Starting phenix.real_space_refine on Sat Jan 18 17:33:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gk2_51414/01_2025/9gk2_51414.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gk2_51414/01_2025/9gk2_51414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gk2_51414/01_2025/9gk2_51414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gk2_51414/01_2025/9gk2_51414.map" model { file = "/net/cci-nas-00/data/ceres_data/9gk2_51414/01_2025/9gk2_51414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gk2_51414/01_2025/9gk2_51414.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 3 Type Number sf(0) Gaussians C 37656 2.51 5 N 10260 2.21 5 O 12600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 434 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 60516 Number of models: 1 Model: "" Number of chains: 18 Chain: "G" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3362 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 420} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3362 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 420} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3362 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 420} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3362 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 420} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3362 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 420} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3362 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 420} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3362 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 420} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3362 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 420} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3362 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 420} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3362 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 420} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3362 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 420} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3362 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 420} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3362 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 420} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3362 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 420} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3362 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 420} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3362 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 420} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3362 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 420} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3362 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 420} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 24.63, per 1000 atoms: 0.41 Number of scatterers: 60516 At special positions: 0 Unit cell: (369.91, 372.75, 117.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 12600 8.00 N 10260 7.00 C 37656 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: 11.69 Conformation dependent library (CDL) restraints added in 6.3 seconds 15480 Ramachandran restraints generated. 7740 Oldfield, 0 Emsley, 7740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15120 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 0 sheets defined 75.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'G' and resid 60 through 81 removed outlier: 3.762A pdb=" N THR G 71 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR G 74 " --> pdb=" O SER G 70 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLU G 77 " --> pdb=" O ALA G 73 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N PHE G 78 " --> pdb=" O TYR G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 91 Processing helix chain 'G' and resid 103 through 162 removed outlier: 3.526A pdb=" N ALA G 107 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA G 161 " --> pdb=" O LEU G 157 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE G 162 " --> pdb=" O ARG G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 174 Processing helix chain 'G' and resid 175 through 186 Processing helix chain 'G' and resid 212 through 235 removed outlier: 3.567A pdb=" N ALA G 216 " --> pdb=" O GLN G 212 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU G 232 " --> pdb=" O ASP G 228 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TRP G 233 " --> pdb=" O ALA G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 286 Proline residue: G 271 - end of helix removed outlier: 3.628A pdb=" N GLN G 284 " --> pdb=" O ASN G 280 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS G 285 " --> pdb=" O LEU G 281 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N SER G 286 " --> pdb=" O GLU G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 321 removed outlier: 3.690A pdb=" N ARG G 291 " --> pdb=" O ASP G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 342 removed outlier: 4.082A pdb=" N HIS G 338 " --> pdb=" O THR G 334 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR G 339 " --> pdb=" O LEU G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 367 Processing helix chain 'G' and resid 380 through 406 removed outlier: 3.989A pdb=" N TYR G 384 " --> pdb=" O GLU G 380 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU G 400 " --> pdb=" O TYR G 396 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 463 removed outlier: 3.577A pdb=" N VAL G 413 " --> pdb=" O PRO G 409 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA G 463 " --> pdb=" O LEU G 459 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 81 removed outlier: 3.764A pdb=" N THR H 71 " --> pdb=" O LEU H 67 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR H 74 " --> pdb=" O SER H 70 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLU H 77 " --> pdb=" O ALA H 73 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N PHE H 78 " --> pdb=" O TYR H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 91 Processing helix chain 'H' and resid 103 through 162 removed outlier: 3.525A pdb=" N ALA H 107 " --> pdb=" O SER H 103 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA H 161 " --> pdb=" O LEU H 157 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE H 162 " --> pdb=" O ARG H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 174 Processing helix chain 'H' and resid 175 through 186 Processing helix chain 'H' and resid 212 through 235 removed outlier: 3.567A pdb=" N ALA H 216 " --> pdb=" O GLN H 212 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU H 232 " --> pdb=" O ASP H 228 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TRP H 233 " --> pdb=" O ALA H 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 286 Proline residue: H 271 - end of helix removed outlier: 3.628A pdb=" N GLN H 284 " --> pdb=" O ASN H 280 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS H 285 " --> pdb=" O LEU H 281 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER H 286 " --> pdb=" O GLU H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 321 removed outlier: 3.689A pdb=" N ARG H 291 " --> pdb=" O ASP H 287 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 342 removed outlier: 4.082A pdb=" N HIS H 338 " --> pdb=" O THR H 334 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR H 339 " --> pdb=" O LEU H 335 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 367 Processing helix chain 'H' and resid 380 through 406 removed outlier: 3.990A pdb=" N TYR H 384 " --> pdb=" O GLU H 380 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU H 400 " --> pdb=" O TYR H 396 " (cutoff:3.500A) Processing helix chain 'H' and resid 406 through 463 removed outlier: 3.577A pdb=" N VAL H 413 " --> pdb=" O PRO H 409 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA H 463 " --> pdb=" O LEU H 459 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 81 removed outlier: 3.764A pdb=" N THR I 71 " --> pdb=" O LEU I 67 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR I 74 " --> pdb=" O SER I 70 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLU I 77 " --> pdb=" O ALA I 73 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N PHE I 78 " --> pdb=" O TYR I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 91 Processing helix chain 'I' and resid 103 through 162 removed outlier: 3.524A pdb=" N ALA I 107 " --> pdb=" O SER I 103 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA I 161 " --> pdb=" O LEU I 157 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE I 162 " --> pdb=" O ARG I 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 174 Processing helix chain 'I' and resid 175 through 186 Processing helix chain 'I' and resid 212 through 235 removed outlier: 3.567A pdb=" N ALA I 216 " --> pdb=" O GLN I 212 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU I 232 " --> pdb=" O ASP I 228 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TRP I 233 " --> pdb=" O ALA I 229 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 286 Proline residue: I 271 - end of helix removed outlier: 3.627A pdb=" N GLN I 284 " --> pdb=" O ASN I 280 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS I 285 " --> pdb=" O LEU I 281 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER I 286 " --> pdb=" O GLU I 282 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 321 removed outlier: 3.688A pdb=" N ARG I 291 " --> pdb=" O ASP I 287 " (cutoff:3.500A) Processing helix chain 'I' and resid 334 through 342 removed outlier: 4.082A pdb=" N HIS I 338 " --> pdb=" O THR I 334 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR I 339 " --> pdb=" O LEU I 335 " (cutoff:3.500A) Processing helix chain 'I' and resid 342 through 367 Processing helix chain 'I' and resid 380 through 406 removed outlier: 3.989A pdb=" N TYR I 384 " --> pdb=" O GLU I 380 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU I 400 " --> pdb=" O TYR I 396 " (cutoff:3.500A) Processing helix chain 'I' and resid 406 through 463 removed outlier: 3.578A pdb=" N VAL I 413 " --> pdb=" O PRO I 409 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA I 463 " --> pdb=" O LEU I 459 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 81 removed outlier: 3.764A pdb=" N THR J 71 " --> pdb=" O LEU J 67 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR J 74 " --> pdb=" O SER J 70 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLU J 77 " --> pdb=" O ALA J 73 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N PHE J 78 " --> pdb=" O TYR J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 91 Processing helix chain 'J' and resid 103 through 162 removed outlier: 3.525A pdb=" N ALA J 107 " --> pdb=" O SER J 103 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA J 161 " --> pdb=" O LEU J 157 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE J 162 " --> pdb=" O ARG J 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 174 Processing helix chain 'J' and resid 175 through 186 Processing helix chain 'J' and resid 212 through 235 removed outlier: 3.567A pdb=" N ALA J 216 " --> pdb=" O GLN J 212 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU J 232 " --> pdb=" O ASP J 228 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TRP J 233 " --> pdb=" O ALA J 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 250 through 286 Proline residue: J 271 - end of helix removed outlier: 3.628A pdb=" N GLN J 284 " --> pdb=" O ASN J 280 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS J 285 " --> pdb=" O LEU J 281 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER J 286 " --> pdb=" O GLU J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 321 removed outlier: 3.690A pdb=" N ARG J 291 " --> pdb=" O ASP J 287 " (cutoff:3.500A) Processing helix chain 'J' and resid 334 through 342 removed outlier: 4.081A pdb=" N HIS J 338 " --> pdb=" O THR J 334 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR J 339 " --> pdb=" O LEU J 335 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 367 Processing helix chain 'J' and resid 380 through 406 removed outlier: 3.990A pdb=" N TYR J 384 " --> pdb=" O GLU J 380 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU J 400 " --> pdb=" O TYR J 396 " (cutoff:3.500A) Processing helix chain 'J' and resid 406 through 463 removed outlier: 3.577A pdb=" N VAL J 413 " --> pdb=" O PRO J 409 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA J 463 " --> pdb=" O LEU J 459 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 81 removed outlier: 3.763A pdb=" N THR K 71 " --> pdb=" O LEU K 67 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR K 74 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLU K 77 " --> pdb=" O ALA K 73 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N PHE K 78 " --> pdb=" O TYR K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 91 Processing helix chain 'K' and resid 103 through 162 removed outlier: 3.524A pdb=" N ALA K 107 " --> pdb=" O SER K 103 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA K 161 " --> pdb=" O LEU K 157 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE K 162 " --> pdb=" O ARG K 158 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 174 Processing helix chain 'K' and resid 175 through 186 Processing helix chain 'K' and resid 212 through 235 removed outlier: 3.567A pdb=" N ALA K 216 " --> pdb=" O GLN K 212 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU K 232 " --> pdb=" O ASP K 228 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TRP K 233 " --> pdb=" O ALA K 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 250 through 286 Proline residue: K 271 - end of helix removed outlier: 3.628A pdb=" N GLN K 284 " --> pdb=" O ASN K 280 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS K 285 " --> pdb=" O LEU K 281 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER K 286 " --> pdb=" O GLU K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 321 removed outlier: 3.691A pdb=" N ARG K 291 " --> pdb=" O ASP K 287 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 342 removed outlier: 4.082A pdb=" N HIS K 338 " --> pdb=" O THR K 334 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR K 339 " --> pdb=" O LEU K 335 " (cutoff:3.500A) Processing helix chain 'K' and resid 342 through 367 Processing helix chain 'K' and resid 380 through 406 removed outlier: 3.990A pdb=" N TYR K 384 " --> pdb=" O GLU K 380 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU K 400 " --> pdb=" O TYR K 396 " (cutoff:3.500A) Processing helix chain 'K' and resid 406 through 463 removed outlier: 3.578A pdb=" N VAL K 413 " --> pdb=" O PRO K 409 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA K 463 " --> pdb=" O LEU K 459 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 81 removed outlier: 3.763A pdb=" N THR L 71 " --> pdb=" O LEU L 67 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR L 74 " --> pdb=" O SER L 70 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLU L 77 " --> pdb=" O ALA L 73 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N PHE L 78 " --> pdb=" O TYR L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 91 Processing helix chain 'L' and resid 103 through 162 removed outlier: 3.525A pdb=" N ALA L 107 " --> pdb=" O SER L 103 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA L 161 " --> pdb=" O LEU L 157 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE L 162 " --> pdb=" O ARG L 158 " (cutoff:3.500A) Processing helix chain 'L' and resid 171 through 174 Processing helix chain 'L' and resid 175 through 186 Processing helix chain 'L' and resid 212 through 235 removed outlier: 3.566A pdb=" N ALA L 216 " --> pdb=" O GLN L 212 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU L 232 " --> pdb=" O ASP L 228 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TRP L 233 " --> pdb=" O ALA L 229 " (cutoff:3.500A) Processing helix chain 'L' and resid 250 through 286 Proline residue: L 271 - end of helix removed outlier: 3.628A pdb=" N GLN L 284 " --> pdb=" O ASN L 280 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS L 285 " --> pdb=" O LEU L 281 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER L 286 " --> pdb=" O GLU L 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 321 removed outlier: 3.689A pdb=" N ARG L 291 " --> pdb=" O ASP L 287 " (cutoff:3.500A) Processing helix chain 'L' and resid 334 through 342 removed outlier: 4.081A pdb=" N HIS L 338 " --> pdb=" O THR L 334 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR L 339 " --> pdb=" O LEU L 335 " (cutoff:3.500A) Processing helix chain 'L' and resid 342 through 367 Processing helix chain 'L' and resid 380 through 406 removed outlier: 3.990A pdb=" N TYR L 384 " --> pdb=" O GLU L 380 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU L 400 " --> pdb=" O TYR L 396 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 463 removed outlier: 3.578A pdb=" N VAL L 413 " --> pdb=" O PRO L 409 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA L 463 " --> pdb=" O LEU L 459 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 81 removed outlier: 3.763A pdb=" N THR M 71 " --> pdb=" O LEU M 67 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR M 74 " --> pdb=" O SER M 70 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLU M 77 " --> pdb=" O ALA M 73 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N PHE M 78 " --> pdb=" O TYR M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 91 Processing helix chain 'M' and resid 103 through 162 removed outlier: 3.525A pdb=" N ALA M 107 " --> pdb=" O SER M 103 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA M 161 " --> pdb=" O LEU M 157 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE M 162 " --> pdb=" O ARG M 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 174 Processing helix chain 'M' and resid 175 through 186 Processing helix chain 'M' and resid 212 through 235 removed outlier: 3.566A pdb=" N ALA M 216 " --> pdb=" O GLN M 212 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU M 232 " --> pdb=" O ASP M 228 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TRP M 233 " --> pdb=" O ALA M 229 " (cutoff:3.500A) Processing helix chain 'M' and resid 250 through 286 Proline residue: M 271 - end of helix removed outlier: 3.629A pdb=" N GLN M 284 " --> pdb=" O ASN M 280 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS M 285 " --> pdb=" O LEU M 281 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER M 286 " --> pdb=" O GLU M 282 " (cutoff:3.500A) Processing helix chain 'M' and resid 287 through 321 removed outlier: 3.689A pdb=" N ARG M 291 " --> pdb=" O ASP M 287 " (cutoff:3.500A) Processing helix chain 'M' and resid 334 through 342 removed outlier: 4.081A pdb=" N HIS M 338 " --> pdb=" O THR M 334 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR M 339 " --> pdb=" O LEU M 335 " (cutoff:3.500A) Processing helix chain 'M' and resid 342 through 367 Processing helix chain 'M' and resid 380 through 406 removed outlier: 3.990A pdb=" N TYR M 384 " --> pdb=" O GLU M 380 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU M 400 " --> pdb=" O TYR M 396 " (cutoff:3.500A) Processing helix chain 'M' and resid 406 through 463 removed outlier: 3.578A pdb=" N VAL M 413 " --> pdb=" O PRO M 409 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA M 463 " --> pdb=" O LEU M 459 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 81 removed outlier: 3.763A pdb=" N THR N 71 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR N 74 " --> pdb=" O SER N 70 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLU N 77 " --> pdb=" O ALA N 73 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N PHE N 78 " --> pdb=" O TYR N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 91 Processing helix chain 'N' and resid 103 through 162 removed outlier: 3.525A pdb=" N ALA N 107 " --> pdb=" O SER N 103 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA N 161 " --> pdb=" O LEU N 157 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE N 162 " --> pdb=" O ARG N 158 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 174 Processing helix chain 'N' and resid 175 through 186 Processing helix chain 'N' and resid 212 through 235 removed outlier: 3.567A pdb=" N ALA N 216 " --> pdb=" O GLN N 212 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU N 232 " --> pdb=" O ASP N 228 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TRP N 233 " --> pdb=" O ALA N 229 " (cutoff:3.500A) Processing helix chain 'N' and resid 250 through 286 Proline residue: N 271 - end of helix removed outlier: 3.629A pdb=" N GLN N 284 " --> pdb=" O ASN N 280 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS N 285 " --> pdb=" O LEU N 281 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER N 286 " --> pdb=" O GLU N 282 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 321 removed outlier: 3.690A pdb=" N ARG N 291 " --> pdb=" O ASP N 287 " (cutoff:3.500A) Processing helix chain 'N' and resid 334 through 342 removed outlier: 4.081A pdb=" N HIS N 338 " --> pdb=" O THR N 334 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR N 339 " --> pdb=" O LEU N 335 " (cutoff:3.500A) Processing helix chain 'N' and resid 342 through 367 Processing helix chain 'N' and resid 380 through 406 removed outlier: 3.991A pdb=" N TYR N 384 " --> pdb=" O GLU N 380 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU N 400 " --> pdb=" O TYR N 396 " (cutoff:3.500A) Processing helix chain 'N' and resid 406 through 463 removed outlier: 3.579A pdb=" N VAL N 413 " --> pdb=" O PRO N 409 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA N 463 " --> pdb=" O LEU N 459 " (cutoff:3.500A) Processing helix chain 'O' and resid 60 through 81 removed outlier: 3.764A pdb=" N THR O 71 " --> pdb=" O LEU O 67 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR O 74 " --> pdb=" O SER O 70 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLU O 77 " --> pdb=" O ALA O 73 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N PHE O 78 " --> pdb=" O TYR O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 91 Processing helix chain 'O' and resid 103 through 162 removed outlier: 3.526A pdb=" N ALA O 107 " --> pdb=" O SER O 103 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA O 161 " --> pdb=" O LEU O 157 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE O 162 " --> pdb=" O ARG O 158 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 174 Processing helix chain 'O' and resid 175 through 186 Processing helix chain 'O' and resid 212 through 235 removed outlier: 3.567A pdb=" N ALA O 216 " --> pdb=" O GLN O 212 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU O 232 " --> pdb=" O ASP O 228 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TRP O 233 " --> pdb=" O ALA O 229 " (cutoff:3.500A) Processing helix chain 'O' and resid 250 through 286 Proline residue: O 271 - end of helix removed outlier: 3.627A pdb=" N GLN O 284 " --> pdb=" O ASN O 280 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS O 285 " --> pdb=" O LEU O 281 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER O 286 " --> pdb=" O GLU O 282 " (cutoff:3.500A) Processing helix chain 'O' and resid 287 through 321 removed outlier: 3.689A pdb=" N ARG O 291 " --> pdb=" O ASP O 287 " (cutoff:3.500A) Processing helix chain 'O' and resid 334 through 342 removed outlier: 4.082A pdb=" N HIS O 338 " --> pdb=" O THR O 334 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR O 339 " --> pdb=" O LEU O 335 " (cutoff:3.500A) Processing helix chain 'O' and resid 342 through 367 Processing helix chain 'O' and resid 380 through 406 removed outlier: 3.988A pdb=" N TYR O 384 " --> pdb=" O GLU O 380 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU O 400 " --> pdb=" O TYR O 396 " (cutoff:3.500A) Processing helix chain 'O' and resid 406 through 463 removed outlier: 3.578A pdb=" N VAL O 413 " --> pdb=" O PRO O 409 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA O 463 " --> pdb=" O LEU O 459 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 81 removed outlier: 3.762A pdb=" N THR P 71 " --> pdb=" O LEU P 67 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR P 74 " --> pdb=" O SER P 70 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLU P 77 " --> pdb=" O ALA P 73 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N PHE P 78 " --> pdb=" O TYR P 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 91 Processing helix chain 'P' and resid 103 through 162 removed outlier: 3.525A pdb=" N ALA P 107 " --> pdb=" O SER P 103 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA P 161 " --> pdb=" O LEU P 157 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE P 162 " --> pdb=" O ARG P 158 " (cutoff:3.500A) Processing helix chain 'P' and resid 171 through 174 Processing helix chain 'P' and resid 175 through 186 Processing helix chain 'P' and resid 212 through 235 removed outlier: 3.567A pdb=" N ALA P 216 " --> pdb=" O GLN P 212 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU P 232 " --> pdb=" O ASP P 228 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TRP P 233 " --> pdb=" O ALA P 229 " (cutoff:3.500A) Processing helix chain 'P' and resid 250 through 286 Proline residue: P 271 - end of helix removed outlier: 3.627A pdb=" N GLN P 284 " --> pdb=" O ASN P 280 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS P 285 " --> pdb=" O LEU P 281 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER P 286 " --> pdb=" O GLU P 282 " (cutoff:3.500A) Processing helix chain 'P' and resid 287 through 321 removed outlier: 3.688A pdb=" N ARG P 291 " --> pdb=" O ASP P 287 " (cutoff:3.500A) Processing helix chain 'P' and resid 334 through 342 removed outlier: 4.082A pdb=" N HIS P 338 " --> pdb=" O THR P 334 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR P 339 " --> pdb=" O LEU P 335 " (cutoff:3.500A) Processing helix chain 'P' and resid 342 through 367 Processing helix chain 'P' and resid 380 through 406 removed outlier: 3.989A pdb=" N TYR P 384 " --> pdb=" O GLU P 380 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU P 400 " --> pdb=" O TYR P 396 " (cutoff:3.500A) Processing helix chain 'P' and resid 406 through 463 removed outlier: 3.580A pdb=" N VAL P 413 " --> pdb=" O PRO P 409 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA P 463 " --> pdb=" O LEU P 459 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 81 removed outlier: 3.764A pdb=" N THR Q 71 " --> pdb=" O LEU Q 67 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR Q 74 " --> pdb=" O SER Q 70 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLU Q 77 " --> pdb=" O ALA Q 73 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N PHE Q 78 " --> pdb=" O TYR Q 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 91 Processing helix chain 'Q' and resid 103 through 162 removed outlier: 3.526A pdb=" N ALA Q 107 " --> pdb=" O SER Q 103 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA Q 161 " --> pdb=" O LEU Q 157 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE Q 162 " --> pdb=" O ARG Q 158 " (cutoff:3.500A) Processing helix chain 'Q' and resid 171 through 174 Processing helix chain 'Q' and resid 175 through 186 Processing helix chain 'Q' and resid 212 through 235 removed outlier: 3.566A pdb=" N ALA Q 216 " --> pdb=" O GLN Q 212 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU Q 232 " --> pdb=" O ASP Q 228 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TRP Q 233 " --> pdb=" O ALA Q 229 " (cutoff:3.500A) Processing helix chain 'Q' and resid 250 through 286 Proline residue: Q 271 - end of helix removed outlier: 3.628A pdb=" N GLN Q 284 " --> pdb=" O ASN Q 280 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS Q 285 " --> pdb=" O LEU Q 281 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER Q 286 " --> pdb=" O GLU Q 282 " (cutoff:3.500A) Processing helix chain 'Q' and resid 287 through 321 removed outlier: 3.689A pdb=" N ARG Q 291 " --> pdb=" O ASP Q 287 " (cutoff:3.500A) Processing helix chain 'Q' and resid 334 through 342 removed outlier: 4.082A pdb=" N HIS Q 338 " --> pdb=" O THR Q 334 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR Q 339 " --> pdb=" O LEU Q 335 " (cutoff:3.500A) Processing helix chain 'Q' and resid 342 through 367 Processing helix chain 'Q' and resid 380 through 406 removed outlier: 3.989A pdb=" N TYR Q 384 " --> pdb=" O GLU Q 380 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU Q 400 " --> pdb=" O TYR Q 396 " (cutoff:3.500A) Processing helix chain 'Q' and resid 406 through 463 removed outlier: 3.578A pdb=" N VAL Q 413 " --> pdb=" O PRO Q 409 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA Q 463 " --> pdb=" O LEU Q 459 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 81 removed outlier: 3.763A pdb=" N THR R 71 " --> pdb=" O LEU R 67 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR R 74 " --> pdb=" O SER R 70 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLU R 77 " --> pdb=" O ALA R 73 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N PHE R 78 " --> pdb=" O TYR R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 91 Processing helix chain 'R' and resid 103 through 162 removed outlier: 3.525A pdb=" N ALA R 107 " --> pdb=" O SER R 103 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA R 161 " --> pdb=" O LEU R 157 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE R 162 " --> pdb=" O ARG R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 174 Processing helix chain 'R' and resid 175 through 186 Processing helix chain 'R' and resid 212 through 235 removed outlier: 3.567A pdb=" N ALA R 216 " --> pdb=" O GLN R 212 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU R 232 " --> pdb=" O ASP R 228 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TRP R 233 " --> pdb=" O ALA R 229 " (cutoff:3.500A) Processing helix chain 'R' and resid 250 through 286 Proline residue: R 271 - end of helix removed outlier: 3.628A pdb=" N GLN R 284 " --> pdb=" O ASN R 280 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS R 285 " --> pdb=" O LEU R 281 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER R 286 " --> pdb=" O GLU R 282 " (cutoff:3.500A) Processing helix chain 'R' and resid 287 through 321 removed outlier: 3.691A pdb=" N ARG R 291 " --> pdb=" O ASP R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 334 through 342 removed outlier: 4.082A pdb=" N HIS R 338 " --> pdb=" O THR R 334 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR R 339 " --> pdb=" O LEU R 335 " (cutoff:3.500A) Processing helix chain 'R' and resid 342 through 367 Processing helix chain 'R' and resid 380 through 406 removed outlier: 3.989A pdb=" N TYR R 384 " --> pdb=" O GLU R 380 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU R 400 " --> pdb=" O TYR R 396 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 463 removed outlier: 3.578A pdb=" N VAL R 413 " --> pdb=" O PRO R 409 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA R 463 " --> pdb=" O LEU R 459 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 81 removed outlier: 3.764A pdb=" N THR S 71 " --> pdb=" O LEU S 67 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR S 74 " --> pdb=" O SER S 70 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLU S 77 " --> pdb=" O ALA S 73 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N PHE S 78 " --> pdb=" O TYR S 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 91 Processing helix chain 'S' and resid 103 through 162 removed outlier: 3.524A pdb=" N ALA S 107 " --> pdb=" O SER S 103 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA S 161 " --> pdb=" O LEU S 157 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE S 162 " --> pdb=" O ARG S 158 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 174 Processing helix chain 'S' and resid 175 through 186 Processing helix chain 'S' and resid 212 through 235 removed outlier: 3.566A pdb=" N ALA S 216 " --> pdb=" O GLN S 212 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU S 232 " --> pdb=" O ASP S 228 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TRP S 233 " --> pdb=" O ALA S 229 " (cutoff:3.500A) Processing helix chain 'S' and resid 250 through 286 Proline residue: S 271 - end of helix removed outlier: 3.628A pdb=" N GLN S 284 " --> pdb=" O ASN S 280 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS S 285 " --> pdb=" O LEU S 281 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER S 286 " --> pdb=" O GLU S 282 " (cutoff:3.500A) Processing helix chain 'S' and resid 287 through 321 removed outlier: 3.689A pdb=" N ARG S 291 " --> pdb=" O ASP S 287 " (cutoff:3.500A) Processing helix chain 'S' and resid 334 through 342 removed outlier: 4.080A pdb=" N HIS S 338 " --> pdb=" O THR S 334 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR S 339 " --> pdb=" O LEU S 335 " (cutoff:3.500A) Processing helix chain 'S' and resid 342 through 367 Processing helix chain 'S' and resid 380 through 406 removed outlier: 3.991A pdb=" N TYR S 384 " --> pdb=" O GLU S 380 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU S 400 " --> pdb=" O TYR S 396 " (cutoff:3.500A) Processing helix chain 'S' and resid 406 through 463 removed outlier: 3.578A pdb=" N VAL S 413 " --> pdb=" O PRO S 409 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA S 463 " --> pdb=" O LEU S 459 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 81 removed outlier: 3.763A pdb=" N THR T 71 " --> pdb=" O LEU T 67 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR T 74 " --> pdb=" O SER T 70 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLU T 77 " --> pdb=" O ALA T 73 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N PHE T 78 " --> pdb=" O TYR T 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 91 Processing helix chain 'T' and resid 103 through 162 removed outlier: 3.525A pdb=" N ALA T 107 " --> pdb=" O SER T 103 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA T 161 " --> pdb=" O LEU T 157 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE T 162 " --> pdb=" O ARG T 158 " (cutoff:3.500A) Processing helix chain 'T' and resid 171 through 174 Processing helix chain 'T' and resid 175 through 186 Processing helix chain 'T' and resid 212 through 235 removed outlier: 3.567A pdb=" N ALA T 216 " --> pdb=" O GLN T 212 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU T 232 " --> pdb=" O ASP T 228 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TRP T 233 " --> pdb=" O ALA T 229 " (cutoff:3.500A) Processing helix chain 'T' and resid 250 through 286 Proline residue: T 271 - end of helix removed outlier: 3.627A pdb=" N GLN T 284 " --> pdb=" O ASN T 280 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS T 285 " --> pdb=" O LEU T 281 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER T 286 " --> pdb=" O GLU T 282 " (cutoff:3.500A) Processing helix chain 'T' and resid 287 through 321 removed outlier: 3.690A pdb=" N ARG T 291 " --> pdb=" O ASP T 287 " (cutoff:3.500A) Processing helix chain 'T' and resid 334 through 342 removed outlier: 4.081A pdb=" N HIS T 338 " --> pdb=" O THR T 334 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR T 339 " --> pdb=" O LEU T 335 " (cutoff:3.500A) Processing helix chain 'T' and resid 342 through 367 Processing helix chain 'T' and resid 380 through 406 removed outlier: 3.991A pdb=" N TYR T 384 " --> pdb=" O GLU T 380 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU T 400 " --> pdb=" O TYR T 396 " (cutoff:3.500A) Processing helix chain 'T' and resid 406 through 463 removed outlier: 3.578A pdb=" N VAL T 413 " --> pdb=" O PRO T 409 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA T 463 " --> pdb=" O LEU T 459 " (cutoff:3.500A) Processing helix chain 'U' and resid 60 through 81 removed outlier: 3.763A pdb=" N THR U 71 " --> pdb=" O LEU U 67 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR U 74 " --> pdb=" O SER U 70 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLU U 77 " --> pdb=" O ALA U 73 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N PHE U 78 " --> pdb=" O TYR U 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 91 Processing helix chain 'U' and resid 103 through 162 removed outlier: 3.525A pdb=" N ALA U 107 " --> pdb=" O SER U 103 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA U 161 " --> pdb=" O LEU U 157 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE U 162 " --> pdb=" O ARG U 158 " (cutoff:3.500A) Processing helix chain 'U' and resid 171 through 174 Processing helix chain 'U' and resid 175 through 186 Processing helix chain 'U' and resid 212 through 235 removed outlier: 3.565A pdb=" N ALA U 216 " --> pdb=" O GLN U 212 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU U 232 " --> pdb=" O ASP U 228 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TRP U 233 " --> pdb=" O ALA U 229 " (cutoff:3.500A) Processing helix chain 'U' and resid 250 through 286 Proline residue: U 271 - end of helix removed outlier: 3.626A pdb=" N GLN U 284 " --> pdb=" O ASN U 280 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS U 285 " --> pdb=" O LEU U 281 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER U 286 " --> pdb=" O GLU U 282 " (cutoff:3.500A) Processing helix chain 'U' and resid 287 through 321 removed outlier: 3.690A pdb=" N ARG U 291 " --> pdb=" O ASP U 287 " (cutoff:3.500A) Processing helix chain 'U' and resid 334 through 342 removed outlier: 4.082A pdb=" N HIS U 338 " --> pdb=" O THR U 334 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR U 339 " --> pdb=" O LEU U 335 " (cutoff:3.500A) Processing helix chain 'U' and resid 342 through 367 Processing helix chain 'U' and resid 380 through 406 removed outlier: 3.991A pdb=" N TYR U 384 " --> pdb=" O GLU U 380 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU U 400 " --> pdb=" O TYR U 396 " (cutoff:3.500A) Processing helix chain 'U' and resid 406 through 463 removed outlier: 3.576A pdb=" N VAL U 413 " --> pdb=" O PRO U 409 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA U 463 " --> pdb=" O LEU U 459 " (cutoff:3.500A) Processing helix chain 'V' and resid 60 through 81 removed outlier: 3.762A pdb=" N THR V 71 " --> pdb=" O LEU V 67 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR V 74 " --> pdb=" O SER V 70 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLU V 77 " --> pdb=" O ALA V 73 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N PHE V 78 " --> pdb=" O TYR V 74 " (cutoff:3.500A) Processing helix chain 'V' and resid 82 through 91 Processing helix chain 'V' and resid 103 through 162 removed outlier: 3.524A pdb=" N ALA V 107 " --> pdb=" O SER V 103 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA V 161 " --> pdb=" O LEU V 157 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE V 162 " --> pdb=" O ARG V 158 " (cutoff:3.500A) Processing helix chain 'V' and resid 171 through 174 Processing helix chain 'V' and resid 175 through 186 Processing helix chain 'V' and resid 212 through 235 removed outlier: 3.567A pdb=" N ALA V 216 " --> pdb=" O GLN V 212 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU V 232 " --> pdb=" O ASP V 228 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TRP V 233 " --> pdb=" O ALA V 229 " (cutoff:3.500A) Processing helix chain 'V' and resid 250 through 286 Proline residue: V 271 - end of helix removed outlier: 3.629A pdb=" N GLN V 284 " --> pdb=" O ASN V 280 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS V 285 " --> pdb=" O LEU V 281 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER V 286 " --> pdb=" O GLU V 282 " (cutoff:3.500A) Processing helix chain 'V' and resid 287 through 321 removed outlier: 3.689A pdb=" N ARG V 291 " --> pdb=" O ASP V 287 " (cutoff:3.500A) Processing helix chain 'V' and resid 334 through 342 removed outlier: 4.081A pdb=" N HIS V 338 " --> pdb=" O THR V 334 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR V 339 " --> pdb=" O LEU V 335 " (cutoff:3.500A) Processing helix chain 'V' and resid 342 through 367 Processing helix chain 'V' and resid 380 through 406 removed outlier: 3.990A pdb=" N TYR V 384 " --> pdb=" O GLU V 380 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU V 400 " --> pdb=" O TYR V 396 " (cutoff:3.500A) Processing helix chain 'V' and resid 406 through 463 removed outlier: 3.577A pdb=" N VAL V 413 " --> pdb=" O PRO V 409 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA V 463 " --> pdb=" O LEU V 459 " (cutoff:3.500A) Processing helix chain 'W' and resid 60 through 81 removed outlier: 3.764A pdb=" N THR W 71 " --> pdb=" O LEU W 67 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR W 74 " --> pdb=" O SER W 70 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU W 77 " --> pdb=" O ALA W 73 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N PHE W 78 " --> pdb=" O TYR W 74 " (cutoff:3.500A) Processing helix chain 'W' and resid 82 through 91 Processing helix chain 'W' and resid 103 through 162 removed outlier: 3.525A pdb=" N ALA W 107 " --> pdb=" O SER W 103 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA W 161 " --> pdb=" O LEU W 157 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE W 162 " --> pdb=" O ARG W 158 " (cutoff:3.500A) Processing helix chain 'W' and resid 171 through 174 Processing helix chain 'W' and resid 175 through 186 Processing helix chain 'W' and resid 212 through 235 removed outlier: 3.569A pdb=" N ALA W 216 " --> pdb=" O GLN W 212 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU W 232 " --> pdb=" O ASP W 228 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TRP W 233 " --> pdb=" O ALA W 229 " (cutoff:3.500A) Processing helix chain 'W' and resid 250 through 286 Proline residue: W 271 - end of helix removed outlier: 3.627A pdb=" N GLN W 284 " --> pdb=" O ASN W 280 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS W 285 " --> pdb=" O LEU W 281 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER W 286 " --> pdb=" O GLU W 282 " (cutoff:3.500A) Processing helix chain 'W' and resid 287 through 321 removed outlier: 3.689A pdb=" N ARG W 291 " --> pdb=" O ASP W 287 " (cutoff:3.500A) Processing helix chain 'W' and resid 334 through 342 removed outlier: 4.081A pdb=" N HIS W 338 " --> pdb=" O THR W 334 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR W 339 " --> pdb=" O LEU W 335 " (cutoff:3.500A) Processing helix chain 'W' and resid 342 through 367 Processing helix chain 'W' and resid 380 through 406 removed outlier: 3.988A pdb=" N TYR W 384 " --> pdb=" O GLU W 380 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU W 400 " --> pdb=" O TYR W 396 " (cutoff:3.500A) Processing helix chain 'W' and resid 406 through 463 removed outlier: 3.578A pdb=" N VAL W 413 " --> pdb=" O PRO W 409 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA W 463 " --> pdb=" O LEU W 459 " (cutoff:3.500A) Processing helix chain 'X' and resid 60 through 81 removed outlier: 3.763A pdb=" N THR X 71 " --> pdb=" O LEU X 67 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR X 74 " --> pdb=" O SER X 70 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLU X 77 " --> pdb=" O ALA X 73 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N PHE X 78 " --> pdb=" O TYR X 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 91 Processing helix chain 'X' and resid 103 through 162 removed outlier: 3.525A pdb=" N ALA X 107 " --> pdb=" O SER X 103 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA X 161 " --> pdb=" O LEU X 157 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE X 162 " --> pdb=" O ARG X 158 " (cutoff:3.500A) Processing helix chain 'X' and resid 171 through 174 Processing helix chain 'X' and resid 175 through 186 Processing helix chain 'X' and resid 212 through 235 removed outlier: 3.567A pdb=" N ALA X 216 " --> pdb=" O GLN X 212 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU X 232 " --> pdb=" O ASP X 228 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TRP X 233 " --> pdb=" O ALA X 229 " (cutoff:3.500A) Processing helix chain 'X' and resid 250 through 286 Proline residue: X 271 - end of helix removed outlier: 3.627A pdb=" N GLN X 284 " --> pdb=" O ASN X 280 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS X 285 " --> pdb=" O LEU X 281 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER X 286 " --> pdb=" O GLU X 282 " (cutoff:3.500A) Processing helix chain 'X' and resid 287 through 321 removed outlier: 3.689A pdb=" N ARG X 291 " --> pdb=" O ASP X 287 " (cutoff:3.500A) Processing helix chain 'X' and resid 334 through 342 removed outlier: 4.082A pdb=" N HIS X 338 " --> pdb=" O THR X 334 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR X 339 " --> pdb=" O LEU X 335 " (cutoff:3.500A) Processing helix chain 'X' and resid 342 through 367 Processing helix chain 'X' and resid 380 through 406 removed outlier: 3.989A pdb=" N TYR X 384 " --> pdb=" O GLU X 380 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU X 400 " --> pdb=" O TYR X 396 " (cutoff:3.500A) Processing helix chain 'X' and resid 406 through 463 removed outlier: 3.578A pdb=" N VAL X 413 " --> pdb=" O PRO X 409 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA X 463 " --> pdb=" O LEU X 459 " (cutoff:3.500A) 4572 hydrogen bonds defined for protein. 13662 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 17.87 Time building geometry restraints manager: 13.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.23: 906 1.23 - 1.31: 10635 1.31 - 1.39: 14553 1.39 - 1.47: 9057 1.47 - 1.55: 26355 Bond restraints: 61506 Sorted by residual: bond pdb=" CA THR P 40 " pdb=" C THR P 40 " ideal model delta sigma weight residual 1.533 1.491 0.042 5.60e-03 3.19e+04 5.61e+01 bond pdb=" C ASN G 38 " pdb=" O ASN G 38 " ideal model delta sigma weight residual 1.234 1.151 0.083 1.19e-02 7.06e+03 4.91e+01 bond pdb=" C ASN J 38 " pdb=" O ASN J 38 " ideal model delta sigma weight residual 1.234 1.156 0.079 1.29e-02 6.01e+03 3.73e+01 bond pdb=" C ASN K 38 " pdb=" O ASN K 38 " ideal model delta sigma weight residual 1.235 1.159 0.076 1.26e-02 6.30e+03 3.65e+01 bond pdb=" C ASN H 38 " pdb=" O ASN H 38 " ideal model delta sigma weight residual 1.233 1.156 0.077 1.35e-02 5.49e+03 3.27e+01 ... (remaining 61501 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 82851 2.87 - 5.73: 872 5.73 - 8.60: 84 8.60 - 11.46: 16 11.46 - 14.33: 3 Bond angle restraints: 83826 Sorted by residual: angle pdb=" C ILE P 39 " pdb=" N THR P 40 " pdb=" CA THR P 40 " ideal model delta sigma weight residual 123.04 113.34 9.70 1.08e+00 8.57e-01 8.06e+01 angle pdb=" C THR P 40 " pdb=" CA THR P 40 " pdb=" CB THR P 40 " ideal model delta sigma weight residual 117.07 105.83 11.24 1.44e+00 4.82e-01 6.10e+01 angle pdb=" N THR L 40 " pdb=" CA THR L 40 " pdb=" C THR L 40 " ideal model delta sigma weight residual 109.59 98.34 11.25 1.47e+00 4.63e-01 5.85e+01 angle pdb=" N THR H 40 " pdb=" CA THR H 40 " pdb=" C THR H 40 " ideal model delta sigma weight residual 109.96 98.81 11.15 1.50e+00 4.44e-01 5.53e+01 angle pdb=" C THR S 40 " pdb=" CA THR S 40 " pdb=" CB THR S 40 " ideal model delta sigma weight residual 110.42 96.09 14.33 1.99e+00 2.53e-01 5.18e+01 ... (remaining 83821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 30978 17.61 - 35.21: 4335 35.21 - 52.82: 1529 52.82 - 70.42: 255 70.42 - 88.03: 145 Dihedral angle restraints: 37242 sinusoidal: 14004 harmonic: 23238 Sorted by residual: dihedral pdb=" C THR O 40 " pdb=" N THR O 40 " pdb=" CA THR O 40 " pdb=" CB THR O 40 " ideal model delta harmonic sigma weight residual -122.00 -108.04 -13.96 0 2.50e+00 1.60e-01 3.12e+01 dihedral pdb=" C ASN S 38 " pdb=" N ASN S 38 " pdb=" CA ASN S 38 " pdb=" CB ASN S 38 " ideal model delta harmonic sigma weight residual -122.60 -109.33 -13.27 0 2.50e+00 1.60e-01 2.82e+01 dihedral pdb=" C THR W 40 " pdb=" N THR W 40 " pdb=" CA THR W 40 " pdb=" CB THR W 40 " ideal model delta harmonic sigma weight residual -122.00 -109.23 -12.77 0 2.50e+00 1.60e-01 2.61e+01 ... (remaining 37239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 8724 0.071 - 0.143: 704 0.143 - 0.214: 32 0.214 - 0.286: 0 0.286 - 0.357: 8 Chirality restraints: 9468 Sorted by residual: chirality pdb=" CA THR U 40 " pdb=" N THR U 40 " pdb=" C THR U 40 " pdb=" CB THR U 40 " both_signs ideal model delta sigma weight residual False 2.53 2.88 -0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA THR O 40 " pdb=" N THR O 40 " pdb=" C THR O 40 " pdb=" CB THR O 40 " both_signs ideal model delta sigma weight residual False 2.53 2.88 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA THR W 40 " pdb=" N THR W 40 " pdb=" C THR W 40 " pdb=" CB THR W 40 " both_signs ideal model delta sigma weight residual False 2.53 2.86 -0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 9465 not shown) Planarity restraints: 11394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE X 37 " -0.027 2.00e-02 2.50e+03 5.75e-02 3.31e+01 pdb=" C PHE X 37 " 0.099 2.00e-02 2.50e+03 pdb=" O PHE X 37 " -0.038 2.00e-02 2.50e+03 pdb=" N ASN X 38 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE S 37 " -0.027 2.00e-02 2.50e+03 5.57e-02 3.10e+01 pdb=" C PHE S 37 " 0.096 2.00e-02 2.50e+03 pdb=" O PHE S 37 " -0.037 2.00e-02 2.50e+03 pdb=" N ASN S 38 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN X 38 " -0.024 2.00e-02 2.50e+03 5.02e-02 2.52e+01 pdb=" C ASN X 38 " 0.087 2.00e-02 2.50e+03 pdb=" O ASN X 38 " -0.033 2.00e-02 2.50e+03 pdb=" N ILE X 39 " -0.030 2.00e-02 2.50e+03 ... (remaining 11391 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 1073 2.64 - 3.21: 56990 3.21 - 3.77: 98571 3.77 - 4.34: 125362 4.34 - 4.90: 213993 Nonbonded interactions: 495989 Sorted by model distance: nonbonded pdb=" OD1 ASP U 98 " pdb=" OH TYR V 384 " model vdw 2.075 3.040 nonbonded pdb=" O THR H 40 " pdb=" C ASN H 41 " model vdw 2.134 3.270 nonbonded pdb=" O THR K 40 " pdb=" C ASN K 41 " model vdw 2.134 3.270 nonbonded pdb=" O THR L 40 " pdb=" C ASN L 41 " model vdw 2.144 3.270 nonbonded pdb=" O TYR V 368 " pdb=" NH1 ARG W 249 " model vdw 2.164 3.120 ... (remaining 495984 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: 0.43 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' selection = chain 'W' selection = chain 'V' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 8.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 2.190 Check model and map are aligned: 0.340 Set scattering table: 0.420 Process input model: 98.280 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 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 0.083 61506 Z= 0.269 Angle : 0.737 14.329 83826 Z= 0.434 Chirality : 0.041 0.357 9468 Planarity : 0.006 0.092 11394 Dihedral : 19.421 88.029 22122 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.07 % Favored : 95.61 % Rotamer: Outliers : 4.15 % Allowed : 35.33 % Favored : 60.52 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.09), residues: 7740 helix: 2.22 (0.06), residues: 5310 sheet: None (None), residues: 0 loop : -2.84 (0.10), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 233 HIS 0.005 0.001 HIS O 251 PHE 0.011 0.002 PHE K 43 TYR 0.016 0.002 TYR S 90 ARG 0.010 0.001 ARG G 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15480 Ramachandran restraints generated. 7740 Oldfield, 0 Emsley, 7740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15480 Ramachandran restraints generated. 7740 Oldfield, 0 Emsley, 7740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1110 residues out of total 6066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 251 poor density : 859 time to evaluate : 4.801 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 167 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8061 (p0) REVERT: G 188 ARG cc_start: 0.6494 (OUTLIER) cc_final: 0.6215 (mpt-90) REVERT: G 306 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7219 (ptt180) REVERT: H 37 PHE cc_start: 0.5626 (m-10) cc_final: 0.5398 (m-80) REVERT: H 167 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8127 (p0) REVERT: H 188 ARG cc_start: 0.6603 (OUTLIER) cc_final: 0.6386 (mmt180) REVERT: H 306 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7257 (ptt180) REVERT: I 167 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.8077 (p0) REVERT: J 167 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8094 (p0) REVERT: K 37 PHE cc_start: 0.5562 (m-10) cc_final: 0.5330 (m-80) REVERT: K 167 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8128 (p0) REVERT: K 306 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7286 (ptt180) REVERT: L 167 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8074 (p0) REVERT: L 188 ARG cc_start: 0.6510 (OUTLIER) cc_final: 0.6252 (mpt-90) REVERT: L 233 TRP cc_start: 0.7750 (m-10) cc_final: 0.7478 (m-10) REVERT: L 306 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7239 (ptt180) REVERT: L 413 VAL cc_start: 0.7948 (t) cc_final: 0.7722 (m) REVERT: M 45 ASP cc_start: 0.7145 (OUTLIER) cc_final: 0.6920 (p0) REVERT: N 167 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8332 (p0) REVERT: N 196 ASP cc_start: 0.6826 (m-30) cc_final: 0.6439 (m-30) REVERT: O 37 PHE cc_start: 0.6097 (m-10) cc_final: 0.5479 (m-80) REVERT: O 188 ARG cc_start: 0.5897 (OUTLIER) cc_final: 0.5609 (tpp80) REVERT: O 462 GLU cc_start: 0.1356 (OUTLIER) cc_final: 0.0458 (mp0) REVERT: P 91 LEU cc_start: 0.5867 (OUTLIER) cc_final: 0.5625 (mt) REVERT: P 174 THR cc_start: 0.7994 (p) cc_final: 0.7753 (p) REVERT: P 239 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7255 (pp) REVERT: P 462 GLU cc_start: -0.0503 (OUTLIER) cc_final: -0.0758 (mt-10) REVERT: Q 239 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7587 (pp) REVERT: R 91 LEU cc_start: 0.5872 (OUTLIER) cc_final: 0.5581 (mt) REVERT: S 91 LEU cc_start: 0.5858 (OUTLIER) cc_final: 0.5622 (mt) REVERT: S 174 THR cc_start: 0.7972 (p) cc_final: 0.7724 (p) REVERT: S 239 ILE cc_start: 0.7749 (OUTLIER) cc_final: 0.7222 (pp) REVERT: S 462 GLU cc_start: -0.0355 (OUTLIER) cc_final: -0.0747 (mt-10) REVERT: T 37 PHE cc_start: 0.6128 (m-10) cc_final: 0.5488 (m-80) REVERT: T 462 GLU cc_start: 0.1343 (OUTLIER) cc_final: 0.0591 (mp0) REVERT: U 196 ASP cc_start: 0.6663 (m-30) cc_final: 0.6311 (m-30) REVERT: U 239 ILE cc_start: 0.7606 (OUTLIER) cc_final: 0.7129 (pp) REVERT: V 462 GLU cc_start: -0.0598 (OUTLIER) cc_final: -0.0800 (mp0) REVERT: W 167 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8339 (p0) REVERT: X 91 LEU cc_start: 0.5850 (OUTLIER) cc_final: 0.5561 (mt) outliers start: 251 outliers final: 101 residues processed: 1076 average time/residue: 1.1476 time to fit residues: 1640.3904 Evaluate side-chains 683 residues out of total 6066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 552 time to evaluate : 4.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 45 ASP Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 188 ARG Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 306 ARG Chi-restraints excluded: chain G residue 378 ASN Chi-restraints excluded: chain G residue 462 GLU Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 45 ASP Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 167 ASP Chi-restraints excluded: chain H residue 188 ARG Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 306 ARG Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 188 ARG Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 462 GLU Chi-restraints excluded: chain J residue 38 ASN Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 167 ASP Chi-restraints excluded: chain J residue 188 ARG Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 378 ASN Chi-restraints excluded: chain J residue 462 GLU Chi-restraints excluded: chain K residue 38 ASN Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 135 SER Chi-restraints excluded: chain K residue 167 ASP Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 239 ILE Chi-restraints excluded: chain K residue 306 ARG Chi-restraints excluded: chain L residue 38 ASN Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 135 SER Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain L residue 188 ARG Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 306 ARG Chi-restraints excluded: chain L residue 378 ASN Chi-restraints excluded: chain L residue 462 GLU Chi-restraints excluded: chain M residue 45 ASP Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 135 SER Chi-restraints excluded: chain M residue 239 ILE Chi-restraints excluded: chain N residue 45 ASP Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 135 SER Chi-restraints excluded: chain N residue 167 ASP Chi-restraints excluded: chain N residue 202 THR Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 306 ARG Chi-restraints excluded: chain N residue 462 GLU Chi-restraints excluded: chain O residue 45 ASP Chi-restraints excluded: chain O residue 135 SER Chi-restraints excluded: chain O residue 188 ARG Chi-restraints excluded: chain O residue 202 THR Chi-restraints excluded: chain O residue 239 ILE Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain O residue 462 GLU Chi-restraints excluded: chain P residue 45 ASP Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 135 SER Chi-restraints excluded: chain P residue 202 THR Chi-restraints excluded: chain P residue 239 ILE Chi-restraints excluded: chain P residue 462 GLU Chi-restraints excluded: chain Q residue 45 ASP Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain Q residue 135 SER Chi-restraints excluded: chain Q residue 202 THR Chi-restraints excluded: chain Q residue 239 ILE Chi-restraints excluded: chain Q residue 241 GLN Chi-restraints excluded: chain Q residue 306 ARG Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 202 THR Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain S residue 45 ASP Chi-restraints excluded: chain S residue 91 LEU Chi-restraints excluded: chain S residue 135 SER Chi-restraints excluded: chain S residue 202 THR Chi-restraints excluded: chain S residue 239 ILE Chi-restraints excluded: chain S residue 306 ARG Chi-restraints excluded: chain S residue 462 GLU Chi-restraints excluded: chain T residue 45 ASP Chi-restraints excluded: chain T residue 135 SER Chi-restraints excluded: chain T residue 202 THR Chi-restraints excluded: chain T residue 239 ILE Chi-restraints excluded: chain T residue 462 GLU Chi-restraints excluded: chain U residue 45 ASP Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 135 SER Chi-restraints excluded: chain U residue 202 THR Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 306 ARG Chi-restraints excluded: chain U residue 355 SER Chi-restraints excluded: chain U residue 462 GLU Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 135 SER Chi-restraints excluded: chain V residue 239 ILE Chi-restraints excluded: chain V residue 462 GLU Chi-restraints excluded: chain W residue 45 ASP Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 135 SER Chi-restraints excluded: chain W residue 167 ASP Chi-restraints excluded: chain W residue 202 THR Chi-restraints excluded: chain W residue 239 ILE Chi-restraints excluded: chain W residue 306 ARG Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 91 LEU Chi-restraints excluded: chain X residue 135 SER Chi-restraints excluded: chain X residue 202 THR Chi-restraints excluded: chain X residue 239 ILE Chi-restraints excluded: chain X residue 306 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 774 random chunks: chunk 653 optimal weight: 10.0000 chunk 586 optimal weight: 8.9990 chunk 325 optimal weight: 1.9990 chunk 200 optimal weight: 5.9990 chunk 395 optimal weight: 10.0000 chunk 313 optimal weight: 4.9990 chunk 606 optimal weight: 1.9990 chunk 234 optimal weight: 5.9990 chunk 368 optimal weight: 0.9980 chunk 451 optimal weight: 0.8980 chunk 702 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 280 ASN ** G 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 280 ASN H 329 ASN I 280 ASN ** I 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 378 ASN I 407 GLN ** I 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 280 ASN ** J 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 280 ASN ** K 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 280 ASN ** L 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN ** M 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 ASN M 378 ASN N 38 ASN ** N 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 ASN N 292 GLN N 324 ASN N 378 ASN ** N 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 280 ASN O 292 GLN O 329 ASN O 378 ASN O 407 GLN ** O 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 280 ASN Q 292 GLN Q 378 ASN ** Q 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 280 ASN R 378 ASN ** S 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 280 ASN T 329 ASN T 378 ASN T 407 GLN ** T 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 241 GLN ** U 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 280 ASN U 378 ASN ** U 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 79 GLN ** V 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 378 ASN ** W 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 251 HIS W 280 ASN W 329 ASN W 378 ASN ** W 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 280 ASN X 378 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.157865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.134122 restraints weight = 107816.790| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 2.93 r_work: 0.4137 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 61506 Z= 0.215 Angle : 0.599 6.440 83826 Z= 0.326 Chirality : 0.040 0.310 9468 Planarity : 0.005 0.062 11394 Dihedral : 6.607 87.359 8772 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.67 % Favored : 96.12 % Rotamer: Outliers : 5.51 % Allowed : 31.37 % Favored : 63.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.09), residues: 7740 helix: 2.52 (0.06), residues: 5436 sheet: None (None), residues: 0 loop : -2.63 (0.10), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP O 233 HIS 0.004 0.001 HIS P 251 PHE 0.017 0.001 PHE U 37 TYR 0.021 0.002 TYR X 153 ARG 0.006 0.001 ARG J 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15480 Ramachandran restraints generated. 7740 Oldfield, 0 Emsley, 7740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15480 Ramachandran restraints generated. 7740 Oldfield, 0 Emsley, 7740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 954 residues out of total 6066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 333 poor density : 621 time to evaluate : 4.981 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 188 ARG cc_start: 0.6300 (OUTLIER) cc_final: 0.6066 (mtt-85) REVERT: G 195 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6223 (mp0) REVERT: G 231 PHE cc_start: 0.7328 (OUTLIER) cc_final: 0.6700 (t80) REVERT: G 233 TRP cc_start: 0.7790 (OUTLIER) cc_final: 0.7050 (m-10) REVERT: G 241 GLN cc_start: 0.9044 (mt0) cc_final: 0.8798 (mm110) REVERT: G 249 ARG cc_start: 0.8123 (ptt-90) cc_final: 0.7871 (ptt-90) REVERT: G 280 ASN cc_start: 0.8043 (OUTLIER) cc_final: 0.7738 (t160) REVERT: H 34 ASN cc_start: 0.5671 (t0) cc_final: 0.5371 (t0) REVERT: H 167 ASP cc_start: 0.8681 (m-30) cc_final: 0.8085 (p0) REVERT: H 188 ARG cc_start: 0.6384 (OUTLIER) cc_final: 0.6093 (mpt-90) REVERT: H 195 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6306 (mp0) REVERT: H 417 ASP cc_start: 0.8420 (m-30) cc_final: 0.8129 (m-30) REVERT: I 195 GLU cc_start: 0.7086 (mm-30) cc_final: 0.6365 (mp0) REVERT: I 417 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.8161 (t0) REVERT: J 34 ASN cc_start: 0.5417 (t0) cc_final: 0.5168 (t0) REVERT: J 195 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6382 (mp0) REVERT: J 241 GLN cc_start: 0.9016 (mt0) cc_final: 0.8544 (mm-40) REVERT: J 417 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8179 (m-30) REVERT: K 34 ASN cc_start: 0.5608 (t0) cc_final: 0.5326 (t0) REVERT: K 167 ASP cc_start: 0.8682 (m-30) cc_final: 0.8087 (p0) REVERT: K 241 GLN cc_start: 0.9019 (mt0) cc_final: 0.8774 (mm110) REVERT: K 417 ASP cc_start: 0.8456 (m-30) cc_final: 0.8043 (m-30) REVERT: L 75 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7591 (mp) REVERT: L 188 ARG cc_start: 0.6246 (OUTLIER) cc_final: 0.5955 (mpt-90) REVERT: L 195 GLU cc_start: 0.6830 (mm-30) cc_final: 0.6171 (mp0) REVERT: L 231 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.6765 (t80) REVERT: L 233 TRP cc_start: 0.7997 (OUTLIER) cc_final: 0.7462 (m-10) REVERT: L 241 GLN cc_start: 0.9028 (mt0) cc_final: 0.8783 (mm-40) REVERT: L 249 ARG cc_start: 0.8102 (ptt-90) cc_final: 0.7837 (ptt-90) REVERT: L 280 ASN cc_start: 0.8067 (OUTLIER) cc_final: 0.7742 (t160) REVERT: L 417 ASP cc_start: 0.8460 (m-30) cc_final: 0.8165 (m-30) REVERT: M 37 PHE cc_start: 0.5024 (m-10) cc_final: 0.4639 (t80) REVERT: M 85 GLU cc_start: 0.9350 (mp0) cc_final: 0.9069 (mp0) REVERT: M 280 ASN cc_start: 0.7828 (OUTLIER) cc_final: 0.7487 (t0) REVERT: M 417 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.8141 (m-30) REVERT: N 226 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7661 (tp30) REVERT: N 241 GLN cc_start: 0.8653 (mt0) cc_final: 0.8327 (tt0) REVERT: N 280 ASN cc_start: 0.7695 (OUTLIER) cc_final: 0.7426 (t160) REVERT: N 417 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7786 (m-30) REVERT: N 426 ASP cc_start: 0.8754 (p0) cc_final: 0.8536 (p0) REVERT: O 75 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7054 (mp) REVERT: O 226 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7313 (tt0) REVERT: O 236 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7472 (tp30) REVERT: O 280 ASN cc_start: 0.7642 (OUTLIER) cc_final: 0.7424 (t0) REVERT: O 414 GLN cc_start: 0.8232 (mt0) cc_final: 0.7976 (mt0) REVERT: O 417 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7703 (m-30) REVERT: O 462 GLU cc_start: 0.2050 (OUTLIER) cc_final: 0.0919 (mp0) REVERT: P 37 PHE cc_start: 0.4933 (m-10) cc_final: 0.4420 (t80) REVERT: P 174 THR cc_start: 0.6805 (p) cc_final: 0.6563 (p) REVERT: P 239 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.6971 (pp) REVERT: P 417 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8083 (m-30) REVERT: Q 91 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6820 (mt) REVERT: Q 239 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7499 (pp) REVERT: Q 280 ASN cc_start: 0.7563 (OUTLIER) cc_final: 0.7337 (t160) REVERT: R 85 GLU cc_start: 0.9342 (mp0) cc_final: 0.9051 (mp0) REVERT: R 280 ASN cc_start: 0.7814 (OUTLIER) cc_final: 0.7545 (t160) REVERT: R 282 GLU cc_start: 0.7553 (tt0) cc_final: 0.7266 (tp30) REVERT: S 37 PHE cc_start: 0.4622 (m-10) cc_final: 0.4242 (t80) REVERT: S 174 THR cc_start: 0.6787 (p) cc_final: 0.6540 (p) REVERT: S 417 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8104 (m-30) REVERT: S 462 GLU cc_start: 0.0284 (OUTLIER) cc_final: 0.0066 (mp0) REVERT: T 75 LEU cc_start: 0.7514 (mt) cc_final: 0.7128 (mp) REVERT: T 188 ARG cc_start: 0.5858 (OUTLIER) cc_final: 0.4860 (mmm-85) REVERT: T 226 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7383 (tt0) REVERT: T 280 ASN cc_start: 0.7655 (OUTLIER) cc_final: 0.7453 (t0) REVERT: T 462 GLU cc_start: 0.2120 (OUTLIER) cc_final: 0.0955 (mp0) REVERT: U 236 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7583 (tp30) REVERT: U 239 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7150 (pp) REVERT: U 280 ASN cc_start: 0.7655 (OUTLIER) cc_final: 0.7404 (t160) REVERT: U 398 LYS cc_start: 0.5870 (OUTLIER) cc_final: 0.5539 (mmpt) REVERT: V 417 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8172 (m-30) REVERT: W 91 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6662 (mt) REVERT: W 188 ARG cc_start: 0.6966 (OUTLIER) cc_final: 0.6443 (mpp80) REVERT: W 280 ASN cc_start: 0.7674 (OUTLIER) cc_final: 0.7357 (t160) REVERT: W 400 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7549 (tp) REVERT: X 85 GLU cc_start: 0.9337 (mp0) cc_final: 0.9057 (mp0) REVERT: X 280 ASN cc_start: 0.7799 (OUTLIER) cc_final: 0.7541 (t160) REVERT: X 282 GLU cc_start: 0.7535 (tt0) cc_final: 0.7255 (tp30) REVERT: X 417 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8193 (m-30) outliers start: 333 outliers final: 129 residues processed: 896 average time/residue: 1.2283 time to fit residues: 1446.8622 Evaluate side-chains 680 residues out of total 6066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 505 time to evaluate : 4.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 45 ASP Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 188 ARG Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 233 TRP Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 280 ASN Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 378 ASN Chi-restraints excluded: chain G residue 404 GLU Chi-restraints excluded: chain G residue 447 GLU Chi-restraints excluded: chain G residue 462 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 45 ASP Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 188 ARG Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 404 GLU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 188 ARG Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 340 SER Chi-restraints excluded: chain I residue 378 ASN Chi-restraints excluded: chain I residue 404 GLU Chi-restraints excluded: chain I residue 417 ASP Chi-restraints excluded: chain I residue 447 GLU Chi-restraints excluded: chain I residue 462 GLU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 135 SER Chi-restraints excluded: chain J residue 188 ARG Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain J residue 417 ASP Chi-restraints excluded: chain J residue 447 GLU Chi-restraints excluded: chain J residue 462 GLU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 239 ILE Chi-restraints excluded: chain K residue 340 SER Chi-restraints excluded: chain K residue 404 GLU Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain L residue 188 ARG Chi-restraints excluded: chain L residue 231 PHE Chi-restraints excluded: chain L residue 233 TRP Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 280 ASN Chi-restraints excluded: chain L residue 378 ASN Chi-restraints excluded: chain L residue 404 GLU Chi-restraints excluded: chain L residue 462 GLU Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 45 ASP Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 167 ASP Chi-restraints excluded: chain M residue 239 ILE Chi-restraints excluded: chain M residue 280 ASN Chi-restraints excluded: chain M residue 299 THR Chi-restraints excluded: chain M residue 417 ASP Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 45 ASP Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 96 SER Chi-restraints excluded: chain N residue 226 GLU Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 280 ASN Chi-restraints excluded: chain N residue 282 GLU Chi-restraints excluded: chain N residue 314 THR Chi-restraints excluded: chain N residue 329 ASN Chi-restraints excluded: chain N residue 378 ASN Chi-restraints excluded: chain N residue 400 LEU Chi-restraints excluded: chain N residue 417 ASP Chi-restraints excluded: chain N residue 462 GLU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 45 ASP Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 196 ASP Chi-restraints excluded: chain O residue 226 GLU Chi-restraints excluded: chain O residue 236 GLU Chi-restraints excluded: chain O residue 239 ILE Chi-restraints excluded: chain O residue 280 ASN Chi-restraints excluded: chain O residue 282 GLU Chi-restraints excluded: chain O residue 378 ASN Chi-restraints excluded: chain O residue 417 ASP Chi-restraints excluded: chain O residue 462 GLU Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 167 ASP Chi-restraints excluded: chain P residue 239 ILE Chi-restraints excluded: chain P residue 417 ASP Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 239 ILE Chi-restraints excluded: chain Q residue 280 ASN Chi-restraints excluded: chain Q residue 307 VAL Chi-restraints excluded: chain Q residue 378 ASN Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 60 THR Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 167 ASP Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 280 ASN Chi-restraints excluded: chain R residue 378 ASN Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 45 ASP Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 239 ILE Chi-restraints excluded: chain S residue 413 VAL Chi-restraints excluded: chain S residue 417 ASP Chi-restraints excluded: chain S residue 462 GLU Chi-restraints excluded: chain T residue 33 THR Chi-restraints excluded: chain T residue 45 ASP Chi-restraints excluded: chain T residue 96 SER Chi-restraints excluded: chain T residue 188 ARG Chi-restraints excluded: chain T residue 196 ASP Chi-restraints excluded: chain T residue 226 GLU Chi-restraints excluded: chain T residue 239 ILE Chi-restraints excluded: chain T residue 280 ASN Chi-restraints excluded: chain T residue 282 GLU Chi-restraints excluded: chain T residue 378 ASN Chi-restraints excluded: chain T residue 462 GLU Chi-restraints excluded: chain U residue 33 THR Chi-restraints excluded: chain U residue 45 ASP Chi-restraints excluded: chain U residue 75 LEU Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 159 ASP Chi-restraints excluded: chain U residue 236 GLU Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 280 ASN Chi-restraints excluded: chain U residue 307 VAL Chi-restraints excluded: chain U residue 378 ASN Chi-restraints excluded: chain U residue 398 LYS Chi-restraints excluded: chain U residue 400 LEU Chi-restraints excluded: chain U residue 462 GLU Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 96 SER Chi-restraints excluded: chain V residue 167 ASP Chi-restraints excluded: chain V residue 239 ILE Chi-restraints excluded: chain V residue 413 VAL Chi-restraints excluded: chain V residue 417 ASP Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 91 LEU Chi-restraints excluded: chain W residue 96 SER Chi-restraints excluded: chain W residue 188 ARG Chi-restraints excluded: chain W residue 239 ILE Chi-restraints excluded: chain W residue 280 ASN Chi-restraints excluded: chain W residue 378 ASN Chi-restraints excluded: chain W residue 400 LEU Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 60 THR Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 167 ASP Chi-restraints excluded: chain X residue 239 ILE Chi-restraints excluded: chain X residue 280 ASN Chi-restraints excluded: chain X residue 299 THR Chi-restraints excluded: chain X residue 378 ASN Chi-restraints excluded: chain X residue 417 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 774 random chunks: chunk 41 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 199 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 366 optimal weight: 1.9990 chunk 512 optimal weight: 10.0000 chunk 596 optimal weight: 2.9990 chunk 392 optimal weight: 9.9990 chunk 332 optimal weight: 9.9990 chunk 271 optimal weight: 2.9990 chunk 293 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 280 ASN ** G 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 378 ASN ** I 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 407 GLN ** K 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 280 ASN ** L 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 ASN M 378 ASN N 280 ASN ** N 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 280 ASN O 329 ASN ** O 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 280 ASN Q 280 ASN Q 378 ASN ** Q 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 280 ASN R 378 ASN ** R 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 280 ASN T 329 ASN ** T 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 280 ASN U 378 ASN U 407 GLN ** U 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 378 ASN ** V 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 280 ASN ** W 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 280 ASN X 378 ASN ** X 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.156286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.132409 restraints weight = 108428.291| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 2.89 r_work: 0.4116 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 61506 Z= 0.224 Angle : 0.586 6.717 83826 Z= 0.318 Chirality : 0.040 0.245 9468 Planarity : 0.004 0.063 11394 Dihedral : 5.918 88.659 8641 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.58 % Favored : 96.21 % Rotamer: Outliers : 4.37 % Allowed : 31.38 % Favored : 64.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.09), residues: 7740 helix: 2.58 (0.07), residues: 5436 sheet: None (None), residues: 0 loop : -2.51 (0.10), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP K 233 HIS 0.003 0.001 HIS H 338 PHE 0.031 0.002 PHE K 37 TYR 0.020 0.002 TYR Q 153 ARG 0.006 0.001 ARG V 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15480 Ramachandran restraints generated. 7740 Oldfield, 0 Emsley, 7740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15480 Ramachandran restraints generated. 7740 Oldfield, 0 Emsley, 7740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 6066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 264 poor density : 568 time to evaluate : 5.169 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: 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: G 34 ASN cc_start: 0.5782 (t0) cc_final: 0.5395 (t0) REVERT: G 75 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7567 (mp) REVERT: G 188 ARG cc_start: 0.6456 (OUTLIER) cc_final: 0.6133 (mtt-85) REVERT: G 195 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6205 (mp0) REVERT: G 223 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7658 (tp) REVERT: G 233 TRP cc_start: 0.7854 (OUTLIER) cc_final: 0.7052 (m-10) REVERT: G 249 ARG cc_start: 0.8202 (ptt-90) cc_final: 0.7944 (ptt-90) REVERT: G 280 ASN cc_start: 0.8117 (OUTLIER) cc_final: 0.7834 (t160) REVERT: H 417 ASP cc_start: 0.8412 (m-30) cc_final: 0.7979 (m-30) REVERT: I 34 ASN cc_start: 0.5669 (t0) cc_final: 0.5291 (t0) REVERT: I 37 PHE cc_start: 0.6581 (m-80) cc_final: 0.6089 (t80) REVERT: I 195 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6372 (mp0) REVERT: I 398 LYS cc_start: 0.6763 (OUTLIER) cc_final: 0.6276 (mttm) REVERT: J 34 ASN cc_start: 0.5764 (t0) cc_final: 0.5482 (t0) REVERT: J 195 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6430 (mp0) REVERT: J 241 GLN cc_start: 0.9062 (mt0) cc_final: 0.8835 (mt0) REVERT: J 398 LYS cc_start: 0.6737 (OUTLIER) cc_final: 0.6255 (mttm) REVERT: J 417 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.8317 (t0) REVERT: K 37 PHE cc_start: 0.5838 (t80) cc_final: 0.5615 (t80) REVERT: K 195 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6367 (mp0) REVERT: K 417 ASP cc_start: 0.8428 (m-30) cc_final: 0.8094 (m-30) REVERT: L 188 ARG cc_start: 0.6406 (OUTLIER) cc_final: 0.6107 (mpt-90) REVERT: L 195 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6221 (mp0) REVERT: L 223 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7646 (tp) REVERT: L 231 PHE cc_start: 0.7285 (OUTLIER) cc_final: 0.6701 (t80) REVERT: L 233 TRP cc_start: 0.8059 (OUTLIER) cc_final: 0.7528 (m-10) REVERT: L 241 GLN cc_start: 0.9044 (mt0) cc_final: 0.8791 (mt0) REVERT: L 280 ASN cc_start: 0.8132 (OUTLIER) cc_final: 0.7836 (t160) REVERT: L 417 ASP cc_start: 0.8458 (m-30) cc_final: 0.8136 (m-30) REVERT: M 37 PHE cc_start: 0.5068 (m-10) cc_final: 0.4620 (t80) REVERT: M 85 GLU cc_start: 0.9314 (mp0) cc_final: 0.9002 (mp0) REVERT: M 280 ASN cc_start: 0.7924 (OUTLIER) cc_final: 0.7577 (t0) REVERT: M 417 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8174 (m-30) REVERT: N 241 GLN cc_start: 0.8700 (mt0) cc_final: 0.8380 (tt0) REVERT: N 280 ASN cc_start: 0.7884 (OUTLIER) cc_final: 0.7595 (t160) REVERT: N 363 GLU cc_start: 0.7880 (tp30) cc_final: 0.7124 (pp20) REVERT: N 417 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7801 (m-30) REVERT: N 426 ASP cc_start: 0.8866 (p0) cc_final: 0.8637 (p0) REVERT: O 75 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7031 (mp) REVERT: O 226 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7385 (tt0) REVERT: O 232 GLU cc_start: 0.7832 (pp20) cc_final: 0.7078 (mp0) REVERT: O 280 ASN cc_start: 0.7814 (OUTLIER) cc_final: 0.7434 (t0) REVERT: O 363 GLU cc_start: 0.7933 (tp30) cc_final: 0.7096 (pp20) REVERT: O 417 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7686 (m-30) REVERT: P 37 PHE cc_start: 0.4909 (m-10) cc_final: 0.4262 (t80) REVERT: P 174 THR cc_start: 0.6881 (p) cc_final: 0.6641 (p) REVERT: P 280 ASN cc_start: 0.7841 (OUTLIER) cc_final: 0.7415 (t0) REVERT: P 417 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8044 (m-30) REVERT: Q 37 PHE cc_start: 0.5698 (t80) cc_final: 0.5258 (t80) REVERT: Q 91 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6891 (mt) REVERT: Q 231 PHE cc_start: 0.7083 (OUTLIER) cc_final: 0.6304 (t80) REVERT: Q 239 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7344 (pp) REVERT: Q 280 ASN cc_start: 0.7753 (OUTLIER) cc_final: 0.7494 (t160) REVERT: Q 363 GLU cc_start: 0.7914 (tp30) cc_final: 0.7143 (pp20) REVERT: Q 410 LEU cc_start: 0.8895 (tp) cc_final: 0.8688 (tp) REVERT: R 37 PHE cc_start: 0.4921 (m-10) cc_final: 0.4437 (t80) REVERT: R 85 GLU cc_start: 0.9319 (mp0) cc_final: 0.8997 (mp0) REVERT: R 280 ASN cc_start: 0.7883 (OUTLIER) cc_final: 0.7665 (t160) REVERT: R 296 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6856 (pp20) REVERT: S 37 PHE cc_start: 0.4373 (m-10) cc_final: 0.3856 (t80) REVERT: S 174 THR cc_start: 0.6886 (p) cc_final: 0.6643 (p) REVERT: S 417 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8099 (m-30) REVERT: T 75 LEU cc_start: 0.7407 (mt) cc_final: 0.7055 (mp) REVERT: T 188 ARG cc_start: 0.5929 (OUTLIER) cc_final: 0.4890 (mmm-85) REVERT: T 226 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7434 (tt0) REVERT: T 232 GLU cc_start: 0.7770 (pp20) cc_final: 0.7045 (mp0) REVERT: T 280 ASN cc_start: 0.7820 (OUTLIER) cc_final: 0.7459 (t0) REVERT: T 363 GLU cc_start: 0.7925 (tp30) cc_final: 0.7096 (pp20) REVERT: U 233 TRP cc_start: 0.7709 (OUTLIER) cc_final: 0.7248 (m-10) REVERT: U 280 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7441 (t160) REVERT: U 363 GLU cc_start: 0.7856 (tp30) cc_final: 0.7085 (pp20) REVERT: V 37 PHE cc_start: 0.4719 (OUTLIER) cc_final: 0.4104 (t80) REVERT: V 417 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8207 (m-30) REVERT: W 37 PHE cc_start: 0.5632 (t80) cc_final: 0.5363 (t80) REVERT: W 91 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6686 (mt) REVERT: W 280 ASN cc_start: 0.7834 (OUTLIER) cc_final: 0.7605 (t160) REVERT: W 363 GLU cc_start: 0.7888 (tp30) cc_final: 0.7129 (pp20) REVERT: W 400 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7621 (tp) REVERT: X 85 GLU cc_start: 0.9328 (mp0) cc_final: 0.9014 (mp0) REVERT: X 280 ASN cc_start: 0.7915 (OUTLIER) cc_final: 0.7699 (t160) REVERT: X 417 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8125 (m-30) outliers start: 264 outliers final: 131 residues processed: 765 average time/residue: 1.1799 time to fit residues: 1211.3156 Evaluate side-chains 657 residues out of total 6066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 484 time to evaluate : 5.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 45 ASP Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 188 ARG Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 233 TRP Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 280 ASN Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 378 ASN Chi-restraints excluded: chain G residue 404 GLU Chi-restraints excluded: chain G residue 447 GLU Chi-restraints excluded: chain G residue 462 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 45 ASP Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 340 SER Chi-restraints excluded: chain H residue 404 GLU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 188 ARG Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 340 SER Chi-restraints excluded: chain I residue 378 ASN Chi-restraints excluded: chain I residue 398 LYS Chi-restraints excluded: chain I residue 404 GLU Chi-restraints excluded: chain I residue 447 GLU Chi-restraints excluded: chain I residue 462 GLU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 135 SER Chi-restraints excluded: chain J residue 188 ARG Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 280 ASN Chi-restraints excluded: chain J residue 340 SER Chi-restraints excluded: chain J residue 378 ASN Chi-restraints excluded: chain J residue 398 LYS Chi-restraints excluded: chain J residue 404 GLU Chi-restraints excluded: chain J residue 417 ASP Chi-restraints excluded: chain J residue 447 GLU Chi-restraints excluded: chain J residue 462 GLU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 239 ILE Chi-restraints excluded: chain K residue 404 GLU Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 129 ILE Chi-restraints excluded: chain L residue 188 ARG Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 231 PHE Chi-restraints excluded: chain L residue 233 TRP Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 280 ASN Chi-restraints excluded: chain L residue 340 SER Chi-restraints excluded: chain L residue 378 ASN Chi-restraints excluded: chain L residue 404 GLU Chi-restraints excluded: chain L residue 462 GLU Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 88 GLU Chi-restraints excluded: chain M residue 167 ASP Chi-restraints excluded: chain M residue 239 ILE Chi-restraints excluded: chain M residue 280 ASN Chi-restraints excluded: chain M residue 299 THR Chi-restraints excluded: chain M residue 413 VAL Chi-restraints excluded: chain M residue 417 ASP Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 233 TRP Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 280 ASN Chi-restraints excluded: chain N residue 329 ASN Chi-restraints excluded: chain N residue 355 SER Chi-restraints excluded: chain N residue 400 LEU Chi-restraints excluded: chain N residue 417 ASP Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 196 ASP Chi-restraints excluded: chain O residue 202 THR Chi-restraints excluded: chain O residue 226 GLU Chi-restraints excluded: chain O residue 239 ILE Chi-restraints excluded: chain O residue 280 ASN Chi-restraints excluded: chain O residue 378 ASN Chi-restraints excluded: chain O residue 417 ASP Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 167 ASP Chi-restraints excluded: chain P residue 239 ILE Chi-restraints excluded: chain P residue 280 ASN Chi-restraints excluded: chain P residue 378 ASN Chi-restraints excluded: chain P residue 413 VAL Chi-restraints excluded: chain P residue 417 ASP Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 196 ASP Chi-restraints excluded: chain Q residue 231 PHE Chi-restraints excluded: chain Q residue 239 ILE Chi-restraints excluded: chain Q residue 280 ASN Chi-restraints excluded: chain Q residue 329 ASN Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain Q residue 378 ASN Chi-restraints excluded: chain R residue 60 THR Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 88 GLU Chi-restraints excluded: chain R residue 167 ASP Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 280 ASN Chi-restraints excluded: chain R residue 296 GLU Chi-restraints excluded: chain R residue 299 THR Chi-restraints excluded: chain R residue 378 ASN Chi-restraints excluded: chain R residue 413 VAL Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 45 ASP Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 239 ILE Chi-restraints excluded: chain S residue 378 ASN Chi-restraints excluded: chain S residue 413 VAL Chi-restraints excluded: chain S residue 417 ASP Chi-restraints excluded: chain T residue 33 THR Chi-restraints excluded: chain T residue 188 ARG Chi-restraints excluded: chain T residue 196 ASP Chi-restraints excluded: chain T residue 202 THR Chi-restraints excluded: chain T residue 226 GLU Chi-restraints excluded: chain T residue 239 ILE Chi-restraints excluded: chain T residue 280 ASN Chi-restraints excluded: chain T residue 355 SER Chi-restraints excluded: chain T residue 378 ASN Chi-restraints excluded: chain U residue 33 THR Chi-restraints excluded: chain U residue 45 ASP Chi-restraints excluded: chain U residue 75 LEU Chi-restraints excluded: chain U residue 159 ASP Chi-restraints excluded: chain U residue 233 TRP Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 280 ASN Chi-restraints excluded: chain U residue 307 VAL Chi-restraints excluded: chain U residue 378 ASN Chi-restraints excluded: chain U residue 400 LEU Chi-restraints excluded: chain U residue 413 VAL Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 37 PHE Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 167 ASP Chi-restraints excluded: chain V residue 239 ILE Chi-restraints excluded: chain V residue 413 VAL Chi-restraints excluded: chain V residue 417 ASP Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 75 LEU Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 91 LEU Chi-restraints excluded: chain W residue 239 ILE Chi-restraints excluded: chain W residue 280 ASN Chi-restraints excluded: chain W residue 378 ASN Chi-restraints excluded: chain W residue 400 LEU Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 60 THR Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 167 ASP Chi-restraints excluded: chain X residue 239 ILE Chi-restraints excluded: chain X residue 280 ASN Chi-restraints excluded: chain X residue 299 THR Chi-restraints excluded: chain X residue 413 VAL Chi-restraints excluded: chain X residue 417 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 774 random chunks: chunk 344 optimal weight: 10.0000 chunk 443 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 480 optimal weight: 20.0000 chunk 145 optimal weight: 1.9990 chunk 185 optimal weight: 0.5980 chunk 216 optimal weight: 9.9990 chunk 427 optimal weight: 20.0000 chunk 657 optimal weight: 9.9990 chunk 691 optimal weight: 5.9990 chunk 581 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 ASN ** G 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 ASN ** I 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 378 ASN ** I 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN L 280 ASN ** L 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 ASN ** N 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 GLN O 329 ASN ** O 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 280 ASN Q 79 GLN Q 184 ASN Q 280 ASN Q 378 ASN ** Q 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 280 ASN R 378 ASN ** S 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 280 ASN ** T 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 280 ASN T 378 ASN ** T 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 280 ASN U 378 ASN ** U 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 280 ASN ** V 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 79 GLN ** W 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 280 ASN X 378 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.155075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.131150 restraints weight = 107064.814| |-----------------------------------------------------------------------------| r_work (start): 0.4270 rms_B_bonded: 2.86 r_work: 0.4123 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 61506 Z= 0.248 Angle : 0.592 11.511 83826 Z= 0.321 Chirality : 0.040 0.310 9468 Planarity : 0.004 0.062 11394 Dihedral : 5.592 86.948 8614 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.49 % Favored : 96.30 % Rotamer: Outliers : 5.09 % Allowed : 30.44 % Favored : 64.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.09), residues: 7740 helix: 2.36 (0.07), residues: 5544 sheet: None (None), residues: 0 loop : -2.37 (0.11), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP S 233 HIS 0.004 0.001 HIS H 338 PHE 0.023 0.002 PHE N 37 TYR 0.020 0.002 TYR V 153 ARG 0.006 0.001 ARG V 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15480 Ramachandran restraints generated. 7740 Oldfield, 0 Emsley, 7740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15480 Ramachandran restraints generated. 7740 Oldfield, 0 Emsley, 7740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 6066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 308 poor density : 561 time to evaluate : 4.991 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 75 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7721 (mp) REVERT: G 188 ARG cc_start: 0.6508 (OUTLIER) cc_final: 0.6174 (mtt-85) REVERT: G 195 GLU cc_start: 0.6868 (mm-30) cc_final: 0.6179 (mp0) REVERT: G 223 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7585 (tp) REVERT: G 231 PHE cc_start: 0.7157 (OUTLIER) cc_final: 0.6593 (t80) REVERT: G 233 TRP cc_start: 0.7933 (OUTLIER) cc_final: 0.7246 (m-10) REVERT: G 249 ARG cc_start: 0.8286 (ptt-90) cc_final: 0.8074 (ptt-90) REVERT: G 280 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7889 (t160) REVERT: H 167 ASP cc_start: 0.8709 (m-30) cc_final: 0.8029 (p0) REVERT: H 195 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6305 (mp0) REVERT: I 37 PHE cc_start: 0.6661 (m-80) cc_final: 0.6043 (t80) REVERT: I 195 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6407 (mp0) REVERT: I 398 LYS cc_start: 0.6749 (OUTLIER) cc_final: 0.6283 (mttm) REVERT: J 195 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6337 (mp0) REVERT: J 241 GLN cc_start: 0.9069 (mt0) cc_final: 0.8788 (mm-40) REVERT: J 398 LYS cc_start: 0.6749 (OUTLIER) cc_final: 0.6290 (mttm) REVERT: K 37 PHE cc_start: 0.5758 (t80) cc_final: 0.5507 (t80) REVERT: L 75 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7717 (mp) REVERT: L 188 ARG cc_start: 0.6455 (OUTLIER) cc_final: 0.6132 (mpt-90) REVERT: L 195 GLU cc_start: 0.6820 (mm-30) cc_final: 0.6196 (mp0) REVERT: L 223 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7587 (tp) REVERT: L 231 PHE cc_start: 0.7220 (OUTLIER) cc_final: 0.6692 (t80) REVERT: L 233 TRP cc_start: 0.8141 (OUTLIER) cc_final: 0.7547 (m-10) REVERT: L 241 GLN cc_start: 0.9081 (mt0) cc_final: 0.8832 (mt0) REVERT: L 280 ASN cc_start: 0.8208 (OUTLIER) cc_final: 0.7887 (t160) REVERT: M 37 PHE cc_start: 0.5083 (OUTLIER) cc_final: 0.4536 (t80) REVERT: M 85 GLU cc_start: 0.9315 (mp0) cc_final: 0.8995 (mp0) REVERT: M 296 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6929 (pp20) REVERT: M 417 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.8176 (m-30) REVERT: N 241 GLN cc_start: 0.8704 (mt0) cc_final: 0.8374 (tt0) REVERT: N 280 ASN cc_start: 0.7902 (OUTLIER) cc_final: 0.7617 (t160) REVERT: N 363 GLU cc_start: 0.7902 (tp30) cc_final: 0.7156 (pp20) REVERT: N 417 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7792 (m-30) REVERT: N 426 ASP cc_start: 0.8866 (p0) cc_final: 0.8658 (p0) REVERT: O 75 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7040 (mp) REVERT: O 226 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7384 (tt0) REVERT: O 232 GLU cc_start: 0.7857 (pp20) cc_final: 0.7019 (mm-30) REVERT: O 363 GLU cc_start: 0.7981 (tp30) cc_final: 0.7175 (pp20) REVERT: O 417 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7642 (m-30) REVERT: P 37 PHE cc_start: 0.4841 (m-10) cc_final: 0.4146 (t80) REVERT: P 85 GLU cc_start: 0.9234 (mp0) cc_final: 0.8955 (mp0) REVERT: P 296 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.7024 (pp20) REVERT: P 417 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.8036 (m-30) REVERT: Q 91 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6907 (mt) REVERT: Q 231 PHE cc_start: 0.7071 (OUTLIER) cc_final: 0.6267 (t80) REVERT: Q 280 ASN cc_start: 0.7900 (OUTLIER) cc_final: 0.7677 (t160) REVERT: Q 363 GLU cc_start: 0.7927 (tp30) cc_final: 0.7212 (pp20) REVERT: Q 410 LEU cc_start: 0.8882 (tp) cc_final: 0.8661 (tp) REVERT: R 85 GLU cc_start: 0.9286 (mp0) cc_final: 0.8965 (mp0) REVERT: R 296 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6884 (pp20) REVERT: S 37 PHE cc_start: 0.4197 (OUTLIER) cc_final: 0.3670 (t80) REVERT: S 296 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.7010 (pp20) REVERT: S 417 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8063 (m-30) REVERT: T 188 ARG cc_start: 0.5947 (OUTLIER) cc_final: 0.4874 (mmm-85) REVERT: T 226 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7445 (tt0) REVERT: T 232 GLU cc_start: 0.7781 (pp20) cc_final: 0.6944 (mm-30) REVERT: T 280 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7634 (t0) REVERT: T 363 GLU cc_start: 0.7981 (tp30) cc_final: 0.7187 (pp20) REVERT: U 280 ASN cc_start: 0.7900 (OUTLIER) cc_final: 0.7636 (t160) REVERT: U 363 GLU cc_start: 0.7949 (tp30) cc_final: 0.7161 (pp20) REVERT: V 37 PHE cc_start: 0.4691 (OUTLIER) cc_final: 0.4040 (t80) REVERT: V 193 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6309 (tt0) REVERT: V 196 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7041 (m-30) REVERT: V 280 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.7446 (t0) REVERT: V 296 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6912 (pp20) REVERT: V 417 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8243 (m-30) REVERT: W 91 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6795 (mt) REVERT: W 188 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.6434 (mpp80) REVERT: W 363 GLU cc_start: 0.7917 (tp30) cc_final: 0.7165 (pp20) REVERT: W 400 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7588 (tp) REVERT: X 37 PHE cc_start: 0.4806 (OUTLIER) cc_final: 0.4166 (t80) REVERT: X 85 GLU cc_start: 0.9284 (mp0) cc_final: 0.8971 (mp0) REVERT: X 280 ASN cc_start: 0.7919 (OUTLIER) cc_final: 0.7719 (t160) REVERT: X 296 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6840 (pp20) REVERT: X 417 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.8124 (m-30) outliers start: 308 outliers final: 139 residues processed: 795 average time/residue: 1.1677 time to fit residues: 1237.2473 Evaluate side-chains 672 residues out of total 6066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 485 time to evaluate : 5.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 45 ASP Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 188 ARG Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 233 TRP Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 280 ASN Chi-restraints excluded: chain G residue 286 SER Chi-restraints excluded: chain G residue 296 GLU Chi-restraints excluded: chain G residue 378 ASN Chi-restraints excluded: chain G residue 404 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 45 ASP Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 286 SER Chi-restraints excluded: chain H residue 404 GLU Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 188 ARG Chi-restraints excluded: chain I residue 196 ASP Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 286 SER Chi-restraints excluded: chain I residue 398 LYS Chi-restraints excluded: chain I residue 404 GLU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 135 SER Chi-restraints excluded: chain J residue 188 ARG Chi-restraints excluded: chain J residue 196 ASP Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 280 ASN Chi-restraints excluded: chain J residue 286 SER Chi-restraints excluded: chain J residue 378 ASN Chi-restraints excluded: chain J residue 398 LYS Chi-restraints excluded: chain J residue 404 GLU Chi-restraints excluded: chain J residue 447 GLU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 239 ILE Chi-restraints excluded: chain K residue 286 SER Chi-restraints excluded: chain K residue 404 GLU Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 188 ARG Chi-restraints excluded: chain L residue 196 ASP Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 231 PHE Chi-restraints excluded: chain L residue 233 TRP Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 280 ASN Chi-restraints excluded: chain L residue 286 SER Chi-restraints excluded: chain L residue 296 GLU Chi-restraints excluded: chain L residue 378 ASN Chi-restraints excluded: chain L residue 404 GLU Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 37 PHE Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 88 GLU Chi-restraints excluded: chain M residue 167 ASP Chi-restraints excluded: chain M residue 239 ILE Chi-restraints excluded: chain M residue 296 GLU Chi-restraints excluded: chain M residue 299 THR Chi-restraints excluded: chain M residue 413 VAL Chi-restraints excluded: chain M residue 417 ASP Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 280 ASN Chi-restraints excluded: chain N residue 307 VAL Chi-restraints excluded: chain N residue 329 ASN Chi-restraints excluded: chain N residue 355 SER Chi-restraints excluded: chain N residue 400 LEU Chi-restraints excluded: chain N residue 417 ASP Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 196 ASP Chi-restraints excluded: chain O residue 202 THR Chi-restraints excluded: chain O residue 226 GLU Chi-restraints excluded: chain O residue 239 ILE Chi-restraints excluded: chain O residue 313 SER Chi-restraints excluded: chain O residue 413 VAL Chi-restraints excluded: chain O residue 417 ASP Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 167 ASP Chi-restraints excluded: chain P residue 239 ILE Chi-restraints excluded: chain P residue 296 GLU Chi-restraints excluded: chain P residue 299 THR Chi-restraints excluded: chain P residue 413 VAL Chi-restraints excluded: chain P residue 417 ASP Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 196 ASP Chi-restraints excluded: chain Q residue 231 PHE Chi-restraints excluded: chain Q residue 239 ILE Chi-restraints excluded: chain Q residue 280 ASN Chi-restraints excluded: chain Q residue 307 VAL Chi-restraints excluded: chain Q residue 329 ASN Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain R residue 60 THR Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 88 GLU Chi-restraints excluded: chain R residue 167 ASP Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 243 ASP Chi-restraints excluded: chain R residue 296 GLU Chi-restraints excluded: chain R residue 299 THR Chi-restraints excluded: chain R residue 378 ASN Chi-restraints excluded: chain R residue 413 VAL Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 37 PHE Chi-restraints excluded: chain S residue 45 ASP Chi-restraints excluded: chain S residue 96 SER Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 239 ILE Chi-restraints excluded: chain S residue 296 GLU Chi-restraints excluded: chain S residue 413 VAL Chi-restraints excluded: chain S residue 417 ASP Chi-restraints excluded: chain T residue 33 THR Chi-restraints excluded: chain T residue 188 ARG Chi-restraints excluded: chain T residue 196 ASP Chi-restraints excluded: chain T residue 202 THR Chi-restraints excluded: chain T residue 226 GLU Chi-restraints excluded: chain T residue 239 ILE Chi-restraints excluded: chain T residue 280 ASN Chi-restraints excluded: chain T residue 313 SER Chi-restraints excluded: chain T residue 329 ASN Chi-restraints excluded: chain T residue 355 SER Chi-restraints excluded: chain T residue 413 VAL Chi-restraints excluded: chain U residue 33 THR Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 75 LEU Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 280 ASN Chi-restraints excluded: chain U residue 307 VAL Chi-restraints excluded: chain U residue 400 LEU Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 37 PHE Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 167 ASP Chi-restraints excluded: chain V residue 193 GLU Chi-restraints excluded: chain V residue 196 ASP Chi-restraints excluded: chain V residue 239 ILE Chi-restraints excluded: chain V residue 280 ASN Chi-restraints excluded: chain V residue 296 GLU Chi-restraints excluded: chain V residue 299 THR Chi-restraints excluded: chain V residue 413 VAL Chi-restraints excluded: chain V residue 417 ASP Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 91 LEU Chi-restraints excluded: chain W residue 188 ARG Chi-restraints excluded: chain W residue 223 LEU Chi-restraints excluded: chain W residue 239 ILE Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain W residue 400 LEU Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 37 PHE Chi-restraints excluded: chain X residue 60 THR Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 167 ASP Chi-restraints excluded: chain X residue 239 ILE Chi-restraints excluded: chain X residue 243 ASP Chi-restraints excluded: chain X residue 280 ASN Chi-restraints excluded: chain X residue 296 GLU Chi-restraints excluded: chain X residue 299 THR Chi-restraints excluded: chain X residue 378 ASN Chi-restraints excluded: chain X residue 413 VAL Chi-restraints excluded: chain X residue 417 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 774 random chunks: chunk 687 optimal weight: 10.0000 chunk 368 optimal weight: 5.9990 chunk 287 optimal weight: 10.0000 chunk 620 optimal weight: 2.9990 chunk 281 optimal weight: 3.9990 chunk 732 optimal weight: 10.0000 chunk 731 optimal weight: 7.9990 chunk 282 optimal weight: 4.9990 chunk 550 optimal weight: 3.9990 chunk 388 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 ASN ** G 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 378 ASN ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 280 ASN ** L 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 407 GLN ** L 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 ASN M 378 ASN N 280 ASN N 378 ASN ** N 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 GLN O 280 ASN ** O 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 378 ASN ** O 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 378 ASN Q 280 ASN Q 378 ASN ** R 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 378 ASN ** S 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 79 GLN ** T 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 280 ASN T 292 GLN T 378 ASN ** T 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 280 ASN U 292 GLN U 378 ASN ** U 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 280 ASN V 378 ASN ** V 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 280 ASN W 378 ASN ** X 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 280 ASN X 378 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.152060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.128185 restraints weight = 109734.290| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 2.83 r_work: 0.4091 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 61506 Z= 0.334 Angle : 0.649 14.003 83826 Z= 0.352 Chirality : 0.043 0.276 9468 Planarity : 0.005 0.065 11394 Dihedral : 5.526 84.251 8597 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.77 % Favored : 96.02 % Rotamer: Outliers : 6.32 % Allowed : 29.58 % Favored : 64.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.09), residues: 7740 helix: 1.97 (0.06), residues: 5562 sheet: None (None), residues: 0 loop : -2.53 (0.11), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.004 TRP R 233 HIS 0.006 0.001 HIS W 251 PHE 0.022 0.002 PHE N 37 TYR 0.022 0.002 TYR R 153 ARG 0.008 0.001 ARG G 443 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15480 Ramachandran restraints generated. 7740 Oldfield, 0 Emsley, 7740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15480 Ramachandran restraints generated. 7740 Oldfield, 0 Emsley, 7740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 6066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 382 poor density : 535 time to evaluate : 5.019 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 75 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7754 (mp) REVERT: G 188 ARG cc_start: 0.6563 (OUTLIER) cc_final: 0.6151 (mpt-90) REVERT: G 195 GLU cc_start: 0.6882 (mm-30) cc_final: 0.6149 (mp0) REVERT: G 231 PHE cc_start: 0.7249 (OUTLIER) cc_final: 0.6715 (t80) REVERT: G 233 TRP cc_start: 0.8041 (OUTLIER) cc_final: 0.7313 (m-10) REVERT: G 280 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.8064 (t160) REVERT: H 112 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6476 (tm-30) REVERT: H 275 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7278 (t0) REVERT: H 380 GLU cc_start: 0.2437 (OUTLIER) cc_final: 0.2121 (pt0) REVERT: I 188 ARG cc_start: 0.6592 (OUTLIER) cc_final: 0.6201 (mpt-90) REVERT: I 195 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6391 (mp0) REVERT: I 398 LYS cc_start: 0.6813 (OUTLIER) cc_final: 0.6343 (mttm) REVERT: J 188 ARG cc_start: 0.6572 (OUTLIER) cc_final: 0.6176 (mpt-90) REVERT: J 195 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6412 (mp0) REVERT: J 241 GLN cc_start: 0.9054 (mt0) cc_final: 0.8683 (mm-40) REVERT: J 398 LYS cc_start: 0.6818 (OUTLIER) cc_final: 0.6340 (mttm) REVERT: K 37 PHE cc_start: 0.5894 (t80) cc_final: 0.5631 (t80) REVERT: K 112 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6476 (tm-30) REVERT: K 275 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7279 (t0) REVERT: K 380 GLU cc_start: 0.2491 (OUTLIER) cc_final: 0.1747 (pt0) REVERT: L 75 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7759 (mp) REVERT: L 195 GLU cc_start: 0.6788 (mm-30) cc_final: 0.6129 (mp0) REVERT: L 231 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.6716 (t80) REVERT: L 233 TRP cc_start: 0.8258 (OUTLIER) cc_final: 0.7635 (m-10) REVERT: L 280 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.8059 (t160) REVERT: M 37 PHE cc_start: 0.5051 (OUTLIER) cc_final: 0.4440 (t80) REVERT: M 157 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7431 (mp) REVERT: M 196 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7175 (m-30) REVERT: M 275 ASP cc_start: 0.7088 (OUTLIER) cc_final: 0.6794 (OUTLIER) REVERT: M 280 ASN cc_start: 0.7831 (OUTLIER) cc_final: 0.7424 (t0) REVERT: M 296 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6978 (pp20) REVERT: M 417 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.8184 (m-30) REVERT: N 241 GLN cc_start: 0.8749 (mt0) cc_final: 0.8381 (tt0) REVERT: N 280 ASN cc_start: 0.8097 (OUTLIER) cc_final: 0.7818 (t160) REVERT: N 306 ARG cc_start: 0.6888 (ptt180) cc_final: 0.6682 (ptp-170) REVERT: N 354 ILE cc_start: 0.6876 (OUTLIER) cc_final: 0.6651 (mp) REVERT: N 363 GLU cc_start: 0.7995 (tp30) cc_final: 0.7227 (pp20) REVERT: O 157 LEU cc_start: 0.7709 (tp) cc_final: 0.7464 (tp) REVERT: O 226 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7385 (tt0) REVERT: O 233 TRP cc_start: 0.7340 (OUTLIER) cc_final: 0.6978 (m-10) REVERT: O 280 ASN cc_start: 0.7926 (OUTLIER) cc_final: 0.7602 (t160) REVERT: O 363 GLU cc_start: 0.8029 (tp30) cc_final: 0.7273 (pp20) REVERT: O 417 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7717 (m-30) REVERT: P 37 PHE cc_start: 0.4778 (OUTLIER) cc_final: 0.4039 (t80) REVERT: P 280 ASN cc_start: 0.7912 (OUTLIER) cc_final: 0.7431 (t0) REVERT: P 296 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.7034 (pp20) REVERT: P 417 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.8000 (m-30) REVERT: Q 91 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6891 (mt) REVERT: Q 231 PHE cc_start: 0.7110 (OUTLIER) cc_final: 0.6262 (t80) REVERT: Q 280 ASN cc_start: 0.8051 (OUTLIER) cc_final: 0.7681 (t160) REVERT: Q 313 SER cc_start: 0.6859 (OUTLIER) cc_final: 0.6379 (p) REVERT: Q 363 GLU cc_start: 0.7978 (tp30) cc_final: 0.7267 (pp20) REVERT: R 37 PHE cc_start: 0.4701 (OUTLIER) cc_final: 0.4089 (t80) REVERT: R 275 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6823 (m-30) REVERT: R 280 ASN cc_start: 0.7459 (OUTLIER) cc_final: 0.7240 (t0) REVERT: R 296 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6949 (pp20) REVERT: S 37 PHE cc_start: 0.4432 (OUTLIER) cc_final: 0.3838 (t80) REVERT: S 280 ASN cc_start: 0.7903 (OUTLIER) cc_final: 0.7450 (t0) REVERT: S 296 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.7010 (pp20) REVERT: S 417 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.8039 (m-30) REVERT: T 188 ARG cc_start: 0.6072 (OUTLIER) cc_final: 0.4949 (mmm-85) REVERT: T 226 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7475 (tt0) REVERT: T 280 ASN cc_start: 0.8128 (OUTLIER) cc_final: 0.7674 (t0) REVERT: T 363 GLU cc_start: 0.8031 (tp30) cc_final: 0.7274 (pp20) REVERT: U 226 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7730 (tt0) REVERT: U 280 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.7848 (t160) REVERT: U 306 ARG cc_start: 0.7009 (ptt180) cc_final: 0.6776 (ptp-170) REVERT: U 363 GLU cc_start: 0.7996 (tp30) cc_final: 0.7227 (pp20) REVERT: V 37 PHE cc_start: 0.4695 (OUTLIER) cc_final: 0.4206 (m-10) REVERT: V 157 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7452 (mp) REVERT: V 193 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6194 (tt0) REVERT: V 275 ASP cc_start: 0.7091 (OUTLIER) cc_final: 0.6807 (m-30) REVERT: V 296 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.7041 (pp20) REVERT: V 417 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8199 (m-30) REVERT: W 91 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6760 (mt) REVERT: W 280 ASN cc_start: 0.7902 (OUTLIER) cc_final: 0.7501 (t160) REVERT: W 363 GLU cc_start: 0.7963 (tp30) cc_final: 0.7266 (pp20) REVERT: W 400 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7587 (tp) REVERT: X 37 PHE cc_start: 0.4654 (OUTLIER) cc_final: 0.3964 (t80) REVERT: X 85 GLU cc_start: 0.9227 (mp0) cc_final: 0.8925 (mp0) REVERT: X 193 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6300 (tt0) REVERT: X 275 ASP cc_start: 0.7038 (OUTLIER) cc_final: 0.6804 (m-30) REVERT: X 280 ASN cc_start: 0.7955 (OUTLIER) cc_final: 0.7707 (t160) REVERT: X 296 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6988 (pp20) REVERT: X 417 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8125 (m-30) outliers start: 382 outliers final: 169 residues processed: 838 average time/residue: 1.1147 time to fit residues: 1259.6405 Evaluate side-chains 714 residues out of total 6066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 478 time to evaluate : 4.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 45 ASP Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 188 ARG Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 233 TRP Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 280 ASN Chi-restraints excluded: chain G residue 286 SER Chi-restraints excluded: chain G residue 296 GLU Chi-restraints excluded: chain G residue 378 ASN Chi-restraints excluded: chain G residue 404 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 45 ASP Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 112 GLU Chi-restraints excluded: chain H residue 196 ASP Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 275 ASP Chi-restraints excluded: chain H residue 286 SER Chi-restraints excluded: chain H residue 313 SER Chi-restraints excluded: chain H residue 380 GLU Chi-restraints excluded: chain H residue 404 GLU Chi-restraints excluded: chain H residue 417 ASP Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 188 ARG Chi-restraints excluded: chain I residue 196 ASP Chi-restraints excluded: chain I residue 212 GLN Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 275 ASP Chi-restraints excluded: chain I residue 286 SER Chi-restraints excluded: chain I residue 398 LYS Chi-restraints excluded: chain I residue 404 GLU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 135 SER Chi-restraints excluded: chain J residue 188 ARG Chi-restraints excluded: chain J residue 196 ASP Chi-restraints excluded: chain J residue 212 GLN Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain J residue 286 SER Chi-restraints excluded: chain J residue 398 LYS Chi-restraints excluded: chain J residue 404 GLU Chi-restraints excluded: chain J residue 447 GLU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 112 GLU Chi-restraints excluded: chain K residue 196 ASP Chi-restraints excluded: chain K residue 239 ILE Chi-restraints excluded: chain K residue 275 ASP Chi-restraints excluded: chain K residue 286 SER Chi-restraints excluded: chain K residue 380 GLU Chi-restraints excluded: chain K residue 404 GLU Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 96 SER Chi-restraints excluded: chain L residue 196 ASP Chi-restraints excluded: chain L residue 231 PHE Chi-restraints excluded: chain L residue 233 TRP Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 280 ASN Chi-restraints excluded: chain L residue 286 SER Chi-restraints excluded: chain L residue 296 GLU Chi-restraints excluded: chain L residue 313 SER Chi-restraints excluded: chain L residue 378 ASN Chi-restraints excluded: chain L residue 404 GLU Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 37 PHE Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 88 GLU Chi-restraints excluded: chain M residue 135 SER Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 167 ASP Chi-restraints excluded: chain M residue 196 ASP Chi-restraints excluded: chain M residue 227 VAL Chi-restraints excluded: chain M residue 239 ILE Chi-restraints excluded: chain M residue 275 ASP Chi-restraints excluded: chain M residue 280 ASN Chi-restraints excluded: chain M residue 296 GLU Chi-restraints excluded: chain M residue 299 THR Chi-restraints excluded: chain M residue 413 VAL Chi-restraints excluded: chain M residue 417 ASP Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 96 SER Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 280 ASN Chi-restraints excluded: chain N residue 307 VAL Chi-restraints excluded: chain N residue 329 ASN Chi-restraints excluded: chain N residue 354 ILE Chi-restraints excluded: chain N residue 355 SER Chi-restraints excluded: chain N residue 400 LEU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 188 ARG Chi-restraints excluded: chain O residue 196 ASP Chi-restraints excluded: chain O residue 202 THR Chi-restraints excluded: chain O residue 226 GLU Chi-restraints excluded: chain O residue 233 TRP Chi-restraints excluded: chain O residue 239 ILE Chi-restraints excluded: chain O residue 280 ASN Chi-restraints excluded: chain O residue 307 VAL Chi-restraints excluded: chain O residue 313 SER Chi-restraints excluded: chain O residue 329 ASN Chi-restraints excluded: chain O residue 413 VAL Chi-restraints excluded: chain O residue 417 ASP Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 37 PHE Chi-restraints excluded: chain P residue 167 ASP Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 239 ILE Chi-restraints excluded: chain P residue 280 ASN Chi-restraints excluded: chain P residue 296 GLU Chi-restraints excluded: chain P residue 299 THR Chi-restraints excluded: chain P residue 380 GLU Chi-restraints excluded: chain P residue 413 VAL Chi-restraints excluded: chain P residue 417 ASP Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain Q residue 91 LEU Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 202 THR Chi-restraints excluded: chain Q residue 231 PHE Chi-restraints excluded: chain Q residue 233 TRP Chi-restraints excluded: chain Q residue 239 ILE Chi-restraints excluded: chain Q residue 280 ASN Chi-restraints excluded: chain Q residue 307 VAL Chi-restraints excluded: chain Q residue 313 SER Chi-restraints excluded: chain Q residue 329 ASN Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain R residue 37 PHE Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 88 GLU Chi-restraints excluded: chain R residue 167 ASP Chi-restraints excluded: chain R residue 227 VAL Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 275 ASP Chi-restraints excluded: chain R residue 280 ASN Chi-restraints excluded: chain R residue 296 GLU Chi-restraints excluded: chain R residue 299 THR Chi-restraints excluded: chain R residue 393 ILE Chi-restraints excluded: chain R residue 413 VAL Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 37 PHE Chi-restraints excluded: chain S residue 45 ASP Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain S residue 239 ILE Chi-restraints excluded: chain S residue 280 ASN Chi-restraints excluded: chain S residue 296 GLU Chi-restraints excluded: chain S residue 299 THR Chi-restraints excluded: chain S residue 380 GLU Chi-restraints excluded: chain S residue 413 VAL Chi-restraints excluded: chain S residue 417 ASP Chi-restraints excluded: chain T residue 33 THR Chi-restraints excluded: chain T residue 51 ILE Chi-restraints excluded: chain T residue 83 VAL Chi-restraints excluded: chain T residue 188 ARG Chi-restraints excluded: chain T residue 196 ASP Chi-restraints excluded: chain T residue 202 THR Chi-restraints excluded: chain T residue 226 GLU Chi-restraints excluded: chain T residue 239 ILE Chi-restraints excluded: chain T residue 280 ASN Chi-restraints excluded: chain T residue 307 VAL Chi-restraints excluded: chain T residue 313 SER Chi-restraints excluded: chain T residue 355 SER Chi-restraints excluded: chain T residue 413 VAL Chi-restraints excluded: chain U residue 33 THR Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 75 LEU Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 226 GLU Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 280 ASN Chi-restraints excluded: chain U residue 307 VAL Chi-restraints excluded: chain U residue 400 LEU Chi-restraints excluded: chain U residue 462 GLU Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 37 PHE Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 135 SER Chi-restraints excluded: chain V residue 157 LEU Chi-restraints excluded: chain V residue 167 ASP Chi-restraints excluded: chain V residue 193 GLU Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain V residue 239 ILE Chi-restraints excluded: chain V residue 275 ASP Chi-restraints excluded: chain V residue 296 GLU Chi-restraints excluded: chain V residue 299 THR Chi-restraints excluded: chain V residue 313 SER Chi-restraints excluded: chain V residue 413 VAL Chi-restraints excluded: chain V residue 417 ASP Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 91 LEU Chi-restraints excluded: chain W residue 96 SER Chi-restraints excluded: chain W residue 223 LEU Chi-restraints excluded: chain W residue 239 ILE Chi-restraints excluded: chain W residue 280 ASN Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain W residue 400 LEU Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 37 PHE Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 167 ASP Chi-restraints excluded: chain X residue 193 GLU Chi-restraints excluded: chain X residue 227 VAL Chi-restraints excluded: chain X residue 239 ILE Chi-restraints excluded: chain X residue 275 ASP Chi-restraints excluded: chain X residue 280 ASN Chi-restraints excluded: chain X residue 296 GLU Chi-restraints excluded: chain X residue 299 THR Chi-restraints excluded: chain X residue 380 GLU Chi-restraints excluded: chain X residue 393 ILE Chi-restraints excluded: chain X residue 413 VAL Chi-restraints excluded: chain X residue 417 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 774 random chunks: chunk 178 optimal weight: 5.9990 chunk 546 optimal weight: 9.9990 chunk 347 optimal weight: 5.9990 chunk 343 optimal weight: 7.9990 chunk 593 optimal weight: 0.9990 chunk 592 optimal weight: 0.0770 chunk 181 optimal weight: 0.6980 chunk 506 optimal weight: 0.3980 chunk 42 optimal weight: 8.9990 chunk 605 optimal weight: 8.9990 chunk 465 optimal weight: 5.9990 overall best weight: 1.6342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 34 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 ASN ** G 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 378 ASN ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 378 ASN ** I 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 378 ASN K 34 ASN K 248 GLN ** K 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 378 ASN ** K 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN ** L 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 280 ASN ** L 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 ASN M 378 ASN ** N 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 ASN N 378 ASN ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 280 ASN ** O 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 378 ASN ** Q 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 446 GLN ** R 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 378 ASN ** T 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 79 GLN ** T 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 280 ASN ** T 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 280 ASN U 378 ASN ** U 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 378 ASN ** V 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 280 ASN W 378 ASN ** X 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 280 ASN X 378 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.154617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.130533 restraints weight = 107444.265| |-----------------------------------------------------------------------------| r_work (start): 0.4254 rms_B_bonded: 3.09 r_work: 0.4109 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 61506 Z= 0.223 Angle : 0.592 14.716 83826 Z= 0.319 Chirality : 0.039 0.253 9468 Planarity : 0.004 0.070 11394 Dihedral : 5.246 90.256 8593 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.26 % Favored : 96.54 % Rotamer: Outliers : 5.16 % Allowed : 31.10 % Favored : 63.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.09), residues: 7740 helix: 2.34 (0.07), residues: 5562 sheet: None (None), residues: 0 loop : -2.45 (0.11), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP R 233 HIS 0.004 0.001 HIS W 251 PHE 0.034 0.002 PHE Q 37 TYR 0.020 0.001 TYR N 153 ARG 0.007 0.000 ARG M 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15480 Ramachandran restraints generated. 7740 Oldfield, 0 Emsley, 7740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15480 Ramachandran restraints generated. 7740 Oldfield, 0 Emsley, 7740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 6066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 312 poor density : 533 time to evaluate : 4.999 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: symmetry clash REVERT: G 75 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7648 (mp) REVERT: G 188 ARG cc_start: 0.6473 (OUTLIER) cc_final: 0.6096 (mpt-90) REVERT: G 233 TRP cc_start: 0.7966 (OUTLIER) cc_final: 0.7377 (m-10) REVERT: G 280 ASN cc_start: 0.8243 (OUTLIER) cc_final: 0.7917 (t160) REVERT: H 112 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6438 (tm-30) REVERT: H 195 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6351 (mp0) REVERT: H 380 GLU cc_start: 0.2410 (OUTLIER) cc_final: 0.2099 (pt0) REVERT: I 398 LYS cc_start: 0.6762 (OUTLIER) cc_final: 0.6273 (mttm) REVERT: J 241 GLN cc_start: 0.9063 (mt0) cc_final: 0.8780 (mm-40) REVERT: J 398 LYS cc_start: 0.6778 (OUTLIER) cc_final: 0.6290 (mttm) REVERT: J 417 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.8425 (t0) REVERT: K 37 PHE cc_start: 0.5748 (t80) cc_final: 0.5452 (t80) REVERT: K 112 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6410 (tm-30) REVERT: K 380 GLU cc_start: 0.2223 (OUTLIER) cc_final: 0.1493 (pt0) REVERT: L 195 GLU cc_start: 0.6801 (mm-30) cc_final: 0.6165 (mp0) REVERT: L 233 TRP cc_start: 0.8154 (OUTLIER) cc_final: 0.7597 (m-10) REVERT: L 280 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7905 (t160) REVERT: M 37 PHE cc_start: 0.4909 (OUTLIER) cc_final: 0.4238 (t80) REVERT: M 85 GLU cc_start: 0.9326 (mp0) cc_final: 0.9007 (mp0) REVERT: M 196 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.6962 (m-30) REVERT: M 280 ASN cc_start: 0.7716 (OUTLIER) cc_final: 0.7408 (t0) REVERT: M 296 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6960 (pp20) REVERT: M 329 ASN cc_start: 0.6794 (m-40) cc_final: 0.6590 (m-40) REVERT: M 417 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8175 (m-30) REVERT: N 241 GLN cc_start: 0.8777 (mt0) cc_final: 0.8430 (tt0) REVERT: N 280 ASN cc_start: 0.7944 (OUTLIER) cc_final: 0.7715 (t160) REVERT: N 313 SER cc_start: 0.7075 (OUTLIER) cc_final: 0.6629 (p) REVERT: N 354 ILE cc_start: 0.6767 (OUTLIER) cc_final: 0.6553 (mp) REVERT: N 363 GLU cc_start: 0.7959 (tp30) cc_final: 0.7191 (pp20) REVERT: O 75 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6972 (mp) REVERT: O 157 LEU cc_start: 0.7648 (tp) cc_final: 0.7428 (tp) REVERT: O 232 GLU cc_start: 0.7668 (pp20) cc_final: 0.6735 (mp0) REVERT: O 280 ASN cc_start: 0.7845 (OUTLIER) cc_final: 0.7364 (t0) REVERT: O 363 GLU cc_start: 0.8010 (tp30) cc_final: 0.7221 (pp20) REVERT: O 417 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7708 (m-30) REVERT: P 34 ASN cc_start: 0.4587 (t0) cc_final: 0.4091 (t0) REVERT: P 37 PHE cc_start: 0.4546 (OUTLIER) cc_final: 0.3832 (t80) REVERT: P 85 GLU cc_start: 0.9213 (mp0) cc_final: 0.8933 (mp0) REVERT: P 296 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.7020 (pp20) REVERT: P 417 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.8032 (m-30) REVERT: Q 188 ARG cc_start: 0.5759 (ttm110) cc_final: 0.5459 (mtt-85) REVERT: Q 231 PHE cc_start: 0.7065 (OUTLIER) cc_final: 0.6219 (t80) REVERT: Q 313 SER cc_start: 0.6875 (OUTLIER) cc_final: 0.6381 (p) REVERT: Q 363 GLU cc_start: 0.7969 (tp30) cc_final: 0.7218 (pp20) REVERT: Q 410 LEU cc_start: 0.8877 (tp) cc_final: 0.8622 (tp) REVERT: Q 415 ASN cc_start: 0.8156 (p0) cc_final: 0.7894 (p0) REVERT: R 37 PHE cc_start: 0.4599 (OUTLIER) cc_final: 0.3964 (t80) REVERT: R 85 GLU cc_start: 0.9264 (mp0) cc_final: 0.8930 (mp0) REVERT: R 275 ASP cc_start: 0.7025 (OUTLIER) cc_final: 0.6814 (m-30) REVERT: R 280 ASN cc_start: 0.7405 (OUTLIER) cc_final: 0.7190 (t0) REVERT: R 296 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6912 (pp20) REVERT: R 329 ASN cc_start: 0.6574 (m-40) cc_final: 0.6346 (m110) REVERT: S 37 PHE cc_start: 0.4154 (OUTLIER) cc_final: 0.3579 (t80) REVERT: S 85 GLU cc_start: 0.9237 (mp0) cc_final: 0.8951 (mp0) REVERT: S 296 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6988 (pp20) REVERT: S 417 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.8013 (m-30) REVERT: T 75 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.6974 (mp) REVERT: T 232 GLU cc_start: 0.7655 (pp20) cc_final: 0.6652 (mp0) REVERT: T 326 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7526 (mm-30) REVERT: T 363 GLU cc_start: 0.8023 (tp30) cc_final: 0.7220 (pp20) REVERT: U 280 ASN cc_start: 0.7935 (OUTLIER) cc_final: 0.7708 (t160) REVERT: U 363 GLU cc_start: 0.7969 (tp30) cc_final: 0.7188 (pp20) REVERT: V 37 PHE cc_start: 0.4556 (OUTLIER) cc_final: 0.4030 (m-10) REVERT: V 193 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6244 (tt0) REVERT: V 196 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.6800 (m-30) REVERT: V 275 ASP cc_start: 0.7005 (OUTLIER) cc_final: 0.6727 (m-30) REVERT: V 296 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6956 (pp20) REVERT: V 417 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8181 (m-30) REVERT: W 91 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6770 (mt) REVERT: W 280 ASN cc_start: 0.7765 (OUTLIER) cc_final: 0.7359 (t160) REVERT: W 363 GLU cc_start: 0.7915 (tp30) cc_final: 0.7222 (pp20) REVERT: X 37 PHE cc_start: 0.4543 (OUTLIER) cc_final: 0.3885 (t80) REVERT: X 85 GLU cc_start: 0.9274 (mp0) cc_final: 0.8933 (mp0) REVERT: X 296 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6939 (pp20) REVERT: X 417 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.8108 (m-30) outliers start: 312 outliers final: 153 residues processed: 772 average time/residue: 1.1107 time to fit residues: 1156.9233 Evaluate side-chains 683 residues out of total 6066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 480 time to evaluate : 4.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 45 ASP Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 188 ARG Chi-restraints excluded: chain G residue 233 TRP Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 280 ASN Chi-restraints excluded: chain G residue 286 SER Chi-restraints excluded: chain G residue 296 GLU Chi-restraints excluded: chain G residue 313 SER Chi-restraints excluded: chain G residue 378 ASN Chi-restraints excluded: chain G residue 404 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 45 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 112 GLU Chi-restraints excluded: chain H residue 196 ASP Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 286 SER Chi-restraints excluded: chain H residue 380 GLU Chi-restraints excluded: chain H residue 404 GLU Chi-restraints excluded: chain H residue 443 ARG Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 188 ARG Chi-restraints excluded: chain I residue 196 ASP Chi-restraints excluded: chain I residue 212 GLN Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 398 LYS Chi-restraints excluded: chain I residue 404 GLU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 135 SER Chi-restraints excluded: chain J residue 188 ARG Chi-restraints excluded: chain J residue 196 ASP Chi-restraints excluded: chain J residue 212 GLN Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 398 LYS Chi-restraints excluded: chain J residue 404 GLU Chi-restraints excluded: chain J residue 417 ASP Chi-restraints excluded: chain J residue 447 GLU Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 112 GLU Chi-restraints excluded: chain K residue 196 ASP Chi-restraints excluded: chain K residue 239 ILE Chi-restraints excluded: chain K residue 286 SER Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 380 GLU Chi-restraints excluded: chain K residue 404 GLU Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 196 ASP Chi-restraints excluded: chain L residue 233 TRP Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 280 ASN Chi-restraints excluded: chain L residue 286 SER Chi-restraints excluded: chain L residue 296 GLU Chi-restraints excluded: chain L residue 313 SER Chi-restraints excluded: chain L residue 378 ASN Chi-restraints excluded: chain L residue 404 GLU Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 37 PHE Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 88 GLU Chi-restraints excluded: chain M residue 167 ASP Chi-restraints excluded: chain M residue 196 ASP Chi-restraints excluded: chain M residue 239 ILE Chi-restraints excluded: chain M residue 280 ASN Chi-restraints excluded: chain M residue 296 GLU Chi-restraints excluded: chain M residue 299 THR Chi-restraints excluded: chain M residue 313 SER Chi-restraints excluded: chain M residue 393 ILE Chi-restraints excluded: chain M residue 413 VAL Chi-restraints excluded: chain M residue 417 ASP Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 280 ASN Chi-restraints excluded: chain N residue 313 SER Chi-restraints excluded: chain N residue 329 ASN Chi-restraints excluded: chain N residue 354 ILE Chi-restraints excluded: chain N residue 355 SER Chi-restraints excluded: chain N residue 400 LEU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 188 ARG Chi-restraints excluded: chain O residue 196 ASP Chi-restraints excluded: chain O residue 202 THR Chi-restraints excluded: chain O residue 239 ILE Chi-restraints excluded: chain O residue 280 ASN Chi-restraints excluded: chain O residue 313 SER Chi-restraints excluded: chain O residue 329 ASN Chi-restraints excluded: chain O residue 413 VAL Chi-restraints excluded: chain O residue 417 ASP Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 37 PHE Chi-restraints excluded: chain P residue 135 SER Chi-restraints excluded: chain P residue 167 ASP Chi-restraints excluded: chain P residue 232 GLU Chi-restraints excluded: chain P residue 239 ILE Chi-restraints excluded: chain P residue 296 GLU Chi-restraints excluded: chain P residue 299 THR Chi-restraints excluded: chain P residue 413 VAL Chi-restraints excluded: chain P residue 417 ASP Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 202 THR Chi-restraints excluded: chain Q residue 231 PHE Chi-restraints excluded: chain Q residue 239 ILE Chi-restraints excluded: chain Q residue 313 SER Chi-restraints excluded: chain Q residue 329 ASN Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain R residue 37 PHE Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 88 GLU Chi-restraints excluded: chain R residue 167 ASP Chi-restraints excluded: chain R residue 232 GLU Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 275 ASP Chi-restraints excluded: chain R residue 280 ASN Chi-restraints excluded: chain R residue 296 GLU Chi-restraints excluded: chain R residue 299 THR Chi-restraints excluded: chain R residue 313 SER Chi-restraints excluded: chain R residue 378 ASN Chi-restraints excluded: chain R residue 413 VAL Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 37 PHE Chi-restraints excluded: chain S residue 45 ASP Chi-restraints excluded: chain S residue 135 SER Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 239 ILE Chi-restraints excluded: chain S residue 296 GLU Chi-restraints excluded: chain S residue 299 THR Chi-restraints excluded: chain S residue 413 VAL Chi-restraints excluded: chain S residue 417 ASP Chi-restraints excluded: chain T residue 33 THR Chi-restraints excluded: chain T residue 51 ILE Chi-restraints excluded: chain T residue 75 LEU Chi-restraints excluded: chain T residue 196 ASP Chi-restraints excluded: chain T residue 202 THR Chi-restraints excluded: chain T residue 239 ILE Chi-restraints excluded: chain T residue 313 SER Chi-restraints excluded: chain T residue 326 GLU Chi-restraints excluded: chain T residue 355 SER Chi-restraints excluded: chain T residue 413 VAL Chi-restraints excluded: chain U residue 33 THR Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 75 LEU Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 234 LEU Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 280 ASN Chi-restraints excluded: chain U residue 400 LEU Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 37 PHE Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 167 ASP Chi-restraints excluded: chain V residue 193 GLU Chi-restraints excluded: chain V residue 196 ASP Chi-restraints excluded: chain V residue 232 GLU Chi-restraints excluded: chain V residue 239 ILE Chi-restraints excluded: chain V residue 275 ASP Chi-restraints excluded: chain V residue 296 GLU Chi-restraints excluded: chain V residue 299 THR Chi-restraints excluded: chain V residue 393 ILE Chi-restraints excluded: chain V residue 413 VAL Chi-restraints excluded: chain V residue 417 ASP Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain W residue 91 LEU Chi-restraints excluded: chain W residue 223 LEU Chi-restraints excluded: chain W residue 239 ILE Chi-restraints excluded: chain W residue 280 ASN Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 37 PHE Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 167 ASP Chi-restraints excluded: chain X residue 232 GLU Chi-restraints excluded: chain X residue 239 ILE Chi-restraints excluded: chain X residue 296 GLU Chi-restraints excluded: chain X residue 299 THR Chi-restraints excluded: chain X residue 313 SER Chi-restraints excluded: chain X residue 413 VAL Chi-restraints excluded: chain X residue 417 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 774 random chunks: chunk 524 optimal weight: 0.8980 chunk 403 optimal weight: 6.9990 chunk 330 optimal weight: 20.0000 chunk 166 optimal weight: 1.9990 chunk 378 optimal weight: 0.9980 chunk 214 optimal weight: 9.9990 chunk 310 optimal weight: 0.8980 chunk 286 optimal weight: 10.0000 chunk 643 optimal weight: 20.0000 chunk 104 optimal weight: 0.5980 chunk 440 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 ASN ** G 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 378 ASN ** G 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 378 ASN ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 ASN ** I 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 378 ASN ** I 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 378 ASN ** K 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 378 ASN ** K 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 248 GLN L 280 ASN ** L 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 ASN M 378 ASN ** N 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 ASN N 378 ASN ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 414 GLN O 446 GLN ** P 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 280 ASN P 378 ASN ** P 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 GLN Q 280 ASN ** R 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 280 ASN S 378 ASN ** T 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 79 GLN T 329 ASN ** T 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 280 ASN U 378 ASN U 407 GLN ** V 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 378 ASN ** V 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 79 GLN ** W 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 329 ASN W 378 ASN W 446 GLN ** X 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.156245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.132495 restraints weight = 106605.392| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 2.89 r_work: 0.4143 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 61506 Z= 0.196 Angle : 0.569 13.249 83826 Z= 0.306 Chirality : 0.038 0.306 9468 Planarity : 0.004 0.074 11394 Dihedral : 5.036 87.653 8590 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.36 % Favored : 96.43 % Rotamer: Outliers : 4.65 % Allowed : 31.68 % Favored : 63.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.09), residues: 7740 helix: 2.64 (0.07), residues: 5544 sheet: None (None), residues: 0 loop : -2.27 (0.11), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP R 233 HIS 0.004 0.001 HIS W 251 PHE 0.027 0.001 PHE Q 37 TYR 0.018 0.001 TYR W 153 ARG 0.008 0.000 ARG V 117 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15480 Ramachandran restraints generated. 7740 Oldfield, 0 Emsley, 7740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15480 Ramachandran restraints generated. 7740 Oldfield, 0 Emsley, 7740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 6066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 281 poor density : 524 time to evaluate : 5.081 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: symmetry clash REVERT: G 75 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7628 (mp) REVERT: G 188 ARG cc_start: 0.6458 (OUTLIER) cc_final: 0.6222 (mpt-90) REVERT: G 233 TRP cc_start: 0.7809 (OUTLIER) cc_final: 0.7368 (m-10) REVERT: H 112 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6488 (tm-30) REVERT: H 195 GLU cc_start: 0.6970 (mm-30) cc_final: 0.6345 (mp0) REVERT: H 380 GLU cc_start: 0.2485 (OUTLIER) cc_final: 0.1942 (mt-10) REVERT: I 195 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6402 (mp0) REVERT: I 280 ASN cc_start: 0.8072 (OUTLIER) cc_final: 0.7668 (t160) REVERT: I 398 LYS cc_start: 0.6743 (OUTLIER) cc_final: 0.6263 (mttm) REVERT: J 34 ASN cc_start: 0.5750 (t0) cc_final: 0.5407 (t0) REVERT: J 37 PHE cc_start: 0.6671 (m-80) cc_final: 0.6129 (t80) REVERT: J 112 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6306 (tm-30) REVERT: J 195 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6402 (mp0) REVERT: J 241 GLN cc_start: 0.9056 (mt0) cc_final: 0.8735 (mm-40) REVERT: J 398 LYS cc_start: 0.6731 (OUTLIER) cc_final: 0.6249 (mttm) REVERT: J 417 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8397 (t0) REVERT: K 34 ASN cc_start: 0.5272 (t0) cc_final: 0.4940 (t0) REVERT: K 37 PHE cc_start: 0.5630 (t80) cc_final: 0.5322 (t80) REVERT: K 112 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6481 (tm-30) REVERT: K 195 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6384 (mp0) REVERT: L 75 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7635 (mp) REVERT: L 195 GLU cc_start: 0.6814 (mm-30) cc_final: 0.6257 (mp0) REVERT: L 233 TRP cc_start: 0.8024 (OUTLIER) cc_final: 0.7547 (m-10) REVERT: M 37 PHE cc_start: 0.4766 (OUTLIER) cc_final: 0.4131 (t80) REVERT: M 85 GLU cc_start: 0.9333 (mp0) cc_final: 0.8996 (mp0) REVERT: M 196 ASP cc_start: 0.7478 (OUTLIER) cc_final: 0.6905 (m-30) REVERT: M 275 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6709 (m-30) REVERT: M 280 ASN cc_start: 0.7575 (OUTLIER) cc_final: 0.7104 (t0) REVERT: M 296 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6931 (pp20) REVERT: M 329 ASN cc_start: 0.6721 (m-40) cc_final: 0.6468 (m-40) REVERT: M 417 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8142 (m-30) REVERT: N 241 GLN cc_start: 0.8741 (mt0) cc_final: 0.8394 (tt0) REVERT: N 313 SER cc_start: 0.7072 (OUTLIER) cc_final: 0.6623 (p) REVERT: N 354 ILE cc_start: 0.6768 (OUTLIER) cc_final: 0.6560 (mp) REVERT: N 363 GLU cc_start: 0.7982 (tp30) cc_final: 0.7179 (pp20) REVERT: N 400 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7542 (tp) REVERT: O 75 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6997 (mp) REVERT: O 188 ARG cc_start: 0.6198 (OUTLIER) cc_final: 0.5747 (mpt-90) REVERT: O 226 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7389 (tt0) REVERT: O 232 GLU cc_start: 0.7638 (pp20) cc_final: 0.6850 (mp0) REVERT: O 363 GLU cc_start: 0.7967 (tp30) cc_final: 0.7169 (pp20) REVERT: O 414 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7956 (mt0) REVERT: O 417 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7681 (m-30) REVERT: P 37 PHE cc_start: 0.4445 (OUTLIER) cc_final: 0.3698 (t80) REVERT: P 85 GLU cc_start: 0.9240 (mp0) cc_final: 0.8962 (mp0) REVERT: P 329 ASN cc_start: 0.6609 (m-40) cc_final: 0.6301 (m-40) REVERT: P 417 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.7968 (m-30) REVERT: Q 280 ASN cc_start: 0.7753 (OUTLIER) cc_final: 0.7409 (t160) REVERT: Q 313 SER cc_start: 0.6967 (OUTLIER) cc_final: 0.6459 (p) REVERT: Q 363 GLU cc_start: 0.7974 (tp30) cc_final: 0.7251 (pp20) REVERT: Q 410 LEU cc_start: 0.8866 (tp) cc_final: 0.8611 (tp) REVERT: Q 415 ASN cc_start: 0.8099 (p0) cc_final: 0.7819 (p0) REVERT: R 37 PHE cc_start: 0.4500 (OUTLIER) cc_final: 0.3886 (t80) REVERT: R 85 GLU cc_start: 0.9279 (mp0) cc_final: 0.8946 (mp0) REVERT: R 232 GLU cc_start: 0.8303 (pp20) cc_final: 0.8032 (pp20) REVERT: R 296 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6882 (pp20) REVERT: S 34 ASN cc_start: 0.4880 (t0) cc_final: 0.4487 (t0) REVERT: S 37 PHE cc_start: 0.4183 (OUTLIER) cc_final: 0.3576 (t80) REVERT: S 85 GLU cc_start: 0.9236 (mp0) cc_final: 0.8959 (mp0) REVERT: S 313 SER cc_start: 0.4624 (OUTLIER) cc_final: 0.4392 (p) REVERT: S 329 ASN cc_start: 0.6508 (m-40) cc_final: 0.6238 (m-40) REVERT: S 417 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.7940 (m-30) REVERT: T 232 GLU cc_start: 0.7590 (pp20) cc_final: 0.6751 (mp0) REVERT: T 363 GLU cc_start: 0.7981 (tp30) cc_final: 0.7186 (pp20) REVERT: U 363 GLU cc_start: 0.7970 (tp30) cc_final: 0.7156 (pp20) REVERT: V 85 GLU cc_start: 0.9356 (mp0) cc_final: 0.9038 (mp0) REVERT: V 193 GLU cc_start: 0.6434 (OUTLIER) cc_final: 0.5914 (tt0) REVERT: V 196 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.6715 (m-30) REVERT: V 232 GLU cc_start: 0.8201 (pp20) cc_final: 0.7114 (mp0) REVERT: V 233 TRP cc_start: 0.7786 (OUTLIER) cc_final: 0.7492 (m-10) REVERT: V 296 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6978 (pp20) REVERT: V 329 ASN cc_start: 0.6819 (m-40) cc_final: 0.6582 (m-40) REVERT: V 417 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8184 (m-30) REVERT: W 363 GLU cc_start: 0.7947 (tp30) cc_final: 0.7222 (pp20) REVERT: W 415 ASN cc_start: 0.8162 (p0) cc_final: 0.7945 (p0) REVERT: X 37 PHE cc_start: 0.4424 (OUTLIER) cc_final: 0.3792 (t80) REVERT: X 85 GLU cc_start: 0.9288 (mp0) cc_final: 0.8961 (mp0) REVERT: X 196 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7273 (m-30) REVERT: X 296 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6852 (pp20) REVERT: X 329 ASN cc_start: 0.6637 (m-40) cc_final: 0.6362 (m110) REVERT: X 417 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.8105 (m-30) outliers start: 281 outliers final: 150 residues processed: 739 average time/residue: 1.1067 time to fit residues: 1107.0927 Evaluate side-chains 680 residues out of total 6066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 485 time to evaluate : 4.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 45 ASP Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 188 ARG Chi-restraints excluded: chain G residue 196 ASP Chi-restraints excluded: chain G residue 233 TRP Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 296 GLU Chi-restraints excluded: chain G residue 313 SER Chi-restraints excluded: chain G residue 404 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 45 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 112 GLU Chi-restraints excluded: chain H residue 196 ASP Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 313 SER Chi-restraints excluded: chain H residue 380 GLU Chi-restraints excluded: chain H residue 404 GLU Chi-restraints excluded: chain H residue 443 ARG Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 188 ARG Chi-restraints excluded: chain I residue 196 ASP Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 398 LYS Chi-restraints excluded: chain I residue 404 GLU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 135 SER Chi-restraints excluded: chain J residue 188 ARG Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 286 SER Chi-restraints excluded: chain J residue 398 LYS Chi-restraints excluded: chain J residue 404 GLU Chi-restraints excluded: chain J residue 417 ASP Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 112 GLU Chi-restraints excluded: chain K residue 196 ASP Chi-restraints excluded: chain K residue 239 ILE Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 404 GLU Chi-restraints excluded: chain K residue 443 ARG Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 233 TRP Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 286 SER Chi-restraints excluded: chain L residue 296 GLU Chi-restraints excluded: chain L residue 313 SER Chi-restraints excluded: chain L residue 378 ASN Chi-restraints excluded: chain L residue 404 GLU Chi-restraints excluded: chain L residue 443 ARG Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 37 PHE Chi-restraints excluded: chain M residue 88 GLU Chi-restraints excluded: chain M residue 151 GLU Chi-restraints excluded: chain M residue 167 ASP Chi-restraints excluded: chain M residue 196 ASP Chi-restraints excluded: chain M residue 239 ILE Chi-restraints excluded: chain M residue 275 ASP Chi-restraints excluded: chain M residue 280 ASN Chi-restraints excluded: chain M residue 296 GLU Chi-restraints excluded: chain M residue 299 THR Chi-restraints excluded: chain M residue 313 SER Chi-restraints excluded: chain M residue 393 ILE Chi-restraints excluded: chain M residue 413 VAL Chi-restraints excluded: chain M residue 417 ASP Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 307 VAL Chi-restraints excluded: chain N residue 313 SER Chi-restraints excluded: chain N residue 329 ASN Chi-restraints excluded: chain N residue 354 ILE Chi-restraints excluded: chain N residue 355 SER Chi-restraints excluded: chain N residue 400 LEU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 188 ARG Chi-restraints excluded: chain O residue 196 ASP Chi-restraints excluded: chain O residue 202 THR Chi-restraints excluded: chain O residue 226 GLU Chi-restraints excluded: chain O residue 239 ILE Chi-restraints excluded: chain O residue 313 SER Chi-restraints excluded: chain O residue 329 ASN Chi-restraints excluded: chain O residue 413 VAL Chi-restraints excluded: chain O residue 414 GLN Chi-restraints excluded: chain O residue 417 ASP Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 37 PHE Chi-restraints excluded: chain P residue 135 SER Chi-restraints excluded: chain P residue 157 LEU Chi-restraints excluded: chain P residue 167 ASP Chi-restraints excluded: chain P residue 232 GLU Chi-restraints excluded: chain P residue 239 ILE Chi-restraints excluded: chain P residue 280 ASN Chi-restraints excluded: chain P residue 299 THR Chi-restraints excluded: chain P residue 321 LEU Chi-restraints excluded: chain P residue 413 VAL Chi-restraints excluded: chain P residue 417 ASP Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 202 THR Chi-restraints excluded: chain Q residue 239 ILE Chi-restraints excluded: chain Q residue 243 ASP Chi-restraints excluded: chain Q residue 280 ASN Chi-restraints excluded: chain Q residue 313 SER Chi-restraints excluded: chain Q residue 329 ASN Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain R residue 37 PHE Chi-restraints excluded: chain R residue 60 THR Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 88 GLU Chi-restraints excluded: chain R residue 167 ASP Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 296 GLU Chi-restraints excluded: chain R residue 299 THR Chi-restraints excluded: chain R residue 413 VAL Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 37 PHE Chi-restraints excluded: chain S residue 135 SER Chi-restraints excluded: chain S residue 157 LEU Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 232 GLU Chi-restraints excluded: chain S residue 239 ILE Chi-restraints excluded: chain S residue 280 ASN Chi-restraints excluded: chain S residue 299 THR Chi-restraints excluded: chain S residue 313 SER Chi-restraints excluded: chain S residue 321 LEU Chi-restraints excluded: chain S residue 413 VAL Chi-restraints excluded: chain S residue 417 ASP Chi-restraints excluded: chain T residue 33 THR Chi-restraints excluded: chain T residue 51 ILE Chi-restraints excluded: chain T residue 196 ASP Chi-restraints excluded: chain T residue 202 THR Chi-restraints excluded: chain T residue 239 ILE Chi-restraints excluded: chain T residue 313 SER Chi-restraints excluded: chain T residue 355 SER Chi-restraints excluded: chain T residue 413 VAL Chi-restraints excluded: chain U residue 33 THR Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 75 LEU Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 234 LEU Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 400 LEU Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 151 GLU Chi-restraints excluded: chain V residue 167 ASP Chi-restraints excluded: chain V residue 193 GLU Chi-restraints excluded: chain V residue 196 ASP Chi-restraints excluded: chain V residue 233 TRP Chi-restraints excluded: chain V residue 239 ILE Chi-restraints excluded: chain V residue 296 GLU Chi-restraints excluded: chain V residue 299 THR Chi-restraints excluded: chain V residue 313 SER Chi-restraints excluded: chain V residue 413 VAL Chi-restraints excluded: chain V residue 417 ASP Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain W residue 223 LEU Chi-restraints excluded: chain W residue 239 ILE Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 37 PHE Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 167 ASP Chi-restraints excluded: chain X residue 196 ASP Chi-restraints excluded: chain X residue 239 ILE Chi-restraints excluded: chain X residue 296 GLU Chi-restraints excluded: chain X residue 299 THR Chi-restraints excluded: chain X residue 340 SER Chi-restraints excluded: chain X residue 413 VAL Chi-restraints excluded: chain X residue 417 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 774 random chunks: chunk 773 optimal weight: 10.0000 chunk 578 optimal weight: 1.9990 chunk 255 optimal weight: 7.9990 chunk 464 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 391 optimal weight: 2.9990 chunk 230 optimal weight: 0.0980 chunk 423 optimal weight: 5.9990 chunk 208 optimal weight: 0.6980 chunk 283 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 378 ASN ** G 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 378 ASN ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 378 ASN ** I 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 378 ASN ** K 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 378 ASN ** K 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 241 GLN L 329 ASN L 378 ASN ** L 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 378 ASN ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 GLN O 280 ASN ** O 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 280 ASN P 378 ASN ** P 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 GLN Q 280 ASN ** R 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 280 ASN ** R 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 280 ASN S 378 ASN ** T 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 79 GLN ** T 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 414 GLN T 446 GLN ** U 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 378 ASN ** V 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 378 ASN ** V 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 79 GLN ** W 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 280 ASN W 329 ASN W 378 ASN ** X 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 280 ASN ** X 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.157967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.134232 restraints weight = 109664.007| |-----------------------------------------------------------------------------| r_work (start): 0.4321 rms_B_bonded: 3.04 r_work: 0.4179 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 61506 Z= 0.182 Angle : 0.560 11.610 83826 Z= 0.300 Chirality : 0.038 0.323 9468 Planarity : 0.004 0.075 11394 Dihedral : 4.744 50.072 8585 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.46 % Favored : 96.34 % Rotamer: Outliers : 4.20 % Allowed : 32.36 % Favored : 63.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.09), residues: 7740 helix: 2.85 (0.07), residues: 5544 sheet: None (None), residues: 0 loop : -2.16 (0.11), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP I 233 HIS 0.004 0.001 HIS W 251 PHE 0.027 0.001 PHE N 37 TYR 0.018 0.001 TYR V 384 ARG 0.012 0.000 ARG Q 188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15480 Ramachandran restraints generated. 7740 Oldfield, 0 Emsley, 7740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15480 Ramachandran restraints generated. 7740 Oldfield, 0 Emsley, 7740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 6066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 254 poor density : 545 time to evaluate : 4.973 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 195 GLU cc_start: 0.6787 (mm-30) cc_final: 0.6470 (mp0) REVERT: G 233 TRP cc_start: 0.7658 (OUTLIER) cc_final: 0.7377 (m-10) REVERT: H 112 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6542 (tm-30) REVERT: H 195 GLU cc_start: 0.6861 (mm-30) cc_final: 0.6373 (mp0) REVERT: I 195 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6515 (mp0) REVERT: I 398 LYS cc_start: 0.6641 (OUTLIER) cc_final: 0.6174 (mttm) REVERT: J 37 PHE cc_start: 0.6551 (m-80) cc_final: 0.6031 (t80) REVERT: J 112 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6253 (tm-30) REVERT: J 195 GLU cc_start: 0.6939 (mm-30) cc_final: 0.6486 (mp0) REVERT: J 241 GLN cc_start: 0.9057 (mt0) cc_final: 0.8826 (mt0) REVERT: J 398 LYS cc_start: 0.6633 (OUTLIER) cc_final: 0.6164 (mttm) REVERT: J 417 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8250 (t0) REVERT: K 37 PHE cc_start: 0.5570 (t80) cc_final: 0.5301 (t80) REVERT: K 112 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6504 (tm-30) REVERT: K 195 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6396 (mp0) REVERT: L 195 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6220 (mp0) REVERT: L 233 TRP cc_start: 0.7922 (OUTLIER) cc_final: 0.7497 (m-10) REVERT: M 37 PHE cc_start: 0.4631 (m-10) cc_final: 0.3983 (t80) REVERT: M 85 GLU cc_start: 0.9314 (mp0) cc_final: 0.8993 (mp0) REVERT: M 196 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.6837 (m-30) REVERT: M 296 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6915 (pp20) REVERT: M 329 ASN cc_start: 0.6775 (m-40) cc_final: 0.6489 (m-40) REVERT: M 417 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8150 (m-30) REVERT: N 196 ASP cc_start: 0.6567 (OUTLIER) cc_final: 0.5926 (m-30) REVERT: N 232 GLU cc_start: 0.7882 (pp20) cc_final: 0.6860 (mp0) REVERT: N 233 TRP cc_start: 0.7567 (m-10) cc_final: 0.7175 (m-10) REVERT: N 241 GLN cc_start: 0.8770 (mt0) cc_final: 0.8412 (tt0) REVERT: N 280 ASN cc_start: 0.7590 (OUTLIER) cc_final: 0.7189 (t0) REVERT: N 313 SER cc_start: 0.7066 (OUTLIER) cc_final: 0.6634 (p) REVERT: N 354 ILE cc_start: 0.6824 (OUTLIER) cc_final: 0.6615 (mp) REVERT: N 363 GLU cc_start: 0.7973 (tp30) cc_final: 0.7188 (pp20) REVERT: N 400 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7535 (tp) REVERT: O 75 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7057 (mp) REVERT: O 280 ASN cc_start: 0.7684 (OUTLIER) cc_final: 0.7357 (t0) REVERT: O 363 GLU cc_start: 0.7959 (tp30) cc_final: 0.7160 (pp20) REVERT: O 417 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7678 (m-30) REVERT: P 37 PHE cc_start: 0.4155 (OUTLIER) cc_final: 0.3486 (t80) REVERT: P 85 GLU cc_start: 0.9213 (mp0) cc_final: 0.8957 (mp0) REVERT: P 196 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.6972 (m-30) REVERT: P 280 ASN cc_start: 0.7054 (OUTLIER) cc_final: 0.6829 (m110) REVERT: P 329 ASN cc_start: 0.6589 (m-40) cc_final: 0.6269 (m-40) REVERT: P 417 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.7961 (m-30) REVERT: Q 313 SER cc_start: 0.6949 (OUTLIER) cc_final: 0.6444 (p) REVERT: Q 363 GLU cc_start: 0.7937 (tp30) cc_final: 0.7185 (pp20) REVERT: Q 410 LEU cc_start: 0.8840 (tp) cc_final: 0.8584 (tp) REVERT: Q 415 ASN cc_start: 0.8050 (p0) cc_final: 0.7773 (p0) REVERT: R 85 GLU cc_start: 0.9269 (mp0) cc_final: 0.8957 (mp0) REVERT: R 296 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6856 (pp20) REVERT: S 37 PHE cc_start: 0.4178 (OUTLIER) cc_final: 0.3610 (t80) REVERT: S 85 GLU cc_start: 0.9231 (mp0) cc_final: 0.8971 (mp0) REVERT: S 196 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.6971 (m-30) REVERT: S 329 ASN cc_start: 0.6626 (m-40) cc_final: 0.6304 (m-40) REVERT: S 417 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8117 (t0) REVERT: T 75 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7024 (mp) REVERT: T 363 GLU cc_start: 0.7956 (tp30) cc_final: 0.7154 (pp20) REVERT: T 414 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7905 (mt0) REVERT: U 37 PHE cc_start: 0.5793 (t80) cc_final: 0.5576 (t80) REVERT: U 280 ASN cc_start: 0.7633 (OUTLIER) cc_final: 0.7302 (t0) REVERT: U 363 GLU cc_start: 0.7989 (tp30) cc_final: 0.7176 (pp20) REVERT: U 400 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7551 (tp) REVERT: V 85 GLU cc_start: 0.9361 (mp0) cc_final: 0.9036 (mp0) REVERT: V 193 GLU cc_start: 0.6135 (OUTLIER) cc_final: 0.5872 (tt0) REVERT: V 196 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.6648 (m-30) REVERT: V 232 GLU cc_start: 0.8232 (pp20) cc_final: 0.7992 (pp20) REVERT: V 296 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.7013 (pp20) REVERT: V 329 ASN cc_start: 0.6796 (m-40) cc_final: 0.6536 (m-40) REVERT: V 417 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8178 (m-30) REVERT: W 232 GLU cc_start: 0.7829 (pp20) cc_final: 0.6619 (mp0) REVERT: W 280 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.7176 (t160) REVERT: W 363 GLU cc_start: 0.7906 (tp30) cc_final: 0.7136 (pp20) REVERT: W 415 ASN cc_start: 0.8062 (p0) cc_final: 0.7797 (p0) REVERT: X 37 PHE cc_start: 0.4169 (OUTLIER) cc_final: 0.3557 (t80) REVERT: X 85 GLU cc_start: 0.9280 (mp0) cc_final: 0.8950 (mp0) REVERT: X 232 GLU cc_start: 0.8301 (pp20) cc_final: 0.7013 (mp0) REVERT: X 233 TRP cc_start: 0.7604 (OUTLIER) cc_final: 0.7367 (m-10) REVERT: X 296 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6826 (pp20) REVERT: X 313 SER cc_start: 0.4690 (OUTLIER) cc_final: 0.4364 (p) REVERT: X 329 ASN cc_start: 0.6726 (m-40) cc_final: 0.6411 (m-40) REVERT: X 417 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.8099 (m-30) outliers start: 254 outliers final: 147 residues processed: 733 average time/residue: 1.1091 time to fit residues: 1107.3301 Evaluate side-chains 671 residues out of total 6066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 482 time to evaluate : 4.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 45 ASP Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 233 TRP Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 286 SER Chi-restraints excluded: chain G residue 296 GLU Chi-restraints excluded: chain G residue 404 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 45 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 112 GLU Chi-restraints excluded: chain H residue 196 ASP Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 243 ASP Chi-restraints excluded: chain H residue 286 SER Chi-restraints excluded: chain H residue 313 SER Chi-restraints excluded: chain H residue 404 GLU Chi-restraints excluded: chain H residue 443 ARG Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 188 ARG Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 398 LYS Chi-restraints excluded: chain I residue 404 GLU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 135 SER Chi-restraints excluded: chain J residue 188 ARG Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 286 SER Chi-restraints excluded: chain J residue 398 LYS Chi-restraints excluded: chain J residue 404 GLU Chi-restraints excluded: chain J residue 417 ASP Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 112 GLU Chi-restraints excluded: chain K residue 239 ILE Chi-restraints excluded: chain K residue 286 SER Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 404 GLU Chi-restraints excluded: chain K residue 443 ARG Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 233 TRP Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 296 GLU Chi-restraints excluded: chain L residue 313 SER Chi-restraints excluded: chain L residue 404 GLU Chi-restraints excluded: chain L residue 443 ARG Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 88 GLU Chi-restraints excluded: chain M residue 135 SER Chi-restraints excluded: chain M residue 151 GLU Chi-restraints excluded: chain M residue 167 ASP Chi-restraints excluded: chain M residue 196 ASP Chi-restraints excluded: chain M residue 296 GLU Chi-restraints excluded: chain M residue 299 THR Chi-restraints excluded: chain M residue 313 SER Chi-restraints excluded: chain M residue 413 VAL Chi-restraints excluded: chain M residue 417 ASP Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 196 ASP Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 280 ASN Chi-restraints excluded: chain N residue 313 SER Chi-restraints excluded: chain N residue 329 ASN Chi-restraints excluded: chain N residue 354 ILE Chi-restraints excluded: chain N residue 355 SER Chi-restraints excluded: chain N residue 400 LEU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 196 ASP Chi-restraints excluded: chain O residue 202 THR Chi-restraints excluded: chain O residue 239 ILE Chi-restraints excluded: chain O residue 243 ASP Chi-restraints excluded: chain O residue 280 ASN Chi-restraints excluded: chain O residue 329 ASN Chi-restraints excluded: chain O residue 417 ASP Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 37 PHE Chi-restraints excluded: chain P residue 135 SER Chi-restraints excluded: chain P residue 157 LEU Chi-restraints excluded: chain P residue 167 ASP Chi-restraints excluded: chain P residue 196 ASP Chi-restraints excluded: chain P residue 232 GLU Chi-restraints excluded: chain P residue 239 ILE Chi-restraints excluded: chain P residue 280 ASN Chi-restraints excluded: chain P residue 321 LEU Chi-restraints excluded: chain P residue 413 VAL Chi-restraints excluded: chain P residue 417 ASP Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 202 THR Chi-restraints excluded: chain Q residue 239 ILE Chi-restraints excluded: chain Q residue 243 ASP Chi-restraints excluded: chain Q residue 307 VAL Chi-restraints excluded: chain Q residue 313 SER Chi-restraints excluded: chain Q residue 329 ASN Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain R residue 60 THR Chi-restraints excluded: chain R residue 88 GLU Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 151 GLU Chi-restraints excluded: chain R residue 167 ASP Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 280 ASN Chi-restraints excluded: chain R residue 296 GLU Chi-restraints excluded: chain R residue 299 THR Chi-restraints excluded: chain R residue 413 VAL Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 37 PHE Chi-restraints excluded: chain S residue 135 SER Chi-restraints excluded: chain S residue 157 LEU Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 196 ASP Chi-restraints excluded: chain S residue 232 GLU Chi-restraints excluded: chain S residue 239 ILE Chi-restraints excluded: chain S residue 275 ASP Chi-restraints excluded: chain S residue 299 THR Chi-restraints excluded: chain S residue 321 LEU Chi-restraints excluded: chain S residue 413 VAL Chi-restraints excluded: chain S residue 417 ASP Chi-restraints excluded: chain T residue 33 THR Chi-restraints excluded: chain T residue 75 LEU Chi-restraints excluded: chain T residue 83 VAL Chi-restraints excluded: chain T residue 196 ASP Chi-restraints excluded: chain T residue 202 THR Chi-restraints excluded: chain T residue 239 ILE Chi-restraints excluded: chain T residue 243 ASP Chi-restraints excluded: chain T residue 355 SER Chi-restraints excluded: chain T residue 413 VAL Chi-restraints excluded: chain T residue 414 GLN Chi-restraints excluded: chain U residue 33 THR Chi-restraints excluded: chain U residue 75 LEU Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 234 LEU Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 280 ASN Chi-restraints excluded: chain U residue 400 LEU Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 151 GLU Chi-restraints excluded: chain V residue 167 ASP Chi-restraints excluded: chain V residue 193 GLU Chi-restraints excluded: chain V residue 196 ASP Chi-restraints excluded: chain V residue 296 GLU Chi-restraints excluded: chain V residue 299 THR Chi-restraints excluded: chain V residue 413 VAL Chi-restraints excluded: chain V residue 417 ASP Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 223 LEU Chi-restraints excluded: chain W residue 239 ILE Chi-restraints excluded: chain W residue 280 ASN Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 37 PHE Chi-restraints excluded: chain X residue 60 THR Chi-restraints excluded: chain X residue 135 SER Chi-restraints excluded: chain X residue 151 GLU Chi-restraints excluded: chain X residue 167 ASP Chi-restraints excluded: chain X residue 233 TRP Chi-restraints excluded: chain X residue 239 ILE Chi-restraints excluded: chain X residue 280 ASN Chi-restraints excluded: chain X residue 296 GLU Chi-restraints excluded: chain X residue 299 THR Chi-restraints excluded: chain X residue 313 SER Chi-restraints excluded: chain X residue 340 SER Chi-restraints excluded: chain X residue 413 VAL Chi-restraints excluded: chain X residue 417 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 774 random chunks: chunk 432 optimal weight: 7.9990 chunk 648 optimal weight: 10.0000 chunk 705 optimal weight: 0.7980 chunk 451 optimal weight: 6.9990 chunk 503 optimal weight: 9.9990 chunk 605 optimal weight: 9.9990 chunk 335 optimal weight: 0.0370 chunk 146 optimal weight: 4.9990 chunk 138 optimal weight: 0.8980 chunk 709 optimal weight: 0.9990 chunk 349 optimal weight: 0.7980 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 378 ASN ** G 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 ASN ** H 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 378 ASN ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 378 ASN ** I 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 329 ASN J 378 ASN ** K 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 378 ASN ** K 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 378 ASN ** L 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 GLN O 280 ASN ** O 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 280 ASN P 378 ASN ** P 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 GLN Q 337 GLN ** R 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 280 ASN ** R 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 79 GLN ** T 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 329 ASN ** T 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 337 GLN ** V 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 79 GLN ** W 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 378 ASN ** W 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 280 ASN X 345 ASN ** X 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.158585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.135413 restraints weight = 105571.809| |-----------------------------------------------------------------------------| r_work (start): 0.4344 rms_B_bonded: 2.86 r_work: 0.4195 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 61506 Z= 0.184 Angle : 0.572 12.453 83826 Z= 0.305 Chirality : 0.038 0.330 9468 Planarity : 0.004 0.088 11394 Dihedral : 4.519 50.934 8572 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.31 % Favored : 96.50 % Rotamer: Outliers : 3.97 % Allowed : 33.00 % Favored : 63.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.09), residues: 7740 helix: 2.94 (0.07), residues: 5544 sheet: None (None), residues: 0 loop : -2.10 (0.12), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP U 233 HIS 0.003 0.001 HIS W 251 PHE 0.026 0.001 PHE N 37 TYR 0.016 0.001 TYR V 384 ARG 0.011 0.000 ARG Q 188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15480 Ramachandran restraints generated. 7740 Oldfield, 0 Emsley, 7740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15480 Ramachandran restraints generated. 7740 Oldfield, 0 Emsley, 7740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 6066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 240 poor density : 509 time to evaluate : 4.924 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: G 37 PHE cc_start: 0.6091 (m-80) cc_final: 0.5841 (t80) REVERT: G 188 ARG cc_start: 0.6426 (OUTLIER) cc_final: 0.6024 (mmt180) REVERT: G 195 GLU cc_start: 0.6770 (mm-30) cc_final: 0.6475 (mp0) REVERT: G 233 TRP cc_start: 0.7613 (OUTLIER) cc_final: 0.7377 (m-10) REVERT: H 112 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6568 (tm-30) REVERT: H 195 GLU cc_start: 0.6894 (mm-30) cc_final: 0.6407 (mp0) REVERT: I 195 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6522 (mp0) REVERT: I 398 LYS cc_start: 0.6614 (OUTLIER) cc_final: 0.6127 (mttm) REVERT: J 37 PHE cc_start: 0.6500 (m-80) cc_final: 0.5918 (t80) REVERT: J 112 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6181 (tm-30) REVERT: J 195 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6497 (mp0) REVERT: J 398 LYS cc_start: 0.6579 (OUTLIER) cc_final: 0.6095 (mttm) REVERT: J 417 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8190 (t0) REVERT: K 37 PHE cc_start: 0.5520 (t80) cc_final: 0.5246 (t80) REVERT: K 112 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6542 (tm-30) REVERT: K 195 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6403 (mp0) REVERT: L 195 GLU cc_start: 0.6774 (mm-30) cc_final: 0.6317 (mp0) REVERT: L 233 TRP cc_start: 0.7891 (OUTLIER) cc_final: 0.7503 (m-10) REVERT: M 37 PHE cc_start: 0.4551 (OUTLIER) cc_final: 0.3867 (t80) REVERT: M 85 GLU cc_start: 0.9351 (mp0) cc_final: 0.9007 (mp0) REVERT: M 196 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.6828 (m-30) REVERT: M 232 GLU cc_start: 0.8192 (pp20) cc_final: 0.6935 (mp0) REVERT: M 233 TRP cc_start: 0.7596 (m-10) cc_final: 0.7305 (m-10) REVERT: M 296 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6918 (pp20) REVERT: M 329 ASN cc_start: 0.6837 (m-40) cc_final: 0.6497 (m-40) REVERT: M 417 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8099 (m-30) REVERT: N 196 ASP cc_start: 0.6573 (OUTLIER) cc_final: 0.5899 (m-30) REVERT: N 232 GLU cc_start: 0.7874 (pp20) cc_final: 0.6729 (mp0) REVERT: N 233 TRP cc_start: 0.7529 (OUTLIER) cc_final: 0.7252 (m-10) REVERT: N 241 GLN cc_start: 0.8753 (mt0) cc_final: 0.8394 (tt0) REVERT: N 280 ASN cc_start: 0.7523 (OUTLIER) cc_final: 0.7178 (t0) REVERT: N 313 SER cc_start: 0.7012 (OUTLIER) cc_final: 0.6564 (p) REVERT: N 354 ILE cc_start: 0.6771 (OUTLIER) cc_final: 0.6565 (mp) REVERT: N 363 GLU cc_start: 0.7972 (tp30) cc_final: 0.7191 (pp20) REVERT: N 400 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7519 (tp) REVERT: O 75 LEU cc_start: 0.7292 (OUTLIER) cc_final: 0.6947 (mp) REVERT: O 280 ASN cc_start: 0.7597 (OUTLIER) cc_final: 0.7352 (t0) REVERT: O 363 GLU cc_start: 0.7875 (tp30) cc_final: 0.7076 (pp20) REVERT: O 417 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7638 (m-30) REVERT: P 85 GLU cc_start: 0.9229 (mp0) cc_final: 0.8959 (mp0) REVERT: P 196 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.6912 (m-30) REVERT: P 209 GLU cc_start: 0.7579 (mp0) cc_final: 0.7025 (mp0) REVERT: P 232 GLU cc_start: 0.8099 (pp20) cc_final: 0.7135 (mp0) REVERT: P 280 ASN cc_start: 0.7048 (OUTLIER) cc_final: 0.6839 (m110) REVERT: P 329 ASN cc_start: 0.6533 (m-40) cc_final: 0.6192 (m-40) REVERT: P 417 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.7937 (m-30) REVERT: Q 232 GLU cc_start: 0.7804 (pp20) cc_final: 0.6709 (mp0) REVERT: Q 280 ASN cc_start: 0.6891 (OUTLIER) cc_final: 0.6542 (t0) REVERT: Q 313 SER cc_start: 0.6914 (OUTLIER) cc_final: 0.6396 (p) REVERT: Q 337 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.7399 (mp10) REVERT: Q 363 GLU cc_start: 0.7900 (tp30) cc_final: 0.7159 (pp20) REVERT: Q 410 LEU cc_start: 0.8835 (tp) cc_final: 0.8588 (tp) REVERT: Q 415 ASN cc_start: 0.8053 (p0) cc_final: 0.7755 (p0) REVERT: R 85 GLU cc_start: 0.9304 (mp0) cc_final: 0.8959 (mp0) REVERT: R 232 GLU cc_start: 0.8177 (pp20) cc_final: 0.7105 (mp0) REVERT: R 233 TRP cc_start: 0.7478 (m-10) cc_final: 0.7272 (m-10) REVERT: R 296 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6855 (pp20) REVERT: R 313 SER cc_start: 0.4650 (OUTLIER) cc_final: 0.4320 (p) REVERT: S 37 PHE cc_start: 0.4000 (OUTLIER) cc_final: 0.3399 (t80) REVERT: S 85 GLU cc_start: 0.9251 (mp0) cc_final: 0.8974 (mp0) REVERT: S 196 ASP cc_start: 0.7605 (OUTLIER) cc_final: 0.6932 (m-30) REVERT: S 209 GLU cc_start: 0.7573 (mp0) cc_final: 0.7012 (mp0) REVERT: S 232 GLU cc_start: 0.8235 (pp20) cc_final: 0.7133 (mp0) REVERT: S 329 ASN cc_start: 0.6474 (m-40) cc_final: 0.6144 (m-40) REVERT: S 417 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8153 (t0) REVERT: T 75 LEU cc_start: 0.7306 (mp) cc_final: 0.6957 (mp) REVERT: T 363 GLU cc_start: 0.7931 (tp30) cc_final: 0.7122 (pp20) REVERT: U 37 PHE cc_start: 0.5714 (t80) cc_final: 0.5487 (t80) REVERT: U 232 GLU cc_start: 0.7904 (pp20) cc_final: 0.6777 (mp0) REVERT: U 233 TRP cc_start: 0.7563 (m-10) cc_final: 0.7212 (m-10) REVERT: U 280 ASN cc_start: 0.7531 (OUTLIER) cc_final: 0.7222 (t0) REVERT: U 337 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.7434 (mt0) REVERT: U 363 GLU cc_start: 0.7955 (tp30) cc_final: 0.7163 (pp20) REVERT: U 400 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7547 (tp) REVERT: V 85 GLU cc_start: 0.9370 (mp0) cc_final: 0.9046 (mp0) REVERT: V 88 GLU cc_start: 0.9358 (pt0) cc_final: 0.9120 (mm-30) REVERT: V 193 GLU cc_start: 0.6034 (OUTLIER) cc_final: 0.5717 (tt0) REVERT: V 196 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.6835 (m-30) REVERT: V 232 GLU cc_start: 0.8181 (pp20) cc_final: 0.7031 (mp0) REVERT: V 296 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6997 (pp20) REVERT: V 313 SER cc_start: 0.4637 (OUTLIER) cc_final: 0.4298 (p) REVERT: V 321 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7921 (mp) REVERT: V 329 ASN cc_start: 0.6819 (m-40) cc_final: 0.6529 (m-40) REVERT: V 417 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.8149 (m-30) REVERT: W 232 GLU cc_start: 0.7841 (pp20) cc_final: 0.6740 (mp0) REVERT: W 363 GLU cc_start: 0.7937 (tp30) cc_final: 0.7147 (pp20) REVERT: W 415 ASN cc_start: 0.8070 (p0) cc_final: 0.7797 (p0) REVERT: X 37 PHE cc_start: 0.4027 (OUTLIER) cc_final: 0.3418 (t80) REVERT: X 85 GLU cc_start: 0.9309 (mp0) cc_final: 0.8981 (mp0) REVERT: X 232 GLU cc_start: 0.8284 (pp20) cc_final: 0.6698 (mp0) REVERT: X 233 TRP cc_start: 0.7542 (m-10) cc_final: 0.7313 (m-10) REVERT: X 296 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6831 (pp20) REVERT: X 313 SER cc_start: 0.4583 (OUTLIER) cc_final: 0.4268 (p) REVERT: X 329 ASN cc_start: 0.6635 (m-40) cc_final: 0.6313 (m-40) REVERT: X 417 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.8089 (m-30) outliers start: 240 outliers final: 145 residues processed: 694 average time/residue: 1.1600 time to fit residues: 1091.0006 Evaluate side-chains 671 residues out of total 6066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 480 time to evaluate : 4.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 45 ASP Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 188 ARG Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 233 TRP Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 286 SER Chi-restraints excluded: chain G residue 404 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 45 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 112 GLU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 243 ASP Chi-restraints excluded: chain H residue 286 SER Chi-restraints excluded: chain H residue 313 SER Chi-restraints excluded: chain H residue 404 GLU Chi-restraints excluded: chain H residue 443 ARG Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 286 SER Chi-restraints excluded: chain I residue 398 LYS Chi-restraints excluded: chain I residue 404 GLU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 135 SER Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 286 SER Chi-restraints excluded: chain J residue 398 LYS Chi-restraints excluded: chain J residue 404 GLU Chi-restraints excluded: chain J residue 417 ASP Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 112 GLU Chi-restraints excluded: chain K residue 196 ASP Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 239 ILE Chi-restraints excluded: chain K residue 286 SER Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 404 GLU Chi-restraints excluded: chain K residue 443 ARG Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 196 ASP Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 233 TRP Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 286 SER Chi-restraints excluded: chain L residue 313 SER Chi-restraints excluded: chain L residue 404 GLU Chi-restraints excluded: chain L residue 443 ARG Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 37 PHE Chi-restraints excluded: chain M residue 88 GLU Chi-restraints excluded: chain M residue 135 SER Chi-restraints excluded: chain M residue 151 GLU Chi-restraints excluded: chain M residue 167 ASP Chi-restraints excluded: chain M residue 196 ASP Chi-restraints excluded: chain M residue 239 ILE Chi-restraints excluded: chain M residue 296 GLU Chi-restraints excluded: chain M residue 299 THR Chi-restraints excluded: chain M residue 313 SER Chi-restraints excluded: chain M residue 413 VAL Chi-restraints excluded: chain M residue 417 ASP Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 196 ASP Chi-restraints excluded: chain N residue 233 TRP Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 280 ASN Chi-restraints excluded: chain N residue 313 SER Chi-restraints excluded: chain N residue 329 ASN Chi-restraints excluded: chain N residue 354 ILE Chi-restraints excluded: chain N residue 355 SER Chi-restraints excluded: chain N residue 400 LEU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 196 ASP Chi-restraints excluded: chain O residue 202 THR Chi-restraints excluded: chain O residue 239 ILE Chi-restraints excluded: chain O residue 243 ASP Chi-restraints excluded: chain O residue 280 ASN Chi-restraints excluded: chain O residue 329 ASN Chi-restraints excluded: chain O residue 417 ASP Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 135 SER Chi-restraints excluded: chain P residue 157 LEU Chi-restraints excluded: chain P residue 167 ASP Chi-restraints excluded: chain P residue 196 ASP Chi-restraints excluded: chain P residue 233 TRP Chi-restraints excluded: chain P residue 239 ILE Chi-restraints excluded: chain P residue 280 ASN Chi-restraints excluded: chain P residue 321 LEU Chi-restraints excluded: chain P residue 413 VAL Chi-restraints excluded: chain P residue 417 ASP Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 202 THR Chi-restraints excluded: chain Q residue 239 ILE Chi-restraints excluded: chain Q residue 243 ASP Chi-restraints excluded: chain Q residue 280 ASN Chi-restraints excluded: chain Q residue 307 VAL Chi-restraints excluded: chain Q residue 313 SER Chi-restraints excluded: chain Q residue 329 ASN Chi-restraints excluded: chain Q residue 337 GLN Chi-restraints excluded: chain R residue 60 THR Chi-restraints excluded: chain R residue 88 GLU Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 167 ASP Chi-restraints excluded: chain R residue 209 GLU Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 280 ASN Chi-restraints excluded: chain R residue 296 GLU Chi-restraints excluded: chain R residue 299 THR Chi-restraints excluded: chain R residue 313 SER Chi-restraints excluded: chain R residue 413 VAL Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 37 PHE Chi-restraints excluded: chain S residue 135 SER Chi-restraints excluded: chain S residue 157 LEU Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 196 ASP Chi-restraints excluded: chain S residue 233 TRP Chi-restraints excluded: chain S residue 239 ILE Chi-restraints excluded: chain S residue 413 VAL Chi-restraints excluded: chain S residue 417 ASP Chi-restraints excluded: chain T residue 33 THR Chi-restraints excluded: chain T residue 83 VAL Chi-restraints excluded: chain T residue 196 ASP Chi-restraints excluded: chain T residue 202 THR Chi-restraints excluded: chain T residue 239 ILE Chi-restraints excluded: chain T residue 243 ASP Chi-restraints excluded: chain T residue 355 SER Chi-restraints excluded: chain T residue 413 VAL Chi-restraints excluded: chain U residue 33 THR Chi-restraints excluded: chain U residue 75 LEU Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 234 LEU Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 243 ASP Chi-restraints excluded: chain U residue 280 ASN Chi-restraints excluded: chain U residue 337 GLN Chi-restraints excluded: chain U residue 400 LEU Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 135 SER Chi-restraints excluded: chain V residue 151 GLU Chi-restraints excluded: chain V residue 167 ASP Chi-restraints excluded: chain V residue 193 GLU Chi-restraints excluded: chain V residue 196 ASP Chi-restraints excluded: chain V residue 239 ILE Chi-restraints excluded: chain V residue 296 GLU Chi-restraints excluded: chain V residue 299 THR Chi-restraints excluded: chain V residue 313 SER Chi-restraints excluded: chain V residue 321 LEU Chi-restraints excluded: chain V residue 413 VAL Chi-restraints excluded: chain V residue 417 ASP Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 223 LEU Chi-restraints excluded: chain W residue 239 ILE Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 37 PHE Chi-restraints excluded: chain X residue 60 THR Chi-restraints excluded: chain X residue 135 SER Chi-restraints excluded: chain X residue 167 ASP Chi-restraints excluded: chain X residue 280 ASN Chi-restraints excluded: chain X residue 296 GLU Chi-restraints excluded: chain X residue 299 THR Chi-restraints excluded: chain X residue 313 SER Chi-restraints excluded: chain X residue 413 VAL Chi-restraints excluded: chain X residue 417 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 774 random chunks: chunk 610 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 470 optimal weight: 20.0000 chunk 734 optimal weight: 10.0000 chunk 452 optimal weight: 0.7980 chunk 212 optimal weight: 9.9990 chunk 125 optimal weight: 0.8980 chunk 515 optimal weight: 50.0000 chunk 211 optimal weight: 3.9990 chunk 529 optimal weight: 0.8980 chunk 169 optimal weight: 9.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 38 ASN ** G 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 378 ASN ** G 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 378 ASN ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 378 ASN ** I 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 378 ASN ** K 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 378 ASN ** K 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 378 ASN ** L 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 ASN ** M 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 329 ASN ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 280 ASN ** O 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 280 ASN P 378 ASN ** P 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 GLN ** R 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 280 ASN R 345 ASN ** R 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 79 GLN ** T 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 329 ASN ** U 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 378 ASN ** V 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 79 GLN ** W 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 280 ASN W 378 ASN ** X 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 280 ASN ** X 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.156255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.132529 restraints weight = 107566.771| |-----------------------------------------------------------------------------| r_work (start): 0.4297 rms_B_bonded: 2.94 r_work: 0.4145 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 61506 Z= 0.227 Angle : 0.600 12.640 83826 Z= 0.322 Chirality : 0.040 0.319 9468 Planarity : 0.004 0.091 11394 Dihedral : 4.551 53.771 8562 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.17 % Favored : 96.64 % Rotamer: Outliers : 3.84 % Allowed : 33.17 % Favored : 63.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.09), residues: 7740 helix: 2.78 (0.06), residues: 5544 sheet: None (None), residues: 0 loop : -2.12 (0.12), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP V 233 HIS 0.005 0.001 HIS W 251 PHE 0.023 0.002 PHE N 37 TYR 0.015 0.001 TYR X 153 ARG 0.013 0.000 ARG Q 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15480 Ramachandran restraints generated. 7740 Oldfield, 0 Emsley, 7740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15480 Ramachandran restraints generated. 7740 Oldfield, 0 Emsley, 7740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 6066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 500 time to evaluate : 4.973 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: G 37 PHE cc_start: 0.6408 (m-80) cc_final: 0.6145 (t80) REVERT: G 188 ARG cc_start: 0.6493 (OUTLIER) cc_final: 0.6069 (mmt180) REVERT: G 195 GLU cc_start: 0.6778 (mm-30) cc_final: 0.6444 (mp0) REVERT: G 233 TRP cc_start: 0.7736 (OUTLIER) cc_final: 0.7409 (m-10) REVERT: H 34 ASN cc_start: 0.5330 (t0) cc_final: 0.4956 (t0) REVERT: H 112 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6610 (tm-30) REVERT: H 195 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6397 (mp0) REVERT: I 188 ARG cc_start: 0.6557 (OUTLIER) cc_final: 0.6274 (mmt180) REVERT: I 195 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6508 (mp0) REVERT: I 398 LYS cc_start: 0.6690 (OUTLIER) cc_final: 0.6236 (mttm) REVERT: J 34 ASN cc_start: 0.5370 (t0) cc_final: 0.5041 (t0) REVERT: J 37 PHE cc_start: 0.6642 (m-80) cc_final: 0.5988 (t80) REVERT: J 112 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6317 (tm-30) REVERT: J 188 ARG cc_start: 0.6565 (OUTLIER) cc_final: 0.6269 (mmt180) REVERT: J 195 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6486 (mp0) REVERT: J 417 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8417 (t0) REVERT: K 37 PHE cc_start: 0.5651 (t80) cc_final: 0.5282 (t80) REVERT: K 112 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6604 (tm-30) REVERT: K 195 GLU cc_start: 0.7048 (mm-30) cc_final: 0.6405 (mp0) REVERT: L 195 GLU cc_start: 0.6757 (mm-30) cc_final: 0.6296 (mp0) REVERT: L 233 TRP cc_start: 0.7969 (OUTLIER) cc_final: 0.7467 (m-10) REVERT: M 37 PHE cc_start: 0.4670 (OUTLIER) cc_final: 0.3988 (t80) REVERT: M 85 GLU cc_start: 0.9344 (mp0) cc_final: 0.8996 (mp0) REVERT: M 117 ARG cc_start: 0.7941 (tpt-90) cc_final: 0.7310 (ttp-170) REVERT: M 196 ASP cc_start: 0.7497 (OUTLIER) cc_final: 0.6912 (m-30) REVERT: M 232 GLU cc_start: 0.8211 (pp20) cc_final: 0.6911 (mp0) REVERT: M 233 TRP cc_start: 0.7715 (m-10) cc_final: 0.7392 (m-10) REVERT: M 296 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6909 (pp20) REVERT: M 321 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7897 (mp) REVERT: M 329 ASN cc_start: 0.6714 (m-40) cc_final: 0.6418 (m-40) REVERT: M 417 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8129 (m-30) REVERT: N 196 ASP cc_start: 0.6675 (OUTLIER) cc_final: 0.5997 (m-30) REVERT: N 232 GLU cc_start: 0.7906 (pp20) cc_final: 0.6757 (mp0) REVERT: N 233 TRP cc_start: 0.7632 (OUTLIER) cc_final: 0.7345 (m-10) REVERT: N 241 GLN cc_start: 0.8762 (mt0) cc_final: 0.8394 (tt0) REVERT: N 280 ASN cc_start: 0.7554 (OUTLIER) cc_final: 0.7177 (t0) REVERT: N 313 SER cc_start: 0.7107 (OUTLIER) cc_final: 0.6673 (p) REVERT: N 354 ILE cc_start: 0.6800 (OUTLIER) cc_final: 0.6594 (mp) REVERT: N 363 GLU cc_start: 0.7986 (tp30) cc_final: 0.7192 (pp20) REVERT: N 400 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7541 (tp) REVERT: O 75 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.6912 (mp) REVERT: O 232 GLU cc_start: 0.7713 (pp20) cc_final: 0.7172 (mm-30) REVERT: O 280 ASN cc_start: 0.7586 (OUTLIER) cc_final: 0.7244 (t0) REVERT: O 363 GLU cc_start: 0.7908 (tp30) cc_final: 0.7110 (pp20) REVERT: O 417 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7625 (m-30) REVERT: P 37 PHE cc_start: 0.4158 (OUTLIER) cc_final: 0.3533 (m-80) REVERT: P 85 GLU cc_start: 0.9230 (mp0) cc_final: 0.8951 (mp0) REVERT: P 196 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7014 (m-30) REVERT: P 329 ASN cc_start: 0.6559 (m-40) cc_final: 0.6249 (m-40) REVERT: P 417 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.7949 (m-30) REVERT: Q 232 GLU cc_start: 0.7788 (pp20) cc_final: 0.6889 (mp0) REVERT: Q 280 ASN cc_start: 0.6908 (OUTLIER) cc_final: 0.6575 (t0) REVERT: Q 313 SER cc_start: 0.6963 (OUTLIER) cc_final: 0.6478 (p) REVERT: Q 363 GLU cc_start: 0.7953 (tp30) cc_final: 0.7222 (pp20) REVERT: Q 410 LEU cc_start: 0.8844 (tp) cc_final: 0.8603 (tp) REVERT: Q 415 ASN cc_start: 0.8067 (p0) cc_final: 0.7779 (p0) REVERT: R 85 GLU cc_start: 0.9288 (mp0) cc_final: 0.8948 (mp0) REVERT: R 196 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7060 (m-30) REVERT: R 232 GLU cc_start: 0.8198 (pp20) cc_final: 0.7102 (mp0) REVERT: R 233 TRP cc_start: 0.7596 (m-10) cc_final: 0.7396 (m-10) REVERT: R 296 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6882 (pp20) REVERT: R 313 SER cc_start: 0.4700 (OUTLIER) cc_final: 0.4364 (p) REVERT: S 37 PHE cc_start: 0.4129 (OUTLIER) cc_final: 0.3649 (t80) REVERT: S 85 GLU cc_start: 0.9224 (mp0) cc_final: 0.8947 (mp0) REVERT: S 196 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7028 (m-30) REVERT: S 329 ASN cc_start: 0.6486 (m-40) cc_final: 0.6155 (m-40) REVERT: S 417 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.7980 (m-30) REVERT: T 232 GLU cc_start: 0.7645 (pp20) cc_final: 0.7076 (mm-30) REVERT: T 363 GLU cc_start: 0.7946 (tp30) cc_final: 0.7184 (pp20) REVERT: U 232 GLU cc_start: 0.7957 (pp20) cc_final: 0.6797 (mp0) REVERT: U 233 TRP cc_start: 0.7528 (m-10) cc_final: 0.7213 (m-10) REVERT: U 280 ASN cc_start: 0.7626 (OUTLIER) cc_final: 0.7307 (t0) REVERT: U 363 GLU cc_start: 0.7985 (tp30) cc_final: 0.7199 (pp20) REVERT: U 400 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7510 (tp) REVERT: V 88 GLU cc_start: 0.9393 (pt0) cc_final: 0.9141 (mm-30) REVERT: V 193 GLU cc_start: 0.6044 (OUTLIER) cc_final: 0.5769 (tt0) REVERT: V 196 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.6875 (m-30) REVERT: V 232 GLU cc_start: 0.8226 (pp20) cc_final: 0.7165 (mp0) REVERT: V 296 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.7015 (pp20) REVERT: V 329 ASN cc_start: 0.6829 (m-40) cc_final: 0.6544 (m-40) REVERT: V 417 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8143 (m-30) REVERT: W 232 GLU cc_start: 0.7912 (pp20) cc_final: 0.6932 (mp0) REVERT: W 280 ASN cc_start: 0.7645 (OUTLIER) cc_final: 0.7282 (t160) REVERT: W 363 GLU cc_start: 0.7946 (tp30) cc_final: 0.7227 (pp20) REVERT: W 415 ASN cc_start: 0.8108 (p0) cc_final: 0.7810 (p0) REVERT: X 37 PHE cc_start: 0.4167 (OUTLIER) cc_final: 0.3540 (t80) REVERT: X 85 GLU cc_start: 0.9290 (mp0) cc_final: 0.8964 (mp0) REVERT: X 232 GLU cc_start: 0.8329 (pp20) cc_final: 0.6719 (mp0) REVERT: X 233 TRP cc_start: 0.7694 (OUTLIER) cc_final: 0.7457 (m-10) REVERT: X 296 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6888 (pp20) REVERT: X 313 SER cc_start: 0.4656 (OUTLIER) cc_final: 0.4325 (p) REVERT: X 329 ASN cc_start: 0.6645 (m-40) cc_final: 0.6326 (m-40) REVERT: X 417 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.8039 (m-30) outliers start: 232 outliers final: 151 residues processed: 680 average time/residue: 1.1052 time to fit residues: 1029.3553 Evaluate side-chains 683 residues out of total 6066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 485 time to evaluate : 4.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 45 ASP Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 188 ARG Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 233 TRP Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 286 SER Chi-restraints excluded: chain G residue 313 SER Chi-restraints excluded: chain G residue 404 GLU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 45 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 112 GLU Chi-restraints excluded: chain H residue 196 ASP Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 243 ASP Chi-restraints excluded: chain H residue 286 SER Chi-restraints excluded: chain H residue 313 SER Chi-restraints excluded: chain H residue 404 GLU Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 188 ARG Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 286 SER Chi-restraints excluded: chain I residue 398 LYS Chi-restraints excluded: chain I residue 404 GLU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 135 SER Chi-restraints excluded: chain J residue 188 ARG Chi-restraints excluded: chain J residue 196 ASP Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 286 SER Chi-restraints excluded: chain J residue 404 GLU Chi-restraints excluded: chain J residue 417 ASP Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 112 GLU Chi-restraints excluded: chain K residue 196 ASP Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 239 ILE Chi-restraints excluded: chain K residue 286 SER Chi-restraints excluded: chain K residue 313 SER Chi-restraints excluded: chain K residue 404 GLU Chi-restraints excluded: chain K residue 443 ARG Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 196 ASP Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 233 TRP Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 286 SER Chi-restraints excluded: chain L residue 313 SER Chi-restraints excluded: chain L residue 404 GLU Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 37 PHE Chi-restraints excluded: chain M residue 88 GLU Chi-restraints excluded: chain M residue 135 SER Chi-restraints excluded: chain M residue 151 GLU Chi-restraints excluded: chain M residue 167 ASP Chi-restraints excluded: chain M residue 196 ASP Chi-restraints excluded: chain M residue 239 ILE Chi-restraints excluded: chain M residue 296 GLU Chi-restraints excluded: chain M residue 299 THR Chi-restraints excluded: chain M residue 313 SER Chi-restraints excluded: chain M residue 321 LEU Chi-restraints excluded: chain M residue 413 VAL Chi-restraints excluded: chain M residue 417 ASP Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 196 ASP Chi-restraints excluded: chain N residue 233 TRP Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 280 ASN Chi-restraints excluded: chain N residue 313 SER Chi-restraints excluded: chain N residue 354 ILE Chi-restraints excluded: chain N residue 355 SER Chi-restraints excluded: chain N residue 400 LEU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 196 ASP Chi-restraints excluded: chain O residue 202 THR Chi-restraints excluded: chain O residue 239 ILE Chi-restraints excluded: chain O residue 243 ASP Chi-restraints excluded: chain O residue 280 ASN Chi-restraints excluded: chain O residue 329 ASN Chi-restraints excluded: chain O residue 417 ASP Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 37 PHE Chi-restraints excluded: chain P residue 135 SER Chi-restraints excluded: chain P residue 157 LEU Chi-restraints excluded: chain P residue 167 ASP Chi-restraints excluded: chain P residue 196 ASP Chi-restraints excluded: chain P residue 239 ILE Chi-restraints excluded: chain P residue 321 LEU Chi-restraints excluded: chain P residue 413 VAL Chi-restraints excluded: chain P residue 417 ASP Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain Q residue 202 THR Chi-restraints excluded: chain Q residue 239 ILE Chi-restraints excluded: chain Q residue 243 ASP Chi-restraints excluded: chain Q residue 280 ASN Chi-restraints excluded: chain Q residue 307 VAL Chi-restraints excluded: chain Q residue 313 SER Chi-restraints excluded: chain Q residue 329 ASN Chi-restraints excluded: chain R residue 60 THR Chi-restraints excluded: chain R residue 88 GLU Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 167 ASP Chi-restraints excluded: chain R residue 196 ASP Chi-restraints excluded: chain R residue 209 GLU Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 280 ASN Chi-restraints excluded: chain R residue 296 GLU Chi-restraints excluded: chain R residue 299 THR Chi-restraints excluded: chain R residue 313 SER Chi-restraints excluded: chain R residue 413 VAL Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 37 PHE Chi-restraints excluded: chain S residue 135 SER Chi-restraints excluded: chain S residue 157 LEU Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 196 ASP Chi-restraints excluded: chain S residue 239 ILE Chi-restraints excluded: chain S residue 321 LEU Chi-restraints excluded: chain S residue 413 VAL Chi-restraints excluded: chain S residue 417 ASP Chi-restraints excluded: chain T residue 33 THR Chi-restraints excluded: chain T residue 51 ILE Chi-restraints excluded: chain T residue 83 VAL Chi-restraints excluded: chain T residue 196 ASP Chi-restraints excluded: chain T residue 202 THR Chi-restraints excluded: chain T residue 239 ILE Chi-restraints excluded: chain T residue 243 ASP Chi-restraints excluded: chain T residue 355 SER Chi-restraints excluded: chain T residue 413 VAL Chi-restraints excluded: chain U residue 33 THR Chi-restraints excluded: chain U residue 75 LEU Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 234 LEU Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 243 ASP Chi-restraints excluded: chain U residue 280 ASN Chi-restraints excluded: chain U residue 400 LEU Chi-restraints excluded: chain V residue 33 THR Chi-restraints excluded: chain V residue 135 SER Chi-restraints excluded: chain V residue 151 GLU Chi-restraints excluded: chain V residue 167 ASP Chi-restraints excluded: chain V residue 193 GLU Chi-restraints excluded: chain V residue 196 ASP Chi-restraints excluded: chain V residue 239 ILE Chi-restraints excluded: chain V residue 296 GLU Chi-restraints excluded: chain V residue 299 THR Chi-restraints excluded: chain V residue 313 SER Chi-restraints excluded: chain V residue 321 LEU Chi-restraints excluded: chain V residue 413 VAL Chi-restraints excluded: chain V residue 417 ASP Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 223 LEU Chi-restraints excluded: chain W residue 239 ILE Chi-restraints excluded: chain W residue 280 ASN Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 37 PHE Chi-restraints excluded: chain X residue 60 THR Chi-restraints excluded: chain X residue 135 SER Chi-restraints excluded: chain X residue 167 ASP Chi-restraints excluded: chain X residue 233 TRP Chi-restraints excluded: chain X residue 239 ILE Chi-restraints excluded: chain X residue 280 ASN Chi-restraints excluded: chain X residue 296 GLU Chi-restraints excluded: chain X residue 299 THR Chi-restraints excluded: chain X residue 313 SER Chi-restraints excluded: chain X residue 413 VAL Chi-restraints excluded: chain X residue 417 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 774 random chunks: chunk 402 optimal weight: 2.9990 chunk 708 optimal weight: 3.9990 chunk 262 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 210 optimal weight: 0.9990 chunk 280 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 690 optimal weight: 5.9990 chunk 582 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 38 ASN ** G 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 378 ASN ** H 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 378 ASN ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 ASN ** I 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 378 ASN ** I 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 378 ASN ** K 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 378 ASN ** K 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 378 ASN ** L 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 280 ASN ** O 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 280 ASN ** P 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 GLN ** R 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 280 ASN ** R 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 79 GLN ** W 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 280 ASN ** W 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 378 ASN ** X 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 280 ASN ** X 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.158089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.134757 restraints weight = 106426.108| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 2.88 r_work: 0.4183 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 61506 Z= 0.188 Angle : 0.583 12.271 83826 Z= 0.312 Chirality : 0.038 0.387 9468 Planarity : 0.004 0.087 11394 Dihedral : 4.428 53.288 8560 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.46 % Favored : 96.34 % Rotamer: Outliers : 3.69 % Allowed : 33.23 % Favored : 63.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.09), residues: 7740 helix: 2.96 (0.06), residues: 5544 sheet: None (None), residues: 0 loop : -2.07 (0.12), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP V 233 HIS 0.004 0.001 HIS W 251 PHE 0.021 0.001 PHE N 37 TYR 0.015 0.001 TYR W 153 ARG 0.008 0.000 ARG V 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 57506.58 seconds wall clock time: 977 minutes 25.81 seconds (58645.81 seconds total)