Starting phenix.real_space_refine on Mon Jan 20 06:41:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9duq_47173/01_2025/9duq_47173.cif Found real_map, /net/cci-nas-00/data/ceres_data/9duq_47173/01_2025/9duq_47173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9duq_47173/01_2025/9duq_47173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9duq_47173/01_2025/9duq_47173.map" model { file = "/net/cci-nas-00/data/ceres_data/9duq_47173/01_2025/9duq_47173.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9duq_47173/01_2025/9duq_47173.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 54 5.49 5 Mg 18 5.21 5 S 450 5.16 5 C 40572 2.51 5 N 11088 2.21 5 O 12357 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 64539 Number of models: 1 Model: "" Number of chains: 45 Chain: "r" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 396 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "B" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "J" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "N" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "P" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "R" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3353 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3356 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "s" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 396 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "t" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 396 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "u" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 396 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "v" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 396 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "w" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 396 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "x" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 396 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "y" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 396 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "z" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 396 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 27.70, per 1000 atoms: 0.43 Number of scatterers: 64539 At special positions: 0 Unit cell: (186.26, 98.69, 293.29, 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 450 16.00 P 54 15.00 Mg 18 11.99 O 12357 8.00 N 11088 7.00 C 40572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 12.45 Conformation dependent library (CDL) restraints added in 6.4 seconds 16110 Ramachandran restraints generated. 8055 Oldfield, 0 Emsley, 8055 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15066 Finding SS restraints... Secondary structure from input PDB file: 360 helices and 47 sheets defined 54.5% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.70 Creating SS restraints... Processing helix chain 'r' and resid 87 through 114 removed outlier: 3.560A pdb=" N LYS r 114 " --> pdb=" O ARG r 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 41 through 48 removed outlier: 3.907A pdb=" N ARG B 48 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 71 through 81 removed outlier: 4.068A pdb=" N MET B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 110 through 128 removed outlier: 3.617A pdb=" N LEU B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 161 Processing helix chain 'B' and resid 182 through 195 removed outlier: 3.864A pdb=" N GLN B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 Processing helix chain 'B' and resid 223 through 238 removed outlier: 3.659A pdb=" N LEU B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 244 Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 287 through 297 Processing helix chain 'B' and resid 298 through 301 removed outlier: 3.641A pdb=" N MET B 301 " --> pdb=" O ALA B 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 298 through 301' Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 324 through 339 Processing helix chain 'B' and resid 340 through 343 Processing helix chain 'B' and resid 383 through 401 removed outlier: 3.807A pdb=" N LEU B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 411 removed outlier: 4.209A pdb=" N TYR B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU B 411 " --> pdb=" O TRP B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 437 removed outlier: 3.833A pdb=" N PHE B 418 " --> pdb=" O ASP B 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.757A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.813A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 removed outlier: 3.597A pdb=" N GLU A 113 " --> pdb=" O ILE A 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 110 through 113' Processing helix chain 'A' and resid 114 through 128 Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.401A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.530A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N GLU A 196 " --> pdb=" O HIS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.583A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.867A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.738A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.600A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 401 removed outlier: 4.134A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 414 through 437 removed outlier: 3.721A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 29 Processing helix chain 'D' and resid 40 through 44 Processing helix chain 'D' and resid 71 through 81 removed outlier: 4.019A pdb=" N MET D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'D' and resid 102 through 108 Processing helix chain 'D' and resid 111 through 129 removed outlier: 4.194A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N SER D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 161 Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.563A pdb=" N ASN D 186 " --> pdb=" O VAL D 182 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN D 193 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU D 196 " --> pdb=" O HIS D 192 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 216 Processing helix chain 'D' and resid 223 through 239 removed outlier: 3.626A pdb=" N LEU D 227 " --> pdb=" O THR D 223 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 244 removed outlier: 3.586A pdb=" N ARG D 243 " --> pdb=" O THR D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 280 through 284 removed outlier: 3.811A pdb=" N ARG D 284 " --> pdb=" O GLN D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 297 through 301 removed outlier: 3.546A pdb=" N ASN D 300 " --> pdb=" O ASP D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 310 Processing helix chain 'D' and resid 324 through 339 Processing helix chain 'D' and resid 340 through 343 removed outlier: 3.640A pdb=" N PHE D 343 " --> pdb=" O SER D 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 340 through 343' Processing helix chain 'D' and resid 384 through 400 removed outlier: 3.627A pdb=" N PHE D 388 " --> pdb=" O ILE D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 410 removed outlier: 3.816A pdb=" N TYR D 408 " --> pdb=" O PHE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 437 removed outlier: 4.044A pdb=" N PHE D 418 " --> pdb=" O ASP D 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 29 Processing helix chain 'C' and resid 48 through 51 removed outlier: 3.968A pdb=" N THR C 51 " --> pdb=" O SER C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 48 through 51' Processing helix chain 'C' and resid 71 through 80 removed outlier: 4.583A pdb=" N ILE C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 114 through 127 Processing helix chain 'C' and resid 143 through 161 removed outlier: 4.513A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 198 removed outlier: 3.518A pdb=" N THR C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N HIS C 192 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLU C 196 " --> pdb=" O HIS C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 223 through 244 removed outlier: 4.867A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 278 through 283 removed outlier: 3.856A pdb=" N TYR C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N HIS C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 278 through 283' Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.706A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 301 removed outlier: 3.664A pdb=" N GLN C 301 " --> pdb=" O PRO C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 338 removed outlier: 3.658A pdb=" N VAL C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 401 removed outlier: 3.979A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.535A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 437 removed outlier: 3.828A pdb=" N PHE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 29 Processing helix chain 'F' and resid 41 through 48 removed outlier: 4.262A pdb=" N ARG F 48 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 51 No H-bonds generated for 'chain 'F' and resid 49 through 51' Processing helix chain 'F' and resid 71 through 81 removed outlier: 4.297A pdb=" N MET F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.522A pdb=" N ILE F 86 " --> pdb=" O PHE F 83 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE F 87 " --> pdb=" O GLY F 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 83 through 87' Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'F' and resid 102 through 108 Processing helix chain 'F' and resid 110 through 129 removed outlier: 3.502A pdb=" N LEU F 114 " --> pdb=" O GLU F 110 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N SER F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS F 129 " --> pdb=" O GLU F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 161 Processing helix chain 'F' and resid 182 through 198 removed outlier: 3.518A pdb=" N ASN F 186 " --> pdb=" O VAL F 182 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN F 193 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU F 196 " --> pdb=" O HIS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 216 Processing helix chain 'F' and resid 223 through 244 removed outlier: 3.853A pdb=" N LEU F 227 " --> pdb=" O THR F 223 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N CYS F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LEU F 242 " --> pdb=" O VAL F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 260 Processing helix chain 'F' and resid 280 through 284 removed outlier: 3.748A pdb=" N ARG F 284 " --> pdb=" O GLN F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 296 Processing helix chain 'F' and resid 306 through 310 Processing helix chain 'F' and resid 324 through 339 removed outlier: 3.829A pdb=" N VAL F 328 " --> pdb=" O SER F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 401 removed outlier: 4.070A pdb=" N LEU F 387 " --> pdb=" O ALA F 383 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE F 391 " --> pdb=" O LEU F 387 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ARG F 401 " --> pdb=" O ALA F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 411 removed outlier: 3.942A pdb=" N TYR F 408 " --> pdb=" O PHE F 404 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU F 411 " --> pdb=" O TRP F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 437 removed outlier: 3.677A pdb=" N PHE F 418 " --> pdb=" O ASP F 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 29 Processing helix chain 'E' and resid 47 through 51 removed outlier: 3.832A pdb=" N ASN E 50 " --> pdb=" O ASP E 47 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR E 51 " --> pdb=" O SER E 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 47 through 51' Processing helix chain 'E' and resid 72 through 81 Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 108 through 127 removed outlier: 3.892A pdb=" N LYS E 112 " --> pdb=" O TYR E 108 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLU E 113 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE E 114 " --> pdb=" O ILE E 110 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASP E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LEU E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 161 removed outlier: 4.418A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 198 removed outlier: 3.525A pdb=" N ASN E 186 " --> pdb=" O VAL E 182 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU E 196 " --> pdb=" O HIS E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 216 Processing helix chain 'E' and resid 223 through 244 removed outlier: 3.606A pdb=" N LEU E 227 " --> pdb=" O THR E 223 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 260 Processing helix chain 'E' and resid 277 through 282 removed outlier: 4.001A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.746A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 338 removed outlier: 3.671A pdb=" N VAL E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 401 removed outlier: 4.333A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS E 401 " --> pdb=" O LEU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 3.830A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 436 removed outlier: 3.824A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 28 Processing helix chain 'H' and resid 40 through 44 Processing helix chain 'H' and resid 48 through 51 removed outlier: 3.675A pdb=" N VAL H 51 " --> pdb=" O ARG H 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 48 through 51' Processing helix chain 'H' and resid 71 through 81 removed outlier: 4.249A pdb=" N MET H 75 " --> pdb=" O GLU H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 102 through 108 Processing helix chain 'H' and resid 110 through 129 removed outlier: 4.425A pdb=" N ASP H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N SER H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 161 Processing helix chain 'H' and resid 182 through 195 removed outlier: 4.696A pdb=" N GLN H 193 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL H 195 " --> pdb=" O VAL H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 216 removed outlier: 3.670A pdb=" N LEU H 209 " --> pdb=" O ASP H 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 238 removed outlier: 3.589A pdb=" N LEU H 227 " --> pdb=" O THR H 223 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL H 238 " --> pdb=" O THR H 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 239 through 244 Processing helix chain 'H' and resid 251 through 260 Processing helix chain 'H' and resid 287 through 297 Processing helix chain 'H' and resid 298 through 301 removed outlier: 3.819A pdb=" N MET H 301 " --> pdb=" O ALA H 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 298 through 301' Processing helix chain 'H' and resid 306 through 310 Processing helix chain 'H' and resid 324 through 339 Processing helix chain 'H' and resid 340 through 343 Processing helix chain 'H' and resid 383 through 401 removed outlier: 4.007A pdb=" N LEU H 387 " --> pdb=" O ALA H 383 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE H 391 " --> pdb=" O LEU H 387 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG H 401 " --> pdb=" O ALA H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 410 removed outlier: 3.780A pdb=" N TYR H 408 " --> pdb=" O PHE H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 437 removed outlier: 3.749A pdb=" N PHE H 418 " --> pdb=" O ASP H 414 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 29 Processing helix chain 'G' and resid 47 through 51 removed outlier: 4.028A pdb=" N ASN G 50 " --> pdb=" O ASP G 47 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR G 51 " --> pdb=" O SER G 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 47 through 51' Processing helix chain 'G' and resid 71 through 81 removed outlier: 4.691A pdb=" N ILE G 75 " --> pdb=" O GLU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 90 No H-bonds generated for 'chain 'G' and resid 88 through 90' Processing helix chain 'G' and resid 102 through 108 Processing helix chain 'G' and resid 111 through 127 removed outlier: 4.523A pdb=" N ASP G 116 " --> pdb=" O LYS G 112 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU G 117 " --> pdb=" O GLU G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 161 removed outlier: 4.510A pdb=" N THR G 150 " --> pdb=" O GLY G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 198 removed outlier: 3.995A pdb=" N THR G 193 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLU G 196 " --> pdb=" O HIS G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 216 removed outlier: 3.577A pdb=" N ILE G 209 " --> pdb=" O ASP G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 244 removed outlier: 4.876A pdb=" N SER G 241 " --> pdb=" O SER G 237 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LEU G 242 " --> pdb=" O ILE G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 260 Processing helix chain 'G' and resid 277 through 284 removed outlier: 3.748A pdb=" N TYR G 282 " --> pdb=" O ALA G 278 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N HIS G 283 " --> pdb=" O GLU G 279 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU G 284 " --> pdb=" O LYS G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 295 Processing helix chain 'G' and resid 296 through 301 removed outlier: 6.300A pdb=" N ALA G 299 " --> pdb=" O PHE G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 310 Processing helix chain 'G' and resid 324 through 337 removed outlier: 3.674A pdb=" N VAL G 328 " --> pdb=" O VAL G 324 " (cutoff:3.500A) Processing helix chain 'G' and resid 384 through 400 removed outlier: 3.820A pdb=" N TRP G 388 " --> pdb=" O ILE G 384 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 410 removed outlier: 3.915A pdb=" N TYR G 408 " --> pdb=" O PHE G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 415 through 437 Processing helix chain 'J' and resid 10 through 29 Processing helix chain 'J' and resid 40 through 44 removed outlier: 3.607A pdb=" N GLN J 43 " --> pdb=" O SER J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 81 removed outlier: 3.993A pdb=" N MET J 75 " --> pdb=" O GLU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.678A pdb=" N PHE J 87 " --> pdb=" O GLY J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 90 No H-bonds generated for 'chain 'J' and resid 88 through 90' Processing helix chain 'J' and resid 102 through 108 Processing helix chain 'J' and resid 111 through 127 removed outlier: 4.027A pdb=" N ASP J 116 " --> pdb=" O ALA J 112 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER J 117 " --> pdb=" O GLU J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 161 Processing helix chain 'J' and resid 182 through 198 removed outlier: 4.221A pdb=" N GLN J 193 " --> pdb=" O LEU J 189 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLU J 196 " --> pdb=" O HIS J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 216 Processing helix chain 'J' and resid 223 through 238 removed outlier: 3.720A pdb=" N LEU J 227 " --> pdb=" O THR J 223 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 244 removed outlier: 3.552A pdb=" N ARG J 243 " --> pdb=" O THR J 239 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 260 Processing helix chain 'J' and resid 287 through 297 Processing helix chain 'J' and resid 306 through 310 Processing helix chain 'J' and resid 324 through 339 Processing helix chain 'J' and resid 340 through 343 Processing helix chain 'J' and resid 383 through 401 removed outlier: 3.753A pdb=" N LEU J 387 " --> pdb=" O ALA J 383 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE J 391 " --> pdb=" O LEU J 387 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG J 401 " --> pdb=" O ALA J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 404 through 410 removed outlier: 4.016A pdb=" N TYR J 408 " --> pdb=" O PHE J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 437 removed outlier: 3.901A pdb=" N PHE J 418 " --> pdb=" O ASP J 414 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 29 Processing helix chain 'I' and resid 48 through 51 removed outlier: 4.056A pdb=" N THR I 51 " --> pdb=" O SER I 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 48 through 51' Processing helix chain 'I' and resid 72 through 80 Processing helix chain 'I' and resid 88 through 90 No H-bonds generated for 'chain 'I' and resid 88 through 90' Processing helix chain 'I' and resid 102 through 108 Processing helix chain 'I' and resid 110 through 113 removed outlier: 3.734A pdb=" N GLU I 113 " --> pdb=" O ILE I 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 110 through 113' Processing helix chain 'I' and resid 114 through 127 Processing helix chain 'I' and resid 143 through 161 removed outlier: 4.415A pdb=" N THR I 150 " --> pdb=" O GLY I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 182 through 198 removed outlier: 3.587A pdb=" N ASN I 186 " --> pdb=" O VAL I 182 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR I 193 " --> pdb=" O LEU I 189 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLU I 196 " --> pdb=" O HIS I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 216 Processing helix chain 'I' and resid 223 through 244 removed outlier: 4.761A pdb=" N SER I 241 " --> pdb=" O SER I 237 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU I 242 " --> pdb=" O ILE I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 260 Processing helix chain 'I' and resid 277 through 284 removed outlier: 3.829A pdb=" N TYR I 282 " --> pdb=" O ALA I 278 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N HIS I 283 " --> pdb=" O GLU I 279 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 296 removed outlier: 3.830A pdb=" N PHE I 296 " --> pdb=" O THR I 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 301 removed outlier: 3.588A pdb=" N GLN I 301 " --> pdb=" O PRO I 298 " (cutoff:3.500A) Processing helix chain 'I' and resid 306 through 310 Processing helix chain 'I' and resid 324 through 338 Processing helix chain 'I' and resid 383 through 401 removed outlier: 4.157A pdb=" N ALA I 387 " --> pdb=" O ALA I 383 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS I 401 " --> pdb=" O LEU I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 404 through 410 removed outlier: 3.812A pdb=" N TYR I 408 " --> pdb=" O PHE I 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 415 through 437 removed outlier: 3.803A pdb=" N SER I 419 " --> pdb=" O GLU I 415 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 29 Processing helix chain 'L' and resid 40 through 44 Processing helix chain 'L' and resid 71 through 81 removed outlier: 3.877A pdb=" N MET L 75 " --> pdb=" O GLU L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 92 Processing helix chain 'L' and resid 102 through 108 Processing helix chain 'L' and resid 110 through 129 removed outlier: 4.340A pdb=" N ASP L 116 " --> pdb=" O ALA L 112 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N SER L 117 " --> pdb=" O GLU L 113 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL L 118 " --> pdb=" O LEU L 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 161 Processing helix chain 'L' and resid 182 through 198 removed outlier: 4.389A pdb=" N GLN L 193 " --> pdb=" O LEU L 189 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLU L 196 " --> pdb=" O HIS L 192 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR L 198 " --> pdb=" O LEU L 194 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 216 Processing helix chain 'L' and resid 223 through 244 removed outlier: 3.720A pdb=" N LEU L 227 " --> pdb=" O THR L 223 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N CYS L 241 " --> pdb=" O GLY L 237 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N LEU L 242 " --> pdb=" O VAL L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 260 Processing helix chain 'L' and resid 287 through 297 Processing helix chain 'L' and resid 306 through 310 Processing helix chain 'L' and resid 324 through 339 Processing helix chain 'L' and resid 340 through 343 removed outlier: 3.558A pdb=" N PHE L 343 " --> pdb=" O SER L 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 340 through 343' Processing helix chain 'L' and resid 383 through 401 removed outlier: 4.028A pdb=" N LEU L 387 " --> pdb=" O ALA L 383 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE L 391 " --> pdb=" O LEU L 387 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG L 401 " --> pdb=" O ALA L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 404 through 412 removed outlier: 4.330A pdb=" N TYR L 408 " --> pdb=" O PHE L 404 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 437 removed outlier: 3.776A pdb=" N PHE L 418 " --> pdb=" O ASP L 414 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 29 Processing helix chain 'K' and resid 47 through 51 removed outlier: 3.720A pdb=" N ASN K 50 " --> pdb=" O ASP K 47 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR K 51 " --> pdb=" O SER K 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 47 through 51' Processing helix chain 'K' and resid 72 through 81 removed outlier: 3.860A pdb=" N VAL K 78 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 90 No H-bonds generated for 'chain 'K' and resid 88 through 90' Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 110 through 113 removed outlier: 3.641A pdb=" N GLU K 113 " --> pdb=" O ILE K 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 110 through 113' Processing helix chain 'K' and resid 114 through 129 removed outlier: 3.610A pdb=" N GLN K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 161 removed outlier: 4.494A pdb=" N THR K 150 " --> pdb=" O GLY K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 198 removed outlier: 4.130A pdb=" N THR K 193 " --> pdb=" O LEU K 189 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLU K 196 " --> pdb=" O HIS K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 205 through 216 Processing helix chain 'K' and resid 223 through 244 removed outlier: 3.618A pdb=" N LEU K 227 " --> pdb=" O THR K 223 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 260 Processing helix chain 'K' and resid 277 through 284 removed outlier: 4.046A pdb=" N TYR K 282 " --> pdb=" O ALA K 278 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N HIS K 283 " --> pdb=" O GLU K 279 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU K 284 " --> pdb=" O LYS K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 296 removed outlier: 3.625A pdb=" N PHE K 296 " --> pdb=" O THR K 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 301 removed outlier: 3.606A pdb=" N GLN K 301 " --> pdb=" O PRO K 298 " (cutoff:3.500A) Processing helix chain 'K' and resid 306 through 310 Processing helix chain 'K' and resid 324 through 338 removed outlier: 3.598A pdb=" N VAL K 328 " --> pdb=" O VAL K 324 " (cutoff:3.500A) Processing helix chain 'K' and resid 384 through 401 removed outlier: 3.520A pdb=" N TRP K 388 " --> pdb=" O ILE K 384 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS K 401 " --> pdb=" O LEU K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 410 removed outlier: 3.795A pdb=" N TYR K 408 " --> pdb=" O PHE K 404 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 436 removed outlier: 3.977A pdb=" N PHE K 418 " --> pdb=" O GLU K 414 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 28 Processing helix chain 'N' and resid 40 through 44 Processing helix chain 'N' and resid 71 through 81 removed outlier: 4.006A pdb=" N MET N 75 " --> pdb=" O GLU N 71 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'N' and resid 102 through 108 Processing helix chain 'N' and resid 109 through 129 removed outlier: 3.637A pdb=" N GLU N 113 " --> pdb=" O THR N 109 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASP N 116 " --> pdb=" O ALA N 112 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N SER N 117 " --> pdb=" O GLU N 113 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL N 118 " --> pdb=" O LEU N 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 143 through 161 removed outlier: 3.622A pdb=" N SER N 147 " --> pdb=" O GLY N 143 " (cutoff:3.500A) Processing helix chain 'N' and resid 182 through 198 removed outlier: 3.527A pdb=" N ASN N 186 " --> pdb=" O VAL N 182 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLN N 193 " --> pdb=" O LEU N 189 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLU N 196 " --> pdb=" O HIS N 192 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR N 198 " --> pdb=" O LEU N 194 " (cutoff:3.500A) Processing helix chain 'N' and resid 205 through 216 removed outlier: 3.518A pdb=" N LEU N 209 " --> pdb=" O ASP N 205 " (cutoff:3.500A) Processing helix chain 'N' and resid 223 through 238 removed outlier: 3.790A pdb=" N LEU N 227 " --> pdb=" O THR N 223 " (cutoff:3.500A) Processing helix chain 'N' and resid 239 through 244 removed outlier: 3.558A pdb=" N ARG N 243 " --> pdb=" O THR N 239 " (cutoff:3.500A) Processing helix chain 'N' and resid 251 through 260 Processing helix chain 'N' and resid 279 through 284 removed outlier: 3.868A pdb=" N GLN N 282 " --> pdb=" O GLY N 279 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG N 284 " --> pdb=" O GLN N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 297 removed outlier: 3.670A pdb=" N ASP N 297 " --> pdb=" O GLN N 293 " (cutoff:3.500A) Processing helix chain 'N' and resid 298 through 301 removed outlier: 3.551A pdb=" N MET N 301 " --> pdb=" O ALA N 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 298 through 301' Processing helix chain 'N' and resid 306 through 310 Processing helix chain 'N' and resid 324 through 338 Processing helix chain 'N' and resid 339 through 343 removed outlier: 3.626A pdb=" N PHE N 343 " --> pdb=" O SER N 340 " (cutoff:3.500A) Processing helix chain 'N' and resid 383 through 401 removed outlier: 3.915A pdb=" N LEU N 387 " --> pdb=" O ALA N 383 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE N 391 " --> pdb=" O LEU N 387 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ARG N 401 " --> pdb=" O ALA N 397 " (cutoff:3.500A) Processing helix chain 'N' and resid 404 through 410 removed outlier: 4.026A pdb=" N TYR N 408 " --> pdb=" O PHE N 404 " (cutoff:3.500A) Processing helix chain 'N' and resid 414 through 437 removed outlier: 3.654A pdb=" N PHE N 418 " --> pdb=" O ASP N 414 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 29 Processing helix chain 'M' and resid 47 through 51 removed outlier: 3.997A pdb=" N ASN M 50 " --> pdb=" O ASP M 47 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR M 51 " --> pdb=" O SER M 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 47 through 51' Processing helix chain 'M' and resid 71 through 81 removed outlier: 4.658A pdb=" N ILE M 75 " --> pdb=" O GLU M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 90 No H-bonds generated for 'chain 'M' and resid 88 through 90' Processing helix chain 'M' and resid 102 through 108 Processing helix chain 'M' and resid 111 through 127 removed outlier: 4.621A pdb=" N ASP M 116 " --> pdb=" O LYS M 112 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LEU M 117 " --> pdb=" O GLU M 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 161 removed outlier: 4.451A pdb=" N THR M 150 " --> pdb=" O GLY M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 182 through 198 removed outlier: 3.509A pdb=" N ASN M 186 " --> pdb=" O VAL M 182 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR M 193 " --> pdb=" O LEU M 189 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLU M 196 " --> pdb=" O HIS M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 216 Processing helix chain 'M' and resid 223 through 244 removed outlier: 3.683A pdb=" N LEU M 227 " --> pdb=" O THR M 223 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N SER M 241 " --> pdb=" O SER M 237 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LEU M 242 " --> pdb=" O ILE M 238 " (cutoff:3.500A) Processing helix chain 'M' and resid 251 through 260 Processing helix chain 'M' and resid 287 through 297 removed outlier: 3.767A pdb=" N PHE M 296 " --> pdb=" O THR M 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 298 through 301 Processing helix chain 'M' and resid 324 through 338 removed outlier: 3.574A pdb=" N VAL M 328 " --> pdb=" O VAL M 324 " (cutoff:3.500A) Processing helix chain 'M' and resid 383 through 400 removed outlier: 4.176A pdb=" N ALA M 387 " --> pdb=" O ALA M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 404 through 410 removed outlier: 3.791A pdb=" N TYR M 408 " --> pdb=" O PHE M 404 " (cutoff:3.500A) Processing helix chain 'M' and resid 414 through 437 removed outlier: 3.920A pdb=" N PHE M 418 " --> pdb=" O GLU M 414 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 28 Processing helix chain 'P' and resid 40 through 44 Processing helix chain 'P' and resid 71 through 81 removed outlier: 4.301A pdb=" N MET P 75 " --> pdb=" O GLU P 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 87 removed outlier: 3.716A pdb=" N ILE P 86 " --> pdb=" O PHE P 83 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE P 87 " --> pdb=" O GLY P 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 83 through 87' Processing helix chain 'P' and resid 88 through 90 No H-bonds generated for 'chain 'P' and resid 88 through 90' Processing helix chain 'P' and resid 102 through 108 Processing helix chain 'P' and resid 111 through 129 removed outlier: 3.708A pdb=" N ASP P 116 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N SER P 117 " --> pdb=" O GLU P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 145 through 161 Processing helix chain 'P' and resid 182 through 198 removed outlier: 3.862A pdb=" N GLN P 193 " --> pdb=" O LEU P 189 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLU P 196 " --> pdb=" O HIS P 192 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR P 198 " --> pdb=" O LEU P 194 " (cutoff:3.500A) Processing helix chain 'P' and resid 206 through 216 Processing helix chain 'P' and resid 223 through 238 removed outlier: 3.713A pdb=" N LEU P 227 " --> pdb=" O THR P 223 " (cutoff:3.500A) Processing helix chain 'P' and resid 239 through 244 Processing helix chain 'P' and resid 251 through 260 Processing helix chain 'P' and resid 280 through 284 removed outlier: 3.597A pdb=" N ARG P 284 " --> pdb=" O GLN P 281 " (cutoff:3.500A) Processing helix chain 'P' and resid 287 through 296 Processing helix chain 'P' and resid 297 through 301 Processing helix chain 'P' and resid 306 through 310 Processing helix chain 'P' and resid 324 through 339 Processing helix chain 'P' and resid 340 through 343 Processing helix chain 'P' and resid 383 through 401 removed outlier: 3.730A pdb=" N LEU P 387 " --> pdb=" O ALA P 383 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE P 391 " --> pdb=" O LEU P 387 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ARG P 401 " --> pdb=" O ALA P 397 " (cutoff:3.500A) Processing helix chain 'P' and resid 404 through 411 removed outlier: 3.890A pdb=" N TYR P 408 " --> pdb=" O PHE P 404 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU P 411 " --> pdb=" O TRP P 407 " (cutoff:3.500A) Processing helix chain 'P' and resid 414 through 437 removed outlier: 3.681A pdb=" N PHE P 418 " --> pdb=" O ASP P 414 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 29 Processing helix chain 'O' and resid 48 through 51 removed outlier: 4.111A pdb=" N THR O 51 " --> pdb=" O SER O 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 48 through 51' Processing helix chain 'O' and resid 71 through 81 removed outlier: 4.604A pdb=" N ILE O 75 " --> pdb=" O GLU O 71 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL O 78 " --> pdb=" O VAL O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 102 through 108 Processing helix chain 'O' and resid 110 through 113 removed outlier: 3.623A pdb=" N GLU O 113 " --> pdb=" O ILE O 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 110 through 113' Processing helix chain 'O' and resid 114 through 127 Processing helix chain 'O' and resid 143 through 161 removed outlier: 4.431A pdb=" N THR O 150 " --> pdb=" O GLY O 146 " (cutoff:3.500A) Processing helix chain 'O' and resid 182 through 198 removed outlier: 3.522A pdb=" N THR O 191 " --> pdb=" O SER O 187 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N HIS O 192 " --> pdb=" O ILE O 188 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR O 193 " --> pdb=" O LEU O 189 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLU O 196 " --> pdb=" O HIS O 192 " (cutoff:3.500A) Processing helix chain 'O' and resid 206 through 216 Processing helix chain 'O' and resid 223 through 244 removed outlier: 3.591A pdb=" N LEU O 227 " --> pdb=" O THR O 223 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N SER O 241 " --> pdb=" O SER O 237 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LEU O 242 " --> pdb=" O ILE O 238 " (cutoff:3.500A) Processing helix chain 'O' and resid 251 through 260 Processing helix chain 'O' and resid 277 through 283 removed outlier: 3.801A pdb=" N TYR O 282 " --> pdb=" O ALA O 278 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N HIS O 283 " --> pdb=" O GLU O 279 " (cutoff:3.500A) Processing helix chain 'O' and resid 287 through 297 removed outlier: 3.735A pdb=" N PHE O 296 " --> pdb=" O THR O 292 " (cutoff:3.500A) Processing helix chain 'O' and resid 298 through 301 Processing helix chain 'O' and resid 324 through 337 removed outlier: 3.586A pdb=" N VAL O 328 " --> pdb=" O VAL O 324 " (cutoff:3.500A) Processing helix chain 'O' and resid 384 through 400 Processing helix chain 'O' and resid 404 through 410 removed outlier: 3.866A pdb=" N TYR O 408 " --> pdb=" O PHE O 404 " (cutoff:3.500A) Processing helix chain 'O' and resid 414 through 437 removed outlier: 3.888A pdb=" N PHE O 418 " --> pdb=" O GLU O 414 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 28 Processing helix chain 'R' and resid 40 through 44 Processing helix chain 'R' and resid 48 through 51 removed outlier: 3.856A pdb=" N VAL R 51 " --> pdb=" O ARG R 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 48 through 51' Processing helix chain 'R' and resid 71 through 81 removed outlier: 3.910A pdb=" N MET R 75 " --> pdb=" O GLU R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 90 No H-bonds generated for 'chain 'R' and resid 88 through 90' Processing helix chain 'R' and resid 102 through 108 Processing helix chain 'R' and resid 109 through 129 removed outlier: 4.409A pdb=" N ASP R 116 " --> pdb=" O ALA R 112 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N SER R 117 " --> pdb=" O GLU R 113 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL R 118 " --> pdb=" O LEU R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 161 Processing helix chain 'R' and resid 182 through 198 removed outlier: 3.969A pdb=" N GLN R 193 " --> pdb=" O LEU R 189 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU R 196 " --> pdb=" O HIS R 192 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR R 198 " --> pdb=" O LEU R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 205 through 216 Processing helix chain 'R' and resid 223 through 244 removed outlier: 3.855A pdb=" N LEU R 227 " --> pdb=" O THR R 223 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR R 239 " --> pdb=" O MET R 235 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N CYS R 241 " --> pdb=" O GLY R 237 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LEU R 242 " --> pdb=" O VAL R 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 260 Processing helix chain 'R' and resid 287 through 297 removed outlier: 3.548A pdb=" N LEU R 291 " --> pdb=" O THR R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 298 through 301 Processing helix chain 'R' and resid 306 through 310 Processing helix chain 'R' and resid 324 through 339 removed outlier: 3.596A pdb=" N VAL R 328 " --> pdb=" O SER R 324 " (cutoff:3.500A) Processing helix chain 'R' and resid 340 through 343 Processing helix chain 'R' and resid 384 through 401 removed outlier: 3.505A pdb=" N PHE R 388 " --> pdb=" O ILE R 384 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE R 391 " --> pdb=" O LEU R 387 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARG R 401 " --> pdb=" O ALA R 397 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 412 removed outlier: 4.438A pdb=" N TYR R 408 " --> pdb=" O PHE R 404 " (cutoff:3.500A) Processing helix chain 'R' and resid 414 through 437 removed outlier: 3.826A pdb=" N PHE R 418 " --> pdb=" O ASP R 414 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 29 Processing helix chain 'Q' and resid 47 through 51 removed outlier: 3.757A pdb=" N ASN Q 50 " --> pdb=" O ASP Q 47 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR Q 51 " --> pdb=" O SER Q 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 47 through 51' Processing helix chain 'Q' and resid 72 through 81 Processing helix chain 'Q' and resid 88 through 90 No H-bonds generated for 'chain 'Q' and resid 88 through 90' Processing helix chain 'Q' and resid 102 through 108 Processing helix chain 'Q' and resid 114 through 127 Processing helix chain 'Q' and resid 143 through 161 removed outlier: 4.386A pdb=" N THR Q 150 " --> pdb=" O GLY Q 146 " (cutoff:3.500A) Processing helix chain 'Q' and resid 182 through 198 removed outlier: 3.709A pdb=" N ASN Q 186 " --> pdb=" O VAL Q 182 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR Q 193 " --> pdb=" O LEU Q 189 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLU Q 196 " --> pdb=" O HIS Q 192 " (cutoff:3.500A) Processing helix chain 'Q' and resid 206 through 216 Processing helix chain 'Q' and resid 223 through 244 removed outlier: 3.505A pdb=" N LEU Q 227 " --> pdb=" O THR Q 223 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N SER Q 241 " --> pdb=" O SER Q 237 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU Q 242 " --> pdb=" O ILE Q 238 " (cutoff:3.500A) Processing helix chain 'Q' and resid 251 through 260 Processing helix chain 'Q' and resid 277 through 282 removed outlier: 3.942A pdb=" N TYR Q 282 " --> pdb=" O ALA Q 278 " (cutoff:3.500A) Processing helix chain 'Q' and resid 287 through 296 removed outlier: 3.672A pdb=" N PHE Q 296 " --> pdb=" O THR Q 292 " (cutoff:3.500A) Processing helix chain 'Q' and resid 324 through 338 removed outlier: 3.631A pdb=" N VAL Q 328 " --> pdb=" O VAL Q 324 " (cutoff:3.500A) Processing helix chain 'Q' and resid 383 through 400 removed outlier: 3.964A pdb=" N ALA Q 387 " --> pdb=" O ALA Q 383 " (cutoff:3.500A) Processing helix chain 'Q' and resid 405 through 410 Processing helix chain 'Q' and resid 414 through 436 removed outlier: 3.647A pdb=" N PHE Q 418 " --> pdb=" O GLU Q 414 " (cutoff:3.500A) Processing helix chain 's' and resid 88 through 114 removed outlier: 3.653A pdb=" N LYS s 114 " --> pdb=" O ARG s 110 " (cutoff:3.500A) Processing helix chain 't' and resid 88 through 114 removed outlier: 3.569A pdb=" N LYS t 114 " --> pdb=" O ARG t 110 " (cutoff:3.500A) Processing helix chain 'u' and resid 88 through 114 removed outlier: 3.627A pdb=" N LYS u 114 " --> pdb=" O ARG u 110 " (cutoff:3.500A) Processing helix chain 'v' and resid 88 through 114 removed outlier: 3.580A pdb=" N LYS v 114 " --> pdb=" O ARG v 110 " (cutoff:3.500A) Processing helix chain 'w' and resid 88 through 114 removed outlier: 3.555A pdb=" N LYS w 114 " --> pdb=" O ARG w 110 " (cutoff:3.500A) Processing helix chain 'x' and resid 88 through 114 removed outlier: 3.689A pdb=" N LYS x 114 " --> pdb=" O ARG x 110 " (cutoff:3.500A) Processing helix chain 'y' and resid 88 through 114 removed outlier: 3.655A pdb=" N LYS y 114 " --> pdb=" O ARG y 110 " (cutoff:3.500A) Processing helix chain 'z' and resid 88 through 114 removed outlier: 3.580A pdb=" N LYS z 114 " --> pdb=" O ARG z 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.802A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU B 3 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N PHE B 135 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL B 5 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N LEU B 137 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE B 7 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N HIS B 139 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ALA B 9 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLN B 133 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ASN B 167 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N PHE B 135 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL B 171 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N HIS B 139 " --> pdb=" O VAL B 171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.802A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU B 3 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N PHE B 135 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL B 5 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N LEU B 137 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE B 7 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N HIS B 139 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ALA B 9 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLN B 133 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ASN B 167 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N PHE B 135 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL B 171 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N HIS B 139 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N MET B 166 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N TYR B 202 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR B 168 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR B 201 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.174A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLU A 3 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY A 134 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.920A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 92 through 94 removed outlier: 8.084A pdb=" N VAL D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU D 67 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ILE D 66 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N HIS D 6 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL D 68 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLN D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLU D 3 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY D 134 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER D 140 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN D 133 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ASN D 167 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N PHE D 135 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N PHE D 169 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU D 137 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL D 171 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N HIS D 139 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N MET D 166 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N TYR D 202 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR D 168 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ILE D 204 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N SER D 170 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR D 201 " --> pdb=" O PHE D 268 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N CYS D 203 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 10.537A pdb=" N PHE D 272 " --> pdb=" O CYS D 203 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N PHE D 267 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N SER D 381 " --> pdb=" O PHE D 267 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 53 through 56 removed outlier: 3.553A pdb=" N LYS D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.318A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N GLU C 3 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY C 134 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLN C 133 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU C 167 " --> pdb=" O GLN C 133 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N PHE C 135 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N PHE C 169 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL C 137 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ILE C 171 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LYS C 166 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N PHE C 202 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLU C 168 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL C 204 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N SER C 170 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 56 removed outlier: 3.684A pdb=" N LYS C 60 " --> pdb=" O THR C 56 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 269 through 273 removed outlier: 6.703A pdb=" N ALA C 374 " --> pdb=" O TYR C 319 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR C 319 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N CYS C 376 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LEU C 317 " --> pdb=" O CYS C 376 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU C 378 " --> pdb=" O CYS C 315 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N CYS C 315 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASN C 380 " --> pdb=" O MET C 313 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 92 through 94 removed outlier: 7.966A pdb=" N VAL F 93 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU F 67 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ILE F 66 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS F 6 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL F 68 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N GLN F 8 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLU F 3 " --> pdb=" O GLY F 134 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N GLN F 136 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL F 5 " --> pdb=" O GLN F 136 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N THR F 138 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE F 7 " --> pdb=" O THR F 138 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N SER F 140 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N ALA F 9 " --> pdb=" O SER F 140 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLN F 133 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ASN F 167 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N PHE F 135 " --> pdb=" O ASN F 167 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N PHE F 169 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU F 137 " --> pdb=" O PHE F 169 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N VAL F 171 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N HIS F 139 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ASP F 205 " --> pdb=" O PRO F 270 " (cutoff:3.500A) removed outlier: 11.938A pdb=" N PHE F 272 " --> pdb=" O ASP F 205 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N PHE F 267 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER F 381 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N LYS F 352 " --> pdb=" O LEU F 313 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL F 315 " --> pdb=" O LYS F 352 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ALA F 354 " --> pdb=" O VAL F 315 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA F 317 " --> pdb=" O ALA F 354 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N CYS F 356 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE F 319 " --> pdb=" O CYS F 356 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 53 through 56 Processing sheet with id=AB4, first strand: chain 'E' and resid 92 through 94 removed outlier: 8.265A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N SER E 140 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N PHE E 135 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N PHE E 169 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL E 137 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ILE E 171 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N HIS E 139 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N SER E 170 " --> pdb=" O VAL E 204 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 53 through 56 removed outlier: 3.858A pdb=" N LYS E 60 " --> pdb=" O THR E 56 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 269 through 273 Processing sheet with id=AB7, first strand: chain 'H' and resid 92 through 94 removed outlier: 8.087A pdb=" N VAL H 93 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LEU H 67 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N GLU H 3 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY H 134 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N SER H 140 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLN H 133 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ASN H 167 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N PHE H 135 " --> pdb=" O ASN H 167 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N PHE H 169 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU H 137 " --> pdb=" O PHE H 169 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL H 171 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N HIS H 139 " --> pdb=" O VAL H 171 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N MET H 166 " --> pdb=" O GLU H 200 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N TYR H 202 " --> pdb=" O MET H 166 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR H 168 " --> pdb=" O TYR H 202 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE H 204 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N SER H 170 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR H 201 " --> pdb=" O PHE H 268 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N CYS H 203 " --> pdb=" O PRO H 270 " (cutoff:3.500A) removed outlier: 10.432A pdb=" N PHE H 272 " --> pdb=" O CYS H 203 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N PHE H 267 " --> pdb=" O SER H 381 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER H 381 " --> pdb=" O PHE H 267 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N LYS H 352 " --> pdb=" O LEU H 313 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL H 315 " --> pdb=" O LYS H 352 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ALA H 354 " --> pdb=" O VAL H 315 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ALA H 317 " --> pdb=" O ALA H 354 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N CYS H 356 " --> pdb=" O ALA H 317 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE H 319 " --> pdb=" O CYS H 356 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 53 through 56 removed outlier: 3.663A pdb=" N LYS H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 92 through 94 removed outlier: 8.512A pdb=" N VAL G 66 " --> pdb=" O CYS G 4 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N SER G 6 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL G 68 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N HIS G 8 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLU G 3 " --> pdb=" O LEU G 132 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY G 134 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N SER G 140 " --> pdb=" O VAL G 9 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLN G 133 " --> pdb=" O SER G 165 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LEU G 167 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N PHE G 135 " --> pdb=" O LEU G 167 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N PHE G 169 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL G 137 " --> pdb=" O PHE G 169 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ILE G 171 " --> pdb=" O VAL G 137 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N HIS G 139 " --> pdb=" O ILE G 171 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LYS G 166 " --> pdb=" O CYS G 200 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N PHE G 202 " --> pdb=" O LYS G 166 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLU G 168 " --> pdb=" O PHE G 202 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 53 through 56 removed outlier: 3.631A pdb=" N LYS G 60 " --> pdb=" O THR G 56 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 269 through 273 removed outlier: 6.610A pdb=" N ALA G 374 " --> pdb=" O TYR G 319 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N TYR G 319 " --> pdb=" O ALA G 374 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N CYS G 376 " --> pdb=" O LEU G 317 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LEU G 317 " --> pdb=" O CYS G 376 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU G 378 " --> pdb=" O CYS G 315 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N CYS G 315 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN G 380 " --> pdb=" O MET G 313 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 92 through 94 removed outlier: 7.884A pdb=" N VAL J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N LEU J 67 " --> pdb=" O VAL J 93 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ILE J 66 " --> pdb=" O ILE J 4 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N HIS J 6 " --> pdb=" O ILE J 66 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL J 68 " --> pdb=" O HIS J 6 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N GLN J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N GLU J 3 " --> pdb=" O LEU J 132 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY J 134 " --> pdb=" O GLU J 3 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N SER J 140 " --> pdb=" O ALA J 9 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS J 139 " --> pdb=" O PHE J 169 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N MET J 166 " --> pdb=" O GLU J 200 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N TYR J 202 " --> pdb=" O MET J 166 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR J 168 " --> pdb=" O TYR J 202 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE J 204 " --> pdb=" O THR J 168 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N SER J 170 " --> pdb=" O ILE J 204 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR J 201 " --> pdb=" O PHE J 268 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N CYS J 203 " --> pdb=" O PRO J 270 " (cutoff:3.500A) removed outlier: 10.724A pdb=" N PHE J 272 " --> pdb=" O CYS J 203 " (cutoff:3.500A) removed outlier: 13.613A pdb=" N ASP J 205 " --> pdb=" O PHE J 272 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N PHE J 267 " --> pdb=" O SER J 381 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N SER J 381 " --> pdb=" O PHE J 267 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 53 through 56 removed outlier: 3.763A pdb=" N LYS J 60 " --> pdb=" O ALA J 56 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 92 through 94 removed outlier: 7.912A pdb=" N ILE I 93 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE I 67 " --> pdb=" O ILE I 93 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N VAL I 66 " --> pdb=" O CYS I 4 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER I 6 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N VAL I 68 " --> pdb=" O SER I 6 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N HIS I 8 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE I 5 " --> pdb=" O LEU I 136 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N PHE I 138 " --> pdb=" O ILE I 5 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE I 7 " --> pdb=" O PHE I 138 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N SER I 140 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N VAL I 9 " --> pdb=" O SER I 140 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N PHE I 135 " --> pdb=" O LEU I 167 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N PHE I 169 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N VAL I 137 " --> pdb=" O PHE I 169 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE I 171 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N HIS I 139 " --> pdb=" O ILE I 171 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 92 through 94 removed outlier: 7.912A pdb=" N ILE I 93 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE I 67 " --> pdb=" O ILE I 93 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N VAL I 66 " --> pdb=" O CYS I 4 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER I 6 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N VAL I 68 " --> pdb=" O SER I 6 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N HIS I 8 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE I 5 " --> pdb=" O LEU I 136 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N PHE I 138 " --> pdb=" O ILE I 5 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE I 7 " --> pdb=" O PHE I 138 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N SER I 140 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N VAL I 9 " --> pdb=" O SER I 140 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N PHE I 135 " --> pdb=" O LEU I 167 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N PHE I 169 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N VAL I 137 " --> pdb=" O PHE I 169 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE I 171 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N HIS I 139 " --> pdb=" O ILE I 171 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 53 through 56 removed outlier: 3.513A pdb=" N LYS I 60 " --> pdb=" O THR I 56 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 272 through 273 removed outlier: 3.670A pdb=" N ALA I 314 " --> pdb=" O ASN I 380 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 93 through 94 removed outlier: 7.922A pdb=" N VAL L 93 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU L 67 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N ILE L 66 " --> pdb=" O ILE L 4 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N HIS L 6 " --> pdb=" O ILE L 66 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N VAL L 68 " --> pdb=" O HIS L 6 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLN L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLU L 3 " --> pdb=" O GLY L 134 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N GLN L 136 " --> pdb=" O GLU L 3 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL L 5 " --> pdb=" O GLN L 136 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N THR L 138 " --> pdb=" O VAL L 5 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE L 7 " --> pdb=" O THR L 138 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N SER L 140 " --> pdb=" O ILE L 7 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ALA L 9 " --> pdb=" O SER L 140 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N HIS L 139 " --> pdb=" O PHE L 169 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR L 201 " --> pdb=" O PHE L 268 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N CYS L 203 " --> pdb=" O PRO L 270 " (cutoff:3.500A) removed outlier: 10.646A pdb=" N PHE L 272 " --> pdb=" O CYS L 203 " (cutoff:3.500A) removed outlier: 13.841A pdb=" N ASP L 205 " --> pdb=" O PHE L 272 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N PHE L 267 " --> pdb=" O SER L 381 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N SER L 381 " --> pdb=" O PHE L 267 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 53 through 56 removed outlier: 3.872A pdb=" N LYS L 60 " --> pdb=" O ALA L 56 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 92 through 94 removed outlier: 8.294A pdb=" N ILE K 93 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N PHE K 67 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N VAL K 66 " --> pdb=" O CYS K 4 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE K 5 " --> pdb=" O LEU K 136 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N PHE K 138 " --> pdb=" O ILE K 5 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE K 7 " --> pdb=" O PHE K 138 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N SER K 140 " --> pdb=" O ILE K 7 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N VAL K 9 " --> pdb=" O SER K 140 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N PHE K 135 " --> pdb=" O LEU K 167 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N PHE K 169 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL K 137 " --> pdb=" O PHE K 169 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N ILE K 171 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N HIS K 139 " --> pdb=" O ILE K 171 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 53 through 56 Processing sheet with id=AD4, first strand: chain 'K' and resid 269 through 273 removed outlier: 3.597A pdb=" N LEU K 318 " --> pdb=" O CYS K 376 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 92 through 94 removed outlier: 8.069A pdb=" N VAL N 93 " --> pdb=" O ALA N 65 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU N 67 " --> pdb=" O VAL N 93 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N ILE N 66 " --> pdb=" O ILE N 4 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N HIS N 6 " --> pdb=" O ILE N 66 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N VAL N 68 " --> pdb=" O HIS N 6 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLN N 8 " --> pdb=" O VAL N 68 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N GLU N 3 " --> pdb=" O LEU N 132 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY N 134 " --> pdb=" O GLU N 3 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL N 5 " --> pdb=" O GLY N 134 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N SER N 140 " --> pdb=" O ALA N 9 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N GLN N 133 " --> pdb=" O ILE N 165 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ASN N 167 " --> pdb=" O GLN N 133 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N PHE N 135 " --> pdb=" O ASN N 167 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N PHE N 169 " --> pdb=" O PHE N 135 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU N 137 " --> pdb=" O PHE N 169 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL N 171 " --> pdb=" O LEU N 137 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N HIS N 139 " --> pdb=" O VAL N 171 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N MET N 166 " --> pdb=" O GLU N 200 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N TYR N 202 " --> pdb=" O MET N 166 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR N 168 " --> pdb=" O TYR N 202 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR N 201 " --> pdb=" O PHE N 268 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE N 267 " --> pdb=" O SER N 381 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N SER N 381 " --> pdb=" O PHE N 267 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 53 through 56 removed outlier: 3.507A pdb=" N VAL N 62 " --> pdb=" O ASN N 54 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS N 60 " --> pdb=" O ALA N 56 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 92 through 94 removed outlier: 8.263A pdb=" N ILE M 93 " --> pdb=" O ALA M 65 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N PHE M 67 " --> pdb=" O ILE M 93 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N VAL M 66 " --> pdb=" O CYS M 4 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N SER M 6 " --> pdb=" O VAL M 66 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL M 68 " --> pdb=" O SER M 6 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N HIS M 8 " --> pdb=" O VAL M 68 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N PHE M 135 " --> pdb=" O LEU M 167 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N PHE M 169 " --> pdb=" O PHE M 135 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N VAL M 137 " --> pdb=" O PHE M 169 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE M 171 " --> pdb=" O VAL M 137 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LYS M 166 " --> pdb=" O CYS M 200 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N PHE M 202 " --> pdb=" O LYS M 166 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU M 168 " --> pdb=" O PHE M 202 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL M 204 " --> pdb=" O GLU M 168 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N SER M 170 " --> pdb=" O VAL M 204 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 53 through 56 removed outlier: 3.610A pdb=" N LYS M 60 " --> pdb=" O THR M 56 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 269 through 270 Processing sheet with id=AE1, first strand: chain 'M' and resid 269 through 270 Processing sheet with id=AE2, first strand: chain 'P' and resid 92 through 93 removed outlier: 8.139A pdb=" N VAL P 93 " --> pdb=" O ALA P 65 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU P 67 " --> pdb=" O VAL P 93 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ILE P 66 " --> pdb=" O ILE P 4 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N HIS P 6 " --> pdb=" O ILE P 66 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL P 68 " --> pdb=" O HIS P 6 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N GLN P 8 " --> pdb=" O VAL P 68 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLU P 3 " --> pdb=" O LEU P 132 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY P 134 " --> pdb=" O GLU P 3 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER P 140 " --> pdb=" O ALA P 9 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLN P 133 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ASN P 167 " --> pdb=" O GLN P 133 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N PHE P 135 " --> pdb=" O ASN P 167 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N PHE P 169 " --> pdb=" O PHE P 135 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU P 137 " --> pdb=" O PHE P 169 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL P 171 " --> pdb=" O LEU P 137 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N HIS P 139 " --> pdb=" O VAL P 171 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR P 201 " --> pdb=" O PHE P 268 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N CYS P 203 " --> pdb=" O PRO P 270 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N PHE P 267 " --> pdb=" O SER P 381 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N SER P 381 " --> pdb=" O PHE P 267 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 53 through 56 removed outlier: 3.620A pdb=" N LYS P 60 " --> pdb=" O ALA P 56 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O' and resid 92 through 94 removed outlier: 8.546A pdb=" N ILE O 93 " --> pdb=" O ALA O 65 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N PHE O 67 " --> pdb=" O ILE O 93 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N PHE O 135 " --> pdb=" O LEU O 167 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N PHE O 169 " --> pdb=" O PHE O 135 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N VAL O 137 " --> pdb=" O PHE O 169 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE O 171 " --> pdb=" O VAL O 137 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LYS O 166 " --> pdb=" O CYS O 200 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N PHE O 202 " --> pdb=" O LYS O 166 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLU O 168 " --> pdb=" O PHE O 202 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N VAL O 204 " --> pdb=" O GLU O 168 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N SER O 170 " --> pdb=" O VAL O 204 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'O' and resid 53 through 55 Processing sheet with id=AE6, first strand: chain 'O' and resid 269 through 273 removed outlier: 3.630A pdb=" N ALA O 314 " --> pdb=" O ASN O 380 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N LYS O 352 " --> pdb=" O MET O 313 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N CYS O 315 " --> pdb=" O LYS O 352 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLY O 354 " --> pdb=" O CYS O 315 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU O 317 " --> pdb=" O GLY O 354 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ASN O 356 " --> pdb=" O LEU O 317 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR O 319 " --> pdb=" O ASN O 356 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 92 through 94 removed outlier: 8.062A pdb=" N VAL R 93 " --> pdb=" O ALA R 65 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU R 67 " --> pdb=" O VAL R 93 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N ILE R 66 " --> pdb=" O ILE R 4 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N HIS R 6 " --> pdb=" O ILE R 66 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL R 68 " --> pdb=" O HIS R 6 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N GLN R 8 " --> pdb=" O VAL R 68 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLU R 3 " --> pdb=" O LEU R 132 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY R 134 " --> pdb=" O GLU R 3 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL R 5 " --> pdb=" O GLY R 134 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N MET R 166 " --> pdb=" O GLU R 200 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N TYR R 202 " --> pdb=" O MET R 166 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR R 168 " --> pdb=" O TYR R 202 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE R 204 " --> pdb=" O THR R 168 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER R 170 " --> pdb=" O ILE R 204 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR R 201 " --> pdb=" O PHE R 268 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N CYS R 203 " --> pdb=" O PRO R 270 " (cutoff:3.500A) removed outlier: 10.670A pdb=" N PHE R 272 " --> pdb=" O CYS R 203 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N PHE R 267 " --> pdb=" O SER R 381 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N SER R 381 " --> pdb=" O PHE R 267 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'R' and resid 53 through 56 removed outlier: 3.816A pdb=" N LYS R 60 " --> pdb=" O ALA R 56 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 92 through 94 removed outlier: 8.316A pdb=" N ILE Q 93 " --> pdb=" O ALA Q 65 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N PHE Q 67 " --> pdb=" O ILE Q 93 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N VAL Q 66 " --> pdb=" O CYS Q 4 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER Q 6 " --> pdb=" O VAL Q 66 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N VAL Q 68 " --> pdb=" O SER Q 6 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N HIS Q 8 " --> pdb=" O VAL Q 68 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N GLU Q 3 " --> pdb=" O GLN Q 133 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE Q 135 " --> pdb=" O GLU Q 3 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE Q 5 " --> pdb=" O PHE Q 135 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N VAL Q 137 " --> pdb=" O ILE Q 5 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE Q 7 " --> pdb=" O VAL Q 137 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N GLN Q 133 " --> pdb=" O SER Q 165 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU Q 167 " --> pdb=" O GLN Q 133 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N PHE Q 135 " --> pdb=" O LEU Q 167 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N PHE Q 169 " --> pdb=" O PHE Q 135 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL Q 137 " --> pdb=" O PHE Q 169 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ILE Q 171 " --> pdb=" O VAL Q 137 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS Q 166 " --> pdb=" O CYS Q 200 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N PHE Q 202 " --> pdb=" O LYS Q 166 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU Q 168 " --> pdb=" O PHE Q 202 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL Q 204 " --> pdb=" O GLU Q 168 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N SER Q 170 " --> pdb=" O VAL Q 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'Q' and resid 53 through 55 Processing sheet with id=AF2, first strand: chain 'Q' and resid 269 through 273 3228 hydrogen bonds defined for protein. 9399 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: 27.69 Time building geometry restraints manager: 14.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 21406 1.35 - 1.47: 15744 1.47 - 1.60: 28018 1.60 - 1.72: 73 1.72 - 1.85: 729 Bond restraints: 65970 Sorted by residual: bond pdb=" CB PRO P 82 " pdb=" CG PRO P 82 " ideal model delta sigma weight residual 1.492 1.640 -0.148 5.00e-02 4.00e+02 8.78e+00 bond pdb=" CA TRP Q 388 " pdb=" CB TRP Q 388 " ideal model delta sigma weight residual 1.529 1.498 0.031 1.64e-02 3.72e+03 3.53e+00 bond pdb=" CA VAL L 288 " pdb=" CB VAL L 288 " ideal model delta sigma weight residual 1.539 1.530 0.009 5.40e-03 3.43e+04 3.01e+00 bond pdb=" CA VAL P 288 " pdb=" CB VAL P 288 " ideal model delta sigma weight residual 1.534 1.546 -0.012 6.80e-03 2.16e+04 2.88e+00 bond pdb=" CB GLU F 422 " pdb=" CG GLU F 422 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.73e+00 ... (remaining 65965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 88113 2.30 - 4.60: 1191 4.60 - 6.90: 136 6.90 - 9.21: 22 9.21 - 11.51: 7 Bond angle restraints: 89469 Sorted by residual: angle pdb=" CA PRO P 82 " pdb=" N PRO P 82 " pdb=" CD PRO P 82 " ideal model delta sigma weight residual 112.00 101.91 10.09 1.40e+00 5.10e-01 5.20e+01 angle pdb=" CA ARG Q 390 " pdb=" CB ARG Q 390 " pdb=" CG ARG Q 390 " ideal model delta sigma weight residual 114.10 124.49 -10.39 2.00e+00 2.50e-01 2.70e+01 angle pdb=" N GLU P 159 " pdb=" CA GLU P 159 " pdb=" CB GLU P 159 " ideal model delta sigma weight residual 110.28 116.98 -6.70 1.55e+00 4.16e-01 1.87e+01 angle pdb=" N GLU M 433 " pdb=" CA GLU M 433 " pdb=" CB GLU M 433 " ideal model delta sigma weight residual 110.30 116.68 -6.38 1.54e+00 4.22e-01 1.71e+01 angle pdb=" C ARG P 158 " pdb=" N GLU P 159 " pdb=" CA GLU P 159 " ideal model delta sigma weight residual 120.31 114.13 6.18 1.52e+00 4.33e-01 1.65e+01 ... (remaining 89464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 38979 35.65 - 71.31: 549 71.31 - 106.96: 36 106.96 - 142.62: 9 142.62 - 178.27: 18 Dihedral angle restraints: 39591 sinusoidal: 16110 harmonic: 23481 Sorted by residual: dihedral pdb=" C5' GTP C 501 " pdb=" O5' GTP C 501 " pdb=" PA GTP C 501 " pdb=" O3A GTP C 501 " ideal model delta sinusoidal sigma weight residual 69.27 -112.46 -178.27 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP Q 501 " pdb=" O5' GTP Q 501 " pdb=" PA GTP Q 501 " pdb=" O3A GTP Q 501 " ideal model delta sinusoidal sigma weight residual 69.27 -112.55 -178.18 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP M 501 " pdb=" O5' GTP M 501 " pdb=" PA GTP M 501 " pdb=" O3A GTP M 501 " ideal model delta sinusoidal sigma weight residual 69.27 -112.72 -178.01 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 39588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 6842 0.047 - 0.093: 2214 0.093 - 0.140: 611 0.140 - 0.187: 36 0.187 - 0.233: 8 Chirality restraints: 9711 Sorted by residual: chirality pdb=" CA ARG Q 390 " pdb=" N ARG Q 390 " pdb=" C ARG Q 390 " pdb=" CB ARG Q 390 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB ILE D 347 " pdb=" CA ILE D 347 " pdb=" CG1 ILE D 347 " pdb=" CG2 ILE D 347 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA GLN L 193 " pdb=" N GLN L 193 " pdb=" C GLN L 193 " pdb=" CB GLN L 193 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 9708 not shown) Planarity restraints: 11637 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG Q 390 " -0.438 9.50e-02 1.11e+02 1.96e-01 2.36e+01 pdb=" NE ARG Q 390 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ARG Q 390 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG Q 390 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG Q 390 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY P 81 " 0.080 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO P 82 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO P 82 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO P 82 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU F 422 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.12e+00 pdb=" CD GLU F 422 " -0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU F 422 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU F 422 " 0.015 2.00e-02 2.50e+03 ... (remaining 11634 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 431 2.49 - 3.09: 46103 3.09 - 3.69: 107211 3.69 - 4.30: 154767 4.30 - 4.90: 256076 Nonbonded interactions: 564588 Sorted by model distance: nonbonded pdb=" O3G GTP A 501 " pdb="MG MG A 502 " model vdw 1.883 2.170 nonbonded pdb=" O3G GTP Q 501 " pdb="MG MG Q 502 " model vdw 1.923 2.170 nonbonded pdb=" O2B G2P R 501 " pdb="MG MG R 502 " model vdw 1.923 2.170 nonbonded pdb=" O2G G2P P 501 " pdb="MG MG P 502 " model vdw 1.925 2.170 nonbonded pdb=" O3G GTP O 501 " pdb="MG MG O 502 " model vdw 1.926 2.170 ... (remaining 564583 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' } ncs_group { reference = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 1.790 Check model and map are aligned: 0.360 Set scattering table: 0.450 Process input model: 114.030 Find NCS groups from input model: 3.100 Set up NCS constraints: 0.530 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:10.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 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 : 0.004 0.148 65970 Z= 0.279 Angle : 0.657 11.508 89469 Z= 0.345 Chirality : 0.048 0.233 9711 Planarity : 0.005 0.196 11637 Dihedral : 14.259 178.273 24525 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.03 % Allowed : 0.19 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.28 (0.09), residues: 8055 helix: 0.97 (0.09), residues: 3600 sheet: 0.20 (0.16), residues: 1161 loop : -0.61 (0.11), residues: 3294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP Q 388 HIS 0.014 0.001 HIS D 192 PHE 0.023 0.002 PHE M 418 TYR 0.028 0.001 TYR K 432 ARG 0.011 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16110 Ramachandran restraints generated. 8055 Oldfield, 0 Emsley, 8055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16110 Ramachandran restraints generated. 8055 Oldfield, 0 Emsley, 8055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1359 residues out of total 6966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1357 time to evaluate : 5.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: r 127 MET cc_start: 0.8217 (mmp) cc_final: 0.7787 (mmp) REVERT: B 19 LYS cc_start: 0.8811 (mmmt) cc_final: 0.8592 (tptp) REVERT: B 31 ASP cc_start: 0.7418 (p0) cc_final: 0.6941 (p0) REVERT: B 47 GLU cc_start: 0.8300 (tp30) cc_final: 0.7600 (tp30) REVERT: B 75 MET cc_start: 0.8724 (mmp) cc_final: 0.8409 (mmp) REVERT: B 105 LYS cc_start: 0.8903 (mtpp) cc_final: 0.8641 (mtpp) REVERT: B 116 ASP cc_start: 0.8165 (m-30) cc_final: 0.7325 (m-30) REVERT: B 120 ASP cc_start: 0.7960 (m-30) cc_final: 0.7742 (m-30) REVERT: B 196 GLU cc_start: 0.8259 (pt0) cc_final: 0.7985 (pt0) REVERT: B 417 GLU cc_start: 0.8232 (tt0) cc_final: 0.7745 (tt0) REVERT: A 112 LYS cc_start: 0.8256 (pttt) cc_final: 0.7666 (pttt) REVERT: A 113 GLU cc_start: 0.7923 (mp0) cc_final: 0.7664 (mp0) REVERT: D 47 GLU cc_start: 0.7625 (pp20) cc_final: 0.7068 (pp20) REVERT: D 71 GLU cc_start: 0.8447 (tp30) cc_final: 0.8179 (tp30) REVERT: D 127 GLU cc_start: 0.7822 (pm20) cc_final: 0.7510 (pm20) REVERT: D 192 HIS cc_start: 0.8731 (OUTLIER) cc_final: 0.8475 (t70) REVERT: D 205 ASP cc_start: 0.7668 (m-30) cc_final: 0.7235 (m-30) REVERT: D 207 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7943 (mm-30) REVERT: D 247 GLN cc_start: 0.8430 (mp10) cc_final: 0.7990 (mp10) REVERT: D 281 GLN cc_start: 0.8518 (pp30) cc_final: 0.8272 (pp30) REVERT: D 302 MET cc_start: 0.8904 (mtm) cc_final: 0.8643 (mtm) REVERT: D 330 GLU cc_start: 0.7965 (mp0) cc_final: 0.7439 (pm20) REVERT: D 345 GLU cc_start: 0.8143 (pm20) cc_final: 0.7924 (pm20) REVERT: D 349 ASN cc_start: 0.6417 (t0) cc_final: 0.6117 (t0) REVERT: D 411 GLU cc_start: 0.6825 (pm20) cc_final: 0.6499 (pm20) REVERT: D 416 MET cc_start: 0.8604 (mmm) cc_final: 0.8371 (tpt) REVERT: D 420 GLU cc_start: 0.8550 (pp20) cc_final: 0.8224 (pp20) REVERT: D 422 GLU cc_start: 0.8128 (tp30) cc_final: 0.7714 (tp30) REVERT: D 427 ASP cc_start: 0.7993 (m-30) cc_final: 0.7636 (m-30) REVERT: C 77 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7845 (tm-30) REVERT: C 103 TYR cc_start: 0.8714 (t80) cc_final: 0.8492 (t80) REVERT: C 115 ILE cc_start: 0.8320 (tp) cc_final: 0.8108 (tp) REVERT: C 377 MET cc_start: 0.8534 (ttp) cc_final: 0.8218 (ttp) REVERT: C 417 GLU cc_start: 0.8253 (tp30) cc_final: 0.7889 (tp30) REVERT: C 420 GLU cc_start: 0.8188 (pt0) cc_final: 0.7840 (pt0) REVERT: C 423 GLU cc_start: 0.8130 (pp20) cc_final: 0.7756 (pp20) REVERT: C 430 LYS cc_start: 0.8659 (tppp) cc_final: 0.8457 (mmmm) REVERT: C 434 GLU cc_start: 0.8214 (pp20) cc_final: 0.7862 (pp20) REVERT: F 47 GLU cc_start: 0.7924 (tp30) cc_final: 0.7588 (tp30) REVERT: F 113 GLU cc_start: 0.8272 (tp30) cc_final: 0.7872 (tp30) REVERT: F 127 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7997 (mm-30) REVERT: F 193 GLN cc_start: 0.7835 (mt0) cc_final: 0.7332 (mt0) REVERT: F 215 ARG cc_start: 0.8950 (mtm-85) cc_final: 0.8279 (mtm110) REVERT: F 235 MET cc_start: 0.8518 (mtt) cc_final: 0.8307 (mtp) REVERT: F 282 GLN cc_start: 0.8480 (pm20) cc_final: 0.8158 (pm20) REVERT: F 299 LYS cc_start: 0.8684 (tptp) cc_final: 0.7944 (tptp) REVERT: F 325 MET cc_start: 0.8611 (mmp) cc_final: 0.8049 (mmp) REVERT: F 345 GLU cc_start: 0.8058 (pp20) cc_final: 0.7826 (tp30) REVERT: F 372 LYS cc_start: 0.8658 (pptt) cc_final: 0.8453 (pptt) REVERT: F 427 ASP cc_start: 0.8122 (m-30) cc_final: 0.7700 (m-30) REVERT: F 433 GLN cc_start: 0.8284 (tp40) cc_final: 0.8075 (tp-100) REVERT: E 24 TYR cc_start: 0.8883 (m-10) cc_final: 0.8594 (m-10) REVERT: E 77 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7944 (mm-30) REVERT: E 113 GLU cc_start: 0.7680 (pp20) cc_final: 0.7426 (pp20) REVERT: E 178 SER cc_start: 0.7884 (p) cc_final: 0.7210 (p) REVERT: E 322 ASP cc_start: 0.8565 (t70) cc_final: 0.8280 (t0) REVERT: E 392 ASP cc_start: 0.8602 (m-30) cc_final: 0.8311 (m-30) REVERT: E 434 GLU cc_start: 0.8346 (pp20) cc_final: 0.7948 (pp20) REVERT: H 1 MET cc_start: 0.7999 (ttm) cc_final: 0.7632 (ttm) REVERT: H 3 GLU cc_start: 0.7260 (mp0) cc_final: 0.6805 (mp0) REVERT: H 26 ASP cc_start: 0.8794 (t70) cc_final: 0.8461 (t0) REVERT: H 47 GLU cc_start: 0.7408 (pp20) cc_final: 0.7174 (pp20) REVERT: H 50 ASN cc_start: 0.8832 (p0) cc_final: 0.8480 (p0) REVERT: H 76 ASP cc_start: 0.8989 (t0) cc_final: 0.8668 (t0) REVERT: H 105 LYS cc_start: 0.9202 (mtpp) cc_final: 0.8840 (mtpp) REVERT: H 156 LYS cc_start: 0.8439 (mmtp) cc_final: 0.7948 (mmtp) REVERT: H 159 GLU cc_start: 0.8113 (mp0) cc_final: 0.7835 (pm20) REVERT: H 199 ASP cc_start: 0.8504 (m-30) cc_final: 0.8182 (m-30) REVERT: H 241 CYS cc_start: 0.8935 (m) cc_final: 0.8714 (m) REVERT: H 259 MET cc_start: 0.8668 (mtp) cc_final: 0.8336 (mtm) REVERT: H 293 GLN cc_start: 0.7939 (pp30) cc_final: 0.7693 (pp30) REVERT: H 325 MET cc_start: 0.8041 (mmm) cc_final: 0.7778 (mmm) REVERT: H 337 ASN cc_start: 0.8383 (m110) cc_final: 0.7941 (m110) REVERT: H 345 GLU cc_start: 0.8218 (tm-30) cc_final: 0.8006 (tm-30) REVERT: H 349 ASN cc_start: 0.6558 (t0) cc_final: 0.6337 (t0) REVERT: H 422 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7730 (tp30) REVERT: H 427 ASP cc_start: 0.8349 (m-30) cc_final: 0.7943 (m-30) REVERT: G 205 ASP cc_start: 0.8520 (p0) cc_final: 0.7938 (p0) REVERT: G 255 PHE cc_start: 0.8029 (t80) cc_final: 0.7533 (t80) REVERT: G 396 ASP cc_start: 0.8525 (m-30) cc_final: 0.8321 (m-30) REVERT: G 423 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7748 (tm-30) REVERT: G 425 MET cc_start: 0.8828 (mmm) cc_final: 0.8516 (tpp) REVERT: G 430 LYS cc_start: 0.8294 (tppp) cc_final: 0.8078 (tppp) REVERT: G 433 GLU cc_start: 0.8171 (tp30) cc_final: 0.7719 (tp30) REVERT: G 434 GLU cc_start: 0.8254 (pp20) cc_final: 0.7773 (pp20) REVERT: J 3 GLU cc_start: 0.7739 (mp0) cc_final: 0.6980 (mp0) REVERT: J 26 ASP cc_start: 0.8308 (t0) cc_final: 0.8076 (t0) REVERT: J 60 LYS cc_start: 0.8332 (tppp) cc_final: 0.7899 (ttmm) REVERT: J 127 GLU cc_start: 0.7576 (pm20) cc_final: 0.7335 (pm20) REVERT: J 166 MET cc_start: 0.8596 (tpp) cc_final: 0.8331 (tpt) REVERT: J 330 GLU cc_start: 0.7940 (pp20) cc_final: 0.7357 (pp20) REVERT: J 338 LYS cc_start: 0.8939 (mmmt) cc_final: 0.8738 (mmmt) REVERT: I 71 GLU cc_start: 0.7711 (pt0) cc_final: 0.7342 (pm20) REVERT: I 154 MET cc_start: 0.8940 (mmt) cc_final: 0.8519 (mmm) REVERT: I 155 GLU cc_start: 0.8327 (mp0) cc_final: 0.7831 (mp0) REVERT: I 249 ASN cc_start: 0.8577 (m-40) cc_final: 0.8362 (m-40) REVERT: I 414 GLU cc_start: 0.8314 (mp0) cc_final: 0.8088 (mp0) REVERT: I 423 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7587 (tm-30) REVERT: I 434 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7841 (mt-10) REVERT: L 71 GLU cc_start: 0.7894 (mp0) cc_final: 0.7550 (mp0) REVERT: L 105 LYS cc_start: 0.8993 (ptmt) cc_final: 0.8615 (ptmm) REVERT: L 113 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7980 (tm-30) REVERT: L 203 CYS cc_start: 0.8856 (t) cc_final: 0.8377 (t) REVERT: L 218 LYS cc_start: 0.9100 (mmtp) cc_final: 0.8662 (mmmm) REVERT: L 281 GLN cc_start: 0.8662 (tm-30) cc_final: 0.7984 (tm-30) REVERT: L 299 LYS cc_start: 0.8746 (tppp) cc_final: 0.8243 (tppp) REVERT: L 323 MET cc_start: 0.8557 (mtp) cc_final: 0.8321 (mtp) REVERT: L 393 GLU cc_start: 0.8390 (pp20) cc_final: 0.7997 (pp20) REVERT: L 433 GLN cc_start: 0.8794 (tp40) cc_final: 0.8465 (tp-100) REVERT: K 24 TYR cc_start: 0.8852 (m-10) cc_final: 0.8554 (m-10) REVERT: K 77 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8224 (mm-30) REVERT: K 96 LYS cc_start: 0.8824 (mmtp) cc_final: 0.8497 (mmtp) REVERT: K 176 GLN cc_start: 0.8915 (mp10) cc_final: 0.8628 (mp10) REVERT: K 433 GLU cc_start: 0.8463 (tp30) cc_final: 0.8203 (tp30) REVERT: K 434 GLU cc_start: 0.8321 (pp20) cc_final: 0.7869 (pp20) REVERT: N 1 MET cc_start: 0.8378 (tpt) cc_final: 0.7719 (tpp) REVERT: N 22 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7970 (tm-30) REVERT: N 50 ASN cc_start: 0.8503 (p0) cc_final: 0.7996 (p0) REVERT: N 59 ASN cc_start: 0.8461 (t0) cc_final: 0.8103 (t0) REVERT: N 60 LYS cc_start: 0.4647 (pttp) cc_final: 0.4423 (pttt) REVERT: N 88 ARG cc_start: 0.6362 (mmp-170) cc_final: 0.5536 (mmp-170) REVERT: N 249 ASN cc_start: 0.8411 (m-40) cc_final: 0.8175 (m-40) REVERT: N 269 MET cc_start: 0.8295 (ttm) cc_final: 0.7997 (mtt) REVERT: N 345 GLU cc_start: 0.8351 (pm20) cc_final: 0.8046 (pm20) REVERT: N 346 TRP cc_start: 0.9277 (p-90) cc_final: 0.9031 (p-90) REVERT: N 349 ASN cc_start: 0.7808 (OUTLIER) cc_final: 0.7572 (p0) REVERT: N 373 MET cc_start: 0.9320 (ptp) cc_final: 0.9046 (ptm) REVERT: N 422 GLU cc_start: 0.8266 (tp30) cc_final: 0.7671 (tp30) REVERT: M 112 LYS cc_start: 0.8309 (pttm) cc_final: 0.8046 (pttm) REVERT: M 123 ARG cc_start: 0.9031 (tmm-80) cc_final: 0.8796 (tmm-80) REVERT: M 220 GLU cc_start: 0.6938 (pp20) cc_final: 0.6453 (pp20) REVERT: M 221 ARG cc_start: 0.8156 (ptp-110) cc_final: 0.7560 (mtm-85) REVERT: M 285 GLN cc_start: 0.8502 (tt0) cc_final: 0.8241 (tt0) REVERT: M 326 LYS cc_start: 0.5781 (mmpt) cc_final: 0.4804 (mptm) REVERT: M 420 GLU cc_start: 0.8068 (pp20) cc_final: 0.7811 (pp20) REVERT: M 423 GLU cc_start: 0.8344 (pp20) cc_final: 0.8025 (pp20) REVERT: M 430 LYS cc_start: 0.8668 (mmmt) cc_final: 0.8121 (mmmm) REVERT: M 433 GLU cc_start: 0.7809 (pm20) cc_final: 0.7246 (pm20) REVERT: P 26 ASP cc_start: 0.8517 (t0) cc_final: 0.8188 (t0) REVERT: P 159 GLU cc_start: 0.7948 (pm20) cc_final: 0.7580 (pm20) REVERT: P 293 GLN cc_start: 0.8378 (pp30) cc_final: 0.7980 (pp30) REVERT: P 393 GLU cc_start: 0.8468 (pp20) cc_final: 0.8233 (pp20) REVERT: O 77 GLU cc_start: 0.8159 (pm20) cc_final: 0.7916 (mp0) REVERT: O 123 ARG cc_start: 0.8943 (tmm-80) cc_final: 0.8544 (tmm-80) REVERT: O 205 ASP cc_start: 0.8187 (t0) cc_final: 0.7899 (t70) REVERT: O 326 LYS cc_start: 0.5523 (mmtp) cc_final: 0.5152 (mmtp) REVERT: O 430 LYS cc_start: 0.8613 (tppp) cc_final: 0.8297 (tppp) REVERT: O 434 GLU cc_start: 0.8365 (pp20) cc_final: 0.8017 (pp20) REVERT: R 47 GLU cc_start: 0.7590 (pp20) cc_final: 0.7363 (tm-30) REVERT: R 60 LYS cc_start: 0.8153 (ptpt) cc_final: 0.7942 (ptpp) REVERT: R 71 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8027 (mp0) REVERT: R 76 ASP cc_start: 0.8635 (t0) cc_final: 0.8345 (t0) REVERT: R 113 GLU cc_start: 0.8295 (tp30) cc_final: 0.8088 (tp30) REVERT: R 116 ASP cc_start: 0.8443 (t70) cc_final: 0.8163 (t0) REVERT: R 159 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7945 (tm-30) REVERT: R 235 MET cc_start: 0.8695 (mtp) cc_final: 0.8436 (mtp) REVERT: R 259 MET cc_start: 0.8822 (mtp) cc_final: 0.8411 (mtt) REVERT: R 281 GLN cc_start: 0.8592 (tp40) cc_final: 0.8164 (tp40) REVERT: R 301 MET cc_start: 0.9302 (mmt) cc_final: 0.9063 (mmp) REVERT: R 349 ASN cc_start: 0.7371 (t0) cc_final: 0.6970 (t0) REVERT: R 387 LEU cc_start: 0.8934 (tt) cc_final: 0.8725 (tt) REVERT: R 393 GLU cc_start: 0.8131 (pp20) cc_final: 0.7868 (pp20) REVERT: R 427 ASP cc_start: 0.8469 (m-30) cc_final: 0.8049 (m-30) REVERT: Q 77 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8437 (tm-30) REVERT: Q 128 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7982 (tm-30) REVERT: Q 313 MET cc_start: 0.8791 (mtm) cc_final: 0.8199 (mtp) REVERT: Q 386 GLU cc_start: 0.8199 (mp0) cc_final: 0.7679 (mp0) REVERT: Q 397 LEU cc_start: 0.9384 (tt) cc_final: 0.8702 (tm) REVERT: Q 430 LYS cc_start: 0.8880 (tppt) cc_final: 0.8608 (tppp) REVERT: Q 433 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7920 (tp30) REVERT: t 93 MET cc_start: 0.8691 (tpt) cc_final: 0.8259 (tpt) REVERT: t 127 MET cc_start: 0.7964 (mmp) cc_final: 0.7683 (mmp) REVERT: v 127 MET cc_start: 0.8105 (mmp) cc_final: 0.7543 (mmp) REVERT: w 93 MET cc_start: 0.8707 (tpt) cc_final: 0.8373 (tpt) REVERT: x 93 MET cc_start: 0.7374 (mmt) cc_final: 0.7099 (mmt) REVERT: x 127 MET cc_start: 0.8186 (tpt) cc_final: 0.7728 (tpt) REVERT: y 127 MET cc_start: 0.8280 (mmp) cc_final: 0.7889 (mmp) REVERT: z 93 MET cc_start: 0.8488 (tpp) cc_final: 0.8019 (tpp) REVERT: z 127 MET cc_start: 0.7946 (mmp) cc_final: 0.7627 (mmp) outliers start: 2 outliers final: 1 residues processed: 1359 average time/residue: 1.8766 time to fit residues: 3126.5168 Evaluate side-chains 1146 residues out of total 6966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1143 time to evaluate : 5.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 192 HIS Chi-restraints excluded: chain K residue 245 ASP Chi-restraints excluded: chain N residue 349 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 801 random chunks: chunk 676 optimal weight: 0.4980 chunk 607 optimal weight: 0.9980 chunk 336 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 409 optimal weight: 7.9990 chunk 324 optimal weight: 4.9990 chunk 627 optimal weight: 2.9990 chunk 242 optimal weight: 0.5980 chunk 381 optimal weight: 4.9990 chunk 467 optimal weight: 3.9990 chunk 727 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN B 433 GLN A 50 ASN A 61 HIS ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 ASN C 256 GLN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 HIS F 293 GLN F 334 ASN E 249 ASN E 256 GLN E 342 GLN H 192 HIS H 197 ASN H 258 ASN ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN G 101 ASN G 133 GLN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 300 ASN ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 101 ASN ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 GLN I 50 ASN I 88 HIS I 266 HIS ** L 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 133 GLN L 136 GLN L 293 GLN L 334 ASN K 107 HIS K 266 HIS K 380 ASN ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 349 ASN ** N 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 102 ASN O 133 GLN O 372 GLN ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 258 ASN R 293 GLN R 334 ASN R 433 GLN Q 249 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.100140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.085499 restraints weight = 120058.298| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.39 r_work: 0.3521 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 65970 Z= 0.214 Angle : 0.615 11.409 89469 Z= 0.316 Chirality : 0.045 0.182 9711 Planarity : 0.004 0.052 11637 Dihedral : 11.127 178.202 9258 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.55 % Allowed : 10.50 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.40 (0.09), residues: 8055 helix: 1.19 (0.09), residues: 3654 sheet: 0.05 (0.15), residues: 1170 loop : -0.64 (0.11), residues: 3231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 346 HIS 0.011 0.001 HIS Q 88 PHE 0.035 0.001 PHE K 255 TYR 0.018 0.001 TYR E 172 ARG 0.010 0.001 ARG H 400 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16110 Ramachandran restraints generated. 8055 Oldfield, 0 Emsley, 8055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16110 Ramachandran restraints generated. 8055 Oldfield, 0 Emsley, 8055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1305 residues out of total 6966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 1198 time to evaluate : 5.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: r 122 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7146 (ptm-80) REVERT: r 127 MET cc_start: 0.8371 (mmp) cc_final: 0.7923 (mmp) REVERT: B 47 GLU cc_start: 0.8617 (tp30) cc_final: 0.7896 (tp30) REVERT: B 76 ASP cc_start: 0.8909 (t0) cc_final: 0.8404 (p0) REVERT: B 116 ASP cc_start: 0.8272 (m-30) cc_final: 0.7481 (m-30) REVERT: B 120 ASP cc_start: 0.8168 (m-30) cc_final: 0.7961 (m-30) REVERT: B 196 GLU cc_start: 0.8597 (pt0) cc_final: 0.8374 (pt0) REVERT: B 283 TYR cc_start: 0.8313 (m-10) cc_final: 0.7744 (m-10) REVERT: B 422 GLU cc_start: 0.8142 (tp30) cc_final: 0.7784 (tp30) REVERT: A 112 LYS cc_start: 0.8446 (pttt) cc_final: 0.8202 (pttt) REVERT: A 113 GLU cc_start: 0.7911 (mp0) cc_final: 0.7630 (mp0) REVERT: A 423 GLU cc_start: 0.8297 (tm-30) cc_final: 0.8071 (pp20) REVERT: D 41 ASP cc_start: 0.8277 (t70) cc_final: 0.7953 (t70) REVERT: D 47 GLU cc_start: 0.7958 (pp20) cc_final: 0.7466 (pp20) REVERT: D 50 ASN cc_start: 0.8846 (p0) cc_final: 0.8366 (p0) REVERT: D 71 GLU cc_start: 0.8494 (tp30) cc_final: 0.8232 (tp30) REVERT: D 159 GLU cc_start: 0.8546 (mt-10) cc_final: 0.7944 (mt-10) REVERT: D 247 GLN cc_start: 0.8634 (mp10) cc_final: 0.8398 (mp10) REVERT: D 281 GLN cc_start: 0.8630 (pp30) cc_final: 0.8386 (pp30) REVERT: D 329 ASP cc_start: 0.8399 (m-30) cc_final: 0.7873 (t70) REVERT: D 330 GLU cc_start: 0.8258 (mp0) cc_final: 0.8034 (pm20) REVERT: D 345 GLU cc_start: 0.8481 (pm20) cc_final: 0.8231 (pm20) REVERT: D 349 ASN cc_start: 0.6404 (t0) cc_final: 0.6181 (t0) REVERT: D 352 LYS cc_start: 0.8503 (tptp) cc_final: 0.8249 (tptt) REVERT: D 416 MET cc_start: 0.8633 (mmm) cc_final: 0.8428 (tpt) REVERT: D 422 GLU cc_start: 0.8064 (tp30) cc_final: 0.7472 (tp30) REVERT: D 427 ASP cc_start: 0.8239 (m-30) cc_final: 0.7709 (m-30) REVERT: D 433 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8292 (tm-30) REVERT: C 77 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8153 (tm-30) REVERT: C 103 TYR cc_start: 0.8727 (t80) cc_final: 0.8127 (t80) REVERT: C 115 ILE cc_start: 0.8238 (tp) cc_final: 0.8031 (tp) REVERT: C 116 ASP cc_start: 0.8537 (p0) cc_final: 0.8319 (p0) REVERT: C 196 GLU cc_start: 0.8210 (mp0) cc_final: 0.7829 (pm20) REVERT: C 417 GLU cc_start: 0.8277 (tp30) cc_final: 0.7918 (tp30) REVERT: C 420 GLU cc_start: 0.8309 (pt0) cc_final: 0.7992 (pt0) REVERT: C 423 GLU cc_start: 0.8385 (pp20) cc_final: 0.8003 (pp20) REVERT: C 434 GLU cc_start: 0.8343 (pp20) cc_final: 0.7977 (pp20) REVERT: F 47 GLU cc_start: 0.8303 (tp30) cc_final: 0.7808 (tp30) REVERT: F 105 LYS cc_start: 0.9186 (mtmt) cc_final: 0.8800 (mtpp) REVERT: F 113 GLU cc_start: 0.8644 (tp30) cc_final: 0.8189 (tp30) REVERT: F 127 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8296 (mm-30) REVERT: F 282 GLN cc_start: 0.8622 (pm20) cc_final: 0.8335 (pm20) REVERT: F 325 MET cc_start: 0.8808 (mmp) cc_final: 0.8503 (mmp) REVERT: F 345 GLU cc_start: 0.8270 (pp20) cc_final: 0.7964 (tp30) REVERT: F 372 LYS cc_start: 0.8874 (pptt) cc_final: 0.8502 (pptt) REVERT: F 398 MET cc_start: 0.9011 (mtm) cc_final: 0.8787 (mtm) REVERT: F 427 ASP cc_start: 0.8289 (m-30) cc_final: 0.7917 (m-30) REVERT: E 24 TYR cc_start: 0.8856 (m-10) cc_final: 0.8575 (m-10) REVERT: E 245 ASP cc_start: 0.8702 (p0) cc_final: 0.8244 (p0) REVERT: E 309 HIS cc_start: 0.8528 (m90) cc_final: 0.7912 (m170) REVERT: E 322 ASP cc_start: 0.8840 (t70) cc_final: 0.8575 (t0) REVERT: E 392 ASP cc_start: 0.8693 (m-30) cc_final: 0.8432 (m-30) REVERT: E 413 MET cc_start: 0.7295 (ttt) cc_final: 0.7023 (ttt) REVERT: E 417 GLU cc_start: 0.8246 (tp30) cc_final: 0.8027 (tp30) REVERT: E 433 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8030 (tm-30) REVERT: E 434 GLU cc_start: 0.8373 (pp20) cc_final: 0.7976 (pp20) REVERT: H 1 MET cc_start: 0.8254 (ttm) cc_final: 0.7468 (ttt) REVERT: H 3 GLU cc_start: 0.7890 (mp0) cc_final: 0.7351 (mp0) REVERT: H 26 ASP cc_start: 0.8909 (t70) cc_final: 0.8578 (t0) REVERT: H 47 GLU cc_start: 0.7781 (pp20) cc_final: 0.7488 (pp20) REVERT: H 50 ASN cc_start: 0.8971 (p0) cc_final: 0.8627 (p0) REVERT: H 76 ASP cc_start: 0.9157 (t0) cc_final: 0.8846 (t0) REVERT: H 105 LYS cc_start: 0.9249 (mtpp) cc_final: 0.8914 (mtpp) REVERT: H 156 LYS cc_start: 0.8704 (mmtp) cc_final: 0.8247 (mmtp) REVERT: H 159 GLU cc_start: 0.8112 (mp0) cc_final: 0.7589 (mp0) REVERT: H 166 MET cc_start: 0.8045 (tpp) cc_final: 0.7687 (tpp) REVERT: H 199 ASP cc_start: 0.8654 (m-30) cc_final: 0.8269 (m-30) REVERT: H 241 CYS cc_start: 0.8945 (m) cc_final: 0.8708 (m) REVERT: H 325 MET cc_start: 0.7893 (mmm) cc_final: 0.7682 (mmm) REVERT: H 337 ASN cc_start: 0.8638 (m110) cc_final: 0.8145 (m110) REVERT: H 338 LYS cc_start: 0.9020 (ptmm) cc_final: 0.8651 (ptmm) REVERT: H 416 MET cc_start: 0.8268 (tpp) cc_final: 0.7965 (mmm) REVERT: H 422 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7850 (tp30) REVERT: H 427 ASP cc_start: 0.8466 (m-30) cc_final: 0.8089 (m-30) REVERT: G 123 ARG cc_start: 0.8946 (tmm-80) cc_final: 0.8661 (tmm-80) REVERT: G 211 ASP cc_start: 0.8825 (t0) cc_final: 0.8416 (t0) REVERT: G 255 PHE cc_start: 0.7959 (t80) cc_final: 0.7498 (t80) REVERT: G 342 GLN cc_start: 0.8171 (mp10) cc_final: 0.7969 (mp10) REVERT: G 423 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8063 (tm-30) REVERT: G 425 MET cc_start: 0.8811 (mmm) cc_final: 0.8536 (tpp) REVERT: G 433 GLU cc_start: 0.8525 (tp30) cc_final: 0.8037 (tp30) REVERT: G 434 GLU cc_start: 0.8352 (pp20) cc_final: 0.7916 (pp20) REVERT: J 3 GLU cc_start: 0.8036 (mp0) cc_final: 0.7286 (mp0) REVERT: J 26 ASP cc_start: 0.8539 (t0) cc_final: 0.8230 (t0) REVERT: J 127 GLU cc_start: 0.7824 (pm20) cc_final: 0.7471 (mp0) REVERT: J 163 ASP cc_start: 0.8489 (p0) cc_final: 0.8239 (p0) REVERT: J 167 ASN cc_start: 0.8867 (m-40) cc_final: 0.8433 (m-40) REVERT: J 207 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8585 (mm-30) REVERT: J 281 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8285 (tm-30) REVERT: J 286 LEU cc_start: 0.9295 (tp) cc_final: 0.9077 (tm) REVERT: J 330 GLU cc_start: 0.7955 (pp20) cc_final: 0.7725 (pp20) REVERT: I 71 GLU cc_start: 0.7723 (pt0) cc_final: 0.7397 (pm20) REVERT: I 76 ASP cc_start: 0.8236 (m-30) cc_final: 0.7887 (m-30) REVERT: I 128 GLN cc_start: 0.8978 (tt0) cc_final: 0.8450 (tm-30) REVERT: I 154 MET cc_start: 0.8983 (mmt) cc_final: 0.8688 (mmm) REVERT: I 211 ASP cc_start: 0.8774 (t0) cc_final: 0.8390 (t0) REVERT: I 251 ASP cc_start: 0.7546 (t0) cc_final: 0.7078 (t70) REVERT: I 423 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7913 (tm-30) REVERT: I 430 LYS cc_start: 0.8553 (mmmm) cc_final: 0.7963 (mmmm) REVERT: I 434 GLU cc_start: 0.8452 (mt-10) cc_final: 0.7953 (mt-10) REVERT: L 1 MET cc_start: 0.9017 (mmm) cc_final: 0.8486 (tpt) REVERT: L 55 GLU cc_start: 0.8107 (tp30) cc_final: 0.7800 (tp30) REVERT: L 71 GLU cc_start: 0.7980 (mp0) cc_final: 0.7595 (mp0) REVERT: L 113 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8416 (tm-30) REVERT: L 133 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7500 (pp30) REVERT: L 203 CYS cc_start: 0.9176 (t) cc_final: 0.8672 (p) REVERT: L 207 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8149 (tp30) REVERT: L 214 PHE cc_start: 0.8462 (m-80) cc_final: 0.8211 (m-80) REVERT: L 247 GLN cc_start: 0.8252 (mp10) cc_final: 0.8020 (mp10) REVERT: L 393 GLU cc_start: 0.8599 (pp20) cc_final: 0.8299 (pp20) REVERT: L 433 GLN cc_start: 0.8881 (tp40) cc_final: 0.8620 (tp-100) REVERT: K 24 TYR cc_start: 0.8886 (m-10) cc_final: 0.8620 (m-10) REVERT: K 96 LYS cc_start: 0.9061 (mmtp) cc_final: 0.8740 (mmtm) REVERT: K 133 GLN cc_start: 0.8444 (mm-40) cc_final: 0.8111 (mm-40) REVERT: K 176 GLN cc_start: 0.8959 (mp10) cc_final: 0.8698 (mp10) REVERT: K 251 ASP cc_start: 0.7376 (t0) cc_final: 0.6896 (t0) REVERT: K 277 SER cc_start: 0.8943 (m) cc_final: 0.8442 (p) REVERT: K 279 GLU cc_start: 0.8211 (pm20) cc_final: 0.7996 (pm20) REVERT: K 433 GLU cc_start: 0.8638 (tp30) cc_final: 0.8418 (tp30) REVERT: K 434 GLU cc_start: 0.8413 (pp20) cc_final: 0.7982 (pp20) REVERT: N 1 MET cc_start: 0.8417 (tpt) cc_final: 0.7776 (tpp) REVERT: N 22 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8170 (tm-30) REVERT: N 50 ASN cc_start: 0.8709 (p0) cc_final: 0.8270 (p0) REVERT: N 59 ASN cc_start: 0.8705 (t0) cc_final: 0.8459 (t0) REVERT: N 60 LYS cc_start: 0.4670 (pttp) cc_final: 0.4151 (pttt) REVERT: N 88 ARG cc_start: 0.6696 (mmp-170) cc_final: 0.5629 (mmp-170) REVERT: N 110 GLU cc_start: 0.7938 (mp0) cc_final: 0.7652 (mp0) REVERT: N 127 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8503 (mm-30) REVERT: N 281 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8682 (tm-30) REVERT: N 293 GLN cc_start: 0.8371 (pp30) cc_final: 0.8169 (pp30) REVERT: N 345 GLU cc_start: 0.8670 (pm20) cc_final: 0.8348 (pm20) REVERT: N 373 MET cc_start: 0.9327 (ptp) cc_final: 0.8970 (ptm) REVERT: N 422 GLU cc_start: 0.8331 (tp30) cc_final: 0.7756 (tp30) REVERT: M 155 GLU cc_start: 0.8601 (pp20) cc_final: 0.8216 (pp20) REVERT: M 203 MET cc_start: 0.9096 (mmm) cc_final: 0.8851 (mmm) REVERT: M 220 GLU cc_start: 0.7499 (pp20) cc_final: 0.7051 (pp20) REVERT: M 221 ARG cc_start: 0.8455 (ptp-110) cc_final: 0.8116 (ptp-110) REVERT: M 285 GLN cc_start: 0.8425 (tt0) cc_final: 0.8122 (tt0) REVERT: M 377 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8526 (ttm) REVERT: M 420 GLU cc_start: 0.8171 (pp20) cc_final: 0.7694 (pp20) REVERT: M 423 GLU cc_start: 0.8473 (pp20) cc_final: 0.8226 (pp20) REVERT: M 430 LYS cc_start: 0.8775 (mmmt) cc_final: 0.8065 (mmmm) REVERT: M 433 GLU cc_start: 0.8129 (pm20) cc_final: 0.7806 (pm20) REVERT: M 434 GLU cc_start: 0.8398 (pp20) cc_final: 0.8188 (pp20) REVERT: M 437 VAL cc_start: 0.9405 (p) cc_final: 0.9079 (m) REVERT: P 26 ASP cc_start: 0.8621 (t0) cc_final: 0.8271 (t0) REVERT: P 127 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8285 (mm-30) REVERT: P 133 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8465 (pt0) REVERT: P 259 MET cc_start: 0.8553 (mtp) cc_final: 0.8319 (mtm) REVERT: P 293 GLN cc_start: 0.8436 (pp30) cc_final: 0.8111 (pp30) REVERT: P 330 GLU cc_start: 0.7789 (tp30) cc_final: 0.7461 (tp30) REVERT: P 337 ASN cc_start: 0.8907 (m110) cc_final: 0.8692 (m-40) REVERT: P 338 LYS cc_start: 0.8884 (mptp) cc_final: 0.8665 (mtmm) REVERT: P 422 GLU cc_start: 0.8135 (tp30) cc_final: 0.7802 (tp30) REVERT: O 71 GLU cc_start: 0.7101 (pm20) cc_final: 0.6727 (mp0) REVERT: O 77 GLU cc_start: 0.8231 (pm20) cc_final: 0.7627 (pm20) REVERT: O 123 ARG cc_start: 0.9213 (tmm-80) cc_final: 0.8806 (ttp80) REVERT: O 154 MET cc_start: 0.9057 (mmm) cc_final: 0.8751 (mmm) REVERT: O 205 ASP cc_start: 0.8016 (t0) cc_final: 0.7806 (t70) REVERT: O 211 ASP cc_start: 0.8592 (t0) cc_final: 0.8381 (t0) REVERT: O 326 LYS cc_start: 0.5681 (mmtp) cc_final: 0.5078 (mmtm) REVERT: O 425 MET cc_start: 0.8751 (mmt) cc_final: 0.8487 (mmm) REVERT: O 430 LYS cc_start: 0.8804 (tppp) cc_final: 0.8494 (tppp) REVERT: O 438 ASP cc_start: 0.8665 (t0) cc_final: 0.8209 (t0) REVERT: R 47 GLU cc_start: 0.7768 (pp20) cc_final: 0.7452 (tm-30) REVERT: R 71 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8143 (mp0) REVERT: R 76 ASP cc_start: 0.8745 (t0) cc_final: 0.8398 (t0) REVERT: R 113 GLU cc_start: 0.8723 (tp30) cc_final: 0.8431 (tp30) REVERT: R 127 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7988 (mm-30) REVERT: R 183 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7856 (mt-10) REVERT: R 259 MET cc_start: 0.8793 (mtp) cc_final: 0.8534 (mtt) REVERT: R 281 GLN cc_start: 0.8880 (tp40) cc_final: 0.8505 (tp40) REVERT: R 301 MET cc_start: 0.9231 (mmt) cc_final: 0.9030 (mmp) REVERT: R 349 ASN cc_start: 0.7686 (t0) cc_final: 0.7262 (t0) REVERT: R 393 GLU cc_start: 0.8359 (pp20) cc_final: 0.8150 (pp20) REVERT: R 427 ASP cc_start: 0.8567 (m-30) cc_final: 0.8176 (m-30) REVERT: Q 77 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8651 (tm-30) REVERT: Q 128 GLN cc_start: 0.8284 (tm-30) cc_final: 0.8036 (tm-30) REVERT: Q 205 ASP cc_start: 0.8012 (m-30) cc_final: 0.7533 (p0) REVERT: Q 302 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8364 (mtm) REVERT: Q 339 ARG cc_start: 0.7986 (tmm160) cc_final: 0.7697 (tmm160) REVERT: Q 357 TYR cc_start: 0.8729 (m-80) cc_final: 0.8525 (m-80) REVERT: Q 377 MET cc_start: 0.9016 (ttp) cc_final: 0.8804 (ttp) REVERT: Q 386 GLU cc_start: 0.8208 (mp0) cc_final: 0.7939 (mp0) REVERT: Q 396 ASP cc_start: 0.8598 (p0) cc_final: 0.8125 (p0) REVERT: Q 397 LEU cc_start: 0.9108 (tt) cc_final: 0.8855 (tm) REVERT: Q 423 GLU cc_start: 0.8788 (pp20) cc_final: 0.8530 (pp20) REVERT: Q 430 LYS cc_start: 0.8942 (tppt) cc_final: 0.8631 (tppp) REVERT: Q 433 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8057 (tp30) REVERT: Q 434 GLU cc_start: 0.8447 (pp20) cc_final: 0.8191 (pp20) REVERT: s 127 MET cc_start: 0.8137 (tpt) cc_final: 0.7730 (tpt) REVERT: t 93 MET cc_start: 0.8866 (tpt) cc_final: 0.8399 (tpt) REVERT: t 127 MET cc_start: 0.8070 (mmp) cc_final: 0.7812 (mmp) REVERT: v 127 MET cc_start: 0.8261 (mmp) cc_final: 0.7680 (mmp) REVERT: w 93 MET cc_start: 0.8774 (tpt) cc_final: 0.8458 (tpt) REVERT: x 93 MET cc_start: 0.7494 (mmt) cc_final: 0.7220 (mmt) REVERT: x 127 MET cc_start: 0.8375 (tpt) cc_final: 0.7915 (tpt) REVERT: y 127 MET cc_start: 0.8498 (mmp) cc_final: 0.8083 (mmp) REVERT: z 93 MET cc_start: 0.8644 (tpp) cc_final: 0.8282 (tpp) REVERT: z 97 TYR cc_start: 0.8405 (t80) cc_final: 0.7634 (t80) REVERT: z 127 MET cc_start: 0.8186 (mmp) cc_final: 0.7838 (mmp) outliers start: 107 outliers final: 32 residues processed: 1232 average time/residue: 1.8147 time to fit residues: 2761.6031 Evaluate side-chains 1167 residues out of total 6966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 1130 time to evaluate : 5.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain r residue 122 ARG Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 432 TYR Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 269 LEU Chi-restraints excluded: chain J residue 333 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 370 LYS Chi-restraints excluded: chain L residue 133 GLN Chi-restraints excluded: chain L residue 427 ASP Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain N residue 129 CYS Chi-restraints excluded: chain N residue 286 LEU Chi-restraints excluded: chain N residue 333 LEU Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 377 MET Chi-restraints excluded: chain P residue 133 GLN Chi-restraints excluded: chain P residue 389 LYS Chi-restraints excluded: chain P residue 405 LEU Chi-restraints excluded: chain R residue 241 CYS Chi-restraints excluded: chain R residue 332 MET Chi-restraints excluded: chain Q residue 302 MET Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain s residue 120 VAL Chi-restraints excluded: chain v residue 120 VAL Chi-restraints excluded: chain x residue 122 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 801 random chunks: chunk 378 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 233 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 780 optimal weight: 0.5980 chunk 671 optimal weight: 9.9990 chunk 412 optimal weight: 4.9990 chunk 299 optimal weight: 6.9990 chunk 432 optimal weight: 0.0970 chunk 414 optimal weight: 0.7980 chunk 218 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS B 133 GLN ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 HIS ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 GLN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 GLN F 192 HIS F 193 GLN F 293 GLN F 334 ASN F 350 ASN F 433 GLN E 249 ASN H 85 GLN H 133 GLN H 192 HIS ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 339 ASN ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN G 15 GLN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 133 GLN ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 433 GLN I 88 HIS I 107 HIS ** L 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 133 GLN L 334 ASN ** L 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 91 GLN M 249 ASN P 336 GLN P 349 ASN O 133 GLN ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 293 GLN R 294 GLN R 334 ASN ** R 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 426 ASN Q 88 HIS Q 249 ASN Q 256 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.100999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.086645 restraints weight = 119460.397| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.39 r_work: 0.3546 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 65970 Z= 0.176 Angle : 0.579 9.828 89469 Z= 0.297 Chirality : 0.044 0.170 9711 Planarity : 0.004 0.057 11637 Dihedral : 10.920 176.506 9252 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.92 % Allowed : 13.35 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.53 (0.10), residues: 8055 helix: 1.38 (0.09), residues: 3627 sheet: -0.07 (0.15), residues: 1188 loop : -0.61 (0.11), residues: 3240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 21 HIS 0.010 0.001 HIS F 192 PHE 0.033 0.001 PHE K 255 TYR 0.017 0.001 TYR G 357 ARG 0.011 0.001 ARG C 2 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16110 Ramachandran restraints generated. 8055 Oldfield, 0 Emsley, 8055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16110 Ramachandran restraints generated. 8055 Oldfield, 0 Emsley, 8055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1309 residues out of total 6966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 1176 time to evaluate : 5.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: r 127 MET cc_start: 0.8393 (mmp) cc_final: 0.7935 (mmp) REVERT: B 47 GLU cc_start: 0.8561 (tp30) cc_final: 0.7865 (tp30) REVERT: B 105 LYS cc_start: 0.8883 (mtpp) cc_final: 0.8622 (mtpp) REVERT: B 116 ASP cc_start: 0.8262 (m-30) cc_final: 0.7488 (m-30) REVERT: B 120 ASP cc_start: 0.8173 (m-30) cc_final: 0.7952 (m-30) REVERT: B 149 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8473 (tpp) REVERT: B 196 GLU cc_start: 0.8590 (pt0) cc_final: 0.8359 (pt0) REVERT: B 282 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8445 (pm20) REVERT: B 283 TYR cc_start: 0.8147 (m-10) cc_final: 0.7929 (m-10) REVERT: B 422 GLU cc_start: 0.8091 (tp30) cc_final: 0.7857 (tp30) REVERT: A 85 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8384 (mt0) REVERT: A 112 LYS cc_start: 0.8463 (pttt) cc_final: 0.7778 (pttt) REVERT: A 209 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8112 (mt) REVERT: A 211 ASP cc_start: 0.8526 (t0) cc_final: 0.8098 (t0) REVERT: A 423 GLU cc_start: 0.8256 (tm-30) cc_final: 0.8032 (pp20) REVERT: D 22 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7571 (tp30) REVERT: D 41 ASP cc_start: 0.8178 (t70) cc_final: 0.7866 (t70) REVERT: D 47 GLU cc_start: 0.8027 (pp20) cc_final: 0.7534 (pp20) REVERT: D 50 ASN cc_start: 0.8858 (p0) cc_final: 0.8376 (p0) REVERT: D 71 GLU cc_start: 0.8448 (tp30) cc_final: 0.8223 (tp30) REVERT: D 105 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8875 (ttpp) REVERT: D 159 GLU cc_start: 0.8580 (mt-10) cc_final: 0.7974 (mt-10) REVERT: D 199 ASP cc_start: 0.8112 (t0) cc_final: 0.7882 (t0) REVERT: D 247 GLN cc_start: 0.8525 (mp10) cc_final: 0.8004 (mp10) REVERT: D 281 GLN cc_start: 0.8539 (pp30) cc_final: 0.8326 (pp30) REVERT: D 329 ASP cc_start: 0.8281 (m-30) cc_final: 0.7968 (t70) REVERT: D 345 GLU cc_start: 0.8452 (pm20) cc_final: 0.8182 (pm20) REVERT: D 349 ASN cc_start: 0.6358 (t0) cc_final: 0.6095 (t0) REVERT: D 398 MET cc_start: 0.9153 (mtp) cc_final: 0.8836 (mtp) REVERT: D 416 MET cc_start: 0.8653 (mmm) cc_final: 0.8434 (tpt) REVERT: D 422 GLU cc_start: 0.8088 (tp30) cc_final: 0.7468 (tp30) REVERT: D 427 ASP cc_start: 0.8203 (m-30) cc_final: 0.7689 (m-30) REVERT: D 433 GLN cc_start: 0.8510 (tm-30) cc_final: 0.8146 (tm-30) REVERT: C 77 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8110 (tm-30) REVERT: C 84 ARG cc_start: 0.8960 (ttp-110) cc_final: 0.8354 (ptp-170) REVERT: C 103 TYR cc_start: 0.8761 (t80) cc_final: 0.8299 (t80) REVERT: C 115 ILE cc_start: 0.8182 (tp) cc_final: 0.7976 (tp) REVERT: C 227 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7821 (mm) REVERT: C 417 GLU cc_start: 0.8018 (tp30) cc_final: 0.7586 (tp30) REVERT: C 420 GLU cc_start: 0.8299 (pt0) cc_final: 0.7946 (pt0) REVERT: C 423 GLU cc_start: 0.8356 (pp20) cc_final: 0.7962 (pp20) REVERT: C 434 GLU cc_start: 0.8320 (pp20) cc_final: 0.7981 (pp20) REVERT: F 47 GLU cc_start: 0.8445 (tp30) cc_final: 0.7860 (tp30) REVERT: F 105 LYS cc_start: 0.9206 (mtmt) cc_final: 0.8927 (mtpp) REVERT: F 113 GLU cc_start: 0.8635 (tp30) cc_final: 0.8172 (tp30) REVERT: F 127 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8252 (mm-30) REVERT: F 247 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7755 (tt0) REVERT: F 282 GLN cc_start: 0.8592 (pm20) cc_final: 0.8310 (pm20) REVERT: F 293 GLN cc_start: 0.6914 (mm-40) cc_final: 0.6661 (mm110) REVERT: F 325 MET cc_start: 0.8777 (mmp) cc_final: 0.8377 (mmp) REVERT: F 330 GLU cc_start: 0.6951 (tp30) cc_final: 0.6237 (tp30) REVERT: F 345 GLU cc_start: 0.8254 (pp20) cc_final: 0.7981 (tp30) REVERT: F 372 LYS cc_start: 0.8918 (pptt) cc_final: 0.8504 (pptt) REVERT: F 398 MET cc_start: 0.8980 (mtm) cc_final: 0.8760 (mtm) REVERT: F 413 MET cc_start: 0.8840 (mtp) cc_final: 0.8555 (mtm) REVERT: F 427 ASP cc_start: 0.8238 (m-30) cc_final: 0.7850 (m-30) REVERT: E 24 TYR cc_start: 0.8833 (m-10) cc_final: 0.8536 (m-10) REVERT: E 245 ASP cc_start: 0.8689 (p0) cc_final: 0.8310 (p0) REVERT: E 251 ASP cc_start: 0.8030 (t0) cc_final: 0.7683 (t0) REVERT: E 322 ASP cc_start: 0.8838 (t70) cc_final: 0.8613 (t0) REVERT: E 339 ARG cc_start: 0.8128 (tmm160) cc_final: 0.7889 (tpm170) REVERT: E 392 ASP cc_start: 0.8733 (m-30) cc_final: 0.8432 (m-30) REVERT: E 413 MET cc_start: 0.7195 (ttt) cc_final: 0.6948 (ttt) REVERT: E 434 GLU cc_start: 0.8294 (pp20) cc_final: 0.7842 (pp20) REVERT: H 1 MET cc_start: 0.8318 (ttm) cc_final: 0.7450 (ttt) REVERT: H 3 GLU cc_start: 0.7821 (mp0) cc_final: 0.7307 (mp0) REVERT: H 26 ASP cc_start: 0.8886 (t70) cc_final: 0.8538 (t0) REVERT: H 47 GLU cc_start: 0.7803 (pp20) cc_final: 0.7448 (pp20) REVERT: H 50 ASN cc_start: 0.8989 (p0) cc_final: 0.8604 (p0) REVERT: H 76 ASP cc_start: 0.9151 (t0) cc_final: 0.8834 (t0) REVERT: H 105 LYS cc_start: 0.9209 (mtpp) cc_final: 0.8860 (mtpp) REVERT: H 133 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8438 (tm-30) REVERT: H 156 LYS cc_start: 0.8716 (mmtp) cc_final: 0.7710 (mmtp) REVERT: H 166 MET cc_start: 0.8016 (tpp) cc_final: 0.7508 (tpp) REVERT: H 199 ASP cc_start: 0.8577 (m-30) cc_final: 0.8057 (m-30) REVERT: H 325 MET cc_start: 0.7931 (mmm) cc_final: 0.7658 (mmm) REVERT: H 337 ASN cc_start: 0.8664 (m110) cc_final: 0.8108 (m110) REVERT: H 416 MET cc_start: 0.8324 (tpp) cc_final: 0.8002 (mmm) REVERT: H 422 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7891 (tp30) REVERT: H 427 ASP cc_start: 0.8459 (m-30) cc_final: 0.8067 (m-30) REVERT: G 123 ARG cc_start: 0.8965 (tmm-80) cc_final: 0.8656 (tmm-80) REVERT: G 154 MET cc_start: 0.8765 (mmm) cc_final: 0.8481 (mtp) REVERT: G 211 ASP cc_start: 0.8788 (t0) cc_final: 0.8292 (t0) REVERT: G 255 PHE cc_start: 0.7947 (t80) cc_final: 0.7539 (t80) REVERT: G 290 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7322 (pm20) REVERT: G 342 GLN cc_start: 0.8192 (mp10) cc_final: 0.7964 (mp10) REVERT: G 423 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8007 (tm-30) REVERT: G 425 MET cc_start: 0.8678 (mmm) cc_final: 0.8440 (tpp) REVERT: G 431 ASP cc_start: 0.8136 (t70) cc_final: 0.7521 (m-30) REVERT: G 433 GLU cc_start: 0.8482 (tp30) cc_final: 0.8010 (tp30) REVERT: G 434 GLU cc_start: 0.8396 (pp20) cc_final: 0.8129 (pp20) REVERT: J 3 GLU cc_start: 0.8014 (mp0) cc_final: 0.6964 (mp0) REVERT: J 26 ASP cc_start: 0.8535 (t0) cc_final: 0.8191 (t0) REVERT: J 76 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8551 (t0) REVERT: J 163 ASP cc_start: 0.8474 (p0) cc_final: 0.8212 (p0) REVERT: J 166 MET cc_start: 0.8690 (tpt) cc_final: 0.8412 (tpt) REVERT: J 167 ASN cc_start: 0.8742 (m-40) cc_final: 0.8362 (m-40) REVERT: J 207 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8519 (mm-30) REVERT: J 281 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8400 (tm-30) REVERT: J 286 LEU cc_start: 0.9283 (tp) cc_final: 0.9013 (tm) REVERT: J 330 GLU cc_start: 0.8022 (pp20) cc_final: 0.7799 (pp20) REVERT: J 358 ILE cc_start: 0.9048 (mm) cc_final: 0.8805 (mp) REVERT: J 414 ASP cc_start: 0.8815 (p0) cc_final: 0.8555 (p0) REVERT: I 71 GLU cc_start: 0.7585 (pt0) cc_final: 0.7215 (pm20) REVERT: I 76 ASP cc_start: 0.8265 (m-30) cc_final: 0.7772 (m-30) REVERT: I 128 GLN cc_start: 0.8992 (tt0) cc_final: 0.8457 (tm-30) REVERT: I 154 MET cc_start: 0.9027 (mmt) cc_final: 0.8738 (mmm) REVERT: I 211 ASP cc_start: 0.8769 (t0) cc_final: 0.8191 (t0) REVERT: I 251 ASP cc_start: 0.7557 (t0) cc_final: 0.7266 (t70) REVERT: I 282 TYR cc_start: 0.8997 (m-80) cc_final: 0.8743 (m-80) REVERT: I 302 MET cc_start: 0.8779 (mmt) cc_final: 0.8543 (mmt) REVERT: I 423 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7856 (tm-30) REVERT: I 430 LYS cc_start: 0.8520 (mmmm) cc_final: 0.7873 (mmmm) REVERT: I 434 GLU cc_start: 0.8473 (mt-10) cc_final: 0.7955 (mt-10) REVERT: L 1 MET cc_start: 0.8953 (mmm) cc_final: 0.8661 (tpt) REVERT: L 55 GLU cc_start: 0.8060 (tp30) cc_final: 0.7736 (tp30) REVERT: L 76 ASP cc_start: 0.8989 (m-30) cc_final: 0.8697 (t0) REVERT: L 105 LYS cc_start: 0.9096 (ptmt) cc_final: 0.8721 (ptmm) REVERT: L 113 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8433 (tm-30) REVERT: L 133 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7505 (pp30) REVERT: L 159 GLU cc_start: 0.7698 (pp20) cc_final: 0.7482 (pp20) REVERT: L 203 CYS cc_start: 0.9198 (t) cc_final: 0.8729 (p) REVERT: L 207 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8188 (tp30) REVERT: L 214 PHE cc_start: 0.8514 (m-80) cc_final: 0.8205 (m-80) REVERT: L 215 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8263 (ptp90) REVERT: L 247 GLN cc_start: 0.8258 (mp10) cc_final: 0.7971 (mp10) REVERT: L 338 LYS cc_start: 0.7004 (tttt) cc_final: 0.6444 (pttt) REVERT: L 433 GLN cc_start: 0.8838 (tp40) cc_final: 0.8570 (tp-100) REVERT: K 24 TYR cc_start: 0.8850 (m-10) cc_final: 0.8616 (m-10) REVERT: K 133 GLN cc_start: 0.8385 (mm-40) cc_final: 0.7973 (mm-40) REVERT: K 176 GLN cc_start: 0.8901 (mp10) cc_final: 0.8594 (mp10) REVERT: K 251 ASP cc_start: 0.7406 (t0) cc_final: 0.6980 (t0) REVERT: K 290 GLU cc_start: 0.8308 (pp20) cc_final: 0.8084 (pp20) REVERT: K 327 ASP cc_start: 0.7886 (p0) cc_final: 0.7682 (p0) REVERT: K 423 GLU cc_start: 0.8179 (pp20) cc_final: 0.7940 (pp20) REVERT: K 433 GLU cc_start: 0.8596 (tp30) cc_final: 0.8346 (tp30) REVERT: K 434 GLU cc_start: 0.8391 (pp20) cc_final: 0.7930 (pp20) REVERT: N 1 MET cc_start: 0.8333 (tpt) cc_final: 0.7805 (tpp) REVERT: N 22 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8107 (tm-30) REVERT: N 50 ASN cc_start: 0.8748 (p0) cc_final: 0.8296 (p0) REVERT: N 59 ASN cc_start: 0.8781 (t0) cc_final: 0.8562 (t0) REVERT: N 60 LYS cc_start: 0.4561 (pttp) cc_final: 0.4136 (pttt) REVERT: N 88 ARG cc_start: 0.6745 (mmp-170) cc_final: 0.5620 (mmp-170) REVERT: N 110 GLU cc_start: 0.8010 (mp0) cc_final: 0.7662 (mp0) REVERT: N 116 ASP cc_start: 0.8681 (t0) cc_final: 0.8457 (t0) REVERT: N 127 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8520 (mm-30) REVERT: N 207 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8282 (mm-30) REVERT: N 281 GLN cc_start: 0.8943 (tm-30) cc_final: 0.8608 (tm-30) REVERT: N 293 GLN cc_start: 0.8397 (pp30) cc_final: 0.8191 (pp30) REVERT: N 338 LYS cc_start: 0.8843 (mtmm) cc_final: 0.8570 (mtmm) REVERT: N 345 GLU cc_start: 0.8668 (pm20) cc_final: 0.8357 (pm20) REVERT: N 373 MET cc_start: 0.9275 (ptp) cc_final: 0.8910 (ptm) REVERT: N 422 GLU cc_start: 0.8378 (tp30) cc_final: 0.7805 (tp30) REVERT: M 85 GLN cc_start: 0.8855 (pt0) cc_final: 0.8618 (pm20) REVERT: M 155 GLU cc_start: 0.8635 (pp20) cc_final: 0.8217 (pp20) REVERT: M 203 MET cc_start: 0.9109 (mmm) cc_final: 0.8627 (mmm) REVERT: M 220 GLU cc_start: 0.7495 (pp20) cc_final: 0.7061 (pp20) REVERT: M 221 ARG cc_start: 0.8484 (ptp-110) cc_final: 0.8132 (ptp-110) REVERT: M 297 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7831 (tm-30) REVERT: M 313 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8697 (mtp) REVERT: M 377 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8574 (ttm) REVERT: M 420 GLU cc_start: 0.8166 (pp20) cc_final: 0.7652 (pp20) REVERT: M 423 GLU cc_start: 0.8528 (pp20) cc_final: 0.8216 (pp20) REVERT: M 430 LYS cc_start: 0.8691 (mmmt) cc_final: 0.7812 (mmmm) REVERT: M 431 ASP cc_start: 0.8287 (t0) cc_final: 0.7950 (t0) REVERT: M 433 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7513 (pm20) REVERT: M 434 GLU cc_start: 0.8441 (pp20) cc_final: 0.8147 (pp20) REVERT: M 437 VAL cc_start: 0.9331 (p) cc_final: 0.8935 (m) REVERT: P 127 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8340 (mm-30) REVERT: P 293 GLN cc_start: 0.8485 (pp30) cc_final: 0.8051 (pp30) REVERT: P 337 ASN cc_start: 0.8969 (m110) cc_final: 0.8763 (m-40) REVERT: P 422 GLU cc_start: 0.8126 (tp30) cc_final: 0.7711 (tp30) REVERT: O 71 GLU cc_start: 0.7078 (pm20) cc_final: 0.6685 (mp0) REVERT: O 77 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.8038 (pm20) REVERT: O 123 ARG cc_start: 0.9192 (tmm-80) cc_final: 0.8787 (ttp80) REVERT: O 154 MET cc_start: 0.9094 (mmm) cc_final: 0.8756 (mmm) REVERT: O 205 ASP cc_start: 0.7975 (t0) cc_final: 0.7764 (t70) REVERT: O 211 ASP cc_start: 0.8624 (t0) cc_final: 0.8342 (t0) REVERT: O 326 LYS cc_start: 0.5615 (mmtp) cc_final: 0.5208 (mmtm) REVERT: O 423 GLU cc_start: 0.8268 (pp20) cc_final: 0.7905 (pp20) REVERT: O 430 LYS cc_start: 0.8793 (tppp) cc_final: 0.8457 (tppp) REVERT: O 431 ASP cc_start: 0.8110 (t70) cc_final: 0.7673 (t0) REVERT: O 434 GLU cc_start: 0.8488 (pp20) cc_final: 0.8122 (pp20) REVERT: O 438 ASP cc_start: 0.8670 (t0) cc_final: 0.8335 (t0) REVERT: R 47 GLU cc_start: 0.7804 (pp20) cc_final: 0.7486 (tm-30) REVERT: R 71 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8133 (mp0) REVERT: R 76 ASP cc_start: 0.8729 (t0) cc_final: 0.8390 (t0) REVERT: R 113 GLU cc_start: 0.8649 (tp30) cc_final: 0.8395 (tp30) REVERT: R 127 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7973 (mm-30) REVERT: R 159 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8051 (pp20) REVERT: R 183 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7969 (mt-10) REVERT: R 204 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8319 (mp) REVERT: R 247 GLN cc_start: 0.8841 (mp10) cc_final: 0.8381 (mm-40) REVERT: R 281 GLN cc_start: 0.8944 (tp40) cc_final: 0.8719 (tp40) REVERT: R 301 MET cc_start: 0.9267 (mmt) cc_final: 0.9059 (mmp) REVERT: R 330 GLU cc_start: 0.6984 (tp30) cc_final: 0.6103 (tp30) REVERT: R 334 ASN cc_start: 0.7490 (m-40) cc_final: 0.7207 (m110) REVERT: R 349 ASN cc_start: 0.7623 (t0) cc_final: 0.7202 (t0) REVERT: R 427 ASP cc_start: 0.8541 (m-30) cc_final: 0.8139 (m-30) REVERT: Q 2 ARG cc_start: 0.8654 (ttp-110) cc_final: 0.8446 (ttp80) REVERT: Q 77 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8593 (tm-30) REVERT: Q 128 GLN cc_start: 0.8279 (tm-30) cc_final: 0.8002 (tm-30) REVERT: Q 205 ASP cc_start: 0.8039 (m-30) cc_final: 0.7474 (p0) REVERT: Q 313 MET cc_start: 0.8723 (mtp) cc_final: 0.8270 (mtp) REVERT: Q 377 MET cc_start: 0.8966 (ttp) cc_final: 0.8716 (ttp) REVERT: Q 386 GLU cc_start: 0.8245 (mp0) cc_final: 0.7883 (mp0) REVERT: Q 397 LEU cc_start: 0.9155 (tt) cc_final: 0.8894 (tm) REVERT: Q 423 GLU cc_start: 0.8787 (pp20) cc_final: 0.8580 (pp20) REVERT: Q 430 LYS cc_start: 0.8939 (tppt) cc_final: 0.8626 (tppp) REVERT: Q 433 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8028 (tp30) REVERT: Q 434 GLU cc_start: 0.8510 (pp20) cc_final: 0.8178 (pp20) REVERT: s 127 MET cc_start: 0.8182 (tpt) cc_final: 0.7915 (tpt) REVERT: t 93 MET cc_start: 0.8875 (tpt) cc_final: 0.8392 (tpt) REVERT: t 127 MET cc_start: 0.8129 (mmp) cc_final: 0.7805 (mmp) REVERT: v 127 MET cc_start: 0.8184 (mmp) cc_final: 0.7626 (mmp) REVERT: w 93 MET cc_start: 0.8766 (tpt) cc_final: 0.8445 (tpt) REVERT: x 93 MET cc_start: 0.7483 (mmt) cc_final: 0.7206 (mmt) REVERT: x 127 MET cc_start: 0.8412 (tpt) cc_final: 0.7951 (tpt) REVERT: y 127 MET cc_start: 0.8429 (mmp) cc_final: 0.8008 (mmp) REVERT: z 93 MET cc_start: 0.8624 (tpp) cc_final: 0.8245 (tpp) REVERT: z 97 TYR cc_start: 0.8390 (t80) cc_final: 0.7652 (t80) REVERT: z 127 MET cc_start: 0.8121 (mmp) cc_final: 0.7757 (mmp) outliers start: 133 outliers final: 41 residues processed: 1229 average time/residue: 1.7973 time to fit residues: 2733.3714 Evaluate side-chains 1190 residues out of total 6966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 1132 time to evaluate : 5.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain r residue 104 GLN Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 133 GLN Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain H residue 133 GLN Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 432 TYR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 315 VAL Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain L residue 133 GLN Chi-restraints excluded: chain L residue 215 ARG Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 68 VAL Chi-restraints excluded: chain N residue 129 CYS Chi-restraints excluded: chain N residue 333 LEU Chi-restraints excluded: chain N residue 402 LYS Chi-restraints excluded: chain N residue 413 MET Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 313 MET Chi-restraints excluded: chain M residue 377 MET Chi-restraints excluded: chain M residue 425 MET Chi-restraints excluded: chain M residue 433 GLU Chi-restraints excluded: chain P residue 389 LYS Chi-restraints excluded: chain P residue 405 LEU Chi-restraints excluded: chain O residue 77 GLU Chi-restraints excluded: chain R residue 149 MET Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 241 CYS Chi-restraints excluded: chain R residue 332 MET Chi-restraints excluded: chain R residue 345 GLU Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain s residue 120 VAL Chi-restraints excluded: chain t residue 120 VAL Chi-restraints excluded: chain x residue 122 ARG Chi-restraints excluded: chain y residue 104 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 801 random chunks: chunk 529 optimal weight: 0.9990 chunk 462 optimal weight: 10.0000 chunk 647 optimal weight: 2.9990 chunk 242 optimal weight: 5.9990 chunk 280 optimal weight: 3.9990 chunk 602 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 449 optimal weight: 0.7980 chunk 614 optimal weight: 0.7980 chunk 197 optimal weight: 5.9990 chunk 292 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN A 15 GLN A 50 ASN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 GLN ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 HIS D 6 HIS ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 GLN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 GLN ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 HIS F 334 ASN E 249 ASN H 96 GLN H 192 HIS ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 339 ASN ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 HIS I 216 ASN I 249 ASN ** L 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 GLN L 293 GLN L 294 GLN L 334 ASN ** N 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 249 ASN M 285 GLN ** P 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 133 GLN ** P 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 282 GLN O 133 GLN ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 293 GLN R 294 GLN R 339 ASN R 433 GLN Q 88 HIS Q 249 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.099998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.085445 restraints weight = 121062.762| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.43 r_work: 0.3529 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 65970 Z= 0.199 Angle : 0.581 9.794 89469 Z= 0.297 Chirality : 0.044 0.246 9711 Planarity : 0.004 0.052 11637 Dihedral : 10.822 176.666 9252 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.31 % Allowed : 15.16 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.61 (0.10), residues: 8055 helix: 1.47 (0.09), residues: 3627 sheet: -0.05 (0.15), residues: 1188 loop : -0.58 (0.11), residues: 3240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 388 HIS 0.011 0.001 HIS Q 88 PHE 0.033 0.001 PHE K 255 TYR 0.023 0.001 TYR E 172 ARG 0.009 0.000 ARG H 400 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16110 Ramachandran restraints generated. 8055 Oldfield, 0 Emsley, 8055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16110 Ramachandran restraints generated. 8055 Oldfield, 0 Emsley, 8055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1310 residues out of total 6966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 1150 time to evaluate : 5.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: r 127 MET cc_start: 0.8390 (mmp) cc_final: 0.7927 (mmp) REVERT: B 47 GLU cc_start: 0.8481 (tp30) cc_final: 0.7731 (tp30) REVERT: B 76 ASP cc_start: 0.8928 (t0) cc_final: 0.8447 (m-30) REVERT: B 116 ASP cc_start: 0.8268 (m-30) cc_final: 0.7569 (m-30) REVERT: B 120 ASP cc_start: 0.8215 (m-30) cc_final: 0.7985 (m-30) REVERT: B 196 GLU cc_start: 0.8537 (pt0) cc_final: 0.8329 (pt0) REVERT: B 282 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8426 (pm20) REVERT: B 325 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8222 (mmm) REVERT: A 85 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8362 (mt0) REVERT: A 112 LYS cc_start: 0.8385 (pttt) cc_final: 0.7820 (pttm) REVERT: A 113 GLU cc_start: 0.7752 (mp0) cc_final: 0.7231 (mp0) REVERT: A 209 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8245 (mt) REVERT: A 211 ASP cc_start: 0.8550 (t0) cc_final: 0.8074 (t0) REVERT: A 423 GLU cc_start: 0.8252 (tm-30) cc_final: 0.8003 (pp20) REVERT: D 22 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7549 (tp30) REVERT: D 41 ASP cc_start: 0.8208 (t70) cc_final: 0.7909 (t70) REVERT: D 47 GLU cc_start: 0.8128 (pp20) cc_final: 0.7533 (pp20) REVERT: D 50 ASN cc_start: 0.8937 (p0) cc_final: 0.8492 (p0) REVERT: D 71 GLU cc_start: 0.8535 (tp30) cc_final: 0.8308 (tp30) REVERT: D 105 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8827 (ttpp) REVERT: D 159 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8103 (mt-10) REVERT: D 199 ASP cc_start: 0.8190 (t0) cc_final: 0.7892 (t0) REVERT: D 345 GLU cc_start: 0.8386 (pm20) cc_final: 0.8135 (pm20) REVERT: D 349 ASN cc_start: 0.6306 (t0) cc_final: 0.6034 (t0) REVERT: D 405 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8254 (mm) REVERT: D 416 MET cc_start: 0.8711 (mmm) cc_final: 0.8448 (tpt) REVERT: D 422 GLU cc_start: 0.8165 (tp30) cc_final: 0.7552 (tp30) REVERT: D 427 ASP cc_start: 0.8136 (m-30) cc_final: 0.7829 (m-30) REVERT: D 433 GLN cc_start: 0.8482 (tm-30) cc_final: 0.8079 (tm-30) REVERT: C 77 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8069 (tm-30) REVERT: C 84 ARG cc_start: 0.9000 (ttp-110) cc_final: 0.8475 (ptp-170) REVERT: C 103 TYR cc_start: 0.8853 (t80) cc_final: 0.8339 (t80) REVERT: C 115 ILE cc_start: 0.8170 (tp) cc_final: 0.7957 (tp) REVERT: C 413 MET cc_start: 0.8541 (ttm) cc_final: 0.8250 (ttp) REVERT: C 420 GLU cc_start: 0.8258 (pt0) cc_final: 0.7965 (pt0) REVERT: C 423 GLU cc_start: 0.8385 (pp20) cc_final: 0.7939 (pp20) REVERT: C 434 GLU cc_start: 0.8333 (pp20) cc_final: 0.7957 (pp20) REVERT: F 26 ASP cc_start: 0.8397 (t0) cc_final: 0.8074 (t0) REVERT: F 47 GLU cc_start: 0.8469 (tp30) cc_final: 0.7847 (tp30) REVERT: F 75 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8234 (mmt) REVERT: F 105 LYS cc_start: 0.9240 (mtmt) cc_final: 0.8929 (mtpp) REVERT: F 127 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8209 (mm-30) REVERT: F 247 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: F 282 GLN cc_start: 0.8614 (pm20) cc_final: 0.8299 (pm20) REVERT: F 293 GLN cc_start: 0.6887 (mm-40) cc_final: 0.6602 (mm110) REVERT: F 325 MET cc_start: 0.8801 (mmp) cc_final: 0.8432 (mmp) REVERT: F 330 GLU cc_start: 0.6967 (tp30) cc_final: 0.6221 (tp30) REVERT: F 345 GLU cc_start: 0.8203 (pp20) cc_final: 0.7961 (tp30) REVERT: F 372 LYS cc_start: 0.8989 (pptt) cc_final: 0.8586 (pptt) REVERT: F 384 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8510 (mm) REVERT: F 398 MET cc_start: 0.8983 (mtm) cc_final: 0.8753 (mtm) REVERT: E 24 TYR cc_start: 0.8818 (m-10) cc_final: 0.8515 (m-10) REVERT: E 245 ASP cc_start: 0.8704 (p0) cc_final: 0.8319 (p0) REVERT: E 251 ASP cc_start: 0.8193 (t0) cc_final: 0.7834 (t70) REVERT: E 392 ASP cc_start: 0.8700 (m-30) cc_final: 0.8405 (m-30) REVERT: E 413 MET cc_start: 0.7364 (ttt) cc_final: 0.7023 (ttt) REVERT: E 434 GLU cc_start: 0.8411 (pp20) cc_final: 0.7923 (pp20) REVERT: H 1 MET cc_start: 0.8412 (ttm) cc_final: 0.7484 (ttt) REVERT: H 3 GLU cc_start: 0.7716 (mp0) cc_final: 0.7276 (mp0) REVERT: H 26 ASP cc_start: 0.8886 (t70) cc_final: 0.8530 (t0) REVERT: H 47 GLU cc_start: 0.7860 (pp20) cc_final: 0.7540 (pp20) REVERT: H 50 ASN cc_start: 0.9060 (p0) cc_final: 0.8630 (p0) REVERT: H 71 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8290 (mm-30) REVERT: H 76 ASP cc_start: 0.9168 (t0) cc_final: 0.8825 (t0) REVERT: H 105 LYS cc_start: 0.9177 (mtpp) cc_final: 0.8817 (mtpp) REVERT: H 156 LYS cc_start: 0.8091 (mmtp) cc_final: 0.7494 (mmtp) REVERT: H 166 MET cc_start: 0.8075 (tpp) cc_final: 0.7518 (tpp) REVERT: H 199 ASP cc_start: 0.8609 (m-30) cc_final: 0.8101 (m-30) REVERT: H 337 ASN cc_start: 0.8738 (m110) cc_final: 0.8127 (m110) REVERT: H 389 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8885 (mtmm) REVERT: H 416 MET cc_start: 0.8361 (tpp) cc_final: 0.7991 (mmm) REVERT: H 422 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7917 (tp30) REVERT: H 427 ASP cc_start: 0.8462 (m-30) cc_final: 0.8085 (m-30) REVERT: G 80 THR cc_start: 0.8980 (m) cc_final: 0.8670 (t) REVERT: G 85 GLN cc_start: 0.8803 (pt0) cc_final: 0.8215 (pp30) REVERT: G 154 MET cc_start: 0.8813 (mmm) cc_final: 0.8528 (mtp) REVERT: G 168 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8425 (pt0) REVERT: G 211 ASP cc_start: 0.8857 (t0) cc_final: 0.8588 (t70) REVERT: G 255 PHE cc_start: 0.7908 (t80) cc_final: 0.7481 (t80) REVERT: G 290 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7419 (pm20) REVERT: G 342 GLN cc_start: 0.8281 (mp10) cc_final: 0.8025 (mp10) REVERT: G 423 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7950 (tm-30) REVERT: G 425 MET cc_start: 0.8694 (mmm) cc_final: 0.8433 (tpp) REVERT: G 431 ASP cc_start: 0.8140 (t70) cc_final: 0.7515 (m-30) REVERT: G 433 GLU cc_start: 0.8510 (tp30) cc_final: 0.8049 (tp30) REVERT: G 434 GLU cc_start: 0.8400 (pp20) cc_final: 0.8137 (pp20) REVERT: J 3 GLU cc_start: 0.7946 (mp0) cc_final: 0.6788 (mp0) REVERT: J 26 ASP cc_start: 0.8535 (t0) cc_final: 0.8183 (t0) REVERT: J 76 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.8581 (t0) REVERT: J 127 GLU cc_start: 0.8162 (mp0) cc_final: 0.7923 (mp0) REVERT: J 149 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8571 (tpp) REVERT: J 163 ASP cc_start: 0.8477 (p0) cc_final: 0.8152 (p0) REVERT: J 166 MET cc_start: 0.8738 (tpt) cc_final: 0.8451 (tpt) REVERT: J 167 ASN cc_start: 0.8757 (m-40) cc_final: 0.8403 (m-40) REVERT: J 207 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8452 (mm-30) REVERT: J 281 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8306 (tm-30) REVERT: J 330 GLU cc_start: 0.8075 (pp20) cc_final: 0.7798 (pp20) REVERT: J 358 ILE cc_start: 0.9036 (mm) cc_final: 0.8823 (mp) REVERT: J 414 ASP cc_start: 0.8825 (p0) cc_final: 0.8540 (p0) REVERT: I 71 GLU cc_start: 0.7553 (pt0) cc_final: 0.7234 (pm20) REVERT: I 76 ASP cc_start: 0.8279 (m-30) cc_final: 0.7703 (m-30) REVERT: I 128 GLN cc_start: 0.9013 (tt0) cc_final: 0.8508 (tm-30) REVERT: I 154 MET cc_start: 0.8972 (mmt) cc_final: 0.8698 (mmm) REVERT: I 211 ASP cc_start: 0.8700 (t0) cc_final: 0.8358 (t0) REVERT: I 282 TYR cc_start: 0.9054 (m-80) cc_final: 0.8835 (m-80) REVERT: I 302 MET cc_start: 0.8689 (mmt) cc_final: 0.8385 (mmt) REVERT: I 423 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7751 (tm-30) REVERT: I 430 LYS cc_start: 0.8464 (mmmm) cc_final: 0.7760 (mmmm) REVERT: I 434 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8149 (mt-10) REVERT: L 1 MET cc_start: 0.9229 (mmm) cc_final: 0.8936 (mmm) REVERT: L 55 GLU cc_start: 0.7959 (tp30) cc_final: 0.7655 (tp30) REVERT: L 76 ASP cc_start: 0.8981 (m-30) cc_final: 0.8699 (t0) REVERT: L 90 ASP cc_start: 0.8706 (t0) cc_final: 0.8473 (p0) REVERT: L 105 LYS cc_start: 0.9087 (ptmt) cc_final: 0.8704 (ptmm) REVERT: L 113 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8333 (tm-30) REVERT: L 127 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7964 (mm-30) REVERT: L 166 MET cc_start: 0.8327 (tpp) cc_final: 0.8126 (tpp) REVERT: L 203 CYS cc_start: 0.9203 (t) cc_final: 0.8736 (p) REVERT: L 207 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8219 (tp30) REVERT: L 281 GLN cc_start: 0.8783 (tm-30) cc_final: 0.8569 (tm-30) REVERT: L 282 GLN cc_start: 0.8283 (pm20) cc_final: 0.8055 (pm20) REVERT: L 299 LYS cc_start: 0.8580 (tppp) cc_final: 0.8280 (tptt) REVERT: L 338 LYS cc_start: 0.6950 (tttt) cc_final: 0.6425 (pttt) REVERT: L 372 LYS cc_start: 0.8709 (pmtt) cc_final: 0.8408 (pptt) REVERT: L 393 GLU cc_start: 0.8653 (pp20) cc_final: 0.8265 (pp20) REVERT: L 427 ASP cc_start: 0.8307 (p0) cc_final: 0.8030 (p0) REVERT: L 433 GLN cc_start: 0.8749 (tp40) cc_final: 0.8524 (tp-100) REVERT: K 24 TYR cc_start: 0.8848 (m-10) cc_final: 0.8597 (m-10) REVERT: K 127 ASP cc_start: 0.8906 (OUTLIER) cc_final: 0.8477 (m-30) REVERT: K 133 GLN cc_start: 0.8388 (mm-40) cc_final: 0.7914 (mm-40) REVERT: K 176 GLN cc_start: 0.9014 (mp10) cc_final: 0.8728 (mp10) REVERT: K 251 ASP cc_start: 0.7452 (t0) cc_final: 0.7005 (t0) REVERT: K 277 SER cc_start: 0.8917 (m) cc_final: 0.8516 (p) REVERT: K 279 GLU cc_start: 0.8207 (pm20) cc_final: 0.8004 (pm20) REVERT: K 290 GLU cc_start: 0.8245 (pp20) cc_final: 0.7965 (pp20) REVERT: K 349 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.8170 (p) REVERT: K 433 GLU cc_start: 0.8781 (tp30) cc_final: 0.8529 (tp30) REVERT: K 434 GLU cc_start: 0.8435 (pp20) cc_final: 0.7971 (pp20) REVERT: N 1 MET cc_start: 0.8492 (tpt) cc_final: 0.8003 (tpp) REVERT: N 22 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8084 (tm-30) REVERT: N 50 ASN cc_start: 0.8828 (p0) cc_final: 0.8370 (p0) REVERT: N 59 ASN cc_start: 0.8738 (t0) cc_final: 0.8520 (t0) REVERT: N 127 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8616 (mm-30) REVERT: N 207 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8089 (tp30) REVERT: N 247 GLN cc_start: 0.8345 (mp10) cc_final: 0.7768 (mp10) REVERT: N 269 MET cc_start: 0.8356 (mtp) cc_final: 0.8151 (mtp) REVERT: N 281 GLN cc_start: 0.8919 (tm-30) cc_final: 0.8495 (tm-30) REVERT: N 338 LYS cc_start: 0.8843 (mtmm) cc_final: 0.8574 (mtmm) REVERT: N 345 GLU cc_start: 0.8714 (pm20) cc_final: 0.8387 (pm20) REVERT: N 373 MET cc_start: 0.9301 (ptp) cc_final: 0.8930 (ptm) REVERT: N 422 GLU cc_start: 0.8428 (tp30) cc_final: 0.7823 (tp30) REVERT: M 85 GLN cc_start: 0.8900 (pt0) cc_final: 0.8677 (pm20) REVERT: M 203 MET cc_start: 0.9186 (mmm) cc_final: 0.8580 (mmm) REVERT: M 220 GLU cc_start: 0.7447 (pp20) cc_final: 0.6941 (pp20) REVERT: M 221 ARG cc_start: 0.8502 (ptp-110) cc_final: 0.8163 (ptp-110) REVERT: M 313 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8601 (mtp) REVERT: M 349 THR cc_start: 0.8499 (OUTLIER) cc_final: 0.8291 (p) REVERT: M 420 GLU cc_start: 0.8279 (pp20) cc_final: 0.7691 (pp20) REVERT: M 423 GLU cc_start: 0.8532 (pp20) cc_final: 0.8223 (pp20) REVERT: M 430 LYS cc_start: 0.8687 (mmmt) cc_final: 0.7779 (mmmm) REVERT: M 433 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7611 (pm20) REVERT: M 434 GLU cc_start: 0.8392 (pp20) cc_final: 0.8137 (pp20) REVERT: P 127 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8264 (mm-30) REVERT: P 133 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8321 (tt0) REVERT: P 293 GLN cc_start: 0.8594 (pp30) cc_final: 0.8122 (pp30) REVERT: P 338 LYS cc_start: 0.8911 (mptp) cc_final: 0.8656 (ptpp) REVERT: P 422 GLU cc_start: 0.8331 (tp30) cc_final: 0.7914 (tp30) REVERT: O 71 GLU cc_start: 0.7143 (pm20) cc_final: 0.6629 (mp0) REVERT: O 123 ARG cc_start: 0.9180 (tmm-80) cc_final: 0.8887 (ttp80) REVERT: O 154 MET cc_start: 0.9122 (mmm) cc_final: 0.8739 (mmm) REVERT: O 205 ASP cc_start: 0.7992 (t0) cc_final: 0.7759 (t70) REVERT: O 211 ASP cc_start: 0.8622 (t0) cc_final: 0.8284 (t0) REVERT: O 326 LYS cc_start: 0.5593 (mmtp) cc_final: 0.5081 (mptm) REVERT: O 423 GLU cc_start: 0.8298 (pp20) cc_final: 0.8022 (pp20) REVERT: O 430 LYS cc_start: 0.8788 (tppp) cc_final: 0.8478 (tppp) REVERT: O 431 ASP cc_start: 0.8183 (t70) cc_final: 0.7973 (t0) REVERT: O 434 GLU cc_start: 0.8499 (pp20) cc_final: 0.8158 (pp20) REVERT: R 47 GLU cc_start: 0.7888 (pp20) cc_final: 0.7564 (tm-30) REVERT: R 76 ASP cc_start: 0.8829 (t0) cc_final: 0.8478 (t0) REVERT: R 113 GLU cc_start: 0.8699 (tp30) cc_final: 0.8445 (tp30) REVERT: R 179 ASP cc_start: 0.7494 (p0) cc_final: 0.7209 (p0) REVERT: R 183 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7840 (mt-10) REVERT: R 204 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8289 (mp) REVERT: R 247 GLN cc_start: 0.8941 (mp10) cc_final: 0.8471 (mm-40) REVERT: R 281 GLN cc_start: 0.9118 (tp40) cc_final: 0.8742 (tp40) REVERT: R 299 LYS cc_start: 0.8178 (tmmt) cc_final: 0.7907 (tmmt) REVERT: R 330 GLU cc_start: 0.6976 (tp30) cc_final: 0.5537 (tp30) REVERT: R 338 LYS cc_start: 0.7027 (pttt) cc_final: 0.6714 (pptt) REVERT: R 349 ASN cc_start: 0.7658 (t0) cc_final: 0.7222 (t0) REVERT: R 373 MET cc_start: 0.8703 (ttp) cc_final: 0.8482 (ttp) REVERT: R 427 ASP cc_start: 0.8545 (m-30) cc_final: 0.8132 (m-30) REVERT: Q 2 ARG cc_start: 0.8613 (ttp-110) cc_final: 0.8342 (ttp80) REVERT: Q 77 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8563 (tm-30) REVERT: Q 128 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8080 (tm-30) REVERT: Q 205 ASP cc_start: 0.8146 (m-30) cc_final: 0.7557 (p0) REVERT: Q 285 GLN cc_start: 0.4745 (mm-40) cc_final: 0.4194 (mm110) REVERT: Q 302 MET cc_start: 0.8591 (mtm) cc_final: 0.8346 (mtm) REVERT: Q 313 MET cc_start: 0.8721 (mtp) cc_final: 0.8241 (mtp) REVERT: Q 357 TYR cc_start: 0.8717 (m-80) cc_final: 0.8391 (m-80) REVERT: Q 377 MET cc_start: 0.8897 (ttp) cc_final: 0.8616 (ttp) REVERT: Q 386 GLU cc_start: 0.8235 (mp0) cc_final: 0.7782 (mp0) REVERT: Q 397 LEU cc_start: 0.9172 (tt) cc_final: 0.8913 (tm) REVERT: Q 423 GLU cc_start: 0.8821 (pp20) cc_final: 0.8575 (pp20) REVERT: Q 430 LYS cc_start: 0.8917 (tppt) cc_final: 0.8596 (tppp) REVERT: Q 433 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8004 (tp30) REVERT: Q 434 GLU cc_start: 0.8603 (pp20) cc_final: 0.8310 (pp20) REVERT: s 127 MET cc_start: 0.8181 (tpt) cc_final: 0.7979 (tpt) REVERT: t 93 MET cc_start: 0.8865 (tpt) cc_final: 0.8370 (tpt) REVERT: t 127 MET cc_start: 0.8117 (mmp) cc_final: 0.7737 (mmp) REVERT: v 127 MET cc_start: 0.8293 (mmp) cc_final: 0.7732 (mmp) REVERT: w 93 MET cc_start: 0.8779 (tpt) cc_final: 0.8465 (tpt) REVERT: x 93 MET cc_start: 0.7587 (mmt) cc_final: 0.7262 (mmt) REVERT: x 127 MET cc_start: 0.8375 (tpt) cc_final: 0.7915 (tpt) REVERT: y 127 MET cc_start: 0.8641 (mmp) cc_final: 0.8216 (mmp) REVERT: z 93 MET cc_start: 0.8597 (tpp) cc_final: 0.8219 (tpp) REVERT: z 97 TYR cc_start: 0.8411 (t80) cc_final: 0.7680 (t80) REVERT: z 127 MET cc_start: 0.8068 (mmp) cc_final: 0.7702 (mmp) outliers start: 160 outliers final: 53 residues processed: 1225 average time/residue: 1.7568 time to fit residues: 2667.1918 Evaluate side-chains 1195 residues out of total 6966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 1121 time to evaluate : 5.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain r residue 104 GLN Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 389 LYS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain H residue 164 ARG Chi-restraints excluded: chain H residue 192 HIS Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 389 LYS Chi-restraints excluded: chain H residue 432 TYR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 269 LEU Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 149 MET Chi-restraints excluded: chain J residue 159 GLU Chi-restraints excluded: chain J residue 315 VAL Chi-restraints excluded: chain I residue 155 GLU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 349 THR Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 68 VAL Chi-restraints excluded: chain N residue 129 CYS Chi-restraints excluded: chain N residue 333 LEU Chi-restraints excluded: chain N residue 402 LYS Chi-restraints excluded: chain N residue 413 MET Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 313 MET Chi-restraints excluded: chain M residue 349 THR Chi-restraints excluded: chain M residue 433 GLU Chi-restraints excluded: chain P residue 37 HIS Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 129 CYS Chi-restraints excluded: chain P residue 133 GLN Chi-restraints excluded: chain P residue 269 MET Chi-restraints excluded: chain P residue 373 MET Chi-restraints excluded: chain P residue 389 LYS Chi-restraints excluded: chain P residue 405 LEU Chi-restraints excluded: chain R residue 149 MET Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 241 CYS Chi-restraints excluded: chain R residue 332 MET Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain s residue 120 VAL Chi-restraints excluded: chain t residue 120 VAL Chi-restraints excluded: chain v residue 131 LEU Chi-restraints excluded: chain x residue 104 GLN Chi-restraints excluded: chain x residue 122 ARG Chi-restraints excluded: chain y residue 104 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 801 random chunks: chunk 568 optimal weight: 10.0000 chunk 208 optimal weight: 0.9980 chunk 446 optimal weight: 0.9980 chunk 611 optimal weight: 3.9990 chunk 507 optimal weight: 0.0870 chunk 548 optimal weight: 2.9990 chunk 333 optimal weight: 0.7980 chunk 257 optimal weight: 7.9990 chunk 162 optimal weight: 0.8980 chunk 315 optimal weight: 1.9990 chunk 269 optimal weight: 7.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 ASN ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 GLN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN D 6 HIS ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 GLN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 HIS F 334 ASN F 349 ASN F 433 GLN E 249 ASN H 85 GLN H 192 HIS ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 HIS I 256 GLN ** L 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 GLN L 247 GLN L 293 GLN ** L 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 334 ASN ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 249 ASN P 102 ASN P 133 GLN ** P 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 433 GLN O 133 GLN ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 293 GLN Q 88 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.101223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.086775 restraints weight = 120480.823| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.43 r_work: 0.3549 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 65970 Z= 0.180 Angle : 0.588 11.950 89469 Z= 0.300 Chirality : 0.043 0.304 9711 Planarity : 0.004 0.050 11637 Dihedral : 10.701 175.061 9252 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.24 % Allowed : 16.54 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.10), residues: 8055 helix: 1.54 (0.09), residues: 3627 sheet: -0.04 (0.16), residues: 1143 loop : -0.53 (0.11), residues: 3285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 21 HIS 0.015 0.001 HIS H 192 PHE 0.033 0.001 PHE K 255 TYR 0.014 0.001 TYR B 61 ARG 0.010 0.000 ARG H 400 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16110 Ramachandran restraints generated. 8055 Oldfield, 0 Emsley, 8055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16110 Ramachandran restraints generated. 8055 Oldfield, 0 Emsley, 8055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1305 residues out of total 6966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 1150 time to evaluate : 5.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: r 127 MET cc_start: 0.8446 (mmp) cc_final: 0.7976 (mmp) REVERT: B 47 GLU cc_start: 0.8478 (tp30) cc_final: 0.7746 (tp30) REVERT: B 76 ASP cc_start: 0.8924 (t0) cc_final: 0.8437 (m-30) REVERT: B 105 LYS cc_start: 0.8916 (mtpp) cc_final: 0.8563 (mtpp) REVERT: B 116 ASP cc_start: 0.8291 (m-30) cc_final: 0.7600 (m-30) REVERT: B 120 ASP cc_start: 0.8210 (m-30) cc_final: 0.7968 (m-30) REVERT: B 196 GLU cc_start: 0.8568 (pt0) cc_final: 0.8361 (pt0) REVERT: B 207 GLU cc_start: 0.8443 (pp20) cc_final: 0.8199 (pp20) REVERT: B 282 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8432 (pm20) REVERT: B 345 GLU cc_start: 0.8102 (pp20) cc_final: 0.7865 (pp20) REVERT: B 422 GLU cc_start: 0.8176 (tp30) cc_final: 0.7792 (tp30) REVERT: A 76 ASP cc_start: 0.8381 (m-30) cc_final: 0.8175 (m-30) REVERT: A 85 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8347 (mt0) REVERT: A 112 LYS cc_start: 0.8384 (pttt) cc_final: 0.7727 (pttm) REVERT: A 113 GLU cc_start: 0.7804 (mp0) cc_final: 0.7207 (mp0) REVERT: A 209 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8188 (mt) REVERT: A 211 ASP cc_start: 0.8593 (t0) cc_final: 0.8091 (t0) REVERT: A 423 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7991 (pp20) REVERT: D 22 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7566 (tp30) REVERT: D 41 ASP cc_start: 0.8089 (t70) cc_final: 0.7782 (t70) REVERT: D 47 GLU cc_start: 0.8133 (pp20) cc_final: 0.7785 (pp20) REVERT: D 50 ASN cc_start: 0.8988 (p0) cc_final: 0.8578 (p0) REVERT: D 105 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8783 (ttpp) REVERT: D 156 LYS cc_start: 0.8713 (mmtt) cc_final: 0.8474 (mmtt) REVERT: D 159 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8121 (mt-10) REVERT: D 199 ASP cc_start: 0.8192 (t0) cc_final: 0.7895 (t0) REVERT: D 278 ARG cc_start: 0.8353 (tpm170) cc_final: 0.8080 (tpm170) REVERT: D 330 GLU cc_start: 0.7815 (pp20) cc_final: 0.7541 (pp20) REVERT: D 345 GLU cc_start: 0.8370 (pm20) cc_final: 0.8094 (pm20) REVERT: D 405 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8212 (mm) REVERT: D 416 MET cc_start: 0.8731 (mmm) cc_final: 0.8448 (tpt) REVERT: D 422 GLU cc_start: 0.8148 (tp30) cc_final: 0.7531 (tp30) REVERT: D 427 ASP cc_start: 0.8172 (m-30) cc_final: 0.7967 (m-30) REVERT: D 433 GLN cc_start: 0.8472 (tm-30) cc_final: 0.8057 (tm-30) REVERT: C 77 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8083 (tm-30) REVERT: C 84 ARG cc_start: 0.8997 (ttp-110) cc_final: 0.8525 (ptp-170) REVERT: C 103 TYR cc_start: 0.8779 (t80) cc_final: 0.8346 (t80) REVERT: C 115 ILE cc_start: 0.8273 (tp) cc_final: 0.8053 (tp) REVERT: C 413 MET cc_start: 0.8465 (ttm) cc_final: 0.8214 (ttp) REVERT: C 420 GLU cc_start: 0.8224 (pt0) cc_final: 0.7992 (pt0) REVERT: C 423 GLU cc_start: 0.8349 (pp20) cc_final: 0.7994 (pp20) REVERT: C 434 GLU cc_start: 0.8334 (pp20) cc_final: 0.7854 (pp20) REVERT: F 1 MET cc_start: 0.8149 (tpp) cc_final: 0.7677 (tpt) REVERT: F 26 ASP cc_start: 0.8230 (t0) cc_final: 0.7905 (t0) REVERT: F 47 GLU cc_start: 0.8459 (tp30) cc_final: 0.7793 (tp30) REVERT: F 75 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8184 (mmt) REVERT: F 105 LYS cc_start: 0.9233 (mtmt) cc_final: 0.8898 (mtpp) REVERT: F 247 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7817 (tt0) REVERT: F 282 GLN cc_start: 0.8621 (pm20) cc_final: 0.8285 (pm20) REVERT: F 293 GLN cc_start: 0.6786 (mm-40) cc_final: 0.6524 (mm110) REVERT: F 325 MET cc_start: 0.8909 (mmp) cc_final: 0.8417 (mmp) REVERT: F 330 GLU cc_start: 0.6893 (tp30) cc_final: 0.6076 (tp30) REVERT: F 345 GLU cc_start: 0.8188 (pp20) cc_final: 0.7966 (tp30) REVERT: F 372 LYS cc_start: 0.8920 (pptt) cc_final: 0.8436 (pptt) REVERT: F 384 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8490 (mm) REVERT: F 398 MET cc_start: 0.8996 (mtm) cc_final: 0.8779 (mtm) REVERT: E 2 ARG cc_start: 0.8626 (ptt90) cc_final: 0.8321 (mtm-85) REVERT: E 24 TYR cc_start: 0.8794 (m-10) cc_final: 0.8460 (m-10) REVERT: E 205 ASP cc_start: 0.8313 (m-30) cc_final: 0.7857 (p0) REVERT: E 245 ASP cc_start: 0.8647 (p0) cc_final: 0.8295 (p0) REVERT: E 251 ASP cc_start: 0.8216 (t0) cc_final: 0.7740 (t70) REVERT: E 392 ASP cc_start: 0.8686 (m-30) cc_final: 0.8361 (m-30) REVERT: E 413 MET cc_start: 0.7269 (ttt) cc_final: 0.6945 (ttt) REVERT: E 434 GLU cc_start: 0.8421 (pp20) cc_final: 0.7910 (pp20) REVERT: H 1 MET cc_start: 0.8392 (ttm) cc_final: 0.7452 (ttt) REVERT: H 3 GLU cc_start: 0.7739 (mp0) cc_final: 0.7324 (mp0) REVERT: H 26 ASP cc_start: 0.8894 (t70) cc_final: 0.8615 (t0) REVERT: H 47 GLU cc_start: 0.7851 (pp20) cc_final: 0.7576 (pp20) REVERT: H 50 ASN cc_start: 0.9069 (p0) cc_final: 0.8648 (p0) REVERT: H 76 ASP cc_start: 0.9126 (t0) cc_final: 0.8801 (t0) REVERT: H 105 LYS cc_start: 0.9173 (mtpp) cc_final: 0.8810 (mtpp) REVERT: H 156 LYS cc_start: 0.7925 (mmtp) cc_final: 0.7494 (mmtp) REVERT: H 166 MET cc_start: 0.8026 (tpp) cc_final: 0.7472 (tpp) REVERT: H 199 ASP cc_start: 0.8613 (m-30) cc_final: 0.8228 (m-30) REVERT: H 281 GLN cc_start: 0.8782 (pp30) cc_final: 0.8436 (tm-30) REVERT: H 337 ASN cc_start: 0.8746 (m110) cc_final: 0.8125 (m110) REVERT: H 389 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8854 (mtmm) REVERT: H 416 MET cc_start: 0.8432 (tpp) cc_final: 0.8055 (mmm) REVERT: H 422 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7895 (tp30) REVERT: H 427 ASP cc_start: 0.8436 (m-30) cc_final: 0.8036 (m-30) REVERT: G 80 THR cc_start: 0.8972 (m) cc_final: 0.8647 (t) REVERT: G 85 GLN cc_start: 0.8798 (pt0) cc_final: 0.8183 (pp30) REVERT: G 154 MET cc_start: 0.8842 (mmm) cc_final: 0.8571 (mtp) REVERT: G 155 GLU cc_start: 0.8501 (pp20) cc_final: 0.8296 (pp20) REVERT: G 168 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8330 (pt0) REVERT: G 211 ASP cc_start: 0.8866 (t0) cc_final: 0.8594 (t70) REVERT: G 255 PHE cc_start: 0.7873 (t80) cc_final: 0.7382 (t80) REVERT: G 290 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7365 (pm20) REVERT: G 342 GLN cc_start: 0.8273 (mp10) cc_final: 0.7995 (mp10) REVERT: G 423 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7902 (tm-30) REVERT: G 425 MET cc_start: 0.8645 (mmm) cc_final: 0.8394 (tpp) REVERT: G 431 ASP cc_start: 0.8125 (t70) cc_final: 0.7470 (m-30) REVERT: G 433 GLU cc_start: 0.8487 (tp30) cc_final: 0.8022 (tp30) REVERT: G 434 GLU cc_start: 0.8415 (pp20) cc_final: 0.8124 (pp20) REVERT: J 3 GLU cc_start: 0.7907 (mp0) cc_final: 0.6956 (mp0) REVERT: J 26 ASP cc_start: 0.8587 (t0) cc_final: 0.8226 (t0) REVERT: J 76 ASP cc_start: 0.8772 (OUTLIER) cc_final: 0.8547 (t0) REVERT: J 127 GLU cc_start: 0.8121 (mp0) cc_final: 0.7747 (mp0) REVERT: J 163 ASP cc_start: 0.8505 (p0) cc_final: 0.8133 (p0) REVERT: J 166 MET cc_start: 0.8761 (tpt) cc_final: 0.8478 (tpt) REVERT: J 196 GLU cc_start: 0.8174 (mp0) cc_final: 0.7875 (mp0) REVERT: J 207 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8431 (mm-30) REVERT: J 281 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8394 (tm-30) REVERT: J 330 GLU cc_start: 0.8123 (pp20) cc_final: 0.7839 (pp20) REVERT: J 414 ASP cc_start: 0.8801 (p0) cc_final: 0.8583 (p0) REVERT: I 71 GLU cc_start: 0.7508 (pt0) cc_final: 0.7012 (pm20) REVERT: I 76 ASP cc_start: 0.8266 (m-30) cc_final: 0.7691 (m-30) REVERT: I 128 GLN cc_start: 0.9013 (tt0) cc_final: 0.8531 (tm-30) REVERT: I 211 ASP cc_start: 0.8728 (t0) cc_final: 0.8393 (t0) REVERT: I 251 ASP cc_start: 0.7400 (t70) cc_final: 0.7016 (t70) REVERT: I 282 TYR cc_start: 0.9024 (m-80) cc_final: 0.8800 (m-80) REVERT: I 423 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7722 (tm-30) REVERT: I 430 LYS cc_start: 0.8464 (mmmm) cc_final: 0.7786 (mmmm) REVERT: I 434 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8110 (mt-10) REVERT: L 1 MET cc_start: 0.9191 (mmm) cc_final: 0.8910 (mmm) REVERT: L 55 GLU cc_start: 0.7886 (tp30) cc_final: 0.7571 (tp30) REVERT: L 113 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8312 (tm-30) REVERT: L 127 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7980 (mm-30) REVERT: L 159 GLU cc_start: 0.7788 (pp20) cc_final: 0.7488 (pp20) REVERT: L 166 MET cc_start: 0.8312 (tpp) cc_final: 0.8091 (tpp) REVERT: L 203 CYS cc_start: 0.9136 (t) cc_final: 0.8758 (p) REVERT: L 207 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8219 (tp30) REVERT: L 214 PHE cc_start: 0.8425 (m-80) cc_final: 0.8082 (m-80) REVERT: L 281 GLN cc_start: 0.8685 (tm-30) cc_final: 0.8481 (tm-30) REVERT: L 299 LYS cc_start: 0.8803 (tppp) cc_final: 0.8307 (tptt) REVERT: L 322 ARG cc_start: 0.8204 (mmp80) cc_final: 0.7747 (mmp80) REVERT: L 351 VAL cc_start: 0.8272 (OUTLIER) cc_final: 0.7971 (t) REVERT: L 372 LYS cc_start: 0.8749 (pmtt) cc_final: 0.8530 (pptt) REVERT: L 393 GLU cc_start: 0.8670 (pp20) cc_final: 0.8307 (pp20) REVERT: L 420 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8041 (pp20) REVERT: L 427 ASP cc_start: 0.8378 (p0) cc_final: 0.8066 (p0) REVERT: K 24 TYR cc_start: 0.8822 (m-10) cc_final: 0.8586 (m-10) REVERT: K 127 ASP cc_start: 0.8929 (OUTLIER) cc_final: 0.8490 (m-30) REVERT: K 133 GLN cc_start: 0.8351 (mm-40) cc_final: 0.8037 (mt0) REVERT: K 176 GLN cc_start: 0.9021 (mp10) cc_final: 0.8727 (mp10) REVERT: K 251 ASP cc_start: 0.7381 (t0) cc_final: 0.6788 (t0) REVERT: K 277 SER cc_start: 0.8913 (m) cc_final: 0.8513 (p) REVERT: K 290 GLU cc_start: 0.8249 (pp20) cc_final: 0.7940 (pp20) REVERT: K 349 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8138 (p) REVERT: K 423 GLU cc_start: 0.8112 (pp20) cc_final: 0.7871 (pp20) REVERT: K 433 GLU cc_start: 0.8783 (tp30) cc_final: 0.8542 (tp30) REVERT: K 434 GLU cc_start: 0.8435 (pp20) cc_final: 0.7970 (pp20) REVERT: N 1 MET cc_start: 0.8548 (tpt) cc_final: 0.8047 (tpp) REVERT: N 22 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8054 (tm-30) REVERT: N 50 ASN cc_start: 0.8854 (p0) cc_final: 0.8389 (p0) REVERT: N 116 ASP cc_start: 0.8648 (t0) cc_final: 0.8331 (t0) REVERT: N 127 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8593 (mm-30) REVERT: N 159 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8212 (mp0) REVERT: N 207 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8179 (mm-30) REVERT: N 269 MET cc_start: 0.8431 (mtp) cc_final: 0.8189 (mtt) REVERT: N 281 GLN cc_start: 0.8906 (tm-30) cc_final: 0.8434 (tm-30) REVERT: N 338 LYS cc_start: 0.8763 (mtmm) cc_final: 0.8363 (mtmm) REVERT: N 345 GLU cc_start: 0.8687 (pm20) cc_final: 0.8357 (pm20) REVERT: N 373 MET cc_start: 0.9291 (ptp) cc_final: 0.8888 (ptm) REVERT: N 422 GLU cc_start: 0.8422 (tp30) cc_final: 0.7799 (tp30) REVERT: N 433 GLN cc_start: 0.8818 (tp40) cc_final: 0.8539 (tp40) REVERT: M 85 GLN cc_start: 0.8888 (pt0) cc_final: 0.8665 (pm20) REVERT: M 203 MET cc_start: 0.9196 (mmm) cc_final: 0.8630 (mmm) REVERT: M 313 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8597 (mtp) REVERT: M 420 GLU cc_start: 0.8275 (pp20) cc_final: 0.7660 (pp20) REVERT: M 423 GLU cc_start: 0.8585 (pp20) cc_final: 0.8298 (pp20) REVERT: M 430 LYS cc_start: 0.8696 (mmmt) cc_final: 0.7800 (mmmm) REVERT: M 431 ASP cc_start: 0.8198 (t0) cc_final: 0.7820 (t0) REVERT: M 433 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7567 (pm20) REVERT: M 434 GLU cc_start: 0.8437 (pp20) cc_final: 0.8161 (pp20) REVERT: P 110 GLU cc_start: 0.7705 (pm20) cc_final: 0.7491 (pm20) REVERT: P 127 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8252 (mm-30) REVERT: P 293 GLN cc_start: 0.8621 (pp30) cc_final: 0.8133 (pp30) REVERT: P 338 LYS cc_start: 0.8996 (mptp) cc_final: 0.8684 (ptpp) REVERT: P 422 GLU cc_start: 0.8306 (tp30) cc_final: 0.7819 (tp30) REVERT: O 71 GLU cc_start: 0.7356 (pm20) cc_final: 0.7065 (mp0) REVERT: O 123 ARG cc_start: 0.9215 (tmm-80) cc_final: 0.8925 (ttp80) REVERT: O 154 MET cc_start: 0.9116 (mmm) cc_final: 0.8693 (mmm) REVERT: O 205 ASP cc_start: 0.7989 (t0) cc_final: 0.7702 (t70) REVERT: O 211 ASP cc_start: 0.8631 (t0) cc_final: 0.8251 (t0) REVERT: O 326 LYS cc_start: 0.5560 (mmtp) cc_final: 0.5167 (mmtm) REVERT: O 423 GLU cc_start: 0.8285 (pp20) cc_final: 0.7978 (pp20) REVERT: O 430 LYS cc_start: 0.8774 (tppp) cc_final: 0.8470 (tppp) REVERT: R 47 GLU cc_start: 0.7914 (pp20) cc_final: 0.7557 (tm-30) REVERT: R 71 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8030 (mp0) REVERT: R 76 ASP cc_start: 0.8805 (t0) cc_final: 0.8439 (p0) REVERT: R 113 GLU cc_start: 0.8667 (tp30) cc_final: 0.8411 (tp30) REVERT: R 127 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7948 (mm-30) REVERT: R 159 GLU cc_start: 0.8357 (tm-30) cc_final: 0.7953 (pp20) REVERT: R 183 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7984 (mt-10) REVERT: R 247 GLN cc_start: 0.8949 (mp10) cc_final: 0.8482 (mm-40) REVERT: R 281 GLN cc_start: 0.9115 (tp40) cc_final: 0.8714 (tp40) REVERT: R 299 LYS cc_start: 0.8169 (tmmt) cc_final: 0.7958 (tmmt) REVERT: R 301 MET cc_start: 0.9249 (mmt) cc_final: 0.9048 (mmp) REVERT: R 330 GLU cc_start: 0.6933 (tp30) cc_final: 0.5660 (tp30) REVERT: R 338 LYS cc_start: 0.7050 (pttt) cc_final: 0.6823 (pptt) REVERT: R 349 ASN cc_start: 0.7603 (t0) cc_final: 0.7164 (t0) REVERT: R 393 GLU cc_start: 0.8317 (pp20) cc_final: 0.8093 (pp20) REVERT: R 427 ASP cc_start: 0.8528 (m-30) cc_final: 0.8118 (m-30) REVERT: Q 2 ARG cc_start: 0.8554 (ttp-110) cc_final: 0.8260 (ttp80) REVERT: Q 77 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8556 (tm-30) REVERT: Q 128 GLN cc_start: 0.8432 (tm-30) cc_final: 0.8086 (tm-30) REVERT: Q 205 ASP cc_start: 0.8149 (m-30) cc_final: 0.7575 (p0) REVERT: Q 285 GLN cc_start: 0.4735 (mm-40) cc_final: 0.4046 (mp10) REVERT: Q 302 MET cc_start: 0.8589 (mtm) cc_final: 0.8362 (mtm) REVERT: Q 313 MET cc_start: 0.8709 (mtp) cc_final: 0.8202 (mtp) REVERT: Q 357 TYR cc_start: 0.8707 (m-80) cc_final: 0.8360 (m-80) REVERT: Q 377 MET cc_start: 0.8875 (ttp) cc_final: 0.8578 (ttp) REVERT: Q 386 GLU cc_start: 0.8204 (mp0) cc_final: 0.7710 (mp0) REVERT: Q 423 GLU cc_start: 0.8847 (pp20) cc_final: 0.8579 (pp20) REVERT: Q 430 LYS cc_start: 0.8905 (tppt) cc_final: 0.8586 (tppp) REVERT: Q 433 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8093 (tp30) REVERT: Q 434 GLU cc_start: 0.8593 (pp20) cc_final: 0.8329 (pp20) REVERT: s 127 MET cc_start: 0.8219 (tpt) cc_final: 0.8010 (tpt) REVERT: t 93 MET cc_start: 0.8894 (tpt) cc_final: 0.8390 (tpt) REVERT: t 127 MET cc_start: 0.8075 (mmp) cc_final: 0.7755 (mmp) REVERT: v 98 LYS cc_start: 0.8817 (mmmt) cc_final: 0.8514 (mmmt) REVERT: v 127 MET cc_start: 0.8257 (mmp) cc_final: 0.7684 (mmp) REVERT: w 93 MET cc_start: 0.8809 (tpt) cc_final: 0.8490 (tpt) REVERT: w 122 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8200 (ptp-170) REVERT: x 127 MET cc_start: 0.8380 (tpt) cc_final: 0.7901 (tpt) REVERT: y 127 MET cc_start: 0.8556 (mmp) cc_final: 0.8103 (mmp) REVERT: z 93 MET cc_start: 0.8597 (tpp) cc_final: 0.8203 (tpp) REVERT: z 97 TYR cc_start: 0.8399 (t80) cc_final: 0.7697 (t80) REVERT: z 127 MET cc_start: 0.8057 (mmp) cc_final: 0.7675 (mmp) outliers start: 155 outliers final: 62 residues processed: 1223 average time/residue: 1.7052 time to fit residues: 2595.4894 Evaluate side-chains 1180 residues out of total 6966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 1098 time to evaluate : 5.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain r residue 104 GLN Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 133 GLN Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 389 LYS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 326 LYS Chi-restraints excluded: chain H residue 389 LYS Chi-restraints excluded: chain H residue 432 TYR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 339 ARG Chi-restraints excluded: chain G residue 402 ARG Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 159 GLU Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain I residue 49 PHE Chi-restraints excluded: chain I residue 155 GLU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 351 VAL Chi-restraints excluded: chain L residue 420 GLU Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 349 THR Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 68 VAL Chi-restraints excluded: chain N residue 129 CYS Chi-restraints excluded: chain N residue 333 LEU Chi-restraints excluded: chain N residue 402 LYS Chi-restraints excluded: chain N residue 413 MET Chi-restraints excluded: chain N residue 425 MET Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 313 MET Chi-restraints excluded: chain M residue 433 GLU Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 373 MET Chi-restraints excluded: chain P residue 389 LYS Chi-restraints excluded: chain P residue 405 LEU Chi-restraints excluded: chain O residue 133 GLN Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 149 MET Chi-restraints excluded: chain R residue 241 CYS Chi-restraints excluded: chain R residue 332 MET Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain s residue 120 VAL Chi-restraints excluded: chain t residue 104 GLN Chi-restraints excluded: chain t residue 120 VAL Chi-restraints excluded: chain u residue 127 MET Chi-restraints excluded: chain v residue 104 GLN Chi-restraints excluded: chain w residue 122 ARG Chi-restraints excluded: chain w residue 127 MET Chi-restraints excluded: chain x residue 104 GLN Chi-restraints excluded: chain y residue 104 GLN Chi-restraints excluded: chain z residue 104 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 801 random chunks: chunk 756 optimal weight: 8.9990 chunk 344 optimal weight: 7.9990 chunk 635 optimal weight: 5.9990 chunk 485 optimal weight: 0.9990 chunk 230 optimal weight: 6.9990 chunk 570 optimal weight: 1.9990 chunk 539 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 204 optimal weight: 6.9990 chunk 715 optimal weight: 9.9990 chunk 199 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN A 50 ASN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 GLN D 197 ASN ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 HIS F 266 HIS F 334 ASN F 349 ASN E 249 ASN H 139 HIS H 192 HIS ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 294 GLN ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 ASN ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 107 HIS I 249 ASN ** L 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 133 GLN L 136 GLN L 293 GLN ** L 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 334 ASN ** N 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 249 ASN P 59 ASN P 133 GLN P 167 ASN ** P 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 433 GLN ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 293 GLN R 394 GLN R 433 GLN Q 88 HIS Q 258 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.098382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.083886 restraints weight = 120427.762| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.39 r_work: 0.3490 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 65970 Z= 0.289 Angle : 0.634 11.560 89469 Z= 0.323 Chirality : 0.046 0.292 9711 Planarity : 0.004 0.053 11637 Dihedral : 10.802 176.202 9252 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.43 % Allowed : 17.46 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.57 (0.10), residues: 8055 helix: 1.37 (0.09), residues: 3681 sheet: -0.07 (0.16), residues: 1143 loop : -0.53 (0.11), residues: 3231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 388 HIS 0.011 0.001 HIS H 192 PHE 0.054 0.002 PHE I 49 TYR 0.022 0.001 TYR J 435 ARG 0.012 0.001 ARG N 322 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16110 Ramachandran restraints generated. 8055 Oldfield, 0 Emsley, 8055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16110 Ramachandran restraints generated. 8055 Oldfield, 0 Emsley, 8055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1315 residues out of total 6966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 1147 time to evaluate : 5.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: r 127 MET cc_start: 0.8557 (mmp) cc_final: 0.8111 (mmp) REVERT: B 47 GLU cc_start: 0.8584 (tp30) cc_final: 0.7866 (tp30) REVERT: B 76 ASP cc_start: 0.8954 (t0) cc_final: 0.8516 (m-30) REVERT: B 105 LYS cc_start: 0.8922 (mtpp) cc_final: 0.8536 (mtpp) REVERT: B 109 THR cc_start: 0.8471 (m) cc_final: 0.8045 (p) REVERT: B 116 ASP cc_start: 0.8314 (m-30) cc_final: 0.7620 (m-30) REVERT: B 120 ASP cc_start: 0.8217 (m-30) cc_final: 0.7983 (m-30) REVERT: B 207 GLU cc_start: 0.8519 (pp20) cc_final: 0.8233 (pp20) REVERT: B 282 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8465 (pm20) REVERT: B 422 GLU cc_start: 0.8133 (tp30) cc_final: 0.7721 (tp30) REVERT: A 85 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8412 (mt0) REVERT: A 112 LYS cc_start: 0.8330 (pttt) cc_final: 0.7629 (pttm) REVERT: A 113 GLU cc_start: 0.7898 (mp0) cc_final: 0.7235 (mp0) REVERT: A 155 GLU cc_start: 0.8457 (pp20) cc_final: 0.8020 (pp20) REVERT: A 209 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8435 (mt) REVERT: A 211 ASP cc_start: 0.8575 (t0) cc_final: 0.8347 (t0) REVERT: A 423 GLU cc_start: 0.8306 (tm-30) cc_final: 0.8101 (pp20) REVERT: D 22 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7583 (tp30) REVERT: D 41 ASP cc_start: 0.8333 (t70) cc_final: 0.8031 (t70) REVERT: D 47 GLU cc_start: 0.8107 (pp20) cc_final: 0.7831 (pp20) REVERT: D 50 ASN cc_start: 0.8935 (p0) cc_final: 0.8517 (p0) REVERT: D 90 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.8304 (p0) REVERT: D 105 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8728 (ttpp) REVERT: D 156 LYS cc_start: 0.8776 (mmtt) cc_final: 0.8567 (mmtt) REVERT: D 159 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8153 (mt-10) REVERT: D 199 ASP cc_start: 0.8414 (t0) cc_final: 0.8072 (t0) REVERT: D 247 GLN cc_start: 0.8569 (mp10) cc_final: 0.8039 (mp10) REVERT: D 278 ARG cc_start: 0.8289 (tpm170) cc_final: 0.7820 (tpm170) REVERT: D 330 GLU cc_start: 0.7868 (pp20) cc_final: 0.7563 (pp20) REVERT: D 345 GLU cc_start: 0.8525 (pm20) cc_final: 0.8260 (pm20) REVERT: D 349 ASN cc_start: 0.6582 (t0) cc_final: 0.6247 (t0) REVERT: D 405 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8386 (mm) REVERT: D 422 GLU cc_start: 0.8111 (tp30) cc_final: 0.7713 (tp30) REVERT: D 433 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8166 (tm-30) REVERT: C 77 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8172 (tm-30) REVERT: C 103 TYR cc_start: 0.8902 (t80) cc_final: 0.8316 (t80) REVERT: C 413 MET cc_start: 0.8607 (ttm) cc_final: 0.8396 (ttp) REVERT: C 417 GLU cc_start: 0.8085 (tp30) cc_final: 0.7595 (tp30) REVERT: C 420 GLU cc_start: 0.8271 (pt0) cc_final: 0.7838 (pt0) REVERT: C 423 GLU cc_start: 0.8456 (pp20) cc_final: 0.8080 (pp20) REVERT: C 434 GLU cc_start: 0.8478 (pp20) cc_final: 0.8004 (pp20) REVERT: F 47 GLU cc_start: 0.8461 (tp30) cc_final: 0.7798 (tp30) REVERT: F 75 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8159 (mmt) REVERT: F 110 GLU cc_start: 0.8446 (pp20) cc_final: 0.8235 (pp20) REVERT: F 113 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7797 (mp0) REVERT: F 247 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7819 (tt0) REVERT: F 282 GLN cc_start: 0.8720 (pm20) cc_final: 0.8378 (pm20) REVERT: F 293 GLN cc_start: 0.6760 (mm-40) cc_final: 0.6544 (mm110) REVERT: F 330 GLU cc_start: 0.6792 (tp30) cc_final: 0.6070 (tp30) REVERT: F 345 GLU cc_start: 0.8230 (pp20) cc_final: 0.7999 (tp30) REVERT: F 372 LYS cc_start: 0.8885 (pptt) cc_final: 0.8360 (pptt) REVERT: F 384 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8544 (mm) REVERT: F 413 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8882 (mtm) REVERT: E 24 TYR cc_start: 0.8848 (m-10) cc_final: 0.8519 (m-10) REVERT: E 205 ASP cc_start: 0.8418 (m-30) cc_final: 0.8146 (p0) REVERT: E 214 ARG cc_start: 0.9239 (OUTLIER) cc_final: 0.8545 (ttm170) REVERT: E 251 ASP cc_start: 0.8250 (t0) cc_final: 0.7938 (t70) REVERT: E 392 ASP cc_start: 0.8752 (m-30) cc_final: 0.8440 (m-30) REVERT: E 434 GLU cc_start: 0.8376 (pp20) cc_final: 0.7847 (pp20) REVERT: H 1 MET cc_start: 0.8484 (ttm) cc_final: 0.7929 (ttm) REVERT: H 3 GLU cc_start: 0.7737 (mp0) cc_final: 0.7319 (mp0) REVERT: H 26 ASP cc_start: 0.8902 (t70) cc_final: 0.8627 (t0) REVERT: H 47 GLU cc_start: 0.7924 (pp20) cc_final: 0.7661 (pp20) REVERT: H 50 ASN cc_start: 0.9034 (p0) cc_final: 0.8623 (p0) REVERT: H 76 ASP cc_start: 0.9163 (t0) cc_final: 0.8817 (t0) REVERT: H 105 LYS cc_start: 0.9186 (mtpp) cc_final: 0.8841 (mtpp) REVERT: H 156 LYS cc_start: 0.8046 (mmtp) cc_final: 0.7395 (mmtm) REVERT: H 166 MET cc_start: 0.8198 (tpp) cc_final: 0.7646 (tpp) REVERT: H 199 ASP cc_start: 0.8726 (m-30) cc_final: 0.8281 (m-30) REVERT: H 416 MET cc_start: 0.8571 (tpp) cc_final: 0.8234 (mmm) REVERT: H 422 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7978 (tp30) REVERT: H 427 ASP cc_start: 0.8457 (m-30) cc_final: 0.8105 (m-30) REVERT: H 433 GLN cc_start: 0.8983 (mm-40) cc_final: 0.8732 (tm-30) REVERT: G 80 THR cc_start: 0.8989 (m) cc_final: 0.8660 (t) REVERT: G 85 GLN cc_start: 0.8815 (pt0) cc_final: 0.8182 (pp30) REVERT: G 154 MET cc_start: 0.8748 (mmm) cc_final: 0.8487 (mtp) REVERT: G 168 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8301 (pt0) REVERT: G 211 ASP cc_start: 0.8832 (t0) cc_final: 0.8510 (t70) REVERT: G 255 PHE cc_start: 0.7950 (t80) cc_final: 0.7473 (t80) REVERT: G 290 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7486 (pm20) REVERT: G 342 GLN cc_start: 0.8252 (mp10) cc_final: 0.7931 (mp10) REVERT: G 423 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8066 (tm-30) REVERT: G 425 MET cc_start: 0.8852 (mmm) cc_final: 0.8546 (tpp) REVERT: G 431 ASP cc_start: 0.8322 (t70) cc_final: 0.7673 (m-30) REVERT: G 433 GLU cc_start: 0.8583 (tp30) cc_final: 0.8140 (tp30) REVERT: G 434 GLU cc_start: 0.8506 (pp20) cc_final: 0.8214 (pp20) REVERT: J 3 GLU cc_start: 0.8023 (mp0) cc_final: 0.6870 (mp0) REVERT: J 26 ASP cc_start: 0.8623 (t0) cc_final: 0.8267 (t0) REVERT: J 76 ASP cc_start: 0.8825 (m-30) cc_final: 0.8604 (t0) REVERT: J 127 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7754 (mp0) REVERT: J 163 ASP cc_start: 0.8455 (p0) cc_final: 0.8111 (p0) REVERT: J 166 MET cc_start: 0.8822 (tpt) cc_final: 0.8587 (tpt) REVERT: J 207 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8572 (mm-30) REVERT: J 281 GLN cc_start: 0.8796 (tm-30) cc_final: 0.8414 (tm-30) REVERT: J 414 ASP cc_start: 0.8787 (p0) cc_final: 0.8530 (p0) REVERT: J 417 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8017 (tm-30) REVERT: I 71 GLU cc_start: 0.7528 (pt0) cc_final: 0.7021 (pm20) REVERT: I 76 ASP cc_start: 0.8398 (m-30) cc_final: 0.7730 (m-30) REVERT: I 128 GLN cc_start: 0.9083 (tt0) cc_final: 0.8526 (tm-30) REVERT: I 154 MET cc_start: 0.9021 (mmt) cc_final: 0.8502 (mmt) REVERT: I 211 ASP cc_start: 0.8702 (t0) cc_final: 0.8308 (t0) REVERT: I 251 ASP cc_start: 0.7487 (t70) cc_final: 0.7121 (t70) REVERT: I 279 GLU cc_start: 0.8326 (pp20) cc_final: 0.8108 (pm20) REVERT: I 423 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7950 (tm-30) REVERT: I 430 LYS cc_start: 0.8607 (mmmm) cc_final: 0.7926 (mmmm) REVERT: I 434 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8274 (mt-10) REVERT: L 1 MET cc_start: 0.9162 (mmm) cc_final: 0.8874 (mmm) REVERT: L 50 ASN cc_start: 0.8752 (p0) cc_final: 0.8546 (p0) REVERT: L 55 GLU cc_start: 0.7933 (tp30) cc_final: 0.7647 (tp30) REVERT: L 105 LYS cc_start: 0.9108 (ptmt) cc_final: 0.8714 (ptmm) REVERT: L 113 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8401 (tm-30) REVERT: L 127 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8217 (mm-30) REVERT: L 133 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.7733 (pp30) REVERT: L 159 GLU cc_start: 0.7909 (pp20) cc_final: 0.7635 (pp20) REVERT: L 166 MET cc_start: 0.8276 (tpp) cc_final: 0.8048 (tpp) REVERT: L 203 CYS cc_start: 0.9087 (t) cc_final: 0.8776 (p) REVERT: L 207 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8212 (tp30) REVERT: L 214 PHE cc_start: 0.8424 (m-80) cc_final: 0.8149 (m-80) REVERT: L 281 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8514 (tm-30) REVERT: L 299 LYS cc_start: 0.8772 (tppp) cc_final: 0.8372 (tptt) REVERT: L 338 LYS cc_start: 0.7041 (tttt) cc_final: 0.6547 (pttt) REVERT: L 420 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8126 (pp20) REVERT: K 24 TYR cc_start: 0.8885 (m-10) cc_final: 0.8634 (m-10) REVERT: K 127 ASP cc_start: 0.9019 (OUTLIER) cc_final: 0.8596 (m-30) REVERT: K 133 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8015 (mm-40) REVERT: K 176 GLN cc_start: 0.9010 (mp10) cc_final: 0.8771 (mp10) REVERT: K 251 ASP cc_start: 0.7529 (t0) cc_final: 0.7052 (t0) REVERT: K 290 GLU cc_start: 0.8312 (pp20) cc_final: 0.8026 (pp20) REVERT: K 309 HIS cc_start: 0.8738 (m170) cc_final: 0.8046 (m170) REVERT: K 386 GLU cc_start: 0.8167 (pp20) cc_final: 0.7827 (pp20) REVERT: K 420 GLU cc_start: 0.8486 (pt0) cc_final: 0.8233 (pt0) REVERT: K 433 GLU cc_start: 0.8677 (tp30) cc_final: 0.8454 (tp30) REVERT: K 434 GLU cc_start: 0.8530 (pp20) cc_final: 0.8055 (pp20) REVERT: N 1 MET cc_start: 0.8760 (tpt) cc_final: 0.8384 (tpp) REVERT: N 22 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8138 (tm-30) REVERT: N 37 HIS cc_start: 0.8245 (m90) cc_final: 0.7821 (m90) REVERT: N 50 ASN cc_start: 0.8879 (p0) cc_final: 0.8465 (p0) REVERT: N 75 MET cc_start: 0.8809 (mmp) cc_final: 0.8582 (mmm) REVERT: N 116 ASP cc_start: 0.8714 (t0) cc_final: 0.8405 (t0) REVERT: N 127 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8556 (mm-30) REVERT: N 159 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8190 (mp0) REVERT: N 207 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8175 (mm-30) REVERT: N 281 GLN cc_start: 0.8939 (tm-30) cc_final: 0.8575 (tm-30) REVERT: N 338 LYS cc_start: 0.8786 (mtmm) cc_final: 0.8385 (mtmm) REVERT: N 345 GLU cc_start: 0.8680 (pm20) cc_final: 0.8367 (pm20) REVERT: N 373 MET cc_start: 0.9286 (ptp) cc_final: 0.8832 (ptm) REVERT: N 422 GLU cc_start: 0.8332 (tp30) cc_final: 0.7729 (tp30) REVERT: N 433 GLN cc_start: 0.8845 (tp40) cc_final: 0.8599 (tp40) REVERT: M 203 MET cc_start: 0.9144 (mmm) cc_final: 0.8679 (mmm) REVERT: M 221 ARG cc_start: 0.8596 (ptp-110) cc_final: 0.7981 (ptp-110) REVERT: M 313 MET cc_start: 0.8920 (mtm) cc_final: 0.8631 (mtp) REVERT: M 420 GLU cc_start: 0.8338 (pp20) cc_final: 0.7729 (pp20) REVERT: M 423 GLU cc_start: 0.8533 (pp20) cc_final: 0.8268 (pp20) REVERT: M 430 LYS cc_start: 0.8781 (mmmt) cc_final: 0.7911 (mmmm) REVERT: M 433 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7790 (pm20) REVERT: M 434 GLU cc_start: 0.8511 (pp20) cc_final: 0.8159 (pp20) REVERT: P 96 GLN cc_start: 0.8270 (pm20) cc_final: 0.8048 (mm-40) REVERT: P 110 GLU cc_start: 0.7773 (pm20) cc_final: 0.7565 (pm20) REVERT: P 127 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8392 (mm-30) REVERT: P 207 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8346 (tm-30) REVERT: P 293 GLN cc_start: 0.8623 (pp30) cc_final: 0.8171 (pp30) REVERT: P 422 GLU cc_start: 0.8237 (tp30) cc_final: 0.7783 (tp30) REVERT: O 73 THR cc_start: 0.8465 (p) cc_final: 0.7495 (p) REVERT: O 77 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7691 (pm20) REVERT: O 123 ARG cc_start: 0.9256 (tmm-80) cc_final: 0.8965 (ttp80) REVERT: O 154 MET cc_start: 0.9109 (mmm) cc_final: 0.8689 (mmm) REVERT: O 205 ASP cc_start: 0.8044 (t0) cc_final: 0.7818 (t70) REVERT: O 211 ASP cc_start: 0.8620 (t0) cc_final: 0.8226 (t0) REVERT: O 251 ASP cc_start: 0.7529 (t0) cc_final: 0.7287 (t0) REVERT: O 326 LYS cc_start: 0.5482 (mmtp) cc_final: 0.4622 (mmtm) REVERT: O 423 GLU cc_start: 0.8341 (pp20) cc_final: 0.7931 (pp20) REVERT: O 430 LYS cc_start: 0.8782 (tppp) cc_final: 0.8504 (tppp) REVERT: O 434 GLU cc_start: 0.8547 (pp20) cc_final: 0.8152 (pp20) REVERT: R 1 MET cc_start: 0.8868 (mmm) cc_final: 0.8645 (tpt) REVERT: R 47 GLU cc_start: 0.7907 (pp20) cc_final: 0.7465 (tm-30) REVERT: R 76 ASP cc_start: 0.8777 (t0) cc_final: 0.8440 (p0) REVERT: R 113 GLU cc_start: 0.8642 (tp30) cc_final: 0.8383 (tp30) REVERT: R 127 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8047 (mm-30) REVERT: R 159 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7992 (pp20) REVERT: R 183 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8107 (mt-10) REVERT: R 281 GLN cc_start: 0.9111 (tp40) cc_final: 0.8695 (tp40) REVERT: R 293 GLN cc_start: 0.6940 (mm-40) cc_final: 0.6727 (mm110) REVERT: R 330 GLU cc_start: 0.6995 (tp30) cc_final: 0.6429 (tp30) REVERT: R 338 LYS cc_start: 0.7422 (pttt) cc_final: 0.7157 (pptt) REVERT: R 349 ASN cc_start: 0.7646 (t0) cc_final: 0.7227 (t0) REVERT: R 427 ASP cc_start: 0.8580 (m-30) cc_final: 0.8192 (m-30) REVERT: Q 2 ARG cc_start: 0.8639 (ttp-110) cc_final: 0.8308 (ttp80) REVERT: Q 77 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8600 (tm-30) REVERT: Q 90 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8590 (mp0) REVERT: Q 128 GLN cc_start: 0.8478 (tm-30) cc_final: 0.8083 (tm-30) REVERT: Q 205 ASP cc_start: 0.8146 (m-30) cc_final: 0.7631 (p0) REVERT: Q 285 GLN cc_start: 0.4848 (mm-40) cc_final: 0.4024 (mp10) REVERT: Q 302 MET cc_start: 0.8693 (mtm) cc_final: 0.8443 (mtm) REVERT: Q 313 MET cc_start: 0.8785 (mtp) cc_final: 0.8322 (mtp) REVERT: Q 357 TYR cc_start: 0.8813 (m-80) cc_final: 0.8435 (m-80) REVERT: Q 386 GLU cc_start: 0.8367 (mp0) cc_final: 0.7873 (mp0) REVERT: Q 423 GLU cc_start: 0.8843 (pp20) cc_final: 0.8613 (pp20) REVERT: Q 430 LYS cc_start: 0.8943 (tppt) cc_final: 0.8513 (tppp) REVERT: Q 433 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8064 (tm-30) REVERT: Q 434 GLU cc_start: 0.8566 (pp20) cc_final: 0.8281 (pp20) REVERT: t 93 MET cc_start: 0.8932 (tpt) cc_final: 0.8403 (tpt) REVERT: t 127 MET cc_start: 0.8052 (mmp) cc_final: 0.7704 (mmp) REVERT: v 98 LYS cc_start: 0.8880 (mmmt) cc_final: 0.8569 (mmmt) REVERT: v 127 MET cc_start: 0.8231 (mmp) cc_final: 0.7679 (mmp) REVERT: w 93 MET cc_start: 0.8848 (tpt) cc_final: 0.8532 (tpt) REVERT: x 93 MET cc_start: 0.7767 (mmt) cc_final: 0.7345 (mmt) REVERT: x 127 MET cc_start: 0.8387 (tpt) cc_final: 0.7950 (tpt) REVERT: y 127 MET cc_start: 0.8594 (mmp) cc_final: 0.8156 (mmp) REVERT: z 93 MET cc_start: 0.8617 (tpp) cc_final: 0.8247 (tpp) REVERT: z 97 TYR cc_start: 0.8423 (t80) cc_final: 0.7718 (t80) REVERT: z 127 MET cc_start: 0.8277 (mmp) cc_final: 0.7881 (mmp) outliers start: 168 outliers final: 64 residues processed: 1233 average time/residue: 1.7626 time to fit residues: 2702.2417 Evaluate side-chains 1179 residues out of total 6966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 1095 time to evaluate : 5.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 133 GLN Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 389 LYS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 192 HIS Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain F residue 413 MET Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain H residue 133 GLN Chi-restraints excluded: chain H residue 192 HIS Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 373 MET Chi-restraints excluded: chain H residue 389 LYS Chi-restraints excluded: chain H residue 425 MET Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 269 LEU Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 339 ARG Chi-restraints excluded: chain G residue 402 ARG Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 127 GLU Chi-restraints excluded: chain J residue 159 GLU Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 315 VAL Chi-restraints excluded: chain J residue 323 MET Chi-restraints excluded: chain I residue 155 GLU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain L residue 133 GLN Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 420 GLU Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 338 LYS Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 68 VAL Chi-restraints excluded: chain N residue 129 CYS Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 333 LEU Chi-restraints excluded: chain N residue 402 LYS Chi-restraints excluded: chain N residue 413 MET Chi-restraints excluded: chain N residue 425 MET Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 433 GLU Chi-restraints excluded: chain P residue 129 CYS Chi-restraints excluded: chain P residue 269 MET Chi-restraints excluded: chain P residue 305 CYS Chi-restraints excluded: chain P residue 373 MET Chi-restraints excluded: chain P residue 389 LYS Chi-restraints excluded: chain P residue 405 LEU Chi-restraints excluded: chain O residue 77 GLU Chi-restraints excluded: chain R residue 149 MET Chi-restraints excluded: chain R residue 332 MET Chi-restraints excluded: chain Q residue 90 GLU Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain t residue 104 GLN Chi-restraints excluded: chain t residue 120 VAL Chi-restraints excluded: chain v residue 104 GLN Chi-restraints excluded: chain x residue 104 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 801 random chunks: chunk 208 optimal weight: 3.9990 chunk 638 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 164 optimal weight: 0.5980 chunk 626 optimal weight: 10.0000 chunk 790 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 758 optimal weight: 8.9990 chunk 199 optimal weight: 1.9990 chunk 313 optimal weight: 10.0000 chunk 308 optimal weight: 5.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN A 50 ASN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 GLN D 293 GLN ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 ASN F 192 HIS F 334 ASN F 349 ASN F 433 GLN E 249 ASN ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 HIS ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 107 HIS ** I 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 GLN L 247 GLN L 293 GLN ** L 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 334 ASN L 336 GLN ** L 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 59 ASN ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 88 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.098303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.083755 restraints weight = 120354.120| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.39 r_work: 0.3486 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 65970 Z= 0.278 Angle : 0.649 13.919 89469 Z= 0.331 Chirality : 0.045 0.313 9711 Planarity : 0.004 0.055 11637 Dihedral : 10.816 176.288 9252 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.04 % Allowed : 19.05 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.10), residues: 8055 helix: 1.38 (0.09), residues: 3663 sheet: -0.12 (0.16), residues: 1143 loop : -0.53 (0.11), residues: 3249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 388 HIS 0.023 0.001 HIS F 192 PHE 0.035 0.001 PHE K 255 TYR 0.022 0.001 TYR P 435 ARG 0.013 0.001 ARG H 400 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16110 Ramachandran restraints generated. 8055 Oldfield, 0 Emsley, 8055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16110 Ramachandran restraints generated. 8055 Oldfield, 0 Emsley, 8055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1275 residues out of total 6966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 1134 time to evaluate : 5.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: r 127 MET cc_start: 0.8562 (mmp) cc_final: 0.8126 (mmp) REVERT: B 1 MET cc_start: 0.8507 (tpt) cc_final: 0.8202 (mmm) REVERT: B 47 GLU cc_start: 0.8599 (tp30) cc_final: 0.7823 (tp30) REVERT: B 105 LYS cc_start: 0.8938 (mtpp) cc_final: 0.8682 (mtpp) REVERT: B 116 ASP cc_start: 0.8255 (m-30) cc_final: 0.7526 (m-30) REVERT: B 120 ASP cc_start: 0.8194 (m-30) cc_final: 0.7957 (m-30) REVERT: B 207 GLU cc_start: 0.8536 (pp20) cc_final: 0.8236 (pp20) REVERT: B 282 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8526 (pm20) REVERT: B 422 GLU cc_start: 0.8140 (tp30) cc_final: 0.7696 (tp30) REVERT: A 85 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8437 (mt0) REVERT: A 112 LYS cc_start: 0.8346 (pttt) cc_final: 0.7585 (pttm) REVERT: A 113 GLU cc_start: 0.7889 (mp0) cc_final: 0.7197 (mp0) REVERT: A 209 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8422 (mt) REVERT: A 211 ASP cc_start: 0.8584 (t0) cc_final: 0.8343 (t0) REVERT: A 423 GLU cc_start: 0.8292 (tm-30) cc_final: 0.8064 (pp20) REVERT: D 22 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7598 (tp30) REVERT: D 41 ASP cc_start: 0.8353 (t70) cc_final: 0.8052 (t70) REVERT: D 47 GLU cc_start: 0.8149 (pp20) cc_final: 0.7811 (pp20) REVERT: D 50 ASN cc_start: 0.8905 (p0) cc_final: 0.8502 (p0) REVERT: D 90 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8274 (p0) REVERT: D 132 LEU cc_start: 0.8699 (tp) cc_final: 0.8477 (mt) REVERT: D 159 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8168 (mt-10) REVERT: D 278 ARG cc_start: 0.8271 (tpm170) cc_final: 0.7766 (tpm170) REVERT: D 330 GLU cc_start: 0.7902 (pp20) cc_final: 0.7574 (pp20) REVERT: D 345 GLU cc_start: 0.8538 (pm20) cc_final: 0.8283 (pm20) REVERT: D 349 ASN cc_start: 0.6631 (t0) cc_final: 0.6295 (t0) REVERT: D 405 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8411 (mm) REVERT: D 422 GLU cc_start: 0.8021 (tp30) cc_final: 0.7454 (tp30) REVERT: D 433 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8129 (tm-30) REVERT: C 77 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8144 (tm-30) REVERT: C 84 ARG cc_start: 0.9023 (ttp-110) cc_final: 0.8781 (ttm110) REVERT: C 103 TYR cc_start: 0.8915 (t80) cc_final: 0.8355 (t80) REVERT: C 163 LYS cc_start: 0.8630 (ttmm) cc_final: 0.8329 (ttmm) REVERT: C 203 MET cc_start: 0.8683 (mmm) cc_final: 0.8411 (mmm) REVERT: C 386 GLU cc_start: 0.8197 (pp20) cc_final: 0.7995 (pp20) REVERT: C 413 MET cc_start: 0.8618 (ttm) cc_final: 0.8417 (ttp) REVERT: C 417 GLU cc_start: 0.8076 (tp30) cc_final: 0.7616 (tp30) REVERT: C 420 GLU cc_start: 0.8251 (pt0) cc_final: 0.7785 (pt0) REVERT: C 423 GLU cc_start: 0.8463 (pp20) cc_final: 0.8087 (pp20) REVERT: C 434 GLU cc_start: 0.8498 (pp20) cc_final: 0.8022 (pp20) REVERT: F 37 HIS cc_start: 0.8669 (OUTLIER) cc_final: 0.7880 (m90) REVERT: F 47 GLU cc_start: 0.8481 (tp30) cc_final: 0.7793 (tp30) REVERT: F 75 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8170 (mmt) REVERT: F 105 LYS cc_start: 0.9275 (mtmt) cc_final: 0.9025 (mtpp) REVERT: F 110 GLU cc_start: 0.8484 (pp20) cc_final: 0.8259 (pp20) REVERT: F 113 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7842 (mp0) REVERT: F 164 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7411 (mmp-170) REVERT: F 247 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7823 (tt0) REVERT: F 282 GLN cc_start: 0.8719 (pm20) cc_final: 0.8405 (pm20) REVERT: F 293 GLN cc_start: 0.6760 (mm-40) cc_final: 0.6533 (mm110) REVERT: F 330 GLU cc_start: 0.6737 (tp30) cc_final: 0.6139 (tp30) REVERT: F 345 GLU cc_start: 0.8250 (pp20) cc_final: 0.7948 (tp30) REVERT: F 372 LYS cc_start: 0.8754 (pptt) cc_final: 0.8254 (pptt) REVERT: F 384 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8508 (mm) REVERT: F 413 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8873 (mtm) REVERT: E 24 TYR cc_start: 0.8842 (m-10) cc_final: 0.8504 (m-10) REVERT: E 73 THR cc_start: 0.8385 (m) cc_final: 0.8136 (m) REVERT: E 205 ASP cc_start: 0.8440 (m-30) cc_final: 0.8175 (p0) REVERT: E 214 ARG cc_start: 0.9258 (OUTLIER) cc_final: 0.8586 (ttm170) REVERT: E 245 ASP cc_start: 0.8692 (p0) cc_final: 0.8236 (p0) REVERT: E 251 ASP cc_start: 0.8299 (t0) cc_final: 0.7908 (t70) REVERT: E 392 ASP cc_start: 0.8726 (m-30) cc_final: 0.8409 (m-30) REVERT: E 413 MET cc_start: 0.7546 (ttt) cc_final: 0.7317 (ttt) REVERT: E 434 GLU cc_start: 0.8367 (pp20) cc_final: 0.7853 (pp20) REVERT: H 1 MET cc_start: 0.8510 (ttm) cc_final: 0.7972 (ttm) REVERT: H 3 GLU cc_start: 0.7751 (mp0) cc_final: 0.7240 (mp0) REVERT: H 26 ASP cc_start: 0.8886 (t70) cc_final: 0.8607 (t0) REVERT: H 47 GLU cc_start: 0.7925 (pp20) cc_final: 0.7643 (pp20) REVERT: H 50 ASN cc_start: 0.9021 (p0) cc_final: 0.8623 (p0) REVERT: H 76 ASP cc_start: 0.9181 (t0) cc_final: 0.8845 (t0) REVERT: H 105 LYS cc_start: 0.9196 (mtpp) cc_final: 0.8871 (mtpp) REVERT: H 133 GLN cc_start: 0.9201 (OUTLIER) cc_final: 0.8452 (tm-30) REVERT: H 156 LYS cc_start: 0.7984 (mmtp) cc_final: 0.7544 (mmtm) REVERT: H 166 MET cc_start: 0.8206 (tpp) cc_final: 0.7670 (tpp) REVERT: H 199 ASP cc_start: 0.8722 (m-30) cc_final: 0.8287 (m-30) REVERT: H 281 GLN cc_start: 0.8823 (pp30) cc_final: 0.8477 (tm-30) REVERT: H 416 MET cc_start: 0.8575 (tpp) cc_final: 0.8218 (mmm) REVERT: H 422 GLU cc_start: 0.8397 (tm-30) cc_final: 0.7918 (tm-30) REVERT: H 427 ASP cc_start: 0.8477 (m-30) cc_final: 0.8135 (m-30) REVERT: H 433 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8745 (tm-30) REVERT: G 85 GLN cc_start: 0.8827 (pt0) cc_final: 0.8173 (pp30) REVERT: G 168 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8232 (pt0) REVERT: G 211 ASP cc_start: 0.8809 (t0) cc_final: 0.8461 (t70) REVERT: G 255 PHE cc_start: 0.7935 (t80) cc_final: 0.7480 (t80) REVERT: G 290 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7561 (pm20) REVERT: G 423 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8090 (tm-30) REVERT: G 425 MET cc_start: 0.8839 (mmm) cc_final: 0.8569 (tpp) REVERT: G 433 GLU cc_start: 0.8602 (tp30) cc_final: 0.8162 (tp30) REVERT: G 434 GLU cc_start: 0.8545 (pp20) cc_final: 0.8185 (pp20) REVERT: J 3 GLU cc_start: 0.7996 (mp0) cc_final: 0.6807 (mp0) REVERT: J 26 ASP cc_start: 0.8657 (t0) cc_final: 0.8306 (t0) REVERT: J 76 ASP cc_start: 0.8833 (OUTLIER) cc_final: 0.8602 (t0) REVERT: J 109 THR cc_start: 0.8755 (m) cc_final: 0.8309 (p) REVERT: J 127 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7768 (mp0) REVERT: J 163 ASP cc_start: 0.8463 (p0) cc_final: 0.8101 (p0) REVERT: J 166 MET cc_start: 0.8827 (tpt) cc_final: 0.8548 (tpt) REVERT: J 196 GLU cc_start: 0.8232 (mp0) cc_final: 0.7904 (mp0) REVERT: J 207 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8555 (mm-30) REVERT: J 281 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8280 (tm-30) REVERT: J 330 GLU cc_start: 0.8104 (pp20) cc_final: 0.7849 (pp20) REVERT: J 417 GLU cc_start: 0.8489 (tm-30) cc_final: 0.7945 (tm-30) REVERT: I 71 GLU cc_start: 0.7480 (pt0) cc_final: 0.7033 (pm20) REVERT: I 76 ASP cc_start: 0.8416 (m-30) cc_final: 0.7722 (m-30) REVERT: I 128 GLN cc_start: 0.9073 (tt0) cc_final: 0.8523 (tm-30) REVERT: I 154 MET cc_start: 0.9007 (mmt) cc_final: 0.8322 (mmt) REVERT: I 155 GLU cc_start: 0.8256 (mp0) cc_final: 0.7525 (mp0) REVERT: I 211 ASP cc_start: 0.8695 (t0) cc_final: 0.8306 (t0) REVERT: I 251 ASP cc_start: 0.7573 (t70) cc_final: 0.7219 (t70) REVERT: I 423 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7996 (tm-30) REVERT: I 430 LYS cc_start: 0.8617 (mmmm) cc_final: 0.7959 (mmmm) REVERT: I 434 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8305 (mt-10) REVERT: L 1 MET cc_start: 0.9094 (mmm) cc_final: 0.8886 (mmm) REVERT: L 113 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8411 (tm-30) REVERT: L 127 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8170 (mm-30) REVERT: L 159 GLU cc_start: 0.7924 (pp20) cc_final: 0.7710 (pp20) REVERT: L 203 CYS cc_start: 0.9078 (t) cc_final: 0.8764 (p) REVERT: L 207 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8239 (tp30) REVERT: L 214 PHE cc_start: 0.8337 (m-80) cc_final: 0.8134 (m-80) REVERT: L 281 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8496 (tm-30) REVERT: L 299 LYS cc_start: 0.8748 (tppp) cc_final: 0.8377 (tptt) REVERT: L 322 ARG cc_start: 0.8083 (mmp80) cc_final: 0.7868 (mmp80) REVERT: L 338 LYS cc_start: 0.7085 (tttt) cc_final: 0.6863 (pttt) REVERT: L 393 GLU cc_start: 0.8705 (pp20) cc_final: 0.8290 (pp20) REVERT: L 420 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8099 (pp20) REVERT: K 24 TYR cc_start: 0.8874 (m-10) cc_final: 0.8618 (m-10) REVERT: K 127 ASP cc_start: 0.9022 (OUTLIER) cc_final: 0.8601 (m-30) REVERT: K 133 GLN cc_start: 0.8508 (mm-40) cc_final: 0.8061 (mm-40) REVERT: K 176 GLN cc_start: 0.9039 (mp10) cc_final: 0.8822 (mp10) REVERT: K 251 ASP cc_start: 0.7497 (t0) cc_final: 0.7036 (t0) REVERT: K 290 GLU cc_start: 0.8233 (pp20) cc_final: 0.8004 (pp20) REVERT: K 386 GLU cc_start: 0.8141 (pp20) cc_final: 0.7782 (pp20) REVERT: K 398 MET cc_start: 0.8883 (tpp) cc_final: 0.8531 (mmm) REVERT: K 433 GLU cc_start: 0.8700 (tp30) cc_final: 0.8452 (tp30) REVERT: K 434 GLU cc_start: 0.8548 (pp20) cc_final: 0.8084 (pp20) REVERT: N 1 MET cc_start: 0.8792 (tpt) cc_final: 0.8454 (tpp) REVERT: N 22 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8136 (tm-30) REVERT: N 37 HIS cc_start: 0.8279 (m90) cc_final: 0.7825 (m90) REVERT: N 50 ASN cc_start: 0.8891 (p0) cc_final: 0.8488 (p0) REVERT: N 75 MET cc_start: 0.8777 (mmp) cc_final: 0.8518 (mmm) REVERT: N 116 ASP cc_start: 0.8731 (t0) cc_final: 0.8431 (t0) REVERT: N 127 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8626 (mm-30) REVERT: N 159 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8256 (mp0) REVERT: N 207 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8105 (tp30) REVERT: N 281 GLN cc_start: 0.8953 (tm-30) cc_final: 0.8535 (tm-30) REVERT: N 325 MET cc_start: 0.7957 (mmm) cc_final: 0.7447 (mtm) REVERT: N 338 LYS cc_start: 0.8772 (mtmm) cc_final: 0.8344 (mtmm) REVERT: N 345 GLU cc_start: 0.8669 (pm20) cc_final: 0.8361 (pm20) REVERT: N 373 MET cc_start: 0.9278 (ptp) cc_final: 0.8836 (ptm) REVERT: N 422 GLU cc_start: 0.8333 (tp30) cc_final: 0.7732 (tp30) REVERT: N 433 GLN cc_start: 0.8848 (tp40) cc_final: 0.8573 (tm-30) REVERT: M 69 ASP cc_start: 0.8190 (t0) cc_final: 0.7892 (t0) REVERT: M 119 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8646 (mm) REVERT: M 203 MET cc_start: 0.9141 (mmm) cc_final: 0.8649 (mmm) REVERT: M 220 GLU cc_start: 0.7467 (pp20) cc_final: 0.6904 (pp20) REVERT: M 221 ARG cc_start: 0.8418 (ptp-110) cc_final: 0.8065 (ptp-110) REVERT: M 302 MET cc_start: 0.8960 (tpp) cc_final: 0.7886 (mpp) REVERT: M 313 MET cc_start: 0.8900 (mtm) cc_final: 0.8637 (mtp) REVERT: M 420 GLU cc_start: 0.8326 (pp20) cc_final: 0.7821 (pp20) REVERT: M 423 GLU cc_start: 0.8598 (pp20) cc_final: 0.8345 (pp20) REVERT: M 430 LYS cc_start: 0.8788 (mmmt) cc_final: 0.8567 (mmmm) REVERT: M 434 GLU cc_start: 0.8583 (pp20) cc_final: 0.8258 (pp20) REVERT: P 110 GLU cc_start: 0.7786 (pm20) cc_final: 0.7571 (pm20) REVERT: P 127 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8405 (mm-30) REVERT: P 293 GLN cc_start: 0.8638 (pp30) cc_final: 0.8163 (pp30) REVERT: P 393 GLU cc_start: 0.8351 (pp20) cc_final: 0.8097 (pp20) REVERT: P 422 GLU cc_start: 0.8210 (tp30) cc_final: 0.7735 (tp30) REVERT: O 73 THR cc_start: 0.8452 (p) cc_final: 0.7481 (p) REVERT: O 77 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7667 (pm20) REVERT: O 123 ARG cc_start: 0.9260 (tmm-80) cc_final: 0.8968 (ttp80) REVERT: O 154 MET cc_start: 0.9100 (mmm) cc_final: 0.8724 (mmm) REVERT: O 211 ASP cc_start: 0.8603 (t0) cc_final: 0.8207 (t0) REVERT: O 245 ASP cc_start: 0.8753 (p0) cc_final: 0.8540 (p0) REVERT: O 326 LYS cc_start: 0.5637 (mmtp) cc_final: 0.4589 (mmtm) REVERT: O 423 GLU cc_start: 0.8368 (pp20) cc_final: 0.8094 (pp20) REVERT: O 430 LYS cc_start: 0.8748 (tppp) cc_final: 0.8458 (tppp) REVERT: O 434 GLU cc_start: 0.8525 (pp20) cc_final: 0.8137 (pp20) REVERT: O 438 ASP cc_start: 0.8542 (t0) cc_final: 0.8324 (t0) REVERT: R 1 MET cc_start: 0.8871 (mmm) cc_final: 0.8593 (tpt) REVERT: R 47 GLU cc_start: 0.7913 (pp20) cc_final: 0.7538 (tm-30) REVERT: R 76 ASP cc_start: 0.8789 (t0) cc_final: 0.8510 (p0) REVERT: R 113 GLU cc_start: 0.8664 (tp30) cc_final: 0.8374 (tp30) REVERT: R 127 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8026 (mm-30) REVERT: R 159 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8048 (pp20) REVERT: R 183 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8129 (mt-10) REVERT: R 259 MET cc_start: 0.8626 (mmm) cc_final: 0.8350 (mtp) REVERT: R 281 GLN cc_start: 0.9076 (tp40) cc_final: 0.8693 (tp40) REVERT: R 330 GLU cc_start: 0.6992 (tp30) cc_final: 0.5912 (tp30) REVERT: R 338 LYS cc_start: 0.7456 (pttt) cc_final: 0.7189 (pptt) REVERT: R 349 ASN cc_start: 0.7653 (t0) cc_final: 0.7246 (t0) REVERT: R 427 ASP cc_start: 0.8569 (m-30) cc_final: 0.8173 (m-30) REVERT: Q 77 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8597 (tm-30) REVERT: Q 90 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8604 (mp0) REVERT: Q 128 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8091 (tm-30) REVERT: Q 205 ASP cc_start: 0.8160 (m-30) cc_final: 0.7627 (p0) REVERT: Q 285 GLN cc_start: 0.4905 (mm-40) cc_final: 0.3977 (mp10) REVERT: Q 302 MET cc_start: 0.8725 (mtm) cc_final: 0.8486 (mtm) REVERT: Q 313 MET cc_start: 0.8746 (mtp) cc_final: 0.8278 (mtp) REVERT: Q 357 TYR cc_start: 0.8843 (m-80) cc_final: 0.8490 (m-80) REVERT: Q 386 GLU cc_start: 0.8379 (mp0) cc_final: 0.7907 (mp0) REVERT: Q 423 GLU cc_start: 0.8835 (pp20) cc_final: 0.8623 (pp20) REVERT: Q 430 LYS cc_start: 0.8954 (tppt) cc_final: 0.8507 (tppp) REVERT: Q 433 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8088 (tm-30) REVERT: Q 434 GLU cc_start: 0.8587 (pp20) cc_final: 0.8285 (pp20) REVERT: s 127 MET cc_start: 0.8118 (tpt) cc_final: 0.7877 (tpt) REVERT: t 93 MET cc_start: 0.8961 (tpt) cc_final: 0.8452 (tpt) REVERT: t 127 MET cc_start: 0.8033 (mmp) cc_final: 0.7678 (mmp) REVERT: v 98 LYS cc_start: 0.8900 (mmmt) cc_final: 0.8579 (mmmt) REVERT: v 127 MET cc_start: 0.8245 (mmp) cc_final: 0.7693 (mmp) REVERT: w 93 MET cc_start: 0.8873 (tpt) cc_final: 0.8566 (tpt) REVERT: w 119 LYS cc_start: 0.8525 (mttt) cc_final: 0.8194 (mttt) REVERT: x 93 MET cc_start: 0.7800 (mmt) cc_final: 0.7364 (mmt) REVERT: x 127 MET cc_start: 0.8436 (tpt) cc_final: 0.7964 (tpt) REVERT: y 127 MET cc_start: 0.8596 (mmp) cc_final: 0.8158 (mmp) REVERT: z 93 MET cc_start: 0.8630 (tpp) cc_final: 0.8257 (tpp) REVERT: z 127 MET cc_start: 0.8283 (mmp) cc_final: 0.7902 (mmp) outliers start: 141 outliers final: 74 residues processed: 1201 average time/residue: 1.7712 time to fit residues: 2644.4210 Evaluate side-chains 1198 residues out of total 6966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 1102 time to evaluate : 5.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain r residue 120 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 389 LYS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 164 ARG Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain F residue 413 MET Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain H residue 133 GLN Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 373 MET Chi-restraints excluded: chain H residue 389 LYS Chi-restraints excluded: chain H residue 405 LEU Chi-restraints excluded: chain H residue 425 MET Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 269 LEU Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 339 ARG Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 127 GLU Chi-restraints excluded: chain J residue 159 GLU Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 315 VAL Chi-restraints excluded: chain J residue 323 MET Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 420 GLU Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 68 VAL Chi-restraints excluded: chain N residue 129 CYS Chi-restraints excluded: chain N residue 199 ASP Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 333 LEU Chi-restraints excluded: chain N residue 393 GLU Chi-restraints excluded: chain N residue 402 LYS Chi-restraints excluded: chain N residue 413 MET Chi-restraints excluded: chain N residue 425 MET Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 211 ASP Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain P residue 37 HIS Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 129 CYS Chi-restraints excluded: chain P residue 305 CYS Chi-restraints excluded: chain P residue 373 MET Chi-restraints excluded: chain P residue 389 LYS Chi-restraints excluded: chain P residue 405 LEU Chi-restraints excluded: chain O residue 77 GLU Chi-restraints excluded: chain O residue 377 MET Chi-restraints excluded: chain R residue 149 MET Chi-restraints excluded: chain R residue 332 MET Chi-restraints excluded: chain Q residue 90 GLU Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain t residue 104 GLN Chi-restraints excluded: chain t residue 120 VAL Chi-restraints excluded: chain v residue 104 GLN Chi-restraints excluded: chain x residue 104 GLN Chi-restraints excluded: chain z residue 104 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 801 random chunks: chunk 508 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 437 optimal weight: 4.9990 chunk 768 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 475 optimal weight: 0.3980 chunk 694 optimal weight: 3.9990 chunk 707 optimal weight: 8.9990 chunk 363 optimal weight: 6.9990 chunk 548 optimal weight: 1.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN A 50 ASN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 GLN ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 HIS F 334 ASN F 349 ASN F 350 ASN E 249 ASN ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 HIS ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 249 ASN ** I 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 372 GLN ** L 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 133 GLN L 293 GLN ** L 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 334 ASN ** N 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 59 ASN P 433 GLN ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 293 GLN ** Q 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 109 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.097954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.083465 restraints weight = 120831.220| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.39 r_work: 0.3482 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 65970 Z= 0.280 Angle : 0.668 13.401 89469 Z= 0.340 Chirality : 0.046 0.330 9711 Planarity : 0.004 0.059 11637 Dihedral : 10.826 176.106 9252 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.29 % Allowed : 19.70 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.51 (0.10), residues: 8055 helix: 1.32 (0.09), residues: 3690 sheet: -0.14 (0.16), residues: 1143 loop : -0.56 (0.11), residues: 3222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 388 HIS 0.011 0.001 HIS H 192 PHE 0.036 0.001 PHE K 255 TYR 0.023 0.001 TYR P 435 ARG 0.014 0.001 ARG H 400 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16110 Ramachandran restraints generated. 8055 Oldfield, 0 Emsley, 8055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16110 Ramachandran restraints generated. 8055 Oldfield, 0 Emsley, 8055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1268 residues out of total 6966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 1110 time to evaluate : 5.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: r 127 MET cc_start: 0.8570 (mmp) cc_final: 0.8135 (mmp) REVERT: B 3 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7194 (mm-30) REVERT: B 47 GLU cc_start: 0.8615 (tp30) cc_final: 0.7949 (tp30) REVERT: B 50 ASN cc_start: 0.8645 (p0) cc_final: 0.8066 (p0) REVERT: B 105 LYS cc_start: 0.8946 (mtpp) cc_final: 0.8674 (mtpp) REVERT: B 116 ASP cc_start: 0.8307 (m-30) cc_final: 0.7595 (m-30) REVERT: B 120 ASP cc_start: 0.8198 (m-30) cc_final: 0.7969 (m-30) REVERT: B 207 GLU cc_start: 0.8562 (pp20) cc_final: 0.8258 (pp20) REVERT: B 282 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8502 (pm20) REVERT: B 330 GLU cc_start: 0.8337 (pp20) cc_final: 0.8129 (pp20) REVERT: B 386 GLU cc_start: 0.8141 (pp20) cc_final: 0.7881 (pp20) REVERT: B 422 GLU cc_start: 0.8176 (tp30) cc_final: 0.7738 (tp30) REVERT: A 85 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8436 (mt0) REVERT: A 112 LYS cc_start: 0.8360 (pttt) cc_final: 0.7568 (pttm) REVERT: A 113 GLU cc_start: 0.7903 (mp0) cc_final: 0.7184 (mp0) REVERT: A 155 GLU cc_start: 0.8484 (pp20) cc_final: 0.8000 (pp20) REVERT: A 209 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8427 (mt) REVERT: A 211 ASP cc_start: 0.8572 (t0) cc_final: 0.8328 (t0) REVERT: A 423 GLU cc_start: 0.8305 (tm-30) cc_final: 0.8098 (pp20) REVERT: D 22 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7597 (tp30) REVERT: D 41 ASP cc_start: 0.8350 (t70) cc_final: 0.7991 (t70) REVERT: D 47 GLU cc_start: 0.8157 (pp20) cc_final: 0.7895 (pp20) REVERT: D 50 ASN cc_start: 0.8906 (p0) cc_final: 0.8509 (p0) REVERT: D 159 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8192 (mt-10) REVERT: D 247 GLN cc_start: 0.8601 (mp10) cc_final: 0.8356 (mp10) REVERT: D 278 ARG cc_start: 0.8279 (tpm170) cc_final: 0.7723 (tpm170) REVERT: D 326 LYS cc_start: 0.8808 (tttp) cc_final: 0.8511 (tttp) REVERT: D 330 GLU cc_start: 0.7911 (pp20) cc_final: 0.7528 (pp20) REVERT: D 345 GLU cc_start: 0.8536 (pm20) cc_final: 0.8284 (pm20) REVERT: D 349 ASN cc_start: 0.6685 (t0) cc_final: 0.6357 (t0) REVERT: D 393 GLU cc_start: 0.8167 (pp20) cc_final: 0.7946 (pp20) REVERT: D 405 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8441 (mm) REVERT: D 422 GLU cc_start: 0.8063 (tp30) cc_final: 0.7488 (tp30) REVERT: D 433 GLN cc_start: 0.8612 (tm-30) cc_final: 0.8142 (tm-30) REVERT: C 77 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8159 (tm-30) REVERT: C 84 ARG cc_start: 0.9020 (ttp-110) cc_final: 0.8767 (ttm110) REVERT: C 103 TYR cc_start: 0.8910 (t80) cc_final: 0.8394 (t80) REVERT: C 119 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8647 (mm) REVERT: C 163 LYS cc_start: 0.8568 (ttmm) cc_final: 0.8283 (ttmm) REVERT: C 203 MET cc_start: 0.8659 (mmm) cc_final: 0.8335 (mmm) REVERT: C 386 GLU cc_start: 0.8200 (pp20) cc_final: 0.7999 (pp20) REVERT: C 417 GLU cc_start: 0.8059 (tp30) cc_final: 0.7624 (tp30) REVERT: C 420 GLU cc_start: 0.8286 (pt0) cc_final: 0.7823 (pt0) REVERT: C 423 GLU cc_start: 0.8462 (pp20) cc_final: 0.8071 (pp20) REVERT: C 434 GLU cc_start: 0.8531 (pp20) cc_final: 0.8083 (pp20) REVERT: F 1 MET cc_start: 0.8169 (tpp) cc_final: 0.7933 (tpt) REVERT: F 47 GLU cc_start: 0.8475 (tp30) cc_final: 0.7808 (tp30) REVERT: F 75 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.8167 (mmt) REVERT: F 105 LYS cc_start: 0.9285 (mtmt) cc_final: 0.9052 (mtpp) REVERT: F 164 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7409 (mmp-170) REVERT: F 247 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7802 (tt0) REVERT: F 282 GLN cc_start: 0.8749 (pm20) cc_final: 0.8444 (pm20) REVERT: F 293 GLN cc_start: 0.6769 (mm-40) cc_final: 0.6526 (mm110) REVERT: F 330 GLU cc_start: 0.6875 (tp30) cc_final: 0.5995 (tp30) REVERT: F 345 GLU cc_start: 0.8281 (pp20) cc_final: 0.7954 (tp30) REVERT: F 372 LYS cc_start: 0.8764 (pptt) cc_final: 0.8254 (pptt) REVERT: F 384 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8537 (mm) REVERT: F 413 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.8914 (mtm) REVERT: E 24 TYR cc_start: 0.8847 (m-10) cc_final: 0.8510 (m-10) REVERT: E 73 THR cc_start: 0.8376 (m) cc_final: 0.8144 (m) REVERT: E 205 ASP cc_start: 0.8412 (m-30) cc_final: 0.8184 (p0) REVERT: E 212 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8444 (mt) REVERT: E 214 ARG cc_start: 0.9229 (OUTLIER) cc_final: 0.8538 (ttm170) REVERT: E 245 ASP cc_start: 0.8703 (p0) cc_final: 0.8244 (p0) REVERT: E 251 ASP cc_start: 0.8333 (t0) cc_final: 0.7906 (t70) REVERT: E 392 ASP cc_start: 0.8731 (m-30) cc_final: 0.8413 (m-30) REVERT: E 434 GLU cc_start: 0.8377 (pp20) cc_final: 0.7853 (pp20) REVERT: H 1 MET cc_start: 0.8508 (ttm) cc_final: 0.7894 (ttm) REVERT: H 3 GLU cc_start: 0.7770 (mp0) cc_final: 0.7314 (mp0) REVERT: H 26 ASP cc_start: 0.8876 (t70) cc_final: 0.8592 (t0) REVERT: H 47 GLU cc_start: 0.7933 (pp20) cc_final: 0.7652 (pp20) REVERT: H 50 ASN cc_start: 0.9030 (p0) cc_final: 0.8635 (p0) REVERT: H 76 ASP cc_start: 0.9161 (t0) cc_final: 0.8837 (t0) REVERT: H 105 LYS cc_start: 0.9186 (mtpp) cc_final: 0.8861 (mtpp) REVERT: H 133 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8649 (tm-30) REVERT: H 156 LYS cc_start: 0.7964 (mmtp) cc_final: 0.7377 (mmtm) REVERT: H 159 GLU cc_start: 0.7730 (pp20) cc_final: 0.7481 (pm20) REVERT: H 166 MET cc_start: 0.8177 (tpp) cc_final: 0.7524 (tpp) REVERT: H 199 ASP cc_start: 0.8750 (m-30) cc_final: 0.8293 (m-30) REVERT: H 281 GLN cc_start: 0.8844 (pp30) cc_final: 0.8453 (tm-30) REVERT: H 416 MET cc_start: 0.8608 (tpp) cc_final: 0.8235 (mmm) REVERT: H 422 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8061 (tm-30) REVERT: H 427 ASP cc_start: 0.8475 (m-30) cc_final: 0.8145 (m-30) REVERT: H 433 GLN cc_start: 0.9004 (mm-40) cc_final: 0.8742 (tm-30) REVERT: G 85 GLN cc_start: 0.8827 (pt0) cc_final: 0.8184 (pp30) REVERT: G 168 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8242 (pt0) REVERT: G 211 ASP cc_start: 0.8807 (t0) cc_final: 0.8450 (t70) REVERT: G 254 GLU cc_start: 0.8412 (tp30) cc_final: 0.8064 (tp30) REVERT: G 255 PHE cc_start: 0.8035 (t80) cc_final: 0.7550 (t80) REVERT: G 290 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7591 (pm20) REVERT: G 423 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8102 (tm-30) REVERT: G 425 MET cc_start: 0.8826 (mmm) cc_final: 0.8553 (tpp) REVERT: G 433 GLU cc_start: 0.8564 (tp30) cc_final: 0.8123 (tp30) REVERT: G 434 GLU cc_start: 0.8546 (pp20) cc_final: 0.8166 (pp20) REVERT: J 3 GLU cc_start: 0.7995 (mp0) cc_final: 0.6810 (mp0) REVERT: J 26 ASP cc_start: 0.8646 (t0) cc_final: 0.8295 (t0) REVERT: J 76 ASP cc_start: 0.8829 (m-30) cc_final: 0.8601 (t0) REVERT: J 109 THR cc_start: 0.8753 (m) cc_final: 0.8261 (p) REVERT: J 127 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7760 (mp0) REVERT: J 163 ASP cc_start: 0.8471 (p0) cc_final: 0.8153 (p0) REVERT: J 166 MET cc_start: 0.8820 (tpt) cc_final: 0.8526 (tpt) REVERT: J 207 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8560 (mm-30) REVERT: J 281 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8289 (tm-30) REVERT: J 330 GLU cc_start: 0.8166 (pp20) cc_final: 0.7946 (pp20) REVERT: J 393 GLU cc_start: 0.8355 (pp20) cc_final: 0.8020 (pp20) REVERT: J 417 GLU cc_start: 0.8460 (tm-30) cc_final: 0.7922 (tm-30) REVERT: I 71 GLU cc_start: 0.7468 (pt0) cc_final: 0.7009 (pm20) REVERT: I 76 ASP cc_start: 0.8406 (m-30) cc_final: 0.7691 (m-30) REVERT: I 128 GLN cc_start: 0.9086 (tt0) cc_final: 0.8530 (tm-30) REVERT: I 154 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8366 (mmt) REVERT: I 155 GLU cc_start: 0.8239 (mp0) cc_final: 0.7646 (mp0) REVERT: I 203 MET cc_start: 0.8745 (mmm) cc_final: 0.8478 (mmm) REVERT: I 211 ASP cc_start: 0.8682 (t0) cc_final: 0.8251 (t0) REVERT: I 251 ASP cc_start: 0.7625 (t70) cc_final: 0.7278 (t70) REVERT: I 326 LYS cc_start: 0.8788 (mtpp) cc_final: 0.8531 (ttmm) REVERT: I 423 GLU cc_start: 0.8252 (tm-30) cc_final: 0.8014 (tm-30) REVERT: I 430 LYS cc_start: 0.8645 (mmmm) cc_final: 0.7988 (mmmm) REVERT: I 434 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8212 (mt-10) REVERT: L 1 MET cc_start: 0.9069 (mmm) cc_final: 0.8773 (mmm) REVERT: L 105 LYS cc_start: 0.9126 (ptmt) cc_final: 0.8732 (ptmm) REVERT: L 113 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8429 (tm-30) REVERT: L 127 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8159 (mm-30) REVERT: L 133 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.7767 (pp30) REVERT: L 159 GLU cc_start: 0.8018 (pp20) cc_final: 0.7809 (pp20) REVERT: L 203 CYS cc_start: 0.8998 (t) cc_final: 0.8723 (p) REVERT: L 207 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8251 (tp30) REVERT: L 281 GLN cc_start: 0.8797 (tm-30) cc_final: 0.8510 (tm-30) REVERT: L 420 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8098 (pp20) REVERT: K 24 TYR cc_start: 0.8879 (m-10) cc_final: 0.8623 (m-10) REVERT: K 77 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8453 (mm-30) REVERT: K 127 ASP cc_start: 0.9009 (OUTLIER) cc_final: 0.8593 (m-30) REVERT: K 290 GLU cc_start: 0.8210 (pp20) cc_final: 0.7995 (pp20) REVERT: K 398 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8512 (mmm) REVERT: K 423 GLU cc_start: 0.8106 (pp20) cc_final: 0.7866 (pp20) REVERT: K 433 GLU cc_start: 0.8620 (tp30) cc_final: 0.8366 (tp30) REVERT: K 434 GLU cc_start: 0.8541 (pp20) cc_final: 0.8209 (pp20) REVERT: N 1 MET cc_start: 0.8822 (tpt) cc_final: 0.8508 (tpp) REVERT: N 22 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8170 (tm-30) REVERT: N 37 HIS cc_start: 0.8274 (m90) cc_final: 0.7813 (m90) REVERT: N 50 ASN cc_start: 0.8901 (p0) cc_final: 0.8515 (p0) REVERT: N 60 LYS cc_start: 0.4170 (pttt) cc_final: 0.3793 (pttt) REVERT: N 75 MET cc_start: 0.8749 (mmp) cc_final: 0.8519 (mmm) REVERT: N 116 ASP cc_start: 0.8736 (t0) cc_final: 0.8414 (t0) REVERT: N 127 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8657 (mm-30) REVERT: N 159 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8278 (mp0) REVERT: N 207 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8140 (tp30) REVERT: N 281 GLN cc_start: 0.8985 (tm-30) cc_final: 0.8578 (tm-30) REVERT: N 305 CYS cc_start: 0.9095 (p) cc_final: 0.8891 (p) REVERT: N 338 LYS cc_start: 0.8769 (mtmm) cc_final: 0.8309 (mtmm) REVERT: N 345 GLU cc_start: 0.8694 (pm20) cc_final: 0.8387 (pm20) REVERT: N 422 GLU cc_start: 0.8349 (tp30) cc_final: 0.7748 (tp30) REVERT: M 85 GLN cc_start: 0.8976 (pt0) cc_final: 0.8658 (pm20) REVERT: M 119 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8647 (mm) REVERT: M 203 MET cc_start: 0.9137 (mmm) cc_final: 0.8628 (mmm) REVERT: M 220 GLU cc_start: 0.7462 (pp20) cc_final: 0.6804 (pp20) REVERT: M 221 ARG cc_start: 0.8422 (ptp-110) cc_final: 0.7960 (ptp-110) REVERT: M 313 MET cc_start: 0.8891 (mtm) cc_final: 0.8650 (mtp) REVERT: M 420 GLU cc_start: 0.8340 (pp20) cc_final: 0.7816 (pp20) REVERT: M 423 GLU cc_start: 0.8598 (pp20) cc_final: 0.8350 (pp20) REVERT: M 430 LYS cc_start: 0.8790 (mmmt) cc_final: 0.8124 (mmmm) REVERT: M 433 GLU cc_start: 0.8241 (pp20) cc_final: 0.7919 (pp20) REVERT: M 434 GLU cc_start: 0.8556 (pp20) cc_final: 0.8194 (pp20) REVERT: P 127 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8410 (mm-30) REVERT: P 293 GLN cc_start: 0.8641 (pp30) cc_final: 0.8153 (pp30) REVERT: P 422 GLU cc_start: 0.8212 (tp30) cc_final: 0.7816 (tp30) REVERT: O 73 THR cc_start: 0.8499 (p) cc_final: 0.7531 (p) REVERT: O 77 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7663 (pm20) REVERT: O 123 ARG cc_start: 0.9275 (tmm-80) cc_final: 0.8859 (ttp80) REVERT: O 154 MET cc_start: 0.9037 (mmm) cc_final: 0.8623 (mmm) REVERT: O 211 ASP cc_start: 0.8575 (t0) cc_final: 0.8151 (t0) REVERT: O 245 ASP cc_start: 0.8727 (p0) cc_final: 0.8521 (p0) REVERT: O 249 ASN cc_start: 0.8792 (m-40) cc_final: 0.8563 (m-40) REVERT: O 326 LYS cc_start: 0.5809 (mmtp) cc_final: 0.4688 (mmtm) REVERT: O 430 LYS cc_start: 0.8762 (tppp) cc_final: 0.8484 (tppp) REVERT: O 434 GLU cc_start: 0.8529 (pp20) cc_final: 0.8110 (pp20) REVERT: O 438 ASP cc_start: 0.8542 (t0) cc_final: 0.8337 (t0) REVERT: R 1 MET cc_start: 0.8882 (mmm) cc_final: 0.8659 (tpt) REVERT: R 47 GLU cc_start: 0.7946 (pp20) cc_final: 0.7464 (tm-30) REVERT: R 113 GLU cc_start: 0.8676 (tp30) cc_final: 0.8386 (tp30) REVERT: R 159 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8041 (pp20) REVERT: R 183 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8139 (mt-10) REVERT: R 281 GLN cc_start: 0.9087 (tp40) cc_final: 0.8704 (tp40) REVERT: R 293 GLN cc_start: 0.6983 (mm-40) cc_final: 0.6725 (mm110) REVERT: R 330 GLU cc_start: 0.6992 (tp30) cc_final: 0.6181 (tp30) REVERT: R 334 ASN cc_start: 0.7449 (m-40) cc_final: 0.6901 (m110) REVERT: R 349 ASN cc_start: 0.7642 (t0) cc_final: 0.7240 (t0) REVERT: R 427 ASP cc_start: 0.8565 (m-30) cc_final: 0.8168 (m-30) REVERT: Q 77 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8601 (tm-30) REVERT: Q 90 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8718 (mp0) REVERT: Q 128 GLN cc_start: 0.8533 (tm-30) cc_final: 0.8107 (tm-30) REVERT: Q 285 GLN cc_start: 0.5000 (mm-40) cc_final: 0.3984 (mp10) REVERT: Q 302 MET cc_start: 0.8801 (mtm) cc_final: 0.8346 (mtm) REVERT: Q 313 MET cc_start: 0.8744 (mtp) cc_final: 0.8273 (mtp) REVERT: Q 357 TYR cc_start: 0.8853 (m-80) cc_final: 0.8518 (m-80) REVERT: Q 386 GLU cc_start: 0.8381 (mp0) cc_final: 0.7954 (mp0) REVERT: Q 423 GLU cc_start: 0.8819 (pp20) cc_final: 0.8605 (pp20) REVERT: Q 430 LYS cc_start: 0.8960 (tppt) cc_final: 0.8513 (tppp) REVERT: Q 433 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8094 (tm-30) REVERT: Q 434 GLU cc_start: 0.8583 (pp20) cc_final: 0.8266 (pp20) REVERT: s 127 MET cc_start: 0.8165 (tpt) cc_final: 0.7846 (tpt) REVERT: t 93 MET cc_start: 0.8963 (tpt) cc_final: 0.8437 (tpt) REVERT: t 127 MET cc_start: 0.8086 (mmp) cc_final: 0.7722 (mmp) REVERT: v 98 LYS cc_start: 0.8919 (mmmt) cc_final: 0.8621 (mmmt) REVERT: v 127 MET cc_start: 0.8314 (mmp) cc_final: 0.7763 (mmp) REVERT: w 93 MET cc_start: 0.8857 (tpt) cc_final: 0.8544 (tpt) REVERT: w 119 LYS cc_start: 0.8553 (mttt) cc_final: 0.8229 (mttt) REVERT: x 127 MET cc_start: 0.8433 (tpt) cc_final: 0.7974 (tpt) REVERT: y 127 MET cc_start: 0.8596 (mmp) cc_final: 0.8170 (mmp) REVERT: z 93 MET cc_start: 0.8627 (tpp) cc_final: 0.8246 (tpp) REVERT: z 127 MET cc_start: 0.8290 (mmp) cc_final: 0.7915 (mmp) outliers start: 158 outliers final: 79 residues processed: 1191 average time/residue: 1.6998 time to fit residues: 2520.3241 Evaluate side-chains 1217 residues out of total 6966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 1113 time to evaluate : 5.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain r residue 120 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 389 LYS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 164 ARG Chi-restraints excluded: chain F residue 192 HIS Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain F residue 413 MET Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain H residue 133 GLN Chi-restraints excluded: chain H residue 192 HIS Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 373 MET Chi-restraints excluded: chain H residue 389 LYS Chi-restraints excluded: chain H residue 405 LEU Chi-restraints excluded: chain H residue 425 MET Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 269 LEU Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 339 ARG Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 127 GLU Chi-restraints excluded: chain J residue 159 GLU Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 315 VAL Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain L residue 133 GLN Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 420 GLU Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 398 MET Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 68 VAL Chi-restraints excluded: chain N residue 129 CYS Chi-restraints excluded: chain N residue 207 GLU Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 333 LEU Chi-restraints excluded: chain N residue 402 LYS Chi-restraints excluded: chain N residue 405 LEU Chi-restraints excluded: chain N residue 413 MET Chi-restraints excluded: chain N residue 425 MET Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 205 ASP Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 425 MET Chi-restraints excluded: chain P residue 37 HIS Chi-restraints excluded: chain P residue 129 CYS Chi-restraints excluded: chain P residue 194 LEU Chi-restraints excluded: chain P residue 269 MET Chi-restraints excluded: chain P residue 305 CYS Chi-restraints excluded: chain P residue 373 MET Chi-restraints excluded: chain P residue 389 LYS Chi-restraints excluded: chain P residue 405 LEU Chi-restraints excluded: chain O residue 77 GLU Chi-restraints excluded: chain R residue 149 MET Chi-restraints excluded: chain R residue 332 MET Chi-restraints excluded: chain Q residue 90 GLU Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain t residue 104 GLN Chi-restraints excluded: chain t residue 120 VAL Chi-restraints excluded: chain v residue 104 GLN Chi-restraints excluded: chain x residue 104 GLN Chi-restraints excluded: chain z residue 104 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 801 random chunks: chunk 96 optimal weight: 2.9990 chunk 611 optimal weight: 9.9990 chunk 213 optimal weight: 1.9990 chunk 798 optimal weight: 9.9990 chunk 459 optimal weight: 6.9990 chunk 570 optimal weight: 2.9990 chunk 780 optimal weight: 10.0000 chunk 539 optimal weight: 0.9980 chunk 430 optimal weight: 10.0000 chunk 464 optimal weight: 0.9990 chunk 660 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 GLN ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 HIS F 334 ASN F 349 ASN F 433 GLN E 249 ASN ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 HIS ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 133 GLN L 334 ASN L 350 ASN ** N 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 59 ASN P 426 ASN ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 339 ASN ** Q 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 109 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.098487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.083988 restraints weight = 120279.387| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.37 r_work: 0.3493 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 65970 Z= 0.259 Angle : 0.688 14.114 89469 Z= 0.349 Chirality : 0.045 0.394 9711 Planarity : 0.004 0.064 11637 Dihedral : 10.801 176.622 9252 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.95 % Allowed : 20.56 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.10), residues: 8055 helix: 1.39 (0.09), residues: 3663 sheet: -0.20 (0.16), residues: 1170 loop : -0.56 (0.11), residues: 3222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 388 HIS 0.022 0.001 HIS H 192 PHE 0.037 0.001 PHE K 255 TYR 0.022 0.001 TYR P 435 ARG 0.014 0.001 ARG H 400 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16110 Ramachandran restraints generated. 8055 Oldfield, 0 Emsley, 8055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16110 Ramachandran restraints generated. 8055 Oldfield, 0 Emsley, 8055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1244 residues out of total 6966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 1109 time to evaluate : 5.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: r 127 MET cc_start: 0.8507 (mmp) cc_final: 0.8091 (mmp) REVERT: B 3 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7158 (mm-30) REVERT: B 47 GLU cc_start: 0.8601 (tp30) cc_final: 0.7889 (tp30) REVERT: B 50 ASN cc_start: 0.8633 (p0) cc_final: 0.7992 (p0) REVERT: B 105 LYS cc_start: 0.8934 (mtpp) cc_final: 0.8670 (mtpp) REVERT: B 116 ASP cc_start: 0.8271 (m-30) cc_final: 0.7534 (m-30) REVERT: B 120 ASP cc_start: 0.8204 (m-30) cc_final: 0.7969 (m-30) REVERT: B 207 GLU cc_start: 0.8522 (pp20) cc_final: 0.8217 (pp20) REVERT: B 282 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8482 (pm20) REVERT: B 330 GLU cc_start: 0.8358 (pp20) cc_final: 0.8137 (pp20) REVERT: B 386 GLU cc_start: 0.8145 (pp20) cc_final: 0.7863 (pp20) REVERT: A 85 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8428 (mt0) REVERT: A 112 LYS cc_start: 0.8430 (pttt) cc_final: 0.7606 (pttm) REVERT: A 113 GLU cc_start: 0.7911 (mp0) cc_final: 0.7185 (mp0) REVERT: A 155 GLU cc_start: 0.8476 (pp20) cc_final: 0.7985 (pp20) REVERT: A 209 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8373 (mt) REVERT: A 211 ASP cc_start: 0.8571 (t0) cc_final: 0.8298 (t0) REVERT: A 423 GLU cc_start: 0.8281 (tm-30) cc_final: 0.8062 (pp20) REVERT: D 22 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7585 (tp30) REVERT: D 41 ASP cc_start: 0.8282 (t70) cc_final: 0.7967 (t70) REVERT: D 47 GLU cc_start: 0.8140 (pp20) cc_final: 0.7912 (pp20) REVERT: D 50 ASN cc_start: 0.8897 (p0) cc_final: 0.8501 (p0) REVERT: D 110 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8346 (mp0) REVERT: D 132 LEU cc_start: 0.8545 (tp) cc_final: 0.8328 (mt) REVERT: D 159 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8185 (mt-10) REVERT: D 247 GLN cc_start: 0.8538 (mp10) cc_final: 0.8224 (mp10) REVERT: D 278 ARG cc_start: 0.8278 (tpm170) cc_final: 0.7743 (tpm170) REVERT: D 326 LYS cc_start: 0.8782 (tttp) cc_final: 0.8566 (tttp) REVERT: D 330 GLU cc_start: 0.7892 (pp20) cc_final: 0.7610 (pp20) REVERT: D 345 GLU cc_start: 0.8531 (pm20) cc_final: 0.8265 (pm20) REVERT: D 349 ASN cc_start: 0.6700 (t0) cc_final: 0.6365 (t0) REVERT: D 405 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8456 (mm) REVERT: D 422 GLU cc_start: 0.8049 (tp30) cc_final: 0.7482 (tp30) REVERT: D 433 GLN cc_start: 0.8617 (tm-30) cc_final: 0.8096 (tm-30) REVERT: C 77 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8160 (tm-30) REVERT: C 84 ARG cc_start: 0.9018 (ttp-110) cc_final: 0.8771 (ttm110) REVERT: C 103 TYR cc_start: 0.8858 (t80) cc_final: 0.8339 (t80) REVERT: C 163 LYS cc_start: 0.8327 (ttmm) cc_final: 0.8040 (ttmm) REVERT: C 203 MET cc_start: 0.8801 (mmm) cc_final: 0.8412 (mmm) REVERT: C 349 THR cc_start: 0.8196 (p) cc_final: 0.7928 (t) REVERT: C 417 GLU cc_start: 0.7995 (tp30) cc_final: 0.7573 (tp30) REVERT: C 420 GLU cc_start: 0.8256 (pt0) cc_final: 0.7821 (pt0) REVERT: C 423 GLU cc_start: 0.8469 (pp20) cc_final: 0.8069 (pp20) REVERT: C 434 GLU cc_start: 0.8504 (pp20) cc_final: 0.7972 (pp20) REVERT: F 47 GLU cc_start: 0.8496 (tp30) cc_final: 0.7783 (tp30) REVERT: F 75 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8156 (mmt) REVERT: F 105 LYS cc_start: 0.9274 (mtmt) cc_final: 0.9048 (mtpp) REVERT: F 159 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7382 (mp0) REVERT: F 247 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7773 (tt0) REVERT: F 282 GLN cc_start: 0.8753 (pm20) cc_final: 0.8442 (pm20) REVERT: F 293 GLN cc_start: 0.6750 (mm-40) cc_final: 0.6546 (mm110) REVERT: F 330 GLU cc_start: 0.6698 (tp30) cc_final: 0.6117 (tp30) REVERT: F 345 GLU cc_start: 0.8271 (pp20) cc_final: 0.7922 (tp30) REVERT: F 372 LYS cc_start: 0.8697 (pptt) cc_final: 0.8177 (pptt) REVERT: F 384 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8507 (mm) REVERT: F 393 GLU cc_start: 0.8421 (pp20) cc_final: 0.8166 (pp20) REVERT: E 2 ARG cc_start: 0.8703 (ptt90) cc_final: 0.8404 (mtm-85) REVERT: E 24 TYR cc_start: 0.8839 (m-10) cc_final: 0.8499 (m-10) REVERT: E 73 THR cc_start: 0.8369 (m) cc_final: 0.8115 (m) REVERT: E 205 ASP cc_start: 0.8371 (m-30) cc_final: 0.8159 (p0) REVERT: E 212 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8490 (mt) REVERT: E 214 ARG cc_start: 0.9220 (OUTLIER) cc_final: 0.8517 (ttm170) REVERT: E 245 ASP cc_start: 0.8674 (p0) cc_final: 0.8222 (p0) REVERT: E 251 ASP cc_start: 0.8392 (t0) cc_final: 0.7917 (t70) REVERT: E 392 ASP cc_start: 0.8732 (m-30) cc_final: 0.8408 (m-30) REVERT: E 434 GLU cc_start: 0.8380 (pp20) cc_final: 0.7861 (pp20) REVERT: H 1 MET cc_start: 0.8474 (ttm) cc_final: 0.7874 (ttm) REVERT: H 3 GLU cc_start: 0.7749 (mp0) cc_final: 0.7322 (mp0) REVERT: H 26 ASP cc_start: 0.8869 (t70) cc_final: 0.8584 (t0) REVERT: H 47 GLU cc_start: 0.7924 (pp20) cc_final: 0.7642 (pp20) REVERT: H 50 ASN cc_start: 0.9021 (p0) cc_final: 0.8636 (p0) REVERT: H 76 ASP cc_start: 0.9170 (t0) cc_final: 0.8834 (t0) REVERT: H 105 LYS cc_start: 0.9213 (mtpp) cc_final: 0.8891 (mtpp) REVERT: H 133 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8634 (tm-30) REVERT: H 156 LYS cc_start: 0.8000 (mmtp) cc_final: 0.7558 (mmtm) REVERT: H 166 MET cc_start: 0.8196 (tpp) cc_final: 0.7584 (tpp) REVERT: H 199 ASP cc_start: 0.8728 (m-30) cc_final: 0.8265 (m-30) REVERT: H 281 GLN cc_start: 0.8830 (pp30) cc_final: 0.8523 (tm-30) REVERT: H 416 MET cc_start: 0.8619 (tpp) cc_final: 0.8286 (mmm) REVERT: H 422 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8088 (tm-30) REVERT: H 427 ASP cc_start: 0.8479 (m-30) cc_final: 0.8145 (m-30) REVERT: H 433 GLN cc_start: 0.8984 (mm-40) cc_final: 0.8588 (tm-30) REVERT: G 168 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8236 (pt0) REVERT: G 172 TYR cc_start: 0.8450 (t80) cc_final: 0.8086 (t80) REVERT: G 203 MET cc_start: 0.8939 (mmm) cc_final: 0.8183 (mmm) REVERT: G 211 ASP cc_start: 0.8820 (t0) cc_final: 0.8455 (t70) REVERT: G 254 GLU cc_start: 0.8399 (tp30) cc_final: 0.8061 (tp30) REVERT: G 255 PHE cc_start: 0.7961 (t80) cc_final: 0.7484 (t80) REVERT: G 290 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7567 (pm20) REVERT: G 402 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8721 (tpp80) REVERT: G 423 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8097 (tm-30) REVERT: G 425 MET cc_start: 0.8832 (mmm) cc_final: 0.8552 (tpp) REVERT: G 433 GLU cc_start: 0.8564 (tp30) cc_final: 0.8124 (tp30) REVERT: G 434 GLU cc_start: 0.8558 (pp20) cc_final: 0.8181 (pp20) REVERT: J 3 GLU cc_start: 0.7985 (mp0) cc_final: 0.6795 (mp0) REVERT: J 26 ASP cc_start: 0.8691 (t0) cc_final: 0.8344 (t0) REVERT: J 76 ASP cc_start: 0.8847 (OUTLIER) cc_final: 0.8624 (t0) REVERT: J 96 GLN cc_start: 0.8585 (pm20) cc_final: 0.8113 (tp40) REVERT: J 109 THR cc_start: 0.8761 (m) cc_final: 0.8304 (p) REVERT: J 127 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7788 (mp0) REVERT: J 163 ASP cc_start: 0.8473 (p0) cc_final: 0.8132 (p0) REVERT: J 166 MET cc_start: 0.8800 (tpt) cc_final: 0.8497 (tpt) REVERT: J 196 GLU cc_start: 0.8177 (mp0) cc_final: 0.7870 (mp0) REVERT: J 207 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8545 (mm-30) REVERT: J 281 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8402 (tm-30) REVERT: J 330 GLU cc_start: 0.8130 (pp20) cc_final: 0.7903 (pp20) REVERT: I 71 GLU cc_start: 0.7706 (pt0) cc_final: 0.7252 (pm20) REVERT: I 76 ASP cc_start: 0.8386 (m-30) cc_final: 0.7674 (m-30) REVERT: I 128 GLN cc_start: 0.9079 (tt0) cc_final: 0.8534 (tm-30) REVERT: I 154 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8369 (mmt) REVERT: I 155 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7614 (mp0) REVERT: I 211 ASP cc_start: 0.8657 (t0) cc_final: 0.8225 (t0) REVERT: I 251 ASP cc_start: 0.7619 (t70) cc_final: 0.7281 (t70) REVERT: I 326 LYS cc_start: 0.8729 (mtpp) cc_final: 0.8464 (ttmm) REVERT: I 423 GLU cc_start: 0.8248 (tm-30) cc_final: 0.8010 (tm-30) REVERT: I 430 LYS cc_start: 0.8644 (mmmm) cc_final: 0.7988 (mmmm) REVERT: I 434 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8222 (mt-10) REVERT: L 1 MET cc_start: 0.9023 (mmm) cc_final: 0.8702 (mmm) REVERT: L 39 ASP cc_start: 0.9172 (p0) cc_final: 0.8870 (p0) REVERT: L 105 LYS cc_start: 0.9121 (ptmt) cc_final: 0.8733 (ptmm) REVERT: L 113 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8419 (tm-30) REVERT: L 127 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8152 (mm-30) REVERT: L 133 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7671 (pp30) REVERT: L 203 CYS cc_start: 0.8991 (t) cc_final: 0.8726 (p) REVERT: L 207 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8286 (tp30) REVERT: L 247 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7597 (tp40) REVERT: L 281 GLN cc_start: 0.8834 (tm-30) cc_final: 0.8500 (tm-30) REVERT: L 322 ARG cc_start: 0.8031 (mmp80) cc_final: 0.7786 (mmp80) REVERT: L 393 GLU cc_start: 0.8667 (pp20) cc_final: 0.8306 (pp20) REVERT: L 420 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8081 (pp20) REVERT: K 24 TYR cc_start: 0.8883 (m-10) cc_final: 0.8639 (m-10) REVERT: K 77 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8528 (mm-30) REVERT: K 96 LYS cc_start: 0.8847 (mmtp) cc_final: 0.8593 (mmtp) REVERT: K 127 ASP cc_start: 0.9000 (OUTLIER) cc_final: 0.8589 (m-30) REVERT: K 155 GLU cc_start: 0.7892 (pp20) cc_final: 0.7625 (pp20) REVERT: K 176 GLN cc_start: 0.9065 (mp10) cc_final: 0.8723 (mp10) REVERT: K 227 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8291 (mt) REVERT: K 290 GLU cc_start: 0.8236 (pp20) cc_final: 0.8001 (pp20) REVERT: K 302 MET cc_start: 0.8201 (mtm) cc_final: 0.7977 (pmm) REVERT: K 398 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8548 (mmm) REVERT: K 420 GLU cc_start: 0.8328 (pt0) cc_final: 0.7896 (pt0) REVERT: K 423 GLU cc_start: 0.8112 (pp20) cc_final: 0.7849 (pp20) REVERT: K 433 GLU cc_start: 0.8655 (tp30) cc_final: 0.8406 (tp30) REVERT: K 434 GLU cc_start: 0.8530 (pp20) cc_final: 0.8257 (pp20) REVERT: N 1 MET cc_start: 0.8864 (tpt) cc_final: 0.8558 (tpp) REVERT: N 22 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8156 (tm-30) REVERT: N 37 HIS cc_start: 0.8292 (m90) cc_final: 0.7831 (m90) REVERT: N 50 ASN cc_start: 0.8921 (p0) cc_final: 0.8544 (p0) REVERT: N 75 MET cc_start: 0.8734 (mmp) cc_final: 0.8498 (mmm) REVERT: N 116 ASP cc_start: 0.8745 (t0) cc_final: 0.8425 (t0) REVERT: N 127 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8656 (mm-30) REVERT: N 159 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8369 (mp0) REVERT: N 207 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8122 (tp30) REVERT: N 281 GLN cc_start: 0.8985 (tm-30) cc_final: 0.8584 (tm-30) REVERT: N 284 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8451 (ptm160) REVERT: N 325 MET cc_start: 0.7974 (mmm) cc_final: 0.7487 (mtm) REVERT: N 338 LYS cc_start: 0.8752 (mtmm) cc_final: 0.8427 (mtmm) REVERT: N 345 GLU cc_start: 0.8699 (pm20) cc_final: 0.8385 (pm20) REVERT: N 422 GLU cc_start: 0.8350 (tp30) cc_final: 0.7752 (tp30) REVERT: M 69 ASP cc_start: 0.8158 (t0) cc_final: 0.7833 (t0) REVERT: M 85 GLN cc_start: 0.8975 (pt0) cc_final: 0.8612 (pm20) REVERT: M 119 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8660 (mm) REVERT: M 203 MET cc_start: 0.9121 (mmm) cc_final: 0.8447 (mmm) REVERT: M 220 GLU cc_start: 0.7424 (pp20) cc_final: 0.6785 (pp20) REVERT: M 221 ARG cc_start: 0.8445 (ptp-110) cc_final: 0.7950 (ptp-110) REVERT: M 302 MET cc_start: 0.8941 (tpp) cc_final: 0.7984 (mpp) REVERT: M 313 MET cc_start: 0.8891 (mtm) cc_final: 0.8605 (mtp) REVERT: M 420 GLU cc_start: 0.8319 (pp20) cc_final: 0.7805 (pp20) REVERT: M 423 GLU cc_start: 0.8603 (pp20) cc_final: 0.8356 (pp20) REVERT: M 430 LYS cc_start: 0.8776 (mmmt) cc_final: 0.8133 (mmmm) REVERT: M 433 GLU cc_start: 0.8227 (pp20) cc_final: 0.7736 (pp20) REVERT: M 434 GLU cc_start: 0.8570 (pp20) cc_final: 0.8250 (pp20) REVERT: P 110 GLU cc_start: 0.7683 (pm20) cc_final: 0.7428 (pm20) REVERT: P 127 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8374 (mm-30) REVERT: P 293 GLN cc_start: 0.8658 (pp30) cc_final: 0.8144 (pp30) REVERT: P 393 GLU cc_start: 0.8332 (pp20) cc_final: 0.8075 (pp20) REVERT: P 422 GLU cc_start: 0.8217 (tp30) cc_final: 0.7773 (tp30) REVERT: O 73 THR cc_start: 0.8501 (p) cc_final: 0.7563 (p) REVERT: O 77 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7674 (pm20) REVERT: O 123 ARG cc_start: 0.9270 (tmm-80) cc_final: 0.8886 (ttp80) REVERT: O 154 MET cc_start: 0.9027 (mmm) cc_final: 0.8608 (mmm) REVERT: O 211 ASP cc_start: 0.8517 (t0) cc_final: 0.8083 (t0) REVERT: O 249 ASN cc_start: 0.8777 (m-40) cc_final: 0.8558 (m-40) REVERT: O 326 LYS cc_start: 0.5758 (mmtp) cc_final: 0.4655 (mmtm) REVERT: O 430 LYS cc_start: 0.8757 (tppp) cc_final: 0.8473 (tppp) REVERT: O 434 GLU cc_start: 0.8527 (pp20) cc_final: 0.8092 (OUTLIER) REVERT: R 1 MET cc_start: 0.8874 (mmm) cc_final: 0.8645 (tpt) REVERT: R 47 GLU cc_start: 0.7949 (pp20) cc_final: 0.7444 (tm-30) REVERT: R 113 GLU cc_start: 0.8677 (tp30) cc_final: 0.8386 (tp30) REVERT: R 127 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7618 (mp0) REVERT: R 183 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8132 (mt-10) REVERT: R 281 GLN cc_start: 0.9089 (tp40) cc_final: 0.8704 (tp40) REVERT: R 330 GLU cc_start: 0.6980 (tp30) cc_final: 0.6134 (tp30) REVERT: R 349 ASN cc_start: 0.7618 (t0) cc_final: 0.7229 (t0) REVERT: R 417 GLU cc_start: 0.8757 (tp30) cc_final: 0.8460 (mm-30) REVERT: R 427 ASP cc_start: 0.8562 (m-30) cc_final: 0.8161 (m-30) REVERT: Q 77 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8597 (tm-30) REVERT: Q 90 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8729 (mp0) REVERT: Q 128 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8081 (tm-30) REVERT: Q 205 ASP cc_start: 0.8036 (m-30) cc_final: 0.7612 (p0) REVERT: Q 285 GLN cc_start: 0.4967 (OUTLIER) cc_final: 0.3902 (mp-120) REVERT: Q 302 MET cc_start: 0.8829 (mtm) cc_final: 0.8474 (mtm) REVERT: Q 313 MET cc_start: 0.8730 (mtp) cc_final: 0.8249 (mtp) REVERT: Q 357 TYR cc_start: 0.8876 (m-80) cc_final: 0.8535 (m-80) REVERT: Q 386 GLU cc_start: 0.8354 (mp0) cc_final: 0.7945 (mp0) REVERT: Q 423 GLU cc_start: 0.8805 (pp20) cc_final: 0.8588 (pp20) REVERT: Q 430 LYS cc_start: 0.8967 (tppt) cc_final: 0.8571 (tppp) REVERT: Q 433 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8101 (tm-30) REVERT: Q 434 GLU cc_start: 0.8570 (pp20) cc_final: 0.8244 (pp20) REVERT: s 104 GLN cc_start: 0.8503 (mt0) cc_final: 0.8289 (mt0) REVERT: s 127 MET cc_start: 0.8163 (tpt) cc_final: 0.7908 (tpt) REVERT: t 93 MET cc_start: 0.8985 (tpt) cc_final: 0.8457 (tpt) REVERT: t 127 MET cc_start: 0.8104 (mmp) cc_final: 0.7748 (mmp) REVERT: v 98 LYS cc_start: 0.8929 (mmmt) cc_final: 0.8639 (mmmt) REVERT: v 127 MET cc_start: 0.8312 (mmp) cc_final: 0.7720 (mmp) REVERT: w 93 MET cc_start: 0.8873 (tpt) cc_final: 0.8564 (tpt) REVERT: w 119 LYS cc_start: 0.8570 (mttt) cc_final: 0.8254 (mttt) REVERT: x 127 MET cc_start: 0.8442 (tpt) cc_final: 0.7990 (tpt) REVERT: y 127 MET cc_start: 0.8527 (mmp) cc_final: 0.8120 (mmp) REVERT: z 93 MET cc_start: 0.8642 (tpp) cc_final: 0.8264 (tpp) REVERT: z 127 MET cc_start: 0.8292 (mmp) cc_final: 0.7911 (mmp) outliers start: 135 outliers final: 76 residues processed: 1178 average time/residue: 1.7586 time to fit residues: 2572.9873 Evaluate side-chains 1198 residues out of total 6966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 1095 time to evaluate : 5.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain r residue 120 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 389 LYS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain H residue 133 GLN Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 373 MET Chi-restraints excluded: chain H residue 389 LYS Chi-restraints excluded: chain H residue 405 LEU Chi-restraints excluded: chain H residue 425 MET Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 269 LEU Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 339 ARG Chi-restraints excluded: chain G residue 402 ARG Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 127 GLU Chi-restraints excluded: chain J residue 159 GLU Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 315 VAL Chi-restraints excluded: chain J residue 414 ASP Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain L residue 133 GLN Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 420 GLU Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 398 MET Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 68 VAL Chi-restraints excluded: chain N residue 129 CYS Chi-restraints excluded: chain N residue 207 GLU Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 284 ARG Chi-restraints excluded: chain N residue 333 LEU Chi-restraints excluded: chain N residue 393 GLU Chi-restraints excluded: chain N residue 402 LYS Chi-restraints excluded: chain N residue 405 LEU Chi-restraints excluded: chain N residue 413 MET Chi-restraints excluded: chain N residue 425 MET Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 205 ASP Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain P residue 129 CYS Chi-restraints excluded: chain P residue 194 LEU Chi-restraints excluded: chain P residue 269 MET Chi-restraints excluded: chain P residue 305 CYS Chi-restraints excluded: chain P residue 338 LYS Chi-restraints excluded: chain P residue 373 MET Chi-restraints excluded: chain P residue 389 LYS Chi-restraints excluded: chain P residue 405 LEU Chi-restraints excluded: chain O residue 77 GLU Chi-restraints excluded: chain R residue 149 MET Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 332 MET Chi-restraints excluded: chain Q residue 90 GLU Chi-restraints excluded: chain Q residue 209 ILE Chi-restraints excluded: chain Q residue 285 GLN Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain t residue 104 GLN Chi-restraints excluded: chain t residue 120 VAL Chi-restraints excluded: chain v residue 104 GLN Chi-restraints excluded: chain w residue 127 MET Chi-restraints excluded: chain x residue 104 GLN Chi-restraints excluded: chain z residue 104 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 801 random chunks: chunk 173 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 497 optimal weight: 2.9990 chunk 151 optimal weight: 0.0470 chunk 726 optimal weight: 9.9990 chunk 600 optimal weight: 0.9990 chunk 327 optimal weight: 1.9990 chunk 737 optimal weight: 5.9990 chunk 433 optimal weight: 5.9990 chunk 758 optimal weight: 7.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN A 50 ASN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 HIS F 334 ASN F 349 ASN E 249 ASN ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 HIS ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 331 GLN ** J 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 249 ASN ** I 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 133 GLN L 334 ASN ** L 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 59 ASN P 133 GLN P 433 GLN ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 293 GLN R 433 GLN Q 88 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.099148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.084638 restraints weight = 120062.058| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.39 r_work: 0.3509 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 65970 Z= 0.233 Angle : 0.692 13.916 89469 Z= 0.351 Chirality : 0.045 0.336 9711 Planarity : 0.004 0.066 11637 Dihedral : 10.745 176.196 9252 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.65 % Allowed : 20.98 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.53 (0.10), residues: 8055 helix: 1.39 (0.09), residues: 3681 sheet: -0.20 (0.16), residues: 1170 loop : -0.59 (0.11), residues: 3204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 388 HIS 0.013 0.001 HIS H 192 PHE 0.037 0.001 PHE K 255 TYR 0.023 0.001 TYR R 435 ARG 0.015 0.001 ARG H 400 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16110 Ramachandran restraints generated. 8055 Oldfield, 0 Emsley, 8055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16110 Ramachandran restraints generated. 8055 Oldfield, 0 Emsley, 8055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1226 residues out of total 6966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 1112 time to evaluate : 5.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: r 127 MET cc_start: 0.8524 (mmp) cc_final: 0.8109 (mmp) REVERT: B 3 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7111 (mm-30) REVERT: B 47 GLU cc_start: 0.8585 (tp30) cc_final: 0.7862 (tp30) REVERT: B 50 ASN cc_start: 0.8635 (p0) cc_final: 0.7936 (p0) REVERT: B 105 LYS cc_start: 0.8938 (mtpp) cc_final: 0.8618 (mtpp) REVERT: B 116 ASP cc_start: 0.8274 (m-30) cc_final: 0.7539 (m-30) REVERT: B 120 ASP cc_start: 0.8186 (m-30) cc_final: 0.7951 (m-30) REVERT: B 207 GLU cc_start: 0.8506 (pp20) cc_final: 0.8188 (pp20) REVERT: B 282 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8492 (pm20) REVERT: B 299 LYS cc_start: 0.8917 (tmmt) cc_final: 0.8592 (ttpp) REVERT: B 330 GLU cc_start: 0.8323 (pp20) cc_final: 0.8097 (pp20) REVERT: B 386 GLU cc_start: 0.8137 (pp20) cc_final: 0.7855 (pp20) REVERT: B 422 GLU cc_start: 0.8161 (tp30) cc_final: 0.7734 (tp30) REVERT: A 49 PHE cc_start: 0.8953 (p90) cc_final: 0.8633 (p90) REVERT: A 85 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8424 (mt0) REVERT: A 112 LYS cc_start: 0.8420 (pttt) cc_final: 0.7564 (pttm) REVERT: A 113 GLU cc_start: 0.7904 (mp0) cc_final: 0.7148 (mp0) REVERT: A 155 GLU cc_start: 0.8480 (pp20) cc_final: 0.8118 (pp20) REVERT: A 203 MET cc_start: 0.8649 (mmm) cc_final: 0.8438 (mmm) REVERT: A 209 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8298 (mt) REVERT: A 211 ASP cc_start: 0.8576 (t0) cc_final: 0.8323 (t0) REVERT: A 423 GLU cc_start: 0.8263 (tm-30) cc_final: 0.8053 (pp20) REVERT: D 3 GLU cc_start: 0.8056 (pp20) cc_final: 0.7838 (pp20) REVERT: D 22 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7577 (tp30) REVERT: D 41 ASP cc_start: 0.8264 (t70) cc_final: 0.7946 (t70) REVERT: D 47 GLU cc_start: 0.8168 (pp20) cc_final: 0.7829 (pp20) REVERT: D 50 ASN cc_start: 0.8912 (p0) cc_final: 0.8513 (p0) REVERT: D 105 LYS cc_start: 0.9187 (ttmt) cc_final: 0.8761 (ttpp) REVERT: D 110 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8292 (mp0) REVERT: D 156 LYS cc_start: 0.8784 (mmtt) cc_final: 0.8517 (mmtt) REVERT: D 159 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8173 (mt-10) REVERT: D 247 GLN cc_start: 0.8550 (mp10) cc_final: 0.8109 (mp10) REVERT: D 278 ARG cc_start: 0.8344 (tpm170) cc_final: 0.7708 (tpm170) REVERT: D 326 LYS cc_start: 0.8749 (tttp) cc_final: 0.8444 (tttp) REVERT: D 330 GLU cc_start: 0.7871 (pp20) cc_final: 0.7484 (pp20) REVERT: D 345 GLU cc_start: 0.8520 (pm20) cc_final: 0.8250 (pm20) REVERT: D 349 ASN cc_start: 0.6639 (t0) cc_final: 0.6312 (t0) REVERT: D 405 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8412 (mm) REVERT: D 422 GLU cc_start: 0.8048 (tp30) cc_final: 0.7468 (tp30) REVERT: D 433 GLN cc_start: 0.8580 (tm-30) cc_final: 0.8067 (tm-30) REVERT: C 77 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8162 (tm-30) REVERT: C 84 ARG cc_start: 0.9001 (ttp-110) cc_final: 0.8769 (ttm110) REVERT: C 103 TYR cc_start: 0.8864 (t80) cc_final: 0.8315 (t80) REVERT: C 163 LYS cc_start: 0.8298 (ttmm) cc_final: 0.8007 (ttmm) REVERT: C 203 MET cc_start: 0.8794 (mmm) cc_final: 0.8426 (mmm) REVERT: C 349 THR cc_start: 0.8221 (p) cc_final: 0.7950 (t) REVERT: C 417 GLU cc_start: 0.7950 (tp30) cc_final: 0.7530 (tp30) REVERT: C 420 GLU cc_start: 0.8245 (pt0) cc_final: 0.7820 (pt0) REVERT: C 423 GLU cc_start: 0.8464 (pp20) cc_final: 0.8058 (pp20) REVERT: C 434 GLU cc_start: 0.8500 (pp20) cc_final: 0.8035 (pp20) REVERT: F 26 ASP cc_start: 0.8447 (t0) cc_final: 0.8145 (t0) REVERT: F 47 GLU cc_start: 0.8523 (tp30) cc_final: 0.7824 (tp30) REVERT: F 75 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8165 (mmt) REVERT: F 105 LYS cc_start: 0.9255 (mtmt) cc_final: 0.9046 (mtpp) REVERT: F 110 GLU cc_start: 0.8396 (pp20) cc_final: 0.8105 (pp20) REVERT: F 159 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7396 (mp0) REVERT: F 247 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7791 (tt0) REVERT: F 282 GLN cc_start: 0.8740 (pm20) cc_final: 0.8425 (pm20) REVERT: F 293 GLN cc_start: 0.6686 (mm-40) cc_final: 0.6420 (mm110) REVERT: F 330 GLU cc_start: 0.6744 (tp30) cc_final: 0.5946 (tp30) REVERT: F 345 GLU cc_start: 0.8292 (pp20) cc_final: 0.7943 (tp30) REVERT: F 372 LYS cc_start: 0.8699 (pptt) cc_final: 0.8175 (pptt) REVERT: F 384 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8510 (mm) REVERT: F 393 GLU cc_start: 0.8409 (pp20) cc_final: 0.8172 (pp20) REVERT: E 2 ARG cc_start: 0.8721 (ptt90) cc_final: 0.8418 (mtm-85) REVERT: E 24 TYR cc_start: 0.8829 (m-10) cc_final: 0.8493 (m-10) REVERT: E 73 THR cc_start: 0.8326 (m) cc_final: 0.8118 (m) REVERT: E 205 ASP cc_start: 0.8398 (m-30) cc_final: 0.8159 (p0) REVERT: E 212 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8476 (mt) REVERT: E 214 ARG cc_start: 0.9213 (OUTLIER) cc_final: 0.8514 (ttm170) REVERT: E 245 ASP cc_start: 0.8671 (p0) cc_final: 0.8213 (p0) REVERT: E 251 ASP cc_start: 0.8348 (t0) cc_final: 0.7839 (t70) REVERT: E 392 ASP cc_start: 0.8742 (m-30) cc_final: 0.8419 (m-30) REVERT: E 434 GLU cc_start: 0.8360 (pp20) cc_final: 0.7831 (pp20) REVERT: H 1 MET cc_start: 0.8449 (ttm) cc_final: 0.7852 (ttm) REVERT: H 3 GLU cc_start: 0.7741 (mp0) cc_final: 0.7356 (mp0) REVERT: H 26 ASP cc_start: 0.8858 (t70) cc_final: 0.8579 (t0) REVERT: H 47 GLU cc_start: 0.7918 (pp20) cc_final: 0.7638 (pp20) REVERT: H 50 ASN cc_start: 0.9017 (p0) cc_final: 0.8635 (p0) REVERT: H 76 ASP cc_start: 0.9173 (t0) cc_final: 0.8841 (t0) REVERT: H 105 LYS cc_start: 0.9207 (mtpp) cc_final: 0.8885 (mtpp) REVERT: H 133 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8645 (tm-30) REVERT: H 156 LYS cc_start: 0.7921 (mmtp) cc_final: 0.7358 (mmtm) REVERT: H 159 GLU cc_start: 0.7760 (pp20) cc_final: 0.7467 (pm20) REVERT: H 166 MET cc_start: 0.8137 (tpp) cc_final: 0.7476 (tpp) REVERT: H 199 ASP cc_start: 0.8724 (m-30) cc_final: 0.8241 (m-30) REVERT: H 416 MET cc_start: 0.8611 (tpp) cc_final: 0.8274 (mmm) REVERT: H 422 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8046 (tm-30) REVERT: H 427 ASP cc_start: 0.8457 (m-30) cc_final: 0.8118 (m-30) REVERT: H 433 GLN cc_start: 0.8964 (mm-40) cc_final: 0.8564 (tm-30) REVERT: G 85 GLN cc_start: 0.8800 (pt0) cc_final: 0.8463 (pm20) REVERT: G 211 ASP cc_start: 0.8815 (t0) cc_final: 0.8517 (t70) REVERT: G 254 GLU cc_start: 0.8368 (tp30) cc_final: 0.8045 (tp30) REVERT: G 255 PHE cc_start: 0.7924 (t80) cc_final: 0.7415 (t80) REVERT: G 290 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7545 (pm20) REVERT: G 423 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8085 (tm-30) REVERT: G 425 MET cc_start: 0.8820 (mmm) cc_final: 0.8536 (tpp) REVERT: G 431 ASP cc_start: 0.8293 (t70) cc_final: 0.7656 (m-30) REVERT: G 433 GLU cc_start: 0.8575 (tp30) cc_final: 0.8145 (tp30) REVERT: G 434 GLU cc_start: 0.8549 (pp20) cc_final: 0.8246 (pp20) REVERT: J 3 GLU cc_start: 0.8054 (mp0) cc_final: 0.6780 (mp0) REVERT: J 26 ASP cc_start: 0.8666 (t0) cc_final: 0.8315 (t0) REVERT: J 76 ASP cc_start: 0.8829 (OUTLIER) cc_final: 0.8603 (t0) REVERT: J 96 GLN cc_start: 0.8541 (pm20) cc_final: 0.8070 (tp40) REVERT: J 109 THR cc_start: 0.8741 (m) cc_final: 0.8285 (p) REVERT: J 127 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7812 (mp0) REVERT: J 163 ASP cc_start: 0.8455 (p0) cc_final: 0.8114 (p0) REVERT: J 166 MET cc_start: 0.8791 (tpt) cc_final: 0.8493 (tpt) REVERT: J 196 GLU cc_start: 0.8179 (mp0) cc_final: 0.7848 (mp0) REVERT: J 207 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8531 (mm-30) REVERT: J 281 GLN cc_start: 0.8882 (tm-30) cc_final: 0.8329 (tm-30) REVERT: J 286 LEU cc_start: 0.9278 (tp) cc_final: 0.8937 (tm) REVERT: J 330 GLU cc_start: 0.8136 (pp20) cc_final: 0.7880 (pp20) REVERT: I 71 GLU cc_start: 0.7733 (pt0) cc_final: 0.7261 (pm20) REVERT: I 76 ASP cc_start: 0.8391 (m-30) cc_final: 0.7677 (m-30) REVERT: I 128 GLN cc_start: 0.9076 (tt0) cc_final: 0.8528 (tm-30) REVERT: I 154 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8484 (mmt) REVERT: I 211 ASP cc_start: 0.8641 (t0) cc_final: 0.8209 (t0) REVERT: I 251 ASP cc_start: 0.7613 (t70) cc_final: 0.7276 (t70) REVERT: I 326 LYS cc_start: 0.8568 (mtpp) cc_final: 0.8304 (ttmm) REVERT: I 423 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7979 (tm-30) REVERT: I 430 LYS cc_start: 0.8614 (mmmm) cc_final: 0.7951 (mmmm) REVERT: I 434 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8212 (mt-10) REVERT: L 1 MET cc_start: 0.9011 (mmm) cc_final: 0.8699 (mmm) REVERT: L 39 ASP cc_start: 0.9164 (p0) cc_final: 0.8868 (p0) REVERT: L 113 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8422 (tm-30) REVERT: L 124 LYS cc_start: 0.8724 (ttmm) cc_final: 0.8501 (ttpp) REVERT: L 127 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8139 (mm-30) REVERT: L 133 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7662 (pp30) REVERT: L 159 GLU cc_start: 0.7879 (pp20) cc_final: 0.7635 (pp20) REVERT: L 203 CYS cc_start: 0.9045 (t) cc_final: 0.8739 (p) REVERT: L 207 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8331 (tp30) REVERT: L 247 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7613 (tp40) REVERT: L 281 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8517 (tm-30) REVERT: L 322 ARG cc_start: 0.8081 (mmp80) cc_final: 0.7815 (mmp80) REVERT: L 393 GLU cc_start: 0.8649 (pp20) cc_final: 0.8271 (pp20) REVERT: L 420 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7950 (pp20) REVERT: K 24 TYR cc_start: 0.8874 (m-10) cc_final: 0.8644 (m-10) REVERT: K 77 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8529 (mm-30) REVERT: K 96 LYS cc_start: 0.8823 (mmtp) cc_final: 0.8579 (mmtp) REVERT: K 127 ASP cc_start: 0.8993 (OUTLIER) cc_final: 0.8577 (m-30) REVERT: K 176 GLN cc_start: 0.9049 (mp10) cc_final: 0.8773 (mp10) REVERT: K 227 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8258 (mt) REVERT: K 290 GLU cc_start: 0.8243 (pp20) cc_final: 0.7994 (pp20) REVERT: K 297 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7864 (tm-30) REVERT: K 302 MET cc_start: 0.8139 (mtm) cc_final: 0.7932 (pmm) REVERT: K 386 GLU cc_start: 0.7975 (pm20) cc_final: 0.7649 (pm20) REVERT: K 398 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8553 (mmm) REVERT: K 420 GLU cc_start: 0.8319 (pt0) cc_final: 0.7969 (pt0) REVERT: K 433 GLU cc_start: 0.8707 (tp30) cc_final: 0.8411 (tp30) REVERT: K 434 GLU cc_start: 0.8539 (pp20) cc_final: 0.8258 (pp20) REVERT: N 1 MET cc_start: 0.8856 (tpt) cc_final: 0.8533 (tpp) REVERT: N 22 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8153 (tm-30) REVERT: N 37 HIS cc_start: 0.8306 (m90) cc_final: 0.7804 (m90) REVERT: N 50 ASN cc_start: 0.8912 (p0) cc_final: 0.8537 (p0) REVERT: N 75 MET cc_start: 0.8741 (mmp) cc_final: 0.8506 (mmm) REVERT: N 116 ASP cc_start: 0.8723 (t0) cc_final: 0.8405 (t0) REVERT: N 127 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8658 (mm-30) REVERT: N 159 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8355 (mp0) REVERT: N 207 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8101 (tp30) REVERT: N 281 GLN cc_start: 0.8970 (tm-30) cc_final: 0.8686 (tm-30) REVERT: N 338 LYS cc_start: 0.8866 (mtmm) cc_final: 0.8616 (mtmm) REVERT: N 345 GLU cc_start: 0.8699 (pm20) cc_final: 0.8380 (pm20) REVERT: N 422 GLU cc_start: 0.8318 (tp30) cc_final: 0.7716 (tp30) REVERT: M 85 GLN cc_start: 0.8958 (pt0) cc_final: 0.8599 (pm20) REVERT: M 98 ASP cc_start: 0.8549 (p0) cc_final: 0.8285 (p0) REVERT: M 119 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8644 (mm) REVERT: M 203 MET cc_start: 0.8997 (mmm) cc_final: 0.8258 (mmm) REVERT: M 220 GLU cc_start: 0.7342 (pp20) cc_final: 0.6763 (pp20) REVERT: M 221 ARG cc_start: 0.8443 (ptp-110) cc_final: 0.7970 (ptp-110) REVERT: M 313 MET cc_start: 0.8889 (mtm) cc_final: 0.8626 (mtp) REVERT: M 420 GLU cc_start: 0.8313 (pp20) cc_final: 0.7833 (pp20) REVERT: M 423 GLU cc_start: 0.8632 (pp20) cc_final: 0.8404 (pp20) REVERT: M 430 LYS cc_start: 0.8776 (mmmt) cc_final: 0.8061 (mmmm) REVERT: M 433 GLU cc_start: 0.8204 (pp20) cc_final: 0.7670 (pp20) REVERT: M 434 GLU cc_start: 0.8550 (pp20) cc_final: 0.8234 (pp20) REVERT: P 22 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7913 (mm-30) REVERT: P 127 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8345 (mm-30) REVERT: P 293 GLN cc_start: 0.8676 (pp30) cc_final: 0.8155 (pp30) REVERT: P 393 GLU cc_start: 0.8343 (pp20) cc_final: 0.8073 (pp20) REVERT: P 422 GLU cc_start: 0.8195 (tp30) cc_final: 0.7746 (tp30) REVERT: O 73 THR cc_start: 0.8486 (p) cc_final: 0.7494 (p) REVERT: O 77 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7651 (pm20) REVERT: O 123 ARG cc_start: 0.9285 (tmm-80) cc_final: 0.9024 (ttp80) REVERT: O 154 MET cc_start: 0.9036 (mmm) cc_final: 0.8621 (mmm) REVERT: O 211 ASP cc_start: 0.8527 (t0) cc_final: 0.8113 (t0) REVERT: O 249 ASN cc_start: 0.8763 (m-40) cc_final: 0.8555 (m-40) REVERT: O 326 LYS cc_start: 0.5668 (mmtp) cc_final: 0.4529 (mmtm) REVERT: O 430 LYS cc_start: 0.8737 (tppp) cc_final: 0.8459 (tppp) REVERT: O 434 GLU cc_start: 0.8519 (pp20) cc_final: 0.8103 (pp20) REVERT: R 1 MET cc_start: 0.8847 (mmm) cc_final: 0.8594 (tpt) REVERT: R 47 GLU cc_start: 0.7942 (pp20) cc_final: 0.7452 (tm-30) REVERT: R 113 GLU cc_start: 0.8657 (tp30) cc_final: 0.8367 (tp30) REVERT: R 127 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7603 (mp0) REVERT: R 159 GLU cc_start: 0.8395 (pp20) cc_final: 0.8172 (pp20) REVERT: R 183 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8139 (mt-10) REVERT: R 207 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8153 (mm-30) REVERT: R 281 GLN cc_start: 0.9098 (tp40) cc_final: 0.8739 (tp40) REVERT: R 293 GLN cc_start: 0.7012 (mm-40) cc_final: 0.6793 (mm110) REVERT: R 330 GLU cc_start: 0.6887 (tp30) cc_final: 0.6127 (tp30) REVERT: R 349 ASN cc_start: 0.7613 (t0) cc_final: 0.7223 (t0) REVERT: R 427 ASP cc_start: 0.8554 (m-30) cc_final: 0.8150 (m-30) REVERT: Q 77 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8610 (tm-30) REVERT: Q 90 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8741 (mp0) REVERT: Q 128 GLN cc_start: 0.8497 (tm-30) cc_final: 0.8068 (tm-30) REVERT: Q 205 ASP cc_start: 0.7987 (m-30) cc_final: 0.7659 (p0) REVERT: Q 285 GLN cc_start: 0.4942 (mm-40) cc_final: 0.3956 (mp10) REVERT: Q 302 MET cc_start: 0.8851 (mtm) cc_final: 0.8274 (mtm) REVERT: Q 313 MET cc_start: 0.8723 (mtp) cc_final: 0.8226 (mtp) REVERT: Q 357 TYR cc_start: 0.8865 (m-80) cc_final: 0.8579 (m-80) REVERT: Q 386 GLU cc_start: 0.8237 (mp0) cc_final: 0.7838 (mp0) REVERT: Q 423 GLU cc_start: 0.8805 (pp20) cc_final: 0.8581 (pp20) REVERT: Q 430 LYS cc_start: 0.9000 (tppt) cc_final: 0.8553 (tppp) REVERT: Q 433 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8065 (tm-30) REVERT: Q 434 GLU cc_start: 0.8573 (pp20) cc_final: 0.8240 (pp20) REVERT: s 104 GLN cc_start: 0.8509 (mt0) cc_final: 0.8298 (mt0) REVERT: s 127 MET cc_start: 0.8127 (tpt) cc_final: 0.7891 (tpt) REVERT: t 93 MET cc_start: 0.9003 (tpt) cc_final: 0.8465 (tpt) REVERT: t 127 MET cc_start: 0.8114 (mmp) cc_final: 0.7759 (mmp) REVERT: v 98 LYS cc_start: 0.8927 (mmmt) cc_final: 0.8636 (mmmt) REVERT: v 127 MET cc_start: 0.8287 (mmp) cc_final: 0.7696 (mmp) REVERT: w 93 MET cc_start: 0.8830 (tpt) cc_final: 0.8514 (tpt) REVERT: w 119 LYS cc_start: 0.8556 (mttt) cc_final: 0.8224 (mttt) REVERT: x 127 MET cc_start: 0.8457 (tpt) cc_final: 0.7970 (tpt) REVERT: y 127 MET cc_start: 0.8483 (mmp) cc_final: 0.8072 (mmp) REVERT: z 93 MET cc_start: 0.8620 (tpp) cc_final: 0.8229 (tpp) REVERT: z 127 MET cc_start: 0.8263 (mmp) cc_final: 0.7867 (mmp) outliers start: 114 outliers final: 73 residues processed: 1173 average time/residue: 1.7702 time to fit residues: 2573.2032 Evaluate side-chains 1190 residues out of total 6966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 1094 time to evaluate : 5.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain r residue 120 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 192 HIS Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain H residue 133 GLN Chi-restraints excluded: chain H residue 192 HIS Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 389 LYS Chi-restraints excluded: chain H residue 405 LEU Chi-restraints excluded: chain H residue 425 MET Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 269 LEU Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 127 GLU Chi-restraints excluded: chain J residue 159 GLU Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 315 VAL Chi-restraints excluded: chain I residue 88 HIS Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain L residue 133 GLN Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 420 GLU Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 398 MET Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 68 VAL Chi-restraints excluded: chain N residue 129 CYS Chi-restraints excluded: chain N residue 220 THR Chi-restraints excluded: chain N residue 333 LEU Chi-restraints excluded: chain N residue 402 LYS Chi-restraints excluded: chain N residue 405 LEU Chi-restraints excluded: chain N residue 413 MET Chi-restraints excluded: chain N residue 425 MET Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 205 ASP Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain P residue 129 CYS Chi-restraints excluded: chain P residue 194 LEU Chi-restraints excluded: chain P residue 269 MET Chi-restraints excluded: chain P residue 305 CYS Chi-restraints excluded: chain P residue 338 LYS Chi-restraints excluded: chain P residue 373 MET Chi-restraints excluded: chain P residue 389 LYS Chi-restraints excluded: chain P residue 405 LEU Chi-restraints excluded: chain O residue 77 GLU Chi-restraints excluded: chain R residue 149 MET Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 332 MET Chi-restraints excluded: chain Q residue 90 GLU Chi-restraints excluded: chain Q residue 209 ILE Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain t residue 104 GLN Chi-restraints excluded: chain t residue 120 VAL Chi-restraints excluded: chain v residue 104 GLN Chi-restraints excluded: chain w residue 127 MET Chi-restraints excluded: chain x residue 104 GLN Chi-restraints excluded: chain z residue 104 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 801 random chunks: chunk 545 optimal weight: 0.8980 chunk 630 optimal weight: 3.9990 chunk 428 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 437 optimal weight: 3.9990 chunk 653 optimal weight: 4.9990 chunk 275 optimal weight: 0.0270 chunk 756 optimal weight: 9.9990 chunk 500 optimal weight: 0.0020 chunk 501 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 overall best weight: 0.7248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN A 50 ASN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 ASN ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 GLN ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 HIS F 334 ASN F 349 ASN F 433 GLN E 249 ASN ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 HIS ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 133 GLN L 334 ASN ** N 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 GLN P 59 ASN ** P 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 88 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.100099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.085613 restraints weight = 119097.164| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.37 r_work: 0.3530 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 65970 Z= 0.214 Angle : 0.692 13.500 89469 Z= 0.351 Chirality : 0.044 0.394 9711 Planarity : 0.004 0.066 11637 Dihedral : 10.679 175.198 9252 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.66 % Allowed : 21.17 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.64 (0.10), residues: 8055 helix: 1.51 (0.09), residues: 3627 sheet: -0.10 (0.16), residues: 1143 loop : -0.55 (0.11), residues: 3285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 388 HIS 0.022 0.001 HIS H 192 PHE 0.037 0.001 PHE K 255 TYR 0.028 0.001 TYR z 123 ARG 0.015 0.001 ARG H 400 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 51398.07 seconds wall clock time: 886 minutes 28.42 seconds (53188.42 seconds total)