Starting phenix.real_space_refine on Tue Sep 24 08:06:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf9_25866/09_2024/7tf9_25866.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf9_25866/09_2024/7tf9_25866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf9_25866/09_2024/7tf9_25866.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf9_25866/09_2024/7tf9_25866.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf9_25866/09_2024/7tf9_25866.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf9_25866/09_2024/7tf9_25866.cif" } resolution = 2.61 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= 0.001 sd= 0.073 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 252 5.16 5 C 31920 2.51 5 N 8372 2.21 5 O 9156 1.98 5 H 140 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 49868 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3494 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3494 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3494 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Chain: "E" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Chain: "F" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3494 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "G" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3494 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "H" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3494 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "I" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3494 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "J" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Chain: "K" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Chain: "L" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Chain: "M" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Chain: "N" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3494 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "O" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3494 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "P" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3494 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "Q" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3494 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "R" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3494 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "S" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3494 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "T" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3494 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "U" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Chain: "V" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Chain: "W" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Chain: "X" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Chain: "Y" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Chain: "Z" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Chain: "a" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Chain: "b" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} 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: 22.68, per 1000 atoms: 0.45 Number of scatterers: 49868 At special positions: 0 Unit cell: (173.36, 169.84, 122.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 252 16.00 Mg 28 11.99 O 9156 8.00 N 8372 7.00 C 31920 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: 9.40 Conformation dependent library (CDL) restraints added in 4.9 seconds 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11732 Finding SS restraints... Secondary structure from input PDB file: 265 helices and 56 sheets defined 46.0% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.29 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: 6.518A pdb=" N PHE A 60 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL A 61 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 62 " --> pdb=" O GLY A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 77 Processing helix chain 'A' and resid 107 through 123 Processing helix chain 'A' and resid 167 through 180 Processing helix chain 'A' and resid 203 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: 5.102A pdb=" N ALA A 287 " --> pdb=" O ARG A 283 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 299 removed outlier: 3.642A pdb=" N ARG A 298 " --> pdb=" O ASN A 294 " (cutoff:3.500A) removed outlier: 3.501A 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: 3.528A 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 371 through 375 Processing helix chain 'A' and resid 376 through 382 removed outlier: 3.638A pdb=" N ALA A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 402 Processing helix chain 'A' and resid 403 through 410 Processing helix chain 'A' and resid 410 through 430 Processing helix chain 'A' and resid 433 through 441 removed outlier: 3.550A 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: 6.523A pdb=" N PHE B 60 " --> pdb=" O ILE B 57 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL B 61 " --> pdb=" O GLU B 58 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG B 62 " --> pdb=" O GLY B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 77 Processing helix chain 'B' and resid 107 through 123 Processing helix chain 'B' and resid 167 through 180 Processing helix chain 'B' and resid 203 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: 5.102A pdb=" N ALA B 287 " --> pdb=" O ARG B 283 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 299 removed outlier: 3.647A pdb=" N ARG B 298 " --> pdb=" O ASN B 294 " (cutoff:3.500A) removed outlier: 3.500A 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: 3.528A 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: 3.639A pdb=" N ALA B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 402 Processing helix chain 'B' and resid 403 through 410 Processing helix chain 'B' and resid 410 through 430 Processing helix chain 'B' and resid 433 through 441 removed outlier: 3.550A 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: 6.519A pdb=" N PHE C 60 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL C 61 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG C 62 " --> pdb=" O GLY C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 77 Processing helix chain 'C' and resid 107 through 123 Processing helix chain 'C' and resid 167 through 180 Processing helix chain 'C' and resid 203 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: 5.102A pdb=" N ALA C 287 " --> pdb=" O ARG C 283 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 299 removed outlier: 3.644A pdb=" N ARG C 298 " --> pdb=" O ASN C 294 " (cutoff:3.500A) removed outlier: 3.500A 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: 3.528A 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 376 through 382 removed outlier: 3.639A pdb=" N ALA C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 402 Processing helix chain 'C' and resid 403 through 410 Processing helix chain 'C' and resid 410 through 430 Processing helix chain 'C' and resid 433 through 441 removed outlier: 3.550A pdb=" N ARG C 437 " --> pdb=" O HIS C 433 " (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: 6.522A pdb=" N PHE F 60 " --> pdb=" O ILE F 57 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL F 61 " --> pdb=" O GLU F 58 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG F 62 " --> pdb=" O GLY F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 77 Processing helix chain 'F' and resid 107 through 123 Processing helix chain 'F' and resid 167 through 180 Processing helix chain 'F' and resid 203 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: 5.102A pdb=" N ALA F 287 " --> pdb=" O ARG F 283 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL F 288 " --> pdb=" O GLY F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 299 removed outlier: 3.571A pdb=" N ARG F 298 " --> pdb=" O ASN F 294 " (cutoff:3.500A) removed outlier: 3.501A 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: 3.528A 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 371 through 375 Processing helix chain 'F' and resid 376 through 382 removed outlier: 3.639A pdb=" N ALA 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 403 through 410 Processing helix chain 'F' and resid 410 through 431 removed outlier: 3.524A pdb=" N ALA F 431 " --> pdb=" O MET F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 439 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: 6.534A pdb=" N PHE G 60 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL G 61 " --> pdb=" O GLU G 58 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG G 62 " --> pdb=" O GLY G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 77 Processing helix chain 'G' and resid 107 through 123 Processing helix chain 'G' and resid 167 through 180 Processing helix chain 'G' and resid 203 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: 5.102A pdb=" N ALA G 287 " --> pdb=" O ARG G 283 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL G 288 " --> pdb=" O GLY G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 299 removed outlier: 3.571A pdb=" N ARG G 298 " --> pdb=" O ASN G 294 " (cutoff:3.500A) removed outlier: 3.500A 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: 3.528A 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 371 through 375 Processing helix chain 'G' and resid 376 through 382 removed outlier: 3.639A pdb=" N ALA 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 403 through 410 Processing helix chain 'G' and resid 410 through 431 Processing helix chain 'G' and resid 435 through 439 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: 6.517A pdb=" N PHE H 60 " --> pdb=" O ILE H 57 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL H 61 " --> pdb=" O GLU H 58 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG H 62 " --> pdb=" O GLY H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 77 Processing helix chain 'H' and resid 107 through 123 Processing helix chain 'H' and resid 167 through 180 Processing helix chain 'H' and resid 203 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: 5.102A pdb=" N ALA H 287 " --> pdb=" O ARG H 283 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL H 288 " --> pdb=" O GLY H 284 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 299 removed outlier: 3.571A pdb=" N ARG H 298 " --> pdb=" O ASN H 294 " (cutoff:3.500A) removed outlier: 3.501A 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: 3.527A 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 371 through 375 Processing helix chain 'H' and resid 376 through 382 removed outlier: 3.638A pdb=" N ALA 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 403 through 410 Processing helix chain 'H' and resid 410 through 431 Processing helix chain 'H' and resid 435 through 439 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: 6.534A pdb=" N PHE I 60 " --> pdb=" O ILE I 57 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL I 61 " --> pdb=" O GLU I 58 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG I 62 " --> pdb=" O GLY I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 77 Processing helix chain 'I' and resid 107 through 123 Processing helix chain 'I' and resid 167 through 180 Processing helix chain 'I' and resid 203 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: 5.102A pdb=" N ALA I 287 " --> pdb=" O ARG I 283 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL I 288 " --> pdb=" O GLY I 284 " (cutoff:3.500A) Processing helix chain 'I' and resid 294 through 299 removed outlier: 3.571A pdb=" N ARG I 298 " --> pdb=" O ASN I 294 " (cutoff:3.500A) removed outlier: 3.500A 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: 3.528A 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 371 through 375 Processing helix chain 'I' and resid 376 through 382 removed outlier: 3.639A pdb=" N ALA I 382 " --> pdb=" O GLU I 378 " (cutoff:3.500A) Processing helix chain 'I' and resid 391 through 402 Processing helix chain 'I' and resid 403 through 410 Processing helix chain 'I' and resid 410 through 431 Processing helix chain 'I' and resid 433 through 441 removed outlier: 3.549A pdb=" N ARG I 437 " --> pdb=" O HIS I 433 " (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: 6.524A pdb=" N PHE N 60 " --> pdb=" O ILE N 57 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL N 61 " --> pdb=" O GLU N 58 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG N 62 " --> pdb=" O GLY N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 74 through 77 Processing helix chain 'N' and resid 107 through 123 Processing helix chain 'N' and resid 167 through 180 Processing helix chain 'N' and resid 203 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: 5.102A pdb=" N ALA N 287 " --> pdb=" O ARG N 283 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL N 288 " --> pdb=" O GLY N 284 " (cutoff:3.500A) Processing helix chain 'N' and resid 294 through 299 removed outlier: 3.637A pdb=" N ARG N 298 " --> pdb=" O ASN N 294 " (cutoff:3.500A) removed outlier: 3.500A 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: 3.528A 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 371 through 375 Processing helix chain 'N' and resid 376 through 382 removed outlier: 3.639A pdb=" N ALA 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 403 through 410 Processing helix chain 'N' and resid 410 through 430 Processing helix chain 'N' and resid 433 through 441 removed outlier: 3.550A 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: 6.525A pdb=" N PHE O 60 " --> pdb=" O ILE O 57 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL O 61 " --> pdb=" O GLU O 58 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG O 62 " --> pdb=" O GLY O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 77 Processing helix chain 'O' and resid 107 through 123 Processing helix chain 'O' and resid 167 through 180 Processing helix chain 'O' and resid 203 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: 5.102A pdb=" N ALA O 287 " --> pdb=" O ARG O 283 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL O 288 " --> pdb=" O GLY O 284 " (cutoff:3.500A) Processing helix chain 'O' and resid 294 through 299 removed outlier: 3.571A pdb=" N ARG O 298 " --> pdb=" O ASN O 294 " (cutoff:3.500A) removed outlier: 3.501A 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: 3.528A 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 371 through 375 Processing helix chain 'O' and resid 376 through 382 removed outlier: 3.638A pdb=" N ALA 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 403 through 410 Processing helix chain 'O' and resid 410 through 430 Processing helix chain 'O' and resid 433 through 441 removed outlier: 3.550A 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: 6.525A pdb=" N PHE P 60 " --> pdb=" O ILE P 57 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL P 61 " --> pdb=" O GLU P 58 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG P 62 " --> pdb=" O GLY P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 74 through 77 Processing helix chain 'P' and resid 107 through 123 Processing helix chain 'P' and resid 167 through 180 Processing helix chain 'P' and resid 203 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: 5.102A pdb=" N ALA P 287 " --> pdb=" O ARG P 283 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL P 288 " --> pdb=" O GLY P 284 " (cutoff:3.500A) Processing helix chain 'P' and resid 294 through 299 removed outlier: 3.571A pdb=" N ARG P 298 " --> pdb=" O ASN P 294 " (cutoff:3.500A) removed outlier: 3.500A 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: 3.527A 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 371 through 375 Processing helix chain 'P' and resid 376 through 382 removed outlier: 3.637A pdb=" N ALA 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 403 through 410 Processing helix chain 'P' and resid 410 through 430 Processing helix chain 'P' and resid 433 through 441 removed outlier: 3.550A 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: 6.524A pdb=" N PHE Q 60 " --> pdb=" O ILE Q 57 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL Q 61 " --> pdb=" O GLU Q 58 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG Q 62 " --> pdb=" O GLY Q 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 77 Processing helix chain 'Q' and resid 107 through 123 Processing helix chain 'Q' and resid 167 through 180 Processing helix chain 'Q' and resid 203 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: 5.102A pdb=" N ALA Q 287 " --> pdb=" O ARG Q 283 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL Q 288 " --> pdb=" O GLY Q 284 " (cutoff:3.500A) Processing helix chain 'Q' and resid 294 through 299 removed outlier: 3.633A pdb=" N ARG Q 298 " --> pdb=" O ASN Q 294 " (cutoff:3.500A) removed outlier: 3.501A 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: 3.528A 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 371 through 375 Processing helix chain 'Q' and resid 376 through 382 removed outlier: 3.638A pdb=" N ALA 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 403 through 410 Processing helix chain 'Q' and resid 410 through 430 Processing helix chain 'Q' and resid 433 through 441 removed outlier: 3.550A 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: 6.534A pdb=" N PHE R 60 " --> pdb=" O ILE R 57 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL R 61 " --> pdb=" O GLU R 58 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG R 62 " --> pdb=" O GLY R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 77 Processing helix chain 'R' and resid 107 through 123 Processing helix chain 'R' and resid 167 through 180 Processing helix chain 'R' and resid 203 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: 5.102A pdb=" N ALA R 287 " --> pdb=" O ARG R 283 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL R 288 " --> pdb=" O GLY R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 299 removed outlier: 3.571A pdb=" N ARG R 298 " --> pdb=" O ASN R 294 " (cutoff:3.500A) removed outlier: 3.500A 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: 3.528A 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 371 through 375 Processing helix chain 'R' and resid 376 through 382 removed outlier: 3.638A pdb=" N ALA R 382 " --> pdb=" O GLU R 378 " (cutoff:3.500A) Processing helix chain 'R' and resid 391 through 402 Processing helix chain 'R' and resid 403 through 410 Processing helix chain 'R' and resid 410 through 431 Processing helix chain 'R' and resid 435 through 439 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: 6.534A pdb=" N PHE S 60 " --> pdb=" O ILE S 57 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL S 61 " --> pdb=" O GLU S 58 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG S 62 " --> pdb=" O GLY S 59 " (cutoff:3.500A) Processing helix chain 'S' and resid 74 through 77 Processing helix chain 'S' and resid 107 through 123 Processing helix chain 'S' and resid 167 through 180 Processing helix chain 'S' and resid 203 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: 5.102A pdb=" N ALA S 287 " --> pdb=" O ARG S 283 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL S 288 " --> pdb=" O GLY S 284 " (cutoff:3.500A) Processing helix chain 'S' and resid 294 through 299 removed outlier: 3.571A pdb=" N ARG S 298 " --> pdb=" O ASN S 294 " (cutoff:3.500A) removed outlier: 3.501A 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: 3.528A 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 371 through 375 Processing helix chain 'S' and resid 376 through 382 removed outlier: 3.639A pdb=" N ALA S 382 " --> pdb=" O GLU S 378 " (cutoff:3.500A) Processing helix chain 'S' and resid 391 through 402 Processing helix chain 'S' and resid 403 through 410 Processing helix chain 'S' and resid 410 through 431 Processing helix chain 'S' and resid 435 through 439 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: 6.534A pdb=" N PHE T 60 " --> pdb=" O ILE T 57 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL T 61 " --> pdb=" O GLU T 58 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG T 62 " --> pdb=" O GLY T 59 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 77 Processing helix chain 'T' and resid 107 through 123 Processing helix chain 'T' and resid 167 through 180 Processing helix chain 'T' and resid 203 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: 5.102A pdb=" N ALA T 287 " --> pdb=" O ARG T 283 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL T 288 " --> pdb=" O GLY T 284 " (cutoff:3.500A) Processing helix chain 'T' and resid 294 through 299 removed outlier: 3.570A pdb=" N ARG T 298 " --> pdb=" O ASN T 294 " (cutoff:3.500A) removed outlier: 3.500A 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: 3.527A 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 376 through 382 removed outlier: 3.639A pdb=" N ALA 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 403 through 410 Processing helix chain 'T' and resid 410 through 431 Processing helix chain 'T' and resid 433 through 441 removed outlier: 3.551A pdb=" N ARG T 437 " --> pdb=" O HIS T 433 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS A 88 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A 92 " --> pdb=" O ARG A 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR A 26 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE A 96 " --> pdb=" O THR A 26 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A 97 " --> pdb=" O TYR A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS A 88 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A 92 " --> pdb=" O ARG A 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR A 26 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE A 96 " --> pdb=" O THR A 26 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 150 removed outlier: 5.299A pdb=" N GLU A 149 " --> pdb=" O LYS A 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 183 through 188 removed outlier: 3.860A pdb=" N ALA A 185 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 197 " --> pdb=" O PRO A 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A 199 " --> pdb=" O PRO A 131 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 126 " --> pdb=" O PHE A 251 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS A 245 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS B 88 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET B 92 " --> pdb=" O ARG B 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR B 26 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ILE B 96 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR B 97 " --> pdb=" O TYR B 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS B 88 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET B 92 " --> pdb=" O ARG B 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR B 26 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ILE B 96 " --> pdb=" O THR B 26 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 150 removed outlier: 5.299A pdb=" N GLU B 149 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 183 through 188 removed outlier: 3.870A pdb=" N ALA B 185 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 197 " --> pdb=" O PRO B 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE B 199 " --> pdb=" O PRO B 131 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 126 " --> pdb=" O PHE B 251 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS B 245 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS C 88 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET C 92 " --> pdb=" O ARG C 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR C 26 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE C 96 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR C 97 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS C 88 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET C 92 " --> pdb=" O ARG C 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR C 26 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE C 96 " --> pdb=" O THR C 26 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 146 through 150 removed outlier: 5.299A pdb=" N GLU C 149 " --> pdb=" O LYS C 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 183 through 188 removed outlier: 3.864A pdb=" N ALA C 185 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE C 197 " --> pdb=" O PRO C 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE C 199 " --> pdb=" O PRO C 131 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU C 126 " --> pdb=" O PHE C 251 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS C 245 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS F 88 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET F 92 " --> pdb=" O ARG F 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR F 26 " --> pdb=" O CYS F 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE F 96 " --> pdb=" O THR F 26 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR F 97 " --> pdb=" O TYR F 69 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS F 88 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET F 92 " --> pdb=" O ARG F 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR F 26 " --> pdb=" O CYS F 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE F 96 " --> pdb=" O THR F 26 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 146 through 150 removed outlier: 5.299A pdb=" N GLU F 149 " --> pdb=" O LYS F 139 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 183 through 188 removed outlier: 3.849A pdb=" N ALA F 185 " --> pdb=" O ASP F 198 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE F 197 " --> pdb=" O PRO F 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE F 199 " --> pdb=" O PRO F 131 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU F 126 " --> pdb=" O PHE F 251 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS F 245 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS G 88 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET G 92 " --> pdb=" O ARG G 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR G 26 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE G 96 " --> pdb=" O THR G 26 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR G 97 " --> pdb=" O TYR G 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS G 88 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET G 92 " --> pdb=" O ARG G 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR G 26 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE G 96 " --> pdb=" O THR G 26 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 146 through 150 removed outlier: 5.299A pdb=" N GLU G 149 " --> pdb=" O LYS G 139 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 183 through 188 removed outlier: 3.852A pdb=" N ALA G 185 " --> pdb=" O ASP G 198 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE G 197 " --> pdb=" O PRO G 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE G 199 " --> pdb=" O PRO G 131 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU G 126 " --> pdb=" O PHE G 251 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS G 245 " --> pdb=" O GLU G 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 32 through 38 removed outlier: 5.548A pdb=" N LYS H 88 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET H 92 " --> pdb=" O ARG H 22 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N THR H 26 " --> pdb=" O CYS H 94 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ILE H 96 " --> pdb=" O THR H 26 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR H 97 " --> pdb=" O TYR H 69 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 32 through 38 removed outlier: 5.548A pdb=" N LYS H 88 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET H 92 " --> pdb=" O ARG H 22 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N THR H 26 " --> pdb=" O CYS H 94 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ILE H 96 " --> pdb=" O THR H 26 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 146 through 150 removed outlier: 5.299A pdb=" N GLU H 149 " --> pdb=" O LYS H 139 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 183 through 188 removed outlier: 3.868A pdb=" N ALA H 185 " --> pdb=" O ASP H 198 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE H 197 " --> pdb=" O PRO H 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE H 199 " --> pdb=" O PRO H 131 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU H 126 " --> pdb=" O PHE H 251 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS H 245 " --> pdb=" O GLU H 132 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS I 88 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET I 92 " --> pdb=" O ARG I 22 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR I 26 " --> pdb=" O CYS I 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE I 96 " --> pdb=" O THR I 26 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR I 97 " --> pdb=" O TYR I 69 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS I 88 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET I 92 " --> pdb=" O ARG I 22 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR I 26 " --> pdb=" O CYS I 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE I 96 " --> pdb=" O THR I 26 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 146 through 150 removed outlier: 5.299A pdb=" N GLU I 149 " --> pdb=" O LYS I 139 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 183 through 188 removed outlier: 3.859A pdb=" N ALA I 185 " --> pdb=" O ASP I 198 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE I 197 " --> pdb=" O PRO I 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE I 199 " --> pdb=" O PRO I 131 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU I 126 " --> pdb=" O PHE I 251 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS I 245 " --> pdb=" O GLU I 132 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS N 88 " --> pdb=" O VAL N 18 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET N 92 " --> pdb=" O ARG N 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR N 26 " --> pdb=" O CYS N 94 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ILE N 96 " --> pdb=" O THR N 26 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR N 97 " --> pdb=" O TYR N 69 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS N 88 " --> pdb=" O VAL N 18 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET N 92 " --> pdb=" O ARG N 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR N 26 " --> pdb=" O CYS N 94 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ILE N 96 " --> pdb=" O THR N 26 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 146 through 150 removed outlier: 5.299A pdb=" N GLU N 149 " --> pdb=" O LYS N 139 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 183 through 188 removed outlier: 3.856A pdb=" N ALA N 185 " --> pdb=" O ASP N 198 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE N 197 " --> pdb=" O PRO N 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE N 199 " --> pdb=" O PRO N 131 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU N 126 " --> pdb=" O PHE N 251 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS N 245 " --> pdb=" O GLU N 132 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS O 88 " --> pdb=" O VAL O 18 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET O 92 " --> pdb=" O ARG O 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR O 26 " --> pdb=" O CYS O 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE O 96 " --> pdb=" O THR O 26 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR O 97 " --> pdb=" O TYR O 69 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS O 88 " --> pdb=" O VAL O 18 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET O 92 " --> pdb=" O ARG O 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR O 26 " --> pdb=" O CYS O 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE O 96 " --> pdb=" O THR O 26 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 146 through 150 removed outlier: 5.299A pdb=" N GLU O 149 " --> pdb=" O LYS O 139 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 183 through 188 removed outlier: 3.865A pdb=" N ALA O 185 " --> pdb=" O ASP O 198 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE O 197 " --> pdb=" O PRO O 133 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE O 199 " --> pdb=" O PRO O 131 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU O 126 " --> pdb=" O PHE O 251 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS O 245 " --> pdb=" O GLU O 132 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'P' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS P 88 " --> pdb=" O VAL P 18 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET P 92 " --> pdb=" O ARG P 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR P 26 " --> pdb=" O CYS P 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE P 96 " --> pdb=" O THR P 26 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR P 97 " --> pdb=" O TYR P 69 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS P 88 " --> pdb=" O VAL P 18 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET P 92 " --> pdb=" O ARG P 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR P 26 " --> pdb=" O CYS P 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE P 96 " --> pdb=" O THR P 26 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 146 through 150 removed outlier: 5.299A pdb=" N GLU P 149 " --> pdb=" O LYS P 139 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 183 through 188 removed outlier: 3.851A pdb=" N ALA P 185 " --> pdb=" O ASP P 198 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE P 197 " --> pdb=" O PRO P 133 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE P 199 " --> pdb=" O PRO P 131 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU P 126 " --> pdb=" O PHE P 251 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS P 245 " --> pdb=" O GLU P 132 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS Q 88 " --> pdb=" O VAL Q 18 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET Q 92 " --> pdb=" O ARG Q 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR Q 26 " --> pdb=" O CYS Q 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE Q 96 " --> pdb=" O THR Q 26 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR Q 97 " --> pdb=" O TYR Q 69 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS Q 88 " --> pdb=" O VAL Q 18 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET Q 92 " --> pdb=" O ARG Q 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR Q 26 " --> pdb=" O CYS Q 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE Q 96 " --> pdb=" O THR Q 26 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 146 through 150 removed outlier: 5.299A pdb=" N GLU Q 149 " --> pdb=" O LYS Q 139 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 183 through 188 removed outlier: 3.858A pdb=" N ALA Q 185 " --> pdb=" O ASP Q 198 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE Q 197 " --> pdb=" O PRO Q 133 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE Q 199 " --> pdb=" O PRO Q 131 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU Q 126 " --> pdb=" O PHE Q 251 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS Q 245 " --> pdb=" O GLU Q 132 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'R' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS R 88 " --> pdb=" O VAL R 18 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET R 92 " --> pdb=" O ARG R 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR R 26 " --> pdb=" O CYS R 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE R 96 " --> pdb=" O THR R 26 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR R 97 " --> pdb=" O TYR R 69 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'R' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS R 88 " --> pdb=" O VAL R 18 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET R 92 " --> pdb=" O ARG R 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR R 26 " --> pdb=" O CYS R 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE R 96 " --> pdb=" O THR R 26 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 146 through 150 removed outlier: 5.299A pdb=" N GLU R 149 " --> pdb=" O LYS R 139 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'R' and resid 183 through 188 removed outlier: 3.860A pdb=" N ALA R 185 " --> pdb=" O ASP R 198 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE R 197 " --> pdb=" O PRO R 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE R 199 " --> pdb=" O PRO R 131 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU R 126 " --> pdb=" O PHE R 251 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS R 245 " --> pdb=" O GLU R 132 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 32 through 38 removed outlier: 5.550A pdb=" N LYS S 88 " --> pdb=" O VAL S 18 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET S 92 " --> pdb=" O ARG S 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR S 26 " --> pdb=" O CYS S 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE S 96 " --> pdb=" O THR S 26 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR S 97 " --> pdb=" O TYR S 69 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'S' and resid 32 through 38 removed outlier: 5.550A pdb=" N LYS S 88 " --> pdb=" O VAL S 18 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET S 92 " --> pdb=" O ARG S 22 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR S 26 " --> pdb=" O CYS S 94 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE S 96 " --> pdb=" O THR S 26 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'S' and resid 146 through 150 removed outlier: 5.299A pdb=" N GLU S 149 " --> pdb=" O LYS S 139 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'S' and resid 183 through 188 removed outlier: 3.845A pdb=" N ALA S 185 " --> pdb=" O ASP S 198 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE S 197 " --> pdb=" O PRO S 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE S 199 " --> pdb=" O PRO S 131 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU S 126 " --> pdb=" O PHE S 251 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS S 245 " --> pdb=" O GLU S 132 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'T' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS T 88 " --> pdb=" O VAL T 18 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET T 92 " --> pdb=" O ARG T 22 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR T 26 " --> pdb=" O CYS T 94 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ILE T 96 " --> pdb=" O THR T 26 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR T 97 " --> pdb=" O TYR T 69 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'T' and resid 32 through 38 removed outlier: 5.549A pdb=" N LYS T 88 " --> pdb=" O VAL T 18 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET T 92 " --> pdb=" O ARG T 22 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR T 26 " --> pdb=" O CYS T 94 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ILE T 96 " --> pdb=" O THR T 26 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'T' and resid 146 through 150 removed outlier: 5.300A pdb=" N GLU T 149 " --> pdb=" O LYS T 139 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'T' and resid 183 through 188 removed outlier: 3.866A pdb=" N ALA T 185 " --> pdb=" O ASP T 198 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE T 197 " --> pdb=" O PRO T 133 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE T 199 " --> pdb=" O PRO T 131 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU T 126 " --> pdb=" O PHE T 251 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS T 245 " --> pdb=" O GLU T 132 " (cutoff:3.500A) 2500 hydrogen bonds defined for protein. 7056 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: 22.81 Time building geometry restraints manager: 11.35 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: 8386 1.31 - 1.48: 19928 1.48 - 1.64: 22170 1.64 - 1.81: 434 Bond restraints: 51058 Sorted by residual: bond pdb=" NE2 GLN I 503 " pdb="HE21 GLN I 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 Q 503 " pdb="HE21 GLN Q 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 N 503 " pdb="HE22 GLN N 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 A 503 " pdb="HE21 GLN A 503 " ideal model delta sigma weight residual 0.860 1.017 -0.157 2.00e-02 2.50e+03 6.12e+01 bond pdb=" NE2 GLN N 503 " pdb="HE21 GLN N 503 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.12e+01 ... (remaining 51053 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 66599 1.78 - 3.56: 2430 3.56 - 5.34: 153 5.34 - 7.12: 48 7.12 - 8.90: 14 Bond angle restraints: 69244 Sorted by residual: angle pdb=" O LEU W 7 " pdb=" C LEU W 7 " pdb=" N PRO W 8 " ideal model delta sigma weight residual 121.37 116.64 4.73 9.00e-01 1.23e+00 2.76e+01 angle pdb=" O LEU D 7 " pdb=" C LEU D 7 " pdb=" N PRO D 8 " ideal model delta sigma weight residual 121.37 116.74 4.63 9.00e-01 1.23e+00 2.65e+01 angle pdb=" O LEU Y 7 " pdb=" C LEU Y 7 " pdb=" N PRO Y 8 " ideal model delta sigma weight residual 121.37 116.81 4.56 9.00e-01 1.23e+00 2.57e+01 angle pdb=" O LEU X 7 " pdb=" C LEU X 7 " pdb=" N PRO X 8 " ideal model delta sigma weight residual 121.37 116.96 4.41 9.00e-01 1.23e+00 2.40e+01 angle pdb=" CA LEU E 7 " pdb=" C LEU E 7 " pdb=" N PRO E 8 " ideal model delta sigma weight residual 117.52 121.07 -3.55 7.90e-01 1.60e+00 2.02e+01 ... (remaining 69239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 27182 17.67 - 35.34: 2318 35.34 - 53.01: 788 53.01 - 70.68: 206 70.68 - 88.35: 40 Dihedral angle restraints: 30534 sinusoidal: 12362 harmonic: 18172 Sorted by residual: dihedral pdb=" CB GLU F 424 " pdb=" CG GLU F 424 " pdb=" CD GLU F 424 " pdb=" OE1 GLU F 424 " ideal model delta sinusoidal sigma weight residual 0.00 88.35 -88.35 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU G 438 " pdb=" CG GLU G 438 " pdb=" CD GLU G 438 " pdb=" OE1 GLU G 438 " ideal model delta sinusoidal sigma weight residual 0.00 87.06 -87.06 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CG ARG H 316 " pdb=" CD ARG H 316 " pdb=" NE ARG H 316 " pdb=" CZ ARG H 316 " ideal model delta sinusoidal sigma weight residual 180.00 136.61 43.39 2 1.50e+01 4.44e-03 1.01e+01 ... (remaining 30531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 5740 0.052 - 0.103: 1243 0.103 - 0.155: 401 0.155 - 0.207: 53 0.207 - 0.258: 25 Chirality restraints: 7462 Sorted by residual: chirality pdb=" CB VAL N 35 " pdb=" CA VAL N 35 " pdb=" CG1 VAL N 35 " pdb=" CG2 VAL N 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB VAL T 35 " pdb=" CA VAL T 35 " pdb=" CG1 VAL T 35 " pdb=" CG2 VAL T 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB VAL B 35 " pdb=" CA VAL B 35 " pdb=" CG1 VAL B 35 " pdb=" CG2 VAL B 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.22 2.00e-01 2.50e+01 1.27e+00 ... (remaining 7459 not shown) Planarity restraints: 9030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 503 " 0.264 2.00e-02 2.50e+03 2.65e-01 1.06e+03 pdb=" CD GLN B 503 " -0.019 2.00e-02 2.50e+03 pdb=" OE1 GLN B 503 " -0.251 2.00e-02 2.50e+03 pdb=" NE2 GLN B 503 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN B 503 " 0.385 2.00e-02 2.50e+03 pdb="HE22 GLN B 503 " -0.376 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN T 503 " -0.262 2.00e-02 2.50e+03 2.63e-01 1.04e+03 pdb=" CD GLN T 503 " 0.019 2.00e-02 2.50e+03 pdb=" OE1 GLN T 503 " 0.249 2.00e-02 2.50e+03 pdb=" NE2 GLN T 503 " 0.003 2.00e-02 2.50e+03 pdb="HE21 GLN T 503 " -0.381 2.00e-02 2.50e+03 pdb="HE22 GLN T 503 " 0.372 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN O 503 " 0.231 2.00e-02 2.50e+03 2.28e-01 7.79e+02 pdb=" CD GLN O 503 " -0.018 2.00e-02 2.50e+03 pdb=" OE1 GLN O 503 " -0.219 2.00e-02 2.50e+03 pdb=" NE2 GLN O 503 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN O 503 " 0.328 2.00e-02 2.50e+03 pdb="HE22 GLN O 503 " -0.320 2.00e-02 2.50e+03 ... (remaining 9027 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.42: 342 2.42 - 2.96: 23994 2.96 - 3.51: 59870 3.51 - 4.05: 93150 4.05 - 4.60: 144831 Nonbonded interactions: 322187 Sorted by model distance: nonbonded pdb=" OE1 GLU O 196 " pdb="MG MG O 501 " model vdw 1.872 2.050 nonbonded pdb=" O GLY I 241 " pdb=" H1 GLN I 503 " model vdw 1.969 2.450 nonbonded pdb=" O GLY C 241 " pdb=" H1 GLN C 503 " model vdw 1.975 2.450 nonbonded pdb=" O GLY S 241 " pdb=" H1 GLN S 503 " model vdw 1.981 2.450 nonbonded pdb=" O GLY G 241 " pdb=" H1 GLN G 503 " model vdw 1.983 2.450 ... (remaining 322182 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: 2.290 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: 1.140 Extract box with map and model: 1.630 Check model and map are aligned: 0.300 Set scattering table: 0.370 Process input model: 95.670 Find NCS groups from input model: 2.200 Set up NCS constraints: 0.460 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:10.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 50918 Z= 0.303 Angle : 0.683 8.899 68936 Z= 0.439 Chirality : 0.050 0.258 7462 Planarity : 0.004 0.033 9030 Dihedral : 15.757 88.346 18788 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.66 % Allowed : 9.25 % Favored : 87.09 % 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: 0.50 (0.11), residues: 6216 helix: 1.79 (0.11), residues: 2338 sheet: -0.69 (0.16), residues: 1078 loop : -0.43 (0.12), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS Q 416 PHE 0.012 0.001 PHE C 60 TYR 0.012 0.001 TYR H 285 ARG 0.009 0.001 ARG G 145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1429 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1238 time to evaluate : 4.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.6657 (mt0) cc_final: 0.6350 (tt0) REVERT: A 29 LEU cc_start: 0.6719 (mm) cc_final: 0.6474 (mt) REVERT: A 63 ILE cc_start: 0.7186 (mt) cc_final: 0.6716 (mm) REVERT: A 67 ASP cc_start: 0.7184 (m-30) cc_final: 0.6843 (m-30) REVERT: A 88 LYS cc_start: 0.5589 (mttp) cc_final: 0.4846 (mmtm) REVERT: A 121 GLU cc_start: 0.5442 (mt-10) cc_final: 0.5166 (tp30) REVERT: A 184 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.5481 (mm-30) REVERT: A 223 ARG cc_start: 0.5668 (ttm-80) cc_final: 0.5294 (ttt180) REVERT: A 268 SER cc_start: 0.6388 (t) cc_final: 0.6046 (p) REVERT: A 315 ASN cc_start: 0.7534 (t0) cc_final: 0.7323 (t0) REVERT: A 316 ARG cc_start: 0.5225 (OUTLIER) cc_final: 0.3896 (tpt170) REVERT: A 347 MET cc_start: 0.6187 (mmm) cc_final: 0.5837 (mmp) REVERT: A 363 THR cc_start: 0.7798 (m) cc_final: 0.7365 (t) REVERT: A 390 GLU cc_start: 0.6548 (pm20) cc_final: 0.5943 (pt0) REVERT: A 401 LYS cc_start: 0.6184 (mtmt) cc_final: 0.5961 (mtpp) REVERT: A 415 GLU cc_start: 0.5349 (mt-10) cc_final: 0.4681 (tt0) REVERT: A 426 ASP cc_start: 0.5849 (t70) cc_final: 0.5235 (m-30) REVERT: A 427 MET cc_start: 0.6335 (mtp) cc_final: 0.6047 (mtp) REVERT: A 429 ARG cc_start: 0.5707 (ttp80) cc_final: 0.5158 (ttt90) REVERT: A 438 GLU cc_start: 0.6058 (mt-10) cc_final: 0.5809 (mt-10) REVERT: A 442 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6886 (mm-30) REVERT: B 16 GLN cc_start: 0.6627 (mt0) cc_final: 0.6348 (tt0) REVERT: B 36 GLU cc_start: 0.6689 (mp0) cc_final: 0.6414 (mp0) REVERT: B 47 ASP cc_start: 0.5494 (m-30) cc_final: 0.5244 (m-30) REVERT: B 73 ASP cc_start: 0.6991 (t0) cc_final: 0.6720 (t70) REVERT: B 75 ASP cc_start: 0.6948 (m-30) cc_final: 0.6704 (m-30) REVERT: B 88 LYS cc_start: 0.5650 (mttp) cc_final: 0.4943 (mttm) REVERT: B 95 ASP cc_start: 0.5927 (m-30) cc_final: 0.5681 (m-30) REVERT: B 100 ASP cc_start: 0.6155 (p0) cc_final: 0.5834 (p0) REVERT: B 117 LYS cc_start: 0.6030 (mmmm) cc_final: 0.5788 (mtmm) REVERT: B 178 GLU cc_start: 0.6692 (tm-30) cc_final: 0.6308 (mt-10) REVERT: B 184 GLU cc_start: 0.6335 (OUTLIER) cc_final: 0.5550 (mm-30) REVERT: B 248 MET cc_start: 0.7702 (ptp) cc_final: 0.7440 (mtt) REVERT: B 268 SER cc_start: 0.6665 (t) cc_final: 0.6405 (p) REVERT: B 303 TYR cc_start: 0.7044 (m-80) cc_final: 0.6841 (m-80) REVERT: B 347 MET cc_start: 0.6109 (mmm) cc_final: 0.5850 (mmp) REVERT: B 370 ARG cc_start: 0.4622 (OUTLIER) cc_final: 0.4112 (tmt-80) REVERT: B 390 GLU cc_start: 0.6445 (pm20) cc_final: 0.5990 (pt0) REVERT: B 411 GLU cc_start: 0.5884 (mp0) cc_final: 0.5619 (mt-10) REVERT: B 415 GLU cc_start: 0.5321 (mt-10) cc_final: 0.4753 (tt0) REVERT: B 424 GLU cc_start: 0.5853 (tt0) cc_final: 0.5637 (tt0) REVERT: B 426 ASP cc_start: 0.5718 (t70) cc_final: 0.5090 (m-30) REVERT: B 429 ARG cc_start: 0.5969 (ttp80) cc_final: 0.5578 (ttt90) REVERT: B 443 ILE cc_start: 0.6479 (mm) cc_final: 0.6267 (mp) REVERT: C 16 GLN cc_start: 0.6719 (mt0) cc_final: 0.6229 (tt0) REVERT: C 19 LYS cc_start: 0.6727 (mmtp) cc_final: 0.6449 (mmmt) REVERT: C 36 GLU cc_start: 0.6687 (mp0) cc_final: 0.6236 (mp0) REVERT: C 63 ILE cc_start: 0.7206 (mt) cc_final: 0.6753 (mm) REVERT: C 88 LYS cc_start: 0.5862 (mttp) cc_final: 0.5221 (mmmt) REVERT: C 92 MET cc_start: 0.7510 (mtm) cc_final: 0.7271 (mtm) REVERT: C 95 ASP cc_start: 0.6142 (m-30) cc_final: 0.5780 (m-30) REVERT: C 100 ASP cc_start: 0.6459 (p0) cc_final: 0.6173 (p0) REVERT: C 121 GLU cc_start: 0.5749 (mt-10) cc_final: 0.5446 (tp30) REVERT: C 178 GLU cc_start: 0.6686 (tm-30) cc_final: 0.6439 (mt-10) REVERT: C 184 GLU cc_start: 0.6246 (OUTLIER) cc_final: 0.5444 (mm-30) REVERT: C 268 SER cc_start: 0.6843 (t) cc_final: 0.6459 (p) REVERT: C 316 ARG cc_start: 0.4926 (OUTLIER) cc_final: 0.3761 (tpt170) REVERT: C 347 MET cc_start: 0.6034 (mmm) cc_final: 0.5734 (mmp) REVERT: C 363 THR cc_start: 0.7886 (m) cc_final: 0.7499 (t) REVERT: C 390 GLU cc_start: 0.6199 (pm20) cc_final: 0.5793 (pt0) REVERT: C 411 GLU cc_start: 0.5511 (mp0) cc_final: 0.5241 (mm-30) REVERT: C 415 GLU cc_start: 0.5453 (mt-10) cc_final: 0.4797 (tt0) REVERT: C 424 GLU cc_start: 0.5683 (tt0) cc_final: 0.5452 (tt0) REVERT: C 426 ASP cc_start: 0.5965 (t70) cc_final: 0.5230 (m-30) REVERT: C 429 ARG cc_start: 0.5813 (ttp80) cc_final: 0.5445 (ttt90) REVERT: C 438 GLU cc_start: 0.5872 (mt-10) cc_final: 0.5596 (mt-10) REVERT: C 442 GLU cc_start: 0.7381 (mm-30) cc_final: 0.5142 (mp0) REVERT: D 9 ARG cc_start: 0.0647 (OUTLIER) cc_final: 0.0053 (mtt180) REVERT: E 6 GLN cc_start: 0.0625 (OUTLIER) cc_final: -0.0109 (pt0) REVERT: E 9 ARG cc_start: 0.1238 (OUTLIER) cc_final: 0.0518 (mmt180) REVERT: F 16 GLN cc_start: 0.6640 (mt0) cc_final: 0.6341 (tt0) REVERT: F 47 ASP cc_start: 0.5339 (m-30) cc_final: 0.5046 (m-30) REVERT: F 63 ILE cc_start: 0.7181 (mt) cc_final: 0.6686 (mm) REVERT: F 67 ASP cc_start: 0.7183 (m-30) cc_final: 0.6819 (m-30) REVERT: F 88 LYS cc_start: 0.5609 (mttp) cc_final: 0.4833 (mmtm) REVERT: F 100 ASP cc_start: 0.6219 (p0) cc_final: 0.6012 (p0) REVERT: F 121 GLU cc_start: 0.5435 (mt-10) cc_final: 0.5227 (tp30) REVERT: F 184 GLU cc_start: 0.6285 (OUTLIER) cc_final: 0.5492 (mm-30) REVERT: F 223 ARG cc_start: 0.5663 (ttm-80) cc_final: 0.5283 (ttt180) REVERT: F 268 SER cc_start: 0.6435 (t) cc_final: 0.6053 (p) REVERT: F 315 ASN cc_start: 0.7537 (t0) cc_final: 0.7320 (t0) REVERT: F 347 MET cc_start: 0.6181 (mmm) cc_final: 0.5833 (mmp) REVERT: F 363 THR cc_start: 0.7819 (m) cc_final: 0.7376 (t) REVERT: F 390 GLU cc_start: 0.6545 (pm20) cc_final: 0.5941 (pt0) REVERT: F 415 GLU cc_start: 0.5479 (mt-10) cc_final: 0.4815 (tt0) REVERT: F 426 ASP cc_start: 0.5465 (t70) cc_final: 0.5074 (m-30) REVERT: F 427 MET cc_start: 0.6644 (OUTLIER) cc_final: 0.6358 (mtp) REVERT: F 429 ARG cc_start: 0.5491 (ttp80) cc_final: 0.4969 (ttt90) REVERT: F 442 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6306 (mm-30) REVERT: F 443 ILE cc_start: 0.5897 (mm) cc_final: 0.5620 (mp) REVERT: G 16 GLN cc_start: 0.6698 (mt0) cc_final: 0.6268 (tt0) REVERT: G 19 LYS cc_start: 0.6703 (mmtp) cc_final: 0.6293 (mmmt) REVERT: G 36 GLU cc_start: 0.6505 (mp0) cc_final: 0.6133 (mp0) REVERT: G 63 ILE cc_start: 0.7181 (mt) cc_final: 0.6759 (mm) REVERT: G 92 MET cc_start: 0.7562 (mtm) cc_final: 0.7157 (mtp) REVERT: G 95 ASP cc_start: 0.6103 (m-30) cc_final: 0.5816 (m-30) REVERT: G 128 ASN cc_start: 0.7408 (m-40) cc_final: 0.6815 (m-40) REVERT: G 178 GLU cc_start: 0.6589 (tm-30) cc_final: 0.6167 (mm-30) REVERT: G 184 GLU cc_start: 0.6312 (OUTLIER) cc_final: 0.5339 (mm-30) REVERT: G 268 SER cc_start: 0.6691 (t) cc_final: 0.6262 (p) REVERT: G 316 ARG cc_start: 0.5383 (OUTLIER) cc_final: 0.4056 (tpt170) REVERT: G 347 MET cc_start: 0.6293 (mmm) cc_final: 0.6019 (mmp) REVERT: G 363 THR cc_start: 0.7668 (m) cc_final: 0.7317 (t) REVERT: G 390 GLU cc_start: 0.6628 (pm20) cc_final: 0.6076 (pt0) REVERT: G 415 GLU cc_start: 0.5727 (mt-10) cc_final: 0.5058 (tt0) REVERT: G 419 GLU cc_start: 0.5569 (tt0) cc_final: 0.5159 (mt-10) REVERT: G 426 ASP cc_start: 0.5272 (t70) cc_final: 0.4611 (m-30) REVERT: G 427 MET cc_start: 0.5934 (mtp) cc_final: 0.5718 (mtp) REVERT: G 429 ARG cc_start: 0.5477 (ttp80) cc_final: 0.5151 (ttt90) REVERT: G 442 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6300 (mm-30) REVERT: G 443 ILE cc_start: 0.5778 (mm) cc_final: 0.5519 (mp) REVERT: H 8 ASP cc_start: 0.6058 (m-30) cc_final: 0.5724 (m-30) REVERT: H 19 LYS cc_start: 0.6782 (mmtp) cc_final: 0.6567 (mmpt) REVERT: H 36 GLU cc_start: 0.6694 (mp0) cc_final: 0.6448 (mt-10) REVERT: H 51 MET cc_start: 0.7484 (mmt) cc_final: 0.7227 (mmt) REVERT: H 63 ILE cc_start: 0.7152 (mt) cc_final: 0.6420 (mm) REVERT: H 88 LYS cc_start: 0.5695 (mttp) cc_final: 0.4996 (mmmt) REVERT: H 95 ASP cc_start: 0.6308 (m-30) cc_final: 0.6021 (m-30) REVERT: H 100 ASP cc_start: 0.6173 (p0) cc_final: 0.5942 (p0) REVERT: H 117 LYS cc_start: 0.6019 (mmmm) cc_final: 0.5713 (mttp) REVERT: H 121 GLU cc_start: 0.5448 (mt-10) cc_final: 0.5213 (tp30) REVERT: H 184 GLU cc_start: 0.6402 (OUTLIER) cc_final: 0.5623 (mm-30) REVERT: H 200 LYS cc_start: 0.6851 (ttmm) cc_final: 0.6568 (mmmt) REVERT: H 232 MET cc_start: 0.7591 (ttm) cc_final: 0.7156 (ttt) REVERT: H 268 SER cc_start: 0.6527 (t) cc_final: 0.6123 (p) REVERT: H 347 MET cc_start: 0.6041 (mmm) cc_final: 0.5798 (mmp) REVERT: H 363 THR cc_start: 0.7733 (m) cc_final: 0.7370 (t) REVERT: H 390 GLU cc_start: 0.6512 (pm20) cc_final: 0.5940 (pt0) REVERT: H 415 GLU cc_start: 0.5531 (mt-10) cc_final: 0.4849 (tt0) REVERT: H 426 ASP cc_start: 0.5222 (t70) cc_final: 0.4668 (m-30) REVERT: H 429 ARG cc_start: 0.5370 (ttp80) cc_final: 0.5117 (ttt90) REVERT: H 442 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6442 (mm-30) REVERT: H 443 ILE cc_start: 0.5796 (mm) cc_final: 0.5429 (mp) REVERT: I 16 GLN cc_start: 0.6697 (mt0) cc_final: 0.6228 (tt0) REVERT: I 19 LYS cc_start: 0.6718 (mmtp) cc_final: 0.6442 (mmmt) REVERT: I 36 GLU cc_start: 0.6682 (mp0) cc_final: 0.6249 (mp0) REVERT: I 63 ILE cc_start: 0.7165 (mt) cc_final: 0.6736 (mm) REVERT: I 88 LYS cc_start: 0.5832 (mttp) cc_final: 0.5156 (mmmt) REVERT: I 95 ASP cc_start: 0.6197 (m-30) cc_final: 0.5852 (m-30) REVERT: I 100 ASP cc_start: 0.6460 (p0) cc_final: 0.6162 (p0) REVERT: I 121 GLU cc_start: 0.5818 (mt-10) cc_final: 0.5510 (tp30) REVERT: I 163 ASP cc_start: 0.3800 (OUTLIER) cc_final: 0.3457 (m-30) REVERT: I 178 GLU cc_start: 0.6692 (tm-30) cc_final: 0.6425 (mt-10) REVERT: I 184 GLU cc_start: 0.6245 (OUTLIER) cc_final: 0.5420 (mm-30) REVERT: I 200 LYS cc_start: 0.6751 (ttmm) cc_final: 0.6526 (mmmm) REVERT: I 232 MET cc_start: 0.7730 (ttm) cc_final: 0.7273 (ttm) REVERT: I 268 SER cc_start: 0.6811 (t) cc_final: 0.6442 (p) REVERT: I 347 MET cc_start: 0.6021 (mmm) cc_final: 0.5750 (mmp) REVERT: I 363 THR cc_start: 0.7871 (m) cc_final: 0.7488 (t) REVERT: I 390 GLU cc_start: 0.6193 (pm20) cc_final: 0.5769 (pt0) REVERT: I 411 GLU cc_start: 0.5486 (mp0) cc_final: 0.5233 (mm-30) REVERT: I 415 GLU cc_start: 0.5576 (mt-10) cc_final: 0.4904 (tt0) REVERT: I 426 ASP cc_start: 0.5433 (t70) cc_final: 0.4777 (m-30) REVERT: I 427 MET cc_start: 0.6004 (mtp) cc_final: 0.5797 (mtp) REVERT: I 429 ARG cc_start: 0.5514 (ttp80) cc_final: 0.5214 (ttt90) REVERT: J 6 GLN cc_start: 0.0849 (OUTLIER) cc_final: -0.0222 (pm20) REVERT: J 7 LEU cc_start: 0.1505 (OUTLIER) cc_final: 0.0720 (mt) REVERT: J 9 ARG cc_start: 0.1311 (OUTLIER) cc_final: 0.0568 (mtt180) REVERT: K 6 GLN cc_start: 0.0494 (OUTLIER) cc_final: -0.0673 (pt0) REVERT: K 7 LEU cc_start: 0.1371 (OUTLIER) cc_final: 0.0990 (mt) REVERT: L 6 GLN cc_start: 0.0729 (OUTLIER) cc_final: -0.0246 (pt0) REVERT: L 7 LEU cc_start: 0.1825 (OUTLIER) cc_final: 0.1414 (mt) REVERT: M 6 GLN cc_start: 0.0646 (OUTLIER) cc_final: -0.0200 (pm20) REVERT: M 7 LEU cc_start: 0.1054 (OUTLIER) cc_final: 0.0586 (mt) REVERT: N 16 GLN cc_start: 0.6732 (mt0) cc_final: 0.6363 (tt0) REVERT: N 19 LYS cc_start: 0.6686 (mmtp) cc_final: 0.6266 (mmmt) REVERT: N 36 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6495 (mp0) REVERT: N 63 ILE cc_start: 0.7144 (mt) cc_final: 0.6654 (mm) REVERT: N 88 LYS cc_start: 0.5810 (mttp) cc_final: 0.5039 (mmtt) REVERT: N 92 MET cc_start: 0.7570 (mtm) cc_final: 0.7164 (mtp) REVERT: N 95 ASP cc_start: 0.6111 (m-30) cc_final: 0.5813 (m-30) REVERT: N 128 ASN cc_start: 0.7411 (m-40) cc_final: 0.6806 (m-40) REVERT: N 178 GLU cc_start: 0.6587 (tm-30) cc_final: 0.6171 (mm-30) REVERT: N 184 GLU cc_start: 0.6265 (OUTLIER) cc_final: 0.5313 (mm-30) REVERT: N 200 LYS cc_start: 0.6944 (ttmm) cc_final: 0.6735 (mmmm) REVERT: N 268 SER cc_start: 0.6667 (t) cc_final: 0.6252 (p) REVERT: N 347 MET cc_start: 0.6284 (mmm) cc_final: 0.6021 (mmp) REVERT: N 363 THR cc_start: 0.7660 (m) cc_final: 0.7311 (t) REVERT: N 390 GLU cc_start: 0.6641 (pm20) cc_final: 0.6084 (pt0) REVERT: N 415 GLU cc_start: 0.5635 (mt-10) cc_final: 0.5003 (tt0) REVERT: N 424 GLU cc_start: 0.5946 (tt0) cc_final: 0.5738 (tt0) REVERT: N 426 ASP cc_start: 0.5840 (t70) cc_final: 0.5229 (m-30) REVERT: N 427 MET cc_start: 0.6286 (mtp) cc_final: 0.5817 (mtp) REVERT: N 429 ARG cc_start: 0.5758 (ttp80) cc_final: 0.5397 (ttt90) REVERT: N 438 GLU cc_start: 0.5757 (mt-10) cc_final: 0.5533 (mt-10) REVERT: N 443 ILE cc_start: 0.6506 (mm) cc_final: 0.6280 (mp) REVERT: O 8 ASP cc_start: 0.6044 (m-30) cc_final: 0.5745 (m-30) REVERT: O 19 LYS cc_start: 0.6764 (mmtp) cc_final: 0.6540 (mmpt) REVERT: O 63 ILE cc_start: 0.7131 (mt) cc_final: 0.6649 (mm) REVERT: O 88 LYS cc_start: 0.5687 (mttp) cc_final: 0.4999 (mmmt) REVERT: O 95 ASP cc_start: 0.6349 (m-30) cc_final: 0.6041 (m-30) REVERT: O 100 ASP cc_start: 0.6200 (p0) cc_final: 0.5975 (p0) REVERT: O 117 LYS cc_start: 0.5877 (mmmm) cc_final: 0.5584 (mttp) REVERT: O 121 GLU cc_start: 0.5524 (mt-10) cc_final: 0.5300 (tp30) REVERT: O 184 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.5623 (mm-30) REVERT: O 200 LYS cc_start: 0.6882 (ttmm) cc_final: 0.6599 (mmmt) REVERT: O 268 SER cc_start: 0.6487 (t) cc_final: 0.6141 (p) REVERT: O 347 MET cc_start: 0.6045 (mmm) cc_final: 0.5796 (mmp) REVERT: O 363 THR cc_start: 0.7949 (m) cc_final: 0.7589 (t) REVERT: O 390 GLU cc_start: 0.6499 (pm20) cc_final: 0.5927 (pt0) REVERT: O 415 GLU cc_start: 0.5297 (mt-10) cc_final: 0.4712 (tt0) REVERT: O 426 ASP cc_start: 0.5875 (t70) cc_final: 0.5172 (m-30) REVERT: O 427 MET cc_start: 0.6348 (mtp) cc_final: 0.6098 (mtp) REVERT: O 429 ARG cc_start: 0.5846 (ttp80) cc_final: 0.5566 (ttt90) REVERT: O 443 ILE cc_start: 0.6453 (mm) cc_final: 0.6231 (mp) REVERT: P 16 GLN cc_start: 0.6569 (mt0) cc_final: 0.6232 (tt0) REVERT: P 19 LYS cc_start: 0.6596 (mmtp) cc_final: 0.6214 (mmtp) REVERT: P 29 LEU cc_start: 0.6805 (mm) cc_final: 0.6516 (mt) REVERT: P 36 GLU cc_start: 0.6491 (mp0) cc_final: 0.6118 (mp0) REVERT: P 63 ILE cc_start: 0.7281 (mt) cc_final: 0.6847 (mm) REVERT: P 88 LYS cc_start: 0.5635 (mttp) cc_final: 0.5407 (mmmm) REVERT: P 117 LYS cc_start: 0.5988 (mmmm) cc_final: 0.5645 (mtmm) REVERT: P 121 GLU cc_start: 0.5471 (mt-10) cc_final: 0.5230 (tp30) REVERT: P 178 GLU cc_start: 0.6721 (tm-30) cc_final: 0.6356 (mt-10) REVERT: P 179 MET cc_start: 0.6504 (ttm) cc_final: 0.6247 (ttm) REVERT: P 184 GLU cc_start: 0.6261 (OUTLIER) cc_final: 0.5457 (mm-30) REVERT: P 223 ARG cc_start: 0.5772 (ttm-80) cc_final: 0.5529 (ttt180) REVERT: P 268 SER cc_start: 0.6388 (t) cc_final: 0.6099 (p) REVERT: P 390 GLU cc_start: 0.6668 (pm20) cc_final: 0.6027 (pt0) REVERT: P 411 GLU cc_start: 0.5380 (mp0) cc_final: 0.5103 (mm-30) REVERT: P 415 GLU cc_start: 0.5675 (mt-10) cc_final: 0.4967 (tt0) REVERT: P 424 GLU cc_start: 0.5795 (tt0) cc_final: 0.5542 (tt0) REVERT: P 426 ASP cc_start: 0.5877 (t70) cc_final: 0.5258 (m-30) REVERT: P 427 MET cc_start: 0.6601 (mtp) cc_final: 0.6179 (mtp) REVERT: P 429 ARG cc_start: 0.5860 (ttp80) cc_final: 0.5491 (ttt90) REVERT: P 442 GLU cc_start: 0.7345 (mm-30) cc_final: 0.5135 (mp0) REVERT: P 443 ILE cc_start: 0.6327 (mm) cc_final: 0.6092 (mp) REVERT: Q 16 GLN cc_start: 0.6988 (mt0) cc_final: 0.6715 (mt0) REVERT: Q 19 LYS cc_start: 0.6630 (mmtp) cc_final: 0.6368 (mmtp) REVERT: Q 51 MET cc_start: 0.7401 (mmt) cc_final: 0.7027 (mmt) REVERT: Q 63 ILE cc_start: 0.7310 (mt) cc_final: 0.6668 (mm) REVERT: Q 67 ASP cc_start: 0.7114 (m-30) cc_final: 0.6688 (m-30) REVERT: Q 88 LYS cc_start: 0.5695 (mttp) cc_final: 0.4960 (mmmt) REVERT: Q 100 ASP cc_start: 0.6336 (p0) cc_final: 0.6086 (p0) REVERT: Q 117 LYS cc_start: 0.6038 (mmmm) cc_final: 0.5831 (mtmm) REVERT: Q 126 GLU cc_start: 0.7097 (pt0) cc_final: 0.6832 (pt0) REVERT: Q 178 GLU cc_start: 0.6468 (tm-30) cc_final: 0.6265 (mt-10) REVERT: Q 184 GLU cc_start: 0.6269 (OUTLIER) cc_final: 0.5711 (mm-30) REVERT: Q 200 LYS cc_start: 0.6821 (ttmm) cc_final: 0.6601 (mmtt) REVERT: Q 223 ARG cc_start: 0.5949 (ttm-80) cc_final: 0.5727 (ttt180) REVERT: Q 268 SER cc_start: 0.6737 (t) cc_final: 0.6302 (p) REVERT: Q 347 MET cc_start: 0.6459 (mmm) cc_final: 0.6191 (mmp) REVERT: Q 363 THR cc_start: 0.7775 (m) cc_final: 0.7392 (t) REVERT: Q 390 GLU cc_start: 0.6450 (pm20) cc_final: 0.5844 (pt0) REVERT: Q 411 GLU cc_start: 0.5438 (mp0) cc_final: 0.5182 (mt-10) REVERT: Q 415 GLU cc_start: 0.5648 (mt-10) cc_final: 0.5026 (tt0) REVERT: Q 426 ASP cc_start: 0.5825 (t70) cc_final: 0.5113 (m-30) REVERT: Q 427 MET cc_start: 0.6293 (mtp) cc_final: 0.6062 (mtp) REVERT: Q 429 ARG cc_start: 0.5808 (ttp80) cc_final: 0.5327 (ttt90) REVERT: Q 442 GLU cc_start: 0.7335 (mm-30) cc_final: 0.5094 (mp0) REVERT: Q 443 ILE cc_start: 0.6477 (mm) cc_final: 0.6119 (mp) REVERT: R 16 GLN cc_start: 0.6975 (mt0) cc_final: 0.6631 (tt0) REVERT: R 19 LYS cc_start: 0.6635 (mmtp) cc_final: 0.6399 (mmtp) REVERT: R 63 ILE cc_start: 0.7305 (mt) cc_final: 0.6833 (mm) REVERT: R 67 ASP cc_start: 0.7139 (m-30) cc_final: 0.6719 (m-30) REVERT: R 88 LYS cc_start: 0.5680 (mttp) cc_final: 0.4957 (mmmt) REVERT: R 100 ASP cc_start: 0.6344 (p0) cc_final: 0.6082 (p0) REVERT: R 117 LYS cc_start: 0.6073 (mmmm) cc_final: 0.5861 (mtmm) REVERT: R 126 GLU cc_start: 0.7093 (pt0) cc_final: 0.6823 (pt0) REVERT: R 178 GLU cc_start: 0.6484 (tm-30) cc_final: 0.6271 (mt-10) REVERT: R 184 GLU cc_start: 0.6245 (OUTLIER) cc_final: 0.5669 (mm-30) REVERT: R 199 PHE cc_start: 0.6459 (m-10) cc_final: 0.6254 (m-10) REVERT: R 200 LYS cc_start: 0.6799 (ttmm) cc_final: 0.6534 (mmtt) REVERT: R 223 ARG cc_start: 0.5954 (ttm-80) cc_final: 0.5714 (ttt180) REVERT: R 268 SER cc_start: 0.6718 (t) cc_final: 0.6294 (p) REVERT: R 316 ARG cc_start: 0.5072 (OUTLIER) cc_final: 0.3859 (tpt170) REVERT: R 347 MET cc_start: 0.6375 (mmm) cc_final: 0.6103 (mmp) REVERT: R 363 THR cc_start: 0.7773 (m) cc_final: 0.7389 (t) REVERT: R 390 GLU cc_start: 0.6464 (pm20) cc_final: 0.5868 (pt0) REVERT: R 411 GLU cc_start: 0.5443 (mp0) cc_final: 0.5186 (mt-10) REVERT: R 415 GLU cc_start: 0.5783 (mt-10) cc_final: 0.5148 (tt0) REVERT: R 426 ASP cc_start: 0.5371 (t70) cc_final: 0.4819 (m-30) REVERT: R 427 MET cc_start: 0.6266 (mtp) cc_final: 0.5905 (mtp) REVERT: R 429 ARG cc_start: 0.5523 (ttp80) cc_final: 0.5107 (ttt90) REVERT: R 442 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.5915 (mm-30) REVERT: S 16 GLN cc_start: 0.6557 (mt0) cc_final: 0.6279 (tt0) REVERT: S 19 LYS cc_start: 0.6607 (mmtp) cc_final: 0.6248 (mmtp) REVERT: S 29 LEU cc_start: 0.6854 (mm) cc_final: 0.6521 (mt) REVERT: S 36 GLU cc_start: 0.6584 (mp0) cc_final: 0.6233 (mp0) REVERT: S 60 PHE cc_start: 0.6986 (p90) cc_final: 0.6737 (p90) REVERT: S 63 ILE cc_start: 0.7237 (mt) cc_final: 0.6753 (mm) REVERT: S 88 LYS cc_start: 0.5663 (mttp) cc_final: 0.5437 (mmmm) REVERT: S 117 LYS cc_start: 0.5938 (mmmm) cc_final: 0.5722 (mtmm) REVERT: S 121 GLU cc_start: 0.5549 (mt-10) cc_final: 0.5301 (tp30) REVERT: S 178 GLU cc_start: 0.6736 (tm-30) cc_final: 0.6340 (mt-10) REVERT: S 179 MET cc_start: 0.6512 (ttm) cc_final: 0.6257 (ttm) REVERT: S 184 GLU cc_start: 0.6329 (OUTLIER) cc_final: 0.5573 (mm-30) REVERT: S 223 ARG cc_start: 0.5746 (ttm-80) cc_final: 0.5507 (ttt180) REVERT: S 268 SER cc_start: 0.6292 (t) cc_final: 0.6027 (p) REVERT: S 347 MET cc_start: 0.6445 (mmm) cc_final: 0.6244 (mmp) REVERT: S 390 GLU cc_start: 0.6662 (pm20) cc_final: 0.6023 (pt0) REVERT: S 411 GLU cc_start: 0.5386 (mp0) cc_final: 0.5099 (mm-30) REVERT: S 415 GLU cc_start: 0.5590 (mt-10) cc_final: 0.4941 (tt0) REVERT: S 426 ASP cc_start: 0.5634 (t70) cc_final: 0.5137 (m-30) REVERT: S 429 ARG cc_start: 0.5584 (ttp80) cc_final: 0.5242 (ttt90) REVERT: S 442 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6381 (mm-30) REVERT: T 16 GLN cc_start: 0.6658 (mt0) cc_final: 0.6383 (tt0) REVERT: T 36 GLU cc_start: 0.6691 (mp0) cc_final: 0.6419 (mp0) REVERT: T 47 ASP cc_start: 0.5585 (m-30) cc_final: 0.5334 (m-30) REVERT: T 73 ASP cc_start: 0.6912 (t0) cc_final: 0.6635 (t70) REVERT: T 75 ASP cc_start: 0.6996 (m-30) cc_final: 0.6723 (m-30) REVERT: T 88 LYS cc_start: 0.5630 (mttp) cc_final: 0.4910 (mttm) REVERT: T 95 ASP cc_start: 0.5991 (m-30) cc_final: 0.5707 (m-30) REVERT: T 100 ASP cc_start: 0.6171 (p0) cc_final: 0.5842 (p0) REVERT: T 178 GLU cc_start: 0.6728 (tm-30) cc_final: 0.6346 (mt-10) REVERT: T 184 GLU cc_start: 0.6331 (OUTLIER) cc_final: 0.5541 (mm-30) REVERT: T 223 ARG cc_start: 0.5913 (ttm-80) cc_final: 0.5706 (ttt180) REVERT: T 268 SER cc_start: 0.6720 (t) cc_final: 0.6450 (p) REVERT: T 303 TYR cc_start: 0.7083 (m-80) cc_final: 0.6859 (m-80) REVERT: T 347 MET cc_start: 0.6119 (mmm) cc_final: 0.5863 (mmp) REVERT: T 390 GLU cc_start: 0.6425 (pm20) cc_final: 0.5957 (pt0) REVERT: T 411 GLU cc_start: 0.5870 (mp0) cc_final: 0.5615 (mt-10) REVERT: T 415 GLU cc_start: 0.5362 (mt-10) cc_final: 0.4776 (tt0) REVERT: T 426 ASP cc_start: 0.5107 (t70) cc_final: 0.4545 (m-30) REVERT: T 429 ARG cc_start: 0.5653 (ttp80) cc_final: 0.5322 (ttt90) REVERT: U 6 GLN cc_start: 0.0385 (OUTLIER) cc_final: -0.0611 (pm20) REVERT: U 7 LEU cc_start: 0.0849 (OUTLIER) cc_final: 0.0401 (mt) REVERT: V 6 GLN cc_start: 0.0418 (OUTLIER) cc_final: -0.0461 (pm20) REVERT: V 7 LEU cc_start: 0.0490 (OUTLIER) cc_final: 0.0037 (mt) REVERT: X 9 ARG cc_start: 0.1350 (OUTLIER) cc_final: 0.0625 (mmt180) REVERT: Y 9 ARG cc_start: 0.0740 (OUTLIER) cc_final: 0.0248 (mmt180) REVERT: Z 6 GLN cc_start: 0.0615 (OUTLIER) cc_final: -0.0213 (pt0) REVERT: Z 10 PHE cc_start: 0.0470 (OUTLIER) cc_final: 0.0201 (m-80) REVERT: a 10 PHE cc_start: 0.0548 (OUTLIER) cc_final: -0.0309 (t80) REVERT: b 6 GLN cc_start: 0.0195 (OUTLIER) cc_final: -0.0717 (pm20) REVERT: b 7 LEU cc_start: 0.0979 (OUTLIER) cc_final: 0.0621 (mt) outliers start: 191 outliers final: 27 residues processed: 1355 average time/residue: 1.3226 time to fit residues: 2225.8591 Evaluate side-chains 947 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 870 time to evaluate : 4.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 370 ARG Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain D residue 9 ARG Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 9 ARG Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 240 ASN Chi-restraints excluded: chain F residue 427 MET Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain G residue 316 ARG Chi-restraints excluded: chain G residue 442 GLU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 184 GLU Chi-restraints excluded: chain H residue 442 GLU Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 240 ASN Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 9 ARG Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 184 GLU Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 184 GLU Chi-restraints excluded: chain P residue 240 ASN Chi-restraints excluded: chain Q residue 35 VAL Chi-restraints excluded: chain Q residue 184 GLU Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 184 GLU Chi-restraints excluded: chain R residue 316 ARG Chi-restraints excluded: chain R residue 442 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 184 GLU Chi-restraints excluded: chain S residue 224 LYS Chi-restraints excluded: chain S residue 240 ASN Chi-restraints excluded: chain S residue 442 GLU Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 184 GLU Chi-restraints excluded: chain T residue 240 ASN Chi-restraints excluded: chain U residue 6 GLN Chi-restraints excluded: chain U residue 7 LEU Chi-restraints excluded: chain U residue 10 PHE Chi-restraints excluded: chain V residue 6 GLN Chi-restraints excluded: chain V residue 7 LEU Chi-restraints excluded: chain V residue 10 PHE Chi-restraints excluded: chain X residue 9 ARG Chi-restraints excluded: chain Y residue 9 ARG Chi-restraints excluded: chain Z residue 6 GLN Chi-restraints excluded: chain Z residue 10 PHE Chi-restraints excluded: chain a residue 10 PHE Chi-restraints excluded: chain b residue 6 GLN Chi-restraints excluded: chain b residue 7 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 520 optimal weight: 6.9990 chunk 466 optimal weight: 6.9990 chunk 259 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 314 optimal weight: 0.9990 chunk 249 optimal weight: 4.9990 chunk 482 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 chunk 293 optimal weight: 6.9990 chunk 359 optimal weight: 4.9990 chunk 559 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 GLN A 281 HIS B 17 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN B 187 HIS ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 ASN C 17 ASN ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN C 281 HIS F 17 ASN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 GLN F 187 HIS F 281 HIS G 17 ASN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 GLN ** G 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN H 34 ASN H 187 HIS ** H 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 17 ASN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 GLN I 281 HIS N 17 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 GLN ** N 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN O 34 ASN O 167 ASN ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 17 ASN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 41 GLN P 187 HIS P 281 HIS Q 17 ASN ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 41 GLN Q 187 HIS ** Q 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 ASN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 187 HIS ** R 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 17 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 187 HIS S 281 HIS T 17 ASN ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 41 GLN ** T 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 315 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 50918 Z= 0.243 Angle : 0.522 4.836 68936 Z= 0.273 Chirality : 0.042 0.151 7462 Planarity : 0.004 0.032 9030 Dihedral : 7.836 67.851 6984 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.67 % Allowed : 13.44 % Favored : 81.88 % 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: 0.67 (0.11), residues: 6216 helix: 2.06 (0.11), residues: 2366 sheet: -0.78 (0.15), residues: 1148 loop : -0.40 (0.12), residues: 2702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP R 435 HIS 0.007 0.001 HIS N 245 PHE 0.017 0.002 PHE I 296 TYR 0.017 0.002 TYR F 285 ARG 0.004 0.001 ARG I 145 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 854 time to evaluate : 4.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.6337 (mt0) cc_final: 0.5831 (tp40) REVERT: A 33 LYS cc_start: 0.6599 (OUTLIER) cc_final: 0.6227 (mmtp) REVERT: A 63 ILE cc_start: 0.7344 (mt) cc_final: 0.6809 (mm) REVERT: A 73 ASP cc_start: 0.6781 (t70) cc_final: 0.6099 (t0) REVERT: A 95 ASP cc_start: 0.6733 (m-30) cc_final: 0.6308 (m-30) REVERT: A 184 GLU cc_start: 0.6436 (tt0) cc_final: 0.6145 (mt-10) REVERT: A 268 SER cc_start: 0.5902 (t) cc_final: 0.5417 (p) REVERT: A 347 MET cc_start: 0.6155 (mmm) cc_final: 0.5777 (mmp) REVERT: A 390 GLU cc_start: 0.6537 (pm20) cc_final: 0.5976 (pt0) REVERT: A 415 GLU cc_start: 0.5182 (mt-10) cc_final: 0.4613 (tt0) REVERT: A 426 ASP cc_start: 0.5382 (t70) cc_final: 0.4759 (m-30) REVERT: A 427 MET cc_start: 0.6323 (mtp) cc_final: 0.5933 (mtp) REVERT: A 429 ARG cc_start: 0.5734 (ttp80) cc_final: 0.5233 (ttt90) REVERT: B 36 GLU cc_start: 0.7200 (mp0) cc_final: 0.6821 (mp0) REVERT: B 47 ASP cc_start: 0.5585 (m-30) cc_final: 0.5305 (m-30) REVERT: B 73 ASP cc_start: 0.6722 (t0) cc_final: 0.6489 (t70) REVERT: B 95 ASP cc_start: 0.6506 (m-30) cc_final: 0.6147 (m-30) REVERT: B 117 LYS cc_start: 0.5863 (mmmm) cc_final: 0.5476 (mttp) REVERT: B 126 GLU cc_start: 0.7667 (pt0) cc_final: 0.6956 (tt0) REVERT: B 159 LEU cc_start: 0.5191 (OUTLIER) cc_final: 0.4917 (tt) REVERT: B 178 GLU cc_start: 0.6530 (tm-30) cc_final: 0.6263 (mt-10) REVERT: B 184 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.5714 (tt0) REVERT: B 347 MET cc_start: 0.6090 (mmm) cc_final: 0.5742 (mmp) REVERT: B 390 GLU cc_start: 0.6353 (pm20) cc_final: 0.5906 (pt0) REVERT: B 411 GLU cc_start: 0.5836 (mp0) cc_final: 0.5564 (mt-10) REVERT: B 415 GLU cc_start: 0.5211 (mt-10) cc_final: 0.4630 (tt0) REVERT: B 426 ASP cc_start: 0.5589 (t70) cc_final: 0.4952 (m-30) REVERT: B 429 ARG cc_start: 0.6091 (ttp80) cc_final: 0.5713 (ttt90) REVERT: B 442 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7019 (mm-30) REVERT: B 443 ILE cc_start: 0.6555 (mm) cc_final: 0.6319 (mp) REVERT: C 95 ASP cc_start: 0.6774 (m-30) cc_final: 0.6387 (m-30) REVERT: C 139 LYS cc_start: 0.6838 (mttt) cc_final: 0.6346 (mttm) REVERT: C 178 GLU cc_start: 0.6608 (tm-30) cc_final: 0.6312 (mt-10) REVERT: C 184 GLU cc_start: 0.6490 (OUTLIER) cc_final: 0.5854 (tt0) REVERT: C 316 ARG cc_start: 0.5220 (OUTLIER) cc_final: 0.4104 (tpt170) REVERT: C 347 MET cc_start: 0.6256 (mmm) cc_final: 0.5880 (mmp) REVERT: C 363 THR cc_start: 0.7910 (m) cc_final: 0.7561 (t) REVERT: C 390 GLU cc_start: 0.6238 (pm20) cc_final: 0.5960 (pt0) REVERT: C 411 GLU cc_start: 0.5491 (mp0) cc_final: 0.5228 (mm-30) REVERT: C 415 GLU cc_start: 0.5204 (mt-10) cc_final: 0.4635 (tt0) REVERT: C 426 ASP cc_start: 0.5561 (t70) cc_final: 0.4974 (m-30) REVERT: C 429 ARG cc_start: 0.5705 (ttp80) cc_final: 0.5305 (ttt90) REVERT: E 6 GLN cc_start: 0.0811 (OUTLIER) cc_final: 0.0156 (pt0) REVERT: F 16 GLN cc_start: 0.6235 (mt0) cc_final: 0.5769 (tp40) REVERT: F 33 LYS cc_start: 0.6664 (OUTLIER) cc_final: 0.6262 (mmtp) REVERT: F 63 ILE cc_start: 0.7356 (mt) cc_final: 0.6816 (mm) REVERT: F 68 MET cc_start: 0.6966 (OUTLIER) cc_final: 0.6640 (mtt) REVERT: F 73 ASP cc_start: 0.6790 (t70) cc_final: 0.6133 (t0) REVERT: F 95 ASP cc_start: 0.6619 (m-30) cc_final: 0.6164 (m-30) REVERT: F 145 ARG cc_start: 0.6300 (mmp80) cc_final: 0.5791 (mtp180) REVERT: F 184 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.6147 (mt-10) REVERT: F 223 ARG cc_start: 0.5546 (ttm-80) cc_final: 0.5114 (ttt180) REVERT: F 268 SER cc_start: 0.5937 (t) cc_final: 0.5456 (p) REVERT: F 347 MET cc_start: 0.6186 (mmm) cc_final: 0.5798 (mmp) REVERT: F 390 GLU cc_start: 0.6488 (pm20) cc_final: 0.5950 (pt0) REVERT: F 415 GLU cc_start: 0.5255 (mt-10) cc_final: 0.4698 (tt0) REVERT: F 426 ASP cc_start: 0.5396 (t70) cc_final: 0.4859 (m-30) REVERT: F 427 MET cc_start: 0.6348 (ttp) cc_final: 0.5883 (mtp) REVERT: F 429 ARG cc_start: 0.5820 (ttp80) cc_final: 0.5287 (ttt90) REVERT: F 442 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6718 (mm-30) REVERT: F 443 ILE cc_start: 0.6343 (mm) cc_final: 0.6107 (mp) REVERT: G 19 LYS cc_start: 0.6447 (mmtp) cc_final: 0.6226 (mmtp) REVERT: G 36 GLU cc_start: 0.7414 (mp0) cc_final: 0.7047 (mp0) REVERT: G 68 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6368 (mtt) REVERT: G 92 MET cc_start: 0.7624 (mtm) cc_final: 0.7236 (mtp) REVERT: G 95 ASP cc_start: 0.6544 (m-30) cc_final: 0.6253 (m-30) REVERT: G 139 LYS cc_start: 0.6991 (mttt) cc_final: 0.6650 (mttm) REVERT: G 178 GLU cc_start: 0.6538 (tm-30) cc_final: 0.6225 (mm-30) REVERT: G 184 GLU cc_start: 0.6443 (OUTLIER) cc_final: 0.5755 (tt0) REVERT: G 347 MET cc_start: 0.6318 (mmm) cc_final: 0.5993 (mmp) REVERT: G 390 GLU cc_start: 0.6585 (pm20) cc_final: 0.6135 (pt0) REVERT: G 415 GLU cc_start: 0.5302 (mt-10) cc_final: 0.4735 (tt0) REVERT: G 426 ASP cc_start: 0.5160 (t70) cc_final: 0.4543 (m-30) REVERT: G 429 ARG cc_start: 0.5803 (ttp80) cc_final: 0.5496 (ttt90) REVERT: G 442 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6730 (mm-30) REVERT: G 443 ILE cc_start: 0.6035 (mm) cc_final: 0.5798 (mp) REVERT: H 8 ASP cc_start: 0.5985 (m-30) cc_final: 0.5772 (m-30) REVERT: H 36 GLU cc_start: 0.7502 (mp0) cc_final: 0.7230 (mp0) REVERT: H 95 ASP cc_start: 0.6612 (m-30) cc_final: 0.6339 (m-30) REVERT: H 121 GLU cc_start: 0.5435 (mt-10) cc_final: 0.5223 (tp30) REVERT: H 163 ASP cc_start: 0.4226 (OUTLIER) cc_final: 0.3938 (m-30) REVERT: H 184 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.5868 (mm-30) REVERT: H 200 LYS cc_start: 0.7058 (ttmm) cc_final: 0.6743 (mmmt) REVERT: H 203 ASP cc_start: 0.6462 (m-30) cc_final: 0.6162 (m-30) REVERT: H 347 MET cc_start: 0.6090 (mmm) cc_final: 0.5770 (mmp) REVERT: H 390 GLU cc_start: 0.6507 (pm20) cc_final: 0.6025 (pt0) REVERT: H 415 GLU cc_start: 0.5217 (mt-10) cc_final: 0.4619 (tt0) REVERT: H 426 ASP cc_start: 0.5349 (t70) cc_final: 0.4769 (m-30) REVERT: H 442 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6616 (mm-30) REVERT: H 443 ILE cc_start: 0.5935 (mm) cc_final: 0.5704 (mp) REVERT: I 16 GLN cc_start: 0.6277 (mt0) cc_final: 0.5868 (tp40) REVERT: I 95 ASP cc_start: 0.6784 (m-30) cc_final: 0.6380 (m-30) REVERT: I 178 GLU cc_start: 0.6559 (tm-30) cc_final: 0.6308 (mt-10) REVERT: I 184 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.5781 (tt0) REVERT: I 200 LYS cc_start: 0.7024 (ttmm) cc_final: 0.6704 (mmmm) REVERT: I 232 MET cc_start: 0.7593 (ttm) cc_final: 0.7244 (ttm) REVERT: I 347 MET cc_start: 0.6257 (mmm) cc_final: 0.5864 (mmp) REVERT: I 363 THR cc_start: 0.7928 (m) cc_final: 0.7575 (t) REVERT: I 390 GLU cc_start: 0.6229 (pm20) cc_final: 0.5956 (pt0) REVERT: I 411 GLU cc_start: 0.5514 (mp0) cc_final: 0.5269 (mm-30) REVERT: I 415 GLU cc_start: 0.5371 (mt-10) cc_final: 0.4763 (tt0) REVERT: I 426 ASP cc_start: 0.5415 (t70) cc_final: 0.4812 (m-30) REVERT: I 427 MET cc_start: 0.5797 (mtp) cc_final: 0.5273 (mtp) REVERT: I 429 ARG cc_start: 0.5835 (ttp80) cc_final: 0.5519 (ttt90) REVERT: J 6 GLN cc_start: 0.1016 (OUTLIER) cc_final: -0.0009 (pm20) REVERT: J 7 LEU cc_start: 0.1799 (OUTLIER) cc_final: 0.0970 (tt) REVERT: L 6 GLN cc_start: 0.0754 (OUTLIER) cc_final: -0.0251 (pt0) REVERT: L 7 LEU cc_start: 0.1747 (OUTLIER) cc_final: 0.1367 (mt) REVERT: N 19 LYS cc_start: 0.6438 (mmtp) cc_final: 0.6221 (mmtp) REVERT: N 68 MET cc_start: 0.7049 (OUTLIER) cc_final: 0.6315 (mtt) REVERT: N 92 MET cc_start: 0.7624 (mtm) cc_final: 0.7239 (mtp) REVERT: N 95 ASP cc_start: 0.6558 (m-30) cc_final: 0.6258 (m-30) REVERT: N 178 GLU cc_start: 0.6535 (tm-30) cc_final: 0.6226 (mm-30) REVERT: N 184 GLU cc_start: 0.6317 (OUTLIER) cc_final: 0.5635 (tt0) REVERT: N 200 LYS cc_start: 0.7090 (ttmm) cc_final: 0.6618 (mmmm) REVERT: N 347 MET cc_start: 0.6313 (mmm) cc_final: 0.5994 (mmp) REVERT: N 390 GLU cc_start: 0.6582 (pm20) cc_final: 0.6158 (pt0) REVERT: N 415 GLU cc_start: 0.5493 (mt-10) cc_final: 0.4944 (tt0) REVERT: N 424 GLU cc_start: 0.6068 (tt0) cc_final: 0.5753 (tt0) REVERT: N 426 ASP cc_start: 0.5343 (t70) cc_final: 0.4747 (m-30) REVERT: N 427 MET cc_start: 0.6469 (mtp) cc_final: 0.5866 (mtp) REVERT: N 429 ARG cc_start: 0.5802 (ttp80) cc_final: 0.5417 (ttt90) REVERT: N 442 GLU cc_start: 0.7278 (mm-30) cc_final: 0.6949 (mm-30) REVERT: N 443 ILE cc_start: 0.6534 (mm) cc_final: 0.6270 (mp) REVERT: O 16 GLN cc_start: 0.6095 (mt0) cc_final: 0.5759 (tp40) REVERT: O 68 MET cc_start: 0.6805 (OUTLIER) cc_final: 0.6276 (mtt) REVERT: O 95 ASP cc_start: 0.6599 (m-30) cc_final: 0.6320 (m-30) REVERT: O 121 GLU cc_start: 0.5475 (mt-10) cc_final: 0.5244 (tp30) REVERT: O 163 ASP cc_start: 0.4357 (OUTLIER) cc_final: 0.4110 (m-30) REVERT: O 184 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.5887 (mm-30) REVERT: O 200 LYS cc_start: 0.7049 (ttmm) cc_final: 0.6736 (mmmt) REVERT: O 203 ASP cc_start: 0.6476 (m-30) cc_final: 0.6186 (m-30) REVERT: O 347 MET cc_start: 0.6126 (mmm) cc_final: 0.5807 (mmp) REVERT: O 390 GLU cc_start: 0.6494 (pm20) cc_final: 0.6021 (pt0) REVERT: O 415 GLU cc_start: 0.5123 (mt-10) cc_final: 0.4523 (tt0) REVERT: O 426 ASP cc_start: 0.5508 (t70) cc_final: 0.4757 (m-30) REVERT: O 429 ARG cc_start: 0.5664 (ttp80) cc_final: 0.5452 (ttt90) REVERT: O 443 ILE cc_start: 0.6254 (mm) cc_final: 0.6025 (mp) REVERT: P 16 GLN cc_start: 0.6167 (mt0) cc_final: 0.5864 (mt0) REVERT: P 19 LYS cc_start: 0.6587 (mmtp) cc_final: 0.6324 (mmtp) REVERT: P 36 GLU cc_start: 0.7518 (mp0) cc_final: 0.7170 (mp0) REVERT: P 63 ILE cc_start: 0.7445 (mt) cc_final: 0.6885 (mm) REVERT: P 68 MET cc_start: 0.7060 (OUTLIER) cc_final: 0.6393 (mtt) REVERT: P 73 ASP cc_start: 0.6890 (t70) cc_final: 0.6452 (t0) REVERT: P 117 LYS cc_start: 0.5875 (mmmm) cc_final: 0.5646 (mtmm) REVERT: P 126 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7690 (tt0) REVERT: P 178 GLU cc_start: 0.6374 (tm-30) cc_final: 0.6052 (mt-10) REVERT: P 179 MET cc_start: 0.6310 (ttm) cc_final: 0.6005 (ttm) REVERT: P 184 GLU cc_start: 0.6348 (OUTLIER) cc_final: 0.6036 (mt-10) REVERT: P 390 GLU cc_start: 0.6521 (pm20) cc_final: 0.5931 (pt0) REVERT: P 411 GLU cc_start: 0.5417 (mp0) cc_final: 0.5100 (mt-10) REVERT: P 415 GLU cc_start: 0.5564 (mt-10) cc_final: 0.4897 (tt0) REVERT: P 426 ASP cc_start: 0.5370 (t70) cc_final: 0.4800 (m-30) REVERT: P 427 MET cc_start: 0.6591 (mtp) cc_final: 0.6239 (mtp) REVERT: P 429 ARG cc_start: 0.5826 (ttp80) cc_final: 0.5397 (ttt90) REVERT: P 442 GLU cc_start: 0.7320 (mm-30) cc_final: 0.6876 (mm-30) REVERT: P 443 ILE cc_start: 0.6319 (mm) cc_final: 0.5945 (mp) REVERT: Q 16 GLN cc_start: 0.6468 (mt0) cc_final: 0.6172 (mm-40) REVERT: Q 67 ASP cc_start: 0.7256 (m-30) cc_final: 0.6877 (m-30) REVERT: Q 73 ASP cc_start: 0.6587 (t70) cc_final: 0.5998 (t0) REVERT: Q 95 ASP cc_start: 0.7073 (m-30) cc_final: 0.6644 (m-30) REVERT: Q 100 ASP cc_start: 0.6221 (p0) cc_final: 0.6007 (p0) REVERT: Q 117 LYS cc_start: 0.5940 (mmmm) cc_final: 0.5690 (mtmm) REVERT: Q 126 GLU cc_start: 0.7273 (pt0) cc_final: 0.6606 (pt0) REVERT: Q 184 GLU cc_start: 0.6236 (OUTLIER) cc_final: 0.5636 (tt0) REVERT: Q 200 LYS cc_start: 0.6981 (ttmm) cc_final: 0.6681 (mmtt) REVERT: Q 347 MET cc_start: 0.6426 (mmm) cc_final: 0.6058 (mmp) REVERT: Q 390 GLU cc_start: 0.6450 (pm20) cc_final: 0.5867 (pt0) REVERT: Q 415 GLU cc_start: 0.5678 (mt-10) cc_final: 0.5087 (tt0) REVERT: Q 426 ASP cc_start: 0.5460 (t70) cc_final: 0.4827 (m-30) REVERT: Q 427 MET cc_start: 0.6526 (mtp) cc_final: 0.6252 (mtp) REVERT: Q 429 ARG cc_start: 0.5543 (ttp80) cc_final: 0.5193 (ttt90) REVERT: Q 442 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6883 (mm-30) REVERT: R 67 ASP cc_start: 0.7242 (m-30) cc_final: 0.6916 (m-30) REVERT: R 73 ASP cc_start: 0.6605 (t70) cc_final: 0.6011 (t0) REVERT: R 95 ASP cc_start: 0.7081 (m-30) cc_final: 0.6653 (m-30) REVERT: R 100 ASP cc_start: 0.6228 (p0) cc_final: 0.6001 (p0) REVERT: R 117 LYS cc_start: 0.5966 (mmmm) cc_final: 0.5726 (mtmm) REVERT: R 126 GLU cc_start: 0.7269 (pt0) cc_final: 0.6599 (pt0) REVERT: R 184 GLU cc_start: 0.6232 (OUTLIER) cc_final: 0.5630 (tt0) REVERT: R 200 LYS cc_start: 0.6983 (ttmm) cc_final: 0.6691 (mmtt) REVERT: R 347 MET cc_start: 0.6427 (mmm) cc_final: 0.6057 (mmp) REVERT: R 390 GLU cc_start: 0.6451 (pm20) cc_final: 0.5828 (pt0) REVERT: R 415 GLU cc_start: 0.5617 (mt-10) cc_final: 0.5008 (tt0) REVERT: R 426 ASP cc_start: 0.5186 (t70) cc_final: 0.4664 (m-30) REVERT: R 427 MET cc_start: 0.5855 (mtp) cc_final: 0.5630 (mtp) REVERT: R 429 ARG cc_start: 0.5728 (ttp80) cc_final: 0.5399 (ttt90) REVERT: R 438 GLU cc_start: 0.5413 (OUTLIER) cc_final: 0.5187 (pt0) REVERT: R 442 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6578 (mm-30) REVERT: S 16 GLN cc_start: 0.6233 (mt0) cc_final: 0.5938 (mt0) REVERT: S 19 LYS cc_start: 0.6588 (mmtp) cc_final: 0.6334 (mmtp) REVERT: S 36 GLU cc_start: 0.7419 (mp0) cc_final: 0.7160 (mp0) REVERT: S 63 ILE cc_start: 0.7424 (mt) cc_final: 0.6839 (mm) REVERT: S 68 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6396 (mtt) REVERT: S 95 ASP cc_start: 0.6738 (m-30) cc_final: 0.6231 (m-30) REVERT: S 121 GLU cc_start: 0.5494 (mt-10) cc_final: 0.5276 (tp30) REVERT: S 126 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7698 (tt0) REVERT: S 178 GLU cc_start: 0.6639 (tm-30) cc_final: 0.6315 (mt-10) REVERT: S 179 MET cc_start: 0.6322 (ttm) cc_final: 0.6046 (ttm) REVERT: S 184 GLU cc_start: 0.6319 (OUTLIER) cc_final: 0.5596 (mm-30) REVERT: S 223 ARG cc_start: 0.6035 (ttm-80) cc_final: 0.5759 (ttt180) REVERT: S 347 MET cc_start: 0.6350 (mmm) cc_final: 0.6029 (mmp) REVERT: S 390 GLU cc_start: 0.6542 (pm20) cc_final: 0.5913 (pt0) REVERT: S 411 GLU cc_start: 0.5377 (mp0) cc_final: 0.5099 (mt-10) REVERT: S 415 GLU cc_start: 0.5623 (mt-10) cc_final: 0.4972 (tt0) REVERT: S 426 ASP cc_start: 0.5225 (t70) cc_final: 0.4726 (m-30) REVERT: S 429 ARG cc_start: 0.5997 (ttp80) cc_final: 0.5642 (ttt90) REVERT: S 442 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6695 (mm-30) REVERT: T 36 GLU cc_start: 0.7212 (mp0) cc_final: 0.6809 (mp0) REVERT: T 47 ASP cc_start: 0.5619 (m-30) cc_final: 0.5355 (m-30) REVERT: T 73 ASP cc_start: 0.6721 (t0) cc_final: 0.6469 (t70) REVERT: T 95 ASP cc_start: 0.6506 (m-30) cc_final: 0.6159 (m-30) REVERT: T 126 GLU cc_start: 0.7632 (pt0) cc_final: 0.6883 (tt0) REVERT: T 159 LEU cc_start: 0.5178 (OUTLIER) cc_final: 0.4891 (tt) REVERT: T 178 GLU cc_start: 0.6540 (tm-30) cc_final: 0.6259 (mt-10) REVERT: T 184 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.5700 (tt0) REVERT: T 347 MET cc_start: 0.6111 (mmm) cc_final: 0.5769 (mmp) REVERT: T 390 GLU cc_start: 0.6393 (pm20) cc_final: 0.5916 (pt0) REVERT: T 411 GLU cc_start: 0.5659 (mp0) cc_final: 0.5345 (mt-10) REVERT: T 415 GLU cc_start: 0.5285 (mt-10) cc_final: 0.4743 (tt0) REVERT: T 426 ASP cc_start: 0.5227 (t70) cc_final: 0.4688 (m-30) REVERT: T 427 MET cc_start: 0.5898 (mtp) cc_final: 0.5684 (mtp) REVERT: T 429 ARG cc_start: 0.6052 (ttp80) cc_final: 0.5724 (ttt90) REVERT: T 442 GLU cc_start: 0.7307 (mm-30) cc_final: 0.6851 (mm-30) REVERT: Z 10 PHE cc_start: 0.0592 (OUTLIER) cc_final: 0.0183 (m-80) REVERT: a 10 PHE cc_start: 0.0661 (OUTLIER) cc_final: -0.0139 (t80) outliers start: 244 outliers final: 59 residues processed: 1027 average time/residue: 1.3504 time to fit residues: 1724.3587 Evaluate side-chains 881 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 781 time to evaluate : 4.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 168 CYS Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 442 GLU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 163 ASP Chi-restraints excluded: chain H residue 184 GLU Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 278 MET Chi-restraints excluded: chain H residue 331 ARG Chi-restraints excluded: chain H residue 355 LEU Chi-restraints excluded: chain H residue 439 GLN Chi-restraints excluded: chain H residue 442 GLU Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 248 MET Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 10 PHE Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 10 PHE Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 68 MET Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 184 GLU Chi-restraints excluded: chain N residue 216 LEU Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 68 MET Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain O residue 163 ASP Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain O residue 278 MET Chi-restraints excluded: chain O residue 355 LEU Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 51 MET Chi-restraints excluded: chain P residue 68 MET Chi-restraints excluded: chain P residue 125 THR Chi-restraints excluded: chain P residue 126 GLU Chi-restraints excluded: chain P residue 184 GLU Chi-restraints excluded: chain P residue 278 MET Chi-restraints excluded: chain Q residue 35 VAL Chi-restraints excluded: chain Q residue 125 THR Chi-restraints excluded: chain Q residue 184 GLU Chi-restraints excluded: chain Q residue 224 LYS Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 184 GLU Chi-restraints excluded: chain R residue 438 GLU Chi-restraints excluded: chain R residue 439 GLN Chi-restraints excluded: chain R residue 442 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 51 MET Chi-restraints excluded: chain S residue 68 MET Chi-restraints excluded: chain S residue 125 THR Chi-restraints excluded: chain S residue 126 GLU Chi-restraints excluded: chain S residue 184 GLU Chi-restraints excluded: chain S residue 442 GLU Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 125 THR Chi-restraints excluded: chain T residue 159 LEU Chi-restraints excluded: chain T residue 184 GLU Chi-restraints excluded: chain T residue 328 LEU Chi-restraints excluded: chain U residue 10 PHE Chi-restraints excluded: chain V residue 10 PHE Chi-restraints excluded: chain Z residue 10 PHE Chi-restraints excluded: chain a residue 10 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 310 optimal weight: 0.8980 chunk 173 optimal weight: 5.9990 chunk 465 optimal weight: 8.9990 chunk 380 optimal weight: 0.0060 chunk 154 optimal weight: 10.0000 chunk 560 optimal weight: 4.9990 chunk 605 optimal weight: 6.9990 chunk 499 optimal weight: 10.0000 chunk 555 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 chunk 449 optimal weight: 2.9990 overall best weight: 2.3802 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 HIS A 225 HIS B 17 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 ASN ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 HIS C 225 HIS ** C 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 ASN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 HIS G 17 ASN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 HIS ** G 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN H 34 ASN ** H 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 315 ASN ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 17 ASN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 187 HIS I 225 HIS N 17 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 225 HIS ** N 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN O 34 ASN O 167 ASN O 187 HIS O 225 HIS ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 315 ASN ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 17 ASN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 128 ASN P 225 HIS ** P 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 17 ASN ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 167 ASN Q 225 HIS ** Q 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 ASN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 225 HIS ** R 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 17 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 128 ASN ** S 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 17 ASN ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 187 HIS T 225 HIS ** T 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 50918 Z= 0.277 Angle : 0.536 4.802 68936 Z= 0.280 Chirality : 0.043 0.153 7462 Planarity : 0.004 0.036 9030 Dihedral : 6.894 71.293 6888 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.91 % Allowed : 14.99 % Favored : 81.10 % 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: 0.44 (0.11), residues: 6216 helix: 1.91 (0.10), residues: 2366 sheet: -0.77 (0.17), residues: 868 loop : -0.69 (0.11), residues: 2982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 435 HIS 0.006 0.001 HIS G 245 PHE 0.017 0.002 PHE P 71 TYR 0.016 0.002 TYR N 285 ARG 0.004 0.001 ARG Q 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 724 time to evaluate : 4.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.6287 (mt0) cc_final: 0.5769 (tp40) REVERT: A 33 LYS cc_start: 0.6693 (OUTLIER) cc_final: 0.6299 (mmtp) REVERT: A 73 ASP cc_start: 0.6676 (t70) cc_final: 0.5850 (t70) REVERT: A 95 ASP cc_start: 0.6863 (m-30) cc_final: 0.6355 (m-30) REVERT: A 184 GLU cc_start: 0.6260 (OUTLIER) cc_final: 0.6006 (mt-10) REVERT: A 203 ASP cc_start: 0.6591 (m-30) cc_final: 0.6381 (m-30) REVERT: A 316 ARG cc_start: 0.5377 (OUTLIER) cc_final: 0.4131 (tpt170) REVERT: A 347 MET cc_start: 0.6122 (mmm) cc_final: 0.5785 (mmp) REVERT: A 390 GLU cc_start: 0.6316 (pm20) cc_final: 0.5898 (pt0) REVERT: A 415 GLU cc_start: 0.5211 (mt-10) cc_final: 0.4643 (tt0) REVERT: A 426 ASP cc_start: 0.5464 (t70) cc_final: 0.4905 (m-30) REVERT: A 427 MET cc_start: 0.6325 (mtp) cc_final: 0.5847 (mtp) REVERT: A 429 ARG cc_start: 0.5852 (ttp80) cc_final: 0.5404 (ttt90) REVERT: B 47 ASP cc_start: 0.5671 (m-30) cc_final: 0.5404 (m-30) REVERT: B 95 ASP cc_start: 0.6863 (m-30) cc_final: 0.6422 (m-30) REVERT: B 117 LYS cc_start: 0.5880 (mmmm) cc_final: 0.5532 (mttp) REVERT: B 126 GLU cc_start: 0.7798 (pt0) cc_final: 0.7249 (tt0) REVERT: B 159 LEU cc_start: 0.5520 (OUTLIER) cc_final: 0.5181 (tt) REVERT: B 178 GLU cc_start: 0.6416 (tm-30) cc_final: 0.6186 (mt-10) REVERT: B 184 GLU cc_start: 0.6501 (tt0) cc_final: 0.5750 (tt0) REVERT: B 347 MET cc_start: 0.6066 (mmm) cc_final: 0.5731 (mmp) REVERT: B 390 GLU cc_start: 0.6339 (pm20) cc_final: 0.5898 (pt0) REVERT: B 411 GLU cc_start: 0.5821 (mp0) cc_final: 0.5577 (mt-10) REVERT: B 415 GLU cc_start: 0.5264 (mt-10) cc_final: 0.4690 (tt0) REVERT: B 426 ASP cc_start: 0.5513 (t70) cc_final: 0.4951 (m-30) REVERT: B 429 ARG cc_start: 0.6139 (ttp80) cc_final: 0.5809 (ttt90) REVERT: B 442 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7147 (mm-30) REVERT: B 443 ILE cc_start: 0.6467 (mm) cc_final: 0.6191 (mp) REVERT: C 95 ASP cc_start: 0.6903 (m-30) cc_final: 0.6532 (m-30) REVERT: C 178 GLU cc_start: 0.6498 (tm-30) cc_final: 0.6226 (mt-10) REVERT: C 184 GLU cc_start: 0.6291 (tt0) cc_final: 0.5700 (tt0) REVERT: C 316 ARG cc_start: 0.5228 (OUTLIER) cc_final: 0.4151 (tpt170) REVERT: C 347 MET cc_start: 0.6157 (mmm) cc_final: 0.5847 (mmp) REVERT: C 415 GLU cc_start: 0.5192 (mt-10) cc_final: 0.4636 (tt0) REVERT: C 426 ASP cc_start: 0.5586 (t70) cc_final: 0.4988 (m-30) REVERT: C 429 ARG cc_start: 0.5943 (ttp80) cc_final: 0.5666 (ttt90) REVERT: C 442 GLU cc_start: 0.7235 (mm-30) cc_final: 0.7029 (mm-30) REVERT: F 16 GLN cc_start: 0.6182 (mt0) cc_final: 0.5678 (tp40) REVERT: F 33 LYS cc_start: 0.6659 (OUTLIER) cc_final: 0.6312 (mmtt) REVERT: F 68 MET cc_start: 0.6898 (OUTLIER) cc_final: 0.6321 (mtt) REVERT: F 73 ASP cc_start: 0.6594 (t70) cc_final: 0.5782 (t70) REVERT: F 95 ASP cc_start: 0.6857 (m-30) cc_final: 0.6359 (m-30) REVERT: F 184 GLU cc_start: 0.6187 (OUTLIER) cc_final: 0.5638 (tt0) REVERT: F 203 ASP cc_start: 0.6593 (m-30) cc_final: 0.6391 (m-30) REVERT: F 347 MET cc_start: 0.6120 (mmm) cc_final: 0.5783 (mmp) REVERT: F 390 GLU cc_start: 0.6306 (pm20) cc_final: 0.5899 (pt0) REVERT: F 415 GLU cc_start: 0.5095 (mt-10) cc_final: 0.4527 (tt0) REVERT: F 426 ASP cc_start: 0.5521 (t70) cc_final: 0.4948 (m-30) REVERT: F 427 MET cc_start: 0.6288 (ttp) cc_final: 0.5911 (mtp) REVERT: F 429 ARG cc_start: 0.5837 (ttp80) cc_final: 0.5356 (ttt90) REVERT: F 439 GLN cc_start: 0.5806 (OUTLIER) cc_final: 0.5512 (mm110) REVERT: F 442 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7134 (mm-30) REVERT: G 16 GLN cc_start: 0.6146 (mt0) cc_final: 0.5943 (mm-40) REVERT: G 92 MET cc_start: 0.7759 (mtm) cc_final: 0.7369 (mtp) REVERT: G 95 ASP cc_start: 0.6829 (m-30) cc_final: 0.6445 (m-30) REVERT: G 139 LYS cc_start: 0.7035 (mttt) cc_final: 0.6712 (mttm) REVERT: G 178 GLU cc_start: 0.6401 (tm-30) cc_final: 0.6165 (mm-30) REVERT: G 184 GLU cc_start: 0.6322 (tt0) cc_final: 0.5770 (tt0) REVERT: G 347 MET cc_start: 0.6266 (mmm) cc_final: 0.5932 (mmp) REVERT: G 390 GLU cc_start: 0.6399 (pm20) cc_final: 0.6072 (pt0) REVERT: G 415 GLU cc_start: 0.5223 (mt-10) cc_final: 0.4668 (tt0) REVERT: G 419 GLU cc_start: 0.5614 (tt0) cc_final: 0.5410 (tt0) REVERT: G 426 ASP cc_start: 0.5184 (t70) cc_final: 0.4578 (m-30) REVERT: G 429 ARG cc_start: 0.5793 (ttp80) cc_final: 0.5421 (ttt90) REVERT: G 443 ILE cc_start: 0.6492 (mm) cc_final: 0.6250 (mp) REVERT: H 36 GLU cc_start: 0.7600 (mt-10) cc_final: 0.6918 (mp0) REVERT: H 95 ASP cc_start: 0.6728 (m-30) cc_final: 0.6375 (m-30) REVERT: H 126 GLU cc_start: 0.7664 (pt0) cc_final: 0.6983 (tt0) REVERT: H 200 LYS cc_start: 0.6978 (ttmm) cc_final: 0.6672 (mmmt) REVERT: H 347 MET cc_start: 0.6109 (mmm) cc_final: 0.5831 (mmp) REVERT: H 390 GLU cc_start: 0.6290 (pm20) cc_final: 0.5923 (pt0) REVERT: H 415 GLU cc_start: 0.5034 (mt-10) cc_final: 0.4477 (tt0) REVERT: H 426 ASP cc_start: 0.5250 (t70) cc_final: 0.4723 (m-30) REVERT: H 442 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7182 (mm-30) REVERT: H 443 ILE cc_start: 0.6240 (mm) cc_final: 0.5947 (mp) REVERT: I 95 ASP cc_start: 0.6900 (m-30) cc_final: 0.6537 (m-30) REVERT: I 163 ASP cc_start: 0.4551 (OUTLIER) cc_final: 0.3064 (m-30) REVERT: I 178 GLU cc_start: 0.6549 (tm-30) cc_final: 0.6287 (mt-10) REVERT: I 184 GLU cc_start: 0.6344 (tt0) cc_final: 0.5601 (tt0) REVERT: I 199 PHE cc_start: 0.6683 (m-10) cc_final: 0.6446 (m-10) REVERT: I 200 LYS cc_start: 0.7176 (ttmm) cc_final: 0.6820 (mmtp) REVERT: I 232 MET cc_start: 0.7638 (ttm) cc_final: 0.7388 (ttm) REVERT: I 347 MET cc_start: 0.6153 (mmm) cc_final: 0.5844 (mmp) REVERT: I 411 GLU cc_start: 0.5461 (mp0) cc_final: 0.5242 (mm-30) REVERT: I 415 GLU cc_start: 0.5148 (mt-10) cc_final: 0.4572 (tt0) REVERT: I 426 ASP cc_start: 0.5377 (t70) cc_final: 0.4839 (m-30) REVERT: I 427 MET cc_start: 0.5859 (mtp) cc_final: 0.5375 (mtp) REVERT: I 429 ARG cc_start: 0.5969 (ttp80) cc_final: 0.5623 (ttt90) REVERT: I 442 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6972 (mm-30) REVERT: N 16 GLN cc_start: 0.6219 (mt0) cc_final: 0.5980 (mm-40) REVERT: N 33 LYS cc_start: 0.6893 (OUTLIER) cc_final: 0.6489 (mmtp) REVERT: N 92 MET cc_start: 0.7760 (mtm) cc_final: 0.7375 (mtp) REVERT: N 95 ASP cc_start: 0.6830 (m-30) cc_final: 0.6459 (m-30) REVERT: N 178 GLU cc_start: 0.6414 (tm-30) cc_final: 0.6181 (mm-30) REVERT: N 184 GLU cc_start: 0.6450 (tt0) cc_final: 0.5692 (tt0) REVERT: N 200 LYS cc_start: 0.7077 (ttmm) cc_final: 0.6726 (mmtt) REVERT: N 347 MET cc_start: 0.6268 (mmm) cc_final: 0.5936 (mmp) REVERT: N 390 GLU cc_start: 0.6409 (pm20) cc_final: 0.6116 (pt0) REVERT: N 415 GLU cc_start: 0.5269 (mt-10) cc_final: 0.4690 (tt0) REVERT: N 426 ASP cc_start: 0.5444 (t70) cc_final: 0.4828 (m-30) REVERT: N 427 MET cc_start: 0.6447 (mtp) cc_final: 0.5986 (mtp) REVERT: N 429 ARG cc_start: 0.5854 (ttp80) cc_final: 0.5429 (ttt90) REVERT: N 442 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6982 (mm-30) REVERT: N 443 ILE cc_start: 0.6444 (mm) cc_final: 0.6177 (mp) REVERT: O 68 MET cc_start: 0.6790 (OUTLIER) cc_final: 0.6158 (mtt) REVERT: O 95 ASP cc_start: 0.6739 (m-30) cc_final: 0.6375 (m-30) REVERT: O 126 GLU cc_start: 0.7701 (pt0) cc_final: 0.7016 (tt0) REVERT: O 200 LYS cc_start: 0.6964 (ttmm) cc_final: 0.6630 (mmtm) REVERT: O 347 MET cc_start: 0.6110 (mmm) cc_final: 0.5834 (mmp) REVERT: O 390 GLU cc_start: 0.6394 (pm20) cc_final: 0.5998 (pt0) REVERT: O 415 GLU cc_start: 0.5052 (mt-10) cc_final: 0.4468 (tt0) REVERT: O 426 ASP cc_start: 0.5505 (t70) cc_final: 0.4801 (m-30) REVERT: O 429 ARG cc_start: 0.5763 (ttp80) cc_final: 0.5551 (ttt90) REVERT: O 443 ILE cc_start: 0.6261 (mm) cc_final: 0.6006 (mp) REVERT: P 16 GLN cc_start: 0.6045 (mt0) cc_final: 0.5742 (mm-40) REVERT: P 19 LYS cc_start: 0.6668 (mmtp) cc_final: 0.6432 (mmtp) REVERT: P 33 LYS cc_start: 0.6710 (OUTLIER) cc_final: 0.6211 (mmtp) REVERT: P 36 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7353 (mp0) REVERT: P 68 MET cc_start: 0.7004 (OUTLIER) cc_final: 0.6398 (mtt) REVERT: P 73 ASP cc_start: 0.6848 (t70) cc_final: 0.6438 (t0) REVERT: P 95 ASP cc_start: 0.6811 (m-30) cc_final: 0.6363 (m-30) REVERT: P 117 LYS cc_start: 0.5790 (mmmm) cc_final: 0.5562 (mtmm) REVERT: P 178 GLU cc_start: 0.6330 (tm-30) cc_final: 0.6101 (mt-10) REVERT: P 184 GLU cc_start: 0.6390 (tt0) cc_final: 0.5737 (tt0) REVERT: P 390 GLU cc_start: 0.6497 (pm20) cc_final: 0.5956 (pt0) REVERT: P 415 GLU cc_start: 0.5460 (mt-10) cc_final: 0.4840 (tt0) REVERT: P 426 ASP cc_start: 0.5239 (t70) cc_final: 0.4684 (m-30) REVERT: P 427 MET cc_start: 0.6475 (mtp) cc_final: 0.6238 (mtp) REVERT: P 429 ARG cc_start: 0.5937 (ttp80) cc_final: 0.5525 (ttt90) REVERT: Q 67 ASP cc_start: 0.7116 (m-30) cc_final: 0.6781 (m-30) REVERT: Q 73 ASP cc_start: 0.6517 (t70) cc_final: 0.5979 (t0) REVERT: Q 95 ASP cc_start: 0.7112 (m-30) cc_final: 0.6723 (m-30) REVERT: Q 126 GLU cc_start: 0.7112 (pt0) cc_final: 0.6363 (pt0) REVERT: Q 184 GLU cc_start: 0.6283 (tt0) cc_final: 0.5639 (tt0) REVERT: Q 200 LYS cc_start: 0.7061 (ttmm) cc_final: 0.6804 (mmtt) REVERT: Q 316 ARG cc_start: 0.5298 (OUTLIER) cc_final: 0.4056 (tpt170) REVERT: Q 390 GLU cc_start: 0.6390 (pm20) cc_final: 0.5887 (pt0) REVERT: Q 415 GLU cc_start: 0.5697 (mt-10) cc_final: 0.5111 (tt0) REVERT: Q 426 ASP cc_start: 0.5411 (t70) cc_final: 0.4801 (m-30) REVERT: Q 429 ARG cc_start: 0.5774 (ttp80) cc_final: 0.5466 (ttt90) REVERT: Q 442 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6946 (mm-30) REVERT: R 73 ASP cc_start: 0.6513 (t70) cc_final: 0.5974 (t0) REVERT: R 95 ASP cc_start: 0.7111 (m-30) cc_final: 0.6723 (m-30) REVERT: R 126 GLU cc_start: 0.7112 (pt0) cc_final: 0.6365 (pt0) REVERT: R 184 GLU cc_start: 0.6284 (tt0) cc_final: 0.5633 (tt0) REVERT: R 200 LYS cc_start: 0.7059 (ttmm) cc_final: 0.6729 (mttm) REVERT: R 390 GLU cc_start: 0.6341 (pm20) cc_final: 0.5848 (pt0) REVERT: R 415 GLU cc_start: 0.5685 (mt-10) cc_final: 0.5101 (tt0) REVERT: R 426 ASP cc_start: 0.5265 (t70) cc_final: 0.4762 (m-30) REVERT: R 429 ARG cc_start: 0.5759 (ttp80) cc_final: 0.5430 (ttt90) REVERT: R 438 GLU cc_start: 0.5694 (OUTLIER) cc_final: 0.5378 (mt-10) REVERT: S 16 GLN cc_start: 0.6041 (mt0) cc_final: 0.5740 (mm-40) REVERT: S 19 LYS cc_start: 0.6669 (mmtp) cc_final: 0.6382 (mmtp) REVERT: S 36 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7323 (mp0) REVERT: S 68 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6417 (mtt) REVERT: S 95 ASP cc_start: 0.6798 (m-30) cc_final: 0.6352 (m-30) REVERT: S 178 GLU cc_start: 0.6362 (tm-30) cc_final: 0.6110 (mt-10) REVERT: S 184 GLU cc_start: 0.6379 (tt0) cc_final: 0.5742 (tt0) REVERT: S 347 MET cc_start: 0.6239 (mmm) cc_final: 0.5917 (mmp) REVERT: S 390 GLU cc_start: 0.6495 (pm20) cc_final: 0.5949 (pt0) REVERT: S 415 GLU cc_start: 0.5525 (mt-10) cc_final: 0.4898 (tt0) REVERT: S 426 ASP cc_start: 0.5239 (t70) cc_final: 0.4766 (m-30) REVERT: S 429 ARG cc_start: 0.5974 (ttp80) cc_final: 0.5569 (ttt90) REVERT: T 47 ASP cc_start: 0.5656 (m-30) cc_final: 0.5413 (m-30) REVERT: T 68 MET cc_start: 0.7051 (OUTLIER) cc_final: 0.6533 (mtt) REVERT: T 95 ASP cc_start: 0.6863 (m-30) cc_final: 0.6427 (m-30) REVERT: T 126 GLU cc_start: 0.7784 (pt0) cc_final: 0.7021 (tt0) REVERT: T 159 LEU cc_start: 0.5544 (OUTLIER) cc_final: 0.5205 (tt) REVERT: T 178 GLU cc_start: 0.6429 (tm-30) cc_final: 0.6184 (mt-10) REVERT: T 184 GLU cc_start: 0.6428 (tt0) cc_final: 0.5699 (tt0) REVERT: T 347 MET cc_start: 0.6069 (mmm) cc_final: 0.5734 (mmp) REVERT: T 390 GLU cc_start: 0.6305 (pm20) cc_final: 0.5872 (pt0) REVERT: T 411 GLU cc_start: 0.5624 (mp0) cc_final: 0.5356 (mt-10) REVERT: T 415 GLU cc_start: 0.5314 (mt-10) cc_final: 0.4737 (tt0) REVERT: T 426 ASP cc_start: 0.5199 (t70) cc_final: 0.4746 (m-30) REVERT: T 429 ARG cc_start: 0.6049 (ttp80) cc_final: 0.5781 (ttt90) REVERT: T 442 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6981 (mm-30) REVERT: V 6 GLN cc_start: 0.0118 (OUTLIER) cc_final: -0.0686 (pt0) REVERT: V 7 LEU cc_start: 0.0768 (OUTLIER) cc_final: 0.0342 (tt) REVERT: Z 10 PHE cc_start: 0.0457 (OUTLIER) cc_final: 0.0184 (m-80) outliers start: 204 outliers final: 74 residues processed: 882 average time/residue: 1.4391 time to fit residues: 1562.4214 Evaluate side-chains 793 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 695 time to evaluate : 4.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 331 ARG Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 168 CYS Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 240 ASN Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 331 ARG Chi-restraints excluded: chain F residue 439 GLN Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 331 ARG Chi-restraints excluded: chain H residue 355 LEU Chi-restraints excluded: chain H residue 442 GLU Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 128 ASN Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 240 ASN Chi-restraints excluded: chain I residue 248 MET Chi-restraints excluded: chain I residue 331 ARG Chi-restraints excluded: chain K residue 10 PHE Chi-restraints excluded: chain N residue 33 LYS Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 68 MET Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain O residue 331 ARG Chi-restraints excluded: chain O residue 355 LEU Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 33 LYS Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 68 MET Chi-restraints excluded: chain P residue 125 THR Chi-restraints excluded: chain P residue 240 ASN Chi-restraints excluded: chain Q residue 35 VAL Chi-restraints excluded: chain Q residue 125 THR Chi-restraints excluded: chain Q residue 216 LEU Chi-restraints excluded: chain Q residue 224 LYS Chi-restraints excluded: chain Q residue 240 ASN Chi-restraints excluded: chain Q residue 316 ARG Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 240 ASN Chi-restraints excluded: chain R residue 438 GLU Chi-restraints excluded: chain R residue 439 GLN Chi-restraints excluded: chain S residue 29 LEU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 68 MET Chi-restraints excluded: chain S residue 125 THR Chi-restraints excluded: chain S residue 200 LYS Chi-restraints excluded: chain S residue 240 ASN Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 68 MET Chi-restraints excluded: chain T residue 125 THR Chi-restraints excluded: chain T residue 128 ASN Chi-restraints excluded: chain T residue 159 LEU Chi-restraints excluded: chain U residue 10 PHE Chi-restraints excluded: chain V residue 6 GLN Chi-restraints excluded: chain V residue 7 LEU Chi-restraints excluded: chain V residue 10 PHE Chi-restraints excluded: chain Z residue 10 PHE Chi-restraints excluded: chain b residue 7 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 553 optimal weight: 0.9980 chunk 421 optimal weight: 0.8980 chunk 290 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 267 optimal weight: 3.9990 chunk 376 optimal weight: 10.0000 chunk 562 optimal weight: 6.9990 chunk 595 optimal weight: 3.9990 chunk 293 optimal weight: 4.9990 chunk 533 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 ASN ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 ASN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 ASN H 225 HIS ** H 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 17 ASN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 151 ASN ** N 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 17 ASN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 17 ASN ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 ASN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 167 ASN ** R 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 17 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 17 ASN ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 50918 Z= 0.191 Angle : 0.464 4.466 68936 Z= 0.244 Chirality : 0.040 0.138 7462 Planarity : 0.004 0.034 9030 Dihedral : 5.648 72.715 6828 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.43 % Allowed : 15.82 % Favored : 80.75 % 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: 0.58 (0.11), residues: 6216 helix: 2.04 (0.10), residues: 2366 sheet: -0.65 (0.17), residues: 1022 loop : -0.61 (0.11), residues: 2828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 435 HIS 0.004 0.001 HIS G 245 PHE 0.011 0.001 PHE H 71 TYR 0.014 0.001 TYR T 285 ARG 0.002 0.000 ARG I 145 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 716 time to evaluate : 4.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.6577 (OUTLIER) cc_final: 0.6137 (mmtp) REVERT: A 73 ASP cc_start: 0.6645 (t70) cc_final: 0.5812 (t70) REVERT: A 95 ASP cc_start: 0.6866 (m-30) cc_final: 0.6439 (m-30) REVERT: A 347 MET cc_start: 0.6117 (mmm) cc_final: 0.5699 (mmp) REVERT: A 390 GLU cc_start: 0.6297 (pm20) cc_final: 0.5943 (pt0) REVERT: A 415 GLU cc_start: 0.5080 (mt-10) cc_final: 0.4495 (tt0) REVERT: A 426 ASP cc_start: 0.5392 (t70) cc_final: 0.4870 (m-30) REVERT: A 427 MET cc_start: 0.6320 (mtp) cc_final: 0.5885 (mtp) REVERT: A 429 ARG cc_start: 0.5783 (ttp80) cc_final: 0.5475 (ttt90) REVERT: B 47 ASP cc_start: 0.5725 (m-30) cc_final: 0.5488 (m-30) REVERT: B 95 ASP cc_start: 0.6803 (m-30) cc_final: 0.6345 (m-30) REVERT: B 117 LYS cc_start: 0.5870 (mmmm) cc_final: 0.5511 (mttp) REVERT: B 159 LEU cc_start: 0.5480 (OUTLIER) cc_final: 0.5177 (tt) REVERT: B 178 GLU cc_start: 0.6467 (tm-30) cc_final: 0.6239 (mt-10) REVERT: B 184 GLU cc_start: 0.6407 (tt0) cc_final: 0.5687 (tt0) REVERT: B 347 MET cc_start: 0.6030 (mmm) cc_final: 0.5713 (mmp) REVERT: B 390 GLU cc_start: 0.6338 (pm20) cc_final: 0.5908 (pt0) REVERT: B 411 GLU cc_start: 0.5617 (mp0) cc_final: 0.5344 (mt-10) REVERT: B 415 GLU cc_start: 0.5260 (mt-10) cc_final: 0.4679 (tt0) REVERT: B 426 ASP cc_start: 0.5423 (t70) cc_final: 0.4886 (m-30) REVERT: B 429 ARG cc_start: 0.6144 (ttp80) cc_final: 0.5799 (ttt90) REVERT: B 442 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7189 (mm-30) REVERT: B 443 ILE cc_start: 0.6479 (mm) cc_final: 0.6229 (mp) REVERT: C 33 LYS cc_start: 0.6601 (OUTLIER) cc_final: 0.6294 (mmtp) REVERT: C 95 ASP cc_start: 0.6910 (m-30) cc_final: 0.6574 (m-30) REVERT: C 139 LYS cc_start: 0.6875 (mttt) cc_final: 0.6374 (mttm) REVERT: C 178 GLU cc_start: 0.6501 (tm-30) cc_final: 0.6233 (mt-10) REVERT: C 184 GLU cc_start: 0.6299 (tt0) cc_final: 0.5667 (tt0) REVERT: C 316 ARG cc_start: 0.5257 (OUTLIER) cc_final: 0.4182 (tpt170) REVERT: C 347 MET cc_start: 0.6150 (mmm) cc_final: 0.5781 (mmp) REVERT: C 415 GLU cc_start: 0.5110 (mt-10) cc_final: 0.4527 (tt0) REVERT: C 426 ASP cc_start: 0.5574 (t70) cc_final: 0.5013 (m-30) REVERT: C 429 ARG cc_start: 0.6038 (ttp80) cc_final: 0.5667 (ttt90) REVERT: F 73 ASP cc_start: 0.6657 (t70) cc_final: 0.5825 (t70) REVERT: F 95 ASP cc_start: 0.6814 (m-30) cc_final: 0.6336 (m-30) REVERT: F 139 LYS cc_start: 0.7055 (mttt) cc_final: 0.6776 (mttm) REVERT: F 184 GLU cc_start: 0.6324 (tt0) cc_final: 0.5700 (tt0) REVERT: F 347 MET cc_start: 0.6114 (mmm) cc_final: 0.5698 (mmp) REVERT: F 390 GLU cc_start: 0.6259 (pm20) cc_final: 0.5919 (pt0) REVERT: F 415 GLU cc_start: 0.5080 (mt-10) cc_final: 0.4515 (tt0) REVERT: F 426 ASP cc_start: 0.5531 (t70) cc_final: 0.4940 (m-30) REVERT: F 427 MET cc_start: 0.6201 (ttp) cc_final: 0.5834 (mtp) REVERT: F 429 ARG cc_start: 0.5777 (ttp80) cc_final: 0.5431 (ttt90) REVERT: F 438 GLU cc_start: 0.5391 (pt0) cc_final: 0.5046 (mt-10) REVERT: F 439 GLN cc_start: 0.5739 (OUTLIER) cc_final: 0.5465 (mm-40) REVERT: G 16 GLN cc_start: 0.6135 (mt0) cc_final: 0.5892 (mm-40) REVERT: G 92 MET cc_start: 0.7785 (mtm) cc_final: 0.7377 (mtp) REVERT: G 95 ASP cc_start: 0.6869 (m-30) cc_final: 0.6465 (m-30) REVERT: G 139 LYS cc_start: 0.7033 (mttt) cc_final: 0.6696 (mttm) REVERT: G 178 GLU cc_start: 0.6388 (tm-30) cc_final: 0.6143 (mm-30) REVERT: G 184 GLU cc_start: 0.6346 (tt0) cc_final: 0.5701 (tt0) REVERT: G 347 MET cc_start: 0.6260 (mmm) cc_final: 0.5952 (mmp) REVERT: G 390 GLU cc_start: 0.6390 (pm20) cc_final: 0.6074 (pt0) REVERT: G 415 GLU cc_start: 0.5096 (mt-10) cc_final: 0.4497 (tt0) REVERT: G 419 GLU cc_start: 0.5567 (tt0) cc_final: 0.5128 (mt-10) REVERT: G 426 ASP cc_start: 0.5192 (t70) cc_final: 0.4537 (m-30) REVERT: G 429 ARG cc_start: 0.5833 (ttp80) cc_final: 0.5480 (ttt90) REVERT: G 438 GLU cc_start: 0.4882 (pt0) cc_final: 0.4645 (mt-10) REVERT: G 442 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6056 (mp0) REVERT: G 443 ILE cc_start: 0.6488 (mm) cc_final: 0.6212 (mp) REVERT: H 95 ASP cc_start: 0.6922 (m-30) cc_final: 0.6553 (m-30) REVERT: H 200 LYS cc_start: 0.6965 (ttmm) cc_final: 0.6682 (mmmt) REVERT: H 347 MET cc_start: 0.6095 (mmm) cc_final: 0.5826 (mmp) REVERT: H 390 GLU cc_start: 0.6282 (pm20) cc_final: 0.5853 (pt0) REVERT: H 415 GLU cc_start: 0.5029 (mt-10) cc_final: 0.4499 (tt0) REVERT: H 426 ASP cc_start: 0.5223 (t70) cc_final: 0.4681 (m-30) REVERT: H 438 GLU cc_start: 0.5320 (pt0) cc_final: 0.4994 (mt-10) REVERT: H 443 ILE cc_start: 0.6222 (mm) cc_final: 0.5937 (mp) REVERT: I 33 LYS cc_start: 0.6649 (OUTLIER) cc_final: 0.6348 (mmtp) REVERT: I 95 ASP cc_start: 0.6912 (m-30) cc_final: 0.6571 (m-30) REVERT: I 178 GLU cc_start: 0.6554 (tm-30) cc_final: 0.6307 (mt-10) REVERT: I 184 GLU cc_start: 0.6338 (tt0) cc_final: 0.5622 (tt0) REVERT: I 200 LYS cc_start: 0.7089 (ttmm) cc_final: 0.6812 (mmtt) REVERT: I 232 MET cc_start: 0.7502 (ttm) cc_final: 0.7225 (ttm) REVERT: I 347 MET cc_start: 0.6146 (mmm) cc_final: 0.5777 (mmp) REVERT: I 415 GLU cc_start: 0.5179 (mt-10) cc_final: 0.4524 (tt0) REVERT: I 419 GLU cc_start: 0.5859 (tt0) cc_final: 0.5347 (mt-10) REVERT: I 426 ASP cc_start: 0.5362 (t70) cc_final: 0.4812 (m-30) REVERT: I 427 MET cc_start: 0.5810 (mtp) cc_final: 0.5339 (mtp) REVERT: I 429 ARG cc_start: 0.5928 (ttp80) cc_final: 0.5580 (ttt90) REVERT: I 442 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7174 (mm-30) REVERT: N 16 GLN cc_start: 0.6135 (mt0) cc_final: 0.5895 (mm-40) REVERT: N 33 LYS cc_start: 0.6715 (OUTLIER) cc_final: 0.6256 (mmmm) REVERT: N 92 MET cc_start: 0.7787 (mtm) cc_final: 0.7438 (mtp) REVERT: N 95 ASP cc_start: 0.6875 (m-30) cc_final: 0.6472 (m-30) REVERT: N 178 GLU cc_start: 0.6627 (tm-30) cc_final: 0.6322 (mm-30) REVERT: N 184 GLU cc_start: 0.6434 (tt0) cc_final: 0.5678 (tt0) REVERT: N 200 LYS cc_start: 0.7076 (ttmm) cc_final: 0.6725 (mmtt) REVERT: N 347 MET cc_start: 0.6244 (mmm) cc_final: 0.5938 (mmp) REVERT: N 390 GLU cc_start: 0.6381 (pm20) cc_final: 0.6077 (pt0) REVERT: N 415 GLU cc_start: 0.5208 (mt-10) cc_final: 0.4629 (tt0) REVERT: N 426 ASP cc_start: 0.5309 (t70) cc_final: 0.4676 (m-30) REVERT: N 427 MET cc_start: 0.6480 (mtp) cc_final: 0.6080 (mtp) REVERT: N 429 ARG cc_start: 0.5850 (ttp80) cc_final: 0.5461 (ttt90) REVERT: N 442 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6917 (mm-30) REVERT: N 443 ILE cc_start: 0.6386 (mm) cc_final: 0.6128 (mp) REVERT: O 95 ASP cc_start: 0.6886 (m-30) cc_final: 0.6517 (m-30) REVERT: O 200 LYS cc_start: 0.6905 (ttmm) cc_final: 0.6600 (mmmt) REVERT: O 347 MET cc_start: 0.6095 (mmm) cc_final: 0.5828 (mmp) REVERT: O 390 GLU cc_start: 0.6368 (pm20) cc_final: 0.5992 (pt0) REVERT: O 415 GLU cc_start: 0.4944 (mt-10) cc_final: 0.4426 (tt0) REVERT: O 426 ASP cc_start: 0.5445 (t70) cc_final: 0.4755 (m-30) REVERT: O 429 ARG cc_start: 0.5810 (ttp80) cc_final: 0.5573 (ttt90) REVERT: O 442 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6754 (mm-30) REVERT: O 443 ILE cc_start: 0.6312 (mm) cc_final: 0.6086 (mp) REVERT: P 16 GLN cc_start: 0.5955 (mt0) cc_final: 0.5665 (mm-40) REVERT: P 19 LYS cc_start: 0.6659 (mmtp) cc_final: 0.6405 (mmtp) REVERT: P 36 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7240 (mp0) REVERT: P 68 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6442 (mtt) REVERT: P 73 ASP cc_start: 0.6869 (t70) cc_final: 0.6454 (t0) REVERT: P 95 ASP cc_start: 0.6857 (m-30) cc_final: 0.6413 (m-30) REVERT: P 117 LYS cc_start: 0.5767 (mmmm) cc_final: 0.5535 (mtmm) REVERT: P 390 GLU cc_start: 0.6444 (pm20) cc_final: 0.5936 (pt0) REVERT: P 415 GLU cc_start: 0.5337 (mt-10) cc_final: 0.4756 (tt0) REVERT: P 426 ASP cc_start: 0.5173 (t70) cc_final: 0.4679 (m-30) REVERT: P 427 MET cc_start: 0.6494 (mtp) cc_final: 0.6178 (mtp) REVERT: P 429 ARG cc_start: 0.5896 (ttp80) cc_final: 0.5492 (ttt90) REVERT: P 442 GLU cc_start: 0.7320 (mt-10) cc_final: 0.7079 (mm-30) REVERT: Q 73 ASP cc_start: 0.6490 (t70) cc_final: 0.5957 (t0) REVERT: Q 95 ASP cc_start: 0.7074 (m-30) cc_final: 0.6676 (m-30) REVERT: Q 126 GLU cc_start: 0.7117 (pt0) cc_final: 0.6350 (pt0) REVERT: Q 200 LYS cc_start: 0.6993 (ttmm) cc_final: 0.6615 (mttt) REVERT: Q 316 ARG cc_start: 0.5267 (OUTLIER) cc_final: 0.4050 (tpt170) REVERT: Q 390 GLU cc_start: 0.6334 (pm20) cc_final: 0.5833 (pt0) REVERT: Q 415 GLU cc_start: 0.5556 (mt-10) cc_final: 0.5024 (tt0) REVERT: Q 426 ASP cc_start: 0.5368 (t70) cc_final: 0.4770 (m-30) REVERT: Q 429 ARG cc_start: 0.5793 (ttp80) cc_final: 0.5451 (ttt90) REVERT: Q 442 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7067 (mm-30) REVERT: R 68 MET cc_start: 0.6834 (OUTLIER) cc_final: 0.6191 (mtt) REVERT: R 73 ASP cc_start: 0.6497 (t70) cc_final: 0.5960 (t0) REVERT: R 95 ASP cc_start: 0.7072 (m-30) cc_final: 0.6674 (m-30) REVERT: R 126 GLU cc_start: 0.7119 (pt0) cc_final: 0.6350 (pt0) REVERT: R 200 LYS cc_start: 0.7067 (ttmm) cc_final: 0.6726 (mttt) REVERT: R 316 ARG cc_start: 0.5232 (OUTLIER) cc_final: 0.4002 (tpt170) REVERT: R 390 GLU cc_start: 0.6345 (pm20) cc_final: 0.5874 (pt0) REVERT: R 415 GLU cc_start: 0.5372 (mt-10) cc_final: 0.4826 (tt0) REVERT: R 426 ASP cc_start: 0.5226 (t70) cc_final: 0.4715 (m-30) REVERT: R 429 ARG cc_start: 0.5766 (ttp80) cc_final: 0.5344 (ttt90) REVERT: R 438 GLU cc_start: 0.5634 (pt0) cc_final: 0.5395 (mt-10) REVERT: S 16 GLN cc_start: 0.5952 (mt0) cc_final: 0.5665 (mm-40) REVERT: S 19 LYS cc_start: 0.6685 (mmtp) cc_final: 0.6429 (mmtp) REVERT: S 68 MET cc_start: 0.7056 (OUTLIER) cc_final: 0.6439 (mtt) REVERT: S 95 ASP cc_start: 0.6743 (m-30) cc_final: 0.6321 (m-30) REVERT: S 178 GLU cc_start: 0.6330 (tm-30) cc_final: 0.6122 (mt-10) REVERT: S 347 MET cc_start: 0.6478 (mmm) cc_final: 0.6154 (mmp) REVERT: S 390 GLU cc_start: 0.6441 (pm20) cc_final: 0.5938 (pt0) REVERT: S 415 GLU cc_start: 0.5390 (mt-10) cc_final: 0.4765 (tt0) REVERT: S 426 ASP cc_start: 0.5204 (t70) cc_final: 0.4730 (m-30) REVERT: S 429 ARG cc_start: 0.6022 (ttp80) cc_final: 0.5615 (ttt90) REVERT: S 438 GLU cc_start: 0.5988 (pt0) cc_final: 0.5590 (pt0) REVERT: S 439 GLN cc_start: 0.5589 (OUTLIER) cc_final: 0.4266 (mp10) REVERT: T 47 ASP cc_start: 0.5712 (m-30) cc_final: 0.5474 (m-30) REVERT: T 95 ASP cc_start: 0.6806 (m-30) cc_final: 0.6343 (m-30) REVERT: T 126 GLU cc_start: 0.7777 (pt0) cc_final: 0.7090 (tt0) REVERT: T 128 ASN cc_start: 0.7483 (OUTLIER) cc_final: 0.7244 (m110) REVERT: T 159 LEU cc_start: 0.5494 (OUTLIER) cc_final: 0.5190 (tt) REVERT: T 178 GLU cc_start: 0.6470 (tm-30) cc_final: 0.6228 (mt-10) REVERT: T 184 GLU cc_start: 0.6415 (tt0) cc_final: 0.5690 (tt0) REVERT: T 347 MET cc_start: 0.6054 (mmm) cc_final: 0.5734 (mmp) REVERT: T 390 GLU cc_start: 0.6326 (pm20) cc_final: 0.5906 (pt0) REVERT: T 411 GLU cc_start: 0.5460 (mp0) cc_final: 0.5181 (mt-10) REVERT: T 415 GLU cc_start: 0.5254 (mt-10) cc_final: 0.4661 (tt0) REVERT: T 419 GLU cc_start: 0.5606 (tt0) cc_final: 0.5185 (mt-10) REVERT: T 426 ASP cc_start: 0.5183 (t70) cc_final: 0.4716 (m-30) REVERT: T 429 ARG cc_start: 0.6027 (ttp80) cc_final: 0.5765 (ttt90) REVERT: T 442 GLU cc_start: 0.7293 (mm-30) cc_final: 0.7049 (mm-30) REVERT: Z 10 PHE cc_start: 0.0227 (OUTLIER) cc_final: -0.0052 (m-80) outliers start: 179 outliers final: 72 residues processed: 835 average time/residue: 1.4239 time to fit residues: 1464.6586 Evaluate side-chains 778 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 689 time to evaluate : 4.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 331 ARG Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 168 CYS Chi-restraints excluded: chain F residue 240 ASN Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 331 ARG Chi-restraints excluded: chain F residue 439 GLN Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 168 CYS Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 439 GLN Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 184 GLU Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 355 LEU Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 128 ASN Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 240 ASN Chi-restraints excluded: chain I residue 248 MET Chi-restraints excluded: chain N residue 29 LEU Chi-restraints excluded: chain N residue 33 LYS Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 216 LEU Chi-restraints excluded: chain N residue 240 ASN Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain O residue 355 LEU Chi-restraints excluded: chain O residue 442 GLU Chi-restraints excluded: chain P residue 68 MET Chi-restraints excluded: chain P residue 125 THR Chi-restraints excluded: chain P residue 240 ASN Chi-restraints excluded: chain Q residue 29 LEU Chi-restraints excluded: chain Q residue 35 VAL Chi-restraints excluded: chain Q residue 125 THR Chi-restraints excluded: chain Q residue 181 PHE Chi-restraints excluded: chain Q residue 216 LEU Chi-restraints excluded: chain Q residue 224 LYS Chi-restraints excluded: chain Q residue 240 ASN Chi-restraints excluded: chain Q residue 316 ARG Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 68 MET Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 181 PHE Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 224 LYS Chi-restraints excluded: chain R residue 240 ASN Chi-restraints excluded: chain R residue 316 ARG Chi-restraints excluded: chain R residue 439 GLN Chi-restraints excluded: chain S residue 68 MET Chi-restraints excluded: chain S residue 125 THR Chi-restraints excluded: chain S residue 439 GLN Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 125 THR Chi-restraints excluded: chain T residue 128 ASN Chi-restraints excluded: chain T residue 159 LEU Chi-restraints excluded: chain V residue 10 PHE Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain Z residue 10 PHE Chi-restraints excluded: chain a residue 10 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 495 optimal weight: 6.9990 chunk 337 optimal weight: 0.0870 chunk 8 optimal weight: 5.9990 chunk 443 optimal weight: 5.9990 chunk 245 optimal weight: 0.9990 chunk 508 optimal weight: 4.9990 chunk 411 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 304 optimal weight: 4.9990 chunk 534 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- 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 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 ASN G 187 HIS ** G 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 151 ASN N 187 HIS ** N 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN O 34 ASN ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 17 ASN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 17 ASN ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 ASN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 17 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 17 ASN ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 50918 Z= 0.339 Angle : 0.559 5.916 68936 Z= 0.292 Chirality : 0.045 0.154 7462 Planarity : 0.005 0.042 9030 Dihedral : 5.726 75.977 6807 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.79 % Allowed : 15.01 % Favored : 81.19 % 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 (0.11), residues: 6216 helix: 1.72 (0.10), residues: 2380 sheet: -0.83 (0.17), residues: 868 loop : -0.69 (0.11), residues: 2968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 435 HIS 0.005 0.001 HIS S 416 PHE 0.015 0.002 PHE O 71 TYR 0.016 0.002 TYR B 285 ARG 0.003 0.001 ARG O 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 676 time to evaluate : 4.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.6661 (OUTLIER) cc_final: 0.6224 (mmtp) REVERT: A 73 ASP cc_start: 0.6680 (t70) cc_final: 0.5821 (t70) REVERT: A 95 ASP cc_start: 0.6928 (m-30) cc_final: 0.6479 (m-30) REVERT: A 316 ARG cc_start: 0.5428 (OUTLIER) cc_final: 0.4141 (tpt170) REVERT: A 390 GLU cc_start: 0.6223 (pm20) cc_final: 0.5886 (pt0) REVERT: A 415 GLU cc_start: 0.5188 (mt-10) cc_final: 0.4595 (tt0) REVERT: A 426 ASP cc_start: 0.5400 (t70) cc_final: 0.4901 (m-30) REVERT: A 427 MET cc_start: 0.6334 (mtp) cc_final: 0.5869 (mtp) REVERT: A 429 ARG cc_start: 0.5949 (ttp80) cc_final: 0.5571 (ttt90) REVERT: B 47 ASP cc_start: 0.5740 (m-30) cc_final: 0.5489 (m-30) REVERT: B 95 ASP cc_start: 0.6801 (m-30) cc_final: 0.6358 (m-30) REVERT: B 117 LYS cc_start: 0.5862 (mmmm) cc_final: 0.5592 (mtmm) REVERT: B 159 LEU cc_start: 0.5556 (OUTLIER) cc_final: 0.5233 (tt) REVERT: B 178 GLU cc_start: 0.6369 (tm-30) cc_final: 0.6152 (mt-10) REVERT: B 184 GLU cc_start: 0.6299 (tt0) cc_final: 0.5619 (tt0) REVERT: B 347 MET cc_start: 0.6023 (mmm) cc_final: 0.5708 (mmp) REVERT: B 390 GLU cc_start: 0.6323 (pm20) cc_final: 0.5902 (pt0) REVERT: B 411 GLU cc_start: 0.5753 (mp0) cc_final: 0.5533 (mt-10) REVERT: B 415 GLU cc_start: 0.5105 (mt-10) cc_final: 0.4562 (tt0) REVERT: B 426 ASP cc_start: 0.5388 (t70) cc_final: 0.4886 (m-30) REVERT: B 429 ARG cc_start: 0.6228 (ttp80) cc_final: 0.5951 (ttt90) REVERT: B 443 ILE cc_start: 0.6441 (mm) cc_final: 0.6107 (mp) REVERT: C 33 LYS cc_start: 0.6709 (OUTLIER) cc_final: 0.6503 (mmmt) REVERT: C 95 ASP cc_start: 0.6864 (m-30) cc_final: 0.6484 (m-30) REVERT: C 178 GLU cc_start: 0.6418 (tm-30) cc_final: 0.6142 (mt-10) REVERT: C 184 GLU cc_start: 0.6257 (tt0) cc_final: 0.5692 (tt0) REVERT: C 316 ARG cc_start: 0.5365 (OUTLIER) cc_final: 0.4202 (tpt170) REVERT: C 347 MET cc_start: 0.6144 (mmm) cc_final: 0.5761 (mmp) REVERT: C 415 GLU cc_start: 0.5145 (mt-10) cc_final: 0.4540 (tt0) REVERT: C 426 ASP cc_start: 0.5496 (t70) cc_final: 0.5038 (m-30) REVERT: C 429 ARG cc_start: 0.6059 (ttp80) cc_final: 0.5724 (ttt90) REVERT: F 33 LYS cc_start: 0.6703 (OUTLIER) cc_final: 0.6347 (mmtt) REVERT: F 73 ASP cc_start: 0.6693 (t70) cc_final: 0.5832 (t70) REVERT: F 95 ASP cc_start: 0.6826 (m-30) cc_final: 0.6359 (m-30) REVERT: F 184 GLU cc_start: 0.6230 (tt0) cc_final: 0.5958 (mt-10) REVERT: F 390 GLU cc_start: 0.6166 (pm20) cc_final: 0.5843 (pt0) REVERT: F 415 GLU cc_start: 0.5207 (mt-10) cc_final: 0.4608 (tt0) REVERT: F 426 ASP cc_start: 0.5564 (t70) cc_final: 0.4957 (m-30) REVERT: F 427 MET cc_start: 0.6343 (ttp) cc_final: 0.5979 (mtp) REVERT: F 429 ARG cc_start: 0.5853 (ttp80) cc_final: 0.5438 (ttt90) REVERT: F 438 GLU cc_start: 0.5509 (OUTLIER) cc_final: 0.5112 (mt-10) REVERT: F 439 GLN cc_start: 0.5806 (OUTLIER) cc_final: 0.5438 (mm110) REVERT: G 16 GLN cc_start: 0.6283 (mt0) cc_final: 0.5992 (mm-40) REVERT: G 92 MET cc_start: 0.7828 (mtm) cc_final: 0.7488 (mtp) REVERT: G 95 ASP cc_start: 0.7063 (m-30) cc_final: 0.6676 (m-30) REVERT: G 178 GLU cc_start: 0.6508 (tm-30) cc_final: 0.6215 (mm-30) REVERT: G 347 MET cc_start: 0.6211 (mmm) cc_final: 0.5904 (mmp) REVERT: G 390 GLU cc_start: 0.6404 (pm20) cc_final: 0.6082 (pt0) REVERT: G 415 GLU cc_start: 0.5124 (mt-10) cc_final: 0.4477 (tt0) REVERT: G 419 GLU cc_start: 0.5553 (tt0) cc_final: 0.5127 (mt-10) REVERT: G 426 ASP cc_start: 0.5189 (t70) cc_final: 0.4599 (m-30) REVERT: G 429 ARG cc_start: 0.5843 (ttp80) cc_final: 0.5529 (ttt90) REVERT: G 438 GLU cc_start: 0.5158 (pt0) cc_final: 0.4812 (mt-10) REVERT: H 95 ASP cc_start: 0.6968 (m-30) cc_final: 0.6610 (m-30) REVERT: H 200 LYS cc_start: 0.7030 (ttmm) cc_final: 0.6723 (mmmt) REVERT: H 347 MET cc_start: 0.6016 (mmm) cc_final: 0.5740 (mmp) REVERT: H 390 GLU cc_start: 0.6243 (pm20) cc_final: 0.5869 (pt0) REVERT: H 415 GLU cc_start: 0.5100 (mt-10) cc_final: 0.4504 (tt0) REVERT: H 426 ASP cc_start: 0.5247 (t70) cc_final: 0.4709 (m-30) REVERT: H 438 GLU cc_start: 0.5632 (pt0) cc_final: 0.5209 (mt-10) REVERT: H 442 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6958 (mm-30) REVERT: H 443 ILE cc_start: 0.6238 (mm) cc_final: 0.6008 (mp) REVERT: I 33 LYS cc_start: 0.6701 (OUTLIER) cc_final: 0.6493 (mmmt) REVERT: I 95 ASP cc_start: 0.6865 (m-30) cc_final: 0.6486 (m-30) REVERT: I 178 GLU cc_start: 0.6425 (tm-30) cc_final: 0.6148 (mt-10) REVERT: I 199 PHE cc_start: 0.6654 (m-10) cc_final: 0.6378 (m-10) REVERT: I 200 LYS cc_start: 0.7112 (ttmm) cc_final: 0.6773 (mmtt) REVERT: I 232 MET cc_start: 0.7584 (ttm) cc_final: 0.7318 (ttm) REVERT: I 347 MET cc_start: 0.6144 (mmm) cc_final: 0.5760 (mmp) REVERT: I 415 GLU cc_start: 0.5117 (mt-10) cc_final: 0.4429 (tt0) REVERT: I 419 GLU cc_start: 0.5903 (tt0) cc_final: 0.5428 (mt-10) REVERT: I 426 ASP cc_start: 0.5331 (t70) cc_final: 0.4832 (m-30) REVERT: I 427 MET cc_start: 0.5822 (mtp) cc_final: 0.5382 (mtp) REVERT: I 429 ARG cc_start: 0.5992 (ttp80) cc_final: 0.5622 (ttt90) REVERT: I 442 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6942 (mm-30) REVERT: N 16 GLN cc_start: 0.6280 (mt0) cc_final: 0.5993 (mm-40) REVERT: N 92 MET cc_start: 0.7820 (mtm) cc_final: 0.7489 (mtp) REVERT: N 95 ASP cc_start: 0.7068 (m-30) cc_final: 0.6683 (m-30) REVERT: N 178 GLU cc_start: 0.6511 (tm-30) cc_final: 0.6217 (mm-30) REVERT: N 200 LYS cc_start: 0.7000 (ttmm) cc_final: 0.6649 (mmtt) REVERT: N 347 MET cc_start: 0.6207 (mmm) cc_final: 0.5901 (mmp) REVERT: N 390 GLU cc_start: 0.6403 (pm20) cc_final: 0.6108 (pt0) REVERT: N 415 GLU cc_start: 0.5223 (mt-10) cc_final: 0.4631 (tt0) REVERT: N 426 ASP cc_start: 0.5365 (t70) cc_final: 0.4782 (m-30) REVERT: N 429 ARG cc_start: 0.5836 (ttp80) cc_final: 0.5488 (ttt90) REVERT: N 442 GLU cc_start: 0.7291 (mm-30) cc_final: 0.7040 (mm-30) REVERT: O 95 ASP cc_start: 0.6932 (m-30) cc_final: 0.6568 (m-30) REVERT: O 200 LYS cc_start: 0.6991 (ttmm) cc_final: 0.6643 (mmmt) REVERT: O 347 MET cc_start: 0.6017 (mmm) cc_final: 0.5742 (mmp) REVERT: O 390 GLU cc_start: 0.6324 (pm20) cc_final: 0.5969 (pt0) REVERT: O 415 GLU cc_start: 0.5091 (mt-10) cc_final: 0.4521 (tt0) REVERT: O 426 ASP cc_start: 0.5439 (t70) cc_final: 0.4821 (m-30) REVERT: O 429 ARG cc_start: 0.5883 (ttp80) cc_final: 0.5647 (ttt90) REVERT: O 442 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6784 (mm-30) REVERT: O 443 ILE cc_start: 0.6399 (mm) cc_final: 0.6123 (mp) REVERT: P 16 GLN cc_start: 0.6009 (mt0) cc_final: 0.5705 (mm-40) REVERT: P 36 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7389 (mt-10) REVERT: P 68 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6370 (mtt) REVERT: P 73 ASP cc_start: 0.6838 (t70) cc_final: 0.6473 (t0) REVERT: P 95 ASP cc_start: 0.6879 (m-30) cc_final: 0.6466 (m-30) REVERT: P 102 THR cc_start: 0.6099 (m) cc_final: 0.5549 (p) REVERT: P 126 GLU cc_start: 0.7969 (tt0) cc_final: 0.7379 (tt0) REVERT: P 163 ASP cc_start: 0.4313 (OUTLIER) cc_final: 0.2689 (m-30) REVERT: P 224 LYS cc_start: 0.5749 (OUTLIER) cc_final: 0.5512 (mtpp) REVERT: P 390 GLU cc_start: 0.6499 (pm20) cc_final: 0.6010 (pt0) REVERT: P 415 GLU cc_start: 0.5169 (mt-10) cc_final: 0.4575 (tt0) REVERT: P 426 ASP cc_start: 0.5209 (t70) cc_final: 0.4740 (m-30) REVERT: P 427 MET cc_start: 0.6569 (mtp) cc_final: 0.6277 (mtp) REVERT: P 429 ARG cc_start: 0.5951 (ttp80) cc_final: 0.5581 (ttt90) REVERT: Q 73 ASP cc_start: 0.6576 (t70) cc_final: 0.6050 (t0) REVERT: Q 95 ASP cc_start: 0.7121 (m-30) cc_final: 0.6743 (m-30) REVERT: Q 126 GLU cc_start: 0.7351 (pt0) cc_final: 0.6560 (pt0) REVERT: Q 200 LYS cc_start: 0.7181 (ttmm) cc_final: 0.6770 (mttt) REVERT: Q 316 ARG cc_start: 0.5335 (OUTLIER) cc_final: 0.4040 (tpt170) REVERT: Q 390 GLU cc_start: 0.6348 (pm20) cc_final: 0.5828 (pt0) REVERT: Q 415 GLU cc_start: 0.5592 (mt-10) cc_final: 0.5032 (tt0) REVERT: Q 426 ASP cc_start: 0.5323 (t70) cc_final: 0.4788 (m-30) REVERT: Q 429 ARG cc_start: 0.5889 (ttp80) cc_final: 0.5571 (ttt90) REVERT: Q 442 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6926 (mm-30) REVERT: R 73 ASP cc_start: 0.6562 (t70) cc_final: 0.6091 (t0) REVERT: R 95 ASP cc_start: 0.7115 (m-30) cc_final: 0.6738 (m-30) REVERT: R 126 GLU cc_start: 0.7355 (pt0) cc_final: 0.6560 (pt0) REVERT: R 200 LYS cc_start: 0.7127 (ttmm) cc_final: 0.6737 (mttt) REVERT: R 316 ARG cc_start: 0.5379 (OUTLIER) cc_final: 0.4108 (tpt170) REVERT: R 390 GLU cc_start: 0.6344 (pm20) cc_final: 0.5847 (pt0) REVERT: R 415 GLU cc_start: 0.5568 (mt-10) cc_final: 0.5008 (tt0) REVERT: R 426 ASP cc_start: 0.5259 (t70) cc_final: 0.4767 (m-30) REVERT: R 429 ARG cc_start: 0.5864 (ttp80) cc_final: 0.5558 (ttt90) REVERT: R 438 GLU cc_start: 0.5624 (OUTLIER) cc_final: 0.5337 (mt-10) REVERT: S 16 GLN cc_start: 0.5945 (mt0) cc_final: 0.5651 (mm-40) REVERT: S 36 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7278 (mt-10) REVERT: S 68 MET cc_start: 0.7124 (OUTLIER) cc_final: 0.6408 (mtt) REVERT: S 95 ASP cc_start: 0.6812 (m-30) cc_final: 0.6403 (m-30) REVERT: S 102 THR cc_start: 0.6128 (m) cc_final: 0.5579 (p) REVERT: S 159 LEU cc_start: 0.5613 (OUTLIER) cc_final: 0.5367 (tt) REVERT: S 163 ASP cc_start: 0.4329 (OUTLIER) cc_final: 0.2703 (m-30) REVERT: S 178 GLU cc_start: 0.6332 (tm-30) cc_final: 0.6063 (mt-10) REVERT: S 347 MET cc_start: 0.6177 (mmm) cc_final: 0.5870 (mmp) REVERT: S 390 GLU cc_start: 0.6494 (pm20) cc_final: 0.5994 (pt0) REVERT: S 415 GLU cc_start: 0.5198 (mt-10) cc_final: 0.4603 (tt0) REVERT: S 426 ASP cc_start: 0.5233 (t70) cc_final: 0.4787 (m-30) REVERT: S 429 ARG cc_start: 0.6066 (ttp80) cc_final: 0.5645 (ttt90) REVERT: S 438 GLU cc_start: 0.6070 (pt0) cc_final: 0.5714 (pt0) REVERT: S 439 GLN cc_start: 0.5757 (OUTLIER) cc_final: 0.4367 (mp10) REVERT: S 442 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6945 (mm-30) REVERT: T 47 ASP cc_start: 0.5738 (m-30) cc_final: 0.5483 (m-30) REVERT: T 95 ASP cc_start: 0.6800 (m-30) cc_final: 0.6360 (m-30) REVERT: T 159 LEU cc_start: 0.5560 (OUTLIER) cc_final: 0.5234 (tt) REVERT: T 178 GLU cc_start: 0.6371 (tm-30) cc_final: 0.6153 (mt-10) REVERT: T 184 GLU cc_start: 0.6305 (tt0) cc_final: 0.5624 (tt0) REVERT: T 347 MET cc_start: 0.6026 (mmm) cc_final: 0.5709 (mmp) REVERT: T 390 GLU cc_start: 0.6313 (pm20) cc_final: 0.5907 (pt0) REVERT: T 415 GLU cc_start: 0.5130 (mt-10) cc_final: 0.4520 (tt0) REVERT: T 419 GLU cc_start: 0.5699 (tt0) cc_final: 0.5248 (mt-10) REVERT: T 426 ASP cc_start: 0.5234 (t70) cc_final: 0.4770 (m-30) REVERT: T 429 ARG cc_start: 0.6186 (ttp80) cc_final: 0.5877 (ttt90) REVERT: T 442 GLU cc_start: 0.7270 (mm-30) cc_final: 0.7043 (mm-30) REVERT: Z 6 GLN cc_start: 0.0307 (OUTLIER) cc_final: -0.0268 (pt0) REVERT: Z 10 PHE cc_start: 0.0184 (OUTLIER) cc_final: -0.0068 (m-80) outliers start: 198 outliers final: 78 residues processed: 828 average time/residue: 1.4348 time to fit residues: 1461.3937 Evaluate side-chains 772 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 669 time to evaluate : 4.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 331 ARG Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 168 CYS Chi-restraints excluded: chain F residue 200 LYS Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 240 ASN Chi-restraints excluded: chain F residue 278 MET Chi-restraints excluded: chain F residue 331 ARG Chi-restraints excluded: chain F residue 421 LYS Chi-restraints excluded: chain F residue 438 GLU Chi-restraints excluded: chain F residue 439 GLN Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 168 CYS Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 355 LEU Chi-restraints excluded: chain H residue 442 GLU Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 128 ASN Chi-restraints excluded: chain I residue 168 CYS Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 240 ASN Chi-restraints excluded: chain I residue 248 MET Chi-restraints excluded: chain N residue 29 LEU Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 168 CYS Chi-restraints excluded: chain N residue 216 LEU Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain O residue 355 LEU Chi-restraints excluded: chain O residue 442 GLU Chi-restraints excluded: chain P residue 15 GLU Chi-restraints excluded: chain P residue 68 MET Chi-restraints excluded: chain P residue 125 THR Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 224 LYS Chi-restraints excluded: chain P residue 331 ARG Chi-restraints excluded: chain Q residue 35 VAL Chi-restraints excluded: chain Q residue 125 THR Chi-restraints excluded: chain Q residue 224 LYS Chi-restraints excluded: chain Q residue 240 ASN Chi-restraints excluded: chain Q residue 316 ARG Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 224 LYS Chi-restraints excluded: chain R residue 240 ASN Chi-restraints excluded: chain R residue 316 ARG Chi-restraints excluded: chain R residue 438 GLU Chi-restraints excluded: chain R residue 439 GLN Chi-restraints excluded: chain S residue 15 GLU Chi-restraints excluded: chain S residue 29 LEU Chi-restraints excluded: chain S residue 68 MET Chi-restraints excluded: chain S residue 125 THR Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 163 ASP Chi-restraints excluded: chain S residue 331 ARG Chi-restraints excluded: chain S residue 439 GLN Chi-restraints excluded: chain S residue 442 GLU Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 125 THR Chi-restraints excluded: chain T residue 159 LEU Chi-restraints excluded: chain T residue 168 CYS Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain Y residue 10 PHE Chi-restraints excluded: chain Z residue 6 GLN Chi-restraints excluded: chain Z residue 10 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 200 optimal weight: 8.9990 chunk 536 optimal weight: 4.9990 chunk 117 optimal weight: 0.1980 chunk 349 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 596 optimal weight: 7.9990 chunk 494 optimal weight: 2.9990 chunk 275 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 197 optimal weight: 0.6980 chunk 312 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 225 HIS ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 ASN ** F 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 ASN ** G 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 ASN ** H 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 167 ASN ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 17 ASN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 17 ASN ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 ASN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 167 ASN ** R 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 17 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 17 ASN ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 50918 Z= 0.115 Angle : 0.416 4.063 68936 Z= 0.220 Chirality : 0.038 0.128 7462 Planarity : 0.003 0.065 9030 Dihedral : 4.975 74.305 6805 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.51 % Allowed : 16.60 % Favored : 80.89 % 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: 0.75 (0.11), residues: 6216 helix: 2.17 (0.10), residues: 2408 sheet: -0.62 (0.16), residues: 1162 loop : -0.50 (0.12), residues: 2646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 435 HIS 0.003 0.001 HIS N 416 PHE 0.008 0.001 PHE G 124 TYR 0.012 0.001 TYR N 285 ARG 0.003 0.000 ARG I 145 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 723 time to evaluate : 4.466 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.6581 (OUTLIER) cc_final: 0.6147 (mmtp) REVERT: A 73 ASP cc_start: 0.6615 (t70) cc_final: 0.6166 (t0) REVERT: A 95 ASP cc_start: 0.6827 (m-30) cc_final: 0.6402 (m-30) REVERT: A 347 MET cc_start: 0.5989 (mmm) cc_final: 0.5662 (mmp) REVERT: A 390 GLU cc_start: 0.6164 (pm20) cc_final: 0.5862 (pt0) REVERT: A 415 GLU cc_start: 0.5067 (mt-10) cc_final: 0.4495 (tt0) REVERT: A 426 ASP cc_start: 0.5369 (t70) cc_final: 0.4846 (m-30) REVERT: A 427 MET cc_start: 0.6245 (mtp) cc_final: 0.5775 (mtp) REVERT: A 429 ARG cc_start: 0.5756 (ttp80) cc_final: 0.5374 (ttt90) REVERT: B 47 ASP cc_start: 0.5685 (m-30) cc_final: 0.5445 (m-30) REVERT: B 95 ASP cc_start: 0.6818 (m-30) cc_final: 0.6411 (m-30) REVERT: B 178 GLU cc_start: 0.6484 (tm-30) cc_final: 0.6237 (mt-10) REVERT: B 184 GLU cc_start: 0.6315 (tt0) cc_final: 0.5669 (tt0) REVERT: B 347 MET cc_start: 0.6027 (mmm) cc_final: 0.5661 (mmp) REVERT: B 390 GLU cc_start: 0.6329 (pm20) cc_final: 0.5856 (pt0) REVERT: B 411 GLU cc_start: 0.5329 (mp0) cc_final: 0.5091 (mt-10) REVERT: B 415 GLU cc_start: 0.5085 (mt-10) cc_final: 0.4595 (tt0) REVERT: B 426 ASP cc_start: 0.5291 (t70) cc_final: 0.4754 (m-30) REVERT: B 429 ARG cc_start: 0.5979 (ttp80) cc_final: 0.5731 (ttt90) REVERT: B 442 GLU cc_start: 0.7318 (mt-10) cc_final: 0.7083 (mm-30) REVERT: B 443 ILE cc_start: 0.6524 (mm) cc_final: 0.6290 (mp) REVERT: C 33 LYS cc_start: 0.6440 (OUTLIER) cc_final: 0.6142 (mmtp) REVERT: C 95 ASP cc_start: 0.6970 (m-30) cc_final: 0.6635 (m-30) REVERT: C 139 LYS cc_start: 0.6874 (mttt) cc_final: 0.6368 (mttm) REVERT: C 178 GLU cc_start: 0.6464 (tm-30) cc_final: 0.6237 (mt-10) REVERT: C 184 GLU cc_start: 0.6239 (tt0) cc_final: 0.5772 (tt0) REVERT: C 316 ARG cc_start: 0.5176 (OUTLIER) cc_final: 0.4202 (tpt170) REVERT: C 347 MET cc_start: 0.6140 (mmm) cc_final: 0.5750 (mmp) REVERT: C 411 GLU cc_start: 0.5892 (mm-30) cc_final: 0.5424 (mt-10) REVERT: C 415 GLU cc_start: 0.5185 (mt-10) cc_final: 0.4556 (tt0) REVERT: C 419 GLU cc_start: 0.5818 (tt0) cc_final: 0.5321 (mt-10) REVERT: C 426 ASP cc_start: 0.5407 (t70) cc_final: 0.4862 (m-30) REVERT: C 429 ARG cc_start: 0.5883 (ttp80) cc_final: 0.5591 (ttt90) REVERT: E 6 GLN cc_start: 0.0243 (OUTLIER) cc_final: -0.0353 (pt0) REVERT: F 33 LYS cc_start: 0.6701 (OUTLIER) cc_final: 0.6317 (mmtp) REVERT: F 73 ASP cc_start: 0.6629 (t70) cc_final: 0.6166 (t0) REVERT: F 95 ASP cc_start: 0.6794 (m-30) cc_final: 0.6366 (m-30) REVERT: F 347 MET cc_start: 0.5990 (mmm) cc_final: 0.5661 (mmp) REVERT: F 390 GLU cc_start: 0.6108 (pm20) cc_final: 0.5807 (pt0) REVERT: F 415 GLU cc_start: 0.5083 (mt-10) cc_final: 0.4514 (tt0) REVERT: F 426 ASP cc_start: 0.5494 (t70) cc_final: 0.4943 (m-30) REVERT: F 427 MET cc_start: 0.6187 (ttp) cc_final: 0.5896 (mtp) REVERT: F 429 ARG cc_start: 0.5729 (ttp80) cc_final: 0.5410 (ttt90) REVERT: F 439 GLN cc_start: 0.5739 (OUTLIER) cc_final: 0.5505 (mm-40) REVERT: G 16 GLN cc_start: 0.6058 (mt0) cc_final: 0.5799 (mm-40) REVERT: G 92 MET cc_start: 0.7787 (mtm) cc_final: 0.7426 (mtp) REVERT: G 95 ASP cc_start: 0.6921 (m-30) cc_final: 0.6625 (m-30) REVERT: G 178 GLU cc_start: 0.6356 (tm-30) cc_final: 0.6056 (mm-30) REVERT: G 347 MET cc_start: 0.6274 (mmm) cc_final: 0.5981 (mmp) REVERT: G 390 GLU cc_start: 0.6363 (pm20) cc_final: 0.6063 (pt0) REVERT: G 415 GLU cc_start: 0.5056 (mt-10) cc_final: 0.4431 (tt0) REVERT: G 419 GLU cc_start: 0.5445 (tt0) cc_final: 0.5048 (mt-10) REVERT: G 426 ASP cc_start: 0.5069 (t70) cc_final: 0.4515 (m-30) REVERT: H 95 ASP cc_start: 0.6800 (m-30) cc_final: 0.6500 (m-30) REVERT: H 200 LYS cc_start: 0.6904 (ttmm) cc_final: 0.6592 (mmmt) REVERT: H 347 MET cc_start: 0.6113 (mmm) cc_final: 0.5853 (mmp) REVERT: H 390 GLU cc_start: 0.6259 (pm20) cc_final: 0.5868 (pt0) REVERT: H 415 GLU cc_start: 0.5001 (mt-10) cc_final: 0.4530 (tt0) REVERT: H 426 ASP cc_start: 0.5202 (t70) cc_final: 0.4649 (m-30) REVERT: H 438 GLU cc_start: 0.5406 (pt0) cc_final: 0.5167 (mt-10) REVERT: H 443 ILE cc_start: 0.6331 (mm) cc_final: 0.6119 (mp) REVERT: I 33 LYS cc_start: 0.6448 (OUTLIER) cc_final: 0.6149 (mmtp) REVERT: I 95 ASP cc_start: 0.6974 (m-30) cc_final: 0.6639 (m-30) REVERT: I 178 GLU cc_start: 0.6522 (tm-30) cc_final: 0.6310 (mt-10) REVERT: I 200 LYS cc_start: 0.7073 (ttmm) cc_final: 0.6752 (mmtt) REVERT: I 232 MET cc_start: 0.7397 (ttm) cc_final: 0.7135 (ttm) REVERT: I 347 MET cc_start: 0.6121 (mmm) cc_final: 0.5738 (mmp) REVERT: I 415 GLU cc_start: 0.5171 (mt-10) cc_final: 0.4561 (tt0) REVERT: I 419 GLU cc_start: 0.5802 (tt0) cc_final: 0.5338 (mt-10) REVERT: I 426 ASP cc_start: 0.5285 (t70) cc_final: 0.4700 (m-30) REVERT: I 427 MET cc_start: 0.5698 (mtp) cc_final: 0.5246 (mtp) REVERT: I 429 ARG cc_start: 0.5811 (ttp80) cc_final: 0.5562 (ttt90) REVERT: I 442 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7149 (mm-30) REVERT: N 16 GLN cc_start: 0.6056 (mt0) cc_final: 0.5800 (mm-40) REVERT: N 92 MET cc_start: 0.7783 (mtm) cc_final: 0.7423 (mtp) REVERT: N 95 ASP cc_start: 0.6906 (m-30) cc_final: 0.6613 (m-30) REVERT: N 139 LYS cc_start: 0.7051 (mttt) cc_final: 0.6706 (mttm) REVERT: N 178 GLU cc_start: 0.6537 (tm-30) cc_final: 0.6224 (mm-30) REVERT: N 200 LYS cc_start: 0.6967 (ttmm) cc_final: 0.6639 (mmtt) REVERT: N 347 MET cc_start: 0.6277 (mmm) cc_final: 0.5985 (mmp) REVERT: N 390 GLU cc_start: 0.6386 (pm20) cc_final: 0.6089 (pt0) REVERT: N 415 GLU cc_start: 0.5055 (mt-10) cc_final: 0.4465 (tt0) REVERT: N 426 ASP cc_start: 0.5167 (t70) cc_final: 0.4652 (m-30) REVERT: N 429 ARG cc_start: 0.5805 (ttp80) cc_final: 0.5510 (ttt90) REVERT: N 442 GLU cc_start: 0.7260 (mm-30) cc_final: 0.7014 (mm-30) REVERT: O 95 ASP cc_start: 0.6808 (m-30) cc_final: 0.6510 (m-30) REVERT: O 200 LYS cc_start: 0.6843 (ttmm) cc_final: 0.6506 (mttm) REVERT: O 347 MET cc_start: 0.6113 (mmm) cc_final: 0.5854 (mmp) REVERT: O 390 GLU cc_start: 0.6340 (pm20) cc_final: 0.5943 (pt0) REVERT: O 415 GLU cc_start: 0.4950 (mt-10) cc_final: 0.4468 (tt0) REVERT: O 426 ASP cc_start: 0.5400 (t70) cc_final: 0.4703 (m-30) REVERT: O 429 ARG cc_start: 0.5746 (ttp80) cc_final: 0.5517 (ttt90) REVERT: O 442 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6795 (mm-30) REVERT: O 443 ILE cc_start: 0.6388 (mm) cc_final: 0.6174 (mp) REVERT: P 16 GLN cc_start: 0.5932 (mt0) cc_final: 0.5665 (mm-40) REVERT: P 68 MET cc_start: 0.6943 (OUTLIER) cc_final: 0.6441 (mtt) REVERT: P 95 ASP cc_start: 0.6854 (m-30) cc_final: 0.6483 (m-30) REVERT: P 126 GLU cc_start: 0.7882 (tt0) cc_final: 0.7278 (tt0) REVERT: P 224 LYS cc_start: 0.5636 (OUTLIER) cc_final: 0.5419 (mtpp) REVERT: P 390 GLU cc_start: 0.6463 (pm20) cc_final: 0.5967 (pt0) REVERT: P 415 GLU cc_start: 0.5298 (mt-10) cc_final: 0.4715 (tt0) REVERT: P 426 ASP cc_start: 0.5124 (t70) cc_final: 0.4631 (m-30) REVERT: P 427 MET cc_start: 0.6382 (mtp) cc_final: 0.6088 (mtp) REVERT: P 429 ARG cc_start: 0.6029 (ttp80) cc_final: 0.5573 (ttt90) REVERT: Q 68 MET cc_start: 0.6704 (OUTLIER) cc_final: 0.5651 (mmt) REVERT: Q 73 ASP cc_start: 0.6537 (t70) cc_final: 0.5984 (t0) REVERT: Q 95 ASP cc_start: 0.7085 (m-30) cc_final: 0.6746 (m-30) REVERT: Q 126 GLU cc_start: 0.7082 (pt0) cc_final: 0.6699 (pt0) REVERT: Q 200 LYS cc_start: 0.7061 (ttmm) cc_final: 0.6687 (mttt) REVERT: Q 224 LYS cc_start: 0.5664 (OUTLIER) cc_final: 0.5364 (ttmm) REVERT: Q 390 GLU cc_start: 0.6331 (pm20) cc_final: 0.5843 (pt0) REVERT: Q 415 GLU cc_start: 0.5320 (mt-10) cc_final: 0.4779 (tt0) REVERT: Q 426 ASP cc_start: 0.5270 (t70) cc_final: 0.4717 (m-30) REVERT: Q 429 ARG cc_start: 0.5660 (ttp80) cc_final: 0.5346 (ttt90) REVERT: Q 442 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7121 (mm-30) REVERT: R 73 ASP cc_start: 0.6550 (t70) cc_final: 0.5989 (t0) REVERT: R 95 ASP cc_start: 0.7093 (m-30) cc_final: 0.6747 (m-30) REVERT: R 126 GLU cc_start: 0.7086 (pt0) cc_final: 0.6551 (tt0) REVERT: R 128 ASN cc_start: 0.7517 (m-40) cc_final: 0.6621 (m-40) REVERT: R 200 LYS cc_start: 0.7066 (ttmm) cc_final: 0.6688 (mttt) REVERT: R 316 ARG cc_start: 0.5258 (OUTLIER) cc_final: 0.4108 (tpt170) REVERT: R 390 GLU cc_start: 0.6323 (pm20) cc_final: 0.5826 (pt0) REVERT: R 415 GLU cc_start: 0.5274 (mt-10) cc_final: 0.4729 (tt0) REVERT: R 426 ASP cc_start: 0.5227 (t70) cc_final: 0.4690 (m-30) REVERT: R 429 ARG cc_start: 0.5697 (ttp80) cc_final: 0.5398 (ttt90) REVERT: S 16 GLN cc_start: 0.5932 (mt0) cc_final: 0.5667 (mm-40) REVERT: S 68 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.6456 (mtt) REVERT: S 95 ASP cc_start: 0.6787 (m-30) cc_final: 0.6393 (m-30) REVERT: S 126 GLU cc_start: 0.7874 (tt0) cc_final: 0.7265 (tt0) REVERT: S 347 MET cc_start: 0.6471 (mmm) cc_final: 0.6094 (mmp) REVERT: S 390 GLU cc_start: 0.6459 (pm20) cc_final: 0.5958 (pt0) REVERT: S 415 GLU cc_start: 0.5177 (mt-10) cc_final: 0.4626 (tt0) REVERT: S 426 ASP cc_start: 0.5129 (t70) cc_final: 0.4668 (m-30) REVERT: S 429 ARG cc_start: 0.5996 (ttp80) cc_final: 0.5615 (ttt90) REVERT: S 438 GLU cc_start: 0.5927 (pt0) cc_final: 0.5332 (mt-10) REVERT: S 439 GLN cc_start: 0.5507 (OUTLIER) cc_final: 0.4229 (mp10) REVERT: T 95 ASP cc_start: 0.6818 (m-30) cc_final: 0.6415 (m-30) REVERT: T 126 GLU cc_start: 0.7654 (pt0) cc_final: 0.7030 (tt0) REVERT: T 178 GLU cc_start: 0.6484 (tm-30) cc_final: 0.6235 (mt-10) REVERT: T 184 GLU cc_start: 0.6321 (tt0) cc_final: 0.5673 (tt0) REVERT: T 347 MET cc_start: 0.6028 (mmm) cc_final: 0.5660 (mmp) REVERT: T 390 GLU cc_start: 0.6313 (pm20) cc_final: 0.5839 (pt0) REVERT: T 415 GLU cc_start: 0.5227 (mt-10) cc_final: 0.4644 (tt0) REVERT: T 419 GLU cc_start: 0.5532 (tt0) cc_final: 0.5139 (mt-10) REVERT: T 426 ASP cc_start: 0.5113 (t70) cc_final: 0.4666 (m-30) REVERT: T 429 ARG cc_start: 0.6048 (ttp80) cc_final: 0.5767 (ttt90) REVERT: Z 6 GLN cc_start: 0.0197 (OUTLIER) cc_final: -0.0444 (pt0) outliers start: 131 outliers final: 44 residues processed: 811 average time/residue: 1.4440 time to fit residues: 1438.8262 Evaluate side-chains 743 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 683 time to evaluate : 4.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 168 CYS Chi-restraints excluded: chain F residue 240 ASN Chi-restraints excluded: chain F residue 331 ARG Chi-restraints excluded: chain F residue 421 LYS Chi-restraints excluded: chain F residue 439 GLN Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 168 CYS Chi-restraints excluded: chain G residue 181 PHE Chi-restraints excluded: chain G residue 224 LYS Chi-restraints excluded: chain G residue 439 GLN Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 168 CYS Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 240 ASN Chi-restraints excluded: chain I residue 248 MET Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 168 CYS Chi-restraints excluded: chain N residue 224 LYS Chi-restraints excluded: chain O residue 101 MET Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain O residue 442 GLU Chi-restraints excluded: chain P residue 68 MET Chi-restraints excluded: chain P residue 125 THR Chi-restraints excluded: chain P residue 181 PHE Chi-restraints excluded: chain P residue 224 LYS Chi-restraints excluded: chain Q residue 68 MET Chi-restraints excluded: chain Q residue 168 CYS Chi-restraints excluded: chain Q residue 181 PHE Chi-restraints excluded: chain Q residue 224 LYS Chi-restraints excluded: chain Q residue 240 ASN Chi-restraints excluded: chain R residue 181 PHE Chi-restraints excluded: chain R residue 224 LYS Chi-restraints excluded: chain R residue 316 ARG Chi-restraints excluded: chain R residue 439 GLN Chi-restraints excluded: chain S residue 68 MET Chi-restraints excluded: chain S residue 125 THR Chi-restraints excluded: chain S residue 181 PHE Chi-restraints excluded: chain S residue 439 GLN Chi-restraints excluded: chain T residue 125 THR Chi-restraints excluded: chain T residue 128 ASN Chi-restraints excluded: chain T residue 168 CYS Chi-restraints excluded: chain T residue 240 ASN Chi-restraints excluded: chain Z residue 6 GLN Chi-restraints excluded: chain a residue 10 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 574 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 339 optimal weight: 0.0870 chunk 435 optimal weight: 0.2980 chunk 337 optimal weight: 1.9990 chunk 501 optimal weight: 10.0000 chunk 332 optimal weight: 9.9990 chunk 593 optimal weight: 5.9990 chunk 371 optimal weight: 5.9990 chunk 361 optimal weight: 6.9990 chunk 274 optimal weight: 5.9990 overall best weight: 2.0764 ------------------------------------------------------------------------------- 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 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 ASN ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 ASN ** C 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN ** F 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 ASN ** G 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 ASN ** H 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN I 167 ASN ** I 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 151 ASN ** N 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 HIS ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 17 ASN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 17 ASN ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 ASN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 17 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 17 ASN ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 50918 Z= 0.241 Angle : 0.487 4.448 68936 Z= 0.254 Chirality : 0.042 0.144 7462 Planarity : 0.004 0.055 9030 Dihedral : 5.094 74.589 6794 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.76 % Allowed : 16.49 % Favored : 80.75 % 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 (0.11), residues: 6216 helix: 2.02 (0.10), residues: 2380 sheet: -0.67 (0.16), residues: 1162 loop : -0.46 (0.12), residues: 2674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP T 435 HIS 0.005 0.001 HIS P 416 PHE 0.011 0.001 PHE O 71 TYR 0.014 0.001 TYR B 285 ARG 0.002 0.000 ARG N 331 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 672 time to evaluate : 4.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6690 (mp) REVERT: A 33 LYS cc_start: 0.6692 (OUTLIER) cc_final: 0.6284 (mmtp) REVERT: A 73 ASP cc_start: 0.6649 (t70) cc_final: 0.5863 (t70) REVERT: A 95 ASP cc_start: 0.6888 (m-30) cc_final: 0.6465 (m-30) REVERT: A 316 ARG cc_start: 0.5318 (OUTLIER) cc_final: 0.4083 (tpt170) REVERT: A 347 MET cc_start: 0.5987 (mmm) cc_final: 0.5663 (mmp) REVERT: A 390 GLU cc_start: 0.6175 (pm20) cc_final: 0.5873 (pt0) REVERT: A 415 GLU cc_start: 0.5226 (mt-10) cc_final: 0.4652 (tt0) REVERT: A 426 ASP cc_start: 0.5343 (t70) cc_final: 0.4884 (m-30) REVERT: A 427 MET cc_start: 0.6328 (mtp) cc_final: 0.5917 (mtp) REVERT: A 429 ARG cc_start: 0.5873 (ttp80) cc_final: 0.5489 (ttt90) REVERT: B 95 ASP cc_start: 0.6853 (m-30) cc_final: 0.6440 (m-30) REVERT: B 159 LEU cc_start: 0.5486 (OUTLIER) cc_final: 0.5189 (tt) REVERT: B 178 GLU cc_start: 0.6425 (tm-30) cc_final: 0.6183 (mt-10) REVERT: B 184 GLU cc_start: 0.6297 (tt0) cc_final: 0.5637 (tt0) REVERT: B 316 ARG cc_start: 0.5274 (OUTLIER) cc_final: 0.4166 (tpt170) REVERT: B 347 MET cc_start: 0.6005 (mmm) cc_final: 0.5629 (mmp) REVERT: B 390 GLU cc_start: 0.6343 (pm20) cc_final: 0.5922 (pt0) REVERT: B 415 GLU cc_start: 0.4978 (mt-10) cc_final: 0.4495 (tt0) REVERT: B 426 ASP cc_start: 0.5386 (t70) cc_final: 0.4882 (m-30) REVERT: B 429 ARG cc_start: 0.6237 (ttp80) cc_final: 0.5909 (ttt90) REVERT: B 442 GLU cc_start: 0.7326 (mt-10) cc_final: 0.7085 (mt-10) REVERT: B 443 ILE cc_start: 0.6488 (mm) cc_final: 0.6257 (mp) REVERT: C 33 LYS cc_start: 0.6632 (OUTLIER) cc_final: 0.6278 (mmtp) REVERT: C 95 ASP cc_start: 0.7022 (m-30) cc_final: 0.6667 (m-30) REVERT: C 178 GLU cc_start: 0.6510 (tm-30) cc_final: 0.6249 (mt-10) REVERT: C 184 GLU cc_start: 0.6283 (tt0) cc_final: 0.5799 (tt0) REVERT: C 316 ARG cc_start: 0.5237 (OUTLIER) cc_final: 0.4156 (tpt170) REVERT: C 347 MET cc_start: 0.6127 (mmm) cc_final: 0.5789 (mmp) REVERT: C 415 GLU cc_start: 0.5031 (mt-10) cc_final: 0.4437 (tt0) REVERT: C 426 ASP cc_start: 0.5470 (t70) cc_final: 0.4979 (m-30) REVERT: C 429 ARG cc_start: 0.5984 (ttp80) cc_final: 0.5678 (ttt90) REVERT: E 6 GLN cc_start: 0.0464 (OUTLIER) cc_final: -0.0118 (pt0) REVERT: F 29 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6649 (mp) REVERT: F 33 LYS cc_start: 0.6666 (OUTLIER) cc_final: 0.6294 (mmtp) REVERT: F 68 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.6237 (mtt) REVERT: F 73 ASP cc_start: 0.6651 (t70) cc_final: 0.5834 (t70) REVERT: F 95 ASP cc_start: 0.6872 (m-30) cc_final: 0.6468 (m-30) REVERT: F 347 MET cc_start: 0.5985 (mmm) cc_final: 0.5660 (mmp) REVERT: F 390 GLU cc_start: 0.6220 (pm20) cc_final: 0.5936 (pt0) REVERT: F 415 GLU cc_start: 0.5227 (mt-10) cc_final: 0.4655 (tt0) REVERT: F 426 ASP cc_start: 0.5567 (t70) cc_final: 0.4977 (m-30) REVERT: F 427 MET cc_start: 0.6190 (ttp) cc_final: 0.5873 (mtp) REVERT: F 429 ARG cc_start: 0.5835 (ttp80) cc_final: 0.5527 (ttt90) REVERT: F 439 GLN cc_start: 0.5749 (OUTLIER) cc_final: 0.5503 (mm-40) REVERT: G 92 MET cc_start: 0.7832 (mtm) cc_final: 0.7533 (mtp) REVERT: G 95 ASP cc_start: 0.6961 (m-30) cc_final: 0.6606 (m-30) REVERT: G 178 GLU cc_start: 0.6449 (tm-30) cc_final: 0.6164 (mm-30) REVERT: G 347 MET cc_start: 0.6234 (mmm) cc_final: 0.5937 (mmp) REVERT: G 390 GLU cc_start: 0.6384 (pm20) cc_final: 0.6080 (pt0) REVERT: G 415 GLU cc_start: 0.5140 (mt-10) cc_final: 0.4515 (tt0) REVERT: G 419 GLU cc_start: 0.5534 (tt0) cc_final: 0.5069 (mt-10) REVERT: G 426 ASP cc_start: 0.5157 (t70) cc_final: 0.4584 (m-30) REVERT: H 95 ASP cc_start: 0.6927 (m-30) cc_final: 0.6618 (m-30) REVERT: H 200 LYS cc_start: 0.6963 (ttmm) cc_final: 0.6636 (mmmt) REVERT: H 347 MET cc_start: 0.6114 (mmm) cc_final: 0.5841 (mmp) REVERT: H 390 GLU cc_start: 0.6226 (pm20) cc_final: 0.5868 (pt0) REVERT: H 415 GLU cc_start: 0.5101 (mt-10) cc_final: 0.4506 (tt0) REVERT: H 426 ASP cc_start: 0.5272 (t70) cc_final: 0.4723 (m-30) REVERT: H 438 GLU cc_start: 0.5490 (pt0) cc_final: 0.5158 (mt-10) REVERT: H 443 ILE cc_start: 0.6218 (mm) cc_final: 0.6013 (mp) REVERT: I 33 LYS cc_start: 0.6622 (OUTLIER) cc_final: 0.6275 (mmtp) REVERT: I 95 ASP cc_start: 0.7019 (m-30) cc_final: 0.6667 (m-30) REVERT: I 178 GLU cc_start: 0.6517 (tm-30) cc_final: 0.6257 (mt-10) REVERT: I 200 LYS cc_start: 0.7118 (ttmm) cc_final: 0.6767 (mmtt) REVERT: I 232 MET cc_start: 0.7529 (ttm) cc_final: 0.7279 (ttm) REVERT: I 347 MET cc_start: 0.6119 (mmm) cc_final: 0.5784 (mmp) REVERT: I 415 GLU cc_start: 0.5127 (mt-10) cc_final: 0.4452 (tt0) REVERT: I 419 GLU cc_start: 0.5856 (tt0) cc_final: 0.5391 (mt-10) REVERT: I 426 ASP cc_start: 0.5365 (t70) cc_final: 0.4832 (m-30) REVERT: I 427 MET cc_start: 0.5786 (mtp) cc_final: 0.5341 (mtp) REVERT: I 429 ARG cc_start: 0.5922 (ttp80) cc_final: 0.5668 (ttt90) REVERT: N 92 MET cc_start: 0.7808 (mtm) cc_final: 0.7510 (mtp) REVERT: N 95 ASP cc_start: 0.6961 (m-30) cc_final: 0.6610 (m-30) REVERT: N 139 LYS cc_start: 0.6978 (mttt) cc_final: 0.6640 (mttm) REVERT: N 178 GLU cc_start: 0.6467 (tm-30) cc_final: 0.6189 (mm-30) REVERT: N 200 LYS cc_start: 0.6963 (ttmm) cc_final: 0.6615 (mmtt) REVERT: N 347 MET cc_start: 0.6236 (mmm) cc_final: 0.5941 (mmp) REVERT: N 390 GLU cc_start: 0.6394 (pm20) cc_final: 0.6095 (pt0) REVERT: N 415 GLU cc_start: 0.5118 (mt-10) cc_final: 0.4541 (tt0) REVERT: N 426 ASP cc_start: 0.5328 (t70) cc_final: 0.4756 (m-30) REVERT: N 429 ARG cc_start: 0.5842 (ttp80) cc_final: 0.5586 (ttt90) REVERT: N 442 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6947 (mm-30) REVERT: O 95 ASP cc_start: 0.6995 (m-30) cc_final: 0.6693 (m-30) REVERT: O 200 LYS cc_start: 0.6911 (ttmm) cc_final: 0.6589 (mttm) REVERT: O 347 MET cc_start: 0.6114 (mmm) cc_final: 0.5841 (mmp) REVERT: O 390 GLU cc_start: 0.6312 (pm20) cc_final: 0.5963 (pt0) REVERT: O 415 GLU cc_start: 0.4968 (mt-10) cc_final: 0.4409 (tt0) REVERT: O 426 ASP cc_start: 0.5463 (t70) cc_final: 0.4797 (m-30) REVERT: O 429 ARG cc_start: 0.5846 (ttp80) cc_final: 0.5623 (ttt90) REVERT: O 442 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6699 (mm-30) REVERT: O 443 ILE cc_start: 0.6412 (mm) cc_final: 0.6182 (mp) REVERT: P 16 GLN cc_start: 0.5919 (mt0) cc_final: 0.5639 (mm-40) REVERT: P 68 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6302 (mtt) REVERT: P 73 ASP cc_start: 0.6821 (t70) cc_final: 0.6442 (t0) REVERT: P 95 ASP cc_start: 0.6927 (m-30) cc_final: 0.6506 (m-30) REVERT: P 126 GLU cc_start: 0.7872 (tt0) cc_final: 0.7318 (tt0) REVERT: P 163 ASP cc_start: 0.4322 (OUTLIER) cc_final: 0.2712 (m-30) REVERT: P 224 LYS cc_start: 0.5721 (OUTLIER) cc_final: 0.5483 (mtpp) REVERT: P 390 GLU cc_start: 0.6512 (pm20) cc_final: 0.5986 (pt0) REVERT: P 415 GLU cc_start: 0.5142 (mt-10) cc_final: 0.4567 (tt0) REVERT: P 426 ASP cc_start: 0.5174 (t70) cc_final: 0.4694 (m-30) REVERT: P 427 MET cc_start: 0.6512 (mtp) cc_final: 0.6232 (mtp) REVERT: P 429 ARG cc_start: 0.5976 (ttp80) cc_final: 0.5523 (ttt90) REVERT: Q 73 ASP cc_start: 0.6504 (t70) cc_final: 0.5948 (t0) REVERT: Q 95 ASP cc_start: 0.7136 (m-30) cc_final: 0.6786 (m-30) REVERT: Q 200 LYS cc_start: 0.7196 (ttmm) cc_final: 0.6756 (mttt) REVERT: Q 316 ARG cc_start: 0.5378 (OUTLIER) cc_final: 0.4177 (tpt170) REVERT: Q 390 GLU cc_start: 0.6330 (pm20) cc_final: 0.5841 (pt0) REVERT: Q 415 GLU cc_start: 0.5530 (mt-10) cc_final: 0.4973 (tt0) REVERT: Q 426 ASP cc_start: 0.5309 (t70) cc_final: 0.4774 (m-30) REVERT: Q 429 ARG cc_start: 0.5710 (ttp80) cc_final: 0.5391 (ttt90) REVERT: Q 442 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7112 (mm-30) REVERT: R 68 MET cc_start: 0.6887 (mmt) cc_final: 0.6587 (mpp) REVERT: R 73 ASP cc_start: 0.6519 (t70) cc_final: 0.5961 (t0) REVERT: R 95 ASP cc_start: 0.7137 (m-30) cc_final: 0.6785 (m-30) REVERT: R 126 GLU cc_start: 0.7302 (pt0) cc_final: 0.6542 (pt0) REVERT: R 200 LYS cc_start: 0.7075 (ttmm) cc_final: 0.6707 (mttt) REVERT: R 316 ARG cc_start: 0.5286 (OUTLIER) cc_final: 0.4090 (tpt170) REVERT: R 390 GLU cc_start: 0.6331 (pm20) cc_final: 0.5821 (pt0) REVERT: R 415 GLU cc_start: 0.5427 (mt-10) cc_final: 0.4861 (tt0) REVERT: R 426 ASP cc_start: 0.5246 (t70) cc_final: 0.4732 (m-30) REVERT: R 429 ARG cc_start: 0.5760 (ttp80) cc_final: 0.5464 (ttt90) REVERT: S 16 GLN cc_start: 0.5916 (mt0) cc_final: 0.5640 (mm-40) REVERT: S 36 GLU cc_start: 0.7352 (mt-10) cc_final: 0.7088 (mt-10) REVERT: S 68 MET cc_start: 0.6972 (OUTLIER) cc_final: 0.6304 (mtt) REVERT: S 95 ASP cc_start: 0.6826 (m-30) cc_final: 0.6408 (m-30) REVERT: S 126 GLU cc_start: 0.7885 (tt0) cc_final: 0.7354 (tt0) REVERT: S 163 ASP cc_start: 0.4360 (OUTLIER) cc_final: 0.2816 (m-30) REVERT: S 347 MET cc_start: 0.6384 (mmm) cc_final: 0.6070 (mmp) REVERT: S 390 GLU cc_start: 0.6508 (pm20) cc_final: 0.5986 (pt0) REVERT: S 415 GLU cc_start: 0.5231 (mt-10) cc_final: 0.4665 (tt0) REVERT: S 426 ASP cc_start: 0.5210 (t70) cc_final: 0.4754 (m-30) REVERT: S 429 ARG cc_start: 0.6050 (ttp80) cc_final: 0.5628 (ttt90) REVERT: S 438 GLU cc_start: 0.6033 (pt0) cc_final: 0.5443 (mt-10) REVERT: S 439 GLN cc_start: 0.5592 (OUTLIER) cc_final: 0.4283 (mp10) REVERT: T 95 ASP cc_start: 0.6836 (m-30) cc_final: 0.6432 (m-30) REVERT: T 126 GLU cc_start: 0.7742 (pt0) cc_final: 0.7285 (tt0) REVERT: T 159 LEU cc_start: 0.5487 (OUTLIER) cc_final: 0.5187 (tt) REVERT: T 178 GLU cc_start: 0.6428 (tm-30) cc_final: 0.6182 (mt-10) REVERT: T 184 GLU cc_start: 0.6292 (tt0) cc_final: 0.5633 (tt0) REVERT: T 203 ASP cc_start: 0.6960 (m-30) cc_final: 0.6722 (m-30) REVERT: T 316 ARG cc_start: 0.5403 (OUTLIER) cc_final: 0.4242 (tpt170) REVERT: T 347 MET cc_start: 0.6007 (mmm) cc_final: 0.5630 (mmp) REVERT: T 390 GLU cc_start: 0.6285 (pm20) cc_final: 0.5798 (pt0) REVERT: T 415 GLU cc_start: 0.5030 (mt-10) cc_final: 0.4489 (tt0) REVERT: T 419 GLU cc_start: 0.5657 (tt0) cc_final: 0.5232 (mt-10) REVERT: T 426 ASP cc_start: 0.5183 (t70) cc_final: 0.4739 (m-30) REVERT: T 429 ARG cc_start: 0.6120 (ttp80) cc_final: 0.5837 (ttt90) REVERT: Z 6 GLN cc_start: 0.0278 (OUTLIER) cc_final: -0.0321 (pt0) outliers start: 144 outliers final: 49 residues processed: 787 average time/residue: 1.4627 time to fit residues: 1414.0204 Evaluate side-chains 748 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 674 time to evaluate : 4.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 316 ARG Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 168 CYS Chi-restraints excluded: chain F residue 200 LYS Chi-restraints excluded: chain F residue 240 ASN Chi-restraints excluded: chain F residue 278 MET Chi-restraints excluded: chain F residue 331 ARG Chi-restraints excluded: chain F residue 421 LYS Chi-restraints excluded: chain F residue 439 GLN Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 168 CYS Chi-restraints excluded: chain G residue 224 LYS Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 168 CYS Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 240 ASN Chi-restraints excluded: chain I residue 248 MET Chi-restraints excluded: chain N residue 29 LEU Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 126 GLU Chi-restraints excluded: chain N residue 168 CYS Chi-restraints excluded: chain N residue 224 LYS Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain O residue 442 GLU Chi-restraints excluded: chain P residue 15 GLU Chi-restraints excluded: chain P residue 68 MET Chi-restraints excluded: chain P residue 125 THR Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 224 LYS Chi-restraints excluded: chain Q residue 125 THR Chi-restraints excluded: chain Q residue 168 CYS Chi-restraints excluded: chain Q residue 240 ASN Chi-restraints excluded: chain Q residue 316 ARG Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 224 LYS Chi-restraints excluded: chain R residue 316 ARG Chi-restraints excluded: chain R residue 439 GLN Chi-restraints excluded: chain S residue 68 MET Chi-restraints excluded: chain S residue 125 THR Chi-restraints excluded: chain S residue 163 ASP Chi-restraints excluded: chain S residue 439 GLN Chi-restraints excluded: chain T residue 125 THR Chi-restraints excluded: chain T residue 128 ASN Chi-restraints excluded: chain T residue 159 LEU Chi-restraints excluded: chain T residue 168 CYS Chi-restraints excluded: chain T residue 240 ASN Chi-restraints excluded: chain T residue 249 SER Chi-restraints excluded: chain T residue 316 ARG Chi-restraints excluded: chain Z residue 6 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 367 optimal weight: 9.9990 chunk 237 optimal weight: 5.9990 chunk 354 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 377 optimal weight: 0.9990 chunk 404 optimal weight: 0.7980 chunk 293 optimal weight: 0.0470 chunk 55 optimal weight: 0.7980 chunk 466 optimal weight: 7.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- 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 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 ASN ** F 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 ASN ** G 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 ASN ** H 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 151 ASN ** N 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 17 ASN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 17 ASN ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 167 ASN ** Q 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 ASN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 167 ASN ** R 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 17 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 50918 Z= 0.151 Angle : 0.436 3.964 68936 Z= 0.229 Chirality : 0.039 0.132 7462 Planarity : 0.003 0.074 9030 Dihedral : 4.852 73.713 6794 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.09 % Allowed : 17.18 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.11), residues: 6216 helix: 2.16 (0.10), residues: 2408 sheet: -0.64 (0.16), residues: 1162 loop : -0.45 (0.12), residues: 2646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 435 HIS 0.003 0.001 HIS N 416 PHE 0.009 0.001 PHE A 296 TYR 0.012 0.001 TYR T 285 ARG 0.003 0.000 ARG I 145 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 693 time to evaluate : 4.523 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.6599 (OUTLIER) cc_final: 0.6200 (mmtp) REVERT: A 73 ASP cc_start: 0.6615 (t70) cc_final: 0.5803 (t70) REVERT: A 95 ASP cc_start: 0.6828 (m-30) cc_final: 0.6387 (m-30) REVERT: A 316 ARG cc_start: 0.5270 (OUTLIER) cc_final: 0.4010 (tpt170) REVERT: A 347 MET cc_start: 0.6014 (mmm) cc_final: 0.5694 (mmp) REVERT: A 390 GLU cc_start: 0.6149 (pm20) cc_final: 0.5841 (pt0) REVERT: A 415 GLU cc_start: 0.5102 (mt-10) cc_final: 0.4533 (tt0) REVERT: A 426 ASP cc_start: 0.5327 (t70) cc_final: 0.4828 (m-30) REVERT: A 427 MET cc_start: 0.6279 (mtp) cc_final: 0.5827 (mtp) REVERT: A 429 ARG cc_start: 0.5856 (ttp80) cc_final: 0.5475 (ttt90) REVERT: B 95 ASP cc_start: 0.7007 (m-30) cc_final: 0.6601 (m-30) REVERT: B 159 LEU cc_start: 0.5391 (OUTLIER) cc_final: 0.5099 (tt) REVERT: B 178 GLU cc_start: 0.6434 (tm-30) cc_final: 0.6172 (mt-10) REVERT: B 184 GLU cc_start: 0.6289 (tt0) cc_final: 0.5656 (tt0) REVERT: B 347 MET cc_start: 0.6027 (mmm) cc_final: 0.5663 (mmp) REVERT: B 390 GLU cc_start: 0.6346 (pm20) cc_final: 0.5921 (pt0) REVERT: B 415 GLU cc_start: 0.5005 (mt-10) cc_final: 0.4540 (tt0) REVERT: B 426 ASP cc_start: 0.5350 (t70) cc_final: 0.4860 (m-30) REVERT: B 429 ARG cc_start: 0.6057 (ttp80) cc_final: 0.5824 (ttt90) REVERT: B 442 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7091 (mt-10) REVERT: B 443 ILE cc_start: 0.6490 (mm) cc_final: 0.6247 (mp) REVERT: C 33 LYS cc_start: 0.6603 (OUTLIER) cc_final: 0.6296 (mmtp) REVERT: C 95 ASP cc_start: 0.6946 (m-30) cc_final: 0.6623 (m-30) REVERT: C 178 GLU cc_start: 0.6507 (tm-30) cc_final: 0.6300 (mt-10) REVERT: C 184 GLU cc_start: 0.6273 (tt0) cc_final: 0.5790 (tt0) REVERT: C 316 ARG cc_start: 0.5141 (OUTLIER) cc_final: 0.4140 (tpt170) REVERT: C 347 MET cc_start: 0.6142 (mmm) cc_final: 0.5812 (mmp) REVERT: C 415 GLU cc_start: 0.4973 (mt-10) cc_final: 0.4344 (tt0) REVERT: C 419 GLU cc_start: 0.5864 (tt0) cc_final: 0.5399 (mt-10) REVERT: C 426 ASP cc_start: 0.5449 (t70) cc_final: 0.4941 (m-30) REVERT: C 429 ARG cc_start: 0.5942 (ttp80) cc_final: 0.5664 (ttt90) REVERT: E 6 GLN cc_start: 0.0410 (OUTLIER) cc_final: -0.0168 (pt0) REVERT: F 33 LYS cc_start: 0.6668 (OUTLIER) cc_final: 0.6325 (mmtp) REVERT: F 68 MET cc_start: 0.6857 (OUTLIER) cc_final: 0.6239 (mtt) REVERT: F 73 ASP cc_start: 0.6642 (t70) cc_final: 0.5837 (t70) REVERT: F 95 ASP cc_start: 0.6819 (m-30) cc_final: 0.6388 (m-30) REVERT: F 347 MET cc_start: 0.6012 (mmm) cc_final: 0.5693 (mmp) REVERT: F 390 GLU cc_start: 0.6163 (pm20) cc_final: 0.5885 (pt0) REVERT: F 415 GLU cc_start: 0.5083 (mt-10) cc_final: 0.4513 (tt0) REVERT: F 426 ASP cc_start: 0.5488 (t70) cc_final: 0.4915 (m-30) REVERT: F 427 MET cc_start: 0.6117 (ttp) cc_final: 0.5823 (mtp) REVERT: F 429 ARG cc_start: 0.5806 (ttp80) cc_final: 0.5531 (ttt90) REVERT: G 92 MET cc_start: 0.7774 (mtm) cc_final: 0.7471 (mtp) REVERT: G 95 ASP cc_start: 0.6908 (m-30) cc_final: 0.6605 (m-30) REVERT: G 178 GLU cc_start: 0.6382 (tm-30) cc_final: 0.6122 (mm-30) REVERT: G 347 MET cc_start: 0.6282 (mmm) cc_final: 0.5991 (mmp) REVERT: G 390 GLU cc_start: 0.6379 (pm20) cc_final: 0.6067 (pt0) REVERT: G 415 GLU cc_start: 0.5075 (mt-10) cc_final: 0.4459 (tt0) REVERT: G 419 GLU cc_start: 0.5484 (tt0) cc_final: 0.5032 (mt-10) REVERT: G 426 ASP cc_start: 0.5063 (t70) cc_final: 0.4570 (m-30) REVERT: H 95 ASP cc_start: 0.6929 (m-30) cc_final: 0.6651 (m-30) REVERT: H 200 LYS cc_start: 0.6903 (ttmm) cc_final: 0.6626 (mmmt) REVERT: H 347 MET cc_start: 0.6105 (mmm) cc_final: 0.5845 (mmp) REVERT: H 390 GLU cc_start: 0.6253 (pm20) cc_final: 0.5890 (pt0) REVERT: H 415 GLU cc_start: 0.5030 (mt-10) cc_final: 0.4496 (tt0) REVERT: H 426 ASP cc_start: 0.5247 (t70) cc_final: 0.4690 (m-30) REVERT: H 438 GLU cc_start: 0.5422 (pt0) cc_final: 0.5186 (mt-10) REVERT: H 443 ILE cc_start: 0.6213 (mm) cc_final: 0.6005 (mp) REVERT: I 33 LYS cc_start: 0.6603 (OUTLIER) cc_final: 0.6296 (mmtp) REVERT: I 95 ASP cc_start: 0.6946 (m-30) cc_final: 0.6624 (m-30) REVERT: I 178 GLU cc_start: 0.6512 (tm-30) cc_final: 0.6294 (mt-10) REVERT: I 200 LYS cc_start: 0.7085 (ttmm) cc_final: 0.6723 (mmtt) REVERT: I 232 MET cc_start: 0.7479 (ttm) cc_final: 0.7271 (ttm) REVERT: I 347 MET cc_start: 0.6120 (mmm) cc_final: 0.5793 (mmp) REVERT: I 415 GLU cc_start: 0.5123 (mt-10) cc_final: 0.4427 (tt0) REVERT: I 419 GLU cc_start: 0.5818 (tt0) cc_final: 0.5365 (mt-10) REVERT: I 426 ASP cc_start: 0.5279 (t70) cc_final: 0.4733 (m-30) REVERT: I 427 MET cc_start: 0.5724 (mtp) cc_final: 0.5283 (mtp) REVERT: I 429 ARG cc_start: 0.5810 (ttp80) cc_final: 0.5565 (ttt90) REVERT: N 92 MET cc_start: 0.7769 (mtm) cc_final: 0.7468 (mtp) REVERT: N 95 ASP cc_start: 0.6909 (m-30) cc_final: 0.6609 (m-30) REVERT: N 139 LYS cc_start: 0.6988 (mttt) cc_final: 0.6657 (mttm) REVERT: N 178 GLU cc_start: 0.6434 (tm-30) cc_final: 0.6131 (mm-30) REVERT: N 200 LYS cc_start: 0.6983 (ttmm) cc_final: 0.6622 (mmtt) REVERT: N 347 MET cc_start: 0.6286 (mmm) cc_final: 0.5997 (mmp) REVERT: N 390 GLU cc_start: 0.6418 (pm20) cc_final: 0.6110 (pt0) REVERT: N 415 GLU cc_start: 0.5071 (mt-10) cc_final: 0.4497 (tt0) REVERT: N 426 ASP cc_start: 0.5334 (t70) cc_final: 0.4746 (m-30) REVERT: N 429 ARG cc_start: 0.5875 (ttp80) cc_final: 0.5614 (ttt90) REVERT: N 442 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6978 (mm-30) REVERT: O 95 ASP cc_start: 0.6926 (m-30) cc_final: 0.6640 (m-30) REVERT: O 200 LYS cc_start: 0.6856 (ttmm) cc_final: 0.6543 (mttm) REVERT: O 347 MET cc_start: 0.6102 (mmm) cc_final: 0.5845 (mmp) REVERT: O 390 GLU cc_start: 0.6307 (pm20) cc_final: 0.5936 (pt0) REVERT: O 415 GLU cc_start: 0.4927 (mt-10) cc_final: 0.4378 (tt0) REVERT: O 426 ASP cc_start: 0.5435 (t70) cc_final: 0.4791 (m-30) REVERT: O 429 ARG cc_start: 0.5805 (ttp80) cc_final: 0.5578 (ttt90) REVERT: O 442 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6803 (mm-30) REVERT: O 443 ILE cc_start: 0.6382 (mm) cc_final: 0.6174 (mp) REVERT: P 16 GLN cc_start: 0.5882 (mt0) cc_final: 0.5645 (mm-40) REVERT: P 68 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.6402 (mtt) REVERT: P 73 ASP cc_start: 0.6843 (t70) cc_final: 0.6451 (t0) REVERT: P 95 ASP cc_start: 0.6834 (m-30) cc_final: 0.6507 (m-30) REVERT: P 126 GLU cc_start: 0.7877 (tt0) cc_final: 0.7247 (tt0) REVERT: P 159 LEU cc_start: 0.5296 (OUTLIER) cc_final: 0.5091 (tt) REVERT: P 224 LYS cc_start: 0.5648 (OUTLIER) cc_final: 0.5396 (mtpp) REVERT: P 390 GLU cc_start: 0.6457 (pm20) cc_final: 0.5975 (pt0) REVERT: P 415 GLU cc_start: 0.5210 (mt-10) cc_final: 0.4634 (tt0) REVERT: P 426 ASP cc_start: 0.5136 (t70) cc_final: 0.4668 (m-30) REVERT: P 427 MET cc_start: 0.6473 (mtp) cc_final: 0.6190 (mtp) REVERT: P 429 ARG cc_start: 0.6049 (ttp80) cc_final: 0.5702 (ttt90) REVERT: Q 73 ASP cc_start: 0.6554 (t70) cc_final: 0.5993 (t0) REVERT: Q 95 ASP cc_start: 0.7101 (m-30) cc_final: 0.6762 (m-30) REVERT: Q 126 GLU cc_start: 0.7204 (pt0) cc_final: 0.6508 (tt0) REVERT: Q 200 LYS cc_start: 0.7069 (ttmm) cc_final: 0.6678 (mttt) REVERT: Q 390 GLU cc_start: 0.6332 (pm20) cc_final: 0.5844 (pt0) REVERT: Q 415 GLU cc_start: 0.5427 (mt-10) cc_final: 0.4870 (tt0) REVERT: Q 426 ASP cc_start: 0.5289 (t70) cc_final: 0.4748 (m-30) REVERT: Q 429 ARG cc_start: 0.5708 (ttp80) cc_final: 0.5388 (ttt90) REVERT: Q 442 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7201 (mm-30) REVERT: R 68 MET cc_start: 0.6831 (mmt) cc_final: 0.6505 (mpp) REVERT: R 73 ASP cc_start: 0.6499 (t70) cc_final: 0.5936 (t0) REVERT: R 95 ASP cc_start: 0.7092 (m-30) cc_final: 0.6762 (m-30) REVERT: R 126 GLU cc_start: 0.7187 (pt0) cc_final: 0.6819 (pt0) REVERT: R 200 LYS cc_start: 0.7047 (ttmm) cc_final: 0.6681 (mttt) REVERT: R 316 ARG cc_start: 0.5252 (OUTLIER) cc_final: 0.4096 (tpt170) REVERT: R 390 GLU cc_start: 0.6328 (pm20) cc_final: 0.5822 (pt0) REVERT: R 415 GLU cc_start: 0.5310 (mt-10) cc_final: 0.4742 (tt0) REVERT: R 426 ASP cc_start: 0.5267 (t70) cc_final: 0.4733 (m-30) REVERT: R 429 ARG cc_start: 0.5819 (ttp80) cc_final: 0.5506 (ttt90) REVERT: S 16 GLN cc_start: 0.5877 (mt0) cc_final: 0.5640 (mm-40) REVERT: S 36 GLU cc_start: 0.7344 (mt-10) cc_final: 0.7116 (mt-10) REVERT: S 68 MET cc_start: 0.6980 (OUTLIER) cc_final: 0.6401 (mtt) REVERT: S 95 ASP cc_start: 0.6810 (m-30) cc_final: 0.6379 (m-30) REVERT: S 126 GLU cc_start: 0.7873 (tt0) cc_final: 0.7231 (tt0) REVERT: S 163 ASP cc_start: 0.4578 (OUTLIER) cc_final: 0.3024 (m-30) REVERT: S 347 MET cc_start: 0.6470 (mmm) cc_final: 0.6099 (mmp) REVERT: S 390 GLU cc_start: 0.6474 (pm20) cc_final: 0.5966 (pt0) REVERT: S 415 GLU cc_start: 0.5192 (mt-10) cc_final: 0.4629 (tt0) REVERT: S 426 ASP cc_start: 0.5170 (t70) cc_final: 0.4693 (m-30) REVERT: S 429 ARG cc_start: 0.6045 (ttp80) cc_final: 0.5653 (ttt90) REVERT: S 438 GLU cc_start: 0.5985 (pt0) cc_final: 0.5420 (mt-10) REVERT: S 439 GLN cc_start: 0.5519 (OUTLIER) cc_final: 0.4239 (mp10) REVERT: T 95 ASP cc_start: 0.7009 (m-30) cc_final: 0.6606 (m-30) REVERT: T 126 GLU cc_start: 0.7631 (pt0) cc_final: 0.7021 (tt0) REVERT: T 159 LEU cc_start: 0.5392 (OUTLIER) cc_final: 0.5099 (tt) REVERT: T 178 GLU cc_start: 0.6436 (tm-30) cc_final: 0.6171 (mt-10) REVERT: T 184 GLU cc_start: 0.6289 (tt0) cc_final: 0.5664 (tt0) REVERT: T 347 MET cc_start: 0.6025 (mmm) cc_final: 0.5658 (mmp) REVERT: T 390 GLU cc_start: 0.6297 (pm20) cc_final: 0.5807 (pt0) REVERT: T 415 GLU cc_start: 0.4990 (mt-10) cc_final: 0.4455 (tt0) REVERT: T 419 GLU cc_start: 0.5575 (tt0) cc_final: 0.5193 (mt-10) REVERT: T 426 ASP cc_start: 0.5137 (t70) cc_final: 0.4698 (m-30) REVERT: T 429 ARG cc_start: 0.6016 (ttp80) cc_final: 0.5731 (ttt90) REVERT: Z 6 GLN cc_start: 0.0053 (OUTLIER) cc_final: -0.0507 (pt0) outliers start: 109 outliers final: 56 residues processed: 781 average time/residue: 1.4877 time to fit residues: 1442.9534 Evaluate side-chains 752 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 677 time to evaluate : 4.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 168 CYS Chi-restraints excluded: chain F residue 181 PHE Chi-restraints excluded: chain F residue 240 ASN Chi-restraints excluded: chain F residue 331 ARG Chi-restraints excluded: chain F residue 421 LYS Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 168 CYS Chi-restraints excluded: chain G residue 181 PHE Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 224 LYS Chi-restraints excluded: chain G residue 439 GLN Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 439 GLN Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 168 CYS Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 240 ASN Chi-restraints excluded: chain I residue 248 MET Chi-restraints excluded: chain M residue 10 PHE Chi-restraints excluded: chain N residue 29 LEU Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 216 LEU Chi-restraints excluded: chain N residue 224 LYS Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain O residue 442 GLU Chi-restraints excluded: chain P residue 68 MET Chi-restraints excluded: chain P residue 125 THR Chi-restraints excluded: chain P residue 159 LEU Chi-restraints excluded: chain P residue 181 PHE Chi-restraints excluded: chain P residue 224 LYS Chi-restraints excluded: chain Q residue 125 THR Chi-restraints excluded: chain Q residue 168 CYS Chi-restraints excluded: chain Q residue 240 ASN Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 181 PHE Chi-restraints excluded: chain R residue 224 LYS Chi-restraints excluded: chain R residue 240 ASN Chi-restraints excluded: chain R residue 316 ARG Chi-restraints excluded: chain R residue 439 GLN Chi-restraints excluded: chain S residue 68 MET Chi-restraints excluded: chain S residue 125 THR Chi-restraints excluded: chain S residue 163 ASP Chi-restraints excluded: chain S residue 240 ASN Chi-restraints excluded: chain S residue 439 GLN Chi-restraints excluded: chain T residue 125 THR Chi-restraints excluded: chain T residue 128 ASN Chi-restraints excluded: chain T residue 159 LEU Chi-restraints excluded: chain T residue 168 CYS Chi-restraints excluded: chain T residue 240 ASN Chi-restraints excluded: chain Z residue 6 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 540 optimal weight: 5.9990 chunk 568 optimal weight: 4.9990 chunk 518 optimal weight: 5.9990 chunk 553 optimal weight: 0.2980 chunk 333 optimal weight: 0.0570 chunk 241 optimal weight: 5.9990 chunk 434 optimal weight: 10.0000 chunk 169 optimal weight: 0.9980 chunk 499 optimal weight: 6.9990 chunk 523 optimal weight: 7.9990 chunk 551 optimal weight: 3.9990 overall best weight: 2.0702 ------------------------------------------------------------------------------- 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 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 ASN ** F 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 ASN ** G 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 ASN ** H 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 17 ASN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 151 ASN ** N 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 17 ASN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 17 ASN ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 167 ASN ** Q 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 ASN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 17 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 50918 Z= 0.242 Angle : 0.490 4.272 68936 Z= 0.256 Chirality : 0.042 0.140 7462 Planarity : 0.004 0.063 9030 Dihedral : 5.101 74.314 6794 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.26 % Allowed : 16.99 % Favored : 80.75 % 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: 0.63 (0.11), residues: 6216 helix: 2.01 (0.10), residues: 2380 sheet: -0.68 (0.16), residues: 1162 loop : -0.47 (0.12), residues: 2674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP T 435 HIS 0.004 0.001 HIS P 416 PHE 0.012 0.002 PHE a 10 TYR 0.014 0.001 TYR B 285 ARG 0.003 0.000 ARG R 437 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 672 time to evaluate : 4.511 Fit side-chains REVERT: A 33 LYS cc_start: 0.6689 (OUTLIER) cc_final: 0.6276 (mmtp) REVERT: A 73 ASP cc_start: 0.6685 (t70) cc_final: 0.5841 (t70) REVERT: A 95 ASP cc_start: 0.6859 (m-30) cc_final: 0.6427 (m-30) REVERT: A 316 ARG cc_start: 0.5263 (OUTLIER) cc_final: 0.4048 (tpt170) REVERT: A 347 MET cc_start: 0.6004 (mmm) cc_final: 0.5695 (mmp) REVERT: A 390 GLU cc_start: 0.6151 (pm20) cc_final: 0.5839 (pt0) REVERT: A 415 GLU cc_start: 0.5129 (mt-10) cc_final: 0.4581 (tt0) REVERT: A 426 ASP cc_start: 0.5332 (t70) cc_final: 0.4866 (m-30) REVERT: A 427 MET cc_start: 0.6266 (mtp) cc_final: 0.5943 (mtp) REVERT: A 429 ARG cc_start: 0.5874 (ttp80) cc_final: 0.5481 (ttt90) REVERT: B 95 ASP cc_start: 0.6968 (m-30) cc_final: 0.6552 (m-30) REVERT: B 159 LEU cc_start: 0.5519 (OUTLIER) cc_final: 0.5240 (tt) REVERT: B 178 GLU cc_start: 0.6422 (tm-30) cc_final: 0.6158 (mt-10) REVERT: B 184 GLU cc_start: 0.6259 (tt0) cc_final: 0.5625 (tt0) REVERT: B 347 MET cc_start: 0.5972 (mmm) cc_final: 0.5599 (mmp) REVERT: B 390 GLU cc_start: 0.6352 (pm20) cc_final: 0.5913 (pt0) REVERT: B 415 GLU cc_start: 0.4981 (mt-10) cc_final: 0.4492 (tt0) REVERT: B 426 ASP cc_start: 0.5388 (t70) cc_final: 0.4870 (m-30) REVERT: B 429 ARG cc_start: 0.6135 (ttp80) cc_final: 0.5852 (ttt90) REVERT: B 442 GLU cc_start: 0.7311 (mt-10) cc_final: 0.7088 (mt-10) REVERT: B 443 ILE cc_start: 0.6478 (mm) cc_final: 0.6246 (mp) REVERT: C 33 LYS cc_start: 0.6621 (OUTLIER) cc_final: 0.6265 (mmtp) REVERT: C 95 ASP cc_start: 0.6974 (m-30) cc_final: 0.6626 (m-30) REVERT: C 178 GLU cc_start: 0.6507 (tm-30) cc_final: 0.6297 (mt-10) REVERT: C 184 GLU cc_start: 0.6248 (tt0) cc_final: 0.5774 (tt0) REVERT: C 316 ARG cc_start: 0.5256 (OUTLIER) cc_final: 0.4176 (tpt170) REVERT: C 347 MET cc_start: 0.6146 (mmm) cc_final: 0.5809 (mmp) REVERT: C 415 GLU cc_start: 0.4941 (mt-10) cc_final: 0.4361 (tt0) REVERT: C 419 GLU cc_start: 0.5898 (tt0) cc_final: 0.5446 (mt-10) REVERT: C 426 ASP cc_start: 0.5465 (t70) cc_final: 0.4978 (m-30) REVERT: C 429 ARG cc_start: 0.5970 (ttp80) cc_final: 0.5696 (ttt90) REVERT: E 6 GLN cc_start: 0.0442 (OUTLIER) cc_final: -0.0138 (pt0) REVERT: F 33 LYS cc_start: 0.6679 (OUTLIER) cc_final: 0.6295 (mmtp) REVERT: F 68 MET cc_start: 0.6865 (OUTLIER) cc_final: 0.6167 (mtt) REVERT: F 73 ASP cc_start: 0.6682 (t70) cc_final: 0.5865 (t70) REVERT: F 95 ASP cc_start: 0.6860 (m-30) cc_final: 0.6433 (m-30) REVERT: F 347 MET cc_start: 0.6003 (mmm) cc_final: 0.5694 (mmp) REVERT: F 390 GLU cc_start: 0.6164 (pm20) cc_final: 0.5883 (pt0) REVERT: F 415 GLU cc_start: 0.5086 (mt-10) cc_final: 0.4506 (tt0) REVERT: F 426 ASP cc_start: 0.5556 (t70) cc_final: 0.4973 (m-30) REVERT: F 427 MET cc_start: 0.6230 (ttp) cc_final: 0.5903 (mtp) REVERT: F 429 ARG cc_start: 0.5878 (ttp80) cc_final: 0.5607 (ttt90) REVERT: G 92 MET cc_start: 0.7786 (mtm) cc_final: 0.7450 (mtp) REVERT: G 95 ASP cc_start: 0.6939 (m-30) cc_final: 0.6575 (m-30) REVERT: G 178 GLU cc_start: 0.6381 (tm-30) cc_final: 0.6125 (mm-30) REVERT: G 347 MET cc_start: 0.6235 (mmm) cc_final: 0.5940 (mmp) REVERT: G 390 GLU cc_start: 0.6383 (pm20) cc_final: 0.6082 (pt0) REVERT: G 415 GLU cc_start: 0.5150 (mt-10) cc_final: 0.4522 (tt0) REVERT: G 419 GLU cc_start: 0.5533 (tt0) cc_final: 0.5077 (mt-10) REVERT: G 426 ASP cc_start: 0.5260 (t70) cc_final: 0.4717 (m-30) REVERT: H 95 ASP cc_start: 0.6968 (m-30) cc_final: 0.6683 (m-30) REVERT: H 200 LYS cc_start: 0.6943 (ttmm) cc_final: 0.6679 (mttm) REVERT: H 347 MET cc_start: 0.6115 (mmm) cc_final: 0.5844 (mmp) REVERT: H 390 GLU cc_start: 0.6226 (pm20) cc_final: 0.5839 (pt0) REVERT: H 415 GLU cc_start: 0.5112 (mt-10) cc_final: 0.4513 (tt0) REVERT: H 426 ASP cc_start: 0.5260 (t70) cc_final: 0.4724 (m-30) REVERT: H 438 GLU cc_start: 0.5477 (pt0) cc_final: 0.5163 (mt-10) REVERT: I 33 LYS cc_start: 0.6672 (OUTLIER) cc_final: 0.6314 (mmtp) REVERT: I 95 ASP cc_start: 0.6975 (m-30) cc_final: 0.6628 (m-30) REVERT: I 163 ASP cc_start: 0.4648 (OUTLIER) cc_final: 0.3677 (m-30) REVERT: I 178 GLU cc_start: 0.6508 (tm-30) cc_final: 0.6294 (mt-10) REVERT: I 200 LYS cc_start: 0.7042 (ttmm) cc_final: 0.6677 (mmtt) REVERT: I 232 MET cc_start: 0.7500 (ttm) cc_final: 0.7257 (ttm) REVERT: I 347 MET cc_start: 0.6126 (mmm) cc_final: 0.5792 (mmp) REVERT: I 415 GLU cc_start: 0.4993 (mt-10) cc_final: 0.4387 (tt0) REVERT: I 419 GLU cc_start: 0.5851 (tt0) cc_final: 0.5387 (mt-10) REVERT: I 426 ASP cc_start: 0.5361 (t70) cc_final: 0.4835 (m-30) REVERT: I 427 MET cc_start: 0.5762 (mtp) cc_final: 0.5327 (mtp) REVERT: I 429 ARG cc_start: 0.5928 (ttp80) cc_final: 0.5688 (ttt90) REVERT: N 92 MET cc_start: 0.7781 (mtm) cc_final: 0.7456 (mtp) REVERT: N 95 ASP cc_start: 0.6964 (m-30) cc_final: 0.6591 (m-30) REVERT: N 178 GLU cc_start: 0.6458 (tm-30) cc_final: 0.6168 (mm-30) REVERT: N 200 LYS cc_start: 0.6955 (ttmm) cc_final: 0.6592 (mmtt) REVERT: N 347 MET cc_start: 0.6240 (mmm) cc_final: 0.5945 (mmp) REVERT: N 390 GLU cc_start: 0.6394 (pm20) cc_final: 0.6098 (pt0) REVERT: N 415 GLU cc_start: 0.5120 (mt-10) cc_final: 0.4536 (tt0) REVERT: N 426 ASP cc_start: 0.5327 (t70) cc_final: 0.4754 (m-30) REVERT: N 429 ARG cc_start: 0.5843 (ttp80) cc_final: 0.5594 (ttt90) REVERT: N 442 GLU cc_start: 0.7260 (mm-30) cc_final: 0.7021 (mm-30) REVERT: O 95 ASP cc_start: 0.6960 (m-30) cc_final: 0.6678 (m-30) REVERT: O 200 LYS cc_start: 0.6904 (ttmm) cc_final: 0.6584 (mttm) REVERT: O 347 MET cc_start: 0.6117 (mmm) cc_final: 0.5845 (mmp) REVERT: O 390 GLU cc_start: 0.6310 (pm20) cc_final: 0.5960 (pt0) REVERT: O 415 GLU cc_start: 0.5006 (mt-10) cc_final: 0.4443 (tt0) REVERT: O 426 ASP cc_start: 0.5478 (t70) cc_final: 0.4870 (m-30) REVERT: O 429 ARG cc_start: 0.5858 (ttp80) cc_final: 0.5635 (ttt90) REVERT: O 442 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6705 (mm-30) REVERT: O 443 ILE cc_start: 0.6397 (mm) cc_final: 0.6164 (mp) REVERT: P 16 GLN cc_start: 0.5943 (mt0) cc_final: 0.5681 (mm-40) REVERT: P 68 MET cc_start: 0.6980 (OUTLIER) cc_final: 0.6312 (mtt) REVERT: P 73 ASP cc_start: 0.6801 (t70) cc_final: 0.6424 (t0) REVERT: P 95 ASP cc_start: 0.6914 (m-30) cc_final: 0.6505 (m-30) REVERT: P 126 GLU cc_start: 0.7875 (tt0) cc_final: 0.7251 (tt0) REVERT: P 159 LEU cc_start: 0.5590 (OUTLIER) cc_final: 0.5370 (tt) REVERT: P 163 ASP cc_start: 0.4579 (OUTLIER) cc_final: 0.3012 (m-30) REVERT: P 224 LYS cc_start: 0.5722 (OUTLIER) cc_final: 0.5430 (mtpp) REVERT: P 390 GLU cc_start: 0.6498 (pm20) cc_final: 0.5985 (pt0) REVERT: P 415 GLU cc_start: 0.5138 (mt-10) cc_final: 0.4556 (tt0) REVERT: P 426 ASP cc_start: 0.5187 (t70) cc_final: 0.4709 (m-30) REVERT: P 427 MET cc_start: 0.6539 (mtp) cc_final: 0.6258 (mtp) REVERT: P 429 ARG cc_start: 0.5991 (ttp80) cc_final: 0.5639 (ttt90) REVERT: Q 68 MET cc_start: 0.6919 (mmt) cc_final: 0.6688 (mpp) REVERT: Q 73 ASP cc_start: 0.6526 (t70) cc_final: 0.5962 (t0) REVERT: Q 95 ASP cc_start: 0.7114 (m-30) cc_final: 0.6773 (m-30) REVERT: Q 200 LYS cc_start: 0.7191 (ttmm) cc_final: 0.6739 (mttt) REVERT: Q 316 ARG cc_start: 0.5386 (OUTLIER) cc_final: 0.4187 (tpt170) REVERT: Q 390 GLU cc_start: 0.6336 (pm20) cc_final: 0.5841 (pt0) REVERT: Q 415 GLU cc_start: 0.5398 (mt-10) cc_final: 0.4917 (tt0) REVERT: Q 426 ASP cc_start: 0.5306 (t70) cc_final: 0.4771 (m-30) REVERT: Q 429 ARG cc_start: 0.5801 (ttp80) cc_final: 0.5475 (ttt90) REVERT: Q 442 GLU cc_start: 0.7278 (mm-30) cc_final: 0.6991 (mm-30) REVERT: R 68 MET cc_start: 0.6921 (mmt) cc_final: 0.6599 (mpp) REVERT: R 73 ASP cc_start: 0.6537 (t70) cc_final: 0.5972 (t0) REVERT: R 95 ASP cc_start: 0.7124 (m-30) cc_final: 0.6783 (m-30) REVERT: R 200 LYS cc_start: 0.7098 (ttmm) cc_final: 0.6700 (mttt) REVERT: R 316 ARG cc_start: 0.5347 (OUTLIER) cc_final: 0.4130 (tpt170) REVERT: R 390 GLU cc_start: 0.6337 (pm20) cc_final: 0.5820 (pt0) REVERT: R 415 GLU cc_start: 0.5348 (mt-10) cc_final: 0.4822 (tt0) REVERT: R 426 ASP cc_start: 0.5260 (t70) cc_final: 0.4747 (m-30) REVERT: R 429 ARG cc_start: 0.5786 (ttp80) cc_final: 0.5531 (ttt90) REVERT: S 16 GLN cc_start: 0.5941 (mt0) cc_final: 0.5680 (mm-40) REVERT: S 68 MET cc_start: 0.6983 (OUTLIER) cc_final: 0.6314 (mtt) REVERT: S 95 ASP cc_start: 0.6821 (m-30) cc_final: 0.6405 (m-30) REVERT: S 126 GLU cc_start: 0.7900 (tt0) cc_final: 0.7538 (tt0) REVERT: S 159 LEU cc_start: 0.5587 (OUTLIER) cc_final: 0.5366 (tt) REVERT: S 163 ASP cc_start: 0.4467 (OUTLIER) cc_final: 0.2916 (m-30) REVERT: S 347 MET cc_start: 0.6385 (mmm) cc_final: 0.6074 (mmp) REVERT: S 390 GLU cc_start: 0.6494 (pm20) cc_final: 0.5985 (pt0) REVERT: S 415 GLU cc_start: 0.5256 (mt-10) cc_final: 0.4669 (tt0) REVERT: S 426 ASP cc_start: 0.5214 (t70) cc_final: 0.4759 (m-30) REVERT: S 429 ARG cc_start: 0.6064 (ttp80) cc_final: 0.5658 (ttt90) REVERT: S 438 GLU cc_start: 0.6026 (pt0) cc_final: 0.5447 (mt-10) REVERT: S 439 GLN cc_start: 0.5640 (OUTLIER) cc_final: 0.4310 (mp10) REVERT: T 95 ASP cc_start: 0.6966 (m-30) cc_final: 0.6554 (m-30) REVERT: T 126 GLU cc_start: 0.7696 (pt0) cc_final: 0.7283 (tt0) REVERT: T 159 LEU cc_start: 0.5519 (OUTLIER) cc_final: 0.5239 (tt) REVERT: T 178 GLU cc_start: 0.6424 (tm-30) cc_final: 0.6158 (mt-10) REVERT: T 184 GLU cc_start: 0.6275 (tt0) cc_final: 0.5636 (tt0) REVERT: T 347 MET cc_start: 0.5971 (mmm) cc_final: 0.5596 (mmp) REVERT: T 390 GLU cc_start: 0.6306 (pm20) cc_final: 0.5842 (pt0) REVERT: T 415 GLU cc_start: 0.5024 (mt-10) cc_final: 0.4490 (tt0) REVERT: T 419 GLU cc_start: 0.5657 (tt0) cc_final: 0.5249 (mt-10) REVERT: T 426 ASP cc_start: 0.5207 (t70) cc_final: 0.4759 (m-30) REVERT: T 429 ARG cc_start: 0.6088 (ttp80) cc_final: 0.5789 (ttt90) REVERT: Z 6 GLN cc_start: 0.0276 (OUTLIER) cc_final: -0.0302 (pt0) outliers start: 118 outliers final: 50 residues processed: 771 average time/residue: 1.4683 time to fit residues: 1400.7353 Evaluate side-chains 744 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 671 time to evaluate : 4.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 168 CYS Chi-restraints excluded: chain F residue 240 ASN Chi-restraints excluded: chain F residue 331 ARG Chi-restraints excluded: chain F residue 421 LYS Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 168 CYS Chi-restraints excluded: chain G residue 181 PHE Chi-restraints excluded: chain G residue 224 LYS Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 168 CYS Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 240 ASN Chi-restraints excluded: chain I residue 248 MET Chi-restraints excluded: chain N residue 29 LEU Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 224 LYS Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain O residue 442 GLU Chi-restraints excluded: chain P residue 15 GLU Chi-restraints excluded: chain P residue 68 MET Chi-restraints excluded: chain P residue 125 THR Chi-restraints excluded: chain P residue 159 LEU Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 181 PHE Chi-restraints excluded: chain P residue 224 LYS Chi-restraints excluded: chain Q residue 125 THR Chi-restraints excluded: chain Q residue 168 CYS Chi-restraints excluded: chain Q residue 240 ASN Chi-restraints excluded: chain Q residue 316 ARG Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 224 LYS Chi-restraints excluded: chain R residue 316 ARG Chi-restraints excluded: chain S residue 15 GLU Chi-restraints excluded: chain S residue 68 MET Chi-restraints excluded: chain S residue 125 THR Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 163 ASP Chi-restraints excluded: chain S residue 439 GLN Chi-restraints excluded: chain T residue 125 THR Chi-restraints excluded: chain T residue 128 ASN Chi-restraints excluded: chain T residue 159 LEU Chi-restraints excluded: chain T residue 168 CYS Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain Z residue 6 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 363 optimal weight: 0.6980 chunk 585 optimal weight: 3.9990 chunk 357 optimal weight: 4.9990 chunk 277 optimal weight: 6.9990 chunk 406 optimal weight: 2.9990 chunk 613 optimal weight: 6.9990 chunk 564 optimal weight: 0.0060 chunk 488 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 377 optimal weight: 0.9990 chunk 299 optimal weight: 6.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- 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 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 ASN ** F 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 ASN ** G 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 ASN ** H 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 151 ASN ** N 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 17 ASN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 17 ASN ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 167 ASN ** Q 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 ASN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 167 ASN ** R 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 17 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 50918 Z= 0.151 Angle : 0.439 3.872 68936 Z= 0.231 Chirality : 0.039 0.133 7462 Planarity : 0.004 0.078 9030 Dihedral : 4.865 73.530 6794 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.69 % Allowed : 17.62 % Favored : 80.70 % 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: 0.76 (0.11), residues: 6216 helix: 2.16 (0.10), residues: 2408 sheet: -0.65 (0.16), residues: 1162 loop : -0.46 (0.12), residues: 2646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 435 HIS 0.004 0.001 HIS N 416 PHE 0.010 0.001 PHE P 20 TYR 0.013 0.001 TYR T 285 ARG 0.003 0.000 ARG I 145 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12432 Ramachandran restraints generated. 6216 Oldfield, 0 Emsley, 6216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 684 time to evaluate : 4.445 Fit side-chains revert: symmetry clash REVERT: A 29 LEU cc_start: 0.6794 (mp) cc_final: 0.6544 (mp) REVERT: A 33 LYS cc_start: 0.6680 (OUTLIER) cc_final: 0.6278 (mmtp) REVERT: A 73 ASP cc_start: 0.6658 (t70) cc_final: 0.5837 (t70) REVERT: A 95 ASP cc_start: 0.6848 (m-30) cc_final: 0.6423 (m-30) REVERT: A 316 ARG cc_start: 0.5221 (OUTLIER) cc_final: 0.3984 (tpt170) REVERT: A 347 MET cc_start: 0.6016 (mmm) cc_final: 0.5700 (mmp) REVERT: A 390 GLU cc_start: 0.6144 (pm20) cc_final: 0.5840 (pt0) REVERT: A 415 GLU cc_start: 0.5056 (mt-10) cc_final: 0.4489 (tt0) REVERT: A 426 ASP cc_start: 0.5320 (t70) cc_final: 0.4832 (m-30) REVERT: A 427 MET cc_start: 0.6320 (mtp) cc_final: 0.5957 (mtp) REVERT: A 429 ARG cc_start: 0.5882 (ttp80) cc_final: 0.5487 (ttt90) REVERT: B 95 ASP cc_start: 0.6957 (m-30) cc_final: 0.6588 (m-30) REVERT: B 159 LEU cc_start: 0.5438 (OUTLIER) cc_final: 0.5148 (tt) REVERT: B 178 GLU cc_start: 0.6440 (tm-30) cc_final: 0.6173 (mt-10) REVERT: B 184 GLU cc_start: 0.6263 (tt0) cc_final: 0.5640 (tt0) REVERT: B 347 MET cc_start: 0.6005 (mmm) cc_final: 0.5639 (mmp) REVERT: B 390 GLU cc_start: 0.6349 (pm20) cc_final: 0.5920 (pt0) REVERT: B 415 GLU cc_start: 0.5013 (mt-10) cc_final: 0.4543 (tt0) REVERT: B 426 ASP cc_start: 0.5369 (t70) cc_final: 0.4873 (m-30) REVERT: B 429 ARG cc_start: 0.6048 (ttp80) cc_final: 0.5819 (ttt90) REVERT: B 442 GLU cc_start: 0.7324 (mt-10) cc_final: 0.7110 (mt-10) REVERT: B 443 ILE cc_start: 0.6475 (mm) cc_final: 0.6243 (mp) REVERT: C 33 LYS cc_start: 0.6603 (OUTLIER) cc_final: 0.6290 (mmtp) REVERT: C 95 ASP cc_start: 0.6985 (m-30) cc_final: 0.6660 (m-30) REVERT: C 178 GLU cc_start: 0.6510 (tm-30) cc_final: 0.6289 (mt-10) REVERT: C 184 GLU cc_start: 0.6257 (tt0) cc_final: 0.5779 (tt0) REVERT: C 316 ARG cc_start: 0.5188 (OUTLIER) cc_final: 0.4174 (tpt170) REVERT: C 347 MET cc_start: 0.6139 (mmm) cc_final: 0.5809 (mmp) REVERT: C 415 GLU cc_start: 0.4875 (mt-10) cc_final: 0.4310 (tt0) REVERT: C 419 GLU cc_start: 0.5882 (tt0) cc_final: 0.5443 (mt-10) REVERT: C 426 ASP cc_start: 0.5443 (t70) cc_final: 0.4940 (m-30) REVERT: C 429 ARG cc_start: 0.5946 (ttp80) cc_final: 0.5662 (ttt90) REVERT: E 6 GLN cc_start: 0.0366 (OUTLIER) cc_final: -0.0205 (pt0) REVERT: F 33 LYS cc_start: 0.6658 (OUTLIER) cc_final: 0.6302 (mmtp) REVERT: F 68 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.6236 (mtt) REVERT: F 73 ASP cc_start: 0.6663 (t70) cc_final: 0.5852 (t70) REVERT: F 95 ASP cc_start: 0.6811 (m-30) cc_final: 0.6378 (m-30) REVERT: F 347 MET cc_start: 0.6015 (mmm) cc_final: 0.5698 (mmp) REVERT: F 390 GLU cc_start: 0.6156 (pm20) cc_final: 0.5885 (pt0) REVERT: F 415 GLU cc_start: 0.5105 (mt-10) cc_final: 0.4538 (tt0) REVERT: F 426 ASP cc_start: 0.5489 (t70) cc_final: 0.4930 (m-30) REVERT: F 427 MET cc_start: 0.6114 (ttp) cc_final: 0.5838 (mtp) REVERT: F 429 ARG cc_start: 0.5798 (ttp80) cc_final: 0.5517 (ttt90) REVERT: G 92 MET cc_start: 0.7778 (mtm) cc_final: 0.7480 (mtp) REVERT: G 95 ASP cc_start: 0.6922 (m-30) cc_final: 0.6606 (m-30) REVERT: G 178 GLU cc_start: 0.6386 (tm-30) cc_final: 0.6121 (mm-30) REVERT: G 347 MET cc_start: 0.6277 (mmm) cc_final: 0.5989 (mmp) REVERT: G 390 GLU cc_start: 0.6372 (pm20) cc_final: 0.6072 (pt0) REVERT: G 415 GLU cc_start: 0.5018 (mt-10) cc_final: 0.4388 (tt0) REVERT: G 419 GLU cc_start: 0.5483 (tt0) cc_final: 0.5030 (mt-10) REVERT: G 426 ASP cc_start: 0.5171 (t70) cc_final: 0.4615 (m-30) REVERT: H 95 ASP cc_start: 0.6933 (m-30) cc_final: 0.6654 (m-30) REVERT: H 200 LYS cc_start: 0.6885 (ttmm) cc_final: 0.6614 (mmmt) REVERT: H 347 MET cc_start: 0.6122 (mmm) cc_final: 0.5852 (mmp) REVERT: H 390 GLU cc_start: 0.6290 (pm20) cc_final: 0.5920 (pt0) REVERT: H 415 GLU cc_start: 0.5061 (mt-10) cc_final: 0.4491 (tt0) REVERT: H 426 ASP cc_start: 0.5252 (t70) cc_final: 0.4697 (m-30) REVERT: H 438 GLU cc_start: 0.5415 (pt0) cc_final: 0.5175 (mt-10) REVERT: I 33 LYS cc_start: 0.6603 (OUTLIER) cc_final: 0.6292 (mmtp) REVERT: I 95 ASP cc_start: 0.7018 (m-30) cc_final: 0.6664 (m-30) REVERT: I 178 GLU cc_start: 0.6513 (tm-30) cc_final: 0.6290 (mt-10) REVERT: I 200 LYS cc_start: 0.7066 (ttmm) cc_final: 0.6673 (mmtt) REVERT: I 232 MET cc_start: 0.7462 (ttm) cc_final: 0.7260 (ttm) REVERT: I 347 MET cc_start: 0.6118 (mmm) cc_final: 0.5792 (mmp) REVERT: I 415 GLU cc_start: 0.5167 (mt-10) cc_final: 0.4449 (tt0) REVERT: I 419 GLU cc_start: 0.5817 (tt0) cc_final: 0.5367 (mt-10) REVERT: I 426 ASP cc_start: 0.5278 (t70) cc_final: 0.4739 (m-30) REVERT: I 427 MET cc_start: 0.5727 (mtp) cc_final: 0.5289 (mtp) REVERT: I 429 ARG cc_start: 0.5891 (ttp80) cc_final: 0.5658 (ttt90) REVERT: N 92 MET cc_start: 0.7804 (mtm) cc_final: 0.7507 (mtp) REVERT: N 95 ASP cc_start: 0.6908 (m-30) cc_final: 0.6610 (m-30) REVERT: N 178 GLU cc_start: 0.6391 (tm-30) cc_final: 0.6127 (mm-30) REVERT: N 200 LYS cc_start: 0.6908 (ttmm) cc_final: 0.6537 (mmtt) REVERT: N 347 MET cc_start: 0.6282 (mmm) cc_final: 0.5995 (mmp) REVERT: N 390 GLU cc_start: 0.6418 (pm20) cc_final: 0.6068 (pt0) REVERT: N 415 GLU cc_start: 0.5158 (mt-10) cc_final: 0.4593 (tt0) REVERT: N 426 ASP cc_start: 0.5333 (t70) cc_final: 0.4749 (m-30) REVERT: N 429 ARG cc_start: 0.5827 (ttp80) cc_final: 0.5585 (ttt90) REVERT: N 442 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6979 (mm-30) REVERT: O 95 ASP cc_start: 0.6929 (m-30) cc_final: 0.6650 (m-30) REVERT: O 200 LYS cc_start: 0.6816 (ttmm) cc_final: 0.6505 (mttm) REVERT: O 224 LYS cc_start: 0.6123 (OUTLIER) cc_final: 0.5884 (mtpp) REVERT: O 347 MET cc_start: 0.6120 (mmm) cc_final: 0.5853 (mmp) REVERT: O 390 GLU cc_start: 0.6292 (pm20) cc_final: 0.5913 (pt0) REVERT: O 415 GLU cc_start: 0.4924 (mt-10) cc_final: 0.4372 (tt0) REVERT: O 426 ASP cc_start: 0.5393 (t70) cc_final: 0.4739 (m-30) REVERT: O 429 ARG cc_start: 0.5819 (ttp80) cc_final: 0.5608 (ttt90) REVERT: O 442 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6806 (mm-30) REVERT: O 443 ILE cc_start: 0.6369 (mm) cc_final: 0.6151 (mp) REVERT: P 16 GLN cc_start: 0.5900 (mt0) cc_final: 0.5660 (mm-40) REVERT: P 68 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.6399 (mtt) REVERT: P 95 ASP cc_start: 0.6823 (m-30) cc_final: 0.6511 (m-30) REVERT: P 126 GLU cc_start: 0.7894 (tt0) cc_final: 0.7315 (tt0) REVERT: P 159 LEU cc_start: 0.5456 (OUTLIER) cc_final: 0.5222 (tt) REVERT: P 163 ASP cc_start: 0.4790 (OUTLIER) cc_final: 0.3318 (m-30) REVERT: P 224 LYS cc_start: 0.5648 (OUTLIER) cc_final: 0.5362 (mtpp) REVERT: P 390 GLU cc_start: 0.6458 (pm20) cc_final: 0.5974 (pt0) REVERT: P 415 GLU cc_start: 0.5206 (mt-10) cc_final: 0.4624 (tt0) REVERT: P 426 ASP cc_start: 0.5143 (t70) cc_final: 0.4673 (m-30) REVERT: P 427 MET cc_start: 0.6487 (mtp) cc_final: 0.6217 (mtp) REVERT: P 429 ARG cc_start: 0.6023 (ttp80) cc_final: 0.5699 (ttt90) REVERT: Q 73 ASP cc_start: 0.6508 (t70) cc_final: 0.5905 (t0) REVERT: Q 95 ASP cc_start: 0.7083 (m-30) cc_final: 0.6760 (m-30) REVERT: Q 200 LYS cc_start: 0.7071 (ttmm) cc_final: 0.6686 (mttt) REVERT: Q 390 GLU cc_start: 0.6329 (pm20) cc_final: 0.5836 (pt0) REVERT: Q 415 GLU cc_start: 0.5299 (mt-10) cc_final: 0.4820 (tt0) REVERT: Q 426 ASP cc_start: 0.5285 (t70) cc_final: 0.4750 (m-30) REVERT: Q 429 ARG cc_start: 0.5674 (ttp80) cc_final: 0.5426 (ttt90) REVERT: Q 442 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7186 (mm-30) REVERT: R 68 MET cc_start: 0.6892 (mmt) cc_final: 0.6576 (mpp) REVERT: R 73 ASP cc_start: 0.6517 (t70) cc_final: 0.5947 (t0) REVERT: R 95 ASP cc_start: 0.7106 (m-30) cc_final: 0.6805 (m-30) REVERT: R 200 LYS cc_start: 0.7075 (ttmm) cc_final: 0.6689 (mttt) REVERT: R 316 ARG cc_start: 0.5297 (OUTLIER) cc_final: 0.4125 (tpt170) REVERT: R 390 GLU cc_start: 0.6331 (pm20) cc_final: 0.5822 (pt0) REVERT: R 415 GLU cc_start: 0.5270 (mt-10) cc_final: 0.4746 (tt0) REVERT: R 426 ASP cc_start: 0.5236 (t70) cc_final: 0.4750 (m-30) REVERT: R 429 ARG cc_start: 0.5831 (ttp80) cc_final: 0.5448 (ttt90) REVERT: S 16 GLN cc_start: 0.5902 (mt0) cc_final: 0.5663 (mm-40) REVERT: S 68 MET cc_start: 0.7007 (OUTLIER) cc_final: 0.6401 (mtt) REVERT: S 95 ASP cc_start: 0.6805 (m-30) cc_final: 0.6374 (m-30) REVERT: S 126 GLU cc_start: 0.7949 (tt0) cc_final: 0.7489 (tt0) REVERT: S 159 LEU cc_start: 0.5418 (OUTLIER) cc_final: 0.5199 (tt) REVERT: S 163 ASP cc_start: 0.4949 (OUTLIER) cc_final: 0.3478 (m-30) REVERT: S 347 MET cc_start: 0.6380 (mmm) cc_final: 0.6015 (mmp) REVERT: S 390 GLU cc_start: 0.6454 (pm20) cc_final: 0.5962 (pt0) REVERT: S 415 GLU cc_start: 0.5219 (mt-10) cc_final: 0.4653 (tt0) REVERT: S 426 ASP cc_start: 0.5187 (t70) cc_final: 0.4714 (m-30) REVERT: S 429 ARG cc_start: 0.6070 (ttp80) cc_final: 0.5671 (ttt90) REVERT: S 438 GLU cc_start: 0.5985 (pt0) cc_final: 0.5447 (mt-10) REVERT: S 439 GLN cc_start: 0.5532 (OUTLIER) cc_final: 0.4252 (mp10) REVERT: T 95 ASP cc_start: 0.6935 (m-30) cc_final: 0.6535 (m-30) REVERT: T 159 LEU cc_start: 0.5436 (OUTLIER) cc_final: 0.5147 (tt) REVERT: T 178 GLU cc_start: 0.6443 (tm-30) cc_final: 0.6173 (mt-10) REVERT: T 184 GLU cc_start: 0.6277 (tt0) cc_final: 0.5653 (tt0) REVERT: T 316 ARG cc_start: 0.5360 (OUTLIER) cc_final: 0.4223 (tpt170) REVERT: T 347 MET cc_start: 0.6002 (mmm) cc_final: 0.5633 (mmp) REVERT: T 390 GLU cc_start: 0.6303 (pm20) cc_final: 0.5805 (pt0) REVERT: T 415 GLU cc_start: 0.4990 (mt-10) cc_final: 0.4460 (tt0) REVERT: T 419 GLU cc_start: 0.5556 (tt0) cc_final: 0.5168 (mt-10) REVERT: T 426 ASP cc_start: 0.5143 (t70) cc_final: 0.4707 (m-30) REVERT: T 429 ARG cc_start: 0.5980 (ttp80) cc_final: 0.5727 (ttt90) REVERT: Z 6 GLN cc_start: 0.0041 (OUTLIER) cc_final: -0.0522 (pt0) outliers start: 88 outliers final: 44 residues processed: 753 average time/residue: 1.4373 time to fit residues: 1328.1283 Evaluate side-chains 744 residues out of total 5446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 677 time to evaluate : 4.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 168 CYS Chi-restraints excluded: chain F residue 181 PHE Chi-restraints excluded: chain F residue 240 ASN Chi-restraints excluded: chain F residue 331 ARG Chi-restraints excluded: chain F residue 421 LYS Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 168 CYS Chi-restraints excluded: chain G residue 224 LYS Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 439 GLN Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 240 ASN Chi-restraints excluded: chain I residue 248 MET Chi-restraints excluded: chain N residue 29 LEU Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 224 LYS Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain O residue 224 LYS Chi-restraints excluded: chain O residue 442 GLU Chi-restraints excluded: chain P residue 68 MET Chi-restraints excluded: chain P residue 125 THR Chi-restraints excluded: chain P residue 159 LEU Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 224 LYS Chi-restraints excluded: chain Q residue 125 THR Chi-restraints excluded: chain Q residue 168 CYS Chi-restraints excluded: chain Q residue 240 ASN Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 240 ASN Chi-restraints excluded: chain R residue 316 ARG Chi-restraints excluded: chain S residue 68 MET Chi-restraints excluded: chain S residue 125 THR Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 163 ASP Chi-restraints excluded: chain S residue 439 GLN Chi-restraints excluded: chain T residue 125 THR Chi-restraints excluded: chain T residue 159 LEU Chi-restraints excluded: chain T residue 249 SER Chi-restraints excluded: chain T residue 316 ARG Chi-restraints excluded: chain Z residue 6 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 388 optimal weight: 10.0000 chunk 520 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 450 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 489 optimal weight: 10.0000 chunk 204 optimal weight: 0.9990 chunk 502 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 ASN F 225 HIS ** F 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 ASN ** G 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 ASN ** H 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN ** I 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 151 ASN ** N 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 HIS ** O 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 17 ASN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 17 ASN ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 ASN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 17 ASN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.137266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.112593 restraints weight = 51141.092| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.52 r_work: 0.3199 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 50918 Z= 0.207 Angle : 0.467 4.093 68936 Z= 0.244 Chirality : 0.041 0.138 7462 Planarity : 0.004 0.067 9030 Dihedral : 4.975 73.719 6794 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.74 % Allowed : 17.56 % Favored : 80.70 % 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 (0.11), residues: 6216 helix: 2.10 (0.10), residues: 2380 sheet: -0.68 (0.16), residues: 1162 loop : -0.44 (0.12), residues: 2674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 435 HIS 0.004 0.001 HIS P 416 PHE 0.011 0.001 PHE Q 296 TYR 0.013 0.001 TYR B 285 ARG 0.002 0.000 ARG I 145 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21218.25 seconds wall clock time: 361 minutes 34.69 seconds (21694.69 seconds total)