Starting phenix.real_space_refine on Sat Oct 12 05:50:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gk2_51414/10_2024/9gk2_51414.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gk2_51414/10_2024/9gk2_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gk2_51414/10_2024/9gk2_51414.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gk2_51414/10_2024/9gk2_51414.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gk2_51414/10_2024/9gk2_51414.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gk2_51414/10_2024/9gk2_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): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 24.00, per 1000 atoms: 0.40 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: 11.41 Conformation dependent library (CDL) restraints added in 5.9 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: 3.19 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: 16.71 Time building geometry restraints manager: 13.51 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: 0.00 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 15.760 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: 0.070 Extract box with map and model: 2.480 Check model and map are aligned: 0.340 Set scattering table: 0.430 Process input model: 96.740 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.330 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:10.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.780 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 251 poor density : 859 time to evaluate : 5.028 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: 1.1569 time to fit residues: 1652.6047 Evaluate side-chains 683 residues out of total 6066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 552 time to evaluate : 4.890 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 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 fitting. rotamer outliers: 333 poor density : 621 time to evaluate : 5.044 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: 0.6620 (OUTLIER) cc_final: 0.6414 (mtt-85) REVERT: G 195 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6621 (mp0) REVERT: G 231 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.7152 (t80) REVERT: G 233 TRP cc_start: 0.7581 (OUTLIER) cc_final: 0.7074 (m-10) REVERT: H 34 ASN cc_start: 0.6284 (t0) cc_final: 0.6036 (t0) REVERT: H 167 ASP cc_start: 0.8585 (m-30) cc_final: 0.8203 (p0) REVERT: H 188 ARG cc_start: 0.6560 (OUTLIER) cc_final: 0.6321 (mpt-90) REVERT: H 195 GLU cc_start: 0.7403 (mm-30) cc_final: 0.6685 (mp0) REVERT: I 195 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6659 (mp0) REVERT: J 34 ASN cc_start: 0.5981 (t0) cc_final: 0.5704 (t0) REVERT: J 195 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6666 (mp0) REVERT: K 34 ASN cc_start: 0.6260 (t0) cc_final: 0.6040 (t0) REVERT: K 167 ASP cc_start: 0.8586 (m-30) cc_final: 0.8205 (p0) REVERT: K 417 ASP cc_start: 0.8175 (m-30) cc_final: 0.7857 (m-30) REVERT: L 188 ARG cc_start: 0.6568 (OUTLIER) cc_final: 0.6302 (mpt-90) REVERT: L 195 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6589 (mp0) REVERT: L 231 PHE cc_start: 0.7897 (OUTLIER) cc_final: 0.7202 (t80) REVERT: L 233 TRP cc_start: 0.7835 (OUTLIER) cc_final: 0.7505 (m-10) REVERT: L 413 VAL cc_start: 0.8045 (t) cc_final: 0.7815 (m) REVERT: N 45 ASP cc_start: 0.7275 (OUTLIER) cc_final: 0.7057 (OUTLIER) REVERT: N 226 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.8017 (tp30) REVERT: O 75 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7464 (mp) REVERT: O 226 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7755 (tt0) REVERT: O 462 GLU cc_start: 0.1247 (OUTLIER) cc_final: 0.0259 (mp0) REVERT: P 37 PHE cc_start: 0.5686 (m-10) cc_final: 0.5431 (t80) REVERT: P 174 THR cc_start: 0.7878 (p) cc_final: 0.7659 (p) REVERT: P 239 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7247 (pp) REVERT: Q 91 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6876 (mt) REVERT: Q 239 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7669 (pp) REVERT: S 174 THR cc_start: 0.7843 (p) cc_final: 0.7623 (p) REVERT: T 75 LEU cc_start: 0.7803 (mt) cc_final: 0.7561 (mp) REVERT: T 188 ARG cc_start: 0.6027 (OUTLIER) cc_final: 0.5178 (mmm-85) REVERT: T 226 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7831 (tt0) REVERT: T 462 GLU cc_start: 0.1230 (OUTLIER) cc_final: 0.0215 (mp0) REVERT: U 239 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7317 (pp) REVERT: W 91 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6836 (mt) REVERT: W 270 GLU cc_start: 0.6408 (mm-30) cc_final: 0.6207 (mm-30) REVERT: W 400 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6973 (tp) outliers start: 333 outliers final: 129 residues processed: 896 average time/residue: 1.2610 time to fit residues: 1477.2012 Evaluate side-chains 651 residues out of total 6066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 502 time to evaluate : 5.009 ------------------------------------------------------------------------------- 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 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 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 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 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 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 299 THR 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 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 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 239 ILE Chi-restraints excluded: chain O residue 282 GLU Chi-restraints excluded: chain O residue 378 ASN 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 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 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 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 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 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 239 ILE 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 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 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 239 ILE 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 299 THR Chi-restraints excluded: chain X residue 378 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 774 random chunks: chunk 390 optimal weight: 9.9990 chunk 218 optimal weight: 0.8980 chunk 584 optimal weight: 5.9990 chunk 478 optimal weight: 8.9990 chunk 193 optimal weight: 8.9990 chunk 704 optimal weight: 1.9990 chunk 760 optimal weight: 0.0570 chunk 627 optimal weight: 3.9990 chunk 698 optimal weight: 5.9990 chunk 240 optimal weight: 0.9990 chunk 564 optimal weight: 8.9990 overall best weight: 1.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** K 241 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 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 ASN N 241 GLN N 378 ASN ** N 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 280 ASN O 329 ASN ** O 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 280 ASN Q 378 ASN ** Q 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 378 ASN ** R 441 GLN ** 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 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 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 378 ASN ** W 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 378 ASN ** X 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.2027 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= 0.221 Angle : 0.588 6.727 83826 Z= 0.318 Chirality : 0.040 0.245 9468 Planarity : 0.004 0.063 11394 Dihedral : 5.906 87.331 8638 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.51 % Favored : 96.28 % Rotamer: Outliers : 4.15 % Allowed : 31.35 % Favored : 64.50 % 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: 1.81 (0.09), residues: 7740 helix: 2.60 (0.06), residues: 5436 sheet: None (None), residues: 0 loop : -2.50 (0.10), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP K 233 HIS 0.004 0.001 HIS W 251 PHE 0.029 0.002 PHE K 37 TYR 0.019 0.002 TYR R 153 ARG 0.005 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 808 residues out of total 6066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 557 time to evaluate : 5.046 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: G 34 ASN cc_start: 0.6213 (t0) cc_final: 0.5854 (t0) REVERT: G 188 ARG cc_start: 0.6731 (OUTLIER) cc_final: 0.6459 (mtt-85) REVERT: G 195 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6629 (mp0) REVERT: G 233 TRP cc_start: 0.7712 (OUTLIER) cc_final: 0.7134 (m-10) REVERT: H 417 ASP cc_start: 0.8111 (m-30) cc_final: 0.7816 (m-30) REVERT: I 34 ASN cc_start: 0.6088 (t0) cc_final: 0.5760 (t0) REVERT: I 37 PHE cc_start: 0.6870 (m-80) cc_final: 0.6605 (t80) REVERT: I 195 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6678 (mp0) REVERT: I 398 LYS cc_start: 0.7087 (OUTLIER) cc_final: 0.6713 (mttm) REVERT: J 195 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6727 (mp0) REVERT: J 398 LYS cc_start: 0.7071 (OUTLIER) cc_final: 0.6702 (mttm) REVERT: K 195 GLU cc_start: 0.7360 (mm-30) cc_final: 0.6743 (mp0) REVERT: L 188 ARG cc_start: 0.6681 (OUTLIER) cc_final: 0.6403 (mpt-90) REVERT: L 195 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6626 (mp0) REVERT: L 233 TRP cc_start: 0.7930 (OUTLIER) cc_final: 0.7605 (m-10) REVERT: L 413 VAL cc_start: 0.8146 (t) cc_final: 0.7860 (m) REVERT: L 417 ASP cc_start: 0.8062 (m-30) cc_final: 0.7810 (m-30) REVERT: N 45 ASP cc_start: 0.7326 (OUTLIER) cc_final: 0.7113 (p0) REVERT: N 226 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7997 (tt0) REVERT: O 75 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7524 (mp) REVERT: P 37 PHE cc_start: 0.5689 (m-10) cc_final: 0.5328 (t80) REVERT: Q 91 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.6903 (mt) REVERT: Q 231 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.6445 (t80) REVERT: Q 239 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7626 (pp) REVERT: Q 410 LEU cc_start: 0.7883 (tp) cc_final: 0.7588 (tp) REVERT: S 174 THR cc_start: 0.7835 (p) cc_final: 0.7634 (p) REVERT: T 75 LEU cc_start: 0.7800 (mt) cc_final: 0.7582 (mp) REVERT: T 188 ARG cc_start: 0.6040 (OUTLIER) cc_final: 0.5156 (mmm-85) REVERT: T 226 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: U 45 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.7150 (OUTLIER) REVERT: U 226 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7996 (tt0) REVERT: U 233 TRP cc_start: 0.7460 (OUTLIER) cc_final: 0.7230 (m-10) REVERT: V 37 PHE cc_start: 0.5691 (OUTLIER) cc_final: 0.5280 (t80) REVERT: W 91 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.6817 (mt) outliers start: 251 outliers final: 129 residues processed: 750 average time/residue: 1.1430 time to fit residues: 1150.9699 Evaluate side-chains 617 residues out of total 6066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 470 time to evaluate : 5.027 ------------------------------------------------------------------------------- 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 188 ARG Chi-restraints excluded: chain G residue 233 TRP Chi-restraints excluded: chain G residue 239 ILE 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 398 LYS Chi-restraints excluded: chain I residue 404 GLU Chi-restraints excluded: chain I residue 447 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 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 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 233 TRP Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 259 LYS 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 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 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 226 GLU 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 314 THR Chi-restraints excluded: chain N residue 329 ASN Chi-restraints excluded: chain N residue 355 SER Chi-restraints excluded: chain N residue 378 ASN 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 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 378 ASN 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 378 ASN Chi-restraints excluded: chain P residue 413 VAL 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 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 299 THR 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 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 226 GLU Chi-restraints excluded: chain U residue 233 TRP Chi-restraints excluded: chain U residue 239 ILE 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 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 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 299 THR Chi-restraints excluded: chain X residue 413 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 774 random chunks: chunk 695 optimal weight: 0.0980 chunk 529 optimal weight: 3.9990 chunk 365 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 336 optimal weight: 4.9990 chunk 472 optimal weight: 4.9990 chunk 706 optimal weight: 3.9990 chunk 748 optimal weight: 3.9990 chunk 369 optimal weight: 6.9990 chunk 669 optimal weight: 0.9990 chunk 201 optimal weight: 6.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- 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 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 414 GLN ** 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 34 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 378 ASN O 38 ASN O 280 ASN O 378 ASN ** O 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 280 ASN Q 79 GLN Q 184 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 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 251 HIS ** W 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 280 ASN X 378 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 61506 Z= 0.269 Angle : 0.608 7.559 83826 Z= 0.330 Chirality : 0.041 0.321 9468 Planarity : 0.004 0.065 11394 Dihedral : 5.592 82.570 8613 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.57 % Favored : 96.23 % Rotamer: Outliers : 5.57 % Allowed : 29.91 % Favored : 64.52 % 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: 1.60 (0.09), residues: 7740 helix: 2.29 (0.06), residues: 5562 sheet: None (None), residues: 0 loop : -2.42 (0.11), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP S 233 HIS 0.004 0.001 HIS H 338 PHE 0.037 0.002 PHE K 37 TYR 0.021 0.002 TYR M 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 880 residues out of total 6066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 337 poor density : 543 time to evaluate : 5.092 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 188 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.6492 (mtt-85) REVERT: G 195 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6626 (mp0) REVERT: G 231 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7172 (t80) REVERT: G 233 TRP cc_start: 0.7893 (OUTLIER) cc_final: 0.7376 (m-10) REVERT: H 195 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6782 (mp0) REVERT: I 188 ARG cc_start: 0.6851 (OUTLIER) cc_final: 0.6485 (mpt-90) REVERT: I 195 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6688 (mp0) REVERT: I 398 LYS cc_start: 0.7194 (OUTLIER) cc_final: 0.6826 (mttm) REVERT: J 188 ARG cc_start: 0.6890 (OUTLIER) cc_final: 0.6529 (mpt-90) REVERT: J 195 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6666 (mp0) REVERT: J 398 LYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6805 (mttm) REVERT: J 417 ASP cc_start: 0.8132 (m-30) cc_final: 0.7847 (m-30) REVERT: K 417 ASP cc_start: 0.8131 (m-30) cc_final: 0.7839 (m-30) REVERT: L 188 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.6475 (mpt-90) REVERT: L 195 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6645 (mp0) REVERT: L 231 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7194 (t80) REVERT: L 233 TRP cc_start: 0.8106 (OUTLIER) cc_final: 0.7678 (m-10) REVERT: L 417 ASP cc_start: 0.8136 (m-30) cc_final: 0.7824 (m-30) REVERT: N 45 ASP cc_start: 0.7293 (OUTLIER) cc_final: 0.7078 (OUTLIER) REVERT: N 226 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7990 (tt0) REVERT: N 410 LEU cc_start: 0.8081 (tp) cc_final: 0.7829 (tp) REVERT: O 75 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7532 (mp) REVERT: O 226 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7813 (tt0) REVERT: P 37 PHE cc_start: 0.5693 (m-10) cc_final: 0.5240 (t80) REVERT: Q 91 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.6877 (mt) REVERT: Q 231 PHE cc_start: 0.7420 (OUTLIER) cc_final: 0.6429 (t80) REVERT: Q 410 LEU cc_start: 0.8035 (tp) cc_final: 0.7722 (tp) REVERT: T 188 ARG cc_start: 0.6039 (OUTLIER) cc_final: 0.5095 (mmm-85) REVERT: T 226 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7870 (tt0) REVERT: U 226 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8011 (tt0) REVERT: V 37 PHE cc_start: 0.5678 (OUTLIER) cc_final: 0.4971 (m-10) REVERT: V 196 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7303 (m-30) REVERT: W 91 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.6812 (mt) REVERT: X 37 PHE cc_start: 0.5399 (OUTLIER) cc_final: 0.5096 (t80) outliers start: 337 outliers final: 154 residues processed: 814 average time/residue: 1.1787 time to fit residues: 1276.4013 Evaluate side-chains 649 residues out of total 6066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 473 time to evaluate : 4.934 ------------------------------------------------------------------------------- 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 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 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 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 196 ASP Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 241 GLN Chi-restraints excluded: chain J residue 280 ASN 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 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 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 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 82 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 299 THR Chi-restraints excluded: chain M residue 393 ILE Chi-restraints excluded: chain M residue 413 VAL 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 226 GLU Chi-restraints excluded: chain N residue 239 ILE 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 O residue 33 THR 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 307 VAL Chi-restraints excluded: chain O residue 313 SER 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 299 THR Chi-restraints excluded: chain P residue 413 VAL 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 233 TRP Chi-restraints excluded: chain Q residue 239 ILE 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 82 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 280 ASN 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 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 378 ASN Chi-restraints excluded: chain S residue 413 VAL 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 307 VAL 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 45 ASP Chi-restraints excluded: chain U residue 75 LEU Chi-restraints excluded: chain U residue 83 VAL 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 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 196 ASP Chi-restraints excluded: chain V residue 239 ILE Chi-restraints excluded: chain V residue 275 ASP Chi-restraints excluded: chain V residue 299 THR Chi-restraints excluded: chain V residue 380 GLU Chi-restraints excluded: chain V residue 413 VAL 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 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 82 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 299 THR Chi-restraints excluded: chain X residue 413 VAL Chi-restraints excluded: chain X residue 415 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 774 random chunks: chunk 623 optimal weight: 9.9990 chunk 424 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 557 optimal weight: 20.0000 chunk 308 optimal weight: 9.9990 chunk 638 optimal weight: 6.9990 chunk 517 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 382 optimal weight: 10.0000 chunk 671 optimal weight: 1.9990 chunk 188 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 38 ASN ** G 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 407 GLN ** G 414 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 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 378 ASN ** K 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN ** L 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 407 GLN ** L 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 ASN N 407 GLN ** N 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 378 ASN ** O 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 280 ASN P 378 ASN Q 378 ASN Q 407 GLN ** Q 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 38 ASN ** 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 79 GLN ** T 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 292 GLN T 378 ASN ** T 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 292 GLN ** 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 378 ASN W 407 GLN ** W 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 280 ASN X 378 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 61506 Z= 0.430 Angle : 0.718 9.432 83826 Z= 0.394 Chirality : 0.046 0.267 9468 Planarity : 0.005 0.079 11394 Dihedral : 5.943 80.105 8601 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.79 % Favored : 96.01 % Rotamer: Outliers : 6.55 % Allowed : 29.68 % Favored : 63.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.09), residues: 7740 helix: 1.60 (0.06), residues: 5454 sheet: None (None), residues: 0 loop : -2.73 (0.10), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.004 TRP R 233 HIS 0.007 0.001 HIS W 251 PHE 0.033 0.003 PHE K 37 TYR 0.023 0.002 TYR V 153 ARG 0.008 0.001 ARG P 427 *********************** 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 888 residues out of total 6066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 396 poor density : 492 time to evaluate : 5.079 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 188 ARG cc_start: 0.6853 (OUTLIER) cc_final: 0.6612 (mmt180) REVERT: G 231 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7264 (t80) REVERT: G 233 TRP cc_start: 0.8128 (OUTLIER) cc_final: 0.7703 (m-10) REVERT: H 275 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.7207 (t0) REVERT: I 188 ARG cc_start: 0.6890 (OUTLIER) cc_final: 0.6560 (mpt-90) REVERT: I 195 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6667 (mp0) REVERT: J 188 ARG cc_start: 0.6901 (OUTLIER) cc_final: 0.6581 (mpt-90) REVERT: J 195 GLU cc_start: 0.7259 (mm-30) cc_final: 0.6704 (mp0) REVERT: J 398 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.7107 (mptm) REVERT: J 417 ASP cc_start: 0.8191 (m-30) cc_final: 0.7891 (m-30) REVERT: K 275 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7214 (t0) REVERT: L 195 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6581 (mp0) REVERT: L 231 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7274 (t80) REVERT: L 233 TRP cc_start: 0.8298 (OUTLIER) cc_final: 0.7755 (m-10) REVERT: M 196 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7527 (m-30) REVERT: N 226 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8095 (tt0) REVERT: N 231 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.6514 (t80) REVERT: N 354 ILE cc_start: 0.7222 (OUTLIER) cc_final: 0.6973 (mp) REVERT: N 380 GLU cc_start: 0.2195 (OUTLIER) cc_final: 0.1337 (pt0) REVERT: O 226 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7831 (tt0) REVERT: P 37 PHE cc_start: 0.5790 (OUTLIER) cc_final: 0.5190 (t80) REVERT: P 231 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.6994 (t80) REVERT: Q 91 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7054 (mt) REVERT: Q 231 PHE cc_start: 0.7466 (OUTLIER) cc_final: 0.6387 (t80) REVERT: R 231 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.7197 (t80) REVERT: S 231 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.6989 (t80) REVERT: T 188 ARG cc_start: 0.6150 (OUTLIER) cc_final: 0.5122 (mmm-85) REVERT: U 226 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8039 (tt0) REVERT: U 354 ILE cc_start: 0.7263 (OUTLIER) cc_final: 0.7056 (mp) REVERT: U 380 GLU cc_start: 0.2434 (OUTLIER) cc_final: 0.1591 (pt0) REVERT: V 37 PHE cc_start: 0.5740 (OUTLIER) cc_final: 0.5039 (m-10) REVERT: V 193 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6016 (tm-30) REVERT: W 91 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.6908 (mt) REVERT: X 37 PHE cc_start: 0.5501 (OUTLIER) cc_final: 0.4881 (m-10) REVERT: X 243 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8302 (t0) outliers start: 396 outliers final: 183 residues processed: 827 average time/residue: 1.1356 time to fit residues: 1256.7880 Evaluate side-chains 651 residues out of total 6066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 437 time to evaluate : 4.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 45 ASP Chi-restraints excluded: chain G residue 51 ILE 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 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 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 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 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 296 GLU 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 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 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 202 THR Chi-restraints excluded: chain I residue 223 LEU 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 462 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 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 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 71 THR Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 96 SER 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 51 ILE 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 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 296 GLU Chi-restraints excluded: chain L residue 378 ASN Chi-restraints excluded: chain L residue 404 GLU 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 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 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 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 231 PHE Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 307 VAL Chi-restraints excluded: chain N residue 354 ILE Chi-restraints excluded: chain N residue 355 SER Chi-restraints excluded: chain N residue 380 GLU 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 96 SER 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 307 VAL Chi-restraints excluded: chain O residue 313 SER 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 227 VAL Chi-restraints excluded: chain P residue 231 PHE Chi-restraints excluded: chain P residue 239 ILE Chi-restraints excluded: chain P residue 299 THR Chi-restraints excluded: chain P residue 306 ARG Chi-restraints excluded: chain P residue 413 VAL 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 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 239 ILE 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 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 231 PHE Chi-restraints excluded: chain R residue 239 ILE 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 45 ASP Chi-restraints excluded: chain S residue 135 SER Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain S residue 231 PHE Chi-restraints excluded: chain S residue 239 ILE Chi-restraints excluded: chain S residue 280 ASN Chi-restraints excluded: chain S residue 378 ASN Chi-restraints excluded: chain S residue 413 VAL 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 96 SER 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 239 ILE 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 45 ASP 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 307 VAL Chi-restraints excluded: chain U residue 329 ASN Chi-restraints excluded: chain U residue 354 ILE Chi-restraints excluded: chain U residue 380 GLU Chi-restraints excluded: chain U residue 393 ILE 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 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 280 ASN Chi-restraints excluded: chain V residue 299 THR Chi-restraints excluded: chain V residue 313 SER Chi-restraints excluded: chain V residue 393 ILE Chi-restraints excluded: chain V residue 413 VAL 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 233 TRP Chi-restraints excluded: chain W residue 239 ILE Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain W residue 329 ASN Chi-restraints excluded: chain W residue 355 SER 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 243 ASP Chi-restraints excluded: chain X residue 299 THR Chi-restraints excluded: chain X residue 413 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 774 random chunks: chunk 251 optimal weight: 1.9990 chunk 673 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 439 optimal weight: 1.9990 chunk 184 optimal weight: 0.7980 chunk 748 optimal weight: 0.0670 chunk 621 optimal weight: 0.9990 chunk 346 optimal weight: 5.9990 chunk 62 optimal weight: 0.2980 chunk 247 optimal weight: 0.8980 chunk 393 optimal weight: 10.0000 overall best weight: 0.6120 ------------------------------------------------------------------------------- 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 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 280 ASN I 329 ASN 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 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 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 378 ASN ** L 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 ASN N 407 GLN O 79 GLN O 280 ASN O 378 ASN ** O 414 GLN ** 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 378 ASN Q 407 GLN ** Q 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 446 GLN ** R 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 280 ASN ** S 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 280 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 378 ASN T 414 GLN ** U 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 280 ASN U 378 ASN ** 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 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 378 ASN W 407 GLN ** X 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 280 ASN X 378 ASN ** X 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 61506 Z= 0.191 Angle : 0.577 7.128 83826 Z= 0.312 Chirality : 0.038 0.254 9468 Planarity : 0.004 0.071 11394 Dihedral : 5.199 81.830 8597 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.28 % Favored : 96.51 % Rotamer: Outliers : 3.82 % Allowed : 32.08 % 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: 1.88 (0.09), residues: 7740 helix: 2.52 (0.07), residues: 5544 sheet: None (None), residues: 0 loop : -2.34 (0.11), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP R 233 HIS 0.003 0.000 HIS W 251 PHE 0.048 0.001 PHE K 37 TYR 0.022 0.001 TYR N 153 ARG 0.008 0.001 ARG W 443 *********************** 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 795 residues out of total 6066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 564 time to evaluate : 5.127 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: H 112 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6809 (tm-30) REVERT: H 195 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6757 (mp0) REVERT: J 398 LYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6890 (mmpt) REVERT: J 417 ASP cc_start: 0.8051 (m-30) cc_final: 0.7777 (m-30) REVERT: K 112 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6814 (tm-30) REVERT: K 195 GLU cc_start: 0.7308 (mm-30) cc_final: 0.6711 (mp0) REVERT: L 195 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6632 (mp0) REVERT: L 233 TRP cc_start: 0.7942 (OUTLIER) cc_final: 0.7658 (m-10) REVERT: M 196 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7211 (m-30) REVERT: N 354 ILE cc_start: 0.7044 (OUTLIER) cc_final: 0.6770 (mp) REVERT: P 37 PHE cc_start: 0.5321 (m-10) cc_final: 0.4836 (t80) REVERT: Q 232 GLU cc_start: 0.7524 (pp20) cc_final: 0.6986 (mp0) REVERT: R 232 GLU cc_start: 0.8063 (pp20) cc_final: 0.7763 (pp20) REVERT: S 313 SER cc_start: 0.5216 (OUTLIER) cc_final: 0.5002 (p) REVERT: V 196 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.6946 (m-30) REVERT: X 232 GLU cc_start: 0.8090 (pp20) cc_final: 0.7815 (pp20) outliers start: 231 outliers final: 103 residues processed: 744 average time/residue: 1.1025 time to fit residues: 1109.4311 Evaluate side-chains 576 residues out of total 6066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 465 time to evaluate : 5.018 ------------------------------------------------------------------------------- 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 223 LEU Chi-restraints excluded: chain G residue 239 ILE 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 83 VAL Chi-restraints excluded: chain H residue 112 GLU Chi-restraints excluded: chain H residue 239 ILE 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 83 VAL Chi-restraints excluded: chain I residue 188 ARG Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 462 GLU 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 239 ILE Chi-restraints excluded: chain J residue 398 LYS 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 112 GLU Chi-restraints excluded: chain K residue 239 ILE 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 223 LEU Chi-restraints excluded: chain L residue 233 TRP Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 404 GLU Chi-restraints excluded: chain L residue 443 ARG Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 88 GLU Chi-restraints excluded: chain M residue 196 ASP Chi-restraints excluded: chain M residue 239 ILE Chi-restraints excluded: chain M residue 299 THR Chi-restraints excluded: chain M residue 393 ILE Chi-restraints excluded: chain M residue 413 VAL Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 280 ASN Chi-restraints excluded: chain N residue 354 ILE Chi-restraints excluded: chain O residue 33 THR 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 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 299 THR Chi-restraints excluded: chain P residue 413 VAL Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 202 THR Chi-restraints excluded: chain Q residue 239 ILE Chi-restraints excluded: chain Q residue 329 ASN Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 88 GLU Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 280 ASN 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 167 ASP Chi-restraints excluded: chain S residue 239 ILE Chi-restraints excluded: chain S residue 299 THR Chi-restraints excluded: chain S residue 313 SER Chi-restraints excluded: chain S residue 413 VAL 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 280 ASN Chi-restraints excluded: chain T residue 413 VAL Chi-restraints excluded: chain U residue 33 THR Chi-restraints excluded: chain U residue 181 ASP Chi-restraints excluded: chain U residue 234 LEU Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 329 ASN 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 196 ASP Chi-restraints excluded: chain V residue 239 ILE Chi-restraints excluded: chain V residue 393 ILE Chi-restraints excluded: chain V residue 413 VAL Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 51 ILE 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 82 THR Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 239 ILE Chi-restraints excluded: chain X residue 299 THR Chi-restraints excluded: chain X residue 313 SER Chi-restraints excluded: chain X residue 413 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 774 random chunks: chunk 722 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 426 optimal weight: 9.9990 chunk 546 optimal weight: 0.8980 chunk 423 optimal weight: 5.9990 chunk 630 optimal weight: 10.0000 chunk 418 optimal weight: 9.9990 chunk 746 optimal weight: 7.9990 chunk 466 optimal weight: 9.9990 chunk 454 optimal weight: 5.9990 chunk 344 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 38 ASN ** G 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 378 ASN ** G 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 378 ASN ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 ASN I 378 ASN ** I 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 280 ASN J 378 ASN K 241 GLN ** 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 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 378 ASN ** L 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 ASN O 280 ASN O 446 GLN ** P 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 378 ASN Q 79 GLN Q 284 GLN Q 378 ASN ** R 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 280 ASN ** S 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 280 ASN S 378 ASN T 79 GLN ** T 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 446 GLN U 280 ASN U 284 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 79 GLN W 378 ASN W 407 GLN ** W 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 446 GLN ** X 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 378 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 61506 Z= 0.390 Angle : 0.704 16.088 83826 Z= 0.383 Chirality : 0.044 0.295 9468 Planarity : 0.005 0.077 11394 Dihedral : 5.438 58.900 8576 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.64 % Favored : 96.14 % Rotamer: Outliers : 5.16 % Allowed : 31.73 % Favored : 63.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.09), residues: 7740 helix: 1.87 (0.06), residues: 5454 sheet: None (None), residues: 0 loop : -2.61 (0.11), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.005 TRP M 233 HIS 0.007 0.001 HIS W 251 PHE 0.033 0.003 PHE K 37 TYR 0.020 0.002 TYR V 153 ARG 0.010 0.001 ARG X 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 784 residues out of total 6066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 472 time to evaluate : 5.078 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: G 188 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6485 (mmt180) REVERT: G 380 GLU cc_start: 0.2563 (OUTLIER) cc_final: 0.2346 (pt0) REVERT: H 112 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6922 (tm-30) REVERT: H 195 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6754 (mp0) REVERT: H 380 GLU cc_start: 0.2663 (OUTLIER) cc_final: 0.2306 (pt0) REVERT: I 195 GLU cc_start: 0.7349 (mm-30) cc_final: 0.6801 (mp0) REVERT: I 398 LYS cc_start: 0.7008 (mptm) cc_final: 0.6675 (mttm) REVERT: J 188 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.6581 (mpt-90) REVERT: J 195 GLU cc_start: 0.7349 (mm-30) cc_final: 0.6792 (mp0) REVERT: J 398 LYS cc_start: 0.7287 (OUTLIER) cc_final: 0.7028 (mmpt) REVERT: J 417 ASP cc_start: 0.8191 (m-30) cc_final: 0.7849 (m-30) REVERT: K 112 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6923 (tm-30) REVERT: K 380 GLU cc_start: 0.2652 (OUTLIER) cc_final: 0.2317 (pt0) REVERT: L 75 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7910 (mp) REVERT: L 195 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6619 (mp0) REVERT: L 233 TRP cc_start: 0.8262 (OUTLIER) cc_final: 0.7755 (m-10) REVERT: L 380 GLU cc_start: 0.2620 (OUTLIER) cc_final: 0.2400 (pt0) REVERT: M 196 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7462 (m-30) REVERT: N 354 ILE cc_start: 0.7215 (OUTLIER) cc_final: 0.6972 (mp) REVERT: P 37 PHE cc_start: 0.5610 (OUTLIER) cc_final: 0.4969 (t80) REVERT: P 313 SER cc_start: 0.5305 (OUTLIER) cc_final: 0.5067 (p) REVERT: Q 232 GLU cc_start: 0.7555 (pp20) cc_final: 0.7065 (mm-30) REVERT: S 313 SER cc_start: 0.5259 (OUTLIER) cc_final: 0.5038 (p) REVERT: U 226 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8047 (tt0) REVERT: U 354 ILE cc_start: 0.7192 (OUTLIER) cc_final: 0.6933 (mp) REVERT: V 37 PHE cc_start: 0.5739 (OUTLIER) cc_final: 0.5025 (m-10) REVERT: V 193 GLU cc_start: 0.6133 (OUTLIER) cc_final: 0.5754 (tm-30) REVERT: V 196 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7345 (m-30) REVERT: X 37 PHE cc_start: 0.5355 (OUTLIER) cc_final: 0.4695 (m-10) outliers start: 312 outliers final: 157 residues processed: 733 average time/residue: 1.1001 time to fit residues: 1091.1546 Evaluate side-chains 619 residues out of total 6066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 440 time to evaluate : 4.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 45 ASP Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 188 ARG Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 380 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 96 SER Chi-restraints excluded: chain H residue 112 GLU Chi-restraints excluded: chain H residue 167 ASP 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 380 GLU Chi-restraints excluded: chain H residue 404 GLU Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 96 SER 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 462 GLU Chi-restraints excluded: chain J residue 33 THR 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 196 ASP Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 280 ASN Chi-restraints excluded: chain J residue 398 LYS 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 112 GLU 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 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 51 ILE 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 202 THR Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 233 TRP Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 380 GLU Chi-restraints excluded: chain L residue 404 GLU 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 167 ASP Chi-restraints excluded: chain M residue 196 ASP Chi-restraints excluded: chain M residue 232 GLU Chi-restraints excluded: chain M residue 239 ILE Chi-restraints excluded: chain M residue 299 THR Chi-restraints excluded: chain M residue 393 ILE Chi-restraints excluded: chain M residue 413 VAL Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 354 ILE Chi-restraints excluded: chain N residue 355 SER Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 164 ILE 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 307 VAL Chi-restraints excluded: chain O residue 313 SER Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 37 PHE Chi-restraints excluded: chain P residue 157 LEU 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 313 SER Chi-restraints excluded: chain P residue 321 LEU Chi-restraints excluded: chain P residue 413 VAL 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 239 ILE Chi-restraints excluded: chain Q residue 243 ASP Chi-restraints excluded: chain Q residue 307 VAL Chi-restraints excluded: chain Q residue 329 ASN Chi-restraints excluded: chain Q residue 354 ILE Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 83 VAL 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 239 ILE Chi-restraints excluded: chain R residue 280 ASN Chi-restraints excluded: chain R residue 299 THR Chi-restraints excluded: chain R residue 313 SER 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 157 LEU 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 313 SER Chi-restraints excluded: chain S residue 321 LEU Chi-restraints excluded: chain S residue 378 ASN Chi-restraints excluded: chain S residue 413 VAL 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 243 ASP 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 U residue 33 THR Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 51 ILE 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 234 LEU 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 329 ASN Chi-restraints excluded: chain U residue 354 ILE 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 135 SER 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 227 VAL Chi-restraints excluded: chain V residue 239 ILE Chi-restraints excluded: chain V residue 299 THR Chi-restraints excluded: chain V residue 313 SER Chi-restraints excluded: chain V residue 393 ILE Chi-restraints excluded: chain V residue 413 VAL Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain W residue 96 SER Chi-restraints excluded: chain W residue 232 GLU Chi-restraints excluded: chain W residue 239 ILE Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain W residue 329 ASN Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 37 PHE Chi-restraints excluded: chain X residue 82 THR Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 135 SER Chi-restraints excluded: chain X residue 167 ASP Chi-restraints excluded: chain X residue 239 ILE Chi-restraints excluded: chain X residue 299 THR Chi-restraints excluded: chain X residue 313 SER Chi-restraints excluded: chain X residue 393 ILE Chi-restraints excluded: chain X residue 413 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 774 random chunks: chunk 461 optimal weight: 6.9990 chunk 297 optimal weight: 20.0000 chunk 445 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 144 optimal weight: 9.9990 chunk 474 optimal weight: 0.0970 chunk 508 optimal weight: 3.9990 chunk 368 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 586 optimal weight: 7.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- 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 ** 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 280 ASN I 378 ASN ** I 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 ASN ** J 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 378 ASN K 34 ASN K 329 ASN 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 329 ASN L 378 ASN ** L 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 378 ASN ** N 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 ASN ** N 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 446 GLN ** O 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 329 ASN ** O 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 378 ASN ** P 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 GLN Q 378 ASN ** Q 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 280 ASN ** S 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 280 ASN S 378 ASN ** T 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 280 ASN ** T 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 378 ASN U 446 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 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 378 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 61506 Z= 0.290 Angle : 0.660 17.280 83826 Z= 0.355 Chirality : 0.041 0.286 9468 Planarity : 0.005 0.083 11394 Dihedral : 5.274 58.175 8568 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.64 % Favored : 96.15 % Rotamer: Outliers : 4.27 % Allowed : 32.62 % Favored : 63.11 % 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: 1.20 (0.09), residues: 7740 helix: 1.98 (0.06), residues: 5562 sheet: None (None), residues: 0 loop : -2.52 (0.11), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.004 TRP X 233 HIS 0.006 0.001 HIS W 251 PHE 0.046 0.002 PHE K 37 TYR 0.021 0.002 TYR W 153 ARG 0.009 0.001 ARG X 117 *********************** 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 737 residues out of total 6066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 479 time to evaluate : 5.096 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: G 188 ARG cc_start: 0.6963 (OUTLIER) cc_final: 0.6413 (mmt180) REVERT: H 112 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6904 (tm-30) REVERT: H 195 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6749 (mp0) REVERT: I 195 GLU cc_start: 0.7342 (mm-30) cc_final: 0.6763 (mp0) REVERT: I 380 GLU cc_start: 0.2865 (OUTLIER) cc_final: 0.2568 (pt0) REVERT: I 398 LYS cc_start: 0.6968 (mptm) cc_final: 0.6615 (mttm) REVERT: J 195 GLU cc_start: 0.7384 (mm-30) cc_final: 0.6780 (mp0) REVERT: J 380 GLU cc_start: 0.3007 (OUTLIER) cc_final: 0.2714 (pt0) REVERT: J 398 LYS cc_start: 0.7229 (OUTLIER) cc_final: 0.6969 (mmpt) REVERT: J 417 ASP cc_start: 0.8156 (m-30) cc_final: 0.7808 (m-30) REVERT: K 112 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6913 (tm-30) REVERT: K 195 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6739 (mp0) REVERT: L 195 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6616 (mp0) REVERT: L 233 TRP cc_start: 0.8172 (OUTLIER) cc_final: 0.7746 (m-10) REVERT: M 196 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7372 (m-30) REVERT: N 226 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: N 354 ILE cc_start: 0.7135 (OUTLIER) cc_final: 0.6856 (mp) REVERT: N 410 LEU cc_start: 0.8036 (tp) cc_final: 0.7709 (tp) REVERT: P 37 PHE cc_start: 0.5470 (OUTLIER) cc_final: 0.4811 (t80) REVERT: P 313 SER cc_start: 0.5290 (OUTLIER) cc_final: 0.5043 (p) REVERT: Q 232 GLU cc_start: 0.7411 (pp20) cc_final: 0.6999 (mm-30) REVERT: R 303 ASP cc_start: 0.6643 (p0) cc_final: 0.6368 (p0) REVERT: S 313 SER cc_start: 0.5223 (OUTLIER) cc_final: 0.5019 (p) REVERT: S 378 ASN cc_start: 0.7209 (OUTLIER) cc_final: 0.6837 (m-40) REVERT: U 354 ILE cc_start: 0.7144 (OUTLIER) cc_final: 0.6873 (mp) REVERT: V 193 GLU cc_start: 0.6049 (OUTLIER) cc_final: 0.5673 (tm-30) REVERT: V 196 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7154 (m-30) REVERT: X 37 PHE cc_start: 0.5269 (OUTLIER) cc_final: 0.4850 (t80) REVERT: X 232 GLU cc_start: 0.8144 (pp20) cc_final: 0.7774 (pp20) outliers start: 258 outliers final: 170 residues processed: 690 average time/residue: 1.1070 time to fit residues: 1036.1207 Evaluate side-chains 638 residues out of total 6066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 450 time to evaluate : 4.983 ------------------------------------------------------------------------------- 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 188 ARG Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 212 GLN Chi-restraints excluded: chain G residue 223 LEU 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 83 VAL Chi-restraints excluded: chain H residue 112 GLU Chi-restraints excluded: chain H residue 167 ASP 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 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 196 ASP Chi-restraints excluded: chain I residue 212 GLN Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 380 GLU Chi-restraints excluded: chain I residue 462 GLU Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 51 ILE 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 196 ASP Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 275 ASP Chi-restraints excluded: chain J residue 380 GLU Chi-restraints excluded: chain J residue 398 LYS 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 167 ASP 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 313 SER 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 202 THR Chi-restraints excluded: chain L residue 212 GLN Chi-restraints excluded: chain L residue 223 LEU 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 404 GLU Chi-restraints excluded: chain M residue 83 VAL 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 227 VAL Chi-restraints excluded: chain M residue 232 GLU Chi-restraints excluded: chain M residue 239 ILE Chi-restraints excluded: chain M residue 299 THR Chi-restraints excluded: chain M residue 313 SER Chi-restraints excluded: chain M residue 380 GLU Chi-restraints excluded: chain M residue 393 ILE Chi-restraints excluded: chain M residue 413 VAL Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 226 GLU Chi-restraints excluded: chain N residue 232 GLU Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 270 GLU 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 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 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 313 SER 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 239 ILE Chi-restraints excluded: chain P residue 313 SER Chi-restraints excluded: chain P residue 321 LEU Chi-restraints excluded: chain P residue 413 VAL 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 239 ILE Chi-restraints excluded: chain Q residue 243 ASP Chi-restraints excluded: chain Q residue 329 ASN Chi-restraints excluded: chain Q residue 354 ILE Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 83 VAL 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 227 VAL Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 299 THR Chi-restraints excluded: chain R residue 313 SER 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 157 LEU Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 239 ILE Chi-restraints excluded: chain S residue 280 ASN Chi-restraints excluded: chain S residue 313 SER Chi-restraints excluded: chain S residue 321 LEU Chi-restraints excluded: chain S residue 378 ASN Chi-restraints excluded: chain S residue 413 VAL Chi-restraints excluded: chain T residue 51 ILE Chi-restraints excluded: chain T residue 83 VAL Chi-restraints excluded: chain T residue 164 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 243 ASP 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 51 ILE Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 232 GLU Chi-restraints excluded: chain U residue 234 LEU Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 270 GLU Chi-restraints excluded: chain U residue 329 ASN Chi-restraints excluded: chain U residue 354 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 232 GLU Chi-restraints excluded: chain V residue 239 ILE Chi-restraints excluded: chain V residue 299 THR Chi-restraints excluded: chain V residue 313 SER Chi-restraints excluded: chain V residue 393 ILE Chi-restraints excluded: chain V residue 413 VAL Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain W residue 196 ASP Chi-restraints excluded: chain W residue 232 GLU Chi-restraints excluded: chain W residue 239 ILE Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain W residue 329 ASN Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 37 PHE Chi-restraints excluded: chain X residue 82 THR Chi-restraints excluded: chain X residue 83 VAL 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 209 GLU Chi-restraints excluded: chain X residue 227 VAL Chi-restraints excluded: chain X residue 239 ILE Chi-restraints excluded: chain X residue 299 THR Chi-restraints excluded: chain X residue 313 SER Chi-restraints excluded: chain X residue 393 ILE Chi-restraints excluded: chain X residue 413 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 774 random chunks: chunk 678 optimal weight: 9.9990 chunk 714 optimal weight: 8.9990 chunk 652 optimal weight: 0.3980 chunk 695 optimal weight: 7.9990 chunk 418 optimal weight: 8.9990 chunk 302 optimal weight: 6.9990 chunk 545 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 628 optimal weight: 8.9990 chunk 657 optimal weight: 10.0000 chunk 692 optimal weight: 2.9990 overall best weight: 5.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 38 ASN ** G 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 378 ASN ** G 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 378 ASN ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 378 ASN ** I 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 280 ASN J 378 ASN K 378 ASN ** K 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 ASN L 378 ASN M 378 ASN ** N 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 ASN N 407 GLN ** N 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 284 GLN ** O 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 378 ASN P 422 GLN Q 378 ASN Q 407 GLN ** Q 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 280 ASN R 324 ASN ** S 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 280 ASN S 324 ASN S 378 ASN ** T 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 378 ASN V 407 GLN ** V 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 38 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 378 ASN X 422 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 61506 Z= 0.506 Angle : 0.794 12.142 83826 Z= 0.434 Chirality : 0.048 0.267 9468 Planarity : 0.006 0.095 11394 Dihedral : 5.965 59.965 8568 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.16 % Favored : 95.63 % Rotamer: Outliers : 5.13 % Allowed : 31.96 % Favored : 62.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.09), residues: 7740 helix: 1.17 (0.06), residues: 5454 sheet: None (None), residues: 0 loop : -2.78 (0.11), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.096 0.006 TRP R 233 HIS 0.008 0.002 HIS W 251 PHE 0.036 0.003 PHE K 37 TYR 0.023 0.003 TYR P 153 ARG 0.010 0.001 ARG X 117 *********************** 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 752 residues out of total 6066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 442 time to evaluate : 5.064 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: G 188 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.6672 (mmt180) REVERT: H 275 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.7240 (t0) REVERT: H 380 GLU cc_start: 0.2613 (OUTLIER) cc_final: 0.2232 (pt0) REVERT: I 188 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.6647 (mpt-90) REVERT: I 195 GLU cc_start: 0.7348 (mm-30) cc_final: 0.6789 (mp0) REVERT: I 380 GLU cc_start: 0.2611 (OUTLIER) cc_final: 0.2239 (pt0) REVERT: I 398 LYS cc_start: 0.7068 (mptm) cc_final: 0.6708 (mttm) REVERT: J 188 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6604 (mpt-90) REVERT: J 195 GLU cc_start: 0.7454 (mm-30) cc_final: 0.6822 (mp0) REVERT: J 380 GLU cc_start: 0.2616 (OUTLIER) cc_final: 0.2251 (pt0) REVERT: K 275 ASP cc_start: 0.7485 (OUTLIER) cc_final: 0.7253 (t0) REVERT: K 380 GLU cc_start: 0.2588 (OUTLIER) cc_final: 0.2208 (pt0) REVERT: L 195 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6575 (mp0) REVERT: L 233 TRP cc_start: 0.8372 (OUTLIER) cc_final: 0.7965 (m-10) REVERT: M 196 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7513 (m-30) REVERT: N 226 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8041 (tt0) REVERT: N 354 ILE cc_start: 0.7290 (OUTLIER) cc_final: 0.7030 (mp) REVERT: O 234 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7435 (mp) REVERT: P 37 PHE cc_start: 0.5861 (OUTLIER) cc_final: 0.5074 (t80) REVERT: P 303 ASP cc_start: 0.6803 (p0) cc_final: 0.6578 (p0) REVERT: P 313 SER cc_start: 0.5336 (OUTLIER) cc_final: 0.5111 (p) REVERT: Q 232 GLU cc_start: 0.7596 (pp20) cc_final: 0.7375 (mm-30) REVERT: Q 233 TRP cc_start: 0.7657 (m-10) cc_final: 0.7354 (m-10) REVERT: S 303 ASP cc_start: 0.6817 (p0) cc_final: 0.6585 (p0) REVERT: S 313 SER cc_start: 0.5226 (OUTLIER) cc_final: 0.5010 (p) REVERT: U 226 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8048 (tt0) REVERT: U 354 ILE cc_start: 0.7264 (OUTLIER) cc_final: 0.7058 (mp) REVERT: V 193 GLU cc_start: 0.6430 (OUTLIER) cc_final: 0.5873 (tm-30) REVERT: V 196 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7496 (m-30) REVERT: W 231 PHE cc_start: 0.7511 (OUTLIER) cc_final: 0.6446 (t80) REVERT: W 233 TRP cc_start: 0.7832 (OUTLIER) cc_final: 0.7554 (m-10) REVERT: X 37 PHE cc_start: 0.5531 (OUTLIER) cc_final: 0.4799 (m-10) outliers start: 310 outliers final: 195 residues processed: 702 average time/residue: 1.1246 time to fit residues: 1066.3556 Evaluate side-chains 647 residues out of total 6066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 428 time to evaluate : 5.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 45 ASP Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 96 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 212 GLN Chi-restraints excluded: chain G residue 223 LEU 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 314 THR 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 167 ASP 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 275 ASP Chi-restraints excluded: chain H residue 286 SER Chi-restraints excluded: chain H residue 296 GLU 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 I residue 33 THR 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 380 GLU Chi-restraints excluded: chain I residue 462 GLU Chi-restraints excluded: chain J residue 33 THR 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 202 THR Chi-restraints excluded: chain J residue 223 LEU 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 380 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 167 ASP 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 275 ASP 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 36 THR Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain L residue 196 ASP Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain L residue 212 GLN Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 233 TRP Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 275 ASP Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 296 GLU Chi-restraints excluded: chain L residue 314 THR Chi-restraints excluded: chain L residue 404 GLU 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 167 ASP Chi-restraints excluded: chain M residue 196 ASP Chi-restraints excluded: chain M residue 227 VAL Chi-restraints excluded: chain M residue 233 TRP Chi-restraints excluded: chain M residue 239 ILE 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 N residue 33 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 96 SER Chi-restraints excluded: chain N residue 226 GLU Chi-restraints excluded: chain N residue 232 GLU 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 O residue 51 ILE Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 196 ASP Chi-restraints excluded: chain O residue 202 THR Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain O residue 239 ILE Chi-restraints excluded: chain O residue 243 ASP Chi-restraints excluded: chain O residue 270 GLU Chi-restraints excluded: chain O residue 307 VAL Chi-restraints excluded: chain O residue 313 SER 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 227 VAL Chi-restraints excluded: chain P residue 239 ILE Chi-restraints excluded: chain P residue 313 SER Chi-restraints excluded: chain P residue 321 LEU Chi-restraints excluded: chain P residue 413 VAL 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 239 ILE Chi-restraints excluded: chain Q residue 243 ASP Chi-restraints excluded: chain Q residue 307 VAL Chi-restraints excluded: chain Q residue 329 ASN Chi-restraints excluded: chain Q residue 354 ILE Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 167 ASP Chi-restraints excluded: chain R residue 227 VAL Chi-restraints excluded: chain R residue 232 GLU Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 263 ASP Chi-restraints excluded: chain R residue 280 ASN 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 135 SER Chi-restraints excluded: chain S residue 157 LEU 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 313 SER Chi-restraints excluded: chain S residue 321 LEU Chi-restraints excluded: chain S residue 413 VAL 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 270 GLU Chi-restraints excluded: chain T residue 307 VAL 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 51 ILE 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 233 TRP Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 243 ASP Chi-restraints excluded: chain U residue 307 VAL Chi-restraints excluded: chain U residue 329 ASN Chi-restraints excluded: chain U residue 354 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 135 SER 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 227 VAL Chi-restraints excluded: chain V residue 232 GLU Chi-restraints excluded: chain V residue 233 TRP Chi-restraints excluded: chain V residue 239 ILE Chi-restraints excluded: chain V residue 299 THR Chi-restraints excluded: chain V residue 313 SER Chi-restraints excluded: chain V residue 393 ILE Chi-restraints excluded: chain V residue 413 VAL Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain W residue 96 SER Chi-restraints excluded: chain W residue 196 ASP Chi-restraints excluded: chain W residue 223 LEU Chi-restraints excluded: chain W residue 231 PHE Chi-restraints excluded: chain W residue 233 TRP Chi-restraints excluded: chain W residue 239 ILE Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain W residue 329 ASN Chi-restraints excluded: chain W residue 355 SER Chi-restraints excluded: chain W residue 413 VAL Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 37 PHE Chi-restraints excluded: chain X residue 82 THR Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 135 SER Chi-restraints excluded: chain X residue 167 ASP Chi-restraints excluded: chain X residue 227 VAL 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 299 THR Chi-restraints excluded: chain X residue 313 SER Chi-restraints excluded: chain X residue 413 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 774 random chunks: chunk 456 optimal weight: 3.9990 chunk 735 optimal weight: 4.9990 chunk 448 optimal weight: 0.7980 chunk 348 optimal weight: 0.8980 chunk 511 optimal weight: 7.9990 chunk 771 optimal weight: 5.9990 chunk 709 optimal weight: 2.9990 chunk 614 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 474 optimal weight: 20.0000 chunk 376 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 378 ASN ** G 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 ASN H 248 GLN ** H 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 378 ASN ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 ASN ** I 248 GLN ** 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 280 ASN J 378 ASN K 34 ASN K 378 ASN ** K 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 ASN ** L 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 378 ASN ** L 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 378 ASN N 280 ASN N 407 GLN ** N 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 378 ASN ** P 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 378 ASN ** Q 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 280 ASN ** S 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 378 ASN ** T 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 280 ASN U 378 ASN ** V 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 378 ASN V 407 GLN ** V 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 284 GLN ** 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 378 ASN ** X 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.3340 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= 0.224 Angle : 0.647 12.561 83826 Z= 0.346 Chirality : 0.040 0.273 9468 Planarity : 0.005 0.091 11394 Dihedral : 5.232 57.112 8568 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.29 % Favored : 96.50 % Rotamer: Outliers : 3.37 % Allowed : 33.71 % Favored : 62.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.09), residues: 7740 helix: 2.23 (0.07), residues: 5544 sheet: None (None), residues: 0 loop : -2.45 (0.11), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.004 TRP V 233 HIS 0.005 0.001 HIS W 251 PHE 0.039 0.002 PHE T 37 TYR 0.023 0.002 TYR W 153 ARG 0.010 0.001 ARG O 443 ********************** 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 697 residues out of total 6066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 493 time to evaluate : 5.036 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 188 ARG cc_start: 0.6909 (OUTLIER) cc_final: 0.6405 (mmt180) REVERT: H 195 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6859 (mp0) REVERT: I 195 GLU cc_start: 0.7325 (mm-30) cc_final: 0.6934 (mp0) REVERT: I 398 LYS cc_start: 0.6904 (mptm) cc_final: 0.6525 (mttm) REVERT: J 195 GLU cc_start: 0.7425 (mm-30) cc_final: 0.6805 (mp0) REVERT: J 398 LYS cc_start: 0.6878 (mptm) cc_final: 0.6642 (mttm) REVERT: K 195 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6742 (mp0) REVERT: L 195 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6624 (mp0) REVERT: L 233 TRP cc_start: 0.8099 (OUTLIER) cc_final: 0.7857 (m-10) REVERT: M 196 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7244 (m-30) REVERT: N 226 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7959 (tt0) REVERT: N 232 GLU cc_start: 0.7492 (pp20) cc_final: 0.7083 (mm-30) REVERT: N 233 TRP cc_start: 0.7436 (m-10) cc_final: 0.7039 (m-10) REVERT: N 354 ILE cc_start: 0.7112 (OUTLIER) cc_final: 0.6828 (mp) REVERT: P 37 PHE cc_start: 0.5400 (OUTLIER) cc_final: 0.4749 (t80) REVERT: P 313 SER cc_start: 0.5241 (OUTLIER) cc_final: 0.5006 (p) REVERT: R 232 GLU cc_start: 0.8139 (pp20) cc_final: 0.7697 (pm20) REVERT: R 303 ASP cc_start: 0.6574 (p0) cc_final: 0.6281 (p0) REVERT: S 313 SER cc_start: 0.5295 (OUTLIER) cc_final: 0.5058 (p) REVERT: U 354 ILE cc_start: 0.7112 (OUTLIER) cc_final: 0.6843 (mp) REVERT: V 196 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.6988 (m-30) REVERT: X 232 GLU cc_start: 0.8024 (pp20) cc_final: 0.7332 (mp0) outliers start: 204 outliers final: 143 residues processed: 664 average time/residue: 1.0879 time to fit residues: 983.5551 Evaluate side-chains 615 residues out of total 6066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 462 time to evaluate : 5.015 ------------------------------------------------------------------------------- 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 188 ARG Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 239 ILE 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 45 ASP Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 167 ASP Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 239 ILE 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 83 VAL 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 462 GLU Chi-restraints excluded: chain J residue 33 THR 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 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 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 91 LEU 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 L residue 36 THR 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 223 LEU Chi-restraints excluded: chain L residue 233 TRP Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 404 GLU Chi-restraints excluded: chain M residue 88 GLU Chi-restraints excluded: chain M residue 135 SER 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 243 ASP Chi-restraints excluded: chain M residue 299 THR Chi-restraints excluded: chain M residue 313 SER Chi-restraints excluded: chain M residue 378 ASN Chi-restraints excluded: chain M residue 393 ILE Chi-restraints excluded: chain M residue 413 VAL Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 96 SER Chi-restraints excluded: chain N residue 226 GLU Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 329 ASN Chi-restraints excluded: chain N residue 354 ILE Chi-restraints excluded: chain O residue 51 ILE 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 P residue 33 THR Chi-restraints excluded: chain P residue 37 PHE Chi-restraints excluded: chain P residue 157 LEU Chi-restraints excluded: chain P residue 167 ASP Chi-restraints excluded: chain P residue 239 ILE Chi-restraints excluded: chain P residue 313 SER Chi-restraints excluded: chain P residue 321 LEU Chi-restraints excluded: chain P residue 413 VAL 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 239 ILE Chi-restraints excluded: chain Q residue 243 ASP Chi-restraints excluded: chain Q residue 329 ASN Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 83 VAL 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 227 VAL Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 280 ASN Chi-restraints excluded: chain R residue 299 THR Chi-restraints excluded: chain R residue 413 VAL 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 239 ILE 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 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 51 ILE Chi-restraints excluded: chain U residue 83 VAL 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 329 ASN Chi-restraints excluded: chain U residue 354 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 196 ASP Chi-restraints excluded: chain V residue 239 ILE Chi-restraints excluded: chain V residue 243 ASP Chi-restraints excluded: chain V residue 299 THR Chi-restraints excluded: chain V residue 378 ASN Chi-restraints excluded: chain V residue 393 ILE Chi-restraints excluded: chain V residue 413 VAL Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain W residue 196 ASP Chi-restraints excluded: chain W residue 239 ILE Chi-restraints excluded: chain X residue 33 THR Chi-restraints excluded: chain X residue 82 THR Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 135 SER Chi-restraints excluded: chain X residue 151 GLU Chi-restraints excluded: chain X residue 227 VAL 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 313 SER Chi-restraints excluded: chain X residue 393 ILE Chi-restraints excluded: chain X residue 413 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 774 random chunks: chunk 487 optimal weight: 0.9980 chunk 654 optimal weight: 5.9990 chunk 188 optimal weight: 0.0030 chunk 566 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 615 optimal weight: 3.9990 chunk 257 optimal weight: 5.9990 chunk 631 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- 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 284 GLN ** H 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 378 ASN ** H 414 GLN ** 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 378 ASN ** K 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 ASN ** L 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 378 ASN ** L 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 378 ASN N 280 ASN ** O 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 378 ASN ** P 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 GLN Q 378 ASN Q 407 GLN ** Q 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 280 ASN ** S 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 378 ASN ** T 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 292 GLN ** T 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 280 ASN 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 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 79 GLN W 378 ASN ** X 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 280 ASN X 378 ASN ** X 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.153961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.129711 restraints weight = 113022.520| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 3.08 r_work: 0.4114 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 61506 Z= 0.237 Angle : 0.656 11.969 83826 Z= 0.351 Chirality : 0.040 0.267 9468 Planarity : 0.005 0.096 11394 Dihedral : 5.077 59.999 8567 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.54 % Favored : 96.25 % Rotamer: Outliers : 3.44 % Allowed : 33.71 % Favored : 62.85 % 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: 1.75 (0.09), residues: 7740 helix: 2.41 (0.07), residues: 5544 sheet: None (None), residues: 0 loop : -2.33 (0.12), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.004 TRP K 233 HIS 0.005 0.001 HIS W 251 PHE 0.047 0.002 PHE H 37 TYR 0.020 0.002 TYR V 153 ARG 0.011 0.001 ARG X 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23569.79 seconds wall clock time: 410 minutes 3.66 seconds (24603.66 seconds total)