OUTLIER) cc_final: 0.5095 (pp) REVERT: A 411 GLU cc_start: 0.5336 (pt0) cc_final: 0.4676 (mm-30) REVERT: A 438 GLU cc_start: 0.5223 (mt-10) cc_final: 0.4923 (mt-10) REVERT: A 441 MET cc_start: 0.6865 (tpp) cc_final: 0.6599 (tpp) REVERT: B 3 LYS cc_start: 0.6579 (tttt) cc_final: 0.6264 (ttmt) REVERT: B 10 GLU cc_start: 0.6015 (OUTLIER) cc_final: 0.5447 (mt-10) REVERT: B 32 ILE cc_start: 0.5692 (mt) cc_final: 0.5368 (mm) REVERT: B 49 LYS cc_start: 0.5829 (mmtt) cc_final: 0.5314 (mmmt) REVERT: B 102 THR cc_start: 0.6140 (m) cc_final: 0.5843 (p) REVERT: B 105 GLU cc_start: 0.6082 (pm20) cc_final: 0.5574 (mp0) REVERT: B 117 LYS cc_start: 0.5767 (tptp) cc_final: 0.5543 (tptm) REVERT: B 182 GLU cc_start: 0.5974 (mt-10) cc_final: 0.5630 (mt-10) REVERT: B 200 LYS cc_start: 0.5798 (mtpp) cc_final: 0.4831 (tptt) REVERT: B 224 LYS cc_start: 0.5651 (ttmm) cc_final: 0.5295 (mtmt) REVERT: B 314 GLN cc_start: 0.6880 (OUTLIER) cc_final: 0.6252 (tt0) REVERT: B 329 SER cc_start: 0.6920 (m) cc_final: 0.6106 (p) REVERT: B 407 LYS cc_start: 0.6081 (mmtm) cc_final: 0.5437 (mtpt) REVERT: B 411 GLU cc_start: 0.5399 (pt0) cc_final: 0.5009 (mm-30) REVERT: B 415 GLU cc_start: 0.5211 (mt-10) cc_final: 0.4419 (tm-30) REVERT: B 441 MET cc_start: 0.6793 (tpp) cc_final: 0.6535 (tpp) REVERT: C 11 LYS cc_start: 0.4689 (tttm) cc_final: 0.4388 (ttpp) REVERT: C 15 GLU cc_start: 0.4216 (OUTLIER) cc_final: 0.3706 (mm-30) REVERT: C 49 LYS cc_start: 0.5865 (mmtt) cc_final: 0.5406 (mmmt) REVERT: C 102 THR cc_start: 0.6221 (m) cc_final: 0.5845 (p) REVERT: C 117 LYS cc_start: 0.5971 (tptm) cc_final: 0.5630 (tptm) REVERT: C 153 LYS cc_start: 0.6034 (mttm) cc_final: 0.4939 (mmmt) REVERT: C 200 LYS cc_start: 0.5846 (mtpp) cc_final: 0.5066 (tptt) REVERT: C 223 ARG cc_start: 0.5153 (ttm-80) cc_final: 0.4785 (tpt170) REVERT: C 269 GLU cc_start: 0.5214 (mm-30) cc_final: 0.4411 (pm20) REVERT: C 314 GLN cc_start: 0.6786 (tt0) cc_final: 0.6512 (tt0) REVERT: C 329 SER cc_start: 0.6974 (m) cc_final: 0.6202 (p) REVERT: C 363 GLU cc_start: 0.6039 (tp30) cc_final: 0.5542 (tt0) REVERT: C 403 GLU cc_start: 0.5600 (tp30) cc_final: 0.4975 (pm20) REVERT: C 411 GLU cc_start: 0.5369 (pt0) cc_final: 0.4518 (mm-30) REVERT: C 415 GLU cc_start: 0.5215 (mt-10) cc_final: 0.4411 (mm-30) REVERT: C 441 MET cc_start: 0.6748 (tpp) cc_final: 0.6235 (tpp) REVERT: F 10 GLU cc_start: 0.5750 (OUTLIER) cc_final: 0.5302 (mt-10) REVERT: F 49 LYS cc_start: 0.5723 (mmtt) cc_final: 0.5262 (mmmt) REVERT: F 102 THR cc_start: 0.6250 (m) cc_final: 0.5775 (p) REVERT: F 148 LEU cc_start: 0.6407 (mt) cc_final: 0.6115 (mp) REVERT: F 153 LYS cc_start: 0.5914 (mttm) cc_final: 0.4833 (mmmt) REVERT: F 182 GLU cc_start: 0.5816 (mt-10) cc_final: 0.5447 (mt-10) REVERT: F 200 LYS cc_start: 0.5623 (mtpp) cc_final: 0.4674 (tptt) REVERT: F 206 ARG cc_start: 0.4790 (ttp80) cc_final: 0.4443 (tpt-90) REVERT: F 224 LYS cc_start: 0.5367 (OUTLIER) cc_final: 0.5035 (mtpp) REVERT: F 269 GLU cc_start: 0.5226 (mm-30) cc_final: 0.4555 (pm20) REVERT: F 280 LYS cc_start: 0.6155 (tttt) cc_final: 0.5928 (tttm) REVERT: F 329 SER cc_start: 0.6894 (m) cc_final: 0.6233 (p) REVERT: F 363 GLU cc_start: 0.5943 (tp30) cc_final: 0.5440 (tt0) REVERT: F 409 LEU cc_start: 0.5309 (OUTLIER) cc_final: 0.5050 (pp) REVERT: F 411 GLU cc_start: 0.5339 (pt0) cc_final: 0.4517 (mm-30) REVERT: F 415 GLU cc_start: 0.5401 (mt-10) cc_final: 0.4624 (mm-30) REVERT: F 441 MET cc_start: 0.6706 (tpp) cc_final: 0.6322 (tpp) REVERT: G 27 ASP cc_start: 0.5353 (p0) cc_final: 0.5071 (p0) REVERT: G 49 LYS cc_start: 0.5622 (mmtt) cc_final: 0.5090 (mmmt) REVERT: G 102 THR cc_start: 0.6343 (m) cc_final: 0.5958 (p) REVERT: G 206 ARG cc_start: 0.5104 (ttt90) cc_final: 0.4682 (tpt-90) REVERT: G 223 ARG cc_start: 0.5339 (ttm-80) cc_final: 0.4991 (tpt170) REVERT: G 261 GLU cc_start: 0.6210 (OUTLIER) cc_final: 0.5873 (mm-30) REVERT: G 314 GLN cc_start: 0.6860 (OUTLIER) cc_final: 0.6582 (tt0) REVERT: G 329 SER cc_start: 0.7031 (m) cc_final: 0.6349 (p) REVERT: G 403 GLU cc_start: 0.5542 (mm-30) cc_final: 0.4981 (pm20) REVERT: G 411 GLU cc_start: 0.5453 (pt0) cc_final: 0.4650 (mm-30) REVERT: G 415 GLU cc_start: 0.5133 (mt-10) cc_final: 0.4460 (mm-30) REVERT: H 27 ASP cc_start: 0.5613 (p0) cc_final: 0.5340 (p0) REVERT: H 32 ILE cc_start: 0.5739 (mt) cc_final: 0.5437 (mm) REVERT: H 49 LYS cc_start: 0.5789 (mmtt) cc_final: 0.5256 (mmmt) REVERT: H 102 THR cc_start: 0.6325 (m) cc_final: 0.5919 (p) REVERT: H 105 GLU cc_start: 0.5814 (pm20) cc_final: 0.5428 (mp0) REVERT: H 117 LYS cc_start: 0.5924 (tptm) cc_final: 0.5687 (tptm) REVERT: H 153 LYS cc_start: 0.5815 (ptpt) cc_final: 0.4849 (mmmt) REVERT: H 200 LYS cc_start: 0.5929 (mtpm) cc_final: 0.4891 (tptt) REVERT: H 206 ARG cc_start: 0.5112 (ttt90) cc_final: 0.4715 (tpt-90) REVERT: H 223 ARG cc_start: 0.5280 (ttm-80) cc_final: 0.4966 (tpt-90) REVERT: H 329 SER cc_start: 0.7037 (m) cc_final: 0.6203 (p) REVERT: H 411 GLU cc_start: 0.5438 (pt0) cc_final: 0.4991 (mm-30) REVERT: H 415 GLU cc_start: 0.5178 (mt-10) cc_final: 0.4494 (tm-30) REVERT: H 431 GLN cc_start: 0.6639 (mm-40) cc_final: 0.6299 (mm-40) REVERT: H 441 MET cc_start: 0.6802 (tpp) cc_final: 0.6235 (tpp) REVERT: I 3 LYS cc_start: 0.6764 (tttt) cc_final: 0.6451 (ttmt) REVERT: I 10 GLU cc_start: 0.5699 (mt-10) cc_final: 0.5432 (mt-10) REVERT: I 49 LYS cc_start: 0.5636 (mmtt) cc_final: 0.5164 (mmmt) REVERT: I 182 GLU cc_start: 0.6092 (mt-10) cc_final: 0.5563 (mt-10) REVERT: I 200 LYS cc_start: 0.5963 (ttmm) cc_final: 0.4868 (tppt) REVERT: I 206 ARG cc_start: 0.4952 (ttp80) cc_final: 0.4481 (tpt-90) REVERT: I 223 ARG cc_start: 0.5138 (ttm-80) cc_final: 0.4732 (tpt-90) REVERT: I 255 VAL cc_start: 0.5987 (m) cc_final: 0.5721 (p) REVERT: I 269 GLU cc_start: 0.5023 (mm-30) cc_final: 0.4489 (pm20) REVERT: I 280 LYS cc_start: 0.6166 (tttt) cc_final: 0.5938 (tttm) REVERT: I 314 GLN cc_start: 0.6949 (tp40) cc_final: 0.6554 (tt0) REVERT: I 329 SER cc_start: 0.7081 (m) cc_final: 0.6237 (p) REVERT: I 363 GLU cc_start: 0.6065 (tp30) cc_final: 0.5455 (tt0) REVERT: I 411 GLU cc_start: 0.5208 (pt0) cc_final: 0.4925 (mm-30) REVERT: I 415 GLU cc_start: 0.4950 (mt-10) cc_final: 0.4129 (tm-30) REVERT: I 441 MET cc_start: 0.6735 (tpp) cc_final: 0.6311 (tpp) REVERT: N 10 GLU cc_start: 0.5766 (OUTLIER) cc_final: 0.5318 (mt-10) REVERT: N 49 LYS cc_start: 0.5782 (mmtt) cc_final: 0.5299 (mmmt) REVERT: N 102 THR cc_start: 0.6250 (m) cc_final: 0.5771 (p) REVERT: N 148 LEU cc_start: 0.6394 (mt) cc_final: 0.6101 (mp) REVERT: N 153 LYS cc_start: 0.5926 (mttm) cc_final: 0.4960 (mmmt) REVERT: N 182 GLU cc_start: 0.5823 (mt-10) cc_final: 0.5456 (mt-10) REVERT: N 200 LYS cc_start: 0.5622 (mtpp) cc_final: 0.4675 (tptt) REVERT: N 206 ARG cc_start: 0.4792 (ttp80) cc_final: 0.4444 (tpt-90) REVERT: N 224 LYS cc_start: 0.5363 (OUTLIER) cc_final: 0.5031 (mtpp) REVERT: N 269 GLU cc_start: 0.5225 (mm-30) cc_final: 0.4553 (pm20) REVERT: N 280 LYS cc_start: 0.6131 (tttt) cc_final: 0.5900 (tttm) REVERT: N 329 SER cc_start: 0.6888 (m) cc_final: 0.6229 (p) REVERT: N 363 GLU cc_start: 0.5952 (tp30) cc_final: 0.5454 (tt0) REVERT: N 403 GLU cc_start: 0.5880 (tp30) cc_final: 0.4974 (mp0) REVERT: N 411 GLU cc_start: 0.5352 (pt0) cc_final: 0.4541 (mm-30) REVERT: N 415 GLU cc_start: 0.5468 (mt-10) cc_final: 0.4634 (mm-30) REVERT: N 441 MET cc_start: 0.6702 (tpp) cc_final: 0.6322 (tpp) REVERT: O 27 ASP cc_start: 0.5347 (p0) cc_final: 0.5067 (p0) REVERT: O 49 LYS cc_start: 0.5629 (mmtt) cc_final: 0.5104 (mmmt) REVERT: O 102 THR cc_start: 0.6341 (m) cc_final: 0.5955 (p) REVERT: O 206 ARG cc_start: 0.5089 (ttt90) cc_final: 0.4667 (tpt-90) REVERT: O 223 ARG cc_start: 0.5327 (ttm-80) cc_final: 0.4987 (tpt170) REVERT: O 314 GLN cc_start: 0.6892 (OUTLIER) cc_final: 0.6373 (tt0) REVERT: O 329 SER cc_start: 0.7014 (m) cc_final: 0.6328 (p) REVERT: O 411 GLU cc_start: 0.5479 (pt0) cc_final: 0.4872 (mm-30) REVERT: O 415 GLU cc_start: 0.5142 (mt-10) cc_final: 0.4321 (tm-30) REVERT: P 10 GLU cc_start: 0.5894 (OUTLIER) cc_final: 0.5359 (mt-10) REVERT: P 27 ASP cc_start: 0.5519 (p0) cc_final: 0.5251 (p0) REVERT: P 32 ILE cc_start: 0.5736 (mt) cc_final: 0.5433 (mm) REVERT: P 49 LYS cc_start: 0.5787 (mmtt) cc_final: 0.5253 (mmmt) REVERT: P 102 THR cc_start: 0.6378 (m) cc_final: 0.5969 (p) REVERT: P 105 GLU cc_start: 0.5817 (pm20) cc_final: 0.5436 (mp0) REVERT: P 153 LYS cc_start: 0.5793 (OUTLIER) cc_final: 0.4707 (mmmt) REVERT: P 200 LYS cc_start: 0.5839 (mtpp) cc_final: 0.4984 (tptt) REVERT: P 206 ARG cc_start: 0.5108 (ttt90) cc_final: 0.4711 (tpt-90) REVERT: P 223 ARG cc_start: 0.5281 (ttm-80) cc_final: 0.4964 (tpt-90) REVERT: P 329 SER cc_start: 0.7054 (m) cc_final: 0.6228 (p) REVERT: P 411 GLU cc_start: 0.5450 (pt0) cc_final: 0.5011 (mm-30) REVERT: P 415 GLU cc_start: 0.5194 (mt-10) cc_final: 0.4513 (tm-30) REVERT: P 431 GLN cc_start: 0.6640 (mm-40) cc_final: 0.6294 (mm-40) REVERT: P 441 MET cc_start: 0.6790 (tpp) cc_final: 0.6219 (tpp) REVERT: Q 27 ASP cc_start: 0.5413 (p0) cc_final: 0.5208 (p0) REVERT: Q 49 LYS cc_start: 0.5650 (mmtt) cc_final: 0.5178 (mmmt) REVERT: Q 102 THR cc_start: 0.6618 (m) cc_final: 0.6256 (p) REVERT: Q 153 LYS cc_start: 0.5913 (mttm) cc_final: 0.4885 (mmmt) REVERT: Q 182 GLU cc_start: 0.6095 (mt-10) cc_final: 0.5568 (mt-10) REVERT: Q 200 LYS cc_start: 0.5966 (ttmm) cc_final: 0.4872 (tppt) REVERT: Q 206 ARG cc_start: 0.4964 (ttp80) cc_final: 0.4493 (tpt-90) REVERT: Q 269 GLU cc_start: 0.5029 (mm-30) cc_final: 0.4495 (pm20) REVERT: Q 280 LYS cc_start: 0.6183 (tttt) cc_final: 0.5954 (tttm) REVERT: Q 314 GLN cc_start: 0.6929 (tp40) cc_final: 0.6541 (tt0) REVERT: Q 329 SER cc_start: 0.7082 (m) cc_final: 0.6237 (p) REVERT: Q 363 GLU cc_start: 0.6064 (tp30) cc_final: 0.5457 (tt0) REVERT: Q 411 GLU cc_start: 0.5245 (pt0) cc_final: 0.4953 (mm-30) REVERT: Q 415 GLU cc_start: 0.4947 (mt-10) cc_final: 0.4126 (tm-30) REVERT: Q 441 MET cc_start: 0.6732 (tpp) cc_final: 0.6302 (tpp) REVERT: R 3 LYS cc_start: 0.7185 (ttmt) cc_final: 0.6929 (ttmm) REVERT: R 11 LYS cc_start: 0.4641 (tttp) cc_final: 0.4343 (ttpp) REVERT: R 15 GLU cc_start: 0.4186 (OUTLIER) cc_final: 0.3734 (mm-30) REVERT: R 32 ILE cc_start: 0.5793 (mp) cc_final: 0.5474 (mp) REVERT: R 49 LYS cc_start: 0.5843 (mmtt) cc_final: 0.5250 (mmmt) REVERT: R 102 THR cc_start: 0.6173 (m) cc_final: 0.5825 (p) REVERT: R 117 LYS cc_start: 0.5824 (tptm) cc_final: 0.5465 (tptm) REVERT: R 148 LEU cc_start: 0.6492 (mt) cc_final: 0.6259 (mt) REVERT: R 182 GLU cc_start: 0.5969 (mt-10) cc_final: 0.5733 (mt-10) REVERT: R 200 LYS cc_start: 0.5978 (ttmm) cc_final: 0.4808 (tppt) REVERT: R 206 ARG cc_start: 0.5069 (ttt90) cc_final: 0.4859 (tpt-90) REVERT: R 314 GLN cc_start: 0.6771 (OUTLIER) cc_final: 0.6307 (tt0) REVERT: R 329 SER cc_start: 0.6792 (m) cc_final: 0.6231 (p) REVERT: R 363 GLU cc_start: 0.6123 (tp30) cc_final: 0.5732 (tt0) REVERT: R 403 GLU cc_start: 0.5825 (tp30) cc_final: 0.5310 (mp0) REVERT: R 407 LYS cc_start: 0.5914 (mmtm) cc_final: 0.5355 (mtpt) REVERT: R 409 LEU cc_start: 0.5470 (OUTLIER) cc_final: 0.5170 (pp) REVERT: R 411 GLU cc_start: 0.5608 (mm-30) cc_final: 0.4915 (tt0) REVERT: R 438 GLU cc_start: 0.5252 (mt-10) cc_final: 0.4973 (mt-10) REVERT: S 3 LYS cc_start: 0.6579 (tttt) cc_final: 0.6274 (ttmt) REVERT: S 10 GLU cc_start: 0.6021 (OUTLIER) cc_final: 0.5609 (mt-10) REVERT: S 11 LYS cc_start: 0.5096 (tttp) cc_final: 0.4725 (ttpp) REVERT: S 49 LYS cc_start: 0.5751 (mmtt) cc_final: 0.5227 (mmmt) REVERT: S 102 THR cc_start: 0.6147 (m) cc_final: 0.5855 (p) REVERT: S 105 GLU cc_start: 0.6181 (pm20) cc_final: 0.5614 (mp0) REVERT: S 153 LYS cc_start: 0.5642 (mmpt) cc_final: 0.5380 (mmmt) REVERT: S 200 LYS cc_start: 0.5806 (mtpp) cc_final: 0.4844 (tptt) REVERT: S 223 ARG cc_start: 0.5110 (ttm-80) cc_final: 0.4763 (tpt-90) REVERT: S 261 GLU cc_start: 0.6155 (OUTLIER) cc_final: 0.5700 (mm-30) REVERT: S 314 GLN cc_start: 0.6871 (OUTLIER) cc_final: 0.6243 (tt0) REVERT: S 329 SER cc_start: 0.6922 (m) cc_final: 0.6109 (p) REVERT: S 407 LYS cc_start: 0.5933 (mmtm) cc_final: 0.5356 (mtpt) REVERT: S 411 GLU cc_start: 0.5292 (pt0) cc_final: 0.4896 (mm-30) REVERT: S 415 GLU cc_start: 0.5224 (mt-10) cc_final: 0.4433 (tm-30) REVERT: S 441 MET cc_start: 0.6791 (tpp) cc_final: 0.6512 (tpp) REVERT: T 11 LYS cc_start: 0.4800 (ttpp) cc_final: 0.4458 (ttpp) REVERT: T 15 GLU cc_start: 0.4498 (OUTLIER) cc_final: 0.4127 (mm-30) REVERT: T 49 LYS cc_start: 0.5847 (mmtt) cc_final: 0.5388 (mmmt) REVERT: T 63 ILE cc_start: 0.6129 (mt) cc_final: 0.5565 (mm) REVERT: T 117 LYS cc_start: 0.6016 (tptm) cc_final: 0.5721 (tptm) REVERT: T 153 LYS cc_start: 0.6017 (mttm) cc_final: 0.4907 (mmmt) REVERT: T 189 GLU cc_start: 0.6227 (OUTLIER) cc_final: 0.5620 (tp30) REVERT: T 200 LYS cc_start: 0.5946 (ttmm) cc_final: 0.5139 (tptp) REVERT: T 223 ARG cc_start: 0.5171 (ttm-80) cc_final: 0.4762 (tpt170) REVERT: T 269 GLU cc_start: 0.5299 (mm-30) cc_final: 0.4493 (pm20) REVERT: T 314 GLN cc_start: 0.6781 (tt0) cc_final: 0.6509 (tt0) REVERT: T 329 SER cc_start: 0.6995 (m) cc_final: 0.6215 (p) REVERT: T 363 GLU cc_start: 0.6050 (tp30) cc_final: 0.5553 (tt0) REVERT: T 411 GLU cc_start: 0.5416 (pt0) cc_final: 0.4618 (mm-30) REVERT: T 441 MET cc_start: 0.6715 (tpp) cc_final: 0.6194 (tpp) outliers start: 93 outliers final: 35 residues processed: 887 average time/residue: 1.5659 time to fit residues: 1686.8029 Evaluate side-chains 882 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 822 time to evaluate : 4.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain E residue 7 MET Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 409 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 261 GLU Chi-restraints excluded: chain G residue 314 GLN Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 167 ASN Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain L residue 7 MET Chi-restraints excluded: chain M residue 7 MET Chi-restraints excluded: chain N residue 10 GLU Chi-restraints excluded: chain N residue 167 ASN Chi-restraints excluded: chain N residue 224 LYS Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 167 ASN Chi-restraints excluded: chain O residue 239 VAL Chi-restraints excluded: chain O residue 314 GLN Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 153 LYS Chi-restraints excluded: chain Q residue 122 LEU Chi-restraints excluded: chain Q residue 167 ASN Chi-restraints excluded: chain R residue 15 GLU Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 314 GLN Chi-restraints excluded: chain R residue 409 LEU Chi-restraints excluded: chain S residue 10 GLU Chi-restraints excluded: chain S residue 239 VAL Chi-restraints excluded: chain S residue 261 GLU Chi-restraints excluded: chain S residue 314 GLN Chi-restraints excluded: chain S residue 409 LEU Chi-restraints excluded: chain T residue 15 GLU Chi-restraints excluded: chain T residue 189 GLU Chi-restraints excluded: chain T residue 224 LYS Chi-restraints excluded: chain U residue 7 MET Chi-restraints excluded: chain W residue 7 MET Chi-restraints excluded: chain Y residue 7 MET Chi-restraints excluded: chain Z residue 7 MET Chi-restraints excluded: chain a residue 7 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 587 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 347 optimal weight: 2.9990 chunk 445 optimal weight: 8.9990 chunk 344 optimal weight: 3.9990 chunk 513 optimal weight: 2.9990 chunk 340 optimal weight: 5.9990 chunk 607 optimal weight: 3.9990 chunk 380 optimal weight: 6.9990 chunk 370 optimal weight: 3.9990 chunk 280 optimal weight: 0.1980 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN A 315 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN B 443 GLN C 17 ASN C 34 ASN C 75 ASN C 167 ASN F 24 GLN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN F 167 ASN F 443 GLN G 24 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN G 167 ASN H 34 ASN H 167 ASN H 443 GLN I 34 ASN I 167 ASN I 266 GLN N 24 GLN N 34 ASN N 167 ASN O 24 GLN ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 ASN O 167 ASN P 34 ASN P 315 ASN P 443 GLN Q 17 ASN Q 34 ASN Q 167 ASN Q 266 GLN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 167 ASN S 34 ASN S 167 ASN S 266 GLN T 17 ASN T 34 ASN T 75 ASN T 167 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5968 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 51450 Z= 0.233 Angle : 0.568 6.080 69650 Z= 0.310 Chirality : 0.044 0.159 7546 Planarity : 0.005 0.087 9184 Dihedral : 5.474 54.517 6852 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.21 % Allowed : 16.40 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.10), residues: 6286 helix: 1.83 (0.10), residues: 2324 sheet: -0.51 (0.16), residues: 882 loop : -0.46 (0.11), residues: 3080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP O 425 HIS 0.007 0.002 HIS O 195 PHE 0.023 0.002 PHE N 285 TYR 0.040 0.003 TYR S 296 ARG 0.007 0.001 ARG S 335 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 962 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 844 time to evaluate : 4.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.4993 (tttp) cc_final: 0.4730 (ttpp) REVERT: A 32 ILE cc_start: 0.5761 (mp) cc_final: 0.5446 (mp) REVERT: A 49 LYS cc_start: 0.5803 (mmtt) cc_final: 0.5209 (mmmt) REVERT: A 102 THR cc_start: 0.6241 (m) cc_final: 0.5883 (p) REVERT: A 117 LYS cc_start: 0.5846 (tptm) cc_final: 0.5534 (tptm) REVERT: A 148 LEU cc_start: 0.6507 (mt) cc_final: 0.6271 (mt) REVERT: A 182 GLU cc_start: 0.5892 (mt-10) cc_final: 0.5664 (mt-10) REVERT: A 200 LYS cc_start: 0.5969 (ttmm) cc_final: 0.4848 (tptt) REVERT: A 314 GLN cc_start: 0.6792 (OUTLIER) cc_final: 0.6257 (tt0) REVERT: A 329 SER cc_start: 0.6816 (m) cc_final: 0.6220 (p) REVERT: A 363 GLU cc_start: 0.6069 (tp30) cc_final: 0.5661 (tt0) REVERT: A 369 ASP cc_start: 0.5465 (OUTLIER) cc_final: 0.4799 (m-30) REVERT: A 403 GLU cc_start: 0.5855 (OUTLIER) cc_final: 0.5218 (tp30) REVERT: A 407 LYS cc_start: 0.5771 (mmtm) cc_final: 0.5257 (mtpt) REVERT: A 411 GLU cc_start: 0.5417 (pt0) cc_final: 0.4798 (mm-30) REVERT: A 441 MET cc_start: 0.6860 (tpp) cc_final: 0.6624 (tpp) REVERT: B 3 LYS cc_start: 0.6617 (tttt) cc_final: 0.6274 (ttmt) REVERT: B 10 GLU cc_start: 0.6024 (OUTLIER) cc_final: 0.5450 (mt-10) REVERT: B 32 ILE cc_start: 0.5700 (mt) cc_final: 0.5418 (mm) REVERT: B 49 LYS cc_start: 0.5823 (mmtt) cc_final: 0.5319 (mmmt) REVERT: B 102 THR cc_start: 0.6365 (OUTLIER) cc_final: 0.5916 (p) REVERT: B 105 GLU cc_start: 0.6092 (pm20) cc_final: 0.5470 (mp0) REVERT: B 117 LYS cc_start: 0.5676 (tptp) cc_final: 0.5416 (tptm) REVERT: B 182 GLU cc_start: 0.6080 (mt-10) cc_final: 0.5733 (mt-10) REVERT: B 200 LYS cc_start: 0.5784 (mtpp) cc_final: 0.4829 (tptt) REVERT: B 224 LYS cc_start: 0.5641 (ttmm) cc_final: 0.5327 (mtmt) REVERT: B 261 GLU cc_start: 0.6132 (OUTLIER) cc_final: 0.5852 (mm-30) REVERT: B 314 GLN cc_start: 0.6816 (OUTLIER) cc_final: 0.6169 (tt0) REVERT: B 329 SER cc_start: 0.6913 (m) cc_final: 0.6100 (p) REVERT: B 385 ILE cc_start: 0.6324 (OUTLIER) cc_final: 0.6062 (mm) REVERT: B 407 LYS cc_start: 0.6145 (mmtm) cc_final: 0.5476 (mtpt) REVERT: B 411 GLU cc_start: 0.5333 (pt0) cc_final: 0.4913 (mm-30) REVERT: B 415 GLU cc_start: 0.5207 (mt-10) cc_final: 0.4440 (tm-30) REVERT: B 441 MET cc_start: 0.6809 (tpp) cc_final: 0.6538 (tpp) REVERT: C 3 LYS cc_start: 0.6823 (tttt) cc_final: 0.6592 (ttmt) REVERT: C 11 LYS cc_start: 0.4778 (tttm) cc_final: 0.4447 (ttpp) REVERT: C 15 GLU cc_start: 0.4309 (OUTLIER) cc_final: 0.3856 (mm-30) REVERT: C 49 LYS cc_start: 0.5853 (mmtt) cc_final: 0.5399 (mmmt) REVERT: C 102 THR cc_start: 0.6295 (m) cc_final: 0.5851 (p) REVERT: C 117 LYS cc_start: 0.5953 (tptm) cc_final: 0.5620 (tptm) REVERT: C 153 LYS cc_start: 0.6030 (mttm) cc_final: 0.5025 (mmmt) REVERT: C 200 LYS cc_start: 0.5741 (mtpp) cc_final: 0.4990 (tptt) REVERT: C 223 ARG cc_start: 0.5019 (ttm-80) cc_final: 0.4654 (tpt170) REVERT: C 269 GLU cc_start: 0.5330 (mm-30) cc_final: 0.4492 (pm20) REVERT: C 314 GLN cc_start: 0.6885 (tt0) cc_final: 0.6613 (tt0) REVERT: C 329 SER cc_start: 0.6988 (m) cc_final: 0.6172 (p) REVERT: C 363 GLU cc_start: 0.6016 (tp30) cc_final: 0.5517 (tt0) REVERT: C 403 GLU cc_start: 0.5675 (tp30) cc_final: 0.5036 (pm20) REVERT: C 411 GLU cc_start: 0.5347 (pt0) cc_final: 0.4589 (mm-30) REVERT: C 441 MET cc_start: 0.6744 (tpp) cc_final: 0.6275 (tpp) REVERT: F 10 GLU cc_start: 0.5759 (OUTLIER) cc_final: 0.5298 (mt-10) REVERT: F 49 LYS cc_start: 0.5790 (mmtt) cc_final: 0.5316 (mmmt) REVERT: F 102 THR cc_start: 0.6278 (OUTLIER) cc_final: 0.5785 (p) REVERT: F 148 LEU cc_start: 0.6427 (mt) cc_final: 0.6141 (mp) REVERT: F 153 LYS cc_start: 0.5911 (mttm) cc_final: 0.4830 (mmmt) REVERT: F 182 GLU cc_start: 0.5903 (mt-10) cc_final: 0.5494 (mt-10) REVERT: F 200 LYS cc_start: 0.5622 (mtpp) cc_final: 0.4659 (tptt) REVERT: F 206 ARG cc_start: 0.4910 (ttp80) cc_final: 0.4527 (tpt-90) REVERT: F 224 LYS cc_start: 0.5318 (OUTLIER) cc_final: 0.4994 (mtpp) REVERT: F 269 GLU cc_start: 0.5313 (mm-30) cc_final: 0.4541 (pm20) REVERT: F 280 LYS cc_start: 0.6176 (tttt) cc_final: 0.5887 (tttm) REVERT: F 329 SER cc_start: 0.6929 (m) cc_final: 0.6257 (p) REVERT: F 363 GLU cc_start: 0.5938 (tp30) cc_final: 0.5431 (tt0) REVERT: F 411 GLU cc_start: 0.5430 (pt0) cc_final: 0.4732 (mm-30) REVERT: F 415 GLU cc_start: 0.5467 (mt-10) cc_final: 0.4667 (mm-30) REVERT: F 441 MET cc_start: 0.6665 (tpp) cc_final: 0.6360 (tpp) REVERT: G 27 ASP cc_start: 0.5491 (p0) cc_final: 0.5273 (p0) REVERT: G 49 LYS cc_start: 0.5674 (mmtt) cc_final: 0.5137 (mmmt) REVERT: G 102 THR cc_start: 0.6328 (m) cc_final: 0.5912 (p) REVERT: G 200 LYS cc_start: 0.6040 (ttmm) cc_final: 0.5045 (tptt) REVERT: G 206 ARG cc_start: 0.5129 (OUTLIER) cc_final: 0.4705 (tpt-90) REVERT: G 223 ARG cc_start: 0.5331 (ttm-80) cc_final: 0.4991 (tpt170) REVERT: G 261 GLU cc_start: 0.6278 (OUTLIER) cc_final: 0.5913 (mm-30) REVERT: G 314 GLN cc_start: 0.6827 (OUTLIER) cc_final: 0.6300 (tt0) REVERT: G 329 SER cc_start: 0.7031 (m) cc_final: 0.6334 (p) REVERT: G 403 GLU cc_start: 0.5641 (mm-30) cc_final: 0.5049 (pm20) REVERT: G 411 GLU cc_start: 0.5586 (pt0) cc_final: 0.4971 (mm-30) REVERT: G 415 GLU cc_start: 0.5171 (mt-10) cc_final: 0.4292 (tm-30) REVERT: H 27 ASP cc_start: 0.5403 (p0) cc_final: 0.5121 (p0) REVERT: H 32 ILE cc_start: 0.5788 (mt) cc_final: 0.5471 (mm) REVERT: H 49 LYS cc_start: 0.5761 (mmtt) cc_final: 0.5250 (mmmt) REVERT: H 102 THR cc_start: 0.6506 (m) cc_final: 0.6040 (p) REVERT: H 105 GLU cc_start: 0.5847 (pm20) cc_final: 0.5484 (mp0) REVERT: H 117 LYS cc_start: 0.5935 (tptm) cc_final: 0.5699 (tptm) REVERT: H 153 LYS cc_start: 0.5907 (ptpt) cc_final: 0.4872 (mmmt) REVERT: H 200 LYS cc_start: 0.5873 (mtpm) cc_final: 0.4869 (tptt) REVERT: H 206 ARG cc_start: 0.5165 (ttt90) cc_final: 0.4753 (tpt-90) REVERT: H 223 ARG cc_start: 0.5300 (ttm-80) cc_final: 0.4734 (ttm-80) REVERT: H 280 LYS cc_start: 0.6266 (tttt) cc_final: 0.6009 (tttm) REVERT: H 329 SER cc_start: 0.7070 (m) cc_final: 0.6243 (p) REVERT: H 411 GLU cc_start: 0.5442 (pt0) cc_final: 0.4975 (mm-30) REVERT: H 415 GLU cc_start: 0.5154 (mt-10) cc_final: 0.4347 (tm-30) REVERT: H 441 MET cc_start: 0.6782 (tpp) cc_final: 0.6246 (tpp) REVERT: I 10 GLU cc_start: 0.5843 (mt-10) cc_final: 0.5577 (mt-10) REVERT: I 49 LYS cc_start: 0.5659 (mmtt) cc_final: 0.5187 (mmmt) REVERT: I 153 LYS cc_start: 0.5939 (mttm) cc_final: 0.4921 (mmmt) REVERT: I 182 GLU cc_start: 0.6114 (mt-10) cc_final: 0.5615 (mt-10) REVERT: I 200 LYS cc_start: 0.5917 (ttmm) cc_final: 0.4891 (tppt) REVERT: I 206 ARG cc_start: 0.4979 (ttp80) cc_final: 0.4491 (tpt-90) REVERT: I 223 ARG cc_start: 0.5174 (ttm-80) cc_final: 0.4686 (tpt170) REVERT: I 280 LYS cc_start: 0.6160 (tttt) cc_final: 0.5925 (tttm) REVERT: I 314 GLN cc_start: 0.6859 (tp40) cc_final: 0.6440 (tt0) REVERT: I 329 SER cc_start: 0.7075 (m) cc_final: 0.6230 (p) REVERT: I 363 GLU cc_start: 0.6059 (tp30) cc_final: 0.5435 (tt0) REVERT: I 411 GLU cc_start: 0.5303 (pt0) cc_final: 0.5017 (mm-30) REVERT: I 415 GLU cc_start: 0.5032 (mt-10) cc_final: 0.4214 (tm-30) REVERT: I 441 MET cc_start: 0.6779 (tpp) cc_final: 0.6356 (tpp) REVERT: N 10 GLU cc_start: 0.5778 (OUTLIER) cc_final: 0.5316 (mt-10) REVERT: N 49 LYS cc_start: 0.5796 (mmtt) cc_final: 0.5320 (mmmt) REVERT: N 102 THR cc_start: 0.6279 (OUTLIER) cc_final: 0.5781 (p) REVERT: N 148 LEU cc_start: 0.6426 (mt) cc_final: 0.6144 (mp) REVERT: N 153 LYS cc_start: 0.5930 (mttm) cc_final: 0.4953 (mmmt) REVERT: N 182 GLU cc_start: 0.5897 (mt-10) cc_final: 0.5490 (mt-10) REVERT: N 200 LYS cc_start: 0.5622 (mtpp) cc_final: 0.4660 (tptt) REVERT: N 206 ARG cc_start: 0.4911 (ttp80) cc_final: 0.4527 (tpt-90) REVERT: N 224 LYS cc_start: 0.5312 (OUTLIER) cc_final: 0.4989 (mtpp) REVERT: N 269 GLU cc_start: 0.5309 (mm-30) cc_final: 0.4538 (pm20) REVERT: N 280 LYS cc_start: 0.6177 (tttt) cc_final: 0.5888 (tttm) REVERT: N 329 SER cc_start: 0.6938 (m) cc_final: 0.6270 (p) REVERT: N 363 GLU cc_start: 0.5954 (tp30) cc_final: 0.5452 (tt0) REVERT: N 403 GLU cc_start: 0.5938 (tp30) cc_final: 0.5032 (mp0) REVERT: N 411 GLU cc_start: 0.5416 (pt0) cc_final: 0.4759 (mm-30) REVERT: N 441 MET cc_start: 0.6671 (tpp) cc_final: 0.6369 (tpp) REVERT: O 27 ASP cc_start: 0.5485 (p0) cc_final: 0.5268 (p0) REVERT: O 49 LYS cc_start: 0.5689 (mmtt) cc_final: 0.5151 (mmmt) REVERT: O 102 THR cc_start: 0.6326 (m) cc_final: 0.5909 (p) REVERT: O 200 LYS cc_start: 0.6051 (ttmm) cc_final: 0.5061 (tptt) REVERT: O 206 ARG cc_start: 0.5143 (OUTLIER) cc_final: 0.4718 (tpt-90) REVERT: O 223 ARG cc_start: 0.5344 (ttm-80) cc_final: 0.4997 (tpt170) REVERT: O 314 GLN cc_start: 0.6854 (OUTLIER) cc_final: 0.6063 (tt0) REVERT: O 329 SER cc_start: 0.7014 (m) cc_final: 0.6315 (p) REVERT: O 411 GLU cc_start: 0.5589 (pt0) cc_final: 0.4976 (mm-30) REVERT: O 415 GLU cc_start: 0.5226 (mt-10) cc_final: 0.4348 (tm-30) REVERT: P 10 GLU cc_start: 0.5946 (OUTLIER) cc_final: 0.5345 (mt-10) REVERT: P 27 ASP cc_start: 0.5512 (p0) cc_final: 0.5224 (p0) REVERT: P 32 ILE cc_start: 0.5784 (mt) cc_final: 0.5465 (mm) REVERT: P 49 LYS cc_start: 0.5614 (mmtt) cc_final: 0.5118 (mmmt) REVERT: P 102 THR cc_start: 0.6488 (m) cc_final: 0.6015 (p) REVERT: P 105 GLU cc_start: 0.5801 (pm20) cc_final: 0.5386 (mp0) REVERT: P 153 LYS cc_start: 0.5774 (OUTLIER) cc_final: 0.4721 (mmmt) REVERT: P 200 LYS cc_start: 0.5773 (mtpp) cc_final: 0.4950 (tptt) REVERT: P 206 ARG cc_start: 0.5161 (ttt90) cc_final: 0.4748 (tpt-90) REVERT: P 223 ARG cc_start: 0.5303 (ttm-80) cc_final: 0.4737 (ttm-80) REVERT: P 329 SER cc_start: 0.7136 (m) cc_final: 0.6281 (p) REVERT: P 411 GLU cc_start: 0.5469 (pt0) cc_final: 0.5004 (mm-30) REVERT: P 415 GLU cc_start: 0.5212 (mt-10) cc_final: 0.4391 (tm-30) REVERT: P 441 MET cc_start: 0.6787 (tpp) cc_final: 0.6247 (tpp) REVERT: Q 27 ASP cc_start: 0.5514 (p0) cc_final: 0.5270 (p0) REVERT: Q 49 LYS cc_start: 0.5673 (mmtt) cc_final: 0.5201 (mmmt) REVERT: Q 102 THR cc_start: 0.6689 (m) cc_final: 0.6296 (p) REVERT: Q 153 LYS cc_start: 0.5925 (mttm) cc_final: 0.4908 (mmmt) REVERT: Q 182 GLU cc_start: 0.6134 (mt-10) cc_final: 0.5625 (mt-10) REVERT: Q 200 LYS cc_start: 0.5920 (ttmm) cc_final: 0.4896 (tppt) REVERT: Q 206 ARG cc_start: 0.4991 (ttp80) cc_final: 0.4504 (tpt-90) REVERT: Q 280 LYS cc_start: 0.6177 (tttt) cc_final: 0.5941 (tttm) REVERT: Q 314 GLN cc_start: 0.6830 (tp40) cc_final: 0.6378 (tt0) REVERT: Q 329 SER cc_start: 0.7077 (m) cc_final: 0.6233 (p) REVERT: Q 363 GLU cc_start: 0.6055 (tp30) cc_final: 0.5428 (tt0) REVERT: Q 407 LYS cc_start: 0.5481 (OUTLIER) cc_final: 0.4929 (mtpt) REVERT: Q 411 GLU cc_start: 0.5326 (pt0) cc_final: 0.5031 (mm-30) REVERT: Q 415 GLU cc_start: 0.5034 (mt-10) cc_final: 0.4217 (tm-30) REVERT: Q 441 MET cc_start: 0.6755 (tpp) cc_final: 0.6327 (tpp) REVERT: R 11 LYS cc_start: 0.4659 (tttp) cc_final: 0.4366 (ttpp) REVERT: R 15 GLU cc_start: 0.4185 (OUTLIER) cc_final: 0.3779 (mm-30) REVERT: R 32 ILE cc_start: 0.5772 (mp) cc_final: 0.5459 (mp) REVERT: R 49 LYS cc_start: 0.5817 (mmtt) cc_final: 0.5225 (mmmt) REVERT: R 102 THR cc_start: 0.6293 (m) cc_final: 0.5916 (p) REVERT: R 117 LYS cc_start: 0.5852 (tptm) cc_final: 0.5534 (tptm) REVERT: R 148 LEU cc_start: 0.6494 (mt) cc_final: 0.6271 (mt) REVERT: R 182 GLU cc_start: 0.5914 (mt-10) cc_final: 0.5683 (mt-10) REVERT: R 200 LYS cc_start: 0.5969 (ttmm) cc_final: 0.4852 (tptt) REVERT: R 314 GLN cc_start: 0.6816 (OUTLIER) cc_final: 0.6321 (tt0) REVERT: R 329 SER cc_start: 0.6805 (m) cc_final: 0.6207 (p) REVERT: R 403 GLU cc_start: 0.5860 (tp30) cc_final: 0.5421 (mp0) REVERT: R 407 LYS cc_start: 0.5920 (mmtm) cc_final: 0.5276 (mtpt) REVERT: R 409 LEU cc_start: 0.5456 (OUTLIER) cc_final: 0.5192 (pp) REVERT: R 411 GLU cc_start: 0.5776 (mm-30) cc_final: 0.5101 (tt0) REVERT: S 3 LYS cc_start: 0.6646 (tttt) cc_final: 0.6331 (ttmt) REVERT: S 10 GLU cc_start: 0.5986 (OUTLIER) cc_final: 0.5597 (mt-10) REVERT: S 11 LYS cc_start: 0.4946 (tttp) cc_final: 0.4601 (ttpp) REVERT: S 49 LYS cc_start: 0.5755 (mmtt) cc_final: 0.5245 (mmmt) REVERT: S 102 THR cc_start: 0.6374 (OUTLIER) cc_final: 0.5929 (p) REVERT: S 105 GLU cc_start: 0.6089 (pm20) cc_final: 0.5412 (mp0) REVERT: S 153 LYS cc_start: 0.5644 (mmpt) cc_final: 0.5392 (mmmt) REVERT: S 200 LYS cc_start: 0.5826 (mtpp) cc_final: 0.4823 (tptt) REVERT: S 223 ARG cc_start: 0.5182 (ttm-80) cc_final: 0.4902 (ttt90) REVERT: S 261 GLU cc_start: 0.6162 (OUTLIER) cc_final: 0.5884 (mm-30) REVERT: S 314 GLN cc_start: 0.6805 (OUTLIER) cc_final: 0.6158 (tt0) REVERT: S 329 SER cc_start: 0.6914 (m) cc_final: 0.6102 (p) REVERT: S 403 GLU cc_start: 0.5745 (tp30) cc_final: 0.5520 (tp30) REVERT: S 407 LYS cc_start: 0.6061 (mmtm) cc_final: 0.5437 (mtpt) REVERT: S 411 GLU cc_start: 0.5328 (pt0) cc_final: 0.4907 (mm-30) REVERT: S 415 GLU cc_start: 0.5219 (mt-10) cc_final: 0.4456 (tm-30) REVERT: T 11 LYS cc_start: 0.4790 (ttpp) cc_final: 0.4420 (ttpp) REVERT: T 15 GLU cc_start: 0.4447 (OUTLIER) cc_final: 0.4133 (mm-30) REVERT: T 49 LYS cc_start: 0.5847 (mmtt) cc_final: 0.5399 (mmmt) REVERT: T 117 LYS cc_start: 0.6014 (tptm) cc_final: 0.5701 (tptm) REVERT: T 153 LYS cc_start: 0.6016 (mttm) cc_final: 0.4899 (mmmt) REVERT: T 189 GLU cc_start: 0.6336 (OUTLIER) cc_final: 0.5704 (tp30) REVERT: T 200 LYS cc_start: 0.5879 (ttmm) cc_final: 0.5056 (tptp) REVERT: T 223 ARG cc_start: 0.5004 (ttm-80) cc_final: 0.4617 (tpt170) REVERT: T 269 GLU cc_start: 0.5395 (mm-30) cc_final: 0.4551 (pm20) REVERT: T 314 GLN cc_start: 0.6884 (OUTLIER) cc_final: 0.6616 (tt0) REVERT: T 329 SER cc_start: 0.6982 (m) cc_final: 0.6175 (p) REVERT: T 363 GLU cc_start: 0.6010 (tp30) cc_final: 0.5527 (tt0) REVERT: T 403 GLU cc_start: 0.5805 (mm-30) cc_final: 0.4975 (pm20) REVERT: T 411 GLU cc_start: 0.5366 (pt0) cc_final: 0.4554 (mm-30) REVERT: T 415 GLU cc_start: 0.5254 (mt-10) cc_final: 0.4455 (mm-30) REVERT: T 441 MET cc_start: 0.6717 (tpp) cc_final: 0.6242 (tpp) outliers start: 118 outliers final: 45 residues processed: 906 average time/residue: 1.5943 time to fit residues: 1752.2896 Evaluate side-chains 911 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 833 time to evaluate : 4.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain E residue 7 MET Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 206 ARG Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 261 GLU Chi-restraints excluded: chain G residue 314 GLN Chi-restraints excluded: chain G residue 409 LEU Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 167 ASN Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain L residue 7 MET Chi-restraints excluded: chain N residue 10 GLU Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 224 LYS Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 206 ARG Chi-restraints excluded: chain O residue 239 VAL Chi-restraints excluded: chain O residue 314 GLN Chi-restraints excluded: chain O residue 409 LEU Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 153 LYS Chi-restraints excluded: chain P residue 239 VAL Chi-restraints excluded: chain Q residue 83 THR Chi-restraints excluded: chain Q residue 122 LEU Chi-restraints excluded: chain Q residue 239 VAL Chi-restraints excluded: chain Q residue 407 LYS Chi-restraints excluded: chain Q residue 409 LEU Chi-restraints excluded: chain R residue 15 GLU Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 314 GLN Chi-restraints excluded: chain R residue 409 LEU Chi-restraints excluded: chain S residue 10 GLU Chi-restraints excluded: chain S residue 83 THR Chi-restraints excluded: chain S residue 102 THR Chi-restraints excluded: chain S residue 239 VAL Chi-restraints excluded: chain S residue 261 GLU Chi-restraints excluded: chain S residue 314 GLN Chi-restraints excluded: chain S residue 409 LEU Chi-restraints excluded: chain T residue 15 GLU Chi-restraints excluded: chain T residue 114 ARG Chi-restraints excluded: chain T residue 189 GLU Chi-restraints excluded: chain T residue 224 LYS Chi-restraints excluded: chain T residue 314 GLN Chi-restraints excluded: chain T residue 409 LEU Chi-restraints excluded: chain U residue 7 MET Chi-restraints excluded: chain W residue 7 MET Chi-restraints excluded: chain Y residue 7 MET Chi-restraints excluded: chain Z residue 7 MET Chi-restraints excluded: chain a residue 7 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 375 optimal weight: 10.0000 chunk 242 optimal weight: 5.9990 chunk 362 optimal weight: 0.9990 chunk 182 optimal weight: 0.5980 chunk 119 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 386 optimal weight: 4.9990 chunk 413 optimal weight: 9.9990 chunk 300 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 477 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN A 315 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN C 34 ASN C 75 ASN C 167 ASN F 24 GLN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN F 167 ASN F 443 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN G 167 ASN G 439 GLN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 ASN H 443 GLN I 34 ASN I 167 ASN I 266 GLN N 24 GLN N 34 ASN N 75 ASN N 167 ASN ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 ASN O 167 ASN P 34 ASN P 443 GLN Q 34 ASN Q 266 GLN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 167 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 ASN S 266 GLN T 34 ASN T 75 ASN T 167 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5959 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 51450 Z= 0.173 Angle : 0.505 5.400 69650 Z= 0.277 Chirality : 0.042 0.147 7546 Planarity : 0.004 0.076 9184 Dihedral : 5.327 53.533 6852 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.02 % Allowed : 16.55 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.10), residues: 6286 helix: 1.92 (0.10), residues: 2324 sheet: -0.53 (0.16), residues: 952 loop : -0.30 (0.11), residues: 3010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP O 425 HIS 0.006 0.001 HIS N 416 PHE 0.019 0.002 PHE Q 285 TYR 0.034 0.002 TYR B 296 ARG 0.005 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 947 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 839 time to evaluate : 4.472 Fit side-chains revert: symmetry clash REVERT: A 3 LYS cc_start: 0.7163 (ttmt) cc_final: 0.6886 (ttmm) REVERT: A 5 THR cc_start: 0.5809 (OUTLIER) cc_final: 0.5313 (t) REVERT: A 11 LYS cc_start: 0.4991 (tttp) cc_final: 0.4727 (ttpp) REVERT: A 32 ILE cc_start: 0.5760 (mp) cc_final: 0.5439 (mp) REVERT: A 49 LYS cc_start: 0.5800 (mmtt) cc_final: 0.5205 (mmmt) REVERT: A 102 THR cc_start: 0.6228 (m) cc_final: 0.5871 (p) REVERT: A 117 LYS cc_start: 0.5846 (tptm) cc_final: 0.5535 (tptm) REVERT: A 148 LEU cc_start: 0.6502 (mt) cc_final: 0.6295 (mt) REVERT: A 182 GLU cc_start: 0.5895 (mt-10) cc_final: 0.5650 (mt-10) REVERT: A 200 LYS cc_start: 0.5971 (ttmm) cc_final: 0.4854 (tptt) REVERT: A 314 GLN cc_start: 0.6742 (OUTLIER) cc_final: 0.6238 (tt0) REVERT: A 329 SER cc_start: 0.6818 (m) cc_final: 0.6210 (p) REVERT: A 363 GLU cc_start: 0.6107 (tp30) cc_final: 0.5731 (tt0) REVERT: A 369 ASP cc_start: 0.5458 (OUTLIER) cc_final: 0.4794 (m-30) REVERT: A 403 GLU cc_start: 0.5827 (OUTLIER) cc_final: 0.5195 (tp30) REVERT: A 407 LYS cc_start: 0.5769 (mmtm) cc_final: 0.5253 (mtpt) REVERT: A 411 GLU cc_start: 0.5415 (pt0) cc_final: 0.4790 (mm-30) REVERT: A 438 GLU cc_start: 0.5201 (mt-10) cc_final: 0.4932 (mt-10) REVERT: A 441 MET cc_start: 0.6843 (tpp) cc_final: 0.6618 (tpp) REVERT: B 3 LYS cc_start: 0.6684 (tttt) cc_final: 0.6395 (ttmt) REVERT: B 10 GLU cc_start: 0.6005 (OUTLIER) cc_final: 0.5431 (mt-10) REVERT: B 32 ILE cc_start: 0.5747 (mt) cc_final: 0.5412 (mm) REVERT: B 49 LYS cc_start: 0.5855 (mmtt) cc_final: 0.5340 (mmmt) REVERT: B 102 THR cc_start: 0.6312 (OUTLIER) cc_final: 0.5890 (p) REVERT: B 105 GLU cc_start: 0.6094 (pm20) cc_final: 0.5490 (mp0) REVERT: B 117 LYS cc_start: 0.5607 (tptp) cc_final: 0.5348 (tptm) REVERT: B 182 GLU cc_start: 0.6049 (mt-10) cc_final: 0.5680 (mt-10) REVERT: B 189 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.5913 (tp30) REVERT: B 200 LYS cc_start: 0.5778 (mtpp) cc_final: 0.4824 (tptt) REVERT: B 206 ARG cc_start: 0.5144 (OUTLIER) cc_final: 0.4095 (tpt-90) REVERT: B 224 LYS cc_start: 0.5649 (ttmm) cc_final: 0.5364 (mtmt) REVERT: B 261 GLU cc_start: 0.6120 (OUTLIER) cc_final: 0.5849 (mm-30) REVERT: B 314 GLN cc_start: 0.6886 (OUTLIER) cc_final: 0.6245 (tt0) REVERT: B 329 SER cc_start: 0.6918 (m) cc_final: 0.6105 (p) REVERT: B 385 ILE cc_start: 0.6263 (OUTLIER) cc_final: 0.6009 (mm) REVERT: B 407 LYS cc_start: 0.6160 (mmtm) cc_final: 0.5486 (mtpt) REVERT: B 411 GLU cc_start: 0.5303 (pt0) cc_final: 0.4909 (mm-30) REVERT: B 415 GLU cc_start: 0.5209 (mt-10) cc_final: 0.4444 (tm-30) REVERT: B 441 MET cc_start: 0.6793 (tpp) cc_final: 0.6545 (tpp) REVERT: C 11 LYS cc_start: 0.4695 (tttm) cc_final: 0.4405 (ttpp) REVERT: C 15 GLU cc_start: 0.4321 (OUTLIER) cc_final: 0.3856 (mm-30) REVERT: C 49 LYS cc_start: 0.5834 (mmtt) cc_final: 0.5383 (mmmt) REVERT: C 102 THR cc_start: 0.6263 (m) cc_final: 0.5844 (p) REVERT: C 117 LYS cc_start: 0.5936 (tptm) cc_final: 0.5608 (tptm) REVERT: C 153 LYS cc_start: 0.6026 (mttm) cc_final: 0.4942 (mmmt) REVERT: C 200 LYS cc_start: 0.5793 (mtpp) cc_final: 0.5072 (tptt) REVERT: C 223 ARG cc_start: 0.5020 (ttm-80) cc_final: 0.4653 (tpt170) REVERT: C 269 GLU cc_start: 0.5204 (mm-30) cc_final: 0.4390 (pm20) REVERT: C 314 GLN cc_start: 0.6882 (OUTLIER) cc_final: 0.6615 (tt0) REVERT: C 329 SER cc_start: 0.6999 (m) cc_final: 0.6192 (p) REVERT: C 363 GLU cc_start: 0.6017 (tp30) cc_final: 0.5517 (tt0) REVERT: C 403 GLU cc_start: 0.5630 (tp30) cc_final: 0.4996 (pm20) REVERT: C 411 GLU cc_start: 0.5334 (pt0) cc_final: 0.4513 (mm-30) REVERT: C 415 GLU cc_start: 0.5226 (mt-10) cc_final: 0.4420 (mm-30) REVERT: C 441 MET cc_start: 0.6722 (tpp) cc_final: 0.6279 (tpp) REVERT: F 10 GLU cc_start: 0.5753 (OUTLIER) cc_final: 0.5293 (mt-10) REVERT: F 49 LYS cc_start: 0.5740 (mmtt) cc_final: 0.5277 (mmmt) REVERT: F 102 THR cc_start: 0.6247 (m) cc_final: 0.5770 (p) REVERT: F 148 LEU cc_start: 0.6425 (mt) cc_final: 0.6142 (mp) REVERT: F 153 LYS cc_start: 0.5909 (mttm) cc_final: 0.4831 (mmmt) REVERT: F 182 GLU cc_start: 0.5892 (mt-10) cc_final: 0.5495 (mt-10) REVERT: F 200 LYS cc_start: 0.5628 (mtpp) cc_final: 0.4670 (tptt) REVERT: F 206 ARG cc_start: 0.4903 (ttp80) cc_final: 0.4539 (tpt-90) REVERT: F 224 LYS cc_start: 0.5369 (OUTLIER) cc_final: 0.5057 (mtpp) REVERT: F 269 GLU cc_start: 0.5305 (mm-30) cc_final: 0.4537 (pm20) REVERT: F 280 LYS cc_start: 0.6203 (tttt) cc_final: 0.5922 (tttm) REVERT: F 329 SER cc_start: 0.6863 (m) cc_final: 0.6205 (p) REVERT: F 363 GLU cc_start: 0.5941 (tp30) cc_final: 0.5434 (tt0) REVERT: F 411 GLU cc_start: 0.5393 (pt0) cc_final: 0.4659 (mm-30) REVERT: F 415 GLU cc_start: 0.5480 (mt-10) cc_final: 0.4671 (mm-30) REVERT: F 441 MET cc_start: 0.6675 (tpp) cc_final: 0.6401 (tpp) REVERT: G 49 LYS cc_start: 0.5684 (mmtt) cc_final: 0.5133 (mmmt) REVERT: G 102 THR cc_start: 0.6315 (m) cc_final: 0.5903 (p) REVERT: G 200 LYS cc_start: 0.6040 (ttmm) cc_final: 0.5078 (tptt) REVERT: G 206 ARG cc_start: 0.5108 (OUTLIER) cc_final: 0.4694 (tpt-90) REVERT: G 223 ARG cc_start: 0.5345 (ttm-80) cc_final: 0.4993 (tpt170) REVERT: G 261 GLU cc_start: 0.6221 (OUTLIER) cc_final: 0.5864 (mm-30) REVERT: G 314 GLN cc_start: 0.6859 (OUTLIER) cc_final: 0.6325 (tt0) REVERT: G 329 SER cc_start: 0.7029 (m) cc_final: 0.6332 (p) REVERT: G 403 GLU cc_start: 0.5612 (mm-30) cc_final: 0.5024 (pm20) REVERT: G 411 GLU cc_start: 0.5520 (pt0) cc_final: 0.4931 (mm-30) REVERT: G 415 GLU cc_start: 0.5173 (mt-10) cc_final: 0.4266 (tm-30) REVERT: H 27 ASP cc_start: 0.5526 (p0) cc_final: 0.5245 (p0) REVERT: H 32 ILE cc_start: 0.5795 (mt) cc_final: 0.5481 (mm) REVERT: H 49 LYS cc_start: 0.5747 (mmtt) cc_final: 0.5235 (mmmt) REVERT: H 102 THR cc_start: 0.6457 (m) cc_final: 0.6008 (p) REVERT: H 105 GLU cc_start: 0.5840 (pm20) cc_final: 0.5429 (mp0) REVERT: H 117 LYS cc_start: 0.5938 (tptm) cc_final: 0.5703 (tptm) REVERT: H 153 LYS cc_start: 0.5848 (ptpt) cc_final: 0.4829 (mmmt) REVERT: H 200 LYS cc_start: 0.5908 (mtpm) cc_final: 0.4900 (tptt) REVERT: H 206 ARG cc_start: 0.5113 (ttt90) cc_final: 0.4705 (tpt-90) REVERT: H 223 ARG cc_start: 0.5292 (ttm-80) cc_final: 0.4971 (tpt-90) REVERT: H 329 SER cc_start: 0.7066 (m) cc_final: 0.6227 (p) REVERT: H 411 GLU cc_start: 0.5445 (pt0) cc_final: 0.4974 (mm-30) REVERT: H 415 GLU cc_start: 0.5107 (mt-10) cc_final: 0.4267 (tm-30) REVERT: H 441 MET cc_start: 0.6778 (tpp) cc_final: 0.6263 (tpp) REVERT: I 10 GLU cc_start: 0.5728 (mt-10) cc_final: 0.5468 (mt-10) REVERT: I 49 LYS cc_start: 0.5670 (mmtt) cc_final: 0.5191 (mmmt) REVERT: I 182 GLU cc_start: 0.6112 (mt-10) cc_final: 0.5606 (mt-10) REVERT: I 200 LYS cc_start: 0.5956 (ttmm) cc_final: 0.4920 (tppt) REVERT: I 206 ARG cc_start: 0.4968 (ttp80) cc_final: 0.4493 (tpt-90) REVERT: I 255 VAL cc_start: 0.6036 (m) cc_final: 0.5781 (p) REVERT: I 280 LYS cc_start: 0.6131 (tttt) cc_final: 0.5896 (tttm) REVERT: I 314 GLN cc_start: 0.6943 (tp40) cc_final: 0.6530 (tt0) REVERT: I 329 SER cc_start: 0.7068 (m) cc_final: 0.6212 (p) REVERT: I 363 GLU cc_start: 0.6066 (tp30) cc_final: 0.5441 (tt0) REVERT: I 411 GLU cc_start: 0.5286 (pt0) cc_final: 0.4991 (mm-30) REVERT: I 415 GLU cc_start: 0.4947 (mt-10) cc_final: 0.4125 (tm-30) REVERT: I 441 MET cc_start: 0.6740 (tpp) cc_final: 0.6333 (tpp) REVERT: N 10 GLU cc_start: 0.5772 (OUTLIER) cc_final: 0.5311 (mt-10) REVERT: N 49 LYS cc_start: 0.5789 (mmtt) cc_final: 0.5309 (mmmt) REVERT: N 102 THR cc_start: 0.6241 (m) cc_final: 0.5767 (p) REVERT: N 148 LEU cc_start: 0.6409 (mt) cc_final: 0.6126 (mp) REVERT: N 153 LYS cc_start: 0.5926 (mttm) cc_final: 0.4963 (mmmt) REVERT: N 182 GLU cc_start: 0.5888 (mt-10) cc_final: 0.5490 (mt-10) REVERT: N 200 LYS cc_start: 0.5626 (mtpp) cc_final: 0.4670 (tptt) REVERT: N 206 ARG cc_start: 0.4903 (ttp80) cc_final: 0.4539 (tpt-90) REVERT: N 224 LYS cc_start: 0.5365 (OUTLIER) cc_final: 0.5052 (mtpp) REVERT: N 269 GLU cc_start: 0.5303 (mm-30) cc_final: 0.4535 (pm20) REVERT: N 280 LYS cc_start: 0.6203 (tttt) cc_final: 0.5924 (tttm) REVERT: N 329 SER cc_start: 0.6859 (m) cc_final: 0.6196 (p) REVERT: N 363 GLU cc_start: 0.5956 (tp30) cc_final: 0.5447 (tt0) REVERT: N 403 GLU cc_start: 0.5873 (tp30) cc_final: 0.4995 (mp0) REVERT: N 411 GLU cc_start: 0.5374 (pt0) cc_final: 0.4723 (mm-30) REVERT: N 441 MET cc_start: 0.6655 (tpp) cc_final: 0.6370 (tpp) REVERT: O 49 LYS cc_start: 0.5697 (mmtt) cc_final: 0.5155 (mmmt) REVERT: O 102 THR cc_start: 0.6313 (m) cc_final: 0.5901 (p) REVERT: O 200 LYS cc_start: 0.6051 (ttmm) cc_final: 0.5094 (tptt) REVERT: O 206 ARG cc_start: 0.5123 (ttt90) cc_final: 0.4707 (tpt-90) REVERT: O 223 ARG cc_start: 0.5350 (ttm-80) cc_final: 0.5000 (tpt170) REVERT: O 314 GLN cc_start: 0.6858 (OUTLIER) cc_final: 0.6330 (tt0) REVERT: O 329 SER cc_start: 0.7013 (m) cc_final: 0.6312 (p) REVERT: O 411 GLU cc_start: 0.5542 (pt0) cc_final: 0.4950 (mm-30) REVERT: O 415 GLU cc_start: 0.5211 (mt-10) cc_final: 0.4312 (tm-30) REVERT: P 10 GLU cc_start: 0.5927 (OUTLIER) cc_final: 0.5363 (mt-10) REVERT: P 27 ASP cc_start: 0.5521 (p0) cc_final: 0.5232 (p0) REVERT: P 32 ILE cc_start: 0.5785 (mt) cc_final: 0.5470 (mm) REVERT: P 49 LYS cc_start: 0.5750 (mmtt) cc_final: 0.5237 (mmmt) REVERT: P 102 THR cc_start: 0.6436 (m) cc_final: 0.5982 (p) REVERT: P 105 GLU cc_start: 0.5831 (pm20) cc_final: 0.5477 (mp0) REVERT: P 153 LYS cc_start: 0.5795 (OUTLIER) cc_final: 0.4725 (mmmt) REVERT: P 200 LYS cc_start: 0.5828 (mtpp) cc_final: 0.4979 (tptt) REVERT: P 206 ARG cc_start: 0.5109 (ttt90) cc_final: 0.4699 (tpt-90) REVERT: P 223 ARG cc_start: 0.5290 (ttm-80) cc_final: 0.4968 (tpt-90) REVERT: P 329 SER cc_start: 0.7134 (m) cc_final: 0.6271 (p) REVERT: P 411 GLU cc_start: 0.5445 (pt0) cc_final: 0.4978 (mm-30) REVERT: P 415 GLU cc_start: 0.5161 (mt-10) cc_final: 0.4309 (tm-30) REVERT: P 441 MET cc_start: 0.6774 (tpp) cc_final: 0.6255 (tpp) REVERT: Q 10 GLU cc_start: 0.6045 (mt-10) cc_final: 0.5611 (mt-10) REVERT: Q 27 ASP cc_start: 0.5485 (p0) cc_final: 0.5237 (p0) REVERT: Q 49 LYS cc_start: 0.5684 (mmtt) cc_final: 0.5206 (mmmt) REVERT: Q 102 THR cc_start: 0.6637 (m) cc_final: 0.6259 (p) REVERT: Q 153 LYS cc_start: 0.5925 (mttm) cc_final: 0.4907 (mmmt) REVERT: Q 182 GLU cc_start: 0.6121 (mt-10) cc_final: 0.5615 (mt-10) REVERT: Q 200 LYS cc_start: 0.5959 (ttmm) cc_final: 0.4925 (tppt) REVERT: Q 206 ARG cc_start: 0.4982 (ttp80) cc_final: 0.4505 (tpt-90) REVERT: Q 255 VAL cc_start: 0.6029 (m) cc_final: 0.5776 (p) REVERT: Q 280 LYS cc_start: 0.6148 (tttt) cc_final: 0.5913 (tttm) REVERT: Q 314 GLN cc_start: 0.6913 (tp40) cc_final: 0.6498 (tt0) REVERT: Q 329 SER cc_start: 0.7069 (m) cc_final: 0.6213 (p) REVERT: Q 363 GLU cc_start: 0.6068 (tp30) cc_final: 0.5529 (tt0) REVERT: Q 407 LYS cc_start: 0.5429 (mttm) cc_final: 0.4882 (mtpt) REVERT: Q 411 GLU cc_start: 0.5317 (pt0) cc_final: 0.5024 (mm-30) REVERT: Q 415 GLU cc_start: 0.4946 (mt-10) cc_final: 0.4122 (tm-30) REVERT: Q 441 MET cc_start: 0.6734 (tpp) cc_final: 0.6323 (tpp) REVERT: R 11 LYS cc_start: 0.4620 (tttp) cc_final: 0.4341 (ttpp) REVERT: R 15 GLU cc_start: 0.4190 (OUTLIER) cc_final: 0.3796 (mm-30) REVERT: R 49 LYS cc_start: 0.5815 (mmtt) cc_final: 0.5217 (mmmt) REVERT: R 102 THR cc_start: 0.6238 (m) cc_final: 0.5865 (p) REVERT: R 117 LYS cc_start: 0.5859 (tptm) cc_final: 0.5531 (tptm) REVERT: R 148 LEU cc_start: 0.6505 (mt) cc_final: 0.6285 (mt) REVERT: R 182 GLU cc_start: 0.5904 (mt-10) cc_final: 0.5667 (mt-10) REVERT: R 200 LYS cc_start: 0.5975 (ttmm) cc_final: 0.4849 (tptt) REVERT: R 314 GLN cc_start: 0.6768 (OUTLIER) cc_final: 0.6307 (tt0) REVERT: R 329 SER cc_start: 0.6803 (m) cc_final: 0.6194 (p) REVERT: R 403 GLU cc_start: 0.5848 (tp30) cc_final: 0.5400 (mp0) REVERT: R 407 LYS cc_start: 0.5924 (mmtm) cc_final: 0.5350 (mtpt) REVERT: R 409 LEU cc_start: 0.5533 (OUTLIER) cc_final: 0.5242 (pp) REVERT: R 411 GLU cc_start: 0.5735 (mm-30) cc_final: 0.5080 (tt0) REVERT: S 3 LYS cc_start: 0.6658 (tttt) cc_final: 0.6371 (ttmt) REVERT: S 10 GLU cc_start: 0.5935 (OUTLIER) cc_final: 0.5539 (mt-10) REVERT: S 11 LYS cc_start: 0.4996 (tttp) cc_final: 0.4637 (ttpp) REVERT: S 49 LYS cc_start: 0.5787 (mmtt) cc_final: 0.5265 (mmmt) REVERT: S 102 THR cc_start: 0.6324 (OUTLIER) cc_final: 0.5904 (p) REVERT: S 105 GLU cc_start: 0.6089 (pm20) cc_final: 0.5476 (mp0) REVERT: S 153 LYS cc_start: 0.5627 (mmpt) cc_final: 0.5377 (mmmt) REVERT: S 200 LYS cc_start: 0.5768 (mtpp) cc_final: 0.4784 (tptt) REVERT: S 206 ARG cc_start: 0.5103 (OUTLIER) cc_final: 0.4070 (tpt-90) REVERT: S 223 ARG cc_start: 0.5099 (ttm-80) cc_final: 0.4816 (ttt90) REVERT: S 261 GLU cc_start: 0.6122 (OUTLIER) cc_final: 0.5855 (mm-30) REVERT: S 314 GLN cc_start: 0.6876 (OUTLIER) cc_final: 0.6234 (tt0) REVERT: S 329 SER cc_start: 0.6919 (m) cc_final: 0.6107 (p) REVERT: S 407 LYS cc_start: 0.6043 (mmtm) cc_final: 0.5430 (mtpt) REVERT: S 411 GLU cc_start: 0.5313 (pt0) cc_final: 0.4921 (mm-30) REVERT: S 415 GLU cc_start: 0.5222 (mt-10) cc_final: 0.4458 (tm-30) REVERT: T 11 LYS cc_start: 0.4783 (ttpp) cc_final: 0.4404 (ttpp) REVERT: T 15 GLU cc_start: 0.4499 (OUTLIER) cc_final: 0.4134 (mm-30) REVERT: T 49 LYS cc_start: 0.5846 (mmtt) cc_final: 0.5395 (mmmt) REVERT: T 117 LYS cc_start: 0.5996 (tptm) cc_final: 0.5686 (tptm) REVERT: T 153 LYS cc_start: 0.6006 (mttm) cc_final: 0.4910 (mmmt) REVERT: T 189 GLU cc_start: 0.6241 (OUTLIER) cc_final: 0.5654 (tp30) REVERT: T 200 LYS cc_start: 0.5933 (ttmm) cc_final: 0.5127 (tptp) REVERT: T 223 ARG cc_start: 0.5011 (ttm-80) cc_final: 0.4619 (tpt170) REVERT: T 269 GLU cc_start: 0.5291 (mm-30) cc_final: 0.4457 (pm20) REVERT: T 314 GLN cc_start: 0.6883 (tt0) cc_final: 0.6614 (tt0) REVERT: T 329 SER cc_start: 0.6993 (m) cc_final: 0.6188 (p) REVERT: T 363 GLU cc_start: 0.6024 (tp30) cc_final: 0.5529 (tt0) REVERT: T 403 GLU cc_start: 0.5476 (mm-30) cc_final: 0.4674 (pm20) REVERT: T 411 GLU cc_start: 0.5386 (pt0) cc_final: 0.4548 (mm-30) REVERT: T 415 GLU cc_start: 0.5228 (mt-10) cc_final: 0.4425 (mm-30) REVERT: T 441 MET cc_start: 0.6712 (tpp) cc_final: 0.6267 (tpp) outliers start: 108 outliers final: 42 residues processed: 898 average time/residue: 1.5795 time to fit residues: 1727.1044 Evaluate side-chains 914 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 839 time to evaluate : 4.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain E residue 7 MET Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 206 ARG Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 261 GLU Chi-restraints excluded: chain G residue 314 GLN Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain L residue 7 MET Chi-restraints excluded: chain N residue 10 GLU Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 224 LYS Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 239 VAL Chi-restraints excluded: chain O residue 314 GLN Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 153 LYS Chi-restraints excluded: chain P residue 239 VAL Chi-restraints excluded: chain Q residue 83 THR Chi-restraints excluded: chain Q residue 122 LEU Chi-restraints excluded: chain Q residue 239 VAL Chi-restraints excluded: chain R residue 15 GLU Chi-restraints excluded: chain R residue 114 ARG Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 314 GLN Chi-restraints excluded: chain R residue 409 LEU Chi-restraints excluded: chain S residue 10 GLU Chi-restraints excluded: chain S residue 102 THR Chi-restraints excluded: chain S residue 206 ARG Chi-restraints excluded: chain S residue 239 VAL Chi-restraints excluded: chain S residue 261 GLU Chi-restraints excluded: chain S residue 314 GLN Chi-restraints excluded: chain S residue 409 LEU Chi-restraints excluded: chain T residue 15 GLU Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 189 GLU Chi-restraints excluded: chain T residue 224 LYS Chi-restraints excluded: chain T residue 409 LEU Chi-restraints excluded: chain U residue 7 MET Chi-restraints excluded: chain V residue 7 MET Chi-restraints excluded: chain W residue 7 MET Chi-restraints excluded: chain Y residue 7 MET Chi-restraints excluded: chain Z residue 7 MET Chi-restraints excluded: chain a residue 7 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 552 optimal weight: 0.5980 chunk 581 optimal weight: 9.9990 chunk 530 optimal weight: 3.9990 chunk 565 optimal weight: 0.0050 chunk 340 optimal weight: 5.9990 chunk 246 optimal weight: 10.0000 chunk 444 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 511 optimal weight: 1.9990 chunk 535 optimal weight: 5.9990 chunk 563 optimal weight: 0.0020 overall best weight: 1.1206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN A 315 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN C 34 ASN C 75 ASN C 167 ASN F 24 GLN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN F 167 ASN F 443 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN G 167 ASN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 ASN H 443 GLN I 34 ASN I 266 GLN N 24 GLN N 34 ASN N 75 ASN N 167 ASN O 17 ASN ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 ASN O 167 ASN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 167 ASN P 443 GLN Q 34 ASN Q 266 GLN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 167 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 ASN S 266 GLN T 34 ASN T 75 ASN T 167 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5950 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 51450 Z= 0.138 Angle : 0.460 4.894 69650 Z= 0.252 Chirality : 0.041 0.139 7546 Planarity : 0.004 0.063 9184 Dihedral : 5.076 51.457 6852 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.71 % Allowed : 16.74 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.10), residues: 6286 helix: 2.11 (0.10), residues: 2324 sheet: -0.45 (0.16), residues: 952 loop : -0.21 (0.11), residues: 3010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 425 HIS 0.004 0.001 HIS N 416 PHE 0.017 0.001 PHE N 285 TYR 0.029 0.002 TYR I 296 ARG 0.008 0.000 ARG G 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 841 time to evaluate : 4.423 Fit side-chains revert: symmetry clash REVERT: A 3 LYS cc_start: 0.7165 (ttmt) cc_final: 0.6890 (ttmm) REVERT: A 5 THR cc_start: 0.5801 (OUTLIER) cc_final: 0.5307 (t) REVERT: A 11 LYS cc_start: 0.4980 (tttp) cc_final: 0.4730 (ttpp) REVERT: A 49 LYS cc_start: 0.5817 (mmtt) cc_final: 0.5219 (mmmt) REVERT: A 102 THR cc_start: 0.6200 (m) cc_final: 0.5849 (p) REVERT: A 117 LYS cc_start: 0.5847 (tptm) cc_final: 0.5505 (tptm) REVERT: A 148 LEU cc_start: 0.6492 (mt) cc_final: 0.6282 (mt) REVERT: A 182 GLU cc_start: 0.5957 (mt-10) cc_final: 0.5693 (mt-10) REVERT: A 200 LYS cc_start: 0.5988 (ttmm) cc_final: 0.4890 (tptt) REVERT: A 314 GLN cc_start: 0.6762 (OUTLIER) cc_final: 0.6262 (tt0) REVERT: A 329 SER cc_start: 0.6894 (m) cc_final: 0.6195 (p) REVERT: A 363 GLU cc_start: 0.6106 (tp30) cc_final: 0.5728 (tt0) REVERT: A 369 ASP cc_start: 0.5389 (OUTLIER) cc_final: 0.4720 (m-30) REVERT: A 403 GLU cc_start: 0.5813 (OUTLIER) cc_final: 0.5183 (tp30) REVERT: A 407 LYS cc_start: 0.5766 (mmtm) cc_final: 0.5252 (mtpt) REVERT: A 411 GLU cc_start: 0.5330 (pt0) cc_final: 0.4692 (mm-30) REVERT: A 438 GLU cc_start: 0.5235 (mt-10) cc_final: 0.4971 (mt-10) REVERT: A 441 MET cc_start: 0.6825 (tpp) cc_final: 0.6603 (tpp) REVERT: B 3 LYS cc_start: 0.6679 (tttt) cc_final: 0.6404 (ttmt) REVERT: B 10 GLU cc_start: 0.6024 (OUTLIER) cc_final: 0.5454 (mt-10) REVERT: B 49 LYS cc_start: 0.5854 (mmtt) cc_final: 0.5337 (mmmt) REVERT: B 102 THR cc_start: 0.6259 (OUTLIER) cc_final: 0.5944 (p) REVERT: B 105 GLU cc_start: 0.6140 (pm20) cc_final: 0.5646 (mp0) REVERT: B 117 LYS cc_start: 0.5622 (tptp) cc_final: 0.5407 (tptm) REVERT: B 167 ASN cc_start: 0.5364 (OUTLIER) cc_final: 0.4204 (m-40) REVERT: B 182 GLU cc_start: 0.6048 (mt-10) cc_final: 0.5708 (mt-10) REVERT: B 200 LYS cc_start: 0.5775 (mtpp) cc_final: 0.4793 (tptt) REVERT: B 224 LYS cc_start: 0.5684 (ttmm) cc_final: 0.5391 (mtmt) REVERT: B 261 GLU cc_start: 0.6138 (OUTLIER) cc_final: 0.5853 (mm-30) REVERT: B 314 GLN cc_start: 0.6878 (OUTLIER) cc_final: 0.6255 (tt0) REVERT: B 329 SER cc_start: 0.6893 (m) cc_final: 0.6085 (p) REVERT: B 407 LYS cc_start: 0.6166 (mmtm) cc_final: 0.5512 (mtpt) REVERT: B 411 GLU cc_start: 0.5364 (pt0) cc_final: 0.4996 (mm-30) REVERT: B 415 GLU cc_start: 0.5201 (mt-10) cc_final: 0.4428 (tm-30) REVERT: B 441 MET cc_start: 0.6761 (tpp) cc_final: 0.6559 (tpp) REVERT: C 11 LYS cc_start: 0.4709 (tttm) cc_final: 0.4417 (ttpp) REVERT: C 15 GLU cc_start: 0.4329 (OUTLIER) cc_final: 0.3842 (mm-30) REVERT: C 49 LYS cc_start: 0.5847 (mmtt) cc_final: 0.5382 (mmmt) REVERT: C 102 THR cc_start: 0.6233 (m) cc_final: 0.5831 (p) REVERT: C 117 LYS cc_start: 0.5907 (tptm) cc_final: 0.5575 (tptm) REVERT: C 153 LYS cc_start: 0.6006 (mttm) cc_final: 0.4919 (mmmt) REVERT: C 200 LYS cc_start: 0.5806 (mtpp) cc_final: 0.5086 (tptt) REVERT: C 223 ARG cc_start: 0.5158 (ttm-80) cc_final: 0.4796 (tpt170) REVERT: C 269 GLU cc_start: 0.5200 (mm-30) cc_final: 0.4395 (pm20) REVERT: C 314 GLN cc_start: 0.6832 (OUTLIER) cc_final: 0.6578 (tt0) REVERT: C 329 SER cc_start: 0.6928 (m) cc_final: 0.6190 (p) REVERT: C 363 GLU cc_start: 0.6022 (tp30) cc_final: 0.5522 (tt0) REVERT: C 403 GLU cc_start: 0.5501 (tp30) cc_final: 0.5007 (pm20) REVERT: C 411 GLU cc_start: 0.5356 (pt0) cc_final: 0.4523 (mm-30) REVERT: C 415 GLU cc_start: 0.5220 (mt-10) cc_final: 0.4415 (mm-30) REVERT: C 441 MET cc_start: 0.6701 (tpp) cc_final: 0.6263 (tpp) REVERT: F 5 THR cc_start: 0.5535 (p) cc_final: 0.5052 (t) REVERT: F 10 GLU cc_start: 0.5753 (OUTLIER) cc_final: 0.5300 (mt-10) REVERT: F 49 LYS cc_start: 0.5741 (mmtt) cc_final: 0.5281 (mmmt) REVERT: F 102 THR cc_start: 0.6236 (m) cc_final: 0.5790 (p) REVERT: F 148 LEU cc_start: 0.6438 (mt) cc_final: 0.6154 (mp) REVERT: F 153 LYS cc_start: 0.5904 (mttm) cc_final: 0.4833 (mmmt) REVERT: F 182 GLU cc_start: 0.5911 (mt-10) cc_final: 0.5533 (mt-10) REVERT: F 200 LYS cc_start: 0.5667 (mtpp) cc_final: 0.4700 (tptt) REVERT: F 206 ARG cc_start: 0.4820 (ttp80) cc_final: 0.4459 (tpt-90) REVERT: F 224 LYS cc_start: 0.5359 (OUTLIER) cc_final: 0.5034 (mtpp) REVERT: F 269 GLU cc_start: 0.5313 (mm-30) cc_final: 0.4585 (pm20) REVERT: F 280 LYS cc_start: 0.6168 (tttt) cc_final: 0.5940 (tttm) REVERT: F 329 SER cc_start: 0.6858 (m) cc_final: 0.6191 (p) REVERT: F 363 GLU cc_start: 0.5936 (tp30) cc_final: 0.5435 (tt0) REVERT: F 411 GLU cc_start: 0.5371 (pt0) cc_final: 0.4625 (mm-30) REVERT: F 415 GLU cc_start: 0.5440 (mt-10) cc_final: 0.4619 (mm-30) REVERT: F 441 MET cc_start: 0.6655 (tpp) cc_final: 0.6378 (tpp) REVERT: G 49 LYS cc_start: 0.5687 (mmtt) cc_final: 0.5192 (mmmt) REVERT: G 102 THR cc_start: 0.6360 (m) cc_final: 0.5958 (p) REVERT: G 206 ARG cc_start: 0.5106 (ttt90) cc_final: 0.4691 (tpt-90) REVERT: G 223 ARG cc_start: 0.5361 (ttm-80) cc_final: 0.5005 (tpt170) REVERT: G 261 GLU cc_start: 0.6160 (OUTLIER) cc_final: 0.5816 (mm-30) REVERT: G 314 GLN cc_start: 0.6857 (OUTLIER) cc_final: 0.6312 (tt0) REVERT: G 329 SER cc_start: 0.7026 (m) cc_final: 0.6319 (p) REVERT: G 403 GLU cc_start: 0.5499 (mm-30) cc_final: 0.4914 (pm20) REVERT: G 411 GLU cc_start: 0.5524 (pt0) cc_final: 0.4701 (mm-30) REVERT: G 415 GLU cc_start: 0.5097 (mt-10) cc_final: 0.4425 (mm-30) REVERT: H 5 THR cc_start: 0.5508 (p) cc_final: 0.5167 (t) REVERT: H 27 ASP cc_start: 0.5537 (p0) cc_final: 0.5252 (p0) REVERT: H 32 ILE cc_start: 0.5752 (mt) cc_final: 0.5444 (mm) REVERT: H 49 LYS cc_start: 0.5787 (mmtt) cc_final: 0.5263 (mmmt) REVERT: H 102 THR cc_start: 0.6448 (m) cc_final: 0.6012 (p) REVERT: H 105 GLU cc_start: 0.5829 (pm20) cc_final: 0.5422 (mp0) REVERT: H 117 LYS cc_start: 0.5915 (tptm) cc_final: 0.5683 (tptm) REVERT: H 153 LYS cc_start: 0.5866 (ptpt) cc_final: 0.4841 (mmmt) REVERT: H 200 LYS cc_start: 0.5919 (mtpm) cc_final: 0.4902 (tptt) REVERT: H 206 ARG cc_start: 0.5121 (ttt90) cc_final: 0.4711 (tpt-90) REVERT: H 223 ARG cc_start: 0.5298 (ttm-80) cc_final: 0.4981 (tpt-90) REVERT: H 329 SER cc_start: 0.7028 (m) cc_final: 0.6187 (p) REVERT: H 411 GLU cc_start: 0.5457 (pt0) cc_final: 0.5008 (mm-30) REVERT: H 415 GLU cc_start: 0.5212 (mt-10) cc_final: 0.4513 (tm-30) REVERT: H 441 MET cc_start: 0.6757 (tpp) cc_final: 0.6252 (tpp) REVERT: I 10 GLU cc_start: 0.5716 (mt-10) cc_final: 0.5459 (mt-10) REVERT: I 49 LYS cc_start: 0.5623 (mmtt) cc_final: 0.5152 (mmmt) REVERT: I 182 GLU cc_start: 0.6068 (mt-10) cc_final: 0.5583 (mt-10) REVERT: I 200 LYS cc_start: 0.5947 (ttmm) cc_final: 0.4883 (tppt) REVERT: I 206 ARG cc_start: 0.4954 (ttp80) cc_final: 0.4485 (tpt-90) REVERT: I 223 ARG cc_start: 0.5129 (ttm-80) cc_final: 0.4724 (tpt-90) REVERT: I 255 VAL cc_start: 0.5987 (m) cc_final: 0.5732 (p) REVERT: I 280 LYS cc_start: 0.6186 (tttt) cc_final: 0.5953 (tttm) REVERT: I 314 GLN cc_start: 0.6951 (tp40) cc_final: 0.6540 (tt0) REVERT: I 329 SER cc_start: 0.7063 (m) cc_final: 0.6197 (p) REVERT: I 363 GLU cc_start: 0.6092 (tp30) cc_final: 0.5555 (tt0) REVERT: I 411 GLU cc_start: 0.5242 (pt0) cc_final: 0.4958 (mm-30) REVERT: I 415 GLU cc_start: 0.4969 (mt-10) cc_final: 0.4152 (tm-30) REVERT: I 441 MET cc_start: 0.6704 (tpp) cc_final: 0.6309 (tpp) REVERT: N 5 THR cc_start: 0.5542 (p) cc_final: 0.5057 (t) REVERT: N 10 GLU cc_start: 0.5770 (OUTLIER) cc_final: 0.5318 (mt-10) REVERT: N 49 LYS cc_start: 0.5797 (mmtt) cc_final: 0.5319 (mmmt) REVERT: N 102 THR cc_start: 0.6249 (m) cc_final: 0.5766 (p) REVERT: N 148 LEU cc_start: 0.6426 (mt) cc_final: 0.6140 (mp) REVERT: N 153 LYS cc_start: 0.5920 (mttm) cc_final: 0.4954 (mmmt) REVERT: N 182 GLU cc_start: 0.5855 (mt-10) cc_final: 0.5468 (mt-10) REVERT: N 200 LYS cc_start: 0.5669 (mtpp) cc_final: 0.4695 (tptt) REVERT: N 206 ARG cc_start: 0.4822 (ttp80) cc_final: 0.4461 (tpt-90) REVERT: N 224 LYS cc_start: 0.5359 (OUTLIER) cc_final: 0.5036 (mtpp) REVERT: N 269 GLU cc_start: 0.5310 (mm-30) cc_final: 0.4576 (pm20) REVERT: N 280 LYS cc_start: 0.6168 (tttt) cc_final: 0.5939 (tttm) REVERT: N 329 SER cc_start: 0.6870 (m) cc_final: 0.6197 (p) REVERT: N 363 GLU cc_start: 0.5947 (tp30) cc_final: 0.5450 (tt0) REVERT: N 403 GLU cc_start: 0.5883 (tp30) cc_final: 0.5223 (pm20) REVERT: N 411 GLU cc_start: 0.5361 (pt0) cc_final: 0.4573 (mm-30) REVERT: N 415 GLU cc_start: 0.5443 (mt-10) cc_final: 0.4611 (mm-30) REVERT: N 441 MET cc_start: 0.6648 (tpp) cc_final: 0.6352 (tpp) REVERT: O 49 LYS cc_start: 0.5707 (mmtt) cc_final: 0.5155 (mmmt) REVERT: O 102 THR cc_start: 0.6356 (m) cc_final: 0.5948 (p) REVERT: O 200 LYS cc_start: 0.6055 (ttmm) cc_final: 0.5068 (tptt) REVERT: O 206 ARG cc_start: 0.5119 (ttt90) cc_final: 0.4702 (tpt-90) REVERT: O 223 ARG cc_start: 0.5364 (ttm-80) cc_final: 0.5010 (tpt170) REVERT: O 314 GLN cc_start: 0.6889 (OUTLIER) cc_final: 0.6363 (tt0) REVERT: O 329 SER cc_start: 0.7010 (m) cc_final: 0.6299 (p) REVERT: O 411 GLU cc_start: 0.5506 (pt0) cc_final: 0.4891 (mm-30) REVERT: O 415 GLU cc_start: 0.5191 (mt-10) cc_final: 0.4273 (tm-30) REVERT: P 5 THR cc_start: 0.5518 (p) cc_final: 0.5168 (t) REVERT: P 10 GLU cc_start: 0.5959 (OUTLIER) cc_final: 0.5374 (mt-10) REVERT: P 19 LYS cc_start: 0.5649 (mmtt) cc_final: 0.5330 (mmmt) REVERT: P 27 ASP cc_start: 0.5493 (p0) cc_final: 0.5208 (p0) REVERT: P 32 ILE cc_start: 0.5750 (mt) cc_final: 0.5442 (mm) REVERT: P 49 LYS cc_start: 0.5789 (mmtt) cc_final: 0.5265 (mmmt) REVERT: P 102 THR cc_start: 0.6442 (m) cc_final: 0.6004 (p) REVERT: P 105 GLU cc_start: 0.5802 (pm20) cc_final: 0.5397 (mp0) REVERT: P 153 LYS cc_start: 0.5805 (OUTLIER) cc_final: 0.4765 (mmmt) REVERT: P 200 LYS cc_start: 0.5838 (mtpp) cc_final: 0.4997 (tptt) REVERT: P 206 ARG cc_start: 0.5116 (ttt90) cc_final: 0.4706 (tpt-90) REVERT: P 223 ARG cc_start: 0.5298 (ttm-80) cc_final: 0.4979 (tpt-90) REVERT: P 329 SER cc_start: 0.7050 (m) cc_final: 0.6197 (p) REVERT: P 411 GLU cc_start: 0.5403 (pt0) cc_final: 0.4948 (mm-30) REVERT: P 415 GLU cc_start: 0.5221 (mt-10) cc_final: 0.4526 (tm-30) REVERT: P 441 MET cc_start: 0.6763 (tpp) cc_final: 0.6254 (tpp) REVERT: Q 27 ASP cc_start: 0.5422 (p0) cc_final: 0.5206 (p0) REVERT: Q 49 LYS cc_start: 0.5639 (mmtt) cc_final: 0.5169 (mmmt) REVERT: Q 102 THR cc_start: 0.6635 (m) cc_final: 0.6267 (p) REVERT: Q 153 LYS cc_start: 0.5925 (mttm) cc_final: 0.4918 (mmmt) REVERT: Q 182 GLU cc_start: 0.6082 (mt-10) cc_final: 0.5591 (mt-10) REVERT: Q 200 LYS cc_start: 0.5951 (ttmm) cc_final: 0.4887 (tppt) REVERT: Q 206 ARG cc_start: 0.4968 (ttp80) cc_final: 0.4498 (tpt-90) REVERT: Q 255 VAL cc_start: 0.5981 (m) cc_final: 0.5727 (p) REVERT: Q 280 LYS cc_start: 0.6202 (tttt) cc_final: 0.5969 (tttm) REVERT: Q 314 GLN cc_start: 0.6942 (tp40) cc_final: 0.6532 (tt0) REVERT: Q 329 SER cc_start: 0.7063 (m) cc_final: 0.6197 (p) REVERT: Q 363 GLU cc_start: 0.6087 (tp30) cc_final: 0.5483 (tt0) REVERT: Q 407 LYS cc_start: 0.5534 (mttm) cc_final: 0.4964 (mtpt) REVERT: Q 411 GLU cc_start: 0.5297 (pt0) cc_final: 0.5000 (mm-30) REVERT: Q 415 GLU cc_start: 0.4967 (mt-10) cc_final: 0.4151 (tm-30) REVERT: Q 441 MET cc_start: 0.6698 (tpp) cc_final: 0.6300 (tpp) REVERT: R 11 LYS cc_start: 0.4627 (tttp) cc_final: 0.4363 (ttpp) REVERT: R 15 GLU cc_start: 0.4210 (OUTLIER) cc_final: 0.3822 (mm-30) REVERT: R 49 LYS cc_start: 0.5844 (mmtt) cc_final: 0.5246 (mmmt) REVERT: R 102 THR cc_start: 0.6226 (m) cc_final: 0.5857 (p) REVERT: R 117 LYS cc_start: 0.5861 (tptm) cc_final: 0.5503 (tptm) REVERT: R 148 LEU cc_start: 0.6491 (mt) cc_final: 0.6272 (mt) REVERT: R 182 GLU cc_start: 0.5937 (mt-10) cc_final: 0.5687 (mt-10) REVERT: R 200 LYS cc_start: 0.5982 (ttmm) cc_final: 0.4885 (tptt) REVERT: R 314 GLN cc_start: 0.6790 (OUTLIER) cc_final: 0.6333 (tt0) REVERT: R 329 SER cc_start: 0.6793 (m) cc_final: 0.6206 (p) REVERT: R 403 GLU cc_start: 0.5911 (tp30) cc_final: 0.5362 (mp0) REVERT: R 407 LYS cc_start: 0.5902 (mmtm) cc_final: 0.5345 (mtpt) REVERT: R 409 LEU cc_start: 0.5496 (OUTLIER) cc_final: 0.5207 (pp) REVERT: R 411 GLU cc_start: 0.5625 (mm-30) cc_final: 0.4927 (tt0) REVERT: R 438 GLU cc_start: 0.5241 (mt-10) cc_final: 0.4987 (mt-10) REVERT: S 3 LYS cc_start: 0.6716 (tttt) cc_final: 0.6454 (ttmt) REVERT: S 10 GLU cc_start: 0.6056 (OUTLIER) cc_final: 0.5691 (mt-10) REVERT: S 11 LYS cc_start: 0.5099 (tttp) cc_final: 0.4730 (ttpp) REVERT: S 49 LYS cc_start: 0.5785 (mmtt) cc_final: 0.5261 (mmmt) REVERT: S 102 THR cc_start: 0.6280 (OUTLIER) cc_final: 0.5954 (p) REVERT: S 105 GLU cc_start: 0.6111 (pm20) cc_final: 0.5624 (mp0) REVERT: S 153 LYS cc_start: 0.5592 (mmpt) cc_final: 0.5338 (mmmt) REVERT: S 167 ASN cc_start: 0.5365 (OUTLIER) cc_final: 0.4174 (m-40) REVERT: S 200 LYS cc_start: 0.5763 (mtpp) cc_final: 0.4787 (tptt) REVERT: S 223 ARG cc_start: 0.5148 (ttm-80) cc_final: 0.4822 (tpt-90) REVERT: S 261 GLU cc_start: 0.6146 (OUTLIER) cc_final: 0.5835 (mm-30) REVERT: S 314 GLN cc_start: 0.6868 (OUTLIER) cc_final: 0.6243 (tt0) REVERT: S 329 SER cc_start: 0.6895 (m) cc_final: 0.6089 (p) REVERT: S 407 LYS cc_start: 0.6020 (mmtm) cc_final: 0.5435 (mtpt) REVERT: S 411 GLU cc_start: 0.5394 (pt0) cc_final: 0.5009 (mm-30) REVERT: S 415 GLU cc_start: 0.5213 (mt-10) cc_final: 0.4441 (tm-30) REVERT: T 11 LYS cc_start: 0.4799 (ttpp) cc_final: 0.4446 (ttpp) REVERT: T 15 GLU cc_start: 0.4466 (OUTLIER) cc_final: 0.4117 (mm-30) REVERT: T 49 LYS cc_start: 0.5860 (mmtt) cc_final: 0.5395 (mmmt) REVERT: T 117 LYS cc_start: 0.6003 (tptm) cc_final: 0.5717 (tptm) REVERT: T 153 LYS cc_start: 0.5998 (mttm) cc_final: 0.4900 (mmmt) REVERT: T 189 GLU cc_start: 0.6254 (OUTLIER) cc_final: 0.5674 (tp30) REVERT: T 200 LYS cc_start: 0.5945 (ttmm) cc_final: 0.5137 (tptp) REVERT: T 223 ARG cc_start: 0.5155 (ttm-80) cc_final: 0.4745 (tpt170) REVERT: T 269 GLU cc_start: 0.5230 (mm-30) cc_final: 0.4413 (pm20) REVERT: T 314 GLN cc_start: 0.6814 (OUTLIER) cc_final: 0.6559 (tt0) REVERT: T 329 SER cc_start: 0.6910 (m) cc_final: 0.6174 (p) REVERT: T 363 GLU cc_start: 0.6058 (tp30) cc_final: 0.5589 (tt0) REVERT: T 403 GLU cc_start: 0.5367 (mm-30) cc_final: 0.4531 (pm20) REVERT: T 411 GLU cc_start: 0.5408 (pt0) cc_final: 0.4626 (mm-30) REVERT: T 441 MET cc_start: 0.6691 (tpp) cc_final: 0.6248 (tpp) outliers start: 91 outliers final: 36 residues processed: 891 average time/residue: 1.5939 time to fit residues: 1719.4682 Evaluate side-chains 896 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 829 time to evaluate : 4.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain E residue 7 MET Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 261 GLU Chi-restraints excluded: chain G residue 314 GLN Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain L residue 7 MET Chi-restraints excluded: chain N residue 10 GLU Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 224 LYS Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 239 VAL Chi-restraints excluded: chain O residue 314 GLN Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 153 LYS Chi-restraints excluded: chain Q residue 83 THR Chi-restraints excluded: chain Q residue 122 LEU Chi-restraints excluded: chain Q residue 239 VAL Chi-restraints excluded: chain R residue 15 GLU Chi-restraints excluded: chain R residue 314 GLN Chi-restraints excluded: chain R residue 409 LEU Chi-restraints excluded: chain S residue 10 GLU Chi-restraints excluded: chain S residue 102 THR Chi-restraints excluded: chain S residue 167 ASN Chi-restraints excluded: chain S residue 239 VAL Chi-restraints excluded: chain S residue 261 GLU Chi-restraints excluded: chain S residue 314 GLN Chi-restraints excluded: chain S residue 409 LEU Chi-restraints excluded: chain T residue 15 GLU Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 114 ARG Chi-restraints excluded: chain T residue 189 GLU Chi-restraints excluded: chain T residue 224 LYS Chi-restraints excluded: chain T residue 314 GLN Chi-restraints excluded: chain U residue 7 MET Chi-restraints excluded: chain V residue 7 MET Chi-restraints excluded: chain W residue 7 MET Chi-restraints excluded: chain Y residue 7 MET Chi-restraints excluded: chain Z residue 7 MET Chi-restraints excluded: chain a residue 7 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 371 optimal weight: 2.9990 chunk 598 optimal weight: 9.9990 chunk 365 optimal weight: 7.9990 chunk 283 optimal weight: 10.0000 chunk 415 optimal weight: 4.9990 chunk 627 optimal weight: 9.9990 chunk 577 optimal weight: 2.9990 chunk 499 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 386 optimal weight: 8.9990 chunk 306 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 167 ASN B 34 ASN B 167 ASN B 245 HIS C 34 ASN C 75 ASN C 167 ASN F 24 GLN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN F 443 GLN G 34 ASN G 75 ASN G 167 ASN H 34 ASN H 443 GLN I 34 ASN I 266 GLN N 24 GLN N 34 ASN N 75 ASN O 34 ASN O 75 ASN P 34 ASN P 443 GLN Q 34 ASN Q 266 GLN R 34 ASN R 167 ASN S 34 ASN S 167 ASN T 34 ASN T 75 ASN T 167 ASN V 4 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5977 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 51450 Z= 0.352 Angle : 0.695 7.605 69650 Z= 0.379 Chirality : 0.049 0.174 7546 Planarity : 0.007 0.128 9184 Dihedral : 5.843 57.107 6850 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.01 % Favored : 94.85 % Rotamer: Outliers : 1.82 % Allowed : 16.82 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.10), residues: 6286 helix: 1.47 (0.10), residues: 2310 sheet: -0.38 (0.17), residues: 812 loop : -0.54 (0.11), residues: 3164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP Q 435 HIS 0.009 0.002 HIS O 195 PHE 0.028 0.003 PHE A 285 TYR 0.048 0.004 TYR Q 296 ARG 0.013 0.001 ARG B 335 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12572 Ramachandran restraints generated. 6286 Oldfield, 0 Emsley, 6286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 843 time to evaluate : 4.484 Fit side-chains revert: symmetry clash REVERT: A 11 LYS cc_start: 0.5009 (tttp) cc_final: 0.4746 (ttpp) REVERT: A 32 ILE cc_start: 0.5753 (mp) cc_final: 0.5443 (mp) REVERT: A 49 LYS cc_start: 0.5804 (mmtt) cc_final: 0.5211 (mmmt) REVERT: A 102 THR cc_start: 0.6282 (m) cc_final: 0.5903 (p) REVERT: A 117 LYS cc_start: 0.5831 (tptm) cc_final: 0.5513 (tptm) REVERT: A 148 LEU cc_start: 0.6504 (mt) cc_final: 0.6294 (mt) REVERT: A 182 GLU cc_start: 0.5979 (mt-10) cc_final: 0.5745 (mt-10) REVERT: A 200 LYS cc_start: 0.5910 (ttmm) cc_final: 0.4869 (tptt) REVERT: A 314 GLN cc_start: 0.6857 (OUTLIER) cc_final: 0.6321 (tt0) REVERT: A 329 SER cc_start: 0.6798 (m) cc_final: 0.6179 (p) REVERT: A 403 GLU cc_start: 0.5882 (OUTLIER) cc_final: 0.5259 (tp30) REVERT: A 407 LYS cc_start: 0.5733 (mmtm) cc_final: 0.5245 (mtpt) REVERT: A 411 GLU cc_start: 0.5514 (pt0) cc_final: 0.4877 (mm-30) REVERT: B 3 LYS cc_start: 0.6582 (tttt) cc_final: 0.6360 (ttmt) REVERT: B 7 GLU cc_start: 0.4678 (mm-30) cc_final: 0.4471 (mm-30) REVERT: B 10 GLU cc_start: 0.6043 (OUTLIER) cc_final: 0.5469 (mt-10) REVERT: B 49 LYS cc_start: 0.5830 (mmtt) cc_final: 0.5345 (mmmt) REVERT: B 102 THR cc_start: 0.6367 (OUTLIER) cc_final: 0.5891 (p) REVERT: B 105 GLU cc_start: 0.6106 (pm20) cc_final: 0.5799 (pm20) REVERT: B 117 LYS cc_start: 0.5785 (tptp) cc_final: 0.5535 (tptm) REVERT: B 182 GLU cc_start: 0.6104 (mt-10) cc_final: 0.5742 (mt-10) REVERT: B 200 LYS cc_start: 0.5790 (mtpp) cc_final: 0.4887 (tptt) REVERT: B 206 ARG cc_start: 0.5238 (OUTLIER) cc_final: 0.4221 (tpt-90) REVERT: B 224 LYS cc_start: 0.5642 (ttmm) cc_final: 0.5339 (mtmt) REVERT: B 261 GLU cc_start: 0.6173 (OUTLIER) cc_final: 0.5851 (mm-30) REVERT: B 314 GLN cc_start: 0.6798 (OUTLIER) cc_final: 0.6165 (tt0) REVERT: B 329 SER cc_start: 0.6903 (m) cc_final: 0.6098 (p) REVERT: B 403 GLU cc_start: 0.5811 (tp30) cc_final: 0.5578 (tp30) REVERT: B 407 LYS cc_start: 0.6173 (mmtm) cc_final: 0.5475 (mtpt) REVERT: B 411 GLU cc_start: 0.5352 (pt0) cc_final: 0.4792 (mm-30) REVERT: B 415 GLU cc_start: 0.5198 (mt-10) cc_final: 0.4488 (mm-30) REVERT: C 49 LYS cc_start: 0.5839 (mmtt) cc_final: 0.5389 (mmmt) REVERT: C 102 THR cc_start: 0.6337 (m) cc_final: 0.5916 (p) REVERT: C 114 ARG cc_start: 0.6701 (OUTLIER) cc_final: 0.5890 (ttm110) REVERT: C 117 LYS cc_start: 0.5839 (tptm) cc_final: 0.5501 (tptm) REVERT: C 153 LYS cc_start: 0.6020 (mttm) cc_final: 0.5048 (mmmt) REVERT: C 200 LYS cc_start: 0.5659 (mtpp) cc_final: 0.4907 (tptt) REVERT: C 223 ARG cc_start: 0.5015 (ttm-80) cc_final: 0.4606 (tpt170) REVERT: C 269 GLU cc_start: 0.5346 (mm-30) cc_final: 0.4489 (pm20) REVERT: C 314 GLN cc_start: 0.6897 (OUTLIER) cc_final: 0.6639 (tt0) REVERT: C 329 SER cc_start: 0.6947 (m) cc_final: 0.6140 (p) REVERT: C 363 GLU cc_start: 0.5994 (tp30) cc_final: 0.5514 (tt0) REVERT: C 403 GLU cc_start: 0.5721 (tp30) cc_final: 0.5255 (pm20) REVERT: C 411 GLU cc_start: 0.5369 (pt0) cc_final: 0.4636 (mm-30) REVERT: C 441 MET cc_start: 0.6668 (tpp) cc_final: 0.6256 (tpp) REVERT: F 10 GLU cc_start: 0.5745 (OUTLIER) cc_final: 0.5262 (mt-10) REVERT: F 49 LYS cc_start: 0.5810 (mmtt) cc_final: 0.5340 (mmmt) REVERT: F 148 LEU cc_start: 0.6366 (mt) cc_final: 0.6053 (mp) REVERT: F 153 LYS cc_start: 0.5925 (mttm) cc_final: 0.4844 (mmmt) REVERT: F 200 LYS cc_start: 0.5622 (mtpp) cc_final: 0.4642 (tptt) REVERT: F 206 ARG cc_start: 0.4905 (ttp80) cc_final: 0.4541 (tpt-90) REVERT: F 224 LYS cc_start: 0.5466 (OUTLIER) cc_final: 0.5143 (mtpp) REVERT: F 269 GLU cc_start: 0.5376 (mm-30) cc_final: 0.4557 (pm20) REVERT: F 329 SER cc_start: 0.6894 (m) cc_final: 0.6237 (p) REVERT: F 363 GLU cc_start: 0.5945 (tp30) cc_final: 0.5442 (tt0) REVERT: F 411 GLU cc_start: 0.5512 (pt0) cc_final: 0.4865 (mm-30) REVERT: F 441 MET cc_start: 0.6668 (tpp) cc_final: 0.6364 (tpp) REVERT: G 49 LYS cc_start: 0.5655 (mmtt) cc_final: 0.5124 (mmmt) REVERT: G 102 THR cc_start: 0.6399 (m) cc_final: 0.5942 (p) REVERT: G 206 ARG cc_start: 0.5151 (OUTLIER) cc_final: 0.4712 (tpt-90) REVERT: G 261 GLU cc_start: 0.6207 (OUTLIER) cc_final: 0.5863 (mm-30) REVERT: G 269 GLU cc_start: 0.5316 (mm-30) cc_final: 0.4953 (tp30) REVERT: G 314 GLN cc_start: 0.6586 (OUTLIER) cc_final: 0.5870 (tt0) REVERT: G 329 SER cc_start: 0.7000 (m) cc_final: 0.6303 (p) REVERT: G 403 GLU cc_start: 0.5795 (mm-30) cc_final: 0.5212 (pm20) REVERT: G 411 GLU cc_start: 0.5615 (pt0) cc_final: 0.4997 (mm-30) REVERT: G 415 GLU cc_start: 0.5207 (mt-10) cc_final: 0.4287 (tm-30) REVERT: H 27 ASP cc_start: 0.5451 (p0) cc_final: 0.5149 (p0) REVERT: H 32 ILE cc_start: 0.5720 (mt) cc_final: 0.5401 (mm) REVERT: H 49 LYS cc_start: 0.5736 (mmtt) cc_final: 0.5243 (mmmt) REVERT: H 102 THR cc_start: 0.6535 (m) cc_final: 0.6066 (p) REVERT: H 105 GLU cc_start: 0.5805 (pm20) cc_final: 0.5544 (pm20) REVERT: H 117 LYS cc_start: 0.5953 (tptm) cc_final: 0.5724 (tptm) REVERT: H 153 LYS cc_start: 0.5794 (ptpt) cc_final: 0.4783 (mmmt) REVERT: H 200 LYS cc_start: 0.5825 (mtpm) cc_final: 0.4845 (tptt) REVERT: H 206 ARG cc_start: 0.5170 (ttt90) cc_final: 0.4753 (tpt-90) REVERT: H 223 ARG cc_start: 0.5299 (ttm-80) cc_final: 0.4971 (tpt-90) REVERT: H 329 SER cc_start: 0.7113 (m) cc_final: 0.6287 (p) REVERT: H 411 GLU cc_start: 0.5481 (pt0) cc_final: 0.5052 (mm-30) REVERT: H 415 GLU cc_start: 0.5184 (mt-10) cc_final: 0.4419 (tm-30) REVERT: H 441 MET cc_start: 0.6685 (tpp) cc_final: 0.6200 (tpp) REVERT: I 49 LYS cc_start: 0.5658 (mmtt) cc_final: 0.5200 (mmmt) REVERT: I 182 GLU cc_start: 0.6114 (mt-10) cc_final: 0.5593 (mt-10) REVERT: I 200 LYS cc_start: 0.5895 (ttmm) cc_final: 0.4905 (tppt) REVERT: I 206 ARG cc_start: 0.5021 (ttp80) cc_final: 0.4597 (tpt-90) REVERT: I 280 LYS cc_start: 0.6079 (tttt) cc_final: 0.5847 (tttm) REVERT: I 314 GLN cc_start: 0.6852 (tp40) cc_final: 0.6414 (tt0) REVERT: I 329 SER cc_start: 0.7074 (m) cc_final: 0.6229 (p) REVERT: I 363 GLU cc_start: 0.6030 (tp30) cc_final: 0.5398 (tt0) REVERT: I 411 GLU cc_start: 0.5334 (pt0) cc_final: 0.5024 (mm-30) REVERT: I 415 GLU cc_start: 0.5029 (mt-10) cc_final: 0.4252 (tm-30) REVERT: I 441 MET cc_start: 0.6814 (tpp) cc_final: 0.6434 (tpp) REVERT: N 49 LYS cc_start: 0.5812 (mmtt) cc_final: 0.5342 (mmmt) REVERT: N 148 LEU cc_start: 0.6355 (mt) cc_final: 0.6041 (mp) REVERT: N 153 LYS cc_start: 0.5921 (mttm) cc_final: 0.4944 (mmmt) REVERT: N 200 LYS cc_start: 0.5617 (mtpp) cc_final: 0.4659 (tptt) REVERT: N 206 ARG cc_start: 0.4907 (ttp80) cc_final: 0.4541 (tpt-90) REVERT: N 224 LYS cc_start: 0.5462 (OUTLIER) cc_final: 0.5139 (mtpp) REVERT: N 269 GLU cc_start: 0.5374 (mm-30) cc_final: 0.4555 (pm20) REVERT: N 329 SER cc_start: 0.6889 (m) cc_final: 0.6221 (p) REVERT: N 363 GLU cc_start: 0.5946 (tp30) cc_final: 0.5430 (tt0) REVERT: N 403 GLU cc_start: 0.5909 (tp30) cc_final: 0.5277 (pm20) REVERT: N 411 GLU cc_start: 0.5472 (pt0) cc_final: 0.4816 (mm-30) REVERT: N 415 GLU cc_start: 0.5505 (mt-10) cc_final: 0.4724 (mm-30) REVERT: N 441 MET cc_start: 0.6653 (tpp) cc_final: 0.6384 (tpp) REVERT: O 49 LYS cc_start: 0.5706 (mmtt) cc_final: 0.5177 (mmmt) REVERT: O 102 THR cc_start: 0.6398 (m) cc_final: 0.5946 (p) REVERT: O 206 ARG cc_start: 0.5137 (ttt90) cc_final: 0.4706 (tpt-90) REVERT: O 223 ARG cc_start: 0.5046 (ttm-80) cc_final: 0.4741 (tpt170) REVERT: O 269 GLU cc_start: 0.5299 (mm-30) cc_final: 0.4938 (tp30) REVERT: O 314 GLN cc_start: 0.6627 (OUTLIER) cc_final: 0.5877 (tt0) REVERT: O 329 SER cc_start: 0.6981 (m) cc_final: 0.6283 (p) REVERT: O 411 GLU cc_start: 0.5619 (pt0) cc_final: 0.5004 (mm-30) REVERT: O 415 GLU cc_start: 0.5234 (mt-10) cc_final: 0.4320 (tm-30) REVERT: P 5 THR cc_start: 0.5460 (p) cc_final: 0.5134 (t) REVERT: P 10 GLU cc_start: 0.5975 (OUTLIER) cc_final: 0.5414 (mt-10) REVERT: P 27 ASP cc_start: 0.5516 (p0) cc_final: 0.5198 (p0) REVERT: P 32 ILE cc_start: 0.5717 (mt) cc_final: 0.5397 (mm) REVERT: P 49 LYS cc_start: 0.5736 (mmtt) cc_final: 0.5248 (mmmt) REVERT: P 102 THR cc_start: 0.6533 (m) cc_final: 0.6059 (p) REVERT: P 153 LYS cc_start: 0.5761 (OUTLIER) cc_final: 0.4739 (mmmt) REVERT: P 200 LYS cc_start: 0.5776 (mtpp) cc_final: 0.4965 (tptt) REVERT: P 206 ARG cc_start: 0.5167 (ttt90) cc_final: 0.4748 (tpt-90) REVERT: P 223 ARG cc_start: 0.5299 (ttm-80) cc_final: 0.4973 (tpt-90) REVERT: P 329 SER cc_start: 0.7136 (m) cc_final: 0.6300 (p) REVERT: P 411 GLU cc_start: 0.5537 (pt0) cc_final: 0.5112 (mm-30) REVERT: P 415 GLU cc_start: 0.5174 (mt-10) cc_final: 0.4387 (tm-30) REVERT: P 441 MET cc_start: 0.6751 (tpp) cc_final: 0.6239 (tpp) REVERT: Q 27 ASP cc_start: 0.5548 (p0) cc_final: 0.5322 (p0) REVERT: Q 49 LYS cc_start: 0.5673 (mmtt) cc_final: 0.5215 (mmmt) REVERT: Q 153 LYS cc_start: 0.5917 (mttm) cc_final: 0.4903 (mmmt) REVERT: Q 182 GLU cc_start: 0.6139 (mt-10) cc_final: 0.5598 (mt-10) REVERT: Q 200 LYS cc_start: 0.5897 (ttmm) cc_final: 0.4907 (tppt) REVERT: Q 206 ARG cc_start: 0.5033 (ttp80) cc_final: 0.4609 (tpt-90) REVERT: Q 269 GLU cc_start: 0.5031 (mm-30) cc_final: 0.4521 (pm20) REVERT: Q 314 GLN cc_start: 0.6872 (tp40) cc_final: 0.6401 (tt0) REVERT: Q 329 SER cc_start: 0.7075 (m) cc_final: 0.6230 (p) REVERT: Q 411 GLU cc_start: 0.5355 (pt0) cc_final: 0.5032 (mm-30) REVERT: Q 415 GLU cc_start: 0.5027 (mt-10) cc_final: 0.4252 (tm-30) REVERT: Q 441 MET cc_start: 0.6810 (tpp) cc_final: 0.6426 (tpp) REVERT: R 11 LYS cc_start: 0.4582 (tttp) cc_final: 0.4347 (ttpp) REVERT: R 15 GLU cc_start: 0.4174 (OUTLIER) cc_final: 0.3933 (mm-30) REVERT: R 49 LYS cc_start: 0.5794 (mmtt) cc_final: 0.5207 (mmmt) REVERT: R 102 THR cc_start: 0.6354 (m) cc_final: 0.5943 (p) REVERT: R 117 LYS cc_start: 0.5812 (tptm) cc_final: 0.5482 (tptm) REVERT: R 148 LEU cc_start: 0.6504 (mt) cc_final: 0.6290 (mt) REVERT: R 182 GLU cc_start: 0.5932 (mt-10) cc_final: 0.5722 (mt-10) REVERT: R 200 LYS cc_start: 0.5912 (ttmm) cc_final: 0.4819 (tptt) REVERT: R 314 GLN cc_start: 0.6857 (OUTLIER) cc_final: 0.6324 (tt0) REVERT: R 329 SER cc_start: 0.6786 (m) cc_final: 0.6166 (p) REVERT: R 403 GLU cc_start: 0.5979 (tp30) cc_final: 0.5250 (pm20) REVERT: R 407 LYS cc_start: 0.5826 (mmtm) cc_final: 0.5311 (mtpt) REVERT: R 409 LEU cc_start: 0.5547 (OUTLIER) cc_final: 0.4911 (mt) REVERT: R 411 GLU cc_start: 0.5828 (mm-30) cc_final: 0.5199 (tt0) REVERT: S 3 LYS cc_start: 0.6596 (tttt) cc_final: 0.6371 (ttmt) REVERT: S 10 GLU cc_start: 0.6000 (OUTLIER) cc_final: 0.5613 (mt-10) REVERT: S 11 LYS cc_start: 0.4794 (tttp) cc_final: 0.4469 (ttpp) REVERT: S 49 LYS cc_start: 0.5764 (mmtt) cc_final: 0.5272 (mmmt) REVERT: S 102 THR cc_start: 0.6379 (OUTLIER) cc_final: 0.5904 (p) REVERT: S 105 GLU cc_start: 0.6118 (pm20) cc_final: 0.5819 (pm20) REVERT: S 153 LYS cc_start: 0.5617 (OUTLIER) cc_final: 0.5349 (mmmt) REVERT: S 200 LYS cc_start: 0.5778 (mtpp) cc_final: 0.4848 (tptt) REVERT: S 206 ARG cc_start: 0.5202 (OUTLIER) cc_final: 0.4196 (tpt-90) REVERT: S 223 ARG cc_start: 0.4988 (ttm-80) cc_final: 0.4721 (ttt90) REVERT: S 261 GLU cc_start: 0.6141 (OUTLIER) cc_final: 0.5828 (mm-30) REVERT: S 314 GLN cc_start: 0.6787 (OUTLIER) cc_final: 0.6154 (tt0) REVERT: S 329 SER cc_start: 0.6903 (m) cc_final: 0.6100 (p) REVERT: S 411 GLU cc_start: 0.5342 (OUTLIER) cc_final: 0.4744 (mm-30) REVERT: S 415 GLU cc_start: 0.5210 (mt-10) cc_final: 0.4500 (mm-30) REVERT: T 11 LYS cc_start: 0.4788 (ttpp) cc_final: 0.4397 (ttpp) REVERT: T 15 GLU cc_start: 0.4518 (OUTLIER) cc_final: 0.4161 (mm-30) REVERT: T 49 LYS cc_start: 0.5851 (mmtt) cc_final: 0.5401 (mmmt) REVERT: T 114 ARG cc_start: 0.6700 (OUTLIER) cc_final: 0.5875 (ttm110) REVERT: T 117 LYS cc_start: 0.6029 (tptm) cc_final: 0.5715 (tptm) REVERT: T 153 LYS cc_start: 0.6009 (mttm) cc_final: 0.4980 (mmmt) REVERT: T 189 GLU cc_start: 0.6325 (OUTLIER) cc_final: 0.5737 (tp30) REVERT: T 200 LYS cc_start: 0.5820 (ttmm) cc_final: 0.4912 (tptt) REVERT: T 223 ARG cc_start: 0.5005 (ttm-80) cc_final: 0.4612 (tpt170) REVERT: T 269 GLU cc_start: 0.5418 (mm-30) cc_final: 0.4572 (pm20) REVERT: T 314 GLN cc_start: 0.6884 (OUTLIER) cc_final: 0.6615 (tt0) REVERT: T 329 SER cc_start: 0.6971 (m) cc_final: 0.6172 (p) REVERT: T 363 GLU cc_start: 0.6019 (tp30) cc_final: 0.5528 (tt0) REVERT: T 403 GLU cc_start: 0.5880 (mm-30) cc_final: 0.5030 (pm20) REVERT: T 411 GLU cc_start: 0.5382 (pt0) cc_final: 0.4588 (mm-30) REVERT: T 415 GLU cc_start: 0.5259 (mt-10) cc_final: 0.4471 (mm-30) REVERT: T 441 MET cc_start: 0.6662 (tpp) cc_final: 0.6248 (tpp) outliers start: 97 outliers final: 38 residues processed: 887 average time/residue: 1.5746 time to fit residues: 1705.6846 Evaluate side-chains 904 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 834 time to evaluate : 4.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain E residue 7 MET Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain G residue 206 ARG Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 261 GLU Chi-restraints excluded: chain G residue 314 GLN Chi-restraints excluded: chain G residue 409 LEU Chi-restraints excluded: chain H residue 239 VAL Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain J residue 7 MET Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain L residue 7 MET Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain N residue 224 LYS Chi-restraints excluded: chain N residue 239 VAL Chi-restraints excluded: chain O residue 239 VAL Chi-restraints excluded: chain O residue 314 GLN Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 153 LYS Chi-restraints excluded: chain P residue 239 VAL Chi-restraints excluded: chain Q residue 122 LEU Chi-restraints excluded: chain Q residue 239 VAL Chi-restraints excluded: chain R residue 15 GLU Chi-restraints excluded: chain R residue 114 ARG Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 314 GLN Chi-restraints excluded: chain R residue 409 LEU Chi-restraints excluded: chain S residue 10 GLU Chi-restraints excluded: chain S residue 102 THR Chi-restraints excluded: chain S residue 153 LYS Chi-restraints excluded: chain S residue 206 ARG Chi-restraints excluded: chain S residue 239 VAL Chi-restraints excluded: chain S residue 261 GLU Chi-restraints excluded: chain S residue 314 GLN Chi-restraints excluded: chain S residue 409 LEU Chi-restraints excluded: chain S residue 411 GLU Chi-restraints excluded: chain T residue 15 GLU Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 114 ARG Chi-restraints excluded: chain T residue 189 GLU Chi-restraints excluded: chain T residue 314 GLN Chi-restraints excluded: chain T residue 409 LEU Chi-restraints excluded: chain U residue 7 MET Chi-restraints excluded: chain V residue 7 MET Chi-restraints excluded: chain W residue 7 MET Chi-restraints excluded: chain Y residue 7 MET Chi-restraints excluded: chain Z residue 7 MET Chi-restraints excluded: chain a residue 7 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 396 optimal weight: 9.9990 chunk 532 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 460 optimal weight: 0.0060 chunk 73 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 500 optimal weight: 4.9990 chunk 209 optimal weight: 0.5980 chunk 514 optimal weight: 8.9990 chunk 63 optimal weight: 0.0270 chunk 92 optimal weight: 2.9990 overall best weight: 1.1258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN A 315 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 ASN C 75 ASN C 167 ASN F 24 GLN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN F 167 ASN F 443 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN G 167 ASN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 ASN H 443 GLN I 34 ASN I 167 ASN I 266 GLN N 24 GLN N 34 ASN N 75 ASN N 167 ASN ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 75 ASN O 167 ASN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 167 ASN P 443 GLN Q 34 ASN Q 167 ASN Q 266 GLN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 167 ASN R 315 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 ASN T 75 ASN T 167 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.211599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.185918 restraints weight = 31429.684| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 0.70 r_work: 0.3981 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3885 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3885 r_free = 0.3885 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3885 r_free = 0.3885 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 51450 Z= 0.141 Angle : 0.469 5.121 69650 Z= 0.257 Chirality : 0.041 0.135 7546 Planarity : 0.004 0.065 9184 Dihedral : 5.186 52.888 6850 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.26 % Favored : 95.72 % Rotamer: Outliers : 1.48 % Allowed : 17.12 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.10), residues: 6286 helix: 1.95 (0.10), residues: 2338 sheet: -0.34 (0.17), residues: 854 loop : -0.50 (0.11), residues: 3094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP P 425 HIS 0.005 0.001 HIS G 195 PHE 0.017 0.001 PHE I 285 TYR 0.031 0.002 TYR I 296 ARG 0.005 0.000 ARG C 170 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24353.78 seconds wall clock time: 414 minutes 12.38 seconds (24852.38 seconds total)