Starting phenix.real_space_refine on Mon Dec 30 05:45:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bm1_16117/12_2024/8bm1_16117.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bm1_16117/12_2024/8bm1_16117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bm1_16117/12_2024/8bm1_16117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bm1_16117/12_2024/8bm1_16117.map" model { file = "/net/cci-nas-00/data/ceres_data/8bm1_16117/12_2024/8bm1_16117.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bm1_16117/12_2024/8bm1_16117.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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: 7 Type Number sf(0) Gaussians K 14 8.98 5 P 42 5.49 5 Mg 14 5.21 5 S 287 5.16 5 C 36757 2.51 5 N 10255 2.21 5 O 14047 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 61416 Number of models: 1 Model: "" Number of chains: 56 Chain: "I" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "W" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 714 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 714 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 714 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 714 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 714 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 714 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 714 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 179 Classifications: {'water': 179} Link IDs: {None: 178} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 112 Classifications: {'water': 112} Link IDs: {None: 111} Chain: "A" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 180 Classifications: {'water': 180} Link IDs: {None: 179} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 115 Classifications: {'water': 115} Link IDs: {None: 114} Chain: "D" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 169 Classifications: {'water': 169} Link IDs: {None: 168} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 107 Classifications: {'water': 107} Link IDs: {None: 106} Chain: "H" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 181 Classifications: {'water': 181} Link IDs: {None: 180} Chain: "J" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "K" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 104 Classifications: {'water': 104} Link IDs: {None: 103} Chain: "L" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 155 Classifications: {'water': 155} Link IDs: {None: 154} Chain: "M" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "O" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 177 Classifications: {'water': 177} Link IDs: {None: 176} Chain: "P" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "Q" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 114 Classifications: {'water': 114} Link IDs: {None: 113} Chain: "R" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 178 Classifications: {'water': 178} Link IDs: {None: 177} Chain: "S" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "T" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 138 Classifications: {'water': 138} Link IDs: {None: 137} Residues with excluded nonbonded symmetry interactions: 7 residue: pdb="MG MG G 601 " occ=0.00 residue: pdb="MG MG C 601 " occ=0.00 residue: pdb="MG MG F 601 " occ=0.00 residue: pdb="MG MG K 601 " occ=0.00 residue: pdb="MG MG N 601 " occ=0.00 residue: pdb="MG MG Q 601 " occ=0.00 residue: pdb="MG MG T 601 " occ=0.00 Time building chain proxies: 28.14, per 1000 atoms: 0.46 Number of scatterers: 61416 At special positions: 0 Unit cell: (152.64, 150.72, 210.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 14 19.00 S 287 16.00 P 42 15.00 Mg 14 11.99 O 14047 8.00 N 10255 7.00 C 36757 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: 11.60 Conformation dependent library (CDL) restraints added in 6.0 seconds 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14462 Finding SS restraints... Secondary structure from input PDB file: 281 helices and 103 sheets defined 54.3% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.56 Creating SS restraints... Processing helix chain 'I' and resid 9 through 29 removed outlier: 3.859A pdb=" N VAL I 29 " --> pdb=" O ASP I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 60 Processing helix chain 'I' and resid 64 through 85 removed outlier: 4.063A pdb=" N VAL I 77 " --> pdb=" O MET I 73 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA I 78 " --> pdb=" O VAL I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 109 Processing helix chain 'I' and resid 112 through 135 Processing helix chain 'I' and resid 140 through 152 Processing helix chain 'I' and resid 155 through 170 Processing helix chain 'I' and resid 201 through 205 Processing helix chain 'I' and resid 233 through 244 Processing helix chain 'I' and resid 255 through 269 removed outlier: 3.717A pdb=" N LEU I 259 " --> pdb=" O GLU I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 284 through 297 Processing helix chain 'I' and resid 338 through 356 Processing helix chain 'I' and resid 358 through 373 Processing helix chain 'I' and resid 385 through 410 Processing helix chain 'I' and resid 416 through 426 Processing helix chain 'I' and resid 433 through 447 Processing helix chain 'I' and resid 448 through 458 Processing helix chain 'I' and resid 461 through 472 Processing helix chain 'I' and resid 497 through 516 removed outlier: 3.549A pdb=" N THR I 516 " --> pdb=" O GLY I 512 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 32 Processing helix chain 'G' and resid 9 through 29 Processing helix chain 'G' and resid 52 through 60 removed outlier: 3.780A pdb=" N VAL G 56 " --> pdb=" O ASP G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 86 removed outlier: 3.952A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA G 78 " --> pdb=" O VAL G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 109 Processing helix chain 'G' and resid 112 through 135 Processing helix chain 'G' and resid 142 through 152 Processing helix chain 'G' and resid 155 through 170 Processing helix chain 'G' and resid 201 through 205 removed outlier: 3.694A pdb=" N PHE G 204 " --> pdb=" O SER G 201 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE G 205 " --> pdb=" O PRO G 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 201 through 205' Processing helix chain 'G' and resid 233 through 244 Processing helix chain 'G' and resid 255 through 267 removed outlier: 4.277A pdb=" N LEU G 259 " --> pdb=" O GLU G 255 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N THR G 261 " --> pdb=" O GLU G 257 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 297 Processing helix chain 'G' and resid 338 through 356 Processing helix chain 'G' and resid 358 through 375 Processing helix chain 'G' and resid 385 through 410 Processing helix chain 'G' and resid 416 through 426 Processing helix chain 'G' and resid 433 through 447 Processing helix chain 'G' and resid 448 through 459 Processing helix chain 'G' and resid 461 through 472 Processing helix chain 'G' and resid 488 through 492 Processing helix chain 'G' and resid 497 through 515 Processing helix chain 'A' and resid 9 through 29 removed outlier: 3.884A pdb=" N VAL A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 64 through 85 removed outlier: 4.043A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 109 Processing helix chain 'A' and resid 112 through 135 Processing helix chain 'A' and resid 140 through 152 Processing helix chain 'A' and resid 155 through 170 Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 255 through 269 Processing helix chain 'A' and resid 283 through 297 Processing helix chain 'A' and resid 338 through 356 Processing helix chain 'A' and resid 358 through 373 Processing helix chain 'A' and resid 385 through 410 Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 433 through 447 Processing helix chain 'A' and resid 448 through 458 Processing helix chain 'A' and resid 461 through 472 Processing helix chain 'A' and resid 497 through 516 removed outlier: 3.689A pdb=" N THR A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'C' and resid 9 through 29 Processing helix chain 'C' and resid 52 through 60 removed outlier: 3.721A pdb=" N VAL C 56 " --> pdb=" O ASP C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 86 removed outlier: 3.943A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 109 Processing helix chain 'C' and resid 112 through 135 Processing helix chain 'C' and resid 137 through 142 Processing helix chain 'C' and resid 143 through 152 Processing helix chain 'C' and resid 155 through 170 Processing helix chain 'C' and resid 201 through 205 removed outlier: 3.614A pdb=" N PHE C 204 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE C 205 " --> pdb=" O PRO C 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 201 through 205' Processing helix chain 'C' and resid 229 through 243 removed outlier: 4.450A pdb=" N MET C 233 " --> pdb=" O ASN C 229 " (cutoff:3.500A) Proline residue: C 235 - end of helix removed outlier: 4.091A pdb=" N LYS C 242 " --> pdb=" O GLU C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 267 removed outlier: 4.338A pdb=" N LEU C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N THR C 261 " --> pdb=" O GLU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 297 Processing helix chain 'C' and resid 338 through 356 Processing helix chain 'C' and resid 358 through 375 Processing helix chain 'C' and resid 385 through 410 Processing helix chain 'C' and resid 416 through 426 Processing helix chain 'C' and resid 433 through 447 Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 461 through 472 Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 497 through 515 Processing helix chain 'D' and resid 9 through 29 removed outlier: 3.882A pdb=" N VAL D 29 " --> pdb=" O ASP D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 60 Processing helix chain 'D' and resid 64 through 86 removed outlier: 3.633A pdb=" N GLU D 76 " --> pdb=" O GLN D 72 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL D 77 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 109 Processing helix chain 'D' and resid 112 through 135 Processing helix chain 'D' and resid 140 through 152 Processing helix chain 'D' and resid 155 through 170 Processing helix chain 'D' and resid 201 through 205 Processing helix chain 'D' and resid 233 through 244 Processing helix chain 'D' and resid 255 through 269 Processing helix chain 'D' and resid 283 through 297 Processing helix chain 'D' and resid 338 through 356 Processing helix chain 'D' and resid 358 through 373 Processing helix chain 'D' and resid 385 through 410 Processing helix chain 'D' and resid 416 through 426 Processing helix chain 'D' and resid 433 through 447 Processing helix chain 'D' and resid 448 through 458 Processing helix chain 'D' and resid 461 through 472 Processing helix chain 'D' and resid 497 through 515 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'F' and resid 9 through 29 Processing helix chain 'F' and resid 52 through 60 removed outlier: 3.771A pdb=" N VAL F 56 " --> pdb=" O ASP F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 86 removed outlier: 3.931A pdb=" N VAL F 77 " --> pdb=" O MET F 73 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA F 78 " --> pdb=" O VAL F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 109 Processing helix chain 'F' and resid 112 through 135 Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 155 through 170 Processing helix chain 'F' and resid 201 through 205 removed outlier: 3.690A pdb=" N PHE F 204 " --> pdb=" O SER F 201 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE F 205 " --> pdb=" O PRO F 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 201 through 205' Processing helix chain 'F' and resid 229 through 244 removed outlier: 4.397A pdb=" N MET F 233 " --> pdb=" O ASN F 229 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 4.001A pdb=" N LYS F 242 " --> pdb=" O GLU F 238 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY F 244 " --> pdb=" O VAL F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 267 Processing helix chain 'F' and resid 281 through 297 Processing helix chain 'F' and resid 338 through 356 Processing helix chain 'F' and resid 358 through 375 Processing helix chain 'F' and resid 385 through 410 Processing helix chain 'F' and resid 416 through 426 Processing helix chain 'F' and resid 433 through 447 Processing helix chain 'F' and resid 448 through 459 Processing helix chain 'F' and resid 461 through 472 Processing helix chain 'F' and resid 488 through 492 Processing helix chain 'F' and resid 497 through 515 Processing helix chain 'H' and resid 9 through 29 removed outlier: 3.899A pdb=" N VAL H 29 " --> pdb=" O ASP H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 60 Processing helix chain 'H' and resid 64 through 85 removed outlier: 4.068A pdb=" N VAL H 77 " --> pdb=" O MET H 73 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA H 78 " --> pdb=" O VAL H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 109 Processing helix chain 'H' and resid 112 through 135 Processing helix chain 'H' and resid 140 through 152 Processing helix chain 'H' and resid 155 through 170 Processing helix chain 'H' and resid 201 through 205 Processing helix chain 'H' and resid 233 through 244 Processing helix chain 'H' and resid 255 through 269 removed outlier: 3.710A pdb=" N LEU H 259 " --> pdb=" O GLU H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 297 Processing helix chain 'H' and resid 338 through 356 Processing helix chain 'H' and resid 358 through 373 Processing helix chain 'H' and resid 385 through 410 Processing helix chain 'H' and resid 416 through 426 Processing helix chain 'H' and resid 433 through 447 Processing helix chain 'H' and resid 448 through 458 Processing helix chain 'H' and resid 461 through 472 Processing helix chain 'H' and resid 497 through 516 removed outlier: 3.604A pdb=" N THR H 516 " --> pdb=" O GLY H 512 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'K' and resid 9 through 29 Processing helix chain 'K' and resid 52 through 60 Processing helix chain 'K' and resid 64 through 86 removed outlier: 3.918A pdb=" N VAL K 77 " --> pdb=" O MET K 73 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA K 78 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 109 Processing helix chain 'K' and resid 112 through 135 Processing helix chain 'K' and resid 137 through 142 Processing helix chain 'K' and resid 143 through 152 Processing helix chain 'K' and resid 155 through 170 Processing helix chain 'K' and resid 201 through 205 removed outlier: 3.751A pdb=" N PHE K 204 " --> pdb=" O SER K 201 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE K 205 " --> pdb=" O PRO K 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 201 through 205' Processing helix chain 'K' and resid 229 through 241 removed outlier: 4.106A pdb=" N MET K 233 " --> pdb=" O ASN K 229 " (cutoff:3.500A) Proline residue: K 235 - end of helix Processing helix chain 'K' and resid 255 through 267 removed outlier: 4.235A pdb=" N THR K 261 " --> pdb=" O GLU K 257 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LEU K 262 " --> pdb=" O ALA K 258 " (cutoff:3.500A) Processing helix chain 'K' and resid 281 through 297 Processing helix chain 'K' and resid 338 through 356 Processing helix chain 'K' and resid 358 through 375 Processing helix chain 'K' and resid 385 through 410 Processing helix chain 'K' and resid 416 through 426 Processing helix chain 'K' and resid 433 through 447 Processing helix chain 'K' and resid 448 through 459 Processing helix chain 'K' and resid 461 through 472 Processing helix chain 'K' and resid 497 through 515 Processing helix chain 'L' and resid 9 through 29 removed outlier: 3.910A pdb=" N VAL L 29 " --> pdb=" O ASP L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 52 through 60 Processing helix chain 'L' and resid 64 through 85 removed outlier: 3.951A pdb=" N VAL L 77 " --> pdb=" O MET L 73 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 109 Processing helix chain 'L' and resid 112 through 135 Processing helix chain 'L' and resid 140 through 152 Processing helix chain 'L' and resid 155 through 170 Processing helix chain 'L' and resid 201 through 205 Processing helix chain 'L' and resid 233 through 244 Processing helix chain 'L' and resid 256 through 269 Processing helix chain 'L' and resid 284 through 297 Processing helix chain 'L' and resid 338 through 356 Processing helix chain 'L' and resid 358 through 373 Processing helix chain 'L' and resid 385 through 410 Processing helix chain 'L' and resid 416 through 426 Processing helix chain 'L' and resid 433 through 447 Processing helix chain 'L' and resid 448 through 458 Processing helix chain 'L' and resid 461 through 472 Processing helix chain 'L' and resid 497 through 516 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'N' and resid 9 through 29 Processing helix chain 'N' and resid 52 through 60 Processing helix chain 'N' and resid 64 through 86 removed outlier: 3.928A pdb=" N VAL N 77 " --> pdb=" O MET N 73 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA N 78 " --> pdb=" O VAL N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 109 Processing helix chain 'N' and resid 112 through 135 Processing helix chain 'N' and resid 137 through 142 Processing helix chain 'N' and resid 143 through 152 Processing helix chain 'N' and resid 155 through 170 Processing helix chain 'N' and resid 201 through 205 removed outlier: 3.612A pdb=" N PHE N 204 " --> pdb=" O SER N 201 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE N 205 " --> pdb=" O PRO N 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 201 through 205' Processing helix chain 'N' and resid 229 through 244 removed outlier: 4.372A pdb=" N MET N 233 " --> pdb=" O ASN N 229 " (cutoff:3.500A) Proline residue: N 235 - end of helix Processing helix chain 'N' and resid 255 through 267 removed outlier: 4.405A pdb=" N LEU N 259 " --> pdb=" O GLU N 255 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N THR N 261 " --> pdb=" O GLU N 257 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU N 262 " --> pdb=" O ALA N 258 " (cutoff:3.500A) Processing helix chain 'N' and resid 281 through 297 Processing helix chain 'N' and resid 338 through 356 Processing helix chain 'N' and resid 358 through 375 Processing helix chain 'N' and resid 385 through 410 Processing helix chain 'N' and resid 416 through 426 Processing helix chain 'N' and resid 433 through 447 Processing helix chain 'N' and resid 448 through 459 Processing helix chain 'N' and resid 461 through 472 Processing helix chain 'N' and resid 497 through 515 Processing helix chain 'O' and resid 9 through 29 removed outlier: 3.896A pdb=" N VAL O 29 " --> pdb=" O ASP O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 52 through 60 Processing helix chain 'O' and resid 64 through 85 removed outlier: 4.020A pdb=" N VAL O 77 " --> pdb=" O MET O 73 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA O 78 " --> pdb=" O VAL O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 88 through 109 Processing helix chain 'O' and resid 112 through 135 Processing helix chain 'O' and resid 140 through 152 Processing helix chain 'O' and resid 155 through 170 Processing helix chain 'O' and resid 201 through 205 Processing helix chain 'O' and resid 233 through 244 Processing helix chain 'O' and resid 255 through 269 removed outlier: 3.731A pdb=" N LEU O 259 " --> pdb=" O GLU O 255 " (cutoff:3.500A) Processing helix chain 'O' and resid 284 through 297 Processing helix chain 'O' and resid 338 through 356 Processing helix chain 'O' and resid 358 through 373 Processing helix chain 'O' and resid 385 through 410 Processing helix chain 'O' and resid 416 through 426 Processing helix chain 'O' and resid 433 through 447 Processing helix chain 'O' and resid 448 through 458 Processing helix chain 'O' and resid 461 through 472 Processing helix chain 'O' and resid 497 through 516 removed outlier: 3.523A pdb=" N THR O 516 " --> pdb=" O GLY O 512 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 32 Processing helix chain 'Q' and resid 9 through 29 Processing helix chain 'Q' and resid 52 through 60 Processing helix chain 'Q' and resid 64 through 86 removed outlier: 4.119A pdb=" N VAL Q 77 " --> pdb=" O MET Q 73 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA Q 78 " --> pdb=" O VAL Q 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 88 through 110 Processing helix chain 'Q' and resid 112 through 135 Processing helix chain 'Q' and resid 137 through 142 Processing helix chain 'Q' and resid 143 through 152 Processing helix chain 'Q' and resid 155 through 170 Processing helix chain 'Q' and resid 201 through 205 removed outlier: 3.616A pdb=" N PHE Q 204 " --> pdb=" O SER Q 201 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE Q 205 " --> pdb=" O PRO Q 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 201 through 205' Processing helix chain 'Q' and resid 229 through 243 removed outlier: 4.290A pdb=" N MET Q 233 " --> pdb=" O ASN Q 229 " (cutoff:3.500A) Proline residue: Q 235 - end of helix Processing helix chain 'Q' and resid 258 through 267 Processing helix chain 'Q' and resid 281 through 297 Processing helix chain 'Q' and resid 338 through 356 Processing helix chain 'Q' and resid 358 through 375 Processing helix chain 'Q' and resid 385 through 410 Processing helix chain 'Q' and resid 416 through 426 Processing helix chain 'Q' and resid 433 through 447 Processing helix chain 'Q' and resid 448 through 459 Processing helix chain 'Q' and resid 461 through 472 Processing helix chain 'Q' and resid 497 through 515 Processing helix chain 'R' and resid 9 through 29 removed outlier: 3.903A pdb=" N VAL R 29 " --> pdb=" O ASP R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 60 Processing helix chain 'R' and resid 64 through 85 removed outlier: 4.061A pdb=" N VAL R 77 " --> pdb=" O MET R 73 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA R 78 " --> pdb=" O VAL R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 109 Processing helix chain 'R' and resid 112 through 135 Processing helix chain 'R' and resid 140 through 152 Processing helix chain 'R' and resid 155 through 170 Processing helix chain 'R' and resid 201 through 205 Processing helix chain 'R' and resid 233 through 244 Processing helix chain 'R' and resid 255 through 269 removed outlier: 3.715A pdb=" N LEU R 259 " --> pdb=" O GLU R 255 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 297 Processing helix chain 'R' and resid 338 through 356 Processing helix chain 'R' and resid 358 through 373 Processing helix chain 'R' and resid 385 through 410 Processing helix chain 'R' and resid 416 through 426 Processing helix chain 'R' and resid 433 through 447 Processing helix chain 'R' and resid 448 through 458 Processing helix chain 'R' and resid 461 through 472 Processing helix chain 'R' and resid 497 through 516 removed outlier: 3.516A pdb=" N THR R 516 " --> pdb=" O GLY R 512 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'T' and resid 9 through 29 Processing helix chain 'T' and resid 52 through 60 Processing helix chain 'T' and resid 64 through 86 removed outlier: 3.818A pdb=" N VAL T 77 " --> pdb=" O MET T 73 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA T 78 " --> pdb=" O VAL T 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 88 through 109 Processing helix chain 'T' and resid 112 through 135 Processing helix chain 'T' and resid 137 through 142 Processing helix chain 'T' and resid 143 through 152 Processing helix chain 'T' and resid 155 through 170 Processing helix chain 'T' and resid 201 through 205 removed outlier: 3.727A pdb=" N PHE T 204 " --> pdb=" O SER T 201 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE T 205 " --> pdb=" O PRO T 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 201 through 205' Processing helix chain 'T' and resid 229 through 241 removed outlier: 4.140A pdb=" N MET T 233 " --> pdb=" O ASN T 229 " (cutoff:3.500A) Proline residue: T 235 - end of helix Processing helix chain 'T' and resid 255 through 267 removed outlier: 3.593A pdb=" N LEU T 259 " --> pdb=" O GLU T 255 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR T 261 " --> pdb=" O GLU T 257 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N LEU T 262 " --> pdb=" O ALA T 258 " (cutoff:3.500A) Processing helix chain 'T' and resid 281 through 297 Processing helix chain 'T' and resid 338 through 356 Processing helix chain 'T' and resid 358 through 375 Processing helix chain 'T' and resid 385 through 410 Processing helix chain 'T' and resid 416 through 426 Processing helix chain 'T' and resid 433 through 447 Processing helix chain 'T' and resid 448 through 459 Processing helix chain 'T' and resid 461 through 472 Processing helix chain 'T' and resid 497 through 515 Processing sheet with id=AA1, first strand: chain 'I' and resid 4 through 8 removed outlier: 7.414A pdb=" N VAL R 39 " --> pdb=" O GLU I 518 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N MET I 520 " --> pdb=" O VAL R 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 48 through 50 removed outlier: 6.639A pdb=" N ASN I 37 " --> pdb=" O CYS A 519 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N VAL A 521 " --> pdb=" O ASN I 37 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL I 39 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N ASP A 523 " --> pdb=" O VAL I 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 174 through 179 removed outlier: 6.348A pdb=" N VAL I 174 " --> pdb=" O ALA I 377 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ILE I 379 " --> pdb=" O VAL I 174 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR I 176 " --> pdb=" O ILE I 379 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL I 381 " --> pdb=" O THR I 176 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N GLU I 178 " --> pdb=" O VAL I 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 213 through 216 removed outlier: 8.451A pdb=" N ILE I 301 " --> pdb=" O ILE I 220 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU I 222 " --> pdb=" O ILE I 301 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 273 through 277 removed outlier: 6.391A pdb=" N LEU I 247 " --> pdb=" O ALA I 274 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL I 276 " --> pdb=" O LEU I 247 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILE I 249 " --> pdb=" O VAL I 276 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE I 219 " --> pdb=" O LEU I 248 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE I 250 " --> pdb=" O PHE I 219 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU I 221 " --> pdb=" O ILE I 250 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ALA I 320 " --> pdb=" O GLY I 335 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLY I 335 " --> pdb=" O ALA I 320 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 411 through 413 Processing sheet with id=AA7, first strand: chain 'I' and resid 476 through 479 Processing sheet with id=AA8, first strand: chain 'W' and resid 3 through 5 removed outlier: 3.683A pdb=" N ARG W 4 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B 93 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE B 64 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE B 11 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N VAL B 43 " --> pdb=" O ARG B 9 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ARG B 9 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ARG B 14 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N GLU B 82 " --> pdb=" O ARG B 14 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'W' and resid 74 through 78 removed outlier: 8.011A pdb=" N GLU W 82 " --> pdb=" O ARG W 14 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ARG W 14 " --> pdb=" O GLU W 82 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG W 9 " --> pdb=" O VAL W 43 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N VAL W 43 " --> pdb=" O ARG W 9 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE W 11 " --> pdb=" O LEU W 41 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE W 64 " --> pdb=" O VAL W 95 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE W 94 " --> pdb=" O ARG S 4 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG S 4 " --> pdb=" O ILE W 94 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'W' and resid 47 through 48 Processing sheet with id=AB2, first strand: chain 'G' and resid 4 through 8 removed outlier: 7.418A pdb=" N VAL C 39 " --> pdb=" O GLU G 518 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N MET G 520 " --> pdb=" O VAL C 39 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 48 through 50 removed outlier: 6.735A pdb=" N ASN G 37 " --> pdb=" O CYS T 519 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N VAL T 521 " --> pdb=" O ASN G 37 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL G 39 " --> pdb=" O VAL T 521 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ASP T 523 " --> pdb=" O VAL G 39 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 175 through 180 Processing sheet with id=AB5, first strand: chain 'G' and resid 193 through 195 removed outlier: 6.640A pdb=" N THR G 330 " --> pdb=" O ILE G 325 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE G 325 " --> pdb=" O THR G 330 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE G 332 " --> pdb=" O VAL G 323 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL G 323 " --> pdb=" O ILE G 332 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASP G 334 " --> pdb=" O LYS G 321 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 193 through 195 removed outlier: 6.640A pdb=" N THR G 330 " --> pdb=" O ILE G 325 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE G 325 " --> pdb=" O THR G 330 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE G 332 " --> pdb=" O VAL G 323 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL G 323 " --> pdb=" O ILE G 332 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASP G 334 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N PHE G 219 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE G 250 " --> pdb=" O PHE G 219 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU G 221 " --> pdb=" O ILE G 250 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU G 247 " --> pdb=" O ALA G 274 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL G 276 " --> pdb=" O LEU G 247 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE G 249 " --> pdb=" O VAL G 276 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 411 through 413 Processing sheet with id=AB8, first strand: chain 'G' and resid 476 through 479 Processing sheet with id=AB9, first strand: chain 'A' and resid 48 through 50 removed outlier: 6.604A pdb=" N ASN A 37 " --> pdb=" O CYS D 519 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N VAL D 521 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL A 39 " --> pdb=" O VAL D 521 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ASP D 523 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 174 through 179 removed outlier: 6.379A pdb=" N VAL A 174 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE A 379 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR A 176 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL A 381 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLU A 178 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 213 through 216 removed outlier: 8.230A pdb=" N ILE A 301 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU A 222 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 273 through 277 removed outlier: 6.305A pdb=" N LEU A 247 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N VAL A 276 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ILE A 249 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N PHE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE A 250 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU A 221 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ALA A 320 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLY A 335 " --> pdb=" O ALA A 320 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 411 through 413 Processing sheet with id=AC5, first strand: chain 'A' and resid 476 through 479 Processing sheet with id=AC6, first strand: chain 'B' and resid 3 through 5 removed outlier: 3.600A pdb=" N ARG B 4 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA E 93 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE E 64 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE E 11 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N VAL E 43 " --> pdb=" O ARG E 9 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ARG E 9 " --> pdb=" O VAL E 43 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ARG E 14 " --> pdb=" O GLU E 82 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N GLU E 82 " --> pdb=" O ARG E 14 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 47 through 48 Processing sheet with id=AC8, first strand: chain 'C' and resid 4 through 8 removed outlier: 5.950A pdb=" N ASN F 37 " --> pdb=" O THR C 517 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS C 519 " --> pdb=" O ASN F 37 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 175 through 180 removed outlier: 6.650A pdb=" N THR C 176 " --> pdb=" O ILE C 379 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL C 381 " --> pdb=" O THR C 176 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N GLU C 178 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 193 through 195 removed outlier: 6.493A pdb=" N ARG C 322 " --> pdb=" O ILE C 333 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL C 323 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 274 through 277 removed outlier: 3.705A pdb=" N ALA C 251 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY C 318 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AD4, first strand: chain 'C' and resid 476 through 479 Processing sheet with id=AD5, first strand: chain 'D' and resid 48 through 50 removed outlier: 7.338A pdb=" N ASN D 37 " --> pdb=" O GLU H 518 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N MET H 520 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL D 39 " --> pdb=" O MET H 520 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N THR H 522 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 174 through 179 removed outlier: 6.395A pdb=" N VAL D 174 " --> pdb=" O ALA D 377 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ILE D 379 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR D 176 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL D 381 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLU D 178 " --> pdb=" O VAL D 381 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 194 through 195 removed outlier: 6.256A pdb=" N GLY D 335 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ALA D 320 " --> pdb=" O GLY D 335 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N PHE D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE D 250 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU D 221 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU D 247 " --> pdb=" O ALA D 274 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL D 276 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILE D 249 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 213 through 216 removed outlier: 8.275A pdb=" N ILE D 301 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU D 222 " --> pdb=" O ILE D 301 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 411 through 413 Processing sheet with id=AE1, first strand: chain 'D' and resid 476 through 479 Processing sheet with id=AE2, first strand: chain 'E' and resid 3 through 5 removed outlier: 3.826A pdb=" N ARG E 4 " --> pdb=" O ILE J 94 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE J 94 " --> pdb=" O ARG E 4 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA J 93 " --> pdb=" O ILE J 66 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE J 64 " --> pdb=" O VAL J 95 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE J 11 " --> pdb=" O LEU J 41 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N VAL J 43 " --> pdb=" O ARG J 9 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG J 9 " --> pdb=" O VAL J 43 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG J 14 " --> pdb=" O GLU J 82 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N GLU J 82 " --> pdb=" O ARG J 14 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 47 through 48 Processing sheet with id=AE4, first strand: chain 'F' and resid 4 through 8 removed outlier: 5.988A pdb=" N ASN K 37 " --> pdb=" O THR F 517 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS F 519 " --> pdb=" O ASN K 37 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 174 through 180 removed outlier: 6.833A pdb=" N VAL F 174 " --> pdb=" O ALA F 377 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE F 379 " --> pdb=" O VAL F 174 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR F 176 " --> pdb=" O ILE F 379 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL F 381 " --> pdb=" O THR F 176 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N GLU F 178 " --> pdb=" O VAL F 381 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 193 through 195 removed outlier: 3.636A pdb=" N VAL F 323 " --> pdb=" O LEU F 215 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 274 through 277 removed outlier: 3.731A pdb=" N ALA F 251 " --> pdb=" O VAL F 276 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N PHE F 219 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ILE F 250 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU F 221 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N ILE F 301 " --> pdb=" O ILE F 220 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU F 222 " --> pdb=" O ILE F 301 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 274 through 277 removed outlier: 3.731A pdb=" N ALA F 251 " --> pdb=" O VAL F 276 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N PHE F 219 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ILE F 250 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU F 221 " --> pdb=" O ILE F 250 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 411 through 413 Processing sheet with id=AF1, first strand: chain 'F' and resid 476 through 479 Processing sheet with id=AF2, first strand: chain 'H' and resid 48 through 50 removed outlier: 7.330A pdb=" N ASN H 37 " --> pdb=" O GLU L 518 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N MET L 520 " --> pdb=" O ASN H 37 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL H 39 " --> pdb=" O MET L 520 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N THR L 522 " --> pdb=" O VAL H 39 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 174 through 179 removed outlier: 6.384A pdb=" N VAL H 174 " --> pdb=" O ALA H 377 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE H 379 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR H 176 " --> pdb=" O ILE H 379 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL H 381 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLU H 178 " --> pdb=" O VAL H 381 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 213 through 216 removed outlier: 8.460A pdb=" N ILE H 301 " --> pdb=" O ILE H 220 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU H 222 " --> pdb=" O ILE H 301 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 273 through 277 removed outlier: 6.420A pdb=" N LEU H 247 " --> pdb=" O ALA H 274 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL H 276 " --> pdb=" O LEU H 247 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ILE H 249 " --> pdb=" O VAL H 276 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ALA H 320 " --> pdb=" O GLY H 335 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY H 335 " --> pdb=" O ALA H 320 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 411 through 413 Processing sheet with id=AF7, first strand: chain 'H' and resid 476 through 479 Processing sheet with id=AF8, first strand: chain 'J' and resid 3 through 5 removed outlier: 3.727A pdb=" N ARG J 4 " --> pdb=" O ILE M 94 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA M 93 " --> pdb=" O ILE M 66 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE M 64 " --> pdb=" O VAL M 95 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE M 11 " --> pdb=" O LEU M 41 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL M 43 " --> pdb=" O ARG M 9 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ARG M 9 " --> pdb=" O VAL M 43 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ARG M 14 " --> pdb=" O GLU M 82 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N GLU M 82 " --> pdb=" O ARG M 14 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 47 through 48 Processing sheet with id=AG1, first strand: chain 'K' and resid 4 through 8 removed outlier: 5.954A pdb=" N ASN N 37 " --> pdb=" O THR K 517 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS K 519 " --> pdb=" O ASN N 37 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 175 through 179 Processing sheet with id=AG3, first strand: chain 'K' and resid 193 through 195 removed outlier: 6.513A pdb=" N ARG K 322 " --> pdb=" O ILE K 333 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL K 323 " --> pdb=" O LEU K 215 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 274 through 277 removed outlier: 5.919A pdb=" N PHE K 219 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE K 250 " --> pdb=" O PHE K 219 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU K 221 " --> pdb=" O ILE K 250 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N ILE K 301 " --> pdb=" O ILE K 220 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LEU K 222 " --> pdb=" O ILE K 301 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 274 through 277 removed outlier: 5.919A pdb=" N PHE K 219 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE K 250 " --> pdb=" O PHE K 219 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU K 221 " --> pdb=" O ILE K 250 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY K 318 " --> pdb=" O ILE K 220 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 411 through 413 Processing sheet with id=AG7, first strand: chain 'K' and resid 476 through 479 Processing sheet with id=AG8, first strand: chain 'L' and resid 48 through 50 removed outlier: 7.359A pdb=" N ASN L 37 " --> pdb=" O GLU O 518 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N MET O 520 " --> pdb=" O ASN L 37 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL L 39 " --> pdb=" O MET O 520 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N THR O 522 " --> pdb=" O VAL L 39 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 174 through 179 removed outlier: 6.351A pdb=" N VAL L 174 " --> pdb=" O ALA L 377 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE L 379 " --> pdb=" O VAL L 174 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR L 176 " --> pdb=" O ILE L 379 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL L 381 " --> pdb=" O THR L 176 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLU L 178 " --> pdb=" O VAL L 381 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 213 through 216 removed outlier: 8.422A pdb=" N ILE L 301 " --> pdb=" O ILE L 220 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU L 222 " --> pdb=" O ILE L 301 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 273 through 277 removed outlier: 6.409A pdb=" N LEU L 247 " --> pdb=" O ALA L 274 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N VAL L 276 " --> pdb=" O LEU L 247 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE L 249 " --> pdb=" O VAL L 276 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE L 219 " --> pdb=" O LEU L 248 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ILE L 250 " --> pdb=" O PHE L 219 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU L 221 " --> pdb=" O ILE L 250 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA L 320 " --> pdb=" O GLY L 335 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLY L 335 " --> pdb=" O ALA L 320 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 226 through 227 Processing sheet with id=AH4, first strand: chain 'L' and resid 411 through 413 Processing sheet with id=AH5, first strand: chain 'L' and resid 476 through 479 Processing sheet with id=AH6, first strand: chain 'M' and resid 3 through 5 removed outlier: 3.852A pdb=" N ARG M 4 " --> pdb=" O ILE P 94 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE P 94 " --> pdb=" O ARG M 4 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE P 64 " --> pdb=" O VAL P 95 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE P 11 " --> pdb=" O LEU P 41 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N VAL P 43 " --> pdb=" O ARG P 9 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ARG P 9 " --> pdb=" O VAL P 43 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ARG P 14 " --> pdb=" O GLU P 82 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N GLU P 82 " --> pdb=" O ARG P 14 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'M' and resid 47 through 48 Processing sheet with id=AH8, first strand: chain 'N' and resid 4 through 8 removed outlier: 5.942A pdb=" N ASN Q 37 " --> pdb=" O THR N 517 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS N 519 " --> pdb=" O ASN Q 37 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'N' and resid 175 through 179 Processing sheet with id=AI1, first strand: chain 'N' and resid 193 through 195 removed outlier: 6.661A pdb=" N THR N 330 " --> pdb=" O ILE N 325 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE N 325 " --> pdb=" O THR N 330 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE N 332 " --> pdb=" O VAL N 323 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL N 323 " --> pdb=" O ILE N 332 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASP N 334 " --> pdb=" O LYS N 321 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N PHE N 219 " --> pdb=" O LEU N 248 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE N 250 " --> pdb=" O PHE N 219 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU N 221 " --> pdb=" O ILE N 250 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU N 247 " --> pdb=" O ALA N 274 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N VAL N 276 " --> pdb=" O LEU N 247 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE N 249 " --> pdb=" O VAL N 276 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'N' and resid 213 through 216 removed outlier: 9.349A pdb=" N ILE N 301 " --> pdb=" O ILE N 220 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU N 222 " --> pdb=" O ILE N 301 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'N' and resid 411 through 413 Processing sheet with id=AI4, first strand: chain 'N' and resid 476 through 479 Processing sheet with id=AI5, first strand: chain 'O' and resid 48 through 50 removed outlier: 6.687A pdb=" N ASN O 37 " --> pdb=" O CYS R 519 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N VAL R 521 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL O 39 " --> pdb=" O VAL R 521 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N ASP R 523 " --> pdb=" O VAL O 39 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'O' and resid 174 through 179 removed outlier: 6.421A pdb=" N VAL O 174 " --> pdb=" O ALA O 377 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE O 379 " --> pdb=" O VAL O 174 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR O 176 " --> pdb=" O ILE O 379 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL O 381 " --> pdb=" O THR O 176 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLU O 178 " --> pdb=" O VAL O 381 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'O' and resid 213 through 216 removed outlier: 8.422A pdb=" N ILE O 301 " --> pdb=" O ILE O 220 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU O 222 " --> pdb=" O ILE O 301 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'O' and resid 273 through 277 removed outlier: 6.403A pdb=" N LEU O 247 " --> pdb=" O ALA O 274 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL O 276 " --> pdb=" O LEU O 247 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ILE O 249 " --> pdb=" O VAL O 276 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N PHE O 219 " --> pdb=" O LEU O 248 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ILE O 250 " --> pdb=" O PHE O 219 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU O 221 " --> pdb=" O ILE O 250 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ALA O 320 " --> pdb=" O GLY O 335 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLY O 335 " --> pdb=" O ALA O 320 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'O' and resid 411 through 413 Processing sheet with id=AJ1, first strand: chain 'O' and resid 476 through 479 Processing sheet with id=AJ2, first strand: chain 'P' and resid 3 through 5 removed outlier: 4.379A pdb=" N ARG P 4 " --> pdb=" O ILE S 94 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE S 94 " --> pdb=" O ARG P 4 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE S 64 " --> pdb=" O VAL S 95 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE S 11 " --> pdb=" O LEU S 41 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VAL S 43 " --> pdb=" O ARG S 9 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ARG S 9 " --> pdb=" O VAL S 43 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ARG S 14 " --> pdb=" O GLU S 82 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N GLU S 82 " --> pdb=" O ARG S 14 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'P' and resid 47 through 48 Processing sheet with id=AJ4, first strand: chain 'Q' and resid 4 through 8 removed outlier: 5.981A pdb=" N ASN T 37 " --> pdb=" O THR Q 517 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS Q 519 " --> pdb=" O ASN T 37 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'Q' and resid 175 through 179 Processing sheet with id=AJ6, first strand: chain 'Q' and resid 193 through 195 removed outlier: 6.463A pdb=" N ARG Q 322 " --> pdb=" O ILE Q 333 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL Q 323 " --> pdb=" O LEU Q 215 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'Q' and resid 274 through 277 removed outlier: 3.804A pdb=" N ALA Q 251 " --> pdb=" O VAL Q 276 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N ILE Q 301 " --> pdb=" O ILE Q 220 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LEU Q 222 " --> pdb=" O ILE Q 301 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'Q' and resid 274 through 277 removed outlier: 3.804A pdb=" N ALA Q 251 " --> pdb=" O VAL Q 276 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'Q' and resid 411 through 413 Processing sheet with id=AK1, first strand: chain 'Q' and resid 476 through 479 Processing sheet with id=AK2, first strand: chain 'R' and resid 174 through 179 removed outlier: 6.406A pdb=" N VAL R 174 " --> pdb=" O ALA R 377 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE R 379 " --> pdb=" O VAL R 174 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR R 176 " --> pdb=" O ILE R 379 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL R 381 " --> pdb=" O THR R 176 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLU R 178 " --> pdb=" O VAL R 381 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'R' and resid 213 through 216 removed outlier: 8.453A pdb=" N ILE R 301 " --> pdb=" O ILE R 220 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU R 222 " --> pdb=" O ILE R 301 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'R' and resid 273 through 277 removed outlier: 6.401A pdb=" N LEU R 247 " --> pdb=" O ALA R 274 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL R 276 " --> pdb=" O LEU R 247 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE R 249 " --> pdb=" O VAL R 276 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE R 219 " --> pdb=" O LEU R 248 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE R 250 " --> pdb=" O PHE R 219 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU R 221 " --> pdb=" O ILE R 250 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ALA R 320 " --> pdb=" O GLY R 335 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY R 335 " --> pdb=" O ALA R 320 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'R' and resid 411 through 413 Processing sheet with id=AK6, first strand: chain 'R' and resid 476 through 479 Processing sheet with id=AK7, first strand: chain 'S' and resid 47 through 48 Processing sheet with id=AK8, first strand: chain 'T' and resid 174 through 180 removed outlier: 6.727A pdb=" N VAL T 174 " --> pdb=" O ALA T 377 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ILE T 379 " --> pdb=" O VAL T 174 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR T 176 " --> pdb=" O ILE T 379 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL T 381 " --> pdb=" O THR T 176 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLU T 178 " --> pdb=" O VAL T 381 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'T' and resid 193 through 195 removed outlier: 6.397A pdb=" N ARG T 322 " --> pdb=" O ILE T 333 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL T 323 " --> pdb=" O LEU T 215 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'T' and resid 274 through 277 removed outlier: 9.152A pdb=" N ILE T 301 " --> pdb=" O ILE T 220 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N LEU T 222 " --> pdb=" O ILE T 301 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'T' and resid 274 through 277 removed outlier: 3.754A pdb=" N GLY T 318 " --> pdb=" O ILE T 220 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'T' and resid 411 through 413 Processing sheet with id=AL4, first strand: chain 'T' and resid 476 through 479 3815 hydrogen bonds defined for protein. 10974 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: 30.33 Time building geometry restraints manager: 13.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 17955 1.33 - 1.45: 5849 1.45 - 1.57: 35368 1.57 - 1.69: 69 1.69 - 1.81: 532 Bond restraints: 59773 Sorted by residual: bond pdb=" C GLY K 244 " pdb=" N LYS K 245 " ideal model delta sigma weight residual 1.332 1.315 0.016 7.50e-03 1.78e+04 4.72e+00 bond pdb=" CG LYS G 242 " pdb=" CD LYS G 242 " ideal model delta sigma weight residual 1.520 1.462 0.058 3.00e-02 1.11e+03 3.75e+00 bond pdb=" CB ASN M 80 " pdb=" CG ASN M 80 " ideal model delta sigma weight residual 1.516 1.562 -0.046 2.50e-02 1.60e+03 3.44e+00 bond pdb=" CB VAL N 236 " pdb=" CG2 VAL N 236 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.25e+00 bond pdb=" C GLY G 244 " pdb=" N LYS G 245 " ideal model delta sigma weight residual 1.340 1.236 0.104 5.87e-02 2.90e+02 3.17e+00 ... (remaining 59768 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 80257 3.36 - 6.71: 482 6.71 - 10.07: 46 10.07 - 13.42: 14 13.42 - 16.78: 2 Bond angle restraints: 80801 Sorted by residual: angle pdb=" CA GLU T 255 " pdb=" CB GLU T 255 " pdb=" CG GLU T 255 " ideal model delta sigma weight residual 114.10 130.88 -16.78 2.00e+00 2.50e-01 7.04e+01 angle pdb=" CA GLU K 255 " pdb=" CB GLU K 255 " pdb=" CG GLU K 255 " ideal model delta sigma weight residual 114.10 130.35 -16.25 2.00e+00 2.50e-01 6.60e+01 angle pdb=" N GLU K 255 " pdb=" CA GLU K 255 " pdb=" CB GLU K 255 " ideal model delta sigma weight residual 109.71 119.35 -9.64 1.54e+00 4.22e-01 3.92e+01 angle pdb=" C LYS K 245 " pdb=" CA LYS K 245 " pdb=" CB LYS K 245 " ideal model delta sigma weight residual 111.01 118.54 -7.53 1.38e+00 5.25e-01 2.98e+01 angle pdb=" N GLU T 255 " pdb=" CA GLU T 255 " pdb=" CB GLU T 255 " ideal model delta sigma weight residual 109.60 118.48 -8.88 1.64e+00 3.72e-01 2.93e+01 ... (remaining 80796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 33213 17.89 - 35.78: 2895 35.78 - 53.67: 874 53.67 - 71.56: 229 71.56 - 89.45: 78 Dihedral angle restraints: 37289 sinusoidal: 14742 harmonic: 22547 Sorted by residual: dihedral pdb=" CG ARG I 284 " pdb=" CD ARG I 284 " pdb=" NE ARG I 284 " pdb=" CZ ARG I 284 " ideal model delta sinusoidal sigma weight residual -90.00 -39.96 -50.04 2 1.50e+01 4.44e-03 1.25e+01 dihedral pdb=" CG ARG F 404 " pdb=" CD ARG F 404 " pdb=" NE ARG F 404 " pdb=" CZ ARG F 404 " ideal model delta sinusoidal sigma weight residual -90.00 -40.28 -49.72 2 1.50e+01 4.44e-03 1.24e+01 dihedral pdb=" CA PHE T 8 " pdb=" C PHE T 8 " pdb=" N GLY T 9 " pdb=" CA GLY T 9 " ideal model delta harmonic sigma weight residual 180.00 162.78 17.22 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 37286 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 7993 0.058 - 0.116: 1569 0.116 - 0.174: 215 0.174 - 0.232: 25 0.232 - 0.290: 5 Chirality restraints: 9807 Sorted by residual: chirality pdb=" CB ILE K 227 " pdb=" CA ILE K 227 " pdb=" CG1 ILE K 227 " pdb=" CG2 ILE K 227 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CG LEU R 365 " pdb=" CB LEU R 365 " pdb=" CD1 LEU R 365 " pdb=" CD2 LEU R 365 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CG LEU H 365 " pdb=" CB LEU H 365 " pdb=" CD1 LEU H 365 " pdb=" CD2 LEU H 365 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 9804 not shown) Planarity restraints: 10507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP K 253 " -0.024 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C ASP K 253 " 0.085 2.00e-02 2.50e+03 pdb=" O ASP K 253 " -0.032 2.00e-02 2.50e+03 pdb=" N VAL K 254 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU T 255 " -0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" CD GLU T 255 " 0.066 2.00e-02 2.50e+03 pdb=" OE1 GLU T 255 " -0.024 2.00e-02 2.50e+03 pdb=" OE2 GLU T 255 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU K 255 " 0.018 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" CD GLU K 255 " -0.065 2.00e-02 2.50e+03 pdb=" OE1 GLU K 255 " 0.024 2.00e-02 2.50e+03 pdb=" OE2 GLU K 255 " 0.023 2.00e-02 2.50e+03 ... (remaining 10504 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.59: 1046 2.59 - 3.23: 62502 3.23 - 3.86: 135818 3.86 - 4.50: 182892 4.50 - 5.14: 278500 Nonbonded interactions: 660758 Sorted by model distance: nonbonded pdb=" O ASN M 80 " pdb=" ND2 ASN M 80 " model vdw 1.948 3.120 nonbonded pdb=" O ASN E 80 " pdb=" ND2 ASN E 80 " model vdw 1.971 3.120 nonbonded pdb=" O ASN J 80 " pdb=" ND2 ASN J 80 " model vdw 1.972 3.120 nonbonded pdb=" O ASN P 80 " pdb=" ND2 ASN P 80 " model vdw 1.975 3.120 nonbonded pdb=" O ASN B 80 " pdb=" ND2 ASN B 80 " model vdw 2.029 3.120 ... (remaining 660753 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 524 or resid 601)) selection = (chain 'C' and (resid 2 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 524 or resid 601)) selection = (chain 'D' and (resid 2 through 524 or resid 601)) selection = (chain 'F' and (resid 2 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 524 or resid 601)) selection = (chain 'G' and (resid 2 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 524 or resid 601)) selection = (chain 'H' and (resid 2 through 524 or resid 601)) selection = (chain 'I' and (resid 2 through 524 or resid 601)) selection = (chain 'K' and (resid 2 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 524 or resid 601)) selection = (chain 'L' and (resid 2 through 524 or resid 601)) selection = (chain 'N' and (resid 2 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 524 or resid 601)) selection = (chain 'O' and (resid 2 through 524 or resid 601)) selection = (chain 'Q' and (resid 2 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 524 or resid 601)) selection = (chain 'R' and (resid 2 through 524 or resid 601)) selection = (chain 'T' and (resid 2 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 524 or resid 601)) } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 6.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 1.800 Check model and map are aligned: 0.340 Set scattering table: 0.440 Process input model: 115.130 Find NCS groups from input model: 2.990 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: 0.020 Load rotamer database and sin/cos tables:11.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 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 0.104 59773 Z= 0.258 Angle : 0.727 16.777 80801 Z= 0.400 Chirality : 0.047 0.290 9807 Planarity : 0.005 0.088 10507 Dihedral : 15.947 89.449 22827 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.82 % Favored : 98.05 % Rotamer: Outliers : 0.81 % Allowed : 18.38 % Favored : 80.81 % 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: 1.10 (0.09), residues: 7959 helix: 1.49 (0.08), residues: 4193 sheet: 0.77 (0.16), residues: 1008 loop : -0.38 (0.11), residues: 2758 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 7 PHE 0.021 0.001 PHE I 219 TYR 0.016 0.002 TYR G 478 ARG 0.019 0.001 ARG R 362 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 700 time to evaluate : 5.105 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: I 69 MET cc_start: 0.8971 (mtp) cc_final: 0.8725 (mtp) REVERT: W 64 ILE cc_start: 0.9129 (mp) cc_final: 0.8922 (mm) REVERT: G 288 MET cc_start: 0.5371 (mpt) cc_final: 0.4444 (ptt) REVERT: C 288 MET cc_start: 0.6504 (mpt) cc_final: 0.5126 (ptt) REVERT: D 73 MET cc_start: 0.8914 (mtm) cc_final: 0.8665 (mtm) REVERT: E 21 SER cc_start: 0.8256 (t) cc_final: 0.7971 (p) REVERT: E 35 SER cc_start: 0.8753 (t) cc_final: 0.8546 (t) REVERT: J 20 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7843 (ttmm) REVERT: J 35 SER cc_start: 0.8811 (t) cc_final: 0.8490 (p) REVERT: J 74 LYS cc_start: 0.8516 (mptm) cc_final: 0.8276 (tttm) REVERT: J 77 LYS cc_start: 0.8695 (tppp) cc_final: 0.8270 (mmmm) REVERT: M 35 SER cc_start: 0.8714 (t) cc_final: 0.8380 (p) REVERT: M 76 GLU cc_start: 0.7547 (tp30) cc_final: 0.7161 (tp30) REVERT: N 288 MET cc_start: 0.4589 (mpt) cc_final: 0.3990 (ptt) REVERT: P 35 SER cc_start: 0.8800 (t) cc_final: 0.8447 (p) REVERT: Q 491 MET cc_start: 0.9430 (mtm) cc_final: 0.9213 (mtp) REVERT: S 76 GLU cc_start: 0.7817 (tp30) cc_final: 0.7581 (tp30) outliers start: 50 outliers final: 14 residues processed: 728 average time/residue: 1.4458 time to fit residues: 1339.1648 Evaluate side-chains 665 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 650 time to evaluate : 5.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain G residue 43 SER Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain H residue 184 GLN Chi-restraints excluded: chain H residue 307 MET Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 80 ASN Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain Q residue 138 CYS Chi-restraints excluded: chain R residue 184 GLN Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 299 THR Chi-restraints excluded: chain S residue 64 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 667 optimal weight: 3.9990 chunk 599 optimal weight: 4.9990 chunk 332 optimal weight: 0.6980 chunk 204 optimal weight: 9.9990 chunk 404 optimal weight: 1.9990 chunk 320 optimal weight: 20.0000 chunk 619 optimal weight: 0.8980 chunk 239 optimal weight: 3.9990 chunk 376 optimal weight: 4.9990 chunk 461 optimal weight: 0.9980 chunk 718 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 319 GLN W 45 ASN A 343 GLN A 352 GLN A 366 GLN B 45 ASN B 80 ASN D 82 ASN E 45 ASN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 319 GLN J 45 ASN M 45 ASN ** O 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 467 ASN R 319 GLN S 45 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 59773 Z= 0.282 Angle : 0.580 8.424 80801 Z= 0.315 Chirality : 0.044 0.186 9807 Planarity : 0.004 0.051 10507 Dihedral : 9.539 89.495 8942 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.01 % Allowed : 0.99 % Favored : 98.99 % Rotamer: Outliers : 2.73 % Allowed : 14.90 % Favored : 82.37 % 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: 1.26 (0.09), residues: 7959 helix: 1.73 (0.08), residues: 4193 sheet: 0.70 (0.15), residues: 1015 loop : -0.44 (0.11), residues: 2751 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 7 PHE 0.014 0.001 PHE K 219 TYR 0.016 0.002 TYR C 478 ARG 0.025 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 679 time to evaluate : 5.099 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: G 267 MET cc_start: 0.2966 (OUTLIER) cc_final: 0.2761 (ppp) REVERT: G 288 MET cc_start: 0.5379 (mpt) cc_final: 0.4689 (ptt) REVERT: C 200 LEU cc_start: 0.3688 (OUTLIER) cc_final: 0.3036 (pt) REVERT: C 288 MET cc_start: 0.6814 (OUTLIER) cc_final: 0.5523 (ptt) REVERT: C 491 MET cc_start: 0.9457 (mtm) cc_final: 0.9197 (mtm) REVERT: D 73 MET cc_start: 0.8949 (mtm) cc_final: 0.8693 (mtm) REVERT: D 321 LYS cc_start: 0.8465 (mppt) cc_final: 0.8159 (mppt) REVERT: F 193 MET cc_start: 0.5297 (OUTLIER) cc_final: 0.4750 (tmt) REVERT: F 267 MET cc_start: 0.2628 (OUTLIER) cc_final: 0.2346 (ppp) REVERT: F 288 MET cc_start: 0.4377 (ptt) cc_final: 0.4051 (mpm) REVERT: F 307 MET cc_start: 0.4750 (mmm) cc_final: 0.4363 (tpt) REVERT: H 233 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.7017 (ttm) REVERT: H 362 ARG cc_start: 0.7716 (ptp90) cc_final: 0.7475 (ttp-110) REVERT: J 74 LYS cc_start: 0.8513 (mptm) cc_final: 0.8275 (tttm) REVERT: J 80 ASN cc_start: 0.7598 (OUTLIER) cc_final: 0.7349 (t0) REVERT: K 267 MET cc_start: 0.1883 (OUTLIER) cc_final: 0.1408 (ppp) REVERT: L 184 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8081 (mp10) REVERT: L 288 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7455 (mpp) REVERT: L 322 ARG cc_start: 0.8049 (mmm-85) cc_final: 0.7663 (ttp80) REVERT: L 325 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8331 (mm) REVERT: L 362 ARG cc_start: 0.7525 (ptp90) cc_final: 0.7284 (ttp-110) REVERT: M 35 SER cc_start: 0.8734 (t) cc_final: 0.8370 (p) REVERT: N 200 LEU cc_start: 0.2595 (OUTLIER) cc_final: 0.2140 (pt) REVERT: N 288 MET cc_start: 0.4626 (OUTLIER) cc_final: 0.4170 (ptt) REVERT: O 184 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8009 (mp10) REVERT: O 220 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8633 (mm) REVERT: P 35 SER cc_start: 0.8833 (t) cc_final: 0.8457 (p) REVERT: Q 267 MET cc_start: 0.1895 (OUTLIER) cc_final: 0.1509 (ppp) REVERT: Q 491 MET cc_start: 0.9426 (mtm) cc_final: 0.9192 (mtp) REVERT: R 233 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6706 (ttm) REVERT: S 74 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8334 (tmtt) REVERT: T 200 LEU cc_start: 0.2345 (OUTLIER) cc_final: 0.1989 (pt) REVERT: T 288 MET cc_start: 0.4931 (OUTLIER) cc_final: 0.4580 (ptt) outliers start: 169 outliers final: 36 residues processed: 776 average time/residue: 1.4795 time to fit residues: 1457.6474 Evaluate side-chains 704 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 648 time to evaluate : 5.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 343 GLN Chi-restraints excluded: chain W residue 87 SER Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 184 GLN Chi-restraints excluded: chain H residue 233 MET Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 80 ASN Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain L residue 184 GLN Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 299 THR Chi-restraints excluded: chain L residue 325 ILE Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 288 MET Chi-restraints excluded: chain O residue 184 GLN Chi-restraints excluded: chain O residue 220 ILE Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain Q residue 138 CYS Chi-restraints excluded: chain Q residue 267 MET Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 184 GLN Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 233 MET Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain S residue 74 LYS Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 288 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 399 optimal weight: 5.9990 chunk 222 optimal weight: 0.0570 chunk 597 optimal weight: 5.9990 chunk 489 optimal weight: 7.9990 chunk 198 optimal weight: 40.0000 chunk 719 optimal weight: 1.9990 chunk 777 optimal weight: 0.9980 chunk 640 optimal weight: 3.9990 chunk 713 optimal weight: 5.9990 chunk 245 optimal weight: 0.7980 chunk 577 optimal weight: 0.9980 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 45 ASN A 352 GLN B 45 ASN E 45 ASN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 ASN L 319 GLN O 319 GLN R 319 GLN S 45 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 59773 Z= 0.204 Angle : 0.522 8.293 80801 Z= 0.284 Chirality : 0.042 0.185 9807 Planarity : 0.003 0.045 10507 Dihedral : 9.296 89.971 8926 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.70 % Allowed : 15.22 % Favored : 82.07 % 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: 1.40 (0.09), residues: 7959 helix: 1.87 (0.08), residues: 4200 sheet: 0.67 (0.15), residues: 1022 loop : -0.42 (0.11), residues: 2737 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS G 401 PHE 0.022 0.001 PHE K 219 TYR 0.015 0.001 TYR D 360 ARG 0.008 0.000 ARG I 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 687 time to evaluate : 5.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 200 LEU cc_start: 0.2455 (OUTLIER) cc_final: 0.2055 (pt) REVERT: G 267 MET cc_start: 0.3031 (OUTLIER) cc_final: 0.2579 (ppp) REVERT: G 288 MET cc_start: 0.5204 (OUTLIER) cc_final: 0.4682 (ptt) REVERT: G 307 MET cc_start: 0.2838 (tpt) cc_final: 0.2623 (mmm) REVERT: C 193 MET cc_start: 0.5443 (OUTLIER) cc_final: 0.4541 (tmt) REVERT: C 200 LEU cc_start: 0.3388 (OUTLIER) cc_final: 0.2782 (pt) REVERT: C 233 MET cc_start: 0.2538 (OUTLIER) cc_final: 0.2252 (ptt) REVERT: C 267 MET cc_start: 0.2671 (OUTLIER) cc_final: 0.2208 (ppp) REVERT: C 288 MET cc_start: 0.6800 (OUTLIER) cc_final: 0.5531 (ptt) REVERT: C 491 MET cc_start: 0.9441 (mtm) cc_final: 0.9139 (mtm) REVERT: E 86 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8279 (ptt) REVERT: F 193 MET cc_start: 0.5297 (OUTLIER) cc_final: 0.4736 (tmt) REVERT: F 267 MET cc_start: 0.2692 (OUTLIER) cc_final: 0.2386 (ppp) REVERT: F 307 MET cc_start: 0.4782 (mmm) cc_final: 0.4383 (tpt) REVERT: H 233 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.7122 (ttm) REVERT: H 267 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8289 (mtt) REVERT: H 307 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.7063 (ptm) REVERT: H 362 ARG cc_start: 0.7620 (ptp90) cc_final: 0.7271 (ttm110) REVERT: J 74 LYS cc_start: 0.8540 (mptm) cc_final: 0.8326 (tttm) REVERT: J 80 ASN cc_start: 0.7621 (OUTLIER) cc_final: 0.7330 (t0) REVERT: K 262 LEU cc_start: -0.1318 (OUTLIER) cc_final: -0.1907 (pp) REVERT: K 267 MET cc_start: 0.1702 (OUTLIER) cc_final: 0.1145 (ppp) REVERT: L 184 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8070 (mp10) REVERT: L 322 ARG cc_start: 0.8029 (mmm-85) cc_final: 0.7749 (ttp80) REVERT: L 325 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8243 (mm) REVERT: L 362 ARG cc_start: 0.7594 (ptp90) cc_final: 0.7330 (ttp-110) REVERT: N 193 MET cc_start: 0.4861 (OUTLIER) cc_final: 0.4215 (tmt) REVERT: N 200 LEU cc_start: 0.2528 (OUTLIER) cc_final: 0.2175 (pt) REVERT: N 288 MET cc_start: 0.4583 (OUTLIER) cc_final: 0.4187 (ptt) REVERT: O 184 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8019 (mp10) REVERT: O 220 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8646 (mm) REVERT: O 322 ARG cc_start: 0.8146 (mmm-85) cc_final: 0.7713 (ttp80) REVERT: P 35 SER cc_start: 0.8856 (t) cc_final: 0.8453 (p) REVERT: Q 267 MET cc_start: 0.1786 (OUTLIER) cc_final: 0.1419 (ppp) REVERT: Q 491 MET cc_start: 0.9378 (mtm) cc_final: 0.9166 (mtp) REVERT: R 63 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7356 (tm-30) REVERT: S 74 LYS cc_start: 0.8736 (tmtt) cc_final: 0.8422 (tmtt) REVERT: S 76 GLU cc_start: 0.7819 (tp30) cc_final: 0.7595 (tp30) REVERT: T 200 LEU cc_start: 0.2281 (OUTLIER) cc_final: 0.1922 (pt) REVERT: T 267 MET cc_start: 0.2004 (OUTLIER) cc_final: 0.1601 (ppp) REVERT: T 288 MET cc_start: 0.5214 (OUTLIER) cc_final: 0.4859 (ptt) outliers start: 167 outliers final: 45 residues processed: 774 average time/residue: 1.4840 time to fit residues: 1456.4802 Evaluate side-chains 732 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 658 time to evaluate : 5.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 86 MET Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 184 GLN Chi-restraints excluded: chain H residue 233 MET Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 307 MET Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 80 ASN Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain L residue 184 GLN Chi-restraints excluded: chain L residue 188 ASP Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 299 THR Chi-restraints excluded: chain L residue 325 ILE Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 288 MET Chi-restraints excluded: chain O residue 176 THR Chi-restraints excluded: chain O residue 184 GLN Chi-restraints excluded: chain O residue 220 ILE Chi-restraints excluded: chain O residue 227 ILE Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain Q residue 138 CYS Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 267 MET Chi-restraints excluded: chain R residue 63 GLU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain S residue 69 ASP Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 245 LYS Chi-restraints excluded: chain T residue 267 MET Chi-restraints excluded: chain T residue 288 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 710 optimal weight: 1.9990 chunk 541 optimal weight: 30.0000 chunk 373 optimal weight: 0.9990 chunk 79 optimal weight: 20.0000 chunk 343 optimal weight: 3.9990 chunk 483 optimal weight: 10.0000 chunk 722 optimal weight: 1.9990 chunk 764 optimal weight: 20.0000 chunk 377 optimal weight: 4.9990 chunk 684 optimal weight: 1.9990 chunk 206 optimal weight: 30.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 45 ASN ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 ASN A 352 GLN B 45 ASN E 45 ASN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 ASN J 7 HIS J 45 ASN L 366 GLN O 112 ASN ** O 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 319 GLN S 45 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 59773 Z= 0.319 Angle : 0.558 8.385 80801 Z= 0.301 Chirality : 0.045 0.216 9807 Planarity : 0.004 0.054 10507 Dihedral : 9.511 89.747 8923 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.77 % Allowed : 15.77 % Favored : 81.46 % 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: 1.23 (0.09), residues: 7959 helix: 1.67 (0.08), residues: 4228 sheet: 0.71 (0.15), residues: 1085 loop : -0.48 (0.11), residues: 2646 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS L 401 PHE 0.015 0.001 PHE N 219 TYR 0.015 0.002 TYR D 360 ARG 0.009 0.001 ARG L 284 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 689 time to evaluate : 5.017 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: G 200 LEU cc_start: 0.2406 (OUTLIER) cc_final: 0.2007 (pt) REVERT: G 267 MET cc_start: 0.3242 (OUTLIER) cc_final: 0.2685 (ppp) REVERT: G 288 MET cc_start: 0.5163 (OUTLIER) cc_final: 0.4581 (ptt) REVERT: G 404 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7558 (mpt90) REVERT: C 193 MET cc_start: 0.5390 (OUTLIER) cc_final: 0.4480 (tmt) REVERT: C 200 LEU cc_start: 0.3227 (OUTLIER) cc_final: 0.2654 (pt) REVERT: C 267 MET cc_start: 0.2928 (OUTLIER) cc_final: 0.2434 (ppp) REVERT: C 288 MET cc_start: 0.6776 (OUTLIER) cc_final: 0.5504 (ptt) REVERT: C 491 MET cc_start: 0.9486 (mtm) cc_final: 0.9154 (mtm) REVERT: D 63 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7336 (tm-30) REVERT: D 366 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7882 (tp40) REVERT: F 193 MET cc_start: 0.5192 (OUTLIER) cc_final: 0.4629 (tmt) REVERT: F 267 MET cc_start: 0.2616 (OUTLIER) cc_final: 0.2324 (ppp) REVERT: F 307 MET cc_start: 0.4772 (mmm) cc_final: 0.4354 (tpt) REVERT: H 63 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7212 (tm-30) REVERT: H 233 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.7158 (ttm) REVERT: H 267 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8273 (mtt) REVERT: H 362 ARG cc_start: 0.7640 (ptp90) cc_final: 0.7427 (ttp-110) REVERT: J 80 ASN cc_start: 0.7669 (OUTLIER) cc_final: 0.7384 (t0) REVERT: K 267 MET cc_start: 0.1496 (OUTLIER) cc_final: 0.0776 (ppp) REVERT: L 325 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8392 (mm) REVERT: L 362 ARG cc_start: 0.7587 (ptp90) cc_final: 0.7380 (ttp-110) REVERT: L 483 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.7380 (mm-30) REVERT: N 193 MET cc_start: 0.4815 (OUTLIER) cc_final: 0.4151 (tmt) REVERT: N 200 LEU cc_start: 0.2403 (OUTLIER) cc_final: 0.2054 (pt) REVERT: N 288 MET cc_start: 0.4605 (OUTLIER) cc_final: 0.4172 (ptt) REVERT: O 160 LYS cc_start: 0.8733 (tmmt) cc_final: 0.8354 (mptp) REVERT: O 184 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.7942 (mp10) REVERT: O 220 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8748 (mm) REVERT: O 322 ARG cc_start: 0.8140 (mmm-85) cc_final: 0.7873 (ttp80) REVERT: P 35 SER cc_start: 0.8860 (t) cc_final: 0.8412 (p) REVERT: Q 267 MET cc_start: 0.1877 (OUTLIER) cc_final: 0.1401 (ppp) REVERT: Q 491 MET cc_start: 0.9400 (mtm) cc_final: 0.9171 (mtp) REVERT: R 63 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7357 (tm-30) REVERT: R 491 MET cc_start: 0.9295 (mtm) cc_final: 0.9011 (mtt) REVERT: S 74 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8406 (tmtt) REVERT: S 76 GLU cc_start: 0.7935 (tp30) cc_final: 0.7615 (tp30) REVERT: T 166 MET cc_start: 0.8530 (mtt) cc_final: 0.8225 (mtt) REVERT: T 200 LEU cc_start: 0.2334 (OUTLIER) cc_final: 0.1958 (pt) REVERT: T 267 MET cc_start: 0.1775 (OUTLIER) cc_final: 0.1227 (ppp) REVERT: T 288 MET cc_start: 0.5228 (OUTLIER) cc_final: 0.4889 (ptt) outliers start: 171 outliers final: 59 residues processed: 778 average time/residue: 1.5078 time to fit residues: 1485.2895 Evaluate side-chains 754 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 666 time to evaluate : 5.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 317 LEU Chi-restraints excluded: chain W residue 3 ILE Chi-restraints excluded: chain W residue 87 SER Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 404 ARG Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 184 GLN Chi-restraints excluded: chain H residue 233 MET Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 80 ASN Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain K residue 132 LYS Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 245 LYS Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 188 ASP Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 299 THR Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 325 ILE Chi-restraints excluded: chain L residue 483 GLU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain N residue 176 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 288 MET Chi-restraints excluded: chain O residue 176 THR Chi-restraints excluded: chain O residue 184 GLN Chi-restraints excluded: chain O residue 220 ILE Chi-restraints excluded: chain O residue 227 ILE Chi-restraints excluded: chain P residue 18 GLU Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain Q residue 138 CYS Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 267 MET Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 63 GLU Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain R residue 299 THR Chi-restraints excluded: chain R residue 307 MET Chi-restraints excluded: chain S residue 74 LYS Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 245 LYS Chi-restraints excluded: chain T residue 267 MET Chi-restraints excluded: chain T residue 288 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 636 optimal weight: 1.9990 chunk 434 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 569 optimal weight: 3.9990 chunk 315 optimal weight: 50.0000 chunk 652 optimal weight: 5.9990 chunk 528 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 390 optimal weight: 0.7980 chunk 686 optimal weight: 0.9990 chunk 192 optimal weight: 0.0970 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 45 ASN ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 GLN E 2 ASN E 45 ASN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 ASN L 366 GLN R 319 GLN R 348 GLN S 45 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 59773 Z= 0.216 Angle : 0.512 8.214 80801 Z= 0.276 Chirality : 0.042 0.183 9807 Planarity : 0.003 0.052 10507 Dihedral : 9.233 89.922 8921 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.25 % Allowed : 16.92 % Favored : 80.83 % 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: 1.35 (0.09), residues: 7959 helix: 1.78 (0.08), residues: 4235 sheet: 0.72 (0.15), residues: 1085 loop : -0.45 (0.11), residues: 2639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 7 PHE 0.014 0.001 PHE N 219 TYR 0.013 0.001 TYR D 360 ARG 0.009 0.000 ARG L 284 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 680 time to evaluate : 5.074 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: G 200 LEU cc_start: 0.2359 (OUTLIER) cc_final: 0.1972 (pt) REVERT: G 267 MET cc_start: 0.3013 (OUTLIER) cc_final: 0.2485 (ppp) REVERT: G 288 MET cc_start: 0.5100 (OUTLIER) cc_final: 0.4582 (ptt) REVERT: G 307 MET cc_start: 0.4456 (mmm) cc_final: 0.3462 (tpt) REVERT: G 404 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7601 (mpt90) REVERT: A 267 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7969 (mtt) REVERT: C 193 MET cc_start: 0.5358 (OUTLIER) cc_final: 0.4452 (tmt) REVERT: C 200 LEU cc_start: 0.3192 (OUTLIER) cc_final: 0.2640 (pt) REVERT: C 262 LEU cc_start: -0.2410 (OUTLIER) cc_final: -0.3117 (pp) REVERT: C 267 MET cc_start: 0.2955 (OUTLIER) cc_final: 0.2381 (ppp) REVERT: C 288 MET cc_start: 0.6757 (OUTLIER) cc_final: 0.5501 (ptt) REVERT: C 365 LEU cc_start: 0.6757 (OUTLIER) cc_final: 0.6222 (tp) REVERT: C 491 MET cc_start: 0.9453 (mtm) cc_final: 0.9158 (mtm) REVERT: D 63 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7329 (tm-30) REVERT: D 362 ARG cc_start: 0.7785 (ttp-110) cc_final: 0.7429 (ptp-110) REVERT: D 366 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7870 (tp40) REVERT: F 193 MET cc_start: 0.5125 (OUTLIER) cc_final: 0.4570 (tmt) REVERT: F 262 LEU cc_start: -0.2015 (OUTLIER) cc_final: -0.2592 (pp) REVERT: F 267 MET cc_start: 0.2586 (OUTLIER) cc_final: 0.2075 (ppp) REVERT: F 307 MET cc_start: 0.4759 (mmm) cc_final: 0.4349 (tpt) REVERT: H 63 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7172 (tm-30) REVERT: H 248 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8778 (tp) REVERT: H 267 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8300 (mtt) REVERT: H 362 ARG cc_start: 0.7597 (ptp90) cc_final: 0.7278 (ttm110) REVERT: J 80 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.7342 (t0) REVERT: K 136 VAL cc_start: 0.8925 (OUTLIER) cc_final: 0.8707 (p) REVERT: K 267 MET cc_start: 0.1358 (OUTLIER) cc_final: 0.0586 (ppp) REVERT: L 325 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8319 (mm) REVERT: L 483 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.7343 (mm-30) REVERT: N 193 MET cc_start: 0.4776 (OUTLIER) cc_final: 0.4108 (tmt) REVERT: N 200 LEU cc_start: 0.2239 (OUTLIER) cc_final: 0.1909 (pt) REVERT: N 288 MET cc_start: 0.4590 (OUTLIER) cc_final: 0.4165 (ptt) REVERT: O 63 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7409 (tm-30) REVERT: O 160 LYS cc_start: 0.8697 (tmmt) cc_final: 0.8294 (mptp) REVERT: O 184 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.7934 (mp10) REVERT: O 220 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8656 (mm) REVERT: O 322 ARG cc_start: 0.8129 (mmm-85) cc_final: 0.7911 (ttp80) REVERT: P 35 SER cc_start: 0.8839 (t) cc_final: 0.8401 (p) REVERT: P 91 ILE cc_start: 0.9196 (mt) cc_final: 0.8956 (mt) REVERT: Q 136 VAL cc_start: 0.8751 (OUTLIER) cc_final: 0.8466 (m) REVERT: Q 267 MET cc_start: 0.1713 (OUTLIER) cc_final: 0.1222 (ppp) REVERT: Q 491 MET cc_start: 0.9363 (mtm) cc_final: 0.9156 (mtp) REVERT: R 63 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7342 (tm-30) REVERT: R 491 MET cc_start: 0.9283 (mtm) cc_final: 0.9016 (mtt) REVERT: S 74 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8375 (tmtt) REVERT: S 75 SER cc_start: 0.9232 (t) cc_final: 0.8961 (m) REVERT: T 166 MET cc_start: 0.8497 (mtt) cc_final: 0.8182 (mtt) REVERT: T 184 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8133 (mm-40) REVERT: T 200 LEU cc_start: 0.2348 (OUTLIER) cc_final: 0.1990 (pt) REVERT: T 267 MET cc_start: 0.1704 (OUTLIER) cc_final: 0.1205 (ppp) REVERT: T 288 MET cc_start: 0.5202 (OUTLIER) cc_final: 0.4842 (ptt) outliers start: 139 outliers final: 49 residues processed: 761 average time/residue: 1.5142 time to fit residues: 1455.4847 Evaluate side-chains 752 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 666 time to evaluate : 4.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain W residue 87 SER Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 404 ARG Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 520 MET Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 80 ASN Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain K residue 132 LYS Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 245 LYS Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 188 ASP Chi-restraints excluded: chain L residue 233 MET Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 299 THR Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 325 ILE Chi-restraints excluded: chain L residue 483 GLU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain N residue 176 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 288 MET Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain O residue 184 GLN Chi-restraints excluded: chain O residue 220 ILE Chi-restraints excluded: chain O residue 273 VAL Chi-restraints excluded: chain P residue 18 GLU Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 138 CYS Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 267 MET Chi-restraints excluded: chain R residue 63 GLU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain R residue 299 THR Chi-restraints excluded: chain R residue 307 MET Chi-restraints excluded: chain S residue 74 LYS Chi-restraints excluded: chain T residue 184 GLN Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 245 LYS Chi-restraints excluded: chain T residue 267 MET Chi-restraints excluded: chain T residue 288 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 257 optimal weight: 7.9990 chunk 688 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 448 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 765 optimal weight: 3.9990 chunk 635 optimal weight: 3.9990 chunk 354 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 253 optimal weight: 2.9990 chunk 401 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 45 ASN W 80 ASN A 352 GLN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 319 GLN J 45 ASN L 343 GLN L 366 GLN R 319 GLN S 45 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 59773 Z= 0.271 Angle : 0.538 12.494 80801 Z= 0.287 Chirality : 0.044 0.199 9807 Planarity : 0.004 0.052 10507 Dihedral : 9.301 89.491 8918 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.38 % Allowed : 17.21 % Favored : 80.41 % 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: 1.28 (0.09), residues: 7959 helix: 1.73 (0.08), residues: 4228 sheet: 0.67 (0.15), residues: 1078 loop : -0.46 (0.11), residues: 2653 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 7 PHE 0.012 0.001 PHE N 219 TYR 0.013 0.001 TYR D 360 ARG 0.010 0.001 ARG L 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 687 time to evaluate : 5.403 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: G 200 LEU cc_start: 0.2391 (OUTLIER) cc_final: 0.1990 (pt) REVERT: G 267 MET cc_start: 0.2639 (OUTLIER) cc_final: 0.2220 (ppp) REVERT: G 288 MET cc_start: 0.5102 (OUTLIER) cc_final: 0.4572 (ptt) REVERT: G 307 MET cc_start: 0.4389 (mmm) cc_final: 0.3490 (tpt) REVERT: G 404 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7614 (mpt90) REVERT: A 220 ILE cc_start: 0.8857 (mm) cc_final: 0.8639 (mm) REVERT: C 193 MET cc_start: 0.5364 (OUTLIER) cc_final: 0.4455 (tmt) REVERT: C 200 LEU cc_start: 0.3226 (OUTLIER) cc_final: 0.2712 (pt) REVERT: C 262 LEU cc_start: -0.2071 (OUTLIER) cc_final: -0.2641 (pp) REVERT: C 267 MET cc_start: 0.2763 (OUTLIER) cc_final: 0.2218 (ppp) REVERT: C 288 MET cc_start: 0.6764 (OUTLIER) cc_final: 0.5521 (ptt) REVERT: C 365 LEU cc_start: 0.6751 (OUTLIER) cc_final: 0.6405 (pp) REVERT: C 491 MET cc_start: 0.9469 (mtm) cc_final: 0.9172 (mtm) REVERT: D 63 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7334 (tm-30) REVERT: D 366 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7859 (tp40) REVERT: E 15 LYS cc_start: 0.7356 (mttm) cc_final: 0.7132 (mttm) REVERT: F 193 MET cc_start: 0.5146 (OUTLIER) cc_final: 0.4573 (tmt) REVERT: F 262 LEU cc_start: -0.2030 (OUTLIER) cc_final: -0.2479 (pp) REVERT: F 267 MET cc_start: 0.2567 (OUTLIER) cc_final: 0.2047 (ppp) REVERT: F 307 MET cc_start: 0.4777 (mmm) cc_final: 0.4362 (tpt) REVERT: H 63 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7178 (tm-30) REVERT: H 160 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8307 (mptp) REVERT: H 184 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8424 (mp10) REVERT: H 267 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8401 (mtt) REVERT: H 483 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7263 (mm-30) REVERT: H 520 MET cc_start: 0.9214 (mtp) cc_final: 0.8938 (mtp) REVERT: J 80 ASN cc_start: 0.7616 (OUTLIER) cc_final: 0.7355 (t0) REVERT: K 136 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8748 (p) REVERT: K 267 MET cc_start: 0.1487 (OUTLIER) cc_final: 0.0756 (pmt) REVERT: K 483 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8025 (mt-10) REVERT: L 184 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8048 (mp10) REVERT: L 325 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8337 (mm) REVERT: L 483 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.7360 (mm-30) REVERT: N 193 MET cc_start: 0.4774 (OUTLIER) cc_final: 0.4084 (tmt) REVERT: N 200 LEU cc_start: 0.2247 (OUTLIER) cc_final: 0.1897 (pt) REVERT: N 288 MET cc_start: 0.4738 (OUTLIER) cc_final: 0.4296 (ptt) REVERT: O 63 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7412 (tm-30) REVERT: O 160 LYS cc_start: 0.8693 (tmmt) cc_final: 0.8298 (mptp) REVERT: O 184 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.7925 (mp10) REVERT: O 220 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8725 (mm) REVERT: P 35 SER cc_start: 0.8854 (t) cc_final: 0.8393 (p) REVERT: P 60 LYS cc_start: 0.9003 (mppt) cc_final: 0.8726 (mmmt) REVERT: P 74 LYS cc_start: 0.8681 (tmtt) cc_final: 0.8415 (tmtt) REVERT: P 91 ILE cc_start: 0.9192 (mt) cc_final: 0.8961 (mt) REVERT: Q 136 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8447 (m) REVERT: Q 193 MET cc_start: 0.5501 (OUTLIER) cc_final: 0.4835 (tmt) REVERT: Q 267 MET cc_start: 0.1673 (OUTLIER) cc_final: 0.1158 (ppp) REVERT: Q 491 MET cc_start: 0.9358 (mtm) cc_final: 0.9157 (mtp) REVERT: R 63 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7354 (tm-30) REVERT: R 267 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8197 (mtt) REVERT: R 491 MET cc_start: 0.9295 (mtm) cc_final: 0.9036 (mtt) REVERT: S 74 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8384 (tmtt) REVERT: S 76 GLU cc_start: 0.7813 (tp30) cc_final: 0.7578 (tp30) REVERT: T 184 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8110 (mm-40) REVERT: T 200 LEU cc_start: 0.2377 (OUTLIER) cc_final: 0.2001 (pt) REVERT: T 267 MET cc_start: 0.1777 (OUTLIER) cc_final: 0.1239 (ppp) REVERT: T 288 MET cc_start: 0.5169 (OUTLIER) cc_final: 0.4828 (ptt) outliers start: 147 outliers final: 62 residues processed: 773 average time/residue: 1.5145 time to fit residues: 1481.8033 Evaluate side-chains 777 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 673 time to evaluate : 5.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 317 LEU Chi-restraints excluded: chain W residue 87 SER Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 404 ARG Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 160 LYS Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 184 GLN Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 483 GLU Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 80 ASN Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain K residue 132 LYS Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 245 LYS Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain K residue 483 GLU Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 184 GLN Chi-restraints excluded: chain L residue 188 ASP Chi-restraints excluded: chain L residue 233 MET Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 299 THR Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 325 ILE Chi-restraints excluded: chain L residue 483 GLU Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 176 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 288 MET Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 176 THR Chi-restraints excluded: chain O residue 184 GLN Chi-restraints excluded: chain O residue 220 ILE Chi-restraints excluded: chain O residue 273 VAL Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 138 CYS Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 193 MET Chi-restraints excluded: chain Q residue 267 MET Chi-restraints excluded: chain R residue 63 GLU Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 267 MET Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain R residue 299 THR Chi-restraints excluded: chain R residue 307 MET Chi-restraints excluded: chain S residue 74 LYS Chi-restraints excluded: chain T residue 184 GLN Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 245 LYS Chi-restraints excluded: chain T residue 267 MET Chi-restraints excluded: chain T residue 288 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 737 optimal weight: 0.6980 chunk 86 optimal weight: 9.9990 chunk 436 optimal weight: 8.9990 chunk 558 optimal weight: 0.8980 chunk 433 optimal weight: 20.0000 chunk 644 optimal weight: 9.9990 chunk 427 optimal weight: 2.9990 chunk 762 optimal weight: 20.0000 chunk 477 optimal weight: 9.9990 chunk 464 optimal weight: 1.9990 chunk 351 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 112 ASN W 45 ASN A 112 ASN A 366 GLN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 ASN L 112 ASN O 366 GLN R 319 GLN S 45 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 59773 Z= 0.285 Angle : 0.546 11.838 80801 Z= 0.292 Chirality : 0.044 0.203 9807 Planarity : 0.004 0.054 10507 Dihedral : 9.332 89.805 8916 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.49 % Allowed : 17.55 % Favored : 79.95 % 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: 1.24 (0.09), residues: 7959 helix: 1.70 (0.08), residues: 4228 sheet: 0.60 (0.15), residues: 1078 loop : -0.45 (0.11), residues: 2653 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 7 PHE 0.011 0.001 PHE N 219 TYR 0.012 0.001 TYR D 360 ARG 0.013 0.001 ARG H 284 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 695 time to evaluate : 5.181 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: G 200 LEU cc_start: 0.2392 (OUTLIER) cc_final: 0.1986 (pt) REVERT: G 288 MET cc_start: 0.5181 (OUTLIER) cc_final: 0.4646 (ptt) REVERT: G 307 MET cc_start: 0.4296 (mmm) cc_final: 0.3471 (tpt) REVERT: G 404 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7630 (mpt90) REVERT: A 111 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8561 (mtp) REVERT: C 200 LEU cc_start: 0.3139 (OUTLIER) cc_final: 0.2623 (pt) REVERT: C 262 LEU cc_start: -0.2268 (OUTLIER) cc_final: -0.2747 (pp) REVERT: C 267 MET cc_start: 0.2644 (OUTLIER) cc_final: 0.2118 (ppp) REVERT: C 288 MET cc_start: 0.6757 (OUTLIER) cc_final: 0.5527 (ptt) REVERT: C 365 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6408 (pp) REVERT: C 491 MET cc_start: 0.9473 (mtm) cc_final: 0.9182 (mtm) REVERT: D 63 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7342 (tm-30) REVERT: D 321 LYS cc_start: 0.8714 (ttmm) cc_final: 0.8510 (ttmm) REVERT: D 362 ARG cc_start: 0.7828 (ttp-110) cc_final: 0.7475 (ptp-110) REVERT: D 366 GLN cc_start: 0.8142 (mm-40) cc_final: 0.7803 (tp40) REVERT: F 193 MET cc_start: 0.5099 (OUTLIER) cc_final: 0.4538 (tmt) REVERT: F 262 LEU cc_start: -0.2118 (OUTLIER) cc_final: -0.2446 (pp) REVERT: F 267 MET cc_start: 0.2437 (OUTLIER) cc_final: 0.1910 (ppp) REVERT: F 307 MET cc_start: 0.4731 (mmm) cc_final: 0.4339 (tpt) REVERT: H 63 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7181 (tm-30) REVERT: H 184 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8408 (mp10) REVERT: H 322 ARG cc_start: 0.8198 (mmm-85) cc_final: 0.7933 (ttp80) REVERT: H 483 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7269 (mm-30) REVERT: J 80 ASN cc_start: 0.7698 (OUTLIER) cc_final: 0.7462 (t0) REVERT: K 136 VAL cc_start: 0.8974 (OUTLIER) cc_final: 0.8764 (p) REVERT: K 267 MET cc_start: 0.1491 (OUTLIER) cc_final: 0.0966 (pmt) REVERT: K 483 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8023 (mt-10) REVERT: L 160 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8500 (mptp) REVERT: L 325 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8183 (mm) REVERT: L 483 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.7353 (mm-30) REVERT: N 193 MET cc_start: 0.4753 (OUTLIER) cc_final: 0.4058 (tmt) REVERT: N 200 LEU cc_start: 0.2153 (OUTLIER) cc_final: 0.1846 (pt) REVERT: N 288 MET cc_start: 0.4724 (OUTLIER) cc_final: 0.4282 (ptt) REVERT: O 63 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7406 (tm-30) REVERT: O 160 LYS cc_start: 0.8686 (tmmt) cc_final: 0.8300 (mptp) REVERT: O 184 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.7915 (mp10) REVERT: O 220 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8749 (mm) REVERT: P 35 SER cc_start: 0.8864 (t) cc_final: 0.8387 (p) REVERT: P 60 LYS cc_start: 0.9016 (mppt) cc_final: 0.8736 (mmmt) REVERT: P 91 ILE cc_start: 0.9212 (mt) cc_final: 0.8993 (mt) REVERT: Q 193 MET cc_start: 0.5420 (OUTLIER) cc_final: 0.4776 (tmt) REVERT: Q 267 MET cc_start: 0.1859 (OUTLIER) cc_final: 0.1352 (ppp) REVERT: Q 288 MET cc_start: 0.5161 (mmt) cc_final: 0.4651 (ptt) REVERT: Q 491 MET cc_start: 0.9373 (mtm) cc_final: 0.9171 (mtp) REVERT: R 63 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7327 (tm-30) REVERT: R 267 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8203 (mtt) REVERT: R 491 MET cc_start: 0.9298 (mtm) cc_final: 0.9035 (mtt) REVERT: S 74 LYS cc_start: 0.8698 (tmtt) cc_final: 0.8384 (tmtt) REVERT: S 76 GLU cc_start: 0.7837 (tp30) cc_final: 0.7564 (tp30) REVERT: T 184 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.8066 (mm-40) REVERT: T 200 LEU cc_start: 0.2338 (OUTLIER) cc_final: 0.1966 (pt) REVERT: T 267 MET cc_start: 0.1850 (OUTLIER) cc_final: 0.1354 (ppp) REVERT: T 288 MET cc_start: 0.5134 (OUTLIER) cc_final: 0.4826 (ptt) outliers start: 154 outliers final: 62 residues processed: 788 average time/residue: 1.5313 time to fit residues: 1523.1309 Evaluate side-chains 780 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 681 time to evaluate : 6.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain I residue 317 LEU Chi-restraints excluded: chain W residue 87 SER Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 404 ARG Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 184 GLN Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 483 GLU Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 80 ASN Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain K residue 132 LYS Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 245 LYS Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain K residue 483 GLU Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 160 LYS Chi-restraints excluded: chain L residue 188 ASP Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 299 THR Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 325 ILE Chi-restraints excluded: chain L residue 483 GLU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 176 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 288 MET Chi-restraints excluded: chain O residue 14 VAL Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain O residue 176 THR Chi-restraints excluded: chain O residue 184 GLN Chi-restraints excluded: chain O residue 220 ILE Chi-restraints excluded: chain O residue 273 VAL Chi-restraints excluded: chain P residue 18 GLU Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain Q residue 138 CYS Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 193 MET Chi-restraints excluded: chain Q residue 267 MET Chi-restraints excluded: chain R residue 63 GLU Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 267 MET Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain R residue 299 THR Chi-restraints excluded: chain R residue 307 MET Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain T residue 184 GLN Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 245 LYS Chi-restraints excluded: chain T residue 267 MET Chi-restraints excluded: chain T residue 288 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 471 optimal weight: 6.9990 chunk 304 optimal weight: 8.9990 chunk 455 optimal weight: 3.9990 chunk 229 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 484 optimal weight: 4.9990 chunk 519 optimal weight: 0.6980 chunk 376 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 599 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 45 ASN H 319 GLN J 45 ASN R 319 GLN R 348 GLN S 45 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 59773 Z= 0.234 Angle : 0.536 11.645 80801 Z= 0.284 Chirality : 0.043 0.203 9807 Planarity : 0.003 0.054 10507 Dihedral : 9.171 88.685 8916 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.14 % Allowed : 18.09 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.09), residues: 7959 helix: 1.78 (0.08), residues: 4228 sheet: 0.60 (0.15), residues: 1078 loop : -0.42 (0.11), residues: 2653 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 7 PHE 0.011 0.001 PHE E 67 TYR 0.012 0.001 TYR D 360 ARG 0.014 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 697 time to evaluate : 5.199 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: G 200 LEU cc_start: 0.2408 (OUTLIER) cc_final: 0.2006 (pt) REVERT: G 267 MET cc_start: 0.1960 (OUTLIER) cc_final: 0.1584 (ppp) REVERT: G 288 MET cc_start: 0.5140 (OUTLIER) cc_final: 0.4609 (ptt) REVERT: G 307 MET cc_start: 0.4323 (mmm) cc_final: 0.3524 (tpt) REVERT: G 404 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7612 (mpt90) REVERT: B 64 ILE cc_start: 0.9308 (mp) cc_final: 0.9056 (mm) REVERT: C 200 LEU cc_start: 0.3071 (OUTLIER) cc_final: 0.2573 (pt) REVERT: C 262 LEU cc_start: -0.2392 (OUTLIER) cc_final: -0.2841 (pp) REVERT: C 267 MET cc_start: 0.2612 (OUTLIER) cc_final: 0.2071 (ppp) REVERT: C 288 MET cc_start: 0.6800 (OUTLIER) cc_final: 0.5619 (ptt) REVERT: C 365 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6380 (pp) REVERT: C 491 MET cc_start: 0.9453 (mtm) cc_final: 0.9188 (mtm) REVERT: D 63 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7348 (tm-30) REVERT: D 366 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7820 (tp40) REVERT: D 483 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.7185 (mm-30) REVERT: F 193 MET cc_start: 0.5106 (OUTLIER) cc_final: 0.4539 (tmt) REVERT: F 262 LEU cc_start: -0.2218 (OUTLIER) cc_final: -0.2472 (pp) REVERT: F 267 MET cc_start: 0.2300 (OUTLIER) cc_final: 0.1767 (ppp) REVERT: F 307 MET cc_start: 0.4742 (mmm) cc_final: 0.4336 (tpt) REVERT: H 63 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7170 (tm-30) REVERT: H 160 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8306 (mptp) REVERT: H 184 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8390 (mp10) REVERT: H 248 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8822 (tp) REVERT: H 322 ARG cc_start: 0.8183 (mmm-85) cc_final: 0.7934 (ttp80) REVERT: H 483 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7263 (mm-30) REVERT: J 9 ARG cc_start: 0.8504 (mtt90) cc_final: 0.8146 (mtt90) REVERT: J 80 ASN cc_start: 0.7742 (OUTLIER) cc_final: 0.7498 (t0) REVERT: K 267 MET cc_start: 0.1259 (OUTLIER) cc_final: 0.0630 (pmt) REVERT: L 160 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8497 (mptp) REVERT: L 325 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8188 (mm) REVERT: L 362 ARG cc_start: 0.7533 (ptp90) cc_final: 0.7316 (ttp-110) REVERT: L 483 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.7349 (mm-30) REVERT: N 193 MET cc_start: 0.4741 (OUTLIER) cc_final: 0.4045 (tmt) REVERT: N 200 LEU cc_start: 0.2048 (OUTLIER) cc_final: 0.1738 (pt) REVERT: N 288 MET cc_start: 0.4799 (OUTLIER) cc_final: 0.4343 (ptt) REVERT: O 160 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8292 (mptp) REVERT: O 184 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.7909 (mp10) REVERT: O 220 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8713 (mm) REVERT: P 35 SER cc_start: 0.8857 (t) cc_final: 0.8378 (p) REVERT: P 60 LYS cc_start: 0.9029 (mppt) cc_final: 0.8759 (mmmt) REVERT: P 91 ILE cc_start: 0.9183 (mt) cc_final: 0.8972 (mt) REVERT: Q 267 MET cc_start: 0.1818 (OUTLIER) cc_final: 0.1352 (ppp) REVERT: Q 288 MET cc_start: 0.5162 (mmt) cc_final: 0.4783 (ptt) REVERT: Q 491 MET cc_start: 0.9346 (mtm) cc_final: 0.9137 (mtp) REVERT: R 63 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7340 (tm-30) REVERT: R 267 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8204 (mtt) REVERT: R 491 MET cc_start: 0.9293 (mtm) cc_final: 0.9020 (mtt) REVERT: S 74 LYS cc_start: 0.8710 (tmtt) cc_final: 0.8388 (tmtt) REVERT: S 76 GLU cc_start: 0.7832 (tp30) cc_final: 0.7531 (tp30) REVERT: T 166 MET cc_start: 0.8504 (mtt) cc_final: 0.8182 (mtt) REVERT: T 184 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.8052 (mm-40) REVERT: T 200 LEU cc_start: 0.2217 (OUTLIER) cc_final: 0.1910 (pt) REVERT: T 267 MET cc_start: 0.1622 (OUTLIER) cc_final: 0.1325 (pmt) REVERT: T 288 MET cc_start: 0.5124 (OUTLIER) cc_final: 0.4807 (ptt) outliers start: 132 outliers final: 54 residues processed: 773 average time/residue: 1.5340 time to fit residues: 1494.5644 Evaluate side-chains 771 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 680 time to evaluate : 5.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain W residue 87 SER Chi-restraints excluded: chain G residue 132 LYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 404 ARG Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 160 LYS Chi-restraints excluded: chain H residue 184 GLN Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 483 GLU Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 80 ASN Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain K residue 132 LYS Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 245 LYS Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 160 LYS Chi-restraints excluded: chain L residue 188 ASP Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 299 THR Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 325 ILE Chi-restraints excluded: chain L residue 483 GLU Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 176 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 288 MET Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 160 LYS Chi-restraints excluded: chain O residue 184 GLN Chi-restraints excluded: chain O residue 220 ILE Chi-restraints excluded: chain O residue 273 VAL Chi-restraints excluded: chain P residue 18 GLU Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 267 MET Chi-restraints excluded: chain R residue 63 GLU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 267 MET Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain R residue 299 THR Chi-restraints excluded: chain R residue 307 MET Chi-restraints excluded: chain S residue 69 ASP Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain T residue 184 GLN Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 245 LYS Chi-restraints excluded: chain T residue 267 MET Chi-restraints excluded: chain T residue 288 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 693 optimal weight: 0.8980 chunk 730 optimal weight: 1.9990 chunk 666 optimal weight: 9.9990 chunk 710 optimal weight: 7.9990 chunk 427 optimal weight: 30.0000 chunk 309 optimal weight: 0.9990 chunk 557 optimal weight: 0.5980 chunk 218 optimal weight: 0.6980 chunk 641 optimal weight: 2.9990 chunk 671 optimal weight: 0.8980 chunk 707 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 45 ASN J 45 ASN R 319 GLN ** R 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 348 GLN S 45 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 59773 Z= 0.195 Angle : 0.531 13.945 80801 Z= 0.280 Chirality : 0.042 0.252 9807 Planarity : 0.003 0.058 10507 Dihedral : 8.934 89.656 8915 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.70 % Allowed : 18.78 % Favored : 79.52 % 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: 1.43 (0.09), residues: 7959 helix: 1.86 (0.08), residues: 4242 sheet: 0.66 (0.15), residues: 1078 loop : -0.38 (0.11), residues: 2639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 7 PHE 0.011 0.001 PHE E 67 TYR 0.011 0.001 TYR D 360 ARG 0.015 0.000 ARG H 284 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 693 time to evaluate : 5.291 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: I 63 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7103 (tm-30) REVERT: G 200 LEU cc_start: 0.2375 (OUTLIER) cc_final: 0.1981 (pt) REVERT: G 267 MET cc_start: 0.1947 (OUTLIER) cc_final: 0.1479 (ppp) REVERT: G 288 MET cc_start: 0.5153 (OUTLIER) cc_final: 0.4640 (ptt) REVERT: G 307 MET cc_start: 0.4151 (mmm) cc_final: 0.3448 (tpt) REVERT: G 404 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7597 (mpt90) REVERT: B 64 ILE cc_start: 0.9316 (mp) cc_final: 0.9074 (mm) REVERT: C 200 LEU cc_start: 0.3118 (OUTLIER) cc_final: 0.2558 (pp) REVERT: C 262 LEU cc_start: -0.2334 (OUTLIER) cc_final: -0.2743 (pp) REVERT: C 267 MET cc_start: 0.2575 (OUTLIER) cc_final: 0.2048 (ppp) REVERT: C 288 MET cc_start: 0.6768 (OUTLIER) cc_final: 0.5597 (ptt) REVERT: C 491 MET cc_start: 0.9423 (mtm) cc_final: 0.9192 (mtm) REVERT: D 63 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7373 (tm-30) REVERT: D 366 GLN cc_start: 0.8115 (mm-40) cc_final: 0.7824 (tp40) REVERT: D 483 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.7188 (mm-30) REVERT: F 193 MET cc_start: 0.5103 (OUTLIER) cc_final: 0.4536 (tmt) REVERT: F 262 LEU cc_start: -0.2088 (OUTLIER) cc_final: -0.2335 (pp) REVERT: F 267 MET cc_start: 0.2325 (OUTLIER) cc_final: 0.1790 (ppp) REVERT: F 307 MET cc_start: 0.4717 (mmm) cc_final: 0.4326 (tpt) REVERT: H 63 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7172 (tm-30) REVERT: H 160 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8314 (mptp) REVERT: H 248 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8778 (tp) REVERT: H 307 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7164 (ptm) REVERT: H 322 ARG cc_start: 0.8162 (mmm-85) cc_final: 0.7942 (ttp80) REVERT: J 9 ARG cc_start: 0.8513 (mtt90) cc_final: 0.8147 (mtt90) REVERT: J 80 ASN cc_start: 0.7748 (OUTLIER) cc_final: 0.7507 (t0) REVERT: K 267 MET cc_start: 0.1336 (OUTLIER) cc_final: 0.0829 (pmt) REVERT: L 325 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.8072 (mm) REVERT: L 362 ARG cc_start: 0.7567 (ptp90) cc_final: 0.7349 (ttp-110) REVERT: N 200 LEU cc_start: 0.1923 (OUTLIER) cc_final: 0.1622 (pt) REVERT: N 288 MET cc_start: 0.4836 (OUTLIER) cc_final: 0.4387 (ptt) REVERT: O 160 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8347 (mptp) REVERT: O 184 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.7957 (mp10) REVERT: O 220 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8677 (mm) REVERT: P 35 SER cc_start: 0.8830 (t) cc_final: 0.8376 (p) REVERT: P 60 LYS cc_start: 0.9039 (mppt) cc_final: 0.8770 (mmmt) REVERT: P 91 ILE cc_start: 0.9163 (mt) cc_final: 0.8942 (mt) REVERT: Q 267 MET cc_start: 0.1845 (OUTLIER) cc_final: 0.1444 (ppp) REVERT: Q 288 MET cc_start: 0.5217 (mmt) cc_final: 0.4964 (ptt) REVERT: Q 491 MET cc_start: 0.9332 (mtm) cc_final: 0.9119 (mtp) REVERT: R 63 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7305 (tm-30) REVERT: R 491 MET cc_start: 0.9265 (mtm) cc_final: 0.8985 (mtt) REVERT: S 9 ARG cc_start: 0.8337 (mtt90) cc_final: 0.8029 (mtt90) REVERT: S 74 LYS cc_start: 0.8698 (tmtt) cc_final: 0.8381 (tmtt) REVERT: T 184 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.8092 (mm-40) REVERT: T 200 LEU cc_start: 0.2206 (OUTLIER) cc_final: 0.1899 (pt) REVERT: T 267 MET cc_start: 0.1403 (OUTLIER) cc_final: 0.1202 (pmt) REVERT: T 288 MET cc_start: 0.5071 (OUTLIER) cc_final: 0.4740 (ptt) outliers start: 105 outliers final: 46 residues processed: 749 average time/residue: 1.5355 time to fit residues: 1449.6662 Evaluate side-chains 760 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 682 time to evaluate : 5.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 GLU Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain W residue 87 SER Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 404 ARG Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 160 LYS Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 307 MET Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 80 ASN Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain K residue 132 LYS Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 245 LYS Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 299 THR Chi-restraints excluded: chain L residue 325 ILE Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 176 THR Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 288 MET Chi-restraints excluded: chain O residue 160 LYS Chi-restraints excluded: chain O residue 184 GLN Chi-restraints excluded: chain O residue 220 ILE Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 267 MET Chi-restraints excluded: chain R residue 63 GLU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain R residue 299 THR Chi-restraints excluded: chain R residue 307 MET Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain T residue 184 GLN Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 245 LYS Chi-restraints excluded: chain T residue 267 MET Chi-restraints excluded: chain T residue 288 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 466 optimal weight: 2.9990 chunk 751 optimal weight: 2.9990 chunk 458 optimal weight: 0.9990 chunk 356 optimal weight: 3.9990 chunk 522 optimal weight: 0.9990 chunk 788 optimal weight: 2.9990 chunk 725 optimal weight: 0.9980 chunk 627 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 484 optimal weight: 5.9990 chunk 384 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 45 ASN D 319 GLN J 45 ASN R 319 GLN ** R 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 348 GLN S 45 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 59773 Z= 0.208 Angle : 0.547 12.938 80801 Z= 0.286 Chirality : 0.042 0.222 9807 Planarity : 0.003 0.069 10507 Dihedral : 8.924 89.911 8915 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.57 % Allowed : 18.98 % Favored : 79.45 % 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: 1.44 (0.09), residues: 7959 helix: 1.87 (0.08), residues: 4242 sheet: 0.66 (0.15), residues: 1078 loop : -0.38 (0.11), residues: 2639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 7 PHE 0.010 0.001 PHE E 67 TYR 0.012 0.001 TYR D 360 ARG 0.015 0.001 ARG H 284 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 687 time to evaluate : 5.082 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: G 200 LEU cc_start: 0.2384 (OUTLIER) cc_final: 0.1987 (pt) REVERT: G 267 MET cc_start: 0.1917 (OUTLIER) cc_final: 0.1547 (ppp) REVERT: G 288 MET cc_start: 0.5147 (OUTLIER) cc_final: 0.4654 (ptt) REVERT: G 307 MET cc_start: 0.4127 (mmm) cc_final: 0.3456 (tpt) REVERT: G 404 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7593 (mpt90) REVERT: B 15 LYS cc_start: 0.7544 (mmtp) cc_final: 0.7190 (mttm) REVERT: B 64 ILE cc_start: 0.9321 (mp) cc_final: 0.9053 (mm) REVERT: C 200 LEU cc_start: 0.3109 (OUTLIER) cc_final: 0.2549 (pp) REVERT: C 262 LEU cc_start: -0.2392 (OUTLIER) cc_final: -0.2753 (pp) REVERT: C 267 MET cc_start: 0.2299 (OUTLIER) cc_final: 0.1730 (ppp) REVERT: C 288 MET cc_start: 0.6761 (OUTLIER) cc_final: 0.5601 (ptt) REVERT: C 365 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6395 (pp) REVERT: C 491 MET cc_start: 0.9413 (mtm) cc_final: 0.9165 (mtm) REVERT: D 63 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7407 (tm-30) REVERT: D 321 LYS cc_start: 0.8678 (ttmm) cc_final: 0.8435 (tttp) REVERT: D 362 ARG cc_start: 0.7797 (ttm110) cc_final: 0.7323 (ptp-110) REVERT: D 366 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7847 (tp40) REVERT: D 483 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.7197 (mm-30) REVERT: D 491 MET cc_start: 0.9360 (mtm) cc_final: 0.9021 (mtp) REVERT: F 193 MET cc_start: 0.5073 (OUTLIER) cc_final: 0.4515 (tmt) REVERT: F 267 MET cc_start: 0.2361 (OUTLIER) cc_final: 0.1809 (ppp) REVERT: F 307 MET cc_start: 0.4723 (mmm) cc_final: 0.4323 (tpt) REVERT: H 63 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7159 (tm-30) REVERT: H 160 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8316 (mptp) REVERT: H 248 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8791 (tp) REVERT: H 307 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7179 (ptm) REVERT: H 322 ARG cc_start: 0.8156 (mmm-85) cc_final: 0.7923 (ttp80) REVERT: J 9 ARG cc_start: 0.8503 (mtt90) cc_final: 0.8197 (mtt90) REVERT: J 80 ASN cc_start: 0.7772 (OUTLIER) cc_final: 0.7535 (t0) REVERT: K 267 MET cc_start: 0.1395 (OUTLIER) cc_final: 0.0957 (pmt) REVERT: K 483 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8008 (mt-10) REVERT: L 325 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.8073 (mm) REVERT: N 200 LEU cc_start: 0.1903 (OUTLIER) cc_final: 0.1602 (pt) REVERT: N 288 MET cc_start: 0.4871 (OUTLIER) cc_final: 0.4429 (ptt) REVERT: O 160 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8348 (mptp) REVERT: O 184 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7953 (mp10) REVERT: O 220 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8666 (mm) REVERT: P 35 SER cc_start: 0.8821 (t) cc_final: 0.8377 (p) REVERT: P 60 LYS cc_start: 0.9037 (mppt) cc_final: 0.8785 (mmmt) REVERT: P 91 ILE cc_start: 0.9151 (mt) cc_final: 0.8930 (mt) REVERT: Q 227 ILE cc_start: -0.2607 (OUTLIER) cc_final: -0.3278 (mp) REVERT: Q 267 MET cc_start: 0.1981 (OUTLIER) cc_final: 0.1559 (ppp) REVERT: Q 491 MET cc_start: 0.9330 (mtm) cc_final: 0.9110 (mtp) REVERT: R 63 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7308 (tm-30) REVERT: R 491 MET cc_start: 0.9266 (mtm) cc_final: 0.8988 (mtt) REVERT: S 74 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8385 (tmtt) REVERT: S 76 GLU cc_start: 0.7767 (tp30) cc_final: 0.7521 (tp30) REVERT: T 184 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8103 (mm-40) REVERT: T 200 LEU cc_start: 0.2086 (OUTLIER) cc_final: 0.1826 (pt) REVERT: T 267 MET cc_start: 0.1239 (OUTLIER) cc_final: 0.0791 (pmt) REVERT: T 288 MET cc_start: 0.5096 (OUTLIER) cc_final: 0.4749 (ptt) outliers start: 97 outliers final: 44 residues processed: 740 average time/residue: 1.5381 time to fit residues: 1437.2482 Evaluate side-chains 752 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 674 time to evaluate : 5.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 273 VAL Chi-restraints excluded: chain I residue 299 THR Chi-restraints excluded: chain W residue 87 SER Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 288 MET Chi-restraints excluded: chain G residue 404 ARG Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 160 LYS Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 307 MET Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 80 ASN Chi-restraints excluded: chain K residue 132 LYS Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 245 LYS Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain K residue 483 GLU Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 299 THR Chi-restraints excluded: chain L residue 325 ILE Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 176 THR Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 288 MET Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 160 LYS Chi-restraints excluded: chain O residue 184 GLN Chi-restraints excluded: chain O residue 220 ILE Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 227 ILE Chi-restraints excluded: chain Q residue 267 MET Chi-restraints excluded: chain R residue 63 GLU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 273 VAL Chi-restraints excluded: chain R residue 299 THR Chi-restraints excluded: chain R residue 307 MET Chi-restraints excluded: chain S residue 74 LYS Chi-restraints excluded: chain S residue 87 SER Chi-restraints excluded: chain T residue 184 GLN Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 245 LYS Chi-restraints excluded: chain T residue 267 MET Chi-restraints excluded: chain T residue 288 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 498 optimal weight: 0.7980 chunk 668 optimal weight: 7.9990 chunk 192 optimal weight: 0.7980 chunk 578 optimal weight: 0.8980 chunk 92 optimal weight: 40.0000 chunk 174 optimal weight: 6.9990 chunk 628 optimal weight: 0.8980 chunk 263 optimal weight: 9.9990 chunk 645 optimal weight: 0.8980 chunk 79 optimal weight: 0.0670 chunk 115 optimal weight: 0.0980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 45 ASN J 45 ASN L 366 GLN R 319 GLN R 453 GLN S 45 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.164863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.117456 restraints weight = 72667.527| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.61 r_work: 0.2997 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 59773 Z= 0.176 Angle : 0.544 12.769 80801 Z= 0.283 Chirality : 0.042 0.209 9807 Planarity : 0.003 0.069 10507 Dihedral : 8.706 88.875 8915 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.50 % Allowed : 19.27 % Favored : 79.23 % 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: 1.54 (0.09), residues: 7959 helix: 2.02 (0.08), residues: 4186 sheet: 0.52 (0.15), residues: 1106 loop : -0.32 (0.11), residues: 2667 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 7 PHE 0.015 0.001 PHE L 219 TYR 0.014 0.001 TYR R 199 ARG 0.015 0.000 ARG L 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20176.66 seconds wall clock time: 350 minutes 27.49 seconds (21027.49 seconds total)