Starting phenix.real_space_refine on Sun Dec 29 22:05:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bmo_16119/12_2024/8bmo_16119.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bmo_16119/12_2024/8bmo_16119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bmo_16119/12_2024/8bmo_16119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bmo_16119/12_2024/8bmo_16119.map" model { file = "/net/cci-nas-00/data/ceres_data/8bmo_16119/12_2024/8bmo_16119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bmo_16119/12_2024/8bmo_16119.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 42 5.49 5 Mg 14 5.21 5 S 287 5.16 5 C 36771 2.51 5 N 10234 2.21 5 O 11998 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 59346 Number of models: 1 Model: "" Number of chains: 35 Chain: "C" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "W" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 714 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 714 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 714 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 714 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 714 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 714 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "T" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 714 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 28.24, per 1000 atoms: 0.48 Number of scatterers: 59346 At special positions: 0 Unit cell: (154.56, 153.6, 210.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 287 16.00 P 42 15.00 Mg 14 11.99 O 11998 8.00 N 10234 7.00 C 36771 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.55 Conformation dependent library (CDL) restraints added in 6.5 seconds 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14476 Finding SS restraints... Secondary structure from input PDB file: 282 helices and 97 sheets defined 54.7% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.95 Creating SS restraints... 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 Processing helix chain 'C' and resid 88 through 110 Processing helix chain 'C' and resid 112 through 135 Processing helix chain 'C' and resid 140 through 152 Processing helix chain 'C' and resid 155 through 169 Processing helix chain 'C' and resid 201 through 205 Processing helix chain 'C' and resid 233 through 244 Processing helix chain 'C' and resid 256 through 269 removed outlier: 3.720A pdb=" N ALA C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 297 removed outlier: 3.532A pdb=" N LYS C 286 " --> pdb=" O GLY C 282 " (cutoff:3.500A) 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 removed outlier: 4.486A pdb=" N GLY C 375 " --> pdb=" O LYS C 371 " (cutoff:3.500A) 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 459 Proline residue: C 450 - end of helix Processing helix chain 'C' and resid 461 through 472 Processing helix chain 'C' and resid 497 through 516 Processing helix chain 'I' and resid 9 through 29 removed outlier: 3.705A pdb=" N VAL I 29 " --> pdb=" O ASP I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 60 removed outlier: 3.598A pdb=" N VAL I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 85 removed outlier: 3.791A pdb=" N GLU I 76 " --> pdb=" O GLN I 72 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL I 77 " --> pdb=" O MET I 73 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA I 78 " --> pdb=" O VAL I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 109 Processing helix chain 'I' and resid 112 through 135 Processing helix chain 'I' and resid 140 through 152 Processing helix chain 'I' and resid 155 through 170 Processing helix chain 'I' and resid 201 through 205 Processing helix chain 'I' and resid 233 through 244 Processing helix chain 'I' and resid 256 through 269 Processing helix chain 'I' and resid 284 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 373 Processing helix chain 'I' and resid 385 through 410 Processing helix chain 'I' and resid 416 through 426 Processing helix chain 'I' and resid 433 through 447 Processing helix chain 'I' and resid 448 through 458 Processing helix chain 'I' and resid 461 through 472 Processing helix chain 'I' and resid 497 through 516 Processing helix chain 'W' and resid 28 through 32 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 Processing helix chain 'A' and resid 88 through 110 Processing helix chain 'A' and resid 112 through 135 Processing helix chain 'A' and resid 140 through 152 Processing helix chain 'A' and resid 155 through 169 removed outlier: 3.507A pdb=" N VAL A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 256 through 267 removed outlier: 3.720A pdb=" N ALA A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) 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 removed outlier: 4.464A pdb=" N GLY A 375 " --> pdb=" O LYS A 371 " (cutoff:3.500A) 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 459 Proline residue: A 450 - end of helix Processing helix chain 'A' and resid 461 through 472 Processing helix chain 'A' and resid 497 through 516 Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.710A pdb=" N VAL B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 removed outlier: 3.664A pdb=" N VAL B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 85 removed outlier: 4.069A pdb=" N VAL B 77 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 3.970A 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 140 through 152 Processing helix chain 'B' and resid 155 through 170 Processing helix chain 'B' and resid 201 through 205 Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 256 through 269 Processing helix chain 'B' and resid 284 through 297 Processing helix chain 'B' and resid 338 through 356 Processing helix chain 'B' and resid 358 through 373 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 459 Processing helix chain 'B' and resid 461 through 472 Processing helix chain 'B' and resid 497 through 516 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.515A pdb=" N ALA D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) 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 Processing helix chain 'E' and resid 88 through 110 Processing helix chain 'E' and resid 112 through 135 Processing helix chain 'E' and resid 140 through 152 Processing helix chain 'E' and resid 155 through 169 Processing helix chain 'E' and resid 201 through 205 Processing helix chain 'E' and resid 233 through 244 Processing helix chain 'E' and resid 256 through 269 removed outlier: 3.763A pdb=" N ALA E 260 " --> pdb=" O GLY E 256 " (cutoff:3.500A) 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 374 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 459 Proline residue: E 450 - end of helix Processing helix chain 'E' and resid 461 through 472 Processing helix chain 'E' and resid 497 through 516 Processing helix chain 'F' and resid 9 through 29 removed outlier: 3.716A pdb=" N VAL F 29 " --> pdb=" O ASP F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 60 removed outlier: 3.579A pdb=" N VAL F 56 " --> pdb=" O ASP F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 85 removed outlier: 4.062A pdb=" N VAL F 77 " --> pdb=" O MET F 73 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA F 78 " --> pdb=" O VAL F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 109 Processing helix chain 'F' and resid 112 through 135 Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 155 through 170 Processing helix chain 'F' and resid 201 through 205 Processing helix chain 'F' and resid 233 through 244 Processing helix chain 'F' and resid 256 through 269 Processing helix chain 'F' and resid 284 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 373 Processing helix chain 'F' and resid 385 through 410 Processing helix chain 'F' and resid 416 through 426 Processing helix chain 'F' and resid 433 through 447 Processing helix chain 'F' and resid 448 through 459 Processing helix chain 'F' and resid 461 through 472 Processing helix chain 'F' and resid 497 through 516 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 87 through 89 No H-bonds generated for 'chain 'G' and resid 87 through 89' 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 Processing helix chain 'H' and resid 88 through 110 Processing helix chain 'H' and resid 112 through 135 Processing helix chain 'H' and resid 140 through 152 Processing helix chain 'H' and resid 155 through 169 Processing helix chain 'H' and resid 201 through 205 Processing helix chain 'H' and resid 233 through 244 Processing helix chain 'H' and resid 256 through 269 removed outlier: 3.752A pdb=" N ALA H 260 " --> pdb=" O GLY H 256 " (cutoff:3.500A) 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 374 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 459 Proline residue: H 450 - end of helix Processing helix chain 'H' and resid 461 through 472 Processing helix chain 'H' and resid 497 through 516 Processing helix chain 'J' and resid 9 through 29 removed outlier: 3.729A pdb=" N VAL J 29 " --> pdb=" O ASP J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 60 removed outlier: 3.656A pdb=" N VAL J 56 " --> pdb=" O ASP J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 85 removed outlier: 4.164A pdb=" N VAL J 77 " --> pdb=" O MET J 73 " (cutoff:3.500A) removed outlier: 3.931A 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 140 through 152 Processing helix chain 'J' and resid 155 through 170 Processing helix chain 'J' and resid 201 through 205 removed outlier: 3.510A pdb=" N PHE J 204 " --> pdb=" O SER J 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 244 Processing helix chain 'J' and resid 256 through 269 Processing helix chain 'J' and resid 284 through 297 Processing helix chain 'J' and resid 338 through 356 Processing helix chain 'J' and resid 358 through 373 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 459 Processing helix chain 'J' and resid 461 through 472 Processing helix chain 'J' and resid 497 through 516 Processing helix chain 'K' and resid 28 through 32 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 Processing helix chain 'L' and resid 88 through 110 Processing helix chain 'L' and resid 112 through 135 Processing helix chain 'L' and resid 140 through 152 Processing helix chain 'L' and resid 155 through 169 Processing helix chain 'L' and resid 201 through 205 Processing helix chain 'L' and resid 233 through 244 Processing helix chain 'L' and resid 256 through 269 removed outlier: 3.789A pdb=" N ALA L 260 " --> pdb=" O GLY L 256 " (cutoff:3.500A) 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 removed outlier: 4.367A pdb=" N GLY L 375 " --> pdb=" O LYS L 371 " (cutoff:3.500A) 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 459 Proline residue: L 450 - end of helix Processing helix chain 'L' and resid 461 through 472 Processing helix chain 'L' and resid 497 through 516 Processing helix chain 'M' and resid 9 through 29 removed outlier: 3.718A pdb=" N VAL M 29 " --> pdb=" O ASP M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 60 removed outlier: 3.682A pdb=" N VAL M 56 " --> pdb=" O ASP M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 85 removed outlier: 4.026A pdb=" N VAL M 77 " --> pdb=" O MET M 73 " (cutoff:3.500A) removed outlier: 3.953A 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 140 through 152 Processing helix chain 'M' and resid 155 through 170 Processing helix chain 'M' and resid 201 through 205 Processing helix chain 'M' and resid 233 through 244 Processing helix chain 'M' and resid 256 through 269 Processing helix chain 'M' and resid 284 through 296 Processing helix chain 'M' and resid 338 through 356 Processing helix chain 'M' and resid 358 through 373 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 459 Processing helix chain 'M' and resid 461 through 472 Processing helix chain 'M' and resid 497 through 516 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.531A pdb=" N ALA N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 29 Processing helix chain 'O' and resid 52 through 60 Processing helix chain 'O' and resid 64 through 86 Processing helix chain 'O' and resid 88 through 110 Processing helix chain 'O' and resid 112 through 135 Processing helix chain 'O' and resid 140 through 152 Processing helix chain 'O' and resid 155 through 169 removed outlier: 3.536A pdb=" N VAL O 169 " --> pdb=" O ALA O 165 " (cutoff:3.500A) Processing helix chain 'O' and resid 201 through 205 Processing helix chain 'O' and resid 233 through 244 Processing helix chain 'O' and resid 256 through 269 removed outlier: 3.908A pdb=" N MET O 267 " --> pdb=" O VAL O 263 " (cutoff:3.500A) Processing helix chain 'O' and resid 282 through 297 Processing helix chain 'O' and resid 308 through 312 Processing helix chain 'O' and resid 338 through 356 Processing helix chain 'O' and resid 358 through 375 removed outlier: 3.818A pdb=" N GLY O 375 " --> pdb=" O LYS O 371 " (cutoff:3.500A) Processing helix chain 'O' and resid 385 through 410 Processing helix chain 'O' and resid 416 through 426 Processing helix chain 'O' and resid 433 through 459 Proline residue: O 450 - end of helix Processing helix chain 'O' and resid 461 through 472 Processing helix chain 'O' and resid 497 through 516 Processing helix chain 'P' and resid 9 through 29 removed outlier: 3.682A pdb=" N VAL P 29 " --> pdb=" O ASP P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 60 removed outlier: 3.722A pdb=" N VAL P 56 " --> pdb=" O ASP P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 64 through 85 removed outlier: 4.163A pdb=" N VAL P 77 " --> pdb=" O MET P 73 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA P 78 " --> pdb=" O VAL P 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 88 through 109 Processing helix chain 'P' and resid 112 through 135 Processing helix chain 'P' and resid 140 through 152 Processing helix chain 'P' and resid 155 through 170 Processing helix chain 'P' and resid 201 through 205 Processing helix chain 'P' and resid 233 through 244 Processing helix chain 'P' and resid 255 through 269 removed outlier: 3.611A pdb=" N LEU P 259 " --> pdb=" O GLU P 255 " (cutoff:3.500A) Processing helix chain 'P' and resid 284 through 297 Processing helix chain 'P' and resid 308 through 312 Processing helix chain 'P' and resid 338 through 356 Processing helix chain 'P' and resid 358 through 373 Processing helix chain 'P' and resid 385 through 410 Processing helix chain 'P' and resid 416 through 426 Processing helix chain 'P' and resid 433 through 447 Processing helix chain 'P' and resid 448 through 459 Processing helix chain 'P' and resid 461 through 472 Processing helix chain 'P' and resid 497 through 516 Processing helix chain 'Q' and resid 28 through 32 Processing helix chain 'R' and resid 9 through 29 Processing helix chain 'R' and resid 52 through 60 Processing helix chain 'R' and resid 64 through 86 Processing helix chain 'R' and resid 88 through 110 Processing helix chain 'R' and resid 112 through 135 Processing helix chain 'R' and resid 140 through 152 Processing helix chain 'R' and resid 155 through 169 Processing helix chain 'R' and resid 201 through 205 Processing helix chain 'R' and resid 230 through 232 No H-bonds generated for 'chain 'R' and resid 230 through 232' Processing helix chain 'R' and resid 233 through 244 Processing helix chain 'R' and resid 256 through 269 Processing helix chain 'R' and resid 282 through 297 Processing helix chain 'R' and resid 308 through 312 Processing helix chain 'R' and resid 338 through 356 Processing helix chain 'R' and resid 358 through 375 removed outlier: 3.849A pdb=" N GLY R 375 " --> pdb=" O LYS R 371 " (cutoff:3.500A) Processing helix chain 'R' and resid 385 through 410 Processing helix chain 'R' and resid 416 through 426 Processing helix chain 'R' and resid 433 through 459 Proline residue: R 450 - end of helix Processing helix chain 'R' and resid 461 through 472 Processing helix chain 'R' and resid 488 through 492 Processing helix chain 'R' and resid 497 through 516 Processing helix chain 'S' and resid 9 through 29 removed outlier: 3.737A pdb=" N VAL S 29 " --> pdb=" O ASP S 25 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 60 removed outlier: 3.610A pdb=" N VAL S 56 " --> pdb=" O ASP S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 64 through 85 removed outlier: 3.788A pdb=" N GLU S 76 " --> pdb=" O GLN S 72 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL S 77 " --> pdb=" O MET S 73 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA S 78 " --> pdb=" O VAL S 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 88 through 109 Processing helix chain 'S' and resid 112 through 135 Processing helix chain 'S' and resid 140 through 152 Processing helix chain 'S' and resid 155 through 170 Processing helix chain 'S' and resid 201 through 205 Processing helix chain 'S' and resid 233 through 244 Processing helix chain 'S' and resid 255 through 269 removed outlier: 3.557A pdb=" N LEU S 259 " --> pdb=" O GLU S 255 " (cutoff:3.500A) Processing helix chain 'S' and resid 284 through 297 Processing helix chain 'S' and resid 308 through 312 Processing helix chain 'S' and resid 338 through 356 Processing helix chain 'S' and resid 358 through 373 Processing helix chain 'S' and resid 385 through 410 Processing helix chain 'S' and resid 416 through 426 Processing helix chain 'S' and resid 433 through 447 Processing helix chain 'S' and resid 448 through 459 Processing helix chain 'S' and resid 461 through 472 Processing helix chain 'S' and resid 488 through 492 Processing helix chain 'S' and resid 497 through 516 Processing helix chain 'T' and resid 28 through 32 removed outlier: 3.501A pdb=" N ALA T 31 " --> pdb=" O THR T 28 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 8 removed outlier: 7.651A pdb=" N VAL A 39 " --> pdb=" O GLU C 518 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N MET C 520 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 48 through 50 removed outlier: 7.481A pdb=" N ASN C 37 " --> pdb=" O GLU R 518 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N MET R 520 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL C 39 " --> pdb=" O MET R 520 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N THR R 522 " --> pdb=" O VAL C 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 174 through 179 Processing sheet with id=AA4, first strand: chain 'C' and resid 193 through 195 removed outlier: 6.265A pdb=" N GLY C 335 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA C 320 " --> pdb=" O GLY C 335 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 193 through 195 removed outlier: 6.265A pdb=" N GLY C 335 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA C 320 " --> pdb=" O GLY C 335 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N PHE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE C 250 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU C 221 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU C 247 " --> pdb=" O ALA C 274 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N VAL C 276 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE C 249 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AA7, first strand: chain 'C' and resid 476 through 479 Processing sheet with id=AA8, first strand: chain 'I' and resid 4 through 8 removed outlier: 7.354A pdb=" N VAL S 39 " --> pdb=" O GLU I 518 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N MET I 520 " --> pdb=" O VAL S 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 48 through 50 removed outlier: 7.325A pdb=" N ASN I 37 " --> pdb=" O GLU B 518 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N MET B 520 " --> pdb=" O ASN I 37 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL I 39 " --> pdb=" O MET B 520 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N THR B 522 " --> pdb=" O VAL I 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 174 through 179 removed outlier: 6.315A pdb=" N VAL I 174 " --> pdb=" O ALA I 377 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ILE I 379 " --> pdb=" O VAL I 174 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR I 176 " --> pdb=" O ILE I 379 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL I 381 " --> pdb=" O THR I 176 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N GLU I 178 " --> pdb=" O VAL I 381 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 213 through 216 removed outlier: 6.573A pdb=" N PHE I 219 " --> pdb=" O LEU I 248 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE I 250 " --> pdb=" O PHE I 219 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU I 221 " --> pdb=" O ILE I 250 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU I 247 " --> pdb=" O ALA I 274 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL I 276 " --> pdb=" O LEU I 247 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ILE I 249 " --> pdb=" O VAL I 276 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 213 through 216 removed outlier: 6.284A pdb=" N ALA I 320 " --> pdb=" O GLY I 335 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLY I 335 " --> pdb=" O ALA I 320 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 411 through 413 Processing sheet with id=AB5, first strand: chain 'I' and resid 476 through 479 Processing sheet with id=AB6, first strand: chain 'W' and resid 3 through 5 removed outlier: 3.958A pdb=" N ARG W 4 " --> pdb=" O ILE D 94 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE D 94 " --> pdb=" O ARG W 4 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE D 64 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE D 11 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL D 43 " --> pdb=" O ARG D 9 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ARG D 9 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ARG D 14 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N GLU D 82 " --> pdb=" O ARG D 14 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'W' and resid 74 through 78 removed outlier: 7.910A pdb=" N GLU W 82 " --> pdb=" O ARG W 14 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ARG W 14 " --> pdb=" O GLU W 82 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ARG W 9 " --> pdb=" O VAL W 43 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N VAL W 43 " --> pdb=" O ARG W 9 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE W 11 " --> pdb=" O LEU W 41 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE W 64 " --> pdb=" O VAL W 95 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE W 94 " --> pdb=" O ARG T 4 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG T 4 " --> pdb=" O ILE W 94 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'W' and resid 47 through 48 Processing sheet with id=AB9, first strand: chain 'A' and resid 4 through 8 removed outlier: 7.687A pdb=" N VAL E 39 " --> pdb=" O GLU A 518 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N MET A 520 " --> pdb=" O VAL E 39 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 174 through 179 Processing sheet with id=AC2, first strand: chain 'A' and resid 193 through 195 Processing sheet with id=AC3, first strand: chain 'A' and resid 273 through 277 removed outlier: 6.601A pdb=" N LEU A 247 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N VAL A 276 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ILE A 249 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N PHE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE A 250 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU A 221 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 411 through 413 Processing sheet with id=AC5, first strand: chain 'A' and resid 476 through 479 Processing sheet with id=AC6, first strand: chain 'B' and resid 48 through 50 removed outlier: 6.657A pdb=" N ASN B 37 " --> pdb=" O CYS F 519 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N VAL F 521 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL B 39 " --> pdb=" O VAL F 521 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N ASP F 523 " --> pdb=" O VAL B 39 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 174 through 179 removed outlier: 6.254A pdb=" N VAL B 174 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ILE B 379 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR B 176 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N VAL B 381 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU B 178 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 213 through 216 removed outlier: 6.536A pdb=" N PHE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE B 250 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU B 221 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU B 247 " --> pdb=" O ALA B 274 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL B 276 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE B 249 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 213 through 216 removed outlier: 6.293A pdb=" N ALA B 320 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLY B 335 " --> pdb=" O ALA B 320 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 411 through 413 Processing sheet with id=AD2, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AD3, first strand: chain 'D' and resid 3 through 5 removed outlier: 3.788A pdb=" N ARG D 4 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE G 94 " --> pdb=" O ARG D 4 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE G 64 " --> pdb=" O VAL G 95 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE G 11 " --> pdb=" O LEU G 41 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ARG G 14 " --> pdb=" O GLU G 82 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N GLU G 82 " --> pdb=" O ARG G 14 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 47 through 48 Processing sheet with id=AD5, first strand: chain 'E' and resid 4 through 8 removed outlier: 7.678A pdb=" N VAL H 39 " --> pdb=" O GLU E 518 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N MET E 520 " --> pdb=" O VAL H 39 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 174 through 179 Processing sheet with id=AD7, first strand: chain 'E' and resid 193 through 195 Processing sheet with id=AD8, first strand: chain 'E' and resid 273 through 277 removed outlier: 6.578A pdb=" N LEU E 247 " --> pdb=" O ALA E 274 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N VAL E 276 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE E 249 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N PHE E 219 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ILE E 250 " --> pdb=" O PHE E 219 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU E 221 " --> pdb=" O ILE E 250 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 411 through 413 Processing sheet with id=AE1, first strand: chain 'E' and resid 476 through 479 Processing sheet with id=AE2, first strand: chain 'F' and resid 48 through 50 removed outlier: 6.700A pdb=" N ASN F 37 " --> pdb=" O CYS J 519 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N VAL J 521 " --> pdb=" O ASN F 37 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL F 39 " --> pdb=" O VAL J 521 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ASP J 523 " --> pdb=" O VAL F 39 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 174 through 179 removed outlier: 6.291A pdb=" N VAL F 174 " --> pdb=" O ALA F 377 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ILE F 379 " --> pdb=" O VAL F 174 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR F 176 " --> pdb=" O ILE F 379 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N VAL F 381 " --> pdb=" O THR F 176 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N GLU F 178 " --> pdb=" O VAL F 381 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 213 through 216 removed outlier: 6.584A pdb=" N PHE F 219 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ILE F 250 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU F 221 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU F 247 " --> pdb=" O ALA F 274 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL F 276 " --> pdb=" O LEU F 247 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE F 249 " --> pdb=" O VAL F 276 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 213 through 216 removed outlier: 6.303A pdb=" N ALA F 320 " --> pdb=" O GLY F 335 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLY F 335 " --> pdb=" O ALA F 320 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 411 through 413 Processing sheet with id=AE7, first strand: chain 'F' and resid 476 through 479 Processing sheet with id=AE8, first strand: chain 'G' and resid 3 through 5 removed outlier: 3.726A pdb=" N ARG G 4 " --> pdb=" O ILE K 94 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE K 94 " --> pdb=" O ARG G 4 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE K 64 " --> pdb=" O VAL K 95 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE K 11 " --> pdb=" O LEU K 41 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N VAL K 43 " --> pdb=" O ARG K 9 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ARG K 9 " --> pdb=" O VAL K 43 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ARG K 14 " --> pdb=" O GLU K 82 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N GLU K 82 " --> pdb=" O ARG K 14 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 47 through 48 Processing sheet with id=AF1, first strand: chain 'H' and resid 4 through 8 removed outlier: 7.677A pdb=" N VAL L 39 " --> pdb=" O GLU H 518 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N MET H 520 " --> pdb=" O VAL L 39 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 174 through 179 Processing sheet with id=AF3, first strand: chain 'H' and resid 193 through 195 removed outlier: 6.270A pdb=" N GLY H 335 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA H 320 " --> pdb=" O GLY H 335 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 193 through 195 removed outlier: 6.270A pdb=" N GLY H 335 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA H 320 " --> pdb=" O GLY H 335 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N PHE H 219 " --> pdb=" O LEU H 248 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE H 250 " --> pdb=" O PHE H 219 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU H 221 " --> pdb=" O ILE H 250 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU H 247 " --> pdb=" O ALA H 274 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N VAL H 276 " --> pdb=" O LEU H 247 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ILE H 249 " --> pdb=" O VAL H 276 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 411 through 413 Processing sheet with id=AF6, first strand: chain 'H' and resid 476 through 479 Processing sheet with id=AF7, first strand: chain 'J' and resid 48 through 50 removed outlier: 6.666A pdb=" N ASN J 37 " --> pdb=" O CYS M 519 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N VAL M 521 " --> pdb=" O ASN J 37 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL J 39 " --> pdb=" O VAL M 521 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ASP M 523 " --> pdb=" O VAL J 39 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 174 through 179 removed outlier: 6.292A pdb=" N VAL J 174 " --> pdb=" O ALA J 377 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE J 379 " --> pdb=" O VAL J 174 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR J 176 " --> pdb=" O ILE J 379 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL J 381 " --> pdb=" O THR J 176 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLU J 178 " --> pdb=" O VAL J 381 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 213 through 216 removed outlier: 6.555A pdb=" N PHE J 219 " --> pdb=" O LEU J 248 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE J 250 " --> pdb=" O PHE J 219 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU J 221 " --> pdb=" O ILE J 250 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU J 247 " --> pdb=" O ALA J 274 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N VAL J 276 " --> pdb=" O LEU J 247 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE J 249 " --> pdb=" O VAL J 276 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 213 through 216 removed outlier: 6.325A pdb=" N ALA J 320 " --> pdb=" O GLY J 335 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLY J 335 " --> pdb=" O ALA J 320 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 411 through 413 Processing sheet with id=AG3, first strand: chain 'J' and resid 476 through 479 Processing sheet with id=AG4, first strand: chain 'K' and resid 3 through 5 removed outlier: 3.642A pdb=" N ARG K 4 " --> pdb=" O ILE N 94 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE N 64 " --> pdb=" O VAL N 95 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE N 11 " --> pdb=" O LEU N 41 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL N 43 " --> pdb=" O ARG N 9 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ARG N 9 " --> pdb=" O VAL N 43 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ARG N 14 " --> pdb=" O GLU N 82 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N GLU N 82 " --> pdb=" O ARG N 14 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 4 through 8 removed outlier: 5.737A pdb=" N ASN O 37 " --> pdb=" O THR L 517 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N CYS L 519 " --> pdb=" O ASN O 37 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 174 through 179 Processing sheet with id=AG7, first strand: chain 'L' and resid 193 through 195 removed outlier: 6.219A pdb=" N GLY L 335 " --> pdb=" O ALA L 320 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ALA L 320 " --> pdb=" O GLY L 335 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 193 through 195 removed outlier: 6.219A pdb=" N GLY L 335 " --> pdb=" O ALA L 320 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ALA L 320 " --> pdb=" O GLY L 335 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N PHE L 219 " --> pdb=" O LEU L 248 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ILE L 250 " --> pdb=" O PHE L 219 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU L 221 " --> pdb=" O ILE L 250 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU L 247 " --> pdb=" O ALA L 274 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N VAL L 276 " --> pdb=" O LEU L 247 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE L 249 " --> pdb=" O VAL L 276 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 411 through 413 Processing sheet with id=AH1, first strand: chain 'L' and resid 476 through 479 Processing sheet with id=AH2, first strand: chain 'M' and resid 48 through 50 removed outlier: 7.320A pdb=" N ASN M 37 " --> pdb=" O GLU P 518 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N MET P 520 " --> pdb=" O ASN M 37 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL M 39 " --> pdb=" O MET P 520 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N THR P 522 " --> pdb=" O VAL M 39 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'M' and resid 174 through 179 removed outlier: 6.277A pdb=" N VAL M 174 " --> pdb=" O ALA M 377 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE M 379 " --> pdb=" O VAL M 174 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR M 176 " --> pdb=" O ILE M 379 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N VAL M 381 " --> pdb=" O THR M 176 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU M 178 " --> pdb=" O VAL M 381 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'M' and resid 213 through 216 removed outlier: 6.549A pdb=" N PHE M 219 " --> pdb=" O LEU M 248 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ILE M 250 " --> pdb=" O PHE M 219 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU M 221 " --> pdb=" O ILE M 250 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU M 247 " --> pdb=" O ALA M 274 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL M 276 " --> pdb=" O LEU M 247 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ILE M 249 " --> pdb=" O VAL M 276 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'M' and resid 213 through 216 removed outlier: 6.238A pdb=" N ALA M 320 " --> pdb=" O GLY M 335 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY M 335 " --> pdb=" O ALA M 320 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'M' and resid 411 through 413 Processing sheet with id=AH7, first strand: chain 'M' and resid 476 through 479 Processing sheet with id=AH8, first strand: chain 'N' and resid 3 through 5 removed outlier: 3.594A pdb=" N ARG N 4 " --> pdb=" O ILE Q 94 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE Q 66 " --> pdb=" O LEU Q 92 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ILE Q 94 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ILE Q 64 " --> pdb=" O ILE Q 94 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE Q 11 " --> pdb=" O LEU Q 41 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N VAL Q 43 " --> pdb=" O ARG Q 9 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ARG Q 9 " --> pdb=" O VAL Q 43 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ARG Q 14 " --> pdb=" O GLU Q 82 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N GLU Q 82 " --> pdb=" O ARG Q 14 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'N' and resid 47 through 48 Processing sheet with id=AI1, first strand: chain 'O' and resid 4 through 8 removed outlier: 7.677A pdb=" N VAL R 39 " --> pdb=" O GLU O 518 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N MET O 520 " --> pdb=" O VAL R 39 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'O' and resid 174 through 179 removed outlier: 3.535A pdb=" N VAL O 381 " --> pdb=" O GLU O 178 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'O' and resid 193 through 195 removed outlier: 6.365A pdb=" N GLY O 335 " --> pdb=" O ALA O 320 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA O 320 " --> pdb=" O GLY O 335 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'O' and resid 193 through 195 removed outlier: 6.365A pdb=" N GLY O 335 " --> pdb=" O ALA O 320 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA O 320 " --> pdb=" O GLY O 335 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N PHE O 219 " --> pdb=" O LEU O 248 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE O 250 " --> pdb=" O PHE O 219 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU O 221 " --> pdb=" O ILE O 250 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU O 247 " --> pdb=" O ALA O 274 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N VAL O 276 " --> pdb=" O LEU O 247 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ILE O 249 " --> pdb=" O VAL O 276 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'O' and resid 411 through 413 Processing sheet with id=AI6, first strand: chain 'O' and resid 476 through 479 Processing sheet with id=AI7, first strand: chain 'P' and resid 48 through 50 removed outlier: 7.233A pdb=" N ASN P 37 " --> pdb=" O GLU S 518 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N MET S 520 " --> pdb=" O ASN P 37 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL P 39 " --> pdb=" O MET S 520 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N THR S 522 " --> pdb=" O VAL P 39 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'P' and resid 174 through 179 removed outlier: 6.315A pdb=" N VAL P 174 " --> pdb=" O ALA P 377 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ILE P 379 " --> pdb=" O VAL P 174 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR P 176 " --> pdb=" O ILE P 379 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL P 381 " --> pdb=" O THR P 176 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLU P 178 " --> pdb=" O VAL P 381 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'P' and resid 194 through 195 removed outlier: 6.492A pdb=" N GLY P 335 " --> pdb=" O ALA P 320 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA P 320 " --> pdb=" O GLY P 335 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE P 219 " --> pdb=" O LEU P 248 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE P 250 " --> pdb=" O PHE P 219 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU P 221 " --> pdb=" O ILE P 250 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU P 247 " --> pdb=" O ALA P 274 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL P 276 " --> pdb=" O LEU P 247 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ILE P 249 " --> pdb=" O VAL P 276 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'P' and resid 213 through 216 removed outlier: 8.466A pdb=" N ILE P 301 " --> pdb=" O ILE P 220 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU P 222 " --> pdb=" O ILE P 301 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'P' and resid 411 through 413 Processing sheet with id=AJ3, first strand: chain 'P' and resid 476 through 479 Processing sheet with id=AJ4, first strand: chain 'Q' and resid 3 through 5 removed outlier: 3.958A pdb=" N ARG Q 4 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE T 94 " --> pdb=" O ARG Q 4 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE T 64 " --> pdb=" O VAL T 95 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE T 11 " --> pdb=" O LEU T 41 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N VAL T 43 " --> pdb=" O ARG T 9 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ARG T 9 " --> pdb=" O VAL T 43 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ARG T 14 " --> pdb=" O GLU T 82 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N GLU T 82 " --> pdb=" O ARG T 14 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'Q' and resid 47 through 48 Processing sheet with id=AJ6, first strand: chain 'R' and resid 174 through 179 Processing sheet with id=AJ7, first strand: chain 'R' and resid 194 through 195 removed outlier: 6.197A pdb=" N GLY R 335 " --> pdb=" O ALA R 320 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA R 320 " --> pdb=" O GLY R 335 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'R' and resid 194 through 195 removed outlier: 6.197A pdb=" N GLY R 335 " --> pdb=" O ALA R 320 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA R 320 " --> pdb=" O GLY R 335 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N PHE R 219 " --> pdb=" O LEU R 248 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'R' and resid 411 through 413 Processing sheet with id=AK1, first strand: chain 'R' and resid 476 through 479 Processing sheet with id=AK2, first strand: chain 'S' and resid 174 through 179 removed outlier: 6.302A pdb=" N VAL S 174 " --> pdb=" O ALA S 377 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE S 379 " --> pdb=" O VAL S 174 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR S 176 " --> pdb=" O ILE S 379 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL S 381 " --> pdb=" O THR S 176 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLU S 178 " --> pdb=" O VAL S 381 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'S' and resid 194 through 195 removed outlier: 6.472A pdb=" N GLY S 335 " --> pdb=" O ALA S 320 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA S 320 " --> pdb=" O GLY S 335 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE S 219 " --> pdb=" O LEU S 248 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ILE S 250 " --> pdb=" O PHE S 219 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU S 221 " --> pdb=" O ILE S 250 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU S 247 " --> pdb=" O ALA S 274 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N VAL S 276 " --> pdb=" O LEU S 247 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE S 249 " --> pdb=" O VAL S 276 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'S' and resid 213 through 216 removed outlier: 8.378A pdb=" N ILE S 301 " --> pdb=" O ILE S 220 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU S 222 " --> pdb=" O ILE S 301 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'S' and resid 411 through 413 Processing sheet with id=AK6, first strand: chain 'S' and resid 476 through 479 Processing sheet with id=AK7, first strand: chain 'T' and resid 47 through 48 3910 hydrogen bonds defined for protein. 11160 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: 32.62 Time building geometry restraints manager: 14.00 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: 20352 1.34 - 1.46: 5735 1.46 - 1.58: 33108 1.58 - 1.70: 53 1.70 - 1.82: 532 Bond restraints: 59780 Sorted by residual: bond pdb=" N GLY M 192 " pdb=" CA GLY M 192 " ideal model delta sigma weight residual 1.452 1.474 -0.022 1.52e-02 4.33e+03 2.11e+00 bond pdb=" N GLY B 192 " pdb=" CA GLY B 192 " ideal model delta sigma weight residual 1.452 1.474 -0.022 1.52e-02 4.33e+03 2.05e+00 bond pdb=" N GLY F 192 " pdb=" CA GLY F 192 " ideal model delta sigma weight residual 1.452 1.474 -0.022 1.52e-02 4.33e+03 2.04e+00 bond pdb=" CA GLY B 192 " pdb=" C GLY B 192 " ideal model delta sigma weight residual 1.514 1.534 -0.019 1.35e-02 5.49e+03 2.00e+00 bond pdb=" N GLY J 192 " pdb=" CA GLY J 192 " ideal model delta sigma weight residual 1.448 1.474 -0.026 1.88e-02 2.83e+03 1.99e+00 ... (remaining 59775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 80065 2.22 - 4.45: 611 4.45 - 6.67: 115 6.67 - 8.89: 24 8.89 - 11.11: 7 Bond angle restraints: 80822 Sorted by residual: angle pdb=" C THR C 266 " pdb=" N MET C 267 " pdb=" CA MET C 267 " ideal model delta sigma weight residual 120.68 113.97 6.71 1.70e+00 3.46e-01 1.56e+01 angle pdb=" CA MET P 267 " pdb=" CB MET P 267 " pdb=" CG MET P 267 " ideal model delta sigma weight residual 114.10 121.71 -7.61 2.00e+00 2.50e-01 1.45e+01 angle pdb=" CA MET C 267 " pdb=" CB MET C 267 " pdb=" CG MET C 267 " ideal model delta sigma weight residual 114.10 121.65 -7.55 2.00e+00 2.50e-01 1.43e+01 angle pdb=" N ILE J 230 " pdb=" CA ILE J 230 " pdb=" C ILE J 230 " ideal model delta sigma weight residual 112.96 109.19 3.77 1.00e+00 1.00e+00 1.42e+01 angle pdb=" N ILE S 230 " pdb=" CA ILE S 230 " pdb=" C ILE S 230 " ideal model delta sigma weight residual 113.42 109.08 4.34 1.17e+00 7.31e-01 1.38e+01 ... (remaining 80817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 32927 17.87 - 35.74: 3219 35.74 - 53.60: 851 53.60 - 71.47: 238 71.47 - 89.34: 61 Dihedral angle restraints: 37296 sinusoidal: 14728 harmonic: 22568 Sorted by residual: dihedral pdb=" CA ILE M 230 " pdb=" C ILE M 230 " pdb=" N ARG M 231 " pdb=" CA ARG M 231 " ideal model delta harmonic sigma weight residual -180.00 -161.11 -18.89 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA THR E 266 " pdb=" C THR E 266 " pdb=" N MET E 267 " pdb=" CA MET E 267 " ideal model delta harmonic sigma weight residual 180.00 161.41 18.59 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA THR H 266 " pdb=" C THR H 266 " pdb=" N MET H 267 " pdb=" CA MET H 267 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 37293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 9363 0.100 - 0.200: 448 0.200 - 0.300: 2 0.300 - 0.400: 0 0.400 - 0.500: 1 Chirality restraints: 9814 Sorted by residual: chirality pdb=" CG LEU C 215 " pdb=" CB LEU C 215 " pdb=" CD1 LEU C 215 " pdb=" CD2 LEU C 215 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.25e+00 chirality pdb=" CB ILE K 25 " pdb=" CA ILE K 25 " pdb=" CG1 ILE K 25 " pdb=" CG2 ILE K 25 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA MET C 267 " pdb=" N MET C 267 " pdb=" C MET C 267 " pdb=" CB MET C 267 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 9811 not shown) Planarity restraints: 10507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA J 260 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" C ALA J 260 " 0.030 2.00e-02 2.50e+03 pdb=" O ALA J 260 " -0.011 2.00e-02 2.50e+03 pdb=" N THR J 261 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 283 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" C ASP B 283 " -0.026 2.00e-02 2.50e+03 pdb=" O ASP B 283 " 0.010 2.00e-02 2.50e+03 pdb=" N ARG B 284 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP H 121 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" CG ASP H 121 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASP H 121 " -0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP H 121 " -0.009 2.00e-02 2.50e+03 ... (remaining 10504 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 465 2.52 - 3.12: 46742 3.12 - 3.71: 100793 3.71 - 4.31: 136214 4.31 - 4.90: 229559 Nonbonded interactions: 513773 Sorted by model distance: nonbonded pdb="MG MG R 601 " pdb=" O1A ATP R 602 " model vdw 1.931 2.170 nonbonded pdb="MG MG L 601 " pdb=" O1A ATP L 602 " model vdw 1.942 2.170 nonbonded pdb="MG MG R 601 " pdb=" O1G ATP R 602 " model vdw 1.954 2.170 nonbonded pdb="MG MG H 601 " pdb=" O1A ATP H 602 " model vdw 1.956 2.170 nonbonded pdb="MG MG A 601 " pdb=" O1A ATP A 602 " model vdw 1.960 2.170 ... (remaining 513768 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 525 or resid 601 through 602)) selection = (chain 'B' and (resid 2 through 196 or (resid 197 and (name N or name CA or name \ C or name O or name CB )) or resid 198 through 525 or resid 601 through 602)) selection = (chain 'C' and (resid 2 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 525 or resid 601 through 602)) selection = (chain 'E' and (resid 2 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 525 or resid 601 through 602)) selection = (chain 'F' and (resid 2 through 196 or (resid 197 and (name N or name CA or name \ C or name O or name CB )) or resid 198 through 525 or resid 601 through 602)) selection = (chain 'H' and (resid 2 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 525 or resid 601 through 602)) selection = (chain 'I' and (resid 2 through 196 or (resid 197 and (name N or name CA or name \ C or name O or name CB )) or resid 198 through 525 or resid 601 through 602)) selection = (chain 'J' and (resid 2 through 196 or (resid 197 and (name N or name CA or name \ C or name O or name CB )) or resid 198 through 525 or resid 601 through 602)) selection = (chain 'L' and (resid 2 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 525 or resid 601 through 602)) selection = (chain 'M' and (resid 2 through 196 or (resid 197 and (name N or name CA or name \ C or name O or name CB )) or resid 198 through 525 or resid 601 through 602)) selection = (chain 'O' and (resid 2 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 525 or resid 601 through 602)) selection = (chain 'P' and (resid 2 through 196 or (resid 197 and (name N or name CA or name \ C or name O or name CB )) or resid 198 through 525 or resid 601 through 602)) selection = (chain 'R' and (resid 2 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 525 or resid 601 through 602)) selection = (chain 'S' and (resid 2 through 196 or (resid 197 and (name N or name CA or name \ C or name O or name CB )) or resid 198 through 525 or resid 601 through 602)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.150 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: 0.100 Extract box with map and model: 1.730 Check model and map are aligned: 0.340 Set scattering table: 0.420 Process input model: 120.130 Find NCS groups from input model: 3.000 Set up NCS constraints: 0.520 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: 0.030 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 59780 Z= 0.244 Angle : 0.555 11.114 80822 Z= 0.298 Chirality : 0.044 0.500 9814 Planarity : 0.003 0.031 10507 Dihedral : 16.091 89.342 22820 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.13 % Allowed : 15.34 % Favored : 84.53 % 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: 1.29 (0.09), residues: 7966 helix: 1.72 (0.08), residues: 4228 sheet: 1.13 (0.17), residues: 875 loop : -0.51 (0.11), residues: 2863 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 401 PHE 0.010 0.001 PHE S 195 TYR 0.011 0.001 TYR K 71 ARG 0.004 0.000 ARG G 47 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 643 time to evaluate : 5.053 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: C 233 MET cc_start: 0.7423 (pmm) cc_final: 0.6974 (pmm) REVERT: I 267 MET cc_start: 0.7901 (mpt) cc_final: 0.7603 (mpt) REVERT: W 51 ASN cc_start: 0.8976 (p0) cc_final: 0.8676 (p0) REVERT: W 55 LYS cc_start: 0.8615 (ttpt) cc_final: 0.8379 (ptpt) REVERT: W 76 GLU cc_start: 0.8288 (tp30) cc_final: 0.8010 (tp30) REVERT: W 87 SER cc_start: 0.8837 (m) cc_final: 0.8475 (t) REVERT: A 219 PHE cc_start: 0.9034 (m-80) cc_final: 0.8574 (m-80) REVERT: A 233 MET cc_start: 0.8996 (pmm) cc_final: 0.8658 (pmm) REVERT: D 16 GLU cc_start: 0.8302 (pp20) cc_final: 0.7705 (pp20) REVERT: D 50 GLU cc_start: 0.7476 (pm20) cc_final: 0.7147 (pm20) REVERT: D 51 ASN cc_start: 0.8696 (p0) cc_final: 0.8399 (p0) REVERT: D 76 GLU cc_start: 0.8364 (tp30) cc_final: 0.7890 (tp30) REVERT: E 193 MET cc_start: 0.7665 (ppp) cc_final: 0.7366 (ppp) REVERT: E 233 MET cc_start: 0.8381 (pmm) cc_final: 0.7557 (pmm) REVERT: G 51 ASN cc_start: 0.8782 (p0) cc_final: 0.8458 (p0) REVERT: G 58 ASP cc_start: 0.8490 (t70) cc_final: 0.8158 (t0) REVERT: G 76 GLU cc_start: 0.8236 (tp30) cc_final: 0.7882 (tp30) REVERT: H 219 PHE cc_start: 0.8972 (m-80) cc_final: 0.8374 (m-80) REVERT: K 51 ASN cc_start: 0.8829 (p0) cc_final: 0.8442 (p0) REVERT: K 76 GLU cc_start: 0.8364 (tp30) cc_final: 0.8004 (tp30) REVERT: L 219 PHE cc_start: 0.8952 (m-80) cc_final: 0.8440 (m-80) REVERT: N 76 GLU cc_start: 0.8445 (tp30) cc_final: 0.8017 (tp30) REVERT: N 88 GLU cc_start: 0.8476 (pp20) cc_final: 0.8228 (tm-30) REVERT: Q 39 GLU cc_start: 0.8319 (pm20) cc_final: 0.7987 (pm20) REVERT: Q 51 ASN cc_start: 0.9104 (p0) cc_final: 0.8714 (p0) REVERT: Q 60 LYS cc_start: 0.8863 (mmtp) cc_final: 0.8652 (mmtm) REVERT: R 193 MET cc_start: 0.7947 (ppp) cc_final: 0.7468 (ppp) REVERT: R 215 LEU cc_start: 0.8714 (mp) cc_final: 0.8281 (mt) REVERT: R 219 PHE cc_start: 0.8951 (m-80) cc_final: 0.8176 (m-80) REVERT: R 389 MET cc_start: 0.2516 (mmm) cc_final: 0.2206 (mmm) REVERT: T 16 GLU cc_start: 0.8329 (pp20) cc_final: 0.7824 (pp20) REVERT: T 20 LYS cc_start: 0.8942 (mtmt) cc_final: 0.8610 (mtpp) REVERT: T 58 ASP cc_start: 0.8629 (m-30) cc_final: 0.8283 (t70) REVERT: T 60 LYS cc_start: 0.8753 (mptt) cc_final: 0.8549 (mptt) REVERT: T 76 GLU cc_start: 0.8152 (tp30) cc_final: 0.7804 (tp30) REVERT: T 77 LYS cc_start: 0.9087 (ptmm) cc_final: 0.8816 (tttp) outliers start: 8 outliers final: 4 residues processed: 647 average time/residue: 0.5584 time to fit residues: 607.6972 Evaluate side-chains 590 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 586 time to evaluate : 4.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain S residue 74 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 667 optimal weight: 0.9990 chunk 599 optimal weight: 8.9990 chunk 332 optimal weight: 5.9990 chunk 204 optimal weight: 2.9990 chunk 404 optimal weight: 0.0060 chunk 320 optimal weight: 3.9990 chunk 619 optimal weight: 4.9990 chunk 239 optimal weight: 1.9990 chunk 376 optimal weight: 6.9990 chunk 461 optimal weight: 0.9980 chunk 718 optimal weight: 9.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 319 GLN ** F 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 265 ASN P 82 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.0781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 59780 Z= 0.218 Angle : 0.523 10.348 80822 Z= 0.281 Chirality : 0.043 0.222 9814 Planarity : 0.003 0.031 10507 Dihedral : 9.094 89.031 8918 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.57 % Allowed : 14.59 % Favored : 83.84 % 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: 1.34 (0.09), residues: 7966 helix: 1.81 (0.08), residues: 4277 sheet: 0.72 (0.16), residues: 1015 loop : -0.52 (0.11), residues: 2674 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS N 7 PHE 0.015 0.001 PHE C 219 TYR 0.017 0.001 TYR O 199 ARG 0.005 0.000 ARG K 9 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 629 time to evaluate : 5.133 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: C 215 LEU cc_start: 0.7244 (mm) cc_final: 0.7005 (mm) REVERT: I 267 MET cc_start: 0.7961 (mpt) cc_final: 0.7566 (mpt) REVERT: I 309 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7840 (mt) REVERT: W 20 LYS cc_start: 0.8935 (mtpt) cc_final: 0.8698 (mtpp) REVERT: W 51 ASN cc_start: 0.9007 (p0) cc_final: 0.8530 (p0) REVERT: W 55 LYS cc_start: 0.8624 (ttpt) cc_final: 0.8359 (ptpt) REVERT: W 76 GLU cc_start: 0.8707 (tp30) cc_final: 0.7892 (tp30) REVERT: W 77 LYS cc_start: 0.8866 (tttp) cc_final: 0.8632 (ttmm) REVERT: W 87 SER cc_start: 0.8843 (m) cc_final: 0.8537 (t) REVERT: A 219 PHE cc_start: 0.9027 (m-80) cc_final: 0.8591 (m-80) REVERT: B 267 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7642 (mpt) REVERT: B 309 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7902 (mt) REVERT: D 16 GLU cc_start: 0.8490 (pp20) cc_final: 0.7766 (pp20) REVERT: D 50 GLU cc_start: 0.7505 (pm20) cc_final: 0.7194 (pm20) REVERT: D 51 ASN cc_start: 0.8606 (p0) cc_final: 0.8336 (p0) REVERT: D 76 GLU cc_start: 0.8388 (tp30) cc_final: 0.7998 (tp30) REVERT: D 88 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8056 (tm-30) REVERT: F 267 MET cc_start: 0.7977 (mpp) cc_final: 0.7629 (mpp) REVERT: F 309 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7689 (mt) REVERT: G 51 ASN cc_start: 0.8728 (p0) cc_final: 0.8444 (p0) REVERT: G 58 ASP cc_start: 0.8489 (t70) cc_final: 0.8229 (t0) REVERT: G 76 GLU cc_start: 0.8421 (tp30) cc_final: 0.7992 (tp30) REVERT: G 77 LYS cc_start: 0.8965 (tttp) cc_final: 0.8707 (tttp) REVERT: H 219 PHE cc_start: 0.8934 (m-80) cc_final: 0.8360 (m-80) REVERT: J 194 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8091 (tm-30) REVERT: J 309 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7771 (mp) REVERT: K 27 LEU cc_start: 0.8740 (mm) cc_final: 0.8538 (mp) REVERT: K 50 GLU cc_start: 0.7293 (pm20) cc_final: 0.7075 (pm20) REVERT: K 51 ASN cc_start: 0.8812 (p0) cc_final: 0.8375 (p0) REVERT: K 76 GLU cc_start: 0.8528 (tp30) cc_final: 0.7810 (tp30) REVERT: L 219 PHE cc_start: 0.8934 (m-80) cc_final: 0.8450 (m-80) REVERT: M 231 ARG cc_start: 0.7963 (mtm110) cc_final: 0.7602 (mtm110) REVERT: M 267 MET cc_start: 0.7996 (mpp) cc_final: 0.7572 (mpp) REVERT: N 76 GLU cc_start: 0.8684 (tp30) cc_final: 0.7931 (tp30) REVERT: N 77 LYS cc_start: 0.8795 (tttm) cc_final: 0.8436 (tptp) REVERT: N 88 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8061 (tm-30) REVERT: O 267 MET cc_start: 0.5725 (mpp) cc_final: 0.4715 (tpt) REVERT: P 229 ASN cc_start: 0.7203 (t0) cc_final: 0.6725 (t0) REVERT: Q 20 LYS cc_start: 0.8853 (mtpt) cc_final: 0.8518 (mtpp) REVERT: Q 51 ASN cc_start: 0.9019 (p0) cc_final: 0.8659 (p0) REVERT: Q 58 ASP cc_start: 0.8373 (t0) cc_final: 0.8111 (t0) REVERT: Q 76 GLU cc_start: 0.8308 (tp30) cc_final: 0.7893 (tp30) REVERT: R 219 PHE cc_start: 0.8927 (m-80) cc_final: 0.8135 (m-80) REVERT: S 267 MET cc_start: 0.7809 (mpt) cc_final: 0.7438 (mpt) REVERT: T 13 LYS cc_start: 0.8910 (ttmm) cc_final: 0.8705 (tttp) REVERT: T 20 LYS cc_start: 0.8835 (mtmt) cc_final: 0.8505 (mtpp) REVERT: T 58 ASP cc_start: 0.8558 (m-30) cc_final: 0.8315 (m-30) REVERT: T 76 GLU cc_start: 0.8417 (tp30) cc_final: 0.7730 (tp30) REVERT: T 77 LYS cc_start: 0.9096 (ptmm) cc_final: 0.8756 (tttp) REVERT: T 88 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8258 (tm-30) outliers start: 97 outliers final: 36 residues processed: 700 average time/residue: 0.5513 time to fit residues: 655.4400 Evaluate side-chains 630 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 587 time to evaluate : 5.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 229 ASN Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain W residue 64 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain J residue 194 GLN Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain J residue 372 LEU Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain O residue 387 VAL Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain P residue 193 MET Chi-restraints excluded: chain Q residue 13 LYS Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 521 VAL Chi-restraints excluded: chain S residue 176 THR Chi-restraints excluded: chain T residue 6 LEU Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain T residue 75 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 399 optimal weight: 4.9990 chunk 222 optimal weight: 9.9990 chunk 597 optimal weight: 20.0000 chunk 489 optimal weight: 50.0000 chunk 198 optimal weight: 10.0000 chunk 719 optimal weight: 5.9990 chunk 777 optimal weight: 3.9990 chunk 640 optimal weight: 9.9990 chunk 713 optimal weight: 9.9990 chunk 245 optimal weight: 6.9990 chunk 577 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 82 ASN I 206 ASN I 319 GLN B 319 GLN B 351 GLN F 82 ASN F 505 GLN J 72 GLN J 82 ASN J 112 ASN ** J 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 319 GLN M 82 ASN M 319 GLN S 82 ASN T 2 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 59780 Z= 0.556 Angle : 0.648 11.041 80822 Z= 0.345 Chirality : 0.049 0.223 9814 Planarity : 0.004 0.048 10507 Dihedral : 9.507 86.318 8911 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.70 % Allowed : 15.16 % Favored : 82.14 % 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: 0.83 (0.09), residues: 7966 helix: 1.32 (0.08), residues: 4312 sheet: 0.32 (0.17), residues: 987 loop : -0.54 (0.11), residues: 2667 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS W 7 PHE 0.012 0.001 PHE B 195 TYR 0.017 0.002 TYR S 199 ARG 0.005 0.000 ARG B 421 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 622 time to evaluate : 5.021 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: C 215 LEU cc_start: 0.7309 (mm) cc_final: 0.7083 (mm) REVERT: C 233 MET cc_start: 0.7539 (pmm) cc_final: 0.7315 (pmm) REVERT: C 389 MET cc_start: 0.2733 (mmm) cc_final: 0.2519 (mmm) REVERT: I 206 ASN cc_start: 0.8514 (m-40) cc_final: 0.8266 (m110) REVERT: I 267 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7608 (mpt) REVERT: I 309 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7939 (mt) REVERT: W 51 ASN cc_start: 0.8992 (p0) cc_final: 0.8514 (p0) REVERT: W 76 GLU cc_start: 0.8560 (tp30) cc_final: 0.8044 (tp30) REVERT: A 121 ASP cc_start: 0.6936 (t0) cc_final: 0.6682 (t0) REVERT: A 219 PHE cc_start: 0.9029 (m-80) cc_final: 0.8521 (m-80) REVERT: A 233 MET cc_start: 0.9000 (pmm) cc_final: 0.8780 (pmm) REVERT: B 193 MET cc_start: 0.7961 (mmm) cc_final: 0.7473 (mmt) REVERT: D 50 GLU cc_start: 0.7592 (pm20) cc_final: 0.7171 (pm20) REVERT: D 51 ASN cc_start: 0.8612 (p0) cc_final: 0.8337 (p0) REVERT: D 76 GLU cc_start: 0.8631 (tp30) cc_final: 0.8139 (tp30) REVERT: D 88 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8027 (tm-30) REVERT: E 121 ASP cc_start: 0.6589 (t0) cc_final: 0.6339 (t0) REVERT: E 514 MET cc_start: 0.8537 (mtm) cc_final: 0.8219 (mtm) REVERT: F 267 MET cc_start: 0.8048 (mpp) cc_final: 0.7772 (mpp) REVERT: F 309 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7703 (mt) REVERT: G 51 ASN cc_start: 0.8703 (p0) cc_final: 0.8473 (p0) REVERT: G 58 ASP cc_start: 0.8533 (t70) cc_final: 0.8206 (t0) REVERT: G 76 GLU cc_start: 0.8506 (tp30) cc_final: 0.8061 (tp30) REVERT: G 77 LYS cc_start: 0.8944 (tttp) cc_final: 0.8650 (tttp) REVERT: H 219 PHE cc_start: 0.8964 (m-80) cc_final: 0.8569 (m-80) REVERT: H 447 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8199 (mtp) REVERT: J 36 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.7276 (mtt180) REVERT: J 194 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.6949 (tm-30) REVERT: J 309 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7818 (mp) REVERT: K 39 GLU cc_start: 0.8465 (pm20) cc_final: 0.8261 (pm20) REVERT: K 51 ASN cc_start: 0.8794 (p0) cc_final: 0.8511 (p0) REVERT: K 76 GLU cc_start: 0.8403 (tp30) cc_final: 0.8033 (tp30) REVERT: L 219 PHE cc_start: 0.8960 (m-80) cc_final: 0.8533 (m-80) REVERT: M 231 ARG cc_start: 0.8073 (mtm110) cc_final: 0.7490 (mtm110) REVERT: M 267 MET cc_start: 0.8056 (mpp) cc_final: 0.7633 (mpt) REVERT: N 76 GLU cc_start: 0.8644 (tp30) cc_final: 0.8075 (tp30) REVERT: N 77 LYS cc_start: 0.8790 (tttm) cc_final: 0.8457 (tptp) REVERT: P 309 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7756 (mt) REVERT: Q 20 LYS cc_start: 0.8847 (mtpt) cc_final: 0.8631 (mtpp) REVERT: Q 51 ASN cc_start: 0.9019 (p0) cc_final: 0.8636 (p0) REVERT: Q 76 GLU cc_start: 0.8518 (tp30) cc_final: 0.8040 (tp30) REVERT: R 121 ASP cc_start: 0.6469 (t0) cc_final: 0.6249 (t0) REVERT: R 215 LEU cc_start: 0.8712 (mp) cc_final: 0.8270 (mt) REVERT: R 219 PHE cc_start: 0.8966 (m-80) cc_final: 0.8404 (m-80) REVERT: R 295 LEU cc_start: 0.9490 (mm) cc_final: 0.9241 (mt) REVERT: S 267 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7522 (mpt) REVERT: S 309 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7946 (mt) REVERT: S 333 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8755 (mt) REVERT: T 13 LYS cc_start: 0.8993 (ttmm) cc_final: 0.8597 (ttmt) REVERT: T 20 LYS cc_start: 0.8845 (mtmt) cc_final: 0.8538 (mtpp) REVERT: T 58 ASP cc_start: 0.8544 (m-30) cc_final: 0.8185 (t70) REVERT: T 60 LYS cc_start: 0.8688 (mptt) cc_final: 0.8469 (mptt) REVERT: T 76 GLU cc_start: 0.8350 (tp30) cc_final: 0.7841 (tp30) outliers start: 167 outliers final: 84 residues processed: 743 average time/residue: 0.5448 time to fit residues: 693.5800 Evaluate side-chains 687 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 592 time to evaluate : 5.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 229 ASN Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 233 MET Chi-restraints excluded: chain I residue 267 MET Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain I residue 435 ASP Chi-restraints excluded: chain W residue 57 LEU Chi-restraints excluded: chain W residue 64 ILE Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 319 GLN Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain J residue 36 ARG Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 194 GLN Chi-restraints excluded: chain J residue 233 MET Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 435 ASP Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 266 THR Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 88 GLU Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 387 VAL Chi-restraints excluded: chain O residue 521 VAL Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain P residue 193 MET Chi-restraints excluded: chain P residue 199 TYR Chi-restraints excluded: chain P residue 213 VAL Chi-restraints excluded: chain P residue 233 MET Chi-restraints excluded: chain P residue 309 LEU Chi-restraints excluded: chain P residue 387 VAL Chi-restraints excluded: chain P residue 435 ASP Chi-restraints excluded: chain Q residue 64 ILE Chi-restraints excluded: chain Q residue 81 GLU Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 521 VAL Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 176 THR Chi-restraints excluded: chain S residue 233 MET Chi-restraints excluded: chain S residue 267 MET Chi-restraints excluded: chain S residue 270 ILE Chi-restraints excluded: chain S residue 307 MET Chi-restraints excluded: chain S residue 309 LEU Chi-restraints excluded: chain S residue 333 ILE Chi-restraints excluded: chain S residue 491 MET Chi-restraints excluded: chain T residue 6 LEU Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 64 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 710 optimal weight: 6.9990 chunk 541 optimal weight: 0.9980 chunk 373 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 343 optimal weight: 1.9990 chunk 483 optimal weight: 30.0000 chunk 722 optimal weight: 0.7980 chunk 764 optimal weight: 0.9980 chunk 377 optimal weight: 30.0000 chunk 684 optimal weight: 0.8980 chunk 206 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 82 ASN B 319 GLN F 82 ASN F 229 ASN J 82 ASN M 82 ASN P 82 ASN ** R 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 59780 Z= 0.198 Angle : 0.525 7.906 80822 Z= 0.281 Chirality : 0.043 0.198 9814 Planarity : 0.003 0.032 10507 Dihedral : 8.896 89.735 8911 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.12 % Allowed : 16.08 % Favored : 81.80 % 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: 1.13 (0.09), residues: 7966 helix: 1.67 (0.08), residues: 4312 sheet: 0.27 (0.16), residues: 1057 loop : -0.56 (0.11), residues: 2597 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS W 7 PHE 0.023 0.001 PHE R 219 TYR 0.017 0.001 TYR R 199 ARG 0.006 0.000 ARG K 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 606 time to evaluate : 5.011 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: I 267 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7718 (mpt) REVERT: I 309 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7886 (mt) REVERT: W 51 ASN cc_start: 0.8951 (p0) cc_final: 0.8445 (p0) REVERT: W 76 GLU cc_start: 0.8364 (tp30) cc_final: 0.7923 (tp30) REVERT: A 121 ASP cc_start: 0.6821 (t0) cc_final: 0.6529 (t0) REVERT: A 219 PHE cc_start: 0.8986 (m-80) cc_final: 0.8530 (m-80) REVERT: B 193 MET cc_start: 0.7897 (mmm) cc_final: 0.7360 (mmt) REVERT: D 50 GLU cc_start: 0.7504 (pm20) cc_final: 0.7076 (pm20) REVERT: D 51 ASN cc_start: 0.8574 (p0) cc_final: 0.8288 (p0) REVERT: D 88 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8067 (tm-30) REVERT: E 121 ASP cc_start: 0.6487 (t0) cc_final: 0.6219 (t0) REVERT: E 514 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8305 (mtt) REVERT: F 194 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8516 (tm-30) REVERT: F 267 MET cc_start: 0.8060 (mpp) cc_final: 0.7600 (mpp) REVERT: F 309 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7645 (mt) REVERT: G 13 LYS cc_start: 0.9106 (tttp) cc_final: 0.8830 (tttp) REVERT: G 51 ASN cc_start: 0.8604 (p0) cc_final: 0.8365 (p0) REVERT: G 58 ASP cc_start: 0.8515 (t70) cc_final: 0.8261 (t0) REVERT: G 76 GLU cc_start: 0.8367 (tp30) cc_final: 0.7966 (tp30) REVERT: G 77 LYS cc_start: 0.8910 (tttp) cc_final: 0.8643 (tttp) REVERT: H 219 PHE cc_start: 0.8899 (m-80) cc_final: 0.8272 (m-80) REVERT: H 295 LEU cc_start: 0.9412 (mm) cc_final: 0.9025 (tp) REVERT: H 447 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8429 (mtp) REVERT: J 194 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8026 (tm-30) REVERT: J 309 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7783 (mp) REVERT: K 27 LEU cc_start: 0.9055 (tp) cc_final: 0.8627 (mp) REVERT: K 39 GLU cc_start: 0.8490 (pm20) cc_final: 0.8045 (pm20) REVERT: K 47 ARG cc_start: 0.8280 (ttm-80) cc_final: 0.8054 (ttm-80) REVERT: K 50 GLU cc_start: 0.7583 (pm20) cc_final: 0.7135 (pm20) REVERT: K 51 ASN cc_start: 0.8772 (p0) cc_final: 0.8399 (p0) REVERT: K 76 GLU cc_start: 0.8319 (tp30) cc_final: 0.7988 (tp30) REVERT: K 84 LEU cc_start: 0.8094 (mt) cc_final: 0.7804 (mt) REVERT: K 86 MET cc_start: 0.7922 (ptp) cc_final: 0.7721 (ptp) REVERT: K 88 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8412 (tm-30) REVERT: L 219 PHE cc_start: 0.8881 (m-80) cc_final: 0.8402 (m-80) REVERT: M 194 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8263 (tm-30) REVERT: N 76 GLU cc_start: 0.8483 (tp30) cc_final: 0.7993 (tp30) REVERT: N 77 LYS cc_start: 0.8743 (tttm) cc_final: 0.8433 (tptp) REVERT: O 195 PHE cc_start: 0.8633 (p90) cc_final: 0.8427 (p90) REVERT: O 267 MET cc_start: 0.5605 (mpp) cc_final: 0.4875 (tpt) REVERT: P 242 LYS cc_start: 0.8899 (mptt) cc_final: 0.8644 (mptt) REVERT: P 267 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7280 (mpt) REVERT: Q 8 ASP cc_start: 0.8203 (p0) cc_final: 0.7419 (p0) REVERT: Q 47 ARG cc_start: 0.8642 (ttm-80) cc_final: 0.7888 (ttm-80) REVERT: Q 51 ASN cc_start: 0.8950 (p0) cc_final: 0.8567 (p0) REVERT: Q 76 GLU cc_start: 0.8355 (tp30) cc_final: 0.8064 (tp30) REVERT: R 215 LEU cc_start: 0.8687 (mp) cc_final: 0.8210 (mt) REVERT: S 267 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7480 (mpt) REVERT: S 309 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7935 (mt) REVERT: T 58 ASP cc_start: 0.8540 (m-30) cc_final: 0.8120 (t0) REVERT: T 60 LYS cc_start: 0.8735 (mptt) cc_final: 0.8487 (mptt) REVERT: T 76 GLU cc_start: 0.8188 (tp30) cc_final: 0.7755 (tp30) REVERT: T 79 ASP cc_start: 0.8815 (p0) cc_final: 0.8523 (p0) outliers start: 131 outliers final: 61 residues processed: 705 average time/residue: 0.5500 time to fit residues: 662.9950 Evaluate side-chains 643 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 570 time to evaluate : 5.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 229 ASN Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain I residue 10 ASN Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 267 MET Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain W residue 64 ILE Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 514 MET Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain J residue 194 GLN Chi-restraints excluded: chain J residue 233 MET Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain J residue 372 LEU Chi-restraints excluded: chain J residue 435 ASP Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 266 THR Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 194 GLN Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain M residue 407 VAL Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 387 VAL Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain P residue 193 MET Chi-restraints excluded: chain P residue 267 MET Chi-restraints excluded: chain P residue 435 ASP Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 64 ILE Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 422 VAL Chi-restraints excluded: chain R residue 521 VAL Chi-restraints excluded: chain S residue 176 THR Chi-restraints excluded: chain S residue 267 MET Chi-restraints excluded: chain S residue 300 VAL Chi-restraints excluded: chain S residue 309 LEU Chi-restraints excluded: chain S residue 407 VAL Chi-restraints excluded: chain T residue 6 LEU Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain T residue 64 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 636 optimal weight: 0.8980 chunk 434 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 569 optimal weight: 0.7980 chunk 315 optimal weight: 8.9990 chunk 652 optimal weight: 9.9990 chunk 528 optimal weight: 0.0370 chunk 0 optimal weight: 7.9990 chunk 390 optimal weight: 6.9990 chunk 686 optimal weight: 9.9990 chunk 192 optimal weight: 6.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 82 ASN I 206 ASN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN G 2 ASN M 82 ASN R 475 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 59780 Z= 0.184 Angle : 0.528 10.566 80822 Z= 0.279 Chirality : 0.043 0.288 9814 Planarity : 0.003 0.031 10507 Dihedral : 8.654 89.963 8911 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.20 % Allowed : 16.58 % Favored : 81.22 % 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: 1.29 (0.09), residues: 7966 helix: 1.84 (0.08), residues: 4312 sheet: 0.31 (0.16), residues: 1057 loop : -0.54 (0.11), residues: 2597 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.000 HIS K 7 PHE 0.013 0.001 PHE C 219 TYR 0.016 0.001 TYR R 199 ARG 0.008 0.000 ARG D 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 595 time to evaluate : 5.066 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: C 447 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.7881 (mpp) REVERT: I 206 ASN cc_start: 0.8486 (m-40) cc_final: 0.8235 (m-40) REVERT: I 309 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7905 (mt) REVERT: W 51 ASN cc_start: 0.8846 (p0) cc_final: 0.8369 (p0) REVERT: W 76 GLU cc_start: 0.8345 (tp30) cc_final: 0.7972 (tp30) REVERT: W 77 LYS cc_start: 0.8713 (tttm) cc_final: 0.8399 (tptp) REVERT: A 121 ASP cc_start: 0.6825 (t0) cc_final: 0.6495 (t0) REVERT: A 219 PHE cc_start: 0.9003 (m-80) cc_final: 0.8550 (m-80) REVERT: B 193 MET cc_start: 0.7865 (mmm) cc_final: 0.7385 (mmt) REVERT: D 50 GLU cc_start: 0.7474 (pm20) cc_final: 0.7027 (pm20) REVERT: D 51 ASN cc_start: 0.8590 (p0) cc_final: 0.8304 (p0) REVERT: D 88 GLU cc_start: 0.8478 (tm-30) cc_final: 0.7949 (tm-30) REVERT: E 121 ASP cc_start: 0.6461 (t0) cc_final: 0.6155 (t0) REVERT: E 447 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8089 (mpp) REVERT: F 194 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8530 (tm-30) REVERT: F 309 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7606 (mt) REVERT: G 51 ASN cc_start: 0.8536 (p0) cc_final: 0.8301 (p0) REVERT: G 58 ASP cc_start: 0.8502 (t70) cc_final: 0.8256 (t0) REVERT: G 76 GLU cc_start: 0.8351 (tp30) cc_final: 0.7961 (tp30) REVERT: G 77 LYS cc_start: 0.8890 (tttp) cc_final: 0.8602 (tttp) REVERT: H 219 PHE cc_start: 0.8861 (m-80) cc_final: 0.8276 (m-80) REVERT: H 447 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8354 (mtp) REVERT: J 194 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8041 (tm-30) REVERT: J 309 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7781 (mp) REVERT: K 27 LEU cc_start: 0.9048 (tp) cc_final: 0.8577 (mp) REVERT: K 51 ASN cc_start: 0.8734 (p0) cc_final: 0.8409 (p0) REVERT: K 76 GLU cc_start: 0.8335 (tp30) cc_final: 0.8069 (tp30) REVERT: K 84 LEU cc_start: 0.8160 (mt) cc_final: 0.7865 (mt) REVERT: K 88 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8375 (tm-30) REVERT: L 219 PHE cc_start: 0.8888 (m-80) cc_final: 0.8376 (m-80) REVERT: L 233 MET cc_start: 0.8964 (pmm) cc_final: 0.8702 (pmm) REVERT: L 447 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8044 (mpp) REVERT: M 194 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8290 (tm-30) REVERT: N 76 GLU cc_start: 0.8414 (tp30) cc_final: 0.7941 (tp30) REVERT: N 77 LYS cc_start: 0.8690 (tttm) cc_final: 0.8373 (tptp) REVERT: O 267 MET cc_start: 0.5657 (mpp) cc_final: 0.5004 (tpt) REVERT: O 447 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8033 (mpp) REVERT: P 267 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7442 (mpt) REVERT: P 289 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9378 (mm) REVERT: Q 51 ASN cc_start: 0.8834 (p0) cc_final: 0.8483 (p0) REVERT: Q 76 GLU cc_start: 0.8378 (tp30) cc_final: 0.7799 (tp30) REVERT: R 215 LEU cc_start: 0.8677 (mp) cc_final: 0.8200 (mt) REVERT: R 295 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9193 (tp) REVERT: S 267 MET cc_start: 0.7900 (mpt) cc_final: 0.7524 (mpt) REVERT: S 309 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7931 (mt) REVERT: T 13 LYS cc_start: 0.9151 (tttp) cc_final: 0.8919 (ttmt) REVERT: T 20 LYS cc_start: 0.8851 (mtmt) cc_final: 0.8560 (mtpp) REVERT: T 55 LYS cc_start: 0.8932 (tppt) cc_final: 0.8564 (ttmm) REVERT: T 58 ASP cc_start: 0.8540 (m-30) cc_final: 0.8099 (t0) REVERT: T 60 LYS cc_start: 0.8752 (mptt) cc_final: 0.8520 (mptt) REVERT: T 76 GLU cc_start: 0.8143 (tp30) cc_final: 0.7743 (tp30) REVERT: T 84 LEU cc_start: 0.8276 (mt) cc_final: 0.7853 (mt) outliers start: 136 outliers final: 73 residues processed: 696 average time/residue: 0.5500 time to fit residues: 655.5542 Evaluate side-chains 653 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 565 time to evaluate : 6.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 229 ASN Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain I residue 10 ASN Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain W residue 64 ILE Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 447 MET Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain J residue 194 GLN Chi-restraints excluded: chain J residue 233 MET Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain J residue 372 LEU Chi-restraints excluded: chain J residue 435 ASP Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 266 THR Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 447 MET Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 194 GLN Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 387 VAL Chi-restraints excluded: chain O residue 447 MET Chi-restraints excluded: chain O residue 521 VAL Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain P residue 193 MET Chi-restraints excluded: chain P residue 267 MET Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 435 ASP Chi-restraints excluded: chain Q residue 64 ILE Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 150 ILE Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 295 LEU Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 521 VAL Chi-restraints excluded: chain S residue 176 THR Chi-restraints excluded: chain S residue 270 ILE Chi-restraints excluded: chain S residue 289 LEU Chi-restraints excluded: chain S residue 300 VAL Chi-restraints excluded: chain S residue 309 LEU Chi-restraints excluded: chain T residue 6 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 257 optimal weight: 4.9990 chunk 688 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 chunk 448 optimal weight: 20.0000 chunk 188 optimal weight: 6.9990 chunk 765 optimal weight: 9.9990 chunk 635 optimal weight: 9.9990 chunk 354 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 253 optimal weight: 7.9990 chunk 401 optimal weight: 0.8980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 319 GLN B 112 ASN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN J 82 ASN J 229 ASN J 319 GLN P 72 GLN P 82 ASN S 82 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 59780 Z= 0.379 Angle : 0.586 9.677 80822 Z= 0.309 Chirality : 0.046 0.266 9814 Planarity : 0.003 0.032 10507 Dihedral : 8.977 89.910 8911 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.30 % Allowed : 17.12 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.09), residues: 7966 helix: 1.65 (0.08), residues: 4312 sheet: 0.26 (0.16), residues: 1057 loop : -0.57 (0.11), residues: 2597 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS W 7 PHE 0.011 0.001 PHE B 195 TYR 0.016 0.002 TYR R 199 ARG 0.005 0.000 ARG D 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 580 time to evaluate : 5.192 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: C 389 MET cc_start: 0.3131 (mmm) cc_final: 0.2780 (mmm) REVERT: C 447 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.7987 (mpp) REVERT: I 206 ASN cc_start: 0.8521 (m-40) cc_final: 0.8238 (m-40) REVERT: I 309 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7884 (mt) REVERT: W 20 LYS cc_start: 0.8628 (mtpp) cc_final: 0.8382 (mmmm) REVERT: W 51 ASN cc_start: 0.8808 (p0) cc_final: 0.8361 (p0) REVERT: W 76 GLU cc_start: 0.8440 (tp30) cc_final: 0.8044 (tp30) REVERT: W 77 LYS cc_start: 0.8715 (tttm) cc_final: 0.8390 (tptp) REVERT: A 121 ASP cc_start: 0.6950 (t0) cc_final: 0.6625 (t0) REVERT: A 219 PHE cc_start: 0.9013 (m-80) cc_final: 0.8529 (m-80) REVERT: B 36 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8515 (mtt90) REVERT: B 193 MET cc_start: 0.7941 (mmm) cc_final: 0.7450 (mmt) REVERT: D 50 GLU cc_start: 0.7568 (pm20) cc_final: 0.7103 (pm20) REVERT: D 51 ASN cc_start: 0.8547 (p0) cc_final: 0.8237 (p0) REVERT: D 88 GLU cc_start: 0.8434 (tm-30) cc_final: 0.7799 (tm-30) REVERT: E 121 ASP cc_start: 0.6554 (t0) cc_final: 0.6284 (t0) REVERT: E 193 MET cc_start: 0.7634 (ppp) cc_final: 0.7355 (ppp) REVERT: E 447 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8339 (mtm) REVERT: F 194 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8496 (tm-30) REVERT: F 309 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7647 (mt) REVERT: G 8 ASP cc_start: 0.8398 (p0) cc_final: 0.8050 (p0) REVERT: G 51 ASN cc_start: 0.8516 (p0) cc_final: 0.8309 (p0) REVERT: G 58 ASP cc_start: 0.8542 (t70) cc_final: 0.8289 (t0) REVERT: G 76 GLU cc_start: 0.8374 (tp30) cc_final: 0.7998 (tp30) REVERT: G 77 LYS cc_start: 0.8886 (tttp) cc_final: 0.8598 (tttp) REVERT: H 193 MET cc_start: 0.7946 (ppp) cc_final: 0.7671 (tmm) REVERT: H 219 PHE cc_start: 0.8873 (m-80) cc_final: 0.8274 (m-80) REVERT: H 447 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8547 (mtp) REVERT: J 194 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8217 (tm-30) REVERT: J 309 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7803 (mp) REVERT: K 27 LEU cc_start: 0.9105 (tp) cc_final: 0.8621 (mp) REVERT: K 39 GLU cc_start: 0.8380 (pm20) cc_final: 0.8170 (pm20) REVERT: K 51 ASN cc_start: 0.8721 (p0) cc_final: 0.8461 (p0) REVERT: K 76 GLU cc_start: 0.8445 (tp30) cc_final: 0.8215 (tp30) REVERT: K 77 LYS cc_start: 0.8517 (tptt) cc_final: 0.7985 (tptp) REVERT: K 84 LEU cc_start: 0.8138 (mt) cc_final: 0.7768 (mt) REVERT: K 88 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8383 (tm-30) REVERT: L 219 PHE cc_start: 0.8907 (m-80) cc_final: 0.8377 (m-80) REVERT: L 447 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8082 (mtp) REVERT: M 194 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.7048 (tm-30) REVERT: N 76 GLU cc_start: 0.8490 (tp30) cc_final: 0.7997 (tp30) REVERT: N 77 LYS cc_start: 0.8731 (tttm) cc_final: 0.8398 (tptp) REVERT: O 447 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8081 (mpp) REVERT: P 229 ASN cc_start: 0.7648 (t0) cc_final: 0.7376 (t0) REVERT: P 242 LYS cc_start: 0.8902 (mptt) cc_final: 0.8686 (mptt) REVERT: Q 13 LYS cc_start: 0.8964 (ttmm) cc_final: 0.8749 (ttmm) REVERT: Q 50 GLU cc_start: 0.7384 (pm20) cc_final: 0.7077 (pm20) REVERT: Q 51 ASN cc_start: 0.8807 (p0) cc_final: 0.8482 (p0) REVERT: Q 55 LYS cc_start: 0.8837 (tppt) cc_final: 0.8464 (ttpp) REVERT: Q 76 GLU cc_start: 0.8417 (tp30) cc_final: 0.8031 (tp30) REVERT: R 215 LEU cc_start: 0.8690 (mp) cc_final: 0.8221 (mt) REVERT: R 295 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9198 (tp) REVERT: S 267 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7641 (mpt) REVERT: S 309 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7902 (mt) REVERT: T 13 LYS cc_start: 0.9124 (tttp) cc_final: 0.8865 (ttmt) REVERT: T 20 LYS cc_start: 0.8883 (mtmt) cc_final: 0.8601 (mtpp) REVERT: T 55 LYS cc_start: 0.8970 (tppt) cc_final: 0.8657 (ttmm) REVERT: T 58 ASP cc_start: 0.8546 (m-30) cc_final: 0.8099 (t0) REVERT: T 60 LYS cc_start: 0.8763 (mptt) cc_final: 0.8522 (mptt) REVERT: T 76 GLU cc_start: 0.8222 (tp30) cc_final: 0.7805 (tp30) outliers start: 142 outliers final: 93 residues processed: 682 average time/residue: 0.5424 time to fit residues: 634.8729 Evaluate side-chains 676 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 568 time to evaluate : 4.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 319 GLN Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain W residue 64 ILE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 447 MET Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain F residue 160 LYS Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 307 MET Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 435 ASP Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain J residue 194 GLN Chi-restraints excluded: chain J residue 233 MET Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain J residue 319 GLN Chi-restraints excluded: chain J residue 372 LEU Chi-restraints excluded: chain J residue 435 ASP Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 266 THR Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 447 MET Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 194 GLN Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain M residue 372 LEU Chi-restraints excluded: chain M residue 420 ILE Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 387 VAL Chi-restraints excluded: chain O residue 447 MET Chi-restraints excluded: chain O residue 521 VAL Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain P residue 193 MET Chi-restraints excluded: chain P residue 435 ASP Chi-restraints excluded: chain Q residue 64 ILE Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 150 ILE Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 295 LEU Chi-restraints excluded: chain R residue 521 VAL Chi-restraints excluded: chain S residue 176 THR Chi-restraints excluded: chain S residue 233 MET Chi-restraints excluded: chain S residue 267 MET Chi-restraints excluded: chain S residue 270 ILE Chi-restraints excluded: chain S residue 289 LEU Chi-restraints excluded: chain S residue 300 VAL Chi-restraints excluded: chain S residue 307 MET Chi-restraints excluded: chain S residue 309 LEU Chi-restraints excluded: chain T residue 6 LEU Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 64 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 737 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 436 optimal weight: 1.9990 chunk 558 optimal weight: 5.9990 chunk 433 optimal weight: 0.4980 chunk 644 optimal weight: 1.9990 chunk 427 optimal weight: 6.9990 chunk 762 optimal weight: 4.9990 chunk 477 optimal weight: 20.0000 chunk 464 optimal weight: 3.9990 chunk 351 optimal weight: 6.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 319 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 ASN J 229 ASN J 319 GLN J 505 GLN M 82 ASN P 82 ASN S 82 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 59780 Z= 0.234 Angle : 0.547 9.645 80822 Z= 0.289 Chirality : 0.044 0.259 9814 Planarity : 0.003 0.030 10507 Dihedral : 8.742 89.540 8911 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.18 % Allowed : 17.54 % Favored : 80.28 % 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: 1.19 (0.09), residues: 7966 helix: 1.74 (0.08), residues: 4312 sheet: 0.27 (0.16), residues: 1057 loop : -0.56 (0.11), residues: 2597 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS W 7 PHE 0.010 0.001 PHE B 195 TYR 0.016 0.001 TYR R 199 ARG 0.007 0.000 ARG D 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 584 time to evaluate : 5.060 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: C 389 MET cc_start: 0.3296 (mmm) cc_final: 0.3039 (mmm) REVERT: C 447 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8003 (mpp) REVERT: I 194 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8241 (tm-30) REVERT: I 206 ASN cc_start: 0.8504 (m-40) cc_final: 0.8268 (m-40) REVERT: I 309 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7903 (mt) REVERT: W 20 LYS cc_start: 0.8596 (mtpp) cc_final: 0.8353 (mmmm) REVERT: W 51 ASN cc_start: 0.8762 (p0) cc_final: 0.8332 (p0) REVERT: W 76 GLU cc_start: 0.8361 (tp30) cc_final: 0.7959 (tp30) REVERT: W 77 LYS cc_start: 0.8697 (tttm) cc_final: 0.8328 (tptp) REVERT: A 121 ASP cc_start: 0.6909 (t0) cc_final: 0.6577 (t0) REVERT: A 219 PHE cc_start: 0.8998 (m-80) cc_final: 0.8568 (m-80) REVERT: B 193 MET cc_start: 0.7903 (mmm) cc_final: 0.7387 (mmt) REVERT: D 50 GLU cc_start: 0.7498 (pm20) cc_final: 0.7036 (pm20) REVERT: D 51 ASN cc_start: 0.8484 (p0) cc_final: 0.8159 (p0) REVERT: D 88 GLU cc_start: 0.8426 (tm-30) cc_final: 0.7818 (tm-30) REVERT: E 121 ASP cc_start: 0.6489 (t0) cc_final: 0.6206 (t0) REVERT: E 447 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8281 (mtm) REVERT: F 194 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8515 (tm-30) REVERT: F 309 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7623 (mt) REVERT: G 47 ARG cc_start: 0.8528 (tpp80) cc_final: 0.8278 (tpp80) REVERT: G 51 ASN cc_start: 0.8482 (p0) cc_final: 0.8281 (p0) REVERT: G 58 ASP cc_start: 0.8515 (t70) cc_final: 0.7962 (t0) REVERT: G 76 GLU cc_start: 0.8355 (tp30) cc_final: 0.7982 (tp30) REVERT: G 77 LYS cc_start: 0.8907 (tttp) cc_final: 0.8645 (tttp) REVERT: G 79 ASP cc_start: 0.8884 (p0) cc_final: 0.8658 (p0) REVERT: H 219 PHE cc_start: 0.8857 (m-80) cc_final: 0.8283 (m-80) REVERT: H 295 LEU cc_start: 0.9269 (mt) cc_final: 0.9024 (tp) REVERT: H 447 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8413 (mtp) REVERT: J 194 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8136 (tm-30) REVERT: J 309 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7786 (mp) REVERT: K 27 LEU cc_start: 0.9106 (tp) cc_final: 0.8609 (mp) REVERT: K 39 GLU cc_start: 0.8403 (pm20) cc_final: 0.8202 (pm20) REVERT: K 47 ARG cc_start: 0.8188 (ttm-80) cc_final: 0.7976 (ttm-80) REVERT: K 51 ASN cc_start: 0.8648 (p0) cc_final: 0.8369 (p0) REVERT: K 76 GLU cc_start: 0.8435 (tp30) cc_final: 0.8219 (tp30) REVERT: K 84 LEU cc_start: 0.8178 (mt) cc_final: 0.7891 (mt) REVERT: K 88 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8287 (tm-30) REVERT: L 219 PHE cc_start: 0.8894 (m-80) cc_final: 0.8370 (m-80) REVERT: L 233 MET cc_start: 0.8931 (pmm) cc_final: 0.8614 (pmm) REVERT: L 447 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8084 (mtp) REVERT: M 194 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.7045 (tm-30) REVERT: N 76 GLU cc_start: 0.8427 (tp30) cc_final: 0.7873 (tp30) REVERT: N 77 LYS cc_start: 0.8720 (tttm) cc_final: 0.8389 (tptp) REVERT: O 267 MET cc_start: 0.5492 (mpp) cc_final: 0.5238 (tpt) REVERT: O 447 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8072 (mpp) REVERT: P 229 ASN cc_start: 0.7540 (t0) cc_final: 0.7216 (t0) REVERT: P 242 LYS cc_start: 0.8949 (mptt) cc_final: 0.8713 (mptt) REVERT: Q 13 LYS cc_start: 0.8963 (ttmm) cc_final: 0.8744 (ttmm) REVERT: Q 39 GLU cc_start: 0.8556 (pm20) cc_final: 0.8302 (pm20) REVERT: Q 51 ASN cc_start: 0.8748 (p0) cc_final: 0.8463 (p0) REVERT: Q 55 LYS cc_start: 0.8797 (tppt) cc_final: 0.8520 (ttpp) REVERT: Q 76 GLU cc_start: 0.8445 (tp30) cc_final: 0.7784 (tp30) REVERT: R 215 LEU cc_start: 0.8683 (mp) cc_final: 0.8216 (mt) REVERT: R 295 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9186 (tp) REVERT: S 267 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7643 (mpt) REVERT: S 309 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7921 (mt) REVERT: T 13 LYS cc_start: 0.9062 (tttp) cc_final: 0.8732 (ttmt) REVERT: T 20 LYS cc_start: 0.8901 (mtmt) cc_final: 0.8620 (mtpp) REVERT: T 58 ASP cc_start: 0.8556 (m-30) cc_final: 0.8095 (t0) REVERT: T 76 GLU cc_start: 0.8121 (tp30) cc_final: 0.7737 (tp30) outliers start: 135 outliers final: 84 residues processed: 690 average time/residue: 0.5517 time to fit residues: 652.6238 Evaluate side-chains 662 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 563 time to evaluate : 5.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 194 GLN Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain W residue 64 ILE Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 447 MET Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain F residue 160 LYS Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 435 ASP Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 438 VAL Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 194 GLN Chi-restraints excluded: chain J residue 233 MET Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain J residue 372 LEU Chi-restraints excluded: chain J residue 435 ASP Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 266 THR Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 447 MET Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 194 GLN Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain M residue 420 ILE Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 387 VAL Chi-restraints excluded: chain O residue 447 MET Chi-restraints excluded: chain O residue 521 VAL Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain P residue 193 MET Chi-restraints excluded: chain P residue 435 ASP Chi-restraints excluded: chain Q residue 64 ILE Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 150 ILE Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 295 LEU Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 521 VAL Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 176 THR Chi-restraints excluded: chain S residue 233 MET Chi-restraints excluded: chain S residue 267 MET Chi-restraints excluded: chain S residue 270 ILE Chi-restraints excluded: chain S residue 289 LEU Chi-restraints excluded: chain S residue 300 VAL Chi-restraints excluded: chain S residue 309 LEU Chi-restraints excluded: chain T residue 6 LEU Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain T residue 57 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 471 optimal weight: 30.0000 chunk 304 optimal weight: 0.9980 chunk 455 optimal weight: 3.9990 chunk 229 optimal weight: 6.9990 chunk 149 optimal weight: 20.0000 chunk 147 optimal weight: 9.9990 chunk 484 optimal weight: 9.9990 chunk 519 optimal weight: 3.9990 chunk 376 optimal weight: 7.9990 chunk 71 optimal weight: 0.0050 chunk 599 optimal weight: 20.0000 overall best weight: 3.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 319 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 366 GLN F 72 GLN J 82 ASN M 82 ASN P 82 ASN S 82 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 59780 Z= 0.367 Angle : 0.595 11.353 80822 Z= 0.313 Chirality : 0.046 0.241 9814 Planarity : 0.003 0.032 10507 Dihedral : 8.940 89.847 8911 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.17 % Allowed : 17.76 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.09), residues: 7966 helix: 1.59 (0.08), residues: 4312 sheet: 0.20 (0.16), residues: 1106 loop : -0.55 (0.11), residues: 2548 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 401 PHE 0.010 0.001 PHE B 195 TYR 0.015 0.002 TYR R 199 ARG 0.007 0.000 ARG D 47 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 580 time to evaluate : 5.287 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: C 389 MET cc_start: 0.3292 (mmm) cc_final: 0.3087 (mmm) REVERT: C 447 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8001 (mtp) REVERT: I 194 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8262 (tm-30) REVERT: I 206 ASN cc_start: 0.8535 (m-40) cc_final: 0.8253 (m-40) REVERT: I 309 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7913 (mt) REVERT: W 20 LYS cc_start: 0.8618 (mtpp) cc_final: 0.8382 (mmmm) REVERT: W 51 ASN cc_start: 0.8738 (p0) cc_final: 0.8311 (p0) REVERT: W 76 GLU cc_start: 0.8433 (tp30) cc_final: 0.7928 (tp30) REVERT: A 121 ASP cc_start: 0.6999 (t0) cc_final: 0.6674 (t0) REVERT: A 219 PHE cc_start: 0.9033 (m-80) cc_final: 0.8556 (m-80) REVERT: D 50 GLU cc_start: 0.7595 (pm20) cc_final: 0.7132 (pm20) REVERT: D 51 ASN cc_start: 0.8512 (p0) cc_final: 0.8170 (p0) REVERT: D 84 LEU cc_start: 0.8225 (mt) cc_final: 0.8024 (mt) REVERT: D 88 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7779 (tm-30) REVERT: E 121 ASP cc_start: 0.6567 (t0) cc_final: 0.6278 (t0) REVERT: E 193 MET cc_start: 0.7695 (ppp) cc_final: 0.7429 (ppp) REVERT: E 447 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8351 (mtm) REVERT: F 194 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8534 (tm-30) REVERT: F 309 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7629 (mt) REVERT: G 47 ARG cc_start: 0.8586 (tpp80) cc_final: 0.8336 (tpp80) REVERT: G 51 ASN cc_start: 0.8452 (p0) cc_final: 0.8243 (p0) REVERT: G 58 ASP cc_start: 0.8460 (t70) cc_final: 0.8184 (t0) REVERT: G 76 GLU cc_start: 0.8381 (tp30) cc_final: 0.7972 (tp30) REVERT: G 79 ASP cc_start: 0.8835 (p0) cc_final: 0.8592 (p0) REVERT: H 219 PHE cc_start: 0.8880 (m-80) cc_final: 0.8269 (m-80) REVERT: H 295 LEU cc_start: 0.9294 (mt) cc_final: 0.9052 (tp) REVERT: H 447 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8558 (mtp) REVERT: J 194 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8251 (tm-30) REVERT: J 309 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7821 (mp) REVERT: K 27 LEU cc_start: 0.9180 (tp) cc_final: 0.8624 (mp) REVERT: K 51 ASN cc_start: 0.8641 (p0) cc_final: 0.8325 (p0) REVERT: K 77 LYS cc_start: 0.8469 (tptt) cc_final: 0.7905 (tptp) REVERT: K 84 LEU cc_start: 0.8123 (mt) cc_final: 0.7848 (mt) REVERT: K 88 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8324 (tm-30) REVERT: L 219 PHE cc_start: 0.8929 (m-80) cc_final: 0.8402 (m-80) REVERT: L 447 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8472 (mtm) REVERT: M 194 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.7106 (tm-30) REVERT: N 76 GLU cc_start: 0.8480 (tp30) cc_final: 0.7893 (tp30) REVERT: N 77 LYS cc_start: 0.8740 (tttm) cc_final: 0.8404 (tptp) REVERT: O 267 MET cc_start: 0.5570 (mpp) cc_final: 0.5206 (tpt) REVERT: O 447 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8104 (mpp) REVERT: P 229 ASN cc_start: 0.7605 (t0) cc_final: 0.7271 (t0) REVERT: P 289 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9368 (mm) REVERT: Q 13 LYS cc_start: 0.8990 (ttmm) cc_final: 0.8774 (ttmm) REVERT: Q 39 GLU cc_start: 0.8580 (pm20) cc_final: 0.8326 (pm20) REVERT: Q 51 ASN cc_start: 0.8658 (p0) cc_final: 0.8362 (p0) REVERT: Q 76 GLU cc_start: 0.8455 (tp30) cc_final: 0.8053 (tp30) REVERT: R 16 MET cc_start: 0.8655 (mmm) cc_final: 0.8347 (mtp) REVERT: R 215 LEU cc_start: 0.8704 (mp) cc_final: 0.8274 (mt) REVERT: R 295 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9186 (tp) REVERT: S 267 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7682 (mpt) REVERT: S 309 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7918 (mt) REVERT: T 13 LYS cc_start: 0.9085 (tttp) cc_final: 0.8865 (ttmt) REVERT: T 20 LYS cc_start: 0.8929 (mtmt) cc_final: 0.8673 (mtpp) REVERT: T 58 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8184 (t0) REVERT: T 76 GLU cc_start: 0.8207 (tp30) cc_final: 0.7786 (tp30) REVERT: T 79 ASP cc_start: 0.8852 (p0) cc_final: 0.8629 (p0) outliers start: 134 outliers final: 98 residues processed: 682 average time/residue: 0.5433 time to fit residues: 637.7370 Evaluate side-chains 677 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 562 time to evaluate : 5.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 194 GLN Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain W residue 64 ILE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 447 MET Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain F residue 160 LYS Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 435 ASP Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 301 ILE Chi-restraints excluded: chain H residue 438 VAL Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 194 GLN Chi-restraints excluded: chain J residue 233 MET Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain J residue 372 LEU Chi-restraints excluded: chain J residue 435 ASP Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 266 THR Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 447 MET Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 194 GLN Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain M residue 372 LEU Chi-restraints excluded: chain M residue 420 ILE Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 387 VAL Chi-restraints excluded: chain O residue 447 MET Chi-restraints excluded: chain O residue 521 VAL Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain P residue 193 MET Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 389 MET Chi-restraints excluded: chain P residue 435 ASP Chi-restraints excluded: chain Q residue 64 ILE Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 150 ILE Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 295 LEU Chi-restraints excluded: chain R residue 422 VAL Chi-restraints excluded: chain R residue 521 VAL Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 176 THR Chi-restraints excluded: chain S residue 233 MET Chi-restraints excluded: chain S residue 267 MET Chi-restraints excluded: chain S residue 270 ILE Chi-restraints excluded: chain S residue 289 LEU Chi-restraints excluded: chain S residue 300 VAL Chi-restraints excluded: chain S residue 309 LEU Chi-restraints excluded: chain S residue 372 LEU Chi-restraints excluded: chain T residue 6 LEU Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 58 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 693 optimal weight: 10.0000 chunk 730 optimal weight: 0.4980 chunk 666 optimal weight: 3.9990 chunk 710 optimal weight: 30.0000 chunk 427 optimal weight: 7.9990 chunk 309 optimal weight: 6.9990 chunk 557 optimal weight: 0.9990 chunk 218 optimal weight: 7.9990 chunk 641 optimal weight: 10.0000 chunk 671 optimal weight: 9.9990 chunk 707 optimal weight: 30.0000 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 366 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 366 GLN J 82 ASN J 319 GLN L 366 GLN O 366 GLN S 112 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 59780 Z= 0.451 Angle : 0.642 12.701 80822 Z= 0.337 Chirality : 0.048 0.261 9814 Planarity : 0.004 0.038 10507 Dihedral : 9.154 86.904 8911 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.51 % Allowed : 17.89 % Favored : 79.60 % 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: 0.87 (0.09), residues: 7966 helix: 1.40 (0.08), residues: 4305 sheet: 0.33 (0.18), residues: 931 loop : -0.58 (0.11), residues: 2730 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS Q 7 PHE 0.010 0.001 PHE P 195 TYR 0.015 0.002 TYR R 199 ARG 0.007 0.000 ARG D 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 580 time to evaluate : 5.098 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: C 447 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8046 (mtp) REVERT: I 36 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8290 (mtt90) REVERT: I 194 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8263 (tm-30) REVERT: I 206 ASN cc_start: 0.8562 (m-40) cc_final: 0.8292 (m-40) REVERT: I 309 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7789 (mt) REVERT: W 51 ASN cc_start: 0.8711 (p0) cc_final: 0.8331 (p0) REVERT: W 76 GLU cc_start: 0.8567 (tp30) cc_final: 0.8051 (tp30) REVERT: W 77 LYS cc_start: 0.8788 (tttp) cc_final: 0.8528 (tptp) REVERT: A 121 ASP cc_start: 0.7026 (t0) cc_final: 0.6674 (t0) REVERT: A 219 PHE cc_start: 0.9031 (m-80) cc_final: 0.8550 (m-80) REVERT: D 50 GLU cc_start: 0.7679 (pm20) cc_final: 0.7215 (pm20) REVERT: D 51 ASN cc_start: 0.8520 (p0) cc_final: 0.8157 (p0) REVERT: D 84 LEU cc_start: 0.8225 (mt) cc_final: 0.8022 (mt) REVERT: D 88 GLU cc_start: 0.8424 (tm-30) cc_final: 0.7891 (tm-30) REVERT: E 121 ASP cc_start: 0.6612 (t0) cc_final: 0.6320 (t0) REVERT: E 447 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8436 (mtm) REVERT: F 194 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.7512 (tm-30) REVERT: F 309 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7631 (mt) REVERT: G 47 ARG cc_start: 0.8654 (tpp80) cc_final: 0.8404 (tpp80) REVERT: G 51 ASN cc_start: 0.8459 (p0) cc_final: 0.8223 (p0) REVERT: G 58 ASP cc_start: 0.8511 (t70) cc_final: 0.8237 (t0) REVERT: G 76 GLU cc_start: 0.8429 (tp30) cc_final: 0.7972 (tp30) REVERT: G 77 LYS cc_start: 0.8949 (tttp) cc_final: 0.8428 (tptp) REVERT: G 79 ASP cc_start: 0.8795 (p0) cc_final: 0.8547 (p0) REVERT: H 121 ASP cc_start: 0.6923 (t0) cc_final: 0.6591 (t0) REVERT: H 219 PHE cc_start: 0.8917 (m-80) cc_final: 0.8317 (m-80) REVERT: H 233 MET cc_start: 0.8889 (pmm) cc_final: 0.8204 (pmm) REVERT: H 295 LEU cc_start: 0.9306 (mt) cc_final: 0.9063 (tp) REVERT: H 447 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8559 (mtp) REVERT: J 194 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8250 (tm-30) REVERT: J 309 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7822 (mp) REVERT: J 483 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7212 (mt-10) REVERT: K 51 ASN cc_start: 0.8559 (p0) cc_final: 0.8289 (p0) REVERT: K 76 GLU cc_start: 0.8381 (tp30) cc_final: 0.8134 (tp30) REVERT: K 77 LYS cc_start: 0.8447 (tptt) cc_final: 0.7960 (tptp) REVERT: K 84 LEU cc_start: 0.8167 (mt) cc_final: 0.7866 (mt) REVERT: K 88 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8443 (tm-30) REVERT: L 219 PHE cc_start: 0.8950 (m-80) cc_final: 0.8418 (m-80) REVERT: L 233 MET cc_start: 0.8954 (pmm) cc_final: 0.8238 (pmm) REVERT: L 447 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8522 (mtm) REVERT: M 194 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.7141 (tm-30) REVERT: N 76 GLU cc_start: 0.8475 (tp30) cc_final: 0.7919 (tp30) REVERT: N 77 LYS cc_start: 0.8764 (tttm) cc_final: 0.8425 (tptp) REVERT: O 267 MET cc_start: 0.5714 (mpp) cc_final: 0.5321 (tpt) REVERT: O 447 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8140 (mpp) REVERT: P 229 ASN cc_start: 0.7579 (t0) cc_final: 0.7252 (t0) REVERT: P 242 LYS cc_start: 0.8968 (mptt) cc_final: 0.8765 (mptt) REVERT: P 289 LEU cc_start: 0.9625 (OUTLIER) cc_final: 0.9361 (mm) REVERT: Q 13 LYS cc_start: 0.9011 (ttmm) cc_final: 0.8722 (ttmm) REVERT: Q 39 GLU cc_start: 0.8600 (pm20) cc_final: 0.8318 (pm20) REVERT: Q 51 ASN cc_start: 0.8655 (p0) cc_final: 0.8360 (p0) REVERT: Q 76 GLU cc_start: 0.8480 (tp30) cc_final: 0.7764 (tp30) REVERT: R 16 MET cc_start: 0.8617 (mmm) cc_final: 0.8404 (mtp) REVERT: R 215 LEU cc_start: 0.8720 (mp) cc_final: 0.8286 (mt) REVERT: R 295 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9179 (tp) REVERT: S 267 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7678 (mpt) REVERT: S 309 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7909 (mt) REVERT: T 20 LYS cc_start: 0.8998 (mtmt) cc_final: 0.8737 (mtpp) REVERT: T 47 ARG cc_start: 0.8709 (ttm-80) cc_final: 0.8419 (ttm-80) REVERT: T 58 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8261 (t0) REVERT: T 68 ASN cc_start: 0.8751 (t0) cc_final: 0.8517 (t0) REVERT: T 76 GLU cc_start: 0.8334 (tp30) cc_final: 0.7908 (tp30) REVERT: T 79 ASP cc_start: 0.8857 (p0) cc_final: 0.8638 (p0) outliers start: 155 outliers final: 108 residues processed: 697 average time/residue: 0.5503 time to fit residues: 656.6045 Evaluate side-chains 700 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 573 time to evaluate : 4.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain I residue 10 ASN Chi-restraints excluded: chain I residue 36 ARG Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 194 GLN Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 447 MET Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain F residue 160 LYS Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 307 MET Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 435 ASP Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 301 ILE Chi-restraints excluded: chain H residue 438 VAL Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 194 GLN Chi-restraints excluded: chain J residue 233 MET Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain J residue 319 GLN Chi-restraints excluded: chain J residue 372 LEU Chi-restraints excluded: chain J residue 435 ASP Chi-restraints excluded: chain J residue 483 GLU Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 266 THR Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 447 MET Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 194 GLN Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain M residue 407 VAL Chi-restraints excluded: chain M residue 420 ILE Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain O residue 69 MET Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 387 VAL Chi-restraints excluded: chain O residue 447 MET Chi-restraints excluded: chain O residue 521 VAL Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain P residue 193 MET Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 387 VAL Chi-restraints excluded: chain P residue 389 MET Chi-restraints excluded: chain P residue 435 ASP Chi-restraints excluded: chain Q residue 64 ILE Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 150 ILE Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 295 LEU Chi-restraints excluded: chain R residue 422 VAL Chi-restraints excluded: chain R residue 521 VAL Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 176 THR Chi-restraints excluded: chain S residue 233 MET Chi-restraints excluded: chain S residue 267 MET Chi-restraints excluded: chain S residue 270 ILE Chi-restraints excluded: chain S residue 289 LEU Chi-restraints excluded: chain S residue 300 VAL Chi-restraints excluded: chain S residue 307 MET Chi-restraints excluded: chain S residue 309 LEU Chi-restraints excluded: chain S residue 372 LEU Chi-restraints excluded: chain T residue 6 LEU Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 58 ASP Chi-restraints excluded: chain T residue 77 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 466 optimal weight: 2.9990 chunk 751 optimal weight: 0.0570 chunk 458 optimal weight: 1.9990 chunk 356 optimal weight: 20.0000 chunk 522 optimal weight: 1.9990 chunk 788 optimal weight: 7.9990 chunk 725 optimal weight: 0.0370 chunk 627 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 484 optimal weight: 8.9990 chunk 384 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 319 GLN I 82 ASN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 GLN F 82 ASN H 366 GLN M 82 ASN P 82 ASN S 82 ASN S 112 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 59780 Z= 0.179 Angle : 0.573 12.135 80822 Z= 0.300 Chirality : 0.043 0.215 9814 Planarity : 0.003 0.037 10507 Dihedral : 8.610 89.785 8911 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.57 % Allowed : 18.64 % Favored : 79.79 % 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: 1.15 (0.09), residues: 7966 helix: 1.70 (0.08), residues: 4312 sheet: 0.36 (0.17), residues: 1001 loop : -0.59 (0.11), residues: 2653 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS Q 7 PHE 0.011 0.001 PHE B 195 TYR 0.016 0.001 TYR R 199 ARG 0.009 0.000 ARG D 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 578 time to evaluate : 5.155 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: C 447 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8005 (mtp) REVERT: I 36 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8359 (mtt90) REVERT: I 194 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8284 (tm-30) REVERT: I 206 ASN cc_start: 0.8526 (m-40) cc_final: 0.8316 (m-40) REVERT: I 309 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7909 (mt) REVERT: W 51 ASN cc_start: 0.8695 (p0) cc_final: 0.8285 (p0) REVERT: W 76 GLU cc_start: 0.8460 (tp30) cc_final: 0.7997 (tp30) REVERT: W 77 LYS cc_start: 0.8742 (tttp) cc_final: 0.8456 (tptp) REVERT: A 121 ASP cc_start: 0.6885 (t0) cc_final: 0.6568 (t0) REVERT: A 219 PHE cc_start: 0.8987 (m-80) cc_final: 0.8534 (m-80) REVERT: B 193 MET cc_start: 0.7895 (mmm) cc_final: 0.7403 (mmt) REVERT: B 389 MET cc_start: 0.8386 (tpp) cc_final: 0.7271 (tpp) REVERT: D 50 GLU cc_start: 0.7530 (pm20) cc_final: 0.7057 (pm20) REVERT: D 51 ASN cc_start: 0.8509 (p0) cc_final: 0.8121 (p0) REVERT: D 88 GLU cc_start: 0.8405 (tm-30) cc_final: 0.7837 (tm-30) REVERT: E 121 ASP cc_start: 0.6467 (t0) cc_final: 0.6162 (t0) REVERT: E 233 MET cc_start: 0.8228 (pmm) cc_final: 0.7586 (pmm) REVERT: E 447 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8261 (mtm) REVERT: F 194 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8570 (tm-30) REVERT: F 309 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7606 (mt) REVERT: G 47 ARG cc_start: 0.8639 (tpp80) cc_final: 0.8406 (tpp80) REVERT: G 51 ASN cc_start: 0.8425 (p0) cc_final: 0.8166 (p0) REVERT: G 58 ASP cc_start: 0.8473 (t70) cc_final: 0.8205 (t0) REVERT: G 63 ASP cc_start: 0.8356 (m-30) cc_final: 0.8140 (t0) REVERT: G 68 ASN cc_start: 0.8408 (t0) cc_final: 0.8181 (t0) REVERT: G 76 GLU cc_start: 0.8383 (tp30) cc_final: 0.7964 (tp30) REVERT: G 77 LYS cc_start: 0.8931 (tttp) cc_final: 0.8442 (tptp) REVERT: G 79 ASP cc_start: 0.8794 (p0) cc_final: 0.8557 (p0) REVERT: H 121 ASP cc_start: 0.6817 (t0) cc_final: 0.6467 (t0) REVERT: H 219 PHE cc_start: 0.8883 (m-80) cc_final: 0.8285 (m-80) REVERT: H 233 MET cc_start: 0.8766 (pmm) cc_final: 0.8086 (pmm) REVERT: H 295 LEU cc_start: 0.9299 (mt) cc_final: 0.9046 (tp) REVERT: H 447 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8481 (mtp) REVERT: J 194 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8188 (tm-30) REVERT: J 309 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7764 (mp) REVERT: K 51 ASN cc_start: 0.8647 (p0) cc_final: 0.8322 (p0) REVERT: K 76 GLU cc_start: 0.8182 (tp30) cc_final: 0.7951 (tp30) REVERT: K 77 LYS cc_start: 0.8388 (tptt) cc_final: 0.7891 (tptp) REVERT: K 86 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.7284 (mtt) REVERT: K 88 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8267 (tm-30) REVERT: L 219 PHE cc_start: 0.8914 (m-80) cc_final: 0.8413 (m-80) REVERT: L 233 MET cc_start: 0.8962 (pmm) cc_final: 0.8287 (pmm) REVERT: L 447 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8196 (mtm) REVERT: M 194 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8398 (tm-30) REVERT: N 64 ILE cc_start: 0.9105 (mp) cc_final: 0.8748 (mt) REVERT: N 76 GLU cc_start: 0.8389 (tp30) cc_final: 0.7995 (tp30) REVERT: N 77 LYS cc_start: 0.8695 (tttm) cc_final: 0.8281 (tptp) REVERT: O 16 MET cc_start: 0.8557 (mtp) cc_final: 0.8342 (mtp) REVERT: O 267 MET cc_start: 0.5709 (mpp) cc_final: 0.5333 (tpt) REVERT: O 447 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8086 (mpp) REVERT: P 229 ASN cc_start: 0.7509 (t0) cc_final: 0.7225 (t0) REVERT: P 242 LYS cc_start: 0.8935 (mptt) cc_final: 0.8687 (mptt) REVERT: P 289 LEU cc_start: 0.9620 (OUTLIER) cc_final: 0.9401 (mm) REVERT: Q 13 LYS cc_start: 0.8990 (ttmm) cc_final: 0.8778 (ttmm) REVERT: Q 39 GLU cc_start: 0.8570 (pm20) cc_final: 0.8316 (pm20) REVERT: Q 51 ASN cc_start: 0.8640 (p0) cc_final: 0.8320 (p0) REVERT: Q 76 GLU cc_start: 0.8407 (tp30) cc_final: 0.7919 (tp30) REVERT: R 215 LEU cc_start: 0.8686 (mp) cc_final: 0.8229 (mt) REVERT: R 288 MET cc_start: 0.8961 (ptp) cc_final: 0.8749 (ptp) REVERT: R 295 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9197 (tp) REVERT: R 389 MET cc_start: 0.2456 (mmm) cc_final: 0.2006 (mmm) REVERT: S 267 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7681 (mpt) REVERT: S 309 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7921 (mt) REVERT: T 13 LYS cc_start: 0.9045 (tttp) cc_final: 0.8827 (ttmt) REVERT: T 20 LYS cc_start: 0.8914 (mtmt) cc_final: 0.8665 (mtpp) REVERT: T 47 ARG cc_start: 0.8585 (ttm-80) cc_final: 0.8310 (ttm-80) REVERT: T 58 ASP cc_start: 0.8581 (m-30) cc_final: 0.8361 (t0) REVERT: T 68 ASN cc_start: 0.8650 (t0) cc_final: 0.8302 (t0) REVERT: T 76 GLU cc_start: 0.8248 (tp30) cc_final: 0.7813 (tp30) REVERT: T 79 ASP cc_start: 0.8874 (p0) cc_final: 0.8664 (p0) outliers start: 97 outliers final: 71 residues processed: 655 average time/residue: 0.5508 time to fit residues: 627.9970 Evaluate side-chains 649 residues out of total 6209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 560 time to evaluate : 5.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain I residue 36 ARG Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 194 GLN Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 447 MET Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 435 ASP Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 301 ILE Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain J residue 194 GLN Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain J residue 372 LEU Chi-restraints excluded: chain J residue 435 ASP Chi-restraints excluded: chain K residue 86 MET Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 266 THR Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 447 MET Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 194 GLN Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain M residue 372 LEU Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 387 VAL Chi-restraints excluded: chain O residue 447 MET Chi-restraints excluded: chain O residue 521 VAL Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain P residue 193 MET Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 435 ASP Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 150 ILE Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 295 LEU Chi-restraints excluded: chain R residue 422 VAL Chi-restraints excluded: chain R residue 521 VAL Chi-restraints excluded: chain S residue 176 THR Chi-restraints excluded: chain S residue 267 MET Chi-restraints excluded: chain S residue 270 ILE Chi-restraints excluded: chain S residue 289 LEU Chi-restraints excluded: chain S residue 300 VAL Chi-restraints excluded: chain S residue 309 LEU Chi-restraints excluded: chain T residue 6 LEU Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain T residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 498 optimal weight: 0.7980 chunk 668 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 578 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 174 optimal weight: 0.9980 chunk 628 optimal weight: 0.9990 chunk 263 optimal weight: 6.9990 chunk 645 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 366 GLN I 82 ASN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 ASN L 366 GLN M 82 ASN O 366 GLN P 82 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.114752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.082214 restraints weight = 127623.976| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.72 r_work: 0.2892 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 59780 Z= 0.187 Angle : 0.568 13.303 80822 Z= 0.296 Chirality : 0.043 0.230 9814 Planarity : 0.003 0.035 10507 Dihedral : 8.410 89.820 8911 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.70 % Allowed : 18.52 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.09), residues: 7966 helix: 1.82 (0.08), residues: 4312 sheet: 0.44 (0.17), residues: 1001 loop : -0.59 (0.11), residues: 2653 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS T 7 PHE 0.010 0.001 PHE P 195 TYR 0.016 0.001 TYR R 199 ARG 0.015 0.000 ARG N 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11118.80 seconds wall clock time: 197 minutes 18.61 seconds (11838.61 seconds total)