Starting phenix.real_space_refine on Sun Dec 29 11:58:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bl2_16100/12_2024/8bl2_16100.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bl2_16100/12_2024/8bl2_16100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bl2_16100/12_2024/8bl2_16100.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bl2_16100/12_2024/8bl2_16100.map" model { file = "/net/cci-nas-00/data/ceres_data/8bl2_16100/12_2024/8bl2_16100.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bl2_16100/12_2024/8bl2_16100.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 280 5.16 5 C 33628 2.51 5 N 9380 2.21 5 O 13770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 57128 Number of models: 1 Model: "" Number of chains: 42 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: 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: "B" 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: "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: 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: "E" 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: "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: 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: 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: "J" 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: "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: 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: "M" 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: "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: "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: "B" 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: "E" 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: "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: "J" 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: "M" 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: "G" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 212 Classifications: {'water': 212} Link IDs: {None: 211} Chain: "A" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 187 Classifications: {'water': 187} Link IDs: {None: 186} Chain: "B" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 200 Classifications: {'water': 200} Link IDs: {None: 199} Chain: "C" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 192 Classifications: {'water': 192} Link IDs: {None: 191} Chain: "D" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 209 Classifications: {'water': 209} Link IDs: {None: 208} Chain: "E" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 178 Classifications: {'water': 178} Link IDs: {None: 177} Chain: "F" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 208 Classifications: {'water': 208} Link IDs: {None: 207} Chain: "H" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 213 Classifications: {'water': 213} Link IDs: {None: 212} Chain: "I" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 192 Classifications: {'water': 192} Link IDs: {None: 191} Chain: "J" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 203 Classifications: {'water': 203} Link IDs: {None: 202} Chain: "K" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 190 Classifications: {'water': 190} Link IDs: {None: 189} Chain: "L" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 202 Classifications: {'water': 202} Link IDs: {None: 201} Chain: "M" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 190 Classifications: {'water': 190} Link IDs: {None: 189} Chain: "N" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 204 Classifications: {'water': 204} Link IDs: {None: 203} Residues with excluded nonbonded symmetry interactions: 14 residue: pdb="MG MG G 601 " occ=0.00 residue: pdb="MG MG A 601 " occ=0.00 residue: pdb="MG MG B 601 " occ=0.00 residue: pdb="MG MG C 601 " occ=0.00 residue: pdb="MG MG D 601 " occ=0.00 residue: pdb="MG MG E 601 " occ=0.00 residue: pdb="MG MG F 601 " occ=0.00 residue: pdb="MG MG H 601 " occ=0.00 residue: pdb="MG MG I 601 " occ=0.00 residue: pdb="MG MG J 601 " occ=0.00 residue: pdb="MG MG K 601 " occ=0.00 residue: pdb="MG MG L 601 " occ=0.00 ... (remaining 2 not shown) Time building chain proxies: 23.74, per 1000 atoms: 0.42 Number of scatterers: 57128 At special positions: 0 Unit cell: (150.72, 151.68, 161.28, 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 280 16.00 P 42 15.00 Mg 14 11.99 O 13770 8.00 N 9380 7.00 C 33628 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: 10.93 Conformation dependent library (CDL) restraints added in 5.6 seconds 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13244 Finding SS restraints... Secondary structure from input PDB file: 294 helices and 98 sheets defined 58.4% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.95 Creating SS restraints... Processing helix chain 'G' and resid 9 through 29 Processing helix chain 'G' and resid 52 through 60 Processing helix chain 'G' and resid 64 through 86 removed outlier: 3.810A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.616A 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 137 through 142 Processing helix chain 'G' and resid 143 through 152 Processing helix chain 'G' and resid 155 through 170 Processing helix chain 'G' and resid 201 through 205 removed outlier: 3.958A pdb=" N ILE G 205 " --> pdb=" O PRO G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 241 Processing helix chain 'G' and resid 259 through 267 Processing helix chain 'G' and resid 282 through 297 Processing helix chain 'G' and resid 308 through 312 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 458 Processing helix chain 'G' and resid 461 through 472 Processing helix chain 'G' and resid 497 through 515 Processing helix chain 'A' and resid 9 through 29 Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 64 through 86 removed outlier: 3.809A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.616A 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 137 through 142 Processing helix chain 'A' and resid 143 through 152 Processing helix chain 'A' and resid 155 through 170 Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.957A pdb=" N ILE A 205 " --> pdb=" O PRO A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 259 through 267 Processing helix chain 'A' and resid 282 through 297 Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 338 through 356 Processing helix chain 'A' and resid 358 through 375 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 515 Processing helix chain 'B' and resid 9 through 29 Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 64 through 86 removed outlier: 3.810A pdb=" N VAL B 77 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 109 Processing helix chain 'B' and resid 112 through 135 Processing helix chain 'B' and resid 137 through 142 Processing helix chain 'B' and resid 143 through 152 Processing helix chain 'B' and resid 155 through 170 Processing helix chain 'B' and resid 201 through 205 removed outlier: 3.957A pdb=" N ILE B 205 " --> pdb=" O PRO B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 259 through 267 Processing helix chain 'B' and resid 282 through 297 Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 338 through 356 Processing helix chain 'B' and resid 358 through 375 Processing helix chain 'B' and resid 385 through 410 Processing helix chain 'B' and resid 416 through 426 Processing helix chain 'B' and resid 433 through 447 Processing helix chain 'B' and resid 448 through 458 Processing helix chain 'B' and resid 461 through 472 Processing helix chain 'B' and resid 497 through 515 Processing helix chain 'C' and resid 9 through 29 Processing helix chain 'C' and resid 52 through 60 Processing helix chain 'C' and resid 64 through 86 removed outlier: 3.810A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.616A 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: 3.957A pdb=" N ILE C 205 " --> pdb=" O PRO C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 241 Processing helix chain 'C' and resid 259 through 267 Processing helix chain 'C' and resid 282 through 297 Processing helix chain 'C' and resid 308 through 312 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 458 Processing helix chain 'C' and resid 461 through 472 Processing helix chain 'C' and resid 497 through 515 Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 52 through 60 Processing helix chain 'D' and resid 64 through 86 removed outlier: 3.809A pdb=" N VAL D 77 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 3.616A 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 137 through 142 Processing helix chain 'D' and resid 143 through 152 Processing helix chain 'D' and resid 155 through 170 Processing helix chain 'D' and resid 201 through 205 removed outlier: 3.957A pdb=" N ILE D 205 " --> pdb=" O PRO D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 241 Processing helix chain 'D' and resid 259 through 267 Processing helix chain 'D' and resid 282 through 297 Processing helix chain 'D' and resid 308 through 312 Processing helix chain 'D' and resid 338 through 356 Processing helix chain 'D' and resid 358 through 375 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 9 through 29 Processing helix chain 'E' and resid 52 through 60 Processing helix chain 'E' and resid 64 through 86 removed outlier: 3.810A pdb=" N VAL E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 109 Processing helix chain 'E' and resid 112 through 135 Processing helix chain 'E' and resid 137 through 142 Processing helix chain 'E' and resid 143 through 152 Processing helix chain 'E' and resid 155 through 170 Processing helix chain 'E' and resid 201 through 205 removed outlier: 3.957A pdb=" N ILE E 205 " --> pdb=" O PRO E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 241 Processing helix chain 'E' and resid 259 through 267 Processing helix chain 'E' and resid 282 through 297 Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 338 through 356 Processing helix chain 'E' and resid 358 through 375 Processing helix chain 'E' and resid 385 through 410 Processing helix chain 'E' and resid 416 through 426 Processing helix chain 'E' and resid 433 through 447 Processing helix chain 'E' and resid 448 through 458 Processing helix chain 'E' and resid 461 through 472 Processing helix chain 'E' and resid 497 through 515 Processing helix chain 'F' and resid 9 through 29 Processing helix chain 'F' and resid 52 through 60 Processing helix chain 'F' and resid 64 through 86 removed outlier: 3.810A pdb=" N VAL F 77 " --> pdb=" O MET F 73 " (cutoff:3.500A) removed outlier: 3.616A 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 137 through 142 Processing helix chain 'F' and resid 143 through 152 Processing helix chain 'F' and resid 155 through 170 Processing helix chain 'F' and resid 201 through 205 removed outlier: 3.957A pdb=" N ILE F 205 " --> pdb=" O PRO F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 241 Processing helix chain 'F' and resid 259 through 267 Processing helix chain 'F' and resid 282 through 297 Processing helix chain 'F' and resid 308 through 312 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 458 Processing helix chain 'F' and resid 461 through 472 Processing helix chain 'F' and resid 497 through 515 Processing helix chain 'H' and resid 9 through 29 Processing helix chain 'H' and resid 52 through 60 Processing helix chain 'H' and resid 64 through 86 removed outlier: 3.809A pdb=" N VAL H 77 " --> pdb=" O MET H 73 " (cutoff:3.500A) removed outlier: 3.616A 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 137 through 142 Processing helix chain 'H' and resid 143 through 152 Processing helix chain 'H' and resid 155 through 170 Processing helix chain 'H' and resid 201 through 205 removed outlier: 3.956A pdb=" N ILE H 205 " --> pdb=" O PRO H 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 241 Processing helix chain 'H' and resid 259 through 267 Processing helix chain 'H' and resid 282 through 297 Processing helix chain 'H' and resid 308 through 312 Processing helix chain 'H' and resid 338 through 356 Processing helix chain 'H' and resid 358 through 375 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 515 Processing helix chain 'I' and resid 9 through 29 Processing helix chain 'I' and resid 52 through 60 Processing helix chain 'I' and resid 64 through 86 removed outlier: 3.810A pdb=" N VAL I 77 " --> pdb=" O MET I 73 " (cutoff:3.500A) removed outlier: 3.616A 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 137 through 142 Processing helix chain 'I' and resid 143 through 152 Processing helix chain 'I' and resid 155 through 170 Processing helix chain 'I' and resid 201 through 205 removed outlier: 3.957A pdb=" N ILE I 205 " --> pdb=" O PRO I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 233 through 241 Processing helix chain 'I' and resid 259 through 267 Processing helix chain 'I' and resid 282 through 297 Processing helix chain 'I' and resid 308 through 312 Processing helix chain 'I' and resid 338 through 356 Processing helix chain 'I' and resid 358 through 375 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 515 Processing helix chain 'J' and resid 9 through 29 Processing helix chain 'J' and resid 52 through 60 Processing helix chain 'J' and resid 64 through 86 removed outlier: 3.810A pdb=" N VAL J 77 " --> pdb=" O MET J 73 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA J 78 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 109 Processing helix chain 'J' and resid 112 through 135 Processing helix chain 'J' and resid 137 through 142 Processing helix chain 'J' and resid 143 through 152 Processing helix chain 'J' and resid 155 through 170 Processing helix chain 'J' and resid 201 through 205 removed outlier: 3.956A pdb=" N ILE J 205 " --> pdb=" O PRO J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 241 Processing helix chain 'J' and resid 259 through 267 Processing helix chain 'J' and resid 282 through 297 Processing helix chain 'J' and resid 308 through 312 Processing helix chain 'J' and resid 338 through 356 Processing helix chain 'J' and resid 358 through 375 Processing helix chain 'J' and resid 385 through 410 Processing helix chain 'J' and resid 416 through 426 Processing helix chain 'J' and resid 433 through 447 Processing helix chain 'J' and resid 448 through 458 Processing helix chain 'J' and resid 461 through 472 Processing helix chain 'J' and resid 497 through 515 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: 3.810A pdb=" N VAL K 77 " --> pdb=" O MET K 73 " (cutoff:3.500A) removed outlier: 3.616A 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: 3.956A pdb=" N ILE K 205 " --> pdb=" O PRO K 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 233 through 241 Processing helix chain 'K' and resid 259 through 267 Processing helix chain 'K' and resid 282 through 297 Processing helix chain 'K' and resid 308 through 312 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 458 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 Processing helix chain 'L' and resid 52 through 60 Processing helix chain 'L' and resid 64 through 86 removed outlier: 3.810A pdb=" N VAL L 77 " --> pdb=" O MET L 73 " (cutoff:3.500A) removed outlier: 3.616A 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 137 through 142 Processing helix chain 'L' and resid 143 through 152 Processing helix chain 'L' and resid 155 through 170 Processing helix chain 'L' and resid 201 through 205 removed outlier: 3.957A pdb=" N ILE L 205 " --> pdb=" O PRO L 202 " (cutoff:3.500A) Processing helix chain 'L' and resid 233 through 241 Processing helix chain 'L' and resid 259 through 267 Processing helix chain 'L' and resid 282 through 297 Processing helix chain 'L' and resid 308 through 312 Processing helix chain 'L' and resid 338 through 356 Processing helix chain 'L' and resid 358 through 375 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 515 Processing helix chain 'M' and resid 9 through 29 Processing helix chain 'M' and resid 52 through 60 Processing helix chain 'M' and resid 64 through 86 removed outlier: 3.810A pdb=" N VAL M 77 " --> pdb=" O MET M 73 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA M 78 " --> pdb=" O VAL M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 109 Processing helix chain 'M' and resid 112 through 135 Processing helix chain 'M' and resid 137 through 142 Processing helix chain 'M' and resid 143 through 152 Processing helix chain 'M' and resid 155 through 170 Processing helix chain 'M' and resid 201 through 205 removed outlier: 3.957A pdb=" N ILE M 205 " --> pdb=" O PRO M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 233 through 241 Processing helix chain 'M' and resid 259 through 267 Processing helix chain 'M' and resid 282 through 297 Processing helix chain 'M' and resid 308 through 312 Processing helix chain 'M' and resid 338 through 356 Processing helix chain 'M' and resid 358 through 375 Processing helix chain 'M' and resid 385 through 410 Processing helix chain 'M' and resid 416 through 426 Processing helix chain 'M' and resid 433 through 447 Processing helix chain 'M' and resid 448 through 458 Processing helix chain 'M' and resid 461 through 472 Processing helix chain 'M' and resid 497 through 515 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: 3.810A pdb=" N VAL N 77 " --> pdb=" O MET N 73 " (cutoff:3.500A) removed outlier: 3.615A 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: 3.957A pdb=" N ILE N 205 " --> pdb=" O PRO N 202 " (cutoff:3.500A) Processing helix chain 'N' and resid 233 through 241 Processing helix chain 'N' and resid 259 through 267 Processing helix chain 'N' and resid 282 through 297 Processing helix chain 'N' and resid 308 through 312 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 458 Processing helix chain 'N' and resid 461 through 472 Processing helix chain 'N' and resid 497 through 515 Processing sheet with id=AA1, first strand: chain 'G' and resid 4 through 8 removed outlier: 7.355A pdb=" N VAL F 39 " --> pdb=" O GLU G 518 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N MET G 520 " --> pdb=" O VAL F 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 48 through 50 removed outlier: 7.461A pdb=" N ASN G 37 " --> pdb=" O GLU A 518 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N MET A 520 " --> pdb=" O ASN G 37 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL G 39 " --> pdb=" O MET A 520 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N THR A 522 " --> pdb=" O VAL G 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 174 through 179 Processing sheet with id=AA4, first strand: chain 'G' and resid 193 through 195 Processing sheet with id=AA5, first strand: chain 'G' and resid 273 through 277 removed outlier: 6.158A pdb=" N LEU G 247 " --> pdb=" O ALA G 274 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL G 276 " --> pdb=" O LEU G 247 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE G 249 " --> pdb=" O VAL G 276 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N ILE G 301 " --> pdb=" O ILE G 220 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N LEU G 222 " --> pdb=" O ILE G 301 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 273 through 277 removed outlier: 6.158A pdb=" N LEU G 247 " --> pdb=" O ALA G 274 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL G 276 " --> pdb=" O LEU G 247 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE G 249 " --> pdb=" O VAL G 276 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 411 through 413 Processing sheet with id=AA8, first strand: chain 'G' and resid 476 through 479 Processing sheet with id=AA9, first strand: chain 'A' and resid 48 through 50 removed outlier: 7.457A pdb=" N ASN A 37 " --> pdb=" O GLU B 518 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N MET B 520 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL A 39 " --> pdb=" O MET B 520 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N THR B 522 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 174 through 179 Processing sheet with id=AB2, first strand: chain 'A' and resid 193 through 195 Processing sheet with id=AB3, first strand: chain 'A' and resid 273 through 277 removed outlier: 6.158A pdb=" N LEU A 247 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL A 276 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE A 249 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 9.593A pdb=" N ILE A 301 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N LEU A 222 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 273 through 277 removed outlier: 6.158A pdb=" N LEU A 247 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL A 276 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE A 249 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 411 through 413 Processing sheet with id=AB6, first strand: chain 'A' and resid 476 through 479 Processing sheet with id=AB7, first strand: chain 'B' and resid 48 through 50 removed outlier: 7.462A pdb=" N ASN B 37 " --> pdb=" O GLU C 518 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N MET C 520 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL B 39 " --> pdb=" O MET C 520 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N THR C 522 " --> pdb=" O VAL B 39 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 174 through 179 Processing sheet with id=AB9, first strand: chain 'B' and resid 193 through 195 Processing sheet with id=AC1, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.158A pdb=" N LEU B 247 " --> pdb=" O ALA B 274 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL B 276 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE B 249 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 9.593A pdb=" N ILE B 301 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N LEU B 222 " --> pdb=" O ILE B 301 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.158A pdb=" N LEU B 247 " --> pdb=" O ALA B 274 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL B 276 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE B 249 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 411 through 413 Processing sheet with id=AC4, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AC5, first strand: chain 'C' and resid 48 through 50 removed outlier: 7.477A pdb=" N ASN C 37 " --> pdb=" O GLU D 518 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N MET D 520 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL C 39 " --> pdb=" O MET D 520 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N THR D 522 " --> pdb=" O VAL C 39 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 174 through 179 Processing sheet with id=AC7, first strand: chain 'C' and resid 193 through 195 Processing sheet with id=AC8, first strand: chain 'C' and resid 273 through 277 removed outlier: 6.158A pdb=" N LEU C 247 " --> pdb=" O ALA C 274 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL C 276 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE C 249 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 9.593A pdb=" N ILE C 301 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LEU C 222 " --> pdb=" O ILE C 301 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 273 through 277 removed outlier: 6.158A pdb=" N LEU C 247 " --> pdb=" O ALA C 274 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL C 276 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE C 249 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AD2, first strand: chain 'C' and resid 476 through 479 Processing sheet with id=AD3, first strand: chain 'D' and resid 48 through 50 removed outlier: 7.456A pdb=" N ASN D 37 " --> pdb=" O GLU E 518 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N MET E 520 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL D 39 " --> pdb=" O MET E 520 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N THR E 522 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 174 through 179 Processing sheet with id=AD5, first strand: chain 'D' and resid 193 through 195 Processing sheet with id=AD6, first strand: chain 'D' and resid 273 through 277 removed outlier: 6.158A pdb=" N LEU D 247 " --> pdb=" O ALA D 274 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL D 276 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE D 249 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N ILE D 301 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N LEU D 222 " --> pdb=" O ILE D 301 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 273 through 277 removed outlier: 6.158A pdb=" N LEU D 247 " --> pdb=" O ALA D 274 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL D 276 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE D 249 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 411 through 413 Processing sheet with id=AD9, first strand: chain 'D' and resid 476 through 479 Processing sheet with id=AE1, first strand: chain 'E' and resid 48 through 50 removed outlier: 7.461A pdb=" N ASN E 37 " --> pdb=" O GLU F 518 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N MET F 520 " --> pdb=" O ASN E 37 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL E 39 " --> pdb=" O MET F 520 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N THR F 522 " --> pdb=" O VAL E 39 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 174 through 179 Processing sheet with id=AE3, first strand: chain 'E' and resid 193 through 195 Processing sheet with id=AE4, first strand: chain 'E' and resid 273 through 277 removed outlier: 6.158A pdb=" N LEU E 247 " --> pdb=" O ALA E 274 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL E 276 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE E 249 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N ILE E 301 " --> pdb=" O ILE E 220 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N LEU E 222 " --> pdb=" O ILE E 301 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 273 through 277 removed outlier: 6.158A pdb=" N LEU E 247 " --> pdb=" O ALA E 274 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL E 276 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE E 249 " --> pdb=" O VAL E 276 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 411 through 413 Processing sheet with id=AE7, first strand: chain 'E' and resid 476 through 479 Processing sheet with id=AE8, first strand: chain 'F' and resid 174 through 179 Processing sheet with id=AE9, first strand: chain 'F' and resid 193 through 195 Processing sheet with id=AF1, first strand: chain 'F' and resid 273 through 277 removed outlier: 6.158A pdb=" N LEU F 247 " --> pdb=" O ALA F 274 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL F 276 " --> pdb=" O LEU F 247 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE F 249 " --> pdb=" O VAL F 276 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N ILE F 301 " --> pdb=" O ILE F 220 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N LEU F 222 " --> pdb=" O ILE F 301 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 273 through 277 removed outlier: 6.158A pdb=" N LEU F 247 " --> pdb=" O ALA F 274 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL F 276 " --> pdb=" O LEU F 247 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE F 249 " --> pdb=" O VAL F 276 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 411 through 413 Processing sheet with id=AF4, first strand: chain 'F' and resid 476 through 479 Processing sheet with id=AF5, first strand: chain 'H' and resid 4 through 8 removed outlier: 5.935A pdb=" N ASN N 37 " --> pdb=" O THR H 517 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS H 519 " --> pdb=" O ASN N 37 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 48 through 50 removed outlier: 6.700A pdb=" N ASN H 37 " --> pdb=" O CYS I 519 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N VAL I 521 " --> pdb=" O ASN H 37 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL H 39 " --> pdb=" O VAL I 521 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N ASP I 523 " --> pdb=" O VAL H 39 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 174 through 179 Processing sheet with id=AF8, first strand: chain 'H' and resid 193 through 195 Processing sheet with id=AF9, first strand: chain 'H' and resid 273 through 277 removed outlier: 6.158A pdb=" N LEU H 247 " --> pdb=" O ALA H 274 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL H 276 " --> pdb=" O LEU H 247 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE H 249 " --> pdb=" O VAL H 276 " (cutoff:3.500A) removed outlier: 9.593A pdb=" N ILE H 301 " --> pdb=" O ILE H 220 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N LEU H 222 " --> pdb=" O ILE H 301 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 273 through 277 removed outlier: 6.158A pdb=" N LEU H 247 " --> pdb=" O ALA H 274 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL H 276 " --> pdb=" O LEU H 247 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE H 249 " --> pdb=" O VAL H 276 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 411 through 413 Processing sheet with id=AG3, first strand: chain 'H' and resid 476 through 479 Processing sheet with id=AG4, first strand: chain 'I' and resid 48 through 50 removed outlier: 7.428A pdb=" N ASN I 37 " --> pdb=" O GLU J 518 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N MET J 520 " --> pdb=" O ASN I 37 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL I 39 " --> pdb=" O MET J 520 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N THR J 522 " --> pdb=" O VAL I 39 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 174 through 179 Processing sheet with id=AG6, first strand: chain 'I' and resid 193 through 195 Processing sheet with id=AG7, first strand: chain 'I' and resid 273 through 277 removed outlier: 6.158A pdb=" N LEU I 247 " --> pdb=" O ALA I 274 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL I 276 " --> pdb=" O LEU I 247 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE I 249 " --> pdb=" O VAL I 276 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N ILE I 301 " --> pdb=" O ILE I 220 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N LEU I 222 " --> pdb=" O ILE I 301 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 273 through 277 removed outlier: 6.158A pdb=" N LEU I 247 " --> pdb=" O ALA I 274 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL I 276 " --> pdb=" O LEU I 247 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE I 249 " --> pdb=" O VAL I 276 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 411 through 413 Processing sheet with id=AH1, first strand: chain 'I' and resid 476 through 479 Processing sheet with id=AH2, first strand: chain 'J' and resid 48 through 50 removed outlier: 6.688A pdb=" N ASN J 37 " --> pdb=" O CYS K 519 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N VAL K 521 " --> pdb=" O ASN J 37 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL J 39 " --> pdb=" O VAL K 521 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N ASP K 523 " --> pdb=" O VAL J 39 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 174 through 179 Processing sheet with id=AH4, first strand: chain 'J' and resid 193 through 195 Processing sheet with id=AH5, first strand: chain 'J' and resid 273 through 277 removed outlier: 6.158A pdb=" N LEU J 247 " --> pdb=" O ALA J 274 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL J 276 " --> pdb=" O LEU J 247 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE J 249 " --> pdb=" O VAL J 276 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N ILE J 301 " --> pdb=" O ILE J 220 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LEU J 222 " --> pdb=" O ILE J 301 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 273 through 277 removed outlier: 6.158A pdb=" N LEU J 247 " --> pdb=" O ALA J 274 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL J 276 " --> pdb=" O LEU J 247 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE J 249 " --> pdb=" O VAL J 276 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 411 through 413 Processing sheet with id=AH8, first strand: chain 'J' and resid 476 through 479 Processing sheet with id=AH9, first strand: chain 'K' and resid 48 through 50 removed outlier: 7.438A pdb=" N ASN K 37 " --> pdb=" O GLU L 518 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N MET L 520 " --> pdb=" O ASN K 37 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL K 39 " --> pdb=" O MET L 520 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N THR L 522 " --> pdb=" O VAL K 39 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'K' and resid 174 through 179 Processing sheet with id=AI2, first strand: chain 'K' and resid 193 through 195 Processing sheet with id=AI3, first strand: chain 'K' and resid 273 through 277 removed outlier: 6.158A pdb=" N LEU K 247 " --> pdb=" O ALA K 274 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL K 276 " --> pdb=" O LEU K 247 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE K 249 " --> pdb=" O VAL K 276 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N ILE K 301 " --> pdb=" O ILE K 220 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N LEU K 222 " --> pdb=" O ILE K 301 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'K' and resid 273 through 277 removed outlier: 6.158A pdb=" N LEU K 247 " --> pdb=" O ALA K 274 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL K 276 " --> pdb=" O LEU K 247 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE K 249 " --> pdb=" O VAL K 276 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'K' and resid 411 through 413 Processing sheet with id=AI6, first strand: chain 'K' and resid 476 through 479 Processing sheet with id=AI7, first strand: chain 'L' and resid 48 through 50 removed outlier: 7.435A pdb=" N ASN L 37 " --> pdb=" O GLU M 518 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N MET M 520 " --> pdb=" O ASN L 37 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL L 39 " --> pdb=" O MET M 520 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N THR M 522 " --> pdb=" O VAL L 39 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'L' and resid 174 through 179 Processing sheet with id=AI9, first strand: chain 'L' and resid 193 through 195 Processing sheet with id=AJ1, first strand: chain 'L' and resid 273 through 277 removed outlier: 6.158A pdb=" N LEU L 247 " --> pdb=" O ALA L 274 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL L 276 " --> pdb=" O LEU L 247 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE L 249 " --> pdb=" O VAL L 276 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N ILE L 301 " --> pdb=" O ILE L 220 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N LEU L 222 " --> pdb=" O ILE L 301 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'L' and resid 273 through 277 removed outlier: 6.158A pdb=" N LEU L 247 " --> pdb=" O ALA L 274 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL L 276 " --> pdb=" O LEU L 247 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE L 249 " --> pdb=" O VAL L 276 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'L' and resid 411 through 413 Processing sheet with id=AJ4, first strand: chain 'L' and resid 476 through 479 Processing sheet with id=AJ5, first strand: chain 'M' and resid 48 through 50 removed outlier: 6.695A pdb=" N ASN M 37 " --> pdb=" O CYS N 519 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N VAL N 521 " --> pdb=" O ASN M 37 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL M 39 " --> pdb=" O VAL N 521 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N ASP N 523 " --> pdb=" O VAL M 39 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'M' and resid 174 through 179 Processing sheet with id=AJ7, first strand: chain 'M' and resid 193 through 195 Processing sheet with id=AJ8, first strand: chain 'M' and resid 273 through 277 removed outlier: 6.158A pdb=" N LEU M 247 " --> pdb=" O ALA M 274 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL M 276 " --> pdb=" O LEU M 247 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE M 249 " --> pdb=" O VAL M 276 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N ILE M 301 " --> pdb=" O ILE M 220 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N LEU M 222 " --> pdb=" O ILE M 301 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'M' and resid 273 through 277 removed outlier: 6.158A pdb=" N LEU M 247 " --> pdb=" O ALA M 274 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL M 276 " --> pdb=" O LEU M 247 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE M 249 " --> pdb=" O VAL M 276 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'M' and resid 411 through 413 Processing sheet with id=AK2, first strand: chain 'M' and resid 476 through 479 Processing sheet with id=AK3, first strand: chain 'N' and resid 174 through 179 Processing sheet with id=AK4, first strand: chain 'N' and resid 193 through 195 Processing sheet with id=AK5, first strand: chain 'N' and resid 273 through 277 removed outlier: 6.158A pdb=" N LEU N 247 " --> pdb=" O ALA N 274 " (cutoff:3.500A) removed outlier: 7.920A 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) removed outlier: 9.593A pdb=" N ILE N 301 " --> pdb=" O ILE N 220 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N LEU N 222 " --> pdb=" O ILE N 301 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'N' and resid 273 through 277 removed outlier: 6.158A pdb=" N LEU N 247 " --> pdb=" O ALA N 274 " (cutoff:3.500A) removed outlier: 7.920A 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=AK7, first strand: chain 'N' and resid 411 through 413 Processing sheet with id=AK8, first strand: chain 'N' and resid 476 through 479 3727 hydrogen bonds defined for protein. 10719 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: 30.91 Time building geometry restraints manager: 12.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 18775 1.34 - 1.46: 5295 1.46 - 1.57: 30110 1.57 - 1.69: 28 1.69 - 1.81: 518 Bond restraints: 54726 Sorted by residual: bond pdb=" CB VAL B 74 " pdb=" CG2 VAL B 74 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.97e+00 bond pdb=" CB VAL N 74 " pdb=" CG2 VAL N 74 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.94e+00 bond pdb=" CB VAL M 74 " pdb=" CG2 VAL M 74 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.93e+00 bond pdb=" CB VAL C 74 " pdb=" CG2 VAL C 74 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.93e+00 bond pdb=" CB VAL I 74 " pdb=" CG2 VAL I 74 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.92e+00 ... (remaining 54721 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 73276 2.29 - 4.57: 602 4.57 - 6.86: 84 6.86 - 9.14: 14 9.14 - 11.43: 14 Bond angle restraints: 73990 Sorted by residual: angle pdb=" CB MET A 267 " pdb=" CG MET A 267 " pdb=" SD MET A 267 " ideal model delta sigma weight residual 112.70 124.13 -11.43 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CB MET I 267 " pdb=" CG MET I 267 " pdb=" SD MET I 267 " ideal model delta sigma weight residual 112.70 124.12 -11.42 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CB MET C 267 " pdb=" CG MET C 267 " pdb=" SD MET C 267 " ideal model delta sigma weight residual 112.70 124.12 -11.42 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CB MET F 267 " pdb=" CG MET F 267 " pdb=" SD MET F 267 " ideal model delta sigma weight residual 112.70 124.12 -11.42 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CB MET G 267 " pdb=" CG MET G 267 " pdb=" SD MET G 267 " ideal model delta sigma weight residual 112.70 124.11 -11.41 3.00e+00 1.11e-01 1.45e+01 ... (remaining 73985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.22: 29103 15.22 - 30.45: 3173 30.45 - 45.67: 1343 45.67 - 60.90: 373 60.90 - 76.12: 168 Dihedral angle restraints: 34160 sinusoidal: 13510 harmonic: 20650 Sorted by residual: dihedral pdb=" CA LYS D 4 " pdb=" C LYS D 4 " pdb=" N ASP D 5 " pdb=" CA ASP D 5 " ideal model delta harmonic sigma weight residual 180.00 160.38 19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA LYS M 4 " pdb=" C LYS M 4 " pdb=" N ASP M 5 " pdb=" CA ASP M 5 " ideal model delta harmonic sigma weight residual 180.00 160.39 19.61 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA LYS B 4 " pdb=" C LYS B 4 " pdb=" N ASP B 5 " pdb=" CA ASP B 5 " ideal model delta harmonic sigma weight residual 180.00 160.40 19.60 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 34157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 5185 0.032 - 0.065: 2628 0.065 - 0.097: 707 0.097 - 0.130: 383 0.130 - 0.162: 71 Chirality restraints: 8974 Sorted by residual: chirality pdb=" CA MET G 447 " pdb=" N MET G 447 " pdb=" C MET G 447 " pdb=" CB MET G 447 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.56e-01 chirality pdb=" CA MET C 447 " pdb=" N MET C 447 " pdb=" C MET C 447 " pdb=" CB MET C 447 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CA MET E 447 " pdb=" N MET E 447 " pdb=" C MET E 447 " pdb=" CB MET E 447 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.45e-01 ... (remaining 8971 not shown) Planarity restraints: 9618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 449 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO D 450 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO D 450 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 450 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 449 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.78e+00 pdb=" N PRO E 450 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO E 450 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 450 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA K 449 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO K 450 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO K 450 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO K 450 " -0.019 5.00e-02 4.00e+02 ... (remaining 9615 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.53: 1158 2.53 - 3.18: 51536 3.18 - 3.83: 130159 3.83 - 4.49: 174288 4.49 - 5.14: 266063 Nonbonded interactions: 623204 Sorted by model distance: nonbonded pdb=" O PHE J 195 " pdb=" O HOH J 701 " model vdw 1.872 3.040 nonbonded pdb=" O THR J 330 " pdb=" O HOH J 701 " model vdw 2.048 3.040 nonbonded pdb="MG MG H 601 " pdb=" O1B ATP H 602 " model vdw 2.055 2.170 nonbonded pdb="MG MG L 601 " pdb=" O1B ATP L 602 " model vdw 2.055 2.170 nonbonded pdb="MG MG E 601 " pdb=" O1B ATP E 602 " model vdw 2.055 2.170 ... (remaining 623199 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 1.600 Check model and map are aligned: 0.320 Set scattering table: 0.400 Process input model: 107.990 Find NCS groups from input model: 2.370 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 54726 Z= 0.315 Angle : 0.592 11.427 73990 Z= 0.318 Chirality : 0.045 0.162 8974 Planarity : 0.003 0.034 9618 Dihedral : 16.845 76.125 20916 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.01 % Allowed : 17.88 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.09), residues: 7294 helix: 1.27 (0.08), residues: 4144 sheet: -0.12 (0.13), residues: 1148 loop : -0.74 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS I 401 PHE 0.006 0.001 PHE L 195 TYR 0.014 0.002 TYR N 478 ARG 0.002 0.000 ARG B 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 338 time to evaluate : 4.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 166 MET cc_start: 0.8206 (mtt) cc_final: 0.7990 (mtp) REVERT: B 166 MET cc_start: 0.8301 (mtt) cc_final: 0.7991 (mtt) REVERT: C 58 ARG cc_start: 0.7996 (mtm-85) cc_final: 0.7708 (mtt-85) REVERT: C 233 MET cc_start: 0.0958 (pmt) cc_final: 0.0700 (pmm) REVERT: C 520 MET cc_start: 0.8838 (mtp) cc_final: 0.8633 (mtp) REVERT: D 166 MET cc_start: 0.8200 (mtt) cc_final: 0.7916 (mtp) REVERT: H 233 MET cc_start: 0.0062 (pmt) cc_final: -0.1182 (tmt) REVERT: I 233 MET cc_start: 0.0316 (pmt) cc_final: -0.0658 (tmt) REVERT: K 386 GLU cc_start: 0.7297 (tp30) cc_final: 0.6877 (mm-30) REVERT: L 73 MET cc_start: 0.8143 (mtm) cc_final: 0.7883 (mtm) REVERT: M 114 MET cc_start: 0.8960 (tpp) cc_final: 0.8665 (tpp) REVERT: N 233 MET cc_start: 0.0426 (pmt) cc_final: -0.0958 (tmt) outliers start: 57 outliers final: 23 residues processed: 395 average time/residue: 1.4350 time to fit residues: 717.4524 Evaluate side-chains 327 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 304 time to evaluate : 4.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 219 PHE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain E residue 219 PHE Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain F residue 219 PHE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain H residue 219 PHE Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain J residue 219 PHE Chi-restraints excluded: chain K residue 236 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 614 optimal weight: 3.9990 chunk 551 optimal weight: 0.0470 chunk 306 optimal weight: 0.6980 chunk 188 optimal weight: 10.0000 chunk 372 optimal weight: 1.9990 chunk 294 optimal weight: 7.9990 chunk 570 optimal weight: 0.8980 chunk 220 optimal weight: 0.7980 chunk 346 optimal weight: 6.9990 chunk 424 optimal weight: 3.9990 chunk 661 optimal weight: 2.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 10 ASN N 10 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 54726 Z= 0.211 Angle : 0.526 10.651 73990 Z= 0.287 Chirality : 0.041 0.164 8974 Planarity : 0.003 0.031 9618 Dihedral : 9.074 79.770 8228 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 3.08 % Allowed : 15.21 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.10), residues: 7294 helix: 1.37 (0.08), residues: 4270 sheet: -0.34 (0.13), residues: 1204 loop : -0.56 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS G 401 PHE 0.015 0.002 PHE J 195 TYR 0.014 0.002 TYR C 478 ARG 0.022 0.000 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 318 time to evaluate : 4.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 10 ASN cc_start: 0.8429 (m-40) cc_final: 0.8147 (t0) REVERT: G 166 MET cc_start: 0.8266 (mtt) cc_final: 0.7848 (mtt) REVERT: A 111 MET cc_start: 0.8391 (mtp) cc_final: 0.8156 (mtp) REVERT: A 166 MET cc_start: 0.8218 (mtt) cc_final: 0.7916 (mtt) REVERT: A 237 LEU cc_start: 0.1358 (OUTLIER) cc_final: 0.1036 (mt) REVERT: A 267 MET cc_start: -0.0819 (pmm) cc_final: -0.1108 (ptp) REVERT: B 166 MET cc_start: 0.8291 (mtt) cc_final: 0.7915 (mtt) REVERT: B 237 LEU cc_start: 0.1344 (OUTLIER) cc_final: 0.1057 (mt) REVERT: C 114 MET cc_start: 0.9282 (tpp) cc_final: 0.9043 (tpp) REVERT: C 237 LEU cc_start: 0.1449 (OUTLIER) cc_final: 0.1179 (mt) REVERT: C 491 MET cc_start: 0.8944 (mtm) cc_final: 0.8586 (mtm) REVERT: D 166 MET cc_start: 0.8179 (mtt) cc_final: 0.7683 (mtt) REVERT: D 233 MET cc_start: 0.0770 (pmt) cc_final: -0.1311 (tmt) REVERT: E 10 ASN cc_start: 0.8442 (m-40) cc_final: 0.8157 (t0) REVERT: E 114 MET cc_start: 0.9254 (tpp) cc_final: 0.9029 (tpp) REVERT: E 142 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.6498 (tptp) REVERT: E 237 LEU cc_start: 0.1534 (OUTLIER) cc_final: 0.0982 (mt) REVERT: H 193 MET cc_start: 0.5230 (OUTLIER) cc_final: 0.4994 (tmt) REVERT: I 174 VAL cc_start: 0.7654 (OUTLIER) cc_final: 0.7417 (p) REVERT: I 193 MET cc_start: 0.4755 (OUTLIER) cc_final: 0.4520 (tmt) REVERT: J 193 MET cc_start: 0.4914 (OUTLIER) cc_final: 0.4669 (tmt) REVERT: J 267 MET cc_start: 0.1182 (pmm) cc_final: -0.1706 (tpt) REVERT: K 193 MET cc_start: 0.5007 (OUTLIER) cc_final: 0.4726 (tmt) REVERT: K 267 MET cc_start: 0.0323 (pmm) cc_final: -0.2098 (tpt) REVERT: L 267 MET cc_start: 0.1154 (pmm) cc_final: -0.1434 (tpt) REVERT: M 114 MET cc_start: 0.9288 (tpp) cc_final: 0.9067 (tpp) outliers start: 174 outliers final: 23 residues processed: 458 average time/residue: 1.4196 time to fit residues: 823.8318 Evaluate side-chains 339 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 306 time to evaluate : 4.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 219 PHE Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 219 PHE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain F residue 219 PHE Chi-restraints excluded: chain H residue 193 MET Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 193 MET Chi-restraints excluded: chain L residue 219 PHE Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 237 LEU Chi-restraints excluded: chain N residue 219 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 367 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 550 optimal weight: 9.9990 chunk 450 optimal weight: 30.0000 chunk 182 optimal weight: 9.9990 chunk 662 optimal weight: 8.9990 chunk 715 optimal weight: 1.9990 chunk 589 optimal weight: 5.9990 chunk 656 optimal weight: 8.9990 chunk 225 optimal weight: 6.9990 chunk 531 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 ASN D 10 ASN I 10 ASN N 10 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 54726 Z= 0.381 Angle : 0.608 9.921 73990 Z= 0.327 Chirality : 0.046 0.257 8974 Planarity : 0.004 0.042 9618 Dihedral : 9.936 89.817 8204 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.91 % Allowed : 14.37 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.09), residues: 7294 helix: 1.32 (0.08), residues: 4242 sheet: -0.35 (0.13), residues: 1246 loop : -0.54 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 401 PHE 0.024 0.001 PHE H 219 TYR 0.018 0.003 TYR N 478 ARG 0.005 0.000 ARG L 452 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 324 time to evaluate : 4.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 10 ASN cc_start: 0.8502 (m-40) cc_final: 0.8184 (t0) REVERT: G 166 MET cc_start: 0.8247 (mtt) cc_final: 0.7720 (mtt) REVERT: G 267 MET cc_start: 0.0211 (OUTLIER) cc_final: -0.1942 (mpp) REVERT: A 111 MET cc_start: 0.8552 (mtp) cc_final: 0.8335 (mtp) REVERT: A 166 MET cc_start: 0.8147 (mtp) cc_final: 0.7704 (mtt) REVERT: A 237 LEU cc_start: 0.1545 (OUTLIER) cc_final: 0.1169 (mt) REVERT: A 267 MET cc_start: -0.0760 (pmm) cc_final: -0.3503 (tpp) REVERT: B 10 ASN cc_start: 0.8414 (OUTLIER) cc_final: 0.8100 (t0) REVERT: B 166 MET cc_start: 0.8240 (mtt) cc_final: 0.7535 (mtt) REVERT: B 237 LEU cc_start: 0.1409 (OUTLIER) cc_final: 0.1073 (mt) REVERT: B 267 MET cc_start: -0.0623 (pmm) cc_final: -0.1805 (mpp) REVERT: C 10 ASN cc_start: 0.8522 (OUTLIER) cc_final: 0.8244 (t0) REVERT: C 237 LEU cc_start: 0.1370 (OUTLIER) cc_final: 0.1082 (mt) REVERT: C 267 MET cc_start: -0.0927 (pmm) cc_final: -0.3519 (tpp) REVERT: C 491 MET cc_start: 0.9191 (mtm) cc_final: 0.8931 (mtm) REVERT: D 166 MET cc_start: 0.8084 (mtt) cc_final: 0.7499 (mtt) REVERT: D 233 MET cc_start: 0.0630 (pmt) cc_final: -0.1378 (tmt) REVERT: E 10 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8191 (t0) REVERT: E 142 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.6662 (tptp) REVERT: E 237 LEU cc_start: 0.1718 (OUTLIER) cc_final: 0.1154 (mt) REVERT: H 193 MET cc_start: 0.5107 (OUTLIER) cc_final: 0.4874 (tmt) REVERT: H 267 MET cc_start: 0.0936 (pmm) cc_final: -0.1465 (tpp) REVERT: I 142 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7130 (tptp) REVERT: I 257 GLU cc_start: 0.0506 (OUTLIER) cc_final: -0.0414 (tt0) REVERT: K 193 MET cc_start: 0.5057 (OUTLIER) cc_final: 0.4840 (tmt) REVERT: K 267 MET cc_start: 0.0959 (pmm) cc_final: -0.1720 (tpp) REVERT: L 111 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8234 (mtp) REVERT: M 267 MET cc_start: 0.1390 (pmm) cc_final: -0.1417 (tpp) REVERT: N 111 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8320 (mtp) REVERT: N 267 MET cc_start: 0.1272 (pmm) cc_final: -0.1698 (tpp) REVERT: N 491 MET cc_start: 0.9200 (mtm) cc_final: 0.8994 (mtm) outliers start: 164 outliers final: 42 residues processed: 448 average time/residue: 1.4480 time to fit residues: 819.2736 Evaluate side-chains 368 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 311 time to evaluate : 4.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 219 PHE Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 366 GLN Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 219 PHE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 219 PHE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 193 MET Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 242 LYS Chi-restraints excluded: chain K residue 144 ILE Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 193 MET Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 219 PHE Chi-restraints excluded: chain L residue 366 GLN Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 237 LEU Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 219 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 654 optimal weight: 10.0000 chunk 497 optimal weight: 50.0000 chunk 343 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 316 optimal weight: 0.8980 chunk 444 optimal weight: 50.0000 chunk 664 optimal weight: 0.9990 chunk 703 optimal weight: 5.9990 chunk 347 optimal weight: 40.0000 chunk 629 optimal weight: 0.9980 chunk 189 optimal weight: 9.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 366 GLN B 10 ASN E 366 GLN M 366 GLN N 10 ASN N 366 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 54726 Z= 0.413 Angle : 0.621 8.626 73990 Z= 0.336 Chirality : 0.047 0.176 8974 Planarity : 0.004 0.049 9618 Dihedral : 9.870 88.970 8204 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.03 % Allowed : 14.46 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.09), residues: 7294 helix: 1.22 (0.08), residues: 4242 sheet: -0.52 (0.13), residues: 1134 loop : -0.40 (0.13), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 401 PHE 0.014 0.001 PHE J 195 TYR 0.018 0.003 TYR N 478 ARG 0.005 0.000 ARG E 445 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 323 time to evaluate : 4.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 10 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.8075 (t0) REVERT: G 267 MET cc_start: 0.0321 (OUTLIER) cc_final: -0.1975 (mpp) REVERT: A 111 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8308 (mtp) REVERT: A 134 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8691 (tp) REVERT: A 166 MET cc_start: 0.8111 (mtp) cc_final: 0.7608 (mtt) REVERT: A 233 MET cc_start: 0.0618 (pmt) cc_final: 0.0293 (pmm) REVERT: A 267 MET cc_start: -0.0575 (pmm) cc_final: -0.1169 (mpp) REVERT: B 166 MET cc_start: 0.8258 (mtt) cc_final: 0.7831 (mtt) REVERT: B 237 LEU cc_start: 0.1539 (OUTLIER) cc_final: 0.1161 (mt) REVERT: B 267 MET cc_start: -0.0494 (pmm) cc_final: -0.1189 (mpp) REVERT: C 237 LEU cc_start: 0.1505 (OUTLIER) cc_final: 0.1211 (mt) REVERT: C 267 MET cc_start: -0.0825 (pmm) cc_final: -0.3376 (tpp) REVERT: D 166 MET cc_start: 0.8075 (mtt) cc_final: 0.7543 (mtt) REVERT: D 267 MET cc_start: -0.0231 (pmm) cc_final: -0.2893 (tpp) REVERT: E 10 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.8113 (t0) REVERT: E 142 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.6718 (tptp) REVERT: E 233 MET cc_start: 0.0882 (OUTLIER) cc_final: 0.0241 (pmm) REVERT: E 267 MET cc_start: 0.0488 (OUTLIER) cc_final: -0.2348 (tpp) REVERT: F 10 ASN cc_start: 0.8381 (OUTLIER) cc_final: 0.8140 (t0) REVERT: F 111 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8210 (mtp) REVERT: H 193 MET cc_start: 0.5217 (OUTLIER) cc_final: 0.4984 (tmt) REVERT: I 142 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7219 (tptp) REVERT: I 193 MET cc_start: 0.4792 (OUTLIER) cc_final: 0.4580 (tmt) REVERT: I 257 GLU cc_start: 0.0640 (OUTLIER) cc_final: -0.0446 (mt-10) REVERT: J 267 MET cc_start: 0.0873 (pmm) cc_final: -0.1696 (tpt) REVERT: K 257 GLU cc_start: 0.0251 (OUTLIER) cc_final: -0.0897 (mt-10) REVERT: L 111 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8250 (mtp) REVERT: M 257 GLU cc_start: 0.0392 (OUTLIER) cc_final: -0.0533 (tt0) REVERT: M 366 GLN cc_start: 0.3760 (OUTLIER) cc_final: 0.3105 (mm110) REVERT: N 111 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8326 (mtp) REVERT: N 257 GLU cc_start: 0.0297 (OUTLIER) cc_final: -0.0467 (tt0) outliers start: 171 outliers final: 59 residues processed: 458 average time/residue: 1.4411 time to fit residues: 835.2484 Evaluate side-chains 394 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 313 time to evaluate : 4.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 10 ASN Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 219 PHE Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 366 GLN Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 219 PHE Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain F residue 10 ASN Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 219 PHE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 193 MET Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 288 MET Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain K residue 144 ILE Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 257 GLU Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 219 PHE Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 257 GLU Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 366 GLN Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 242 LYS Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 366 GLN Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 219 PHE Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 257 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 586 optimal weight: 3.9990 chunk 399 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 523 optimal weight: 1.9990 chunk 290 optimal weight: 10.0000 chunk 600 optimal weight: 9.9990 chunk 486 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 359 optimal weight: 0.5980 chunk 631 optimal weight: 3.9990 chunk 177 optimal weight: 30.0000 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 366 GLN B 366 GLN I 10 ASN ** M 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 10 ASN N 366 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 54726 Z= 0.331 Angle : 0.589 9.696 73990 Z= 0.318 Chirality : 0.044 0.306 8974 Planarity : 0.004 0.040 9618 Dihedral : 9.684 89.244 8204 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.00 % Allowed : 14.57 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.09), residues: 7294 helix: 1.29 (0.08), residues: 4256 sheet: -0.54 (0.13), residues: 1148 loop : -0.39 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS K 401 PHE 0.014 0.001 PHE J 195 TYR 0.016 0.002 TYR F 478 ARG 0.004 0.000 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 322 time to evaluate : 4.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 10 ASN cc_start: 0.8394 (OUTLIER) cc_final: 0.8045 (t0) REVERT: G 267 MET cc_start: 0.0370 (OUTLIER) cc_final: -0.1894 (mpp) REVERT: A 111 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8220 (mtp) REVERT: A 166 MET cc_start: 0.8088 (mtp) cc_final: 0.7622 (mtt) REVERT: A 233 MET cc_start: 0.0611 (OUTLIER) cc_final: 0.0302 (pmm) REVERT: A 237 LEU cc_start: 0.1341 (OUTLIER) cc_final: 0.0947 (mt) REVERT: B 237 LEU cc_start: 0.1437 (OUTLIER) cc_final: 0.1036 (mt) REVERT: B 267 MET cc_start: -0.0760 (pmm) cc_final: -0.1145 (mpp) REVERT: C 237 LEU cc_start: 0.1408 (OUTLIER) cc_final: 0.0974 (mt) REVERT: C 267 MET cc_start: -0.0642 (pmm) cc_final: -0.1027 (mpp) REVERT: D 166 MET cc_start: 0.8020 (mtt) cc_final: 0.7567 (mtt) REVERT: D 267 MET cc_start: -0.0346 (pmm) cc_final: -0.3113 (tpp) REVERT: E 10 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.8096 (t0) REVERT: E 142 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.6711 (tptp) REVERT: E 233 MET cc_start: 0.1004 (pmt) cc_final: 0.0331 (pmm) REVERT: E 237 LEU cc_start: 0.1421 (OUTLIER) cc_final: 0.0799 (mt) REVERT: E 267 MET cc_start: 0.0532 (OUTLIER) cc_final: -0.2395 (tpp) REVERT: F 10 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.8121 (t0) REVERT: H 234 LEU cc_start: 0.0416 (OUTLIER) cc_final: 0.0092 (mt) REVERT: H 267 MET cc_start: 0.0847 (pmm) cc_final: -0.1425 (tpp) REVERT: J 257 GLU cc_start: 0.0970 (OUTLIER) cc_final: -0.0208 (mt-10) REVERT: L 111 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8196 (mtp) REVERT: M 257 GLU cc_start: 0.0400 (OUTLIER) cc_final: -0.0519 (tt0) REVERT: M 267 MET cc_start: 0.0912 (OUTLIER) cc_final: -0.2006 (tpp) REVERT: N 257 GLU cc_start: 0.0360 (OUTLIER) cc_final: -0.0436 (tt0) REVERT: N 267 MET cc_start: 0.1146 (pmm) cc_final: -0.1824 (tpp) outliers start: 169 outliers final: 63 residues processed: 458 average time/residue: 1.4539 time to fit residues: 841.3856 Evaluate side-chains 395 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 314 time to evaluate : 4.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 10 ASN Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 219 PHE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 219 PHE Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain F residue 10 ASN Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 219 PHE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 288 MET Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 257 GLU Chi-restraints excluded: chain K residue 144 ILE Chi-restraints excluded: chain K residue 157 THR Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 257 GLU Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain L residue 157 THR Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 219 PHE Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 257 GLU Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 267 MET Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 219 PHE Chi-restraints excluded: chain N residue 257 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 236 optimal weight: 6.9990 chunk 633 optimal weight: 1.9990 chunk 139 optimal weight: 30.0000 chunk 413 optimal weight: 4.9990 chunk 173 optimal weight: 4.9990 chunk 704 optimal weight: 50.0000 chunk 584 optimal weight: 0.9990 chunk 326 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 232 optimal weight: 20.0000 chunk 369 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 366 GLN ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN C 10 ASN F 366 GLN I 10 ASN K 10 ASN L 366 GLN M 366 GLN N 10 ASN N 366 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 54726 Z= 0.280 Angle : 0.566 9.654 73990 Z= 0.306 Chirality : 0.042 0.164 8974 Planarity : 0.003 0.033 9618 Dihedral : 9.548 88.807 8204 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.61 % Allowed : 15.26 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.09), residues: 7294 helix: 1.37 (0.08), residues: 4256 sheet: -0.49 (0.13), residues: 1148 loop : -0.36 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS K 401 PHE 0.012 0.001 PHE J 195 TYR 0.015 0.002 TYR F 478 ARG 0.003 0.000 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 320 time to evaluate : 4.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 10 ASN cc_start: 0.8367 (OUTLIER) cc_final: 0.8045 (t0) REVERT: G 267 MET cc_start: 0.0416 (OUTLIER) cc_final: -0.1829 (mpp) REVERT: A 111 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8255 (mtp) REVERT: A 134 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8648 (tp) REVERT: A 166 MET cc_start: 0.8120 (mtp) cc_final: 0.7749 (mtt) REVERT: A 233 MET cc_start: 0.0606 (OUTLIER) cc_final: 0.0285 (pmm) REVERT: A 237 LEU cc_start: 0.1385 (OUTLIER) cc_final: 0.1001 (mt) REVERT: A 267 MET cc_start: -0.0720 (pmm) cc_final: -0.3118 (tpp) REVERT: B 142 LYS cc_start: 0.7687 (tptp) cc_final: 0.7466 (tppt) REVERT: B 237 LEU cc_start: 0.1414 (OUTLIER) cc_final: 0.0993 (mt) REVERT: C 237 LEU cc_start: 0.1468 (OUTLIER) cc_final: 0.1017 (mt) REVERT: D 166 MET cc_start: 0.7999 (mtt) cc_final: 0.7511 (mtt) REVERT: D 267 MET cc_start: -0.0340 (pmm) cc_final: -0.3037 (tpp) REVERT: E 10 ASN cc_start: 0.8387 (OUTLIER) cc_final: 0.8081 (t0) REVERT: E 142 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.6710 (tptp) REVERT: E 233 MET cc_start: 0.0804 (OUTLIER) cc_final: 0.0253 (pmm) REVERT: E 267 MET cc_start: 0.0603 (OUTLIER) cc_final: -0.2256 (tpp) REVERT: H 161 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8309 (mp) REVERT: H 267 MET cc_start: 0.0828 (OUTLIER) cc_final: -0.1545 (tpp) REVERT: I 257 GLU cc_start: 0.0780 (OUTLIER) cc_final: -0.0722 (mt-10) REVERT: J 193 MET cc_start: 0.5230 (OUTLIER) cc_final: 0.4972 (tmt) REVERT: J 257 GLU cc_start: 0.0952 (OUTLIER) cc_final: -0.0001 (mt-10) REVERT: J 267 MET cc_start: 0.0249 (pmt) cc_final: -0.0465 (ptp) REVERT: J 288 MET cc_start: 0.3864 (ptp) cc_final: 0.3161 (mmp) REVERT: M 257 GLU cc_start: 0.0526 (OUTLIER) cc_final: -0.0372 (tt0) REVERT: M 267 MET cc_start: 0.1236 (OUTLIER) cc_final: -0.1105 (tpp) REVERT: N 257 GLU cc_start: 0.0552 (OUTLIER) cc_final: -0.0069 (mt-10) outliers start: 147 outliers final: 62 residues processed: 439 average time/residue: 1.4641 time to fit residues: 809.3878 Evaluate side-chains 400 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 318 time to evaluate : 4.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 10 ASN Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 219 PHE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 219 PHE Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 219 PHE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 257 GLU Chi-restraints excluded: chain K residue 144 ILE Chi-restraints excluded: chain K residue 157 THR Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 257 GLU Chi-restraints excluded: chain K residue 288 MET Chi-restraints excluded: chain L residue 157 THR Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 219 PHE Chi-restraints excluded: chain L residue 257 GLU Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 267 MET Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 219 PHE Chi-restraints excluded: chain N residue 257 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 679 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 401 optimal weight: 7.9990 chunk 514 optimal weight: 0.9980 chunk 398 optimal weight: 20.0000 chunk 592 optimal weight: 7.9990 chunk 393 optimal weight: 30.0000 chunk 701 optimal weight: 50.0000 chunk 439 optimal weight: 7.9990 chunk 427 optimal weight: 0.9990 chunk 323 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 366 GLN ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN C 10 ASN I 10 ASN L 366 GLN N 10 ASN N 366 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 54726 Z= 0.339 Angle : 0.601 11.640 73990 Z= 0.323 Chirality : 0.044 0.243 8974 Planarity : 0.004 0.040 9618 Dihedral : 9.712 89.745 8204 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.59 % Allowed : 15.47 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.09), residues: 7294 helix: 1.29 (0.08), residues: 4256 sheet: -0.45 (0.13), residues: 1148 loop : -0.34 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS K 401 PHE 0.010 0.001 PHE J 195 TYR 0.016 0.002 TYR F 478 ARG 0.003 0.000 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 318 time to evaluate : 4.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 10 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.8064 (t0) REVERT: G 267 MET cc_start: 0.0290 (OUTLIER) cc_final: -0.1918 (mpp) REVERT: A 111 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8232 (mtp) REVERT: A 134 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8643 (tp) REVERT: A 166 MET cc_start: 0.8104 (mtp) cc_final: 0.7677 (mtt) REVERT: A 233 MET cc_start: 0.0636 (OUTLIER) cc_final: 0.0309 (pmm) REVERT: A 237 LEU cc_start: 0.1125 (OUTLIER) cc_final: 0.0695 (mt) REVERT: A 267 MET cc_start: -0.0395 (pmm) cc_final: -0.3058 (tpp) REVERT: B 237 LEU cc_start: 0.1383 (OUTLIER) cc_final: 0.0910 (mt) REVERT: B 267 MET cc_start: -0.0030 (OUTLIER) cc_final: -0.2143 (mpp) REVERT: C 237 LEU cc_start: 0.1581 (OUTLIER) cc_final: 0.0976 (mt) REVERT: C 267 MET cc_start: -0.1173 (pmm) cc_final: -0.3261 (tpp) REVERT: D 166 MET cc_start: 0.7991 (mtt) cc_final: 0.7462 (mtt) REVERT: D 267 MET cc_start: -0.0575 (pmm) cc_final: -0.3220 (tpp) REVERT: E 10 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.8081 (t0) REVERT: E 142 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.6742 (tptp) REVERT: E 233 MET cc_start: 0.0800 (OUTLIER) cc_final: 0.0230 (pmm) REVERT: E 267 MET cc_start: 0.0593 (OUTLIER) cc_final: -0.2315 (tpp) REVERT: H 161 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8329 (mp) REVERT: H 234 LEU cc_start: 0.0350 (OUTLIER) cc_final: 0.0104 (mt) REVERT: H 267 MET cc_start: 0.0720 (OUTLIER) cc_final: -0.1631 (tpp) REVERT: I 257 GLU cc_start: 0.0888 (OUTLIER) cc_final: -0.0716 (mt-10) REVERT: J 193 MET cc_start: 0.5211 (OUTLIER) cc_final: 0.4951 (tmt) REVERT: J 257 GLU cc_start: 0.0962 (OUTLIER) cc_final: 0.0139 (mt-10) REVERT: J 267 MET cc_start: 0.0200 (pmt) cc_final: -0.0507 (ptp) REVERT: J 288 MET cc_start: 0.3766 (ptp) cc_final: 0.3208 (mmp) REVERT: K 193 MET cc_start: 0.5056 (OUTLIER) cc_final: 0.4774 (tmt) REVERT: K 234 LEU cc_start: -0.0042 (OUTLIER) cc_final: -0.0367 (mm) REVERT: L 111 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8219 (mtp) REVERT: L 267 MET cc_start: 0.1329 (pmm) cc_final: 0.0983 (pmm) REVERT: M 267 MET cc_start: 0.1141 (OUTLIER) cc_final: -0.1120 (tpp) REVERT: M 366 GLN cc_start: 0.3859 (OUTLIER) cc_final: 0.3392 (mm110) REVERT: N 111 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8321 (mtp) REVERT: N 257 GLU cc_start: 0.0497 (OUTLIER) cc_final: -0.0040 (mt-10) REVERT: N 267 MET cc_start: 0.0893 (pmm) cc_final: -0.2088 (tpp) outliers start: 146 outliers final: 69 residues processed: 438 average time/residue: 1.5026 time to fit residues: 826.2545 Evaluate side-chains 411 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 316 time to evaluate : 4.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 10 ASN Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 219 PHE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 219 PHE Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 219 PHE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 288 MET Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 257 GLU Chi-restraints excluded: chain K residue 144 ILE Chi-restraints excluded: chain K residue 157 THR Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 193 MET Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 257 GLU Chi-restraints excluded: chain K residue 288 MET Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain L residue 157 THR Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 219 PHE Chi-restraints excluded: chain L residue 257 GLU Chi-restraints excluded: chain L residue 366 GLN Chi-restraints excluded: chain M residue 144 ILE Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 267 MET Chi-restraints excluded: chain M residue 366 GLN Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 219 PHE Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 257 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 0.8980 chunk 280 optimal weight: 6.9990 chunk 419 optimal weight: 0.8980 chunk 211 optimal weight: 0.9980 chunk 137 optimal weight: 0.0470 chunk 135 optimal weight: 1.9990 chunk 446 optimal weight: 4.9990 chunk 478 optimal weight: 0.9980 chunk 346 optimal weight: 30.0000 chunk 65 optimal weight: 2.9990 chunk 551 optimal weight: 10.0000 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 366 GLN ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN I 10 ASN L 366 GLN N 10 ASN N 366 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 54726 Z= 0.194 Angle : 0.543 11.631 73990 Z= 0.290 Chirality : 0.041 0.292 8974 Planarity : 0.003 0.031 9618 Dihedral : 9.038 85.079 8204 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.27 % Allowed : 16.06 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.10), residues: 7294 helix: 1.48 (0.08), residues: 4270 sheet: -0.47 (0.13), residues: 1134 loop : -0.33 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS N 401 PHE 0.013 0.001 PHE J 195 TYR 0.012 0.001 TYR A 478 ARG 0.006 0.000 ARG L 368 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 330 time to evaluate : 4.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 267 MET cc_start: 0.0146 (OUTLIER) cc_final: -0.2016 (mpp) REVERT: A 166 MET cc_start: 0.8085 (mtp) cc_final: 0.7650 (mtt) REVERT: A 233 MET cc_start: 0.0612 (OUTLIER) cc_final: 0.0261 (pmm) REVERT: A 237 LEU cc_start: 0.0990 (OUTLIER) cc_final: 0.0581 (mt) REVERT: A 267 MET cc_start: -0.0705 (pmm) cc_final: -0.3198 (tpp) REVERT: B 237 LEU cc_start: 0.1138 (OUTLIER) cc_final: 0.0671 (mt) REVERT: B 267 MET cc_start: -0.0093 (OUTLIER) cc_final: -0.2078 (mpp) REVERT: C 237 LEU cc_start: 0.1583 (OUTLIER) cc_final: 0.1011 (mt) REVERT: C 267 MET cc_start: -0.1288 (pmm) cc_final: -0.3417 (tpp) REVERT: D 166 MET cc_start: 0.7983 (mtt) cc_final: 0.7503 (mtt) REVERT: D 267 MET cc_start: -0.0675 (pmm) cc_final: -0.3321 (tpp) REVERT: E 10 ASN cc_start: 0.8392 (m-40) cc_final: 0.8125 (t0) REVERT: E 142 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.6643 (tptp) REVERT: E 233 MET cc_start: 0.0774 (OUTLIER) cc_final: 0.0209 (pmm) REVERT: I 257 GLU cc_start: 0.0899 (OUTLIER) cc_final: -0.0518 (mt-10) REVERT: I 267 MET cc_start: 0.0087 (pmm) cc_final: -0.1004 (ptp) REVERT: J 142 LYS cc_start: 0.7408 (tptp) cc_final: 0.7185 (tppt) REVERT: J 267 MET cc_start: -0.0180 (pmt) cc_final: -0.0687 (ptp) REVERT: J 288 MET cc_start: 0.3707 (ptp) cc_final: 0.3125 (mmp) REVERT: K 193 MET cc_start: 0.5059 (OUTLIER) cc_final: 0.4765 (tmt) REVERT: M 142 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.6776 (tptp) REVERT: M 257 GLU cc_start: 0.0632 (OUTLIER) cc_final: -0.0312 (tt0) REVERT: M 366 GLN cc_start: 0.3843 (OUTLIER) cc_final: 0.3433 (mm110) REVERT: N 193 MET cc_start: 0.3955 (tpt) cc_final: 0.3414 (tpt) REVERT: N 267 MET cc_start: 0.1139 (pmm) cc_final: -0.1868 (tpp) outliers start: 128 outliers final: 53 residues processed: 431 average time/residue: 1.5659 time to fit residues: 842.4344 Evaluate side-chains 387 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 321 time to evaluate : 4.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 219 PHE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 219 PHE Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 219 PHE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 288 MET Chi-restraints excluded: chain H residue 365 LEU Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 257 GLU Chi-restraints excluded: chain K residue 144 ILE Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 193 MET Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 257 GLU Chi-restraints excluded: chain K residue 288 MET Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 219 PHE Chi-restraints excluded: chain L residue 257 GLU Chi-restraints excluded: chain L residue 366 GLN Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 366 GLN Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 219 PHE Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 257 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 638 optimal weight: 3.9990 chunk 672 optimal weight: 2.9990 chunk 613 optimal weight: 1.9990 chunk 653 optimal weight: 0.8980 chunk 393 optimal weight: 8.9990 chunk 284 optimal weight: 50.0000 chunk 513 optimal weight: 3.9990 chunk 200 optimal weight: 0.6980 chunk 590 optimal weight: 8.9990 chunk 618 optimal weight: 0.9980 chunk 651 optimal weight: 30.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 366 GLN ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN C 10 ASN I 10 ASN L 366 GLN N 10 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 54726 Z= 0.261 Angle : 0.580 12.232 73990 Z= 0.309 Chirality : 0.042 0.241 8974 Planarity : 0.003 0.047 9618 Dihedral : 9.460 89.582 8204 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.91 % Allowed : 16.39 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.09), residues: 7294 helix: 1.43 (0.08), residues: 4284 sheet: -0.35 (0.14), residues: 1120 loop : -0.34 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 401 PHE 0.012 0.001 PHE J 195 TYR 0.014 0.002 TYR F 478 ARG 0.024 0.000 ARG L 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 319 time to evaluate : 4.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 267 MET cc_start: -0.0057 (OUTLIER) cc_final: -0.2157 (mpp) REVERT: A 166 MET cc_start: 0.8079 (mtp) cc_final: 0.7734 (mtt) REVERT: A 233 MET cc_start: 0.0601 (OUTLIER) cc_final: 0.0246 (pmm) REVERT: A 237 LEU cc_start: 0.0927 (OUTLIER) cc_final: 0.0534 (mt) REVERT: A 267 MET cc_start: -0.0701 (pmm) cc_final: -0.3210 (tpp) REVERT: B 142 LYS cc_start: 0.7610 (tptp) cc_final: 0.7390 (tppt) REVERT: B 237 LEU cc_start: 0.1148 (OUTLIER) cc_final: 0.0673 (mt) REVERT: B 267 MET cc_start: -0.0112 (OUTLIER) cc_final: -0.2069 (mpp) REVERT: C 237 LEU cc_start: 0.1460 (OUTLIER) cc_final: 0.0878 (mt) REVERT: C 267 MET cc_start: -0.0937 (pmm) cc_final: -0.3069 (tpp) REVERT: D 166 MET cc_start: 0.7964 (mtt) cc_final: 0.7557 (mtt) REVERT: D 267 MET cc_start: -0.0954 (pmm) cc_final: -0.3416 (tpp) REVERT: E 10 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.8155 (t0) REVERT: E 142 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.6684 (tptp) REVERT: E 233 MET cc_start: 0.0930 (OUTLIER) cc_final: 0.0358 (pmm) REVERT: E 267 MET cc_start: -0.0489 (pmm) cc_final: -0.2810 (tpp) REVERT: I 233 MET cc_start: 0.1201 (pmm) cc_final: -0.0280 (tmt) REVERT: I 257 GLU cc_start: 0.1059 (OUTLIER) cc_final: -0.0327 (mt-10) REVERT: I 267 MET cc_start: 0.0068 (pmm) cc_final: -0.1070 (ptp) REVERT: J 142 LYS cc_start: 0.7571 (tptp) cc_final: 0.7338 (tppt) REVERT: J 267 MET cc_start: -0.0335 (pmt) cc_final: -0.0687 (ptp) REVERT: J 288 MET cc_start: 0.3723 (ptp) cc_final: 0.3151 (mmp) REVERT: K 193 MET cc_start: 0.5073 (OUTLIER) cc_final: 0.4776 (tmt) REVERT: K 234 LEU cc_start: -0.0355 (OUTLIER) cc_final: -0.0713 (mm) REVERT: M 142 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.6822 (tptp) REVERT: M 257 GLU cc_start: 0.0882 (OUTLIER) cc_final: -0.0184 (tt0) REVERT: M 267 MET cc_start: 0.0587 (pmm) cc_final: -0.1752 (tpp) REVERT: M 366 GLN cc_start: 0.3842 (OUTLIER) cc_final: 0.3407 (mm-40) REVERT: N 193 MET cc_start: 0.4031 (tpt) cc_final: 0.3378 (tpt) REVERT: N 257 GLU cc_start: 0.0876 (OUTLIER) cc_final: 0.0143 (mt-10) REVERT: N 267 MET cc_start: 0.1248 (pmm) cc_final: -0.1770 (tpp) outliers start: 108 outliers final: 63 residues processed: 411 average time/residue: 1.5609 time to fit residues: 802.1917 Evaluate side-chains 397 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 318 time to evaluate : 5.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 219 PHE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 219 PHE Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 219 PHE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 288 MET Chi-restraints excluded: chain H residue 365 LEU Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 257 GLU Chi-restraints excluded: chain K residue 144 ILE Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 193 MET Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 257 GLU Chi-restraints excluded: chain K residue 288 MET Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 219 PHE Chi-restraints excluded: chain L residue 257 GLU Chi-restraints excluded: chain L residue 366 GLN Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 227 ILE Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 366 GLN Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 219 PHE Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 237 LEU Chi-restraints excluded: chain N residue 257 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 429 optimal weight: 0.9990 chunk 691 optimal weight: 2.9990 chunk 422 optimal weight: 1.9990 chunk 328 optimal weight: 1.9990 chunk 480 optimal weight: 2.9990 chunk 725 optimal weight: 0.9990 chunk 667 optimal weight: 1.9990 chunk 577 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 446 optimal weight: 7.9990 chunk 354 optimal weight: 2.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 366 GLN ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN C 10 ASN I 10 ASN L 366 GLN N 10 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 54726 Z= 0.251 Angle : 0.576 13.037 73990 Z= 0.308 Chirality : 0.042 0.238 8974 Planarity : 0.003 0.056 9618 Dihedral : 9.403 89.695 8204 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.70 % Allowed : 16.66 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.10), residues: 7294 helix: 1.44 (0.08), residues: 4270 sheet: -0.30 (0.13), residues: 1232 loop : -0.43 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 401 PHE 0.011 0.001 PHE J 195 TYR 0.013 0.002 TYR F 478 ARG 0.003 0.000 ARG F 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 318 time to evaluate : 6.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 267 MET cc_start: 0.0067 (OUTLIER) cc_final: -0.2330 (mpp) REVERT: A 166 MET cc_start: 0.8075 (mtp) cc_final: 0.7720 (mtt) REVERT: A 233 MET cc_start: 0.0591 (OUTLIER) cc_final: 0.0229 (pmm) REVERT: A 237 LEU cc_start: 0.0898 (OUTLIER) cc_final: 0.0502 (mt) REVERT: A 267 MET cc_start: -0.0797 (pmm) cc_final: -0.3289 (tpp) REVERT: B 142 LYS cc_start: 0.7731 (tptp) cc_final: 0.7528 (tppt) REVERT: B 237 LEU cc_start: 0.0680 (OUTLIER) cc_final: 0.0220 (mt) REVERT: B 267 MET cc_start: -0.0198 (OUTLIER) cc_final: -0.2120 (mpp) REVERT: C 237 LEU cc_start: 0.1414 (OUTLIER) cc_final: 0.0824 (mt) REVERT: C 267 MET cc_start: -0.1071 (pmm) cc_final: -0.3176 (tpp) REVERT: D 166 MET cc_start: 0.7945 (mtt) cc_final: 0.7539 (mtt) REVERT: D 267 MET cc_start: -0.0958 (pmm) cc_final: -0.3447 (tpp) REVERT: E 10 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.8141 (t0) REVERT: E 142 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.6678 (tptp) REVERT: E 233 MET cc_start: 0.0910 (OUTLIER) cc_final: 0.0337 (pmm) REVERT: F 267 MET cc_start: -0.0249 (pmt) cc_final: -0.2039 (mpp) REVERT: I 233 MET cc_start: 0.1154 (pmm) cc_final: -0.0348 (tmt) REVERT: I 257 GLU cc_start: 0.0948 (OUTLIER) cc_final: -0.0157 (mt-10) REVERT: I 267 MET cc_start: -0.0039 (pmm) cc_final: -0.1183 (ptp) REVERT: J 142 LYS cc_start: 0.7669 (tptp) cc_final: 0.7458 (tppt) REVERT: J 267 MET cc_start: -0.0460 (pmt) cc_final: -0.0797 (ptp) REVERT: J 288 MET cc_start: 0.3724 (ptp) cc_final: 0.3160 (mmp) REVERT: K 193 MET cc_start: 0.5079 (OUTLIER) cc_final: 0.4770 (tmt) REVERT: K 234 LEU cc_start: -0.0530 (OUTLIER) cc_final: -0.0851 (mm) REVERT: M 142 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.6821 (tptp) REVERT: M 257 GLU cc_start: 0.0912 (OUTLIER) cc_final: -0.0172 (tt0) REVERT: M 267 MET cc_start: 0.0531 (pmm) cc_final: -0.2501 (tpp) REVERT: M 366 GLN cc_start: 0.3874 (OUTLIER) cc_final: 0.3423 (mm-40) REVERT: N 193 MET cc_start: 0.4031 (tpt) cc_final: 0.3379 (tpt) REVERT: N 257 GLU cc_start: 0.0805 (OUTLIER) cc_final: 0.0048 (tt0) REVERT: N 267 MET cc_start: 0.1238 (pmm) cc_final: -0.1787 (tpp) outliers start: 96 outliers final: 66 residues processed: 400 average time/residue: 1.5668 time to fit residues: 783.0000 Evaluate side-chains 397 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 315 time to evaluate : 4.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 219 PHE Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 219 PHE Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 219 PHE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 288 MET Chi-restraints excluded: chain H residue 365 LEU Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 257 GLU Chi-restraints excluded: chain K residue 144 ILE Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 193 MET Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 257 GLU Chi-restraints excluded: chain K residue 288 MET Chi-restraints excluded: chain L residue 157 THR Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 219 PHE Chi-restraints excluded: chain L residue 257 GLU Chi-restraints excluded: chain L residue 366 GLN Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 227 ILE Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 366 GLN Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 219 PHE Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 257 GLU Chi-restraints excluded: chain N residue 366 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 458 optimal weight: 1.9990 chunk 615 optimal weight: 0.9990 chunk 176 optimal weight: 0.0060 chunk 532 optimal weight: 2.9990 chunk 85 optimal weight: 20.0000 chunk 160 optimal weight: 0.4980 chunk 578 optimal weight: 4.9990 chunk 242 optimal weight: 30.0000 chunk 593 optimal weight: 0.3980 chunk 73 optimal weight: 30.0000 chunk 106 optimal weight: 1.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 10 ASN G 366 GLN ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN C 10 ASN I 10 ASN L 366 GLN N 10 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.198503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.141182 restraints weight = 55706.503| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.38 r_work: 0.3234 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 54726 Z= 0.199 Angle : 0.554 12.875 73990 Z= 0.296 Chirality : 0.041 0.227 8974 Planarity : 0.003 0.046 9618 Dihedral : 9.096 87.277 8204 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.72 % Allowed : 16.68 % Favored : 81.60 % 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: 1.01 (0.10), residues: 7294 helix: 1.48 (0.08), residues: 4284 sheet: -0.27 (0.13), residues: 1232 loop : -0.45 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 401 PHE 0.012 0.001 PHE J 195 TYR 0.012 0.001 TYR F 478 ARG 0.020 0.000 ARG L 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13739.79 seconds wall clock time: 241 minutes 26.70 seconds (14486.70 seconds total)